Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 25835) +++ /issm/trunk/configure.ac (revision 25836) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([Ice Sheet System Model (ISSM)],[4.17],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([Ice Sheet System Model (ISSM)],[4.18],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 Index: /issm/trunk/etc/environment.csh =================================================================== --- /issm/trunk/etc/environment.csh (revision 25835) +++ /issm/trunk/etc/environment.csh (revision 25836) @@ -42,4 +42,5 @@ setenv PATH {$DAKOTA_DIR}/bin:{$PATH} setenv MANPATH {$MANPATH}:{$MPI_DIR}/man:{$DAKOTA_DIR}/docs/man:{$DAKOTA_DIR}/docs/man-ref + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$DAKOTA_DIR/lib endif @@ -49,4 +50,5 @@ if (-d $BOOST_DIR) then setenv PATH {$BOOST_DIR}/bin:{$PATH} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$BOOST_DIR/lib endif Index: /issm/trunk/etc/environment.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 25835) +++ /issm/trunk/etc/environment.sh (revision 25836) @@ -148,18 +148,18 @@ path_append(){ #{{{ if [ -d "${1}" ] && [[ ":${PATH}:" != *":${1}:"* ]]; then - path="${1}" + PATH_IN="${1}" if [[ "${ISSM_ARCH}" == "cygwin-intel" ]]; then - path=`cygpath -u "${1}"` - fi - export PATH="${PATH}:${path}" + PATH_IN=`cygpath -u "${1}"` + fi + export PATH="${PATH}:${PATH_IN}" fi } #}}} path_prepend(){ #{{{ if [ -d "${1}" ] && [[ ":${PATH}:" != *":${1}:"* ]]; then - path="${1}" + PATH_IN="${1}" if [[ "${ISSM_ARCH}" == "cygwin-intel" ]]; then - path=`cygpath -u "${1}"` - fi - export PATH="${path}:${PATH}" + PATH_IN=`cygpath -u "${1}"` + fi + export PATH="${PATH_IN}:${PATH}" fi } #}}} @@ -197,5 +197,5 @@ if [ -d "$PETSC_DIR" ]; then export PETSC_DIR - ld_library_path_append "${PETSC_DIR}/lib" + ld_library_path_prepend "${PETSC_DIR}/lib" # In case we have installed MPICH via PETSc @@ -372,4 +372,11 @@ fi +NETCDF_PYTHON_DIR="${ISSM_DIR}/externalpackages/netcdf-python/install" +if [ -d "${NETCDF_PYTHON_DIR}" ]; then + if [ -d "${NETCDF_PYTHON_DIR}/lib/python2.7/site-packages" ]; then + ld_library_path_append "${NETCDF_PYTHON_DIR}/lib/python2.7/site-packages" + fi +fi + HDF5_DIR="${ISSM_DIR}/externalpackages/hdf5/install" if [ -d "${HDF5_DIR}" ]; then @@ -383,11 +390,6 @@ if [ -d "${SQLITE_DIR}" ]; then path_append "${SQLITE_DIR}/bin" + library_path_append "${SQLITE_DIR}/lib" ld_library_path_append "${SQLITE_DIR}/lib" -fi - -PROJ4_DIR="${ISSM_DIR}/externalpackages/proj.4/install" -if [ -d "${PROJ4_DIR}" ]; then - dyld_library_path_prepend "${PROJ4_DIR}/lib" - ld_library_path_prepend "${PROJ4_DIR}/lib" fi @@ -402,4 +404,10 @@ path_prepend "${GDAL_DIR}/bin" ld_library_path_append "${GDAL_DIR}/lib" +fi + +ESMF_DIR="${ISSM_DIR}/externalpackages/esmf/install" +if [ -d "${ESMF_DIR}" ]; then + path_prepend "${ESMF_DIR}/bin" + ld_library_path_append "${ESMF_DIR}/lib/libO/Linux.gfortran.64.mpich.default/" fi Index: /issm/trunk/examples/AMR/mismip.par =================================================================== --- /issm/trunk/examples/AMR/mismip.par (revision 25835) +++ /issm/trunk/examples/AMR/mismip.par (revision 25836) @@ -4,5 +4,5 @@ md.geometry.surface=10*ones(md.mesh.numberofvertices,1); md.geometry.thickness=md.geometry.surface-md.geometry.base; -md.mask.groundedice_levelset=-1*ones(md.mesh.numberofvertices,1); +md.mask.ocean_levelset=-1*ones(md.mesh.numberofvertices,1); % creating basal drag Index: /issm/trunk/examples/EsaGRACE/runme.m =================================================================== --- /issm/trunk/examples/EsaGRACE/runme.m (revision 25835) +++ /issm/trunk/examples/EsaGRACE/runme.m (revision 25836) @@ -50,5 +50,5 @@ md.esa.love_l = love_numbers('l','CF'); md.esa.love_l(nlove+1:end)=[]; - md.mask.groundedice_levelset = ones(md.mesh.numberofvertices,1); + md.mask.ocean_levelset = ones(md.mesh.numberofvertices,1); md.mask.ice_levelset = ones(md.mesh.numberofvertices,1); pos=find(md.esa.deltathickness~=0); Index: /issm/trunk/examples/EsaWahr/runme.m =================================================================== --- /issm/trunk/examples/EsaWahr/runme.m (revision 25835) +++ /issm/trunk/examples/EsaWahr/runme.m (revision 25836) @@ -63,5 +63,5 @@ md.mask.ice_levelset = -ones(md.mesh.numberofvertices,1); - md.mask.groundedice_levelset = ones(md.mesh.numberofvertices,1); + md.mask.ocean_levelset = ones(md.mesh.numberofvertices,1); di=md.materials.rho_ice/md.materials.rho_water; Index: /issm/trunk/examples/Greenland/Greenland.par =================================================================== --- /issm/trunk/examples/Greenland/Greenland.par (revision 25835) +++ /issm/trunk/examples/Greenland/Greenland.par (revision 25836) @@ -45,5 +45,5 @@ disp(' Construct basal friction parameters'); md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); -pos=find(md.mask.groundedice_levelset<0); +pos=find(md.mask.ocean_levelset<0); md.friction.coefficient(pos)=0; %no friction applied on floating ice md.friction.p=ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/ISMIP/CheatyRunme.m =================================================================== --- /issm/trunk/examples/ISMIP/CheatyRunme.m (revision 25835) +++ /issm/trunk/examples/ISMIP/CheatyRunme.m (revision 25836) @@ -45,5 +45,5 @@ % plot the given mask #md.mask to locate the field %-> - plotmodel(md,'data',md.mask.groundedice_levelset); + plotmodel(md,'data',md.mask.ocean_levelset); % save the given model %-> Index: /issm/trunk/examples/IceBridge/Greenland.par =================================================================== --- /issm/trunk/examples/IceBridge/Greenland.par (revision 25835) +++ /issm/trunk/examples/IceBridge/Greenland.par (revision 25836) @@ -68,5 +68,5 @@ disp(' Construct basal friction parameters'); md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); -pos=find(md.mask.groundedice_levelset<0); +pos=find(md.mask.ocean_levelset<0); md.friction.coefficient(pos)=0; %no friction applied on floating ice md.friction.p=ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/IceBridge/Greenland_noOIB.par =================================================================== --- /issm/trunk/examples/IceBridge/Greenland_noOIB.par (revision 25835) +++ /issm/trunk/examples/IceBridge/Greenland_noOIB.par (revision 25836) @@ -45,5 +45,5 @@ disp(' Construct basal friction parameters'); md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); -pos=find(md.mask.groundedice_levelset<0); +pos=find(md.mask.ocean_levelset<0); md.friction.coefficient(pos)=0; %no friction applied on floating ice md.friction.p=ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/IceBridge/Greenland_solution.par =================================================================== --- /issm/trunk/examples/IceBridge/Greenland_solution.par (revision 25835) +++ /issm/trunk/examples/IceBridge/Greenland_solution.par (revision 25836) @@ -72,5 +72,5 @@ disp(' Construct basal friction parameters'); md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); -pos=find(md.mask.groundedice_levelset<0); +pos=find(md.mask.ocean_levelset<0); md.friction.coefficient(pos)=0; %no friction applied on floating ice md.friction.p=ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/IceflowModels/EISMINT.par =================================================================== --- /issm/trunk/examples/IceflowModels/EISMINT.par (revision 25835) +++ /issm/trunk/examples/IceflowModels/EISMINT.par (revision 25836) @@ -11,5 +11,5 @@ disp(' creating drag'); md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/IceflowModels/SquareShelf.par =================================================================== --- /issm/trunk/examples/IceflowModels/SquareShelf.par (revision 25835) +++ /issm/trunk/examples/IceflowModels/SquareShelf.par (revision 25836) @@ -31,5 +31,5 @@ %Friction md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/Inversion/Square.par =================================================================== --- /issm/trunk/examples/Inversion/Square.par (revision 25835) +++ /issm/trunk/examples/Inversion/Square.par (revision 25836) @@ -12,5 +12,5 @@ disp(' creating drag'); md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; md.friction.p = ones(md.mesh.numberofelements,1); md.friction.q = ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/Jakobshavn/Jks.par =================================================================== --- /issm/trunk/examples/Jakobshavn/Jks.par (revision 25835) +++ /issm/trunk/examples/Jakobshavn/Jks.par (revision 25836) @@ -43,5 +43,5 @@ disp(' Construct basal friction parameters'); md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/LcurveAnalysis/Square.par =================================================================== --- /issm/trunk/examples/LcurveAnalysis/Square.par (revision 25835) +++ /issm/trunk/examples/LcurveAnalysis/Square.par (revision 25836) @@ -12,5 +12,5 @@ disp(' creating drag'); md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; md.friction.p = ones(md.mesh.numberofelements,1); md.friction.q = ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/Pig/Pig.par =================================================================== --- /issm/trunk/examples/Pig/Pig.par (revision 25835) +++ /issm/trunk/examples/Pig/Pig.par (revision 25836) @@ -31,5 +31,5 @@ %Get the node numbers of floating nodes -pos=find(md.mask.groundedice_levelset<0); +pos=find(md.mask.ocean_levelset<0); %apply a flotation criterion on the precedingly defined nodes and @@ -102,5 +102,5 @@ %no friction applied on floating ice -pos=find(md.mask.groundedice_levelset<0); +pos=find(md.mask.ocean_levelset<0); md.friction.coefficient(pos)=0; md.groundingline.migration='SubelementMigration'; Index: /issm/trunk/examples/Pig/runme.m =================================================================== --- /issm/trunk/examples/Pig/runme.m (revision 25835) +++ /issm/trunk/examples/Pig/runme.m (revision 25836) @@ -72,9 +72,9 @@ %fill in the md.mask structure - md.mask.groundedice_levelset=groundedice; %ice is grounded for mask equal one + md.mask.ocean_levelset=groundedice; %ice is grounded for mask equal one md.mask.ice_levelset=-1*ones(md.mesh.numberofvertices,1);%ice is present when negatvie %ploting - plotmodel(md,'data',md.mask.groundedice_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') + plotmodel(md,'data',md.mask.ocean_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') % Save model Index: /issm/trunk/examples/Pig2/Pig.par =================================================================== --- /issm/trunk/examples/Pig2/Pig.par (revision 25835) +++ /issm/trunk/examples/Pig2/Pig.par (revision 25836) @@ -31,5 +31,5 @@ %Get the node numbers of floating nodes -pos=find(md.mask.groundedice_levelset<0); +pos=find(md.mask.ocean_levelset<0); %apply a flotation criterion on the precedingly defined nodes and @@ -102,5 +102,5 @@ %no friction applied on floating ice -pos=find(md.mask.groundedice_levelset<0); +pos=find(md.mask.ocean_levelset<0); md.friction.coefficient(pos)=0; md.groundingline.migration='SubelementMigration'; Index: /issm/trunk/examples/Pig2/runme.m =================================================================== --- /issm/trunk/examples/Pig2/runme.m (revision 25835) +++ /issm/trunk/examples/Pig2/runme.m (revision 25836) @@ -60,8 +60,8 @@ %fill in the md.mask structure - md.mask.groundedice_levelset=groundedice; %ice is grounded for mask equal one + md.mask.ocean_levelset=groundedice; %ice is grounded for mask equal one md.mask.ice_levelset=-1*ones(md.mesh.numberofvertices,1);%ice is present when negatvie - plotmodel(md,'data',md.mask.groundedice_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') + plotmodel(md,'data',md.mask.ocean_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') save ./Models/PIG_SetMask md; @@ -100,5 +100,5 @@ md.inversion.min_parameters=md.materials.rheology_B; md.inversion.max_parameters=md.materials.rheology_B; - pos = find(md.mask.groundedice_levelset<0); + pos = find(md.mask.ocean_levelset<0); md.inversion.min_parameters(pos) = cuffey(273); md.inversion.max_parameters(pos) = cuffey(200); @@ -111,5 +111,5 @@ % Solve md.cluster=generic('name',oshostname,'np',2); - mds=extract(md,md.mask.groundedice_levelset<0); + mds=extract(md,md.mask.ocean_levelset<0); mds=solve(mds,'Stressbalance'); Index: /issm/trunk/examples/PigSensitivity/runme.m =================================================================== --- /issm/trunk/examples/PigSensitivity/runme.m (revision 25835) +++ /issm/trunk/examples/PigSensitivity/runme.m (revision 25836) @@ -12,5 +12,5 @@ md.transient.isthermal=0; - pos=find(md.mask.groundedice_levelset<0); + pos=find(md.mask.ocean_levelset<0); md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1); Index: /issm/trunk/examples/SlrFarrell/runme.m =================================================================== --- /issm/trunk/examples/SlrFarrell/runme.m (revision 25835) +++ /issm/trunk/examples/SlrFarrell/runme.m (revision 25836) @@ -84,8 +84,8 @@ md.mask.land_levelset = 1-md.mask.ocean_levelset; md.mask.ice_levelset = ones(md.mesh.numberofvertices,1); - md.mask.groundedice_levelset = -ones(md.mesh.numberofvertices,1); + md.mask.ocean_levelset = -ones(md.mesh.numberofvertices,1); pos=find(md.mesh.lat <-80); md.mask.ice_levelset(pos(1))=-1; % ice yes! - md.mask.groundedice_levelset(pos(1))=1; % ice grounded! + md.mask.ocean_levelset(pos(1))=1; % ice grounded! di=md.materials.rho_ice/md.materials.rho_water; Index: /issm/trunk/examples/SlrGRACE/runme.m =================================================================== --- /issm/trunk/examples/SlrGRACE/runme.m (revision 25835) +++ /issm/trunk/examples/SlrGRACE/runme.m (revision 25836) @@ -85,5 +85,5 @@ md.slr.love_l = love_numbers('l','CM'); md.slr.love_l(nlove+1:end)=[]; - md.mask.groundedice_levelset = ones(md.mesh.numberofvertices,1); + md.mask.ocean_levelset = ones(md.mesh.numberofvertices,1); md.mask.ice_levelset = ones(md.mesh.numberofvertices,1); pos=find(md.slr.deltathickness~=0); Index: /issm/trunk/examples/SlrGRACE_NIMS/runme.m =================================================================== --- /issm/trunk/examples/SlrGRACE_NIMS/runme.m (revision 25835) +++ /issm/trunk/examples/SlrGRACE_NIMS/runme.m (revision 25836) @@ -147,5 +147,5 @@ md.slr.love_l = love_numbers('l','CM'); md.slr.love_l(nlove+1:end)=[]; - md.mask.groundedice_levelset = ones(md.mesh.numberofvertices,1); + md.mask.ocean_levelset = ones(md.mesh.numberofvertices,1); md.mask.ice_levelset = ones(md.mesh.numberofvertices,1); pos=find(md.slr.deltathickness~=0); Index: /issm/trunk/examples/SquareIceShelf/Square.par =================================================================== --- /issm/trunk/examples/SquareIceShelf/Square.par (revision 25835) +++ /issm/trunk/examples/SquareIceShelf/Square.par (revision 25836) @@ -12,5 +12,5 @@ disp(' creating drag'); md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/examples/shakti/moulin.par =================================================================== --- /issm/trunk/examples/shakti/moulin.par (revision 25835) +++ /issm/trunk/examples/shakti/moulin.par (revision 25836) @@ -2,21 +2,21 @@ % Set up bed topography and ice geometry for a tilted 500m thick slab - md.geometry.base = .02*md.mesh.x; - md.geometry.bed = md.geometry.base; - md.geometry.surface = .02*md.mesh.x + 500; - md.geometry.thickness = md.geometry.surface - md.geometry.bed; +md.geometry.base = .02*md.mesh.x; +md.geometry.bed = md.geometry.base; +md.geometry.surface = .02*md.mesh.x + 500; +md.geometry.thickness = md.geometry.surface - md.geometry.bed; % Define ice sliding velocity (m/yr) - md.initialization.vx = 10^-6*md.constants.yts*ones(md.mesh.numberofvertices,1); - md.initialization.vy = zeros(md.mesh.numberofvertices,1); - md.initialization.pressure=zeros(md.mesh.numberofvertices,1); +md.initialization.vx = 10^-6*md.constants.yts*ones(md.mesh.numberofvertices,1); +md.initialization.vy = zeros(md.mesh.numberofvertices,1); +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); md.initialization.pressure=zeros(md.mesh.numberofvertices,1); % Materials - % Ice flow law parameter (note that the standard parameter A=B^(-3)) - md.materials.rheology_B= (5e-25)^(-1/3)*ones(md.mesh.numberofvertices,1); - md.initialization.temperature=(273)*ones(md.mesh.numberofvertices,1); - md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); +% Ice flow law parameter (note that the standard parameter A=B^(-3)) +md.materials.rheology_B= (5e-25)^(-1/3)*ones(md.mesh.numberofvertices,1); +md.initialization.temperature=(273)*ones(md.mesh.numberofvertices,1); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); %Calving @@ -27,5 +27,4 @@ md.friction=frictionshakti(md.friction); md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); - %Numerical parameters @@ -42,17 +41,4 @@ md.timestepping.final_time=3.; -%GIA: -md.gia.lithosphere_thickness=100.*ones(md.mesh.numberofvertices,1); % in km -md.gia.mantle_viscosity=1.0*10^21*ones(md.mesh.numberofvertices,1); % in Pa.s -md.materials.lithosphere_shear_modulus=6.7*10^10; % in Pa -md.materials.lithosphere_density=3.32; % in g/cm^-3 -md.materials.mantle_shear_modulus=1.45*10^11; % in Pa -md.materials.mantle_density=3.34; % in g/cm^-3 - %Boundary conditions: md=SetIceSheetBC(md); - -%Change name so that no test have the same name -A=dbstack; -if (length(A)>2), md.miscellaneous.name=A(3).file(1:end-2); end - Index: /issm/trunk/examples/shakti/moulin.py =================================================================== --- /issm/trunk/examples/shakti/moulin.py (revision 25836) +++ /issm/trunk/examples/shakti/moulin.py (revision 25836) @@ -0,0 +1,57 @@ +import numpy as np +from SetIceSheetBC import SetIceSheetBC +from frictionshakti import frictionshakti +from verbose import verbose + +#Start defining model parameters here +# Set up bed topography and ice geometry for a tilted 500m thick slab +md.geometry.base = .02 * md.mesh.x +md.geometry.bed = md.geometry.base +md.geometry.surface = .02 * md.mesh.x + 500 +md.geometry.thickness = md.geometry.surface - md.geometry.bed + +# Define ice sliding velocity (m / yr) +md.initialization.vx = 1.0e-6 * md.constants.yts * np.ones(md.mesh.numberofvertices) +md.initialization.vy = np.zeros(md.mesh.numberofvertices) +md.initialization.pressure = np.zeros(md.mesh.numberofvertices) + +# Materials +# Ice flow law parameter (note that the standard parameter A = B^(- 3)) +md.materials.rheology_B = 5e-25**(-1 / 3) * np.ones(md.mesh.numberofvertices) +md.initialization.temperature = 273. * np.ones(md.mesh.numberofvertices) +md.materials.rheology_n = 3. * np.ones(md.mesh.numberofelements) + +#Calving +md.calving.calvingrate = np.zeros(md.mesh.numberofvertices) +#md.calving.spclevelset = NaN(md.mesh.numberofvertices, 1) + +# Friction law and coefficient +md.friction = frictionshakti(md) +md.friction.coefficient = 20. * np.ones(md.mesh.numberofvertices) + +#Numerical parameters +#md.stressbalance.viscosity_overshoot = 0.0 +md.masstransport.stabilization = 1. +md.thermal.stabilization = 1. +md.verbose = verbose(0) +md.settings.waitonlock = 30 +md.stressbalance.restol = 0.05 +md.steadystate.reltol = 0.05 +md.stressbalance.reltol = 0.05 +md.stressbalance.abstol = np.nan +md.timestepping.time_step = 1. +md.timestepping.final_time = 3. + +#GIA: +md.gia.lithosphere_thickness = 100. * np.ones(md.mesh.numberofvertices) # in km +md.gia.mantle_viscosity = 1.0e21 * np.ones(md.mesh.numberofvertices) # in Pa.s +md.materials.lithosphere_shear_modulus = 6.7e10 # in Pa +md.materials.lithosphere_density = 3.32 # in g / cm^ - 3 +md.materials.mantle_shear_modulus = 1.45e11 # in Pa +md.materials.mantle_density = 3.34 # in g / cm^ - 3 + +#Boundary conditions: +md = SetIceSheetBC(md) + +#Change name so that no test have the same name +md.private.runtimename = True Index: /issm/trunk/examples/shakti/runme.py =================================================================== --- /issm/trunk/examples/shakti/runme.py (revision 25836) +++ /issm/trunk/examples/shakti/runme.py (revision 25836) @@ -0,0 +1,91 @@ +import numpy as np +from model import * +from solve import solve +from hydrologyshakti import hydrologyshakti +from parameterize import parameterize +from export_netCDF import export_netCDF +from transient import transient +from setmask import setmask +from triangle import triangle + + +steps = [1, 2, 3] + +if 1 in steps: + print(' Step 1: Mesh') + #Generate unstructured mesh on 1, 000 m square with typical element edge length of 20 m + md = triangle(model(), './outline.exp', 20) + export_netCDF(md, 'MoulinMesh.nc') + + +if 2 in steps: + print(' Step 2: Parameterization') + md = loadmodel('MoulinMesh.nc') + md = setmask(md, '', '') + + # Run parameterization script to set up geometry, velocity, material properties, etc. + md = parameterize(md, 'moulin.py') + + # HYDROLOGY SPECIFIC PARAMETERIZATION: + # Change hydrology class to Sommers' SHaKTI model + md.hydrology = hydrologyshakti() + + # Define initial water head such that water pressure is 50% of ice overburden pressure + md.hydrology.head = 0.5 * md.materials.rho_ice / md.materials.rho_freshwater * md.geometry.thickness + md.geometry.base + + # Initial subglacial gap height of 0.01m everywhere + md.hydrology.gap_height = 0.01 * np.ones(md.mesh.numberofelements) + + # Typical bed bump bump spacing (2m) + md.hydrology.bump_spacing = 2 * np.ones(md.mesh.numberofelements) + + # Typical bed bump height (0.1m) + md.hydrology.bump_height = 0.1 * np.ones(md.mesh.numberofelements) + + # Define distributed englacial input to the subglacial system (m / yr) + # Change the value 0.0 to add distributed input + md.hydrology.englacial_input = 0.0 * np.ones(md.mesh.numberofvertices) + + # Initial Reynolds number (start at Re = 1000 everywhere) + md.hydrology.reynolds = 1000. * np.ones(md.mesh.numberofelements) + + # Set up atmospheric pressure Type I boundary condition at left edge of + # domain (outflow, i.e. h = zb at x = xmin) + md.hydrology.spchead = np.nan * np.ones(md.mesh.numberofvertices) + pos = np.where(np.logical_and(md.mesh.vertexonboundary, md.mesh.x == np.nanmin(md.mesh.x))) + md.hydrology.spchead[pos] = md.geometry.base[pos] + + export_netCDF(md, 'MoulinParam.nc') + +if 3 in steps: + print(' Step 3: Solve!') + md = loadmodel('MoulinParam.nc') + + md.transient = transient.deactivateall(md.transient) + md.transient.ishydrology = 1 + + # Specify that you want to run the model on your current computer + # Change the number of processors according to your machine (here np = 4) + md.cluster = generic('np', 2) + + # Define the time stepping scheme: run for 90 days with a time step of 1 hr + md.timestepping.time_step = 3600. / md.constants.yts # Time step (in years) + md.timestepping.final_time = 30. / 365. + + #Add one moulin with steady input at x = 500, y = 500 + DistToCenter = np.sqrt((md.mesh.x - 500)**2 + (md.mesh.y - 500)**2) + loc = np.where(np.nanmin(DistToCenter) == DistToCenter) + time = np.arange(0, md.timestepping.final_time + md.timestepping.time_step, md.timestepping.time_step) + md.hydrology.moulin_input = np.zeros((md.mesh.numberofvertices, len(time))) + md.hydrology.moulin_input = np.vstack((md.hydrology.moulin_input, time)) + md.hydrology.moulin_input[loc, :] = 4 + + # Specify no - flux Type 2 boundary conditions on all edges (except + # the Type 1 condition set at the outflow above) + md.hydrology.neumannflux = np.zeros((md.mesh.numberofelements, len(time))) + md.hydrology.neumannflux = np.vstack((md.hydrology.neumannflux, time)) + + md.verbose.solution = 1 + md = solve(md, 'Transient') + + export_netCDF(md, 'MoulinTransient.nc') Index: /issm/trunk/externalpackages/adjoinablempi/install-linux.sh =================================================================== --- /issm/trunk/externalpackages/adjoinablempi/install-linux.sh (revision 25836) +++ /issm/trunk/externalpackages/adjoinablempi/install-linux.sh (revision 25836) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + + +# Cleanup +rm -rf install src +mkdir install + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz" "adjoinablempi.tar.gz" + +# Unpack source +tar -zxvf adjoinablempi.tar.gz + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/adjoinablempi/install" \ + --libdir="${ISSM_DIR}/externalpackages/adjoinablempi/install/lib" \ + --with-mpi-root="${ISSM_DIR}/externalpackages/petsc/install" \ + --enable-requestOnTrace + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/adjoinablempi/install-mac.sh =================================================================== --- /issm/trunk/externalpackages/adjoinablempi/install-mac.sh (revision 25836) +++ /issm/trunk/externalpackages/adjoinablempi/install-mac.sh (revision 25836) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + + +## Environment +# +#export CPATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc:/usr/include # If path to malloc is not included in shell configuration files, export it here after verifying that the path is correct. +export CFLAGS=-Wno-error=implicit-function-declaration + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz" "adjoinablempi.tar.gz" + +# Unpack source +tar -zxvf adjoinablempi.tar.gz + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/adjoinablempi/install" \ + --libdir="${ISSM_DIR}/externalpackages/adjoinablempi/install/lib" \ + --disable-dependency-tracking \ + --with-mpi-root="${ISSM_DIR}/externalpackages/petsc/install" \ + --enable-requestOnTrace + +# Clean +make clean + +# Compile +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi + +# Install +make install Index: sm/trunk/externalpackages/adjoinablempi/install.sh =================================================================== --- /issm/trunk/externalpackages/adjoinablempi/install.sh (revision 25835) +++ (revision ) @@ -1,38 +1,0 @@ -#!/bin/bash -set -eu - - -# Keeping this for potential future use -#Mercurial cloning: -#hg clone -r 268 http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src - -# Cleanup -rm -rf install src -mkdir install src - -# Download source -${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz" "adjoinablempi.tar.gz" - -# Unpack source -tar -zxvf adjoinablempi.tar.gz - -# Configure -cd src -./configure \ - --prefix="${ISSM_DIR}/externalpackages/adjoinablempi/install" \ - --libdir="${ISSM_DIR}/externalpackages/adjoinablempi/install/lib" \ - --with-mpi-root="${ISSM_DIR}/externalpackages/mpich/install" \ - --enable-requestOnTrace - -# Clean -make clean - -# Compile -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi - -# Install -make install Index: /issm/trunk/externalpackages/adolc/install-mac-with_ampi.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-mac-with_ampi.sh (revision 25836) +++ /issm/trunk/externalpackages/adolc/install-mac-with_ampi.sh (revision 25836) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + + +## Environment +# +export CFLAGS="-O2 -L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi" +export CXXFLAGS="-O2 -L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz" "ADOL-C.tar.gz" + +# Unpack source +tar -zxvf ADOL-C.tar.gz + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/adolc/install" \ + --libdir="${ISSM_DIR}/externalpackages/adolc/install/lib" \ + --with-mpi-root="${ISSM_DIR}/externalpackages/petsc/install" \ + --enable-ampi \ + --with-ampi="${ISSM_DIR}/externalpackages/adjoinablempi/install" \ + --with-soname=adolc \ + --disable-tapedoc-values + +# Compile and install +if [ $# -eq 0 ]; then + make V=1 + make V=1 install +else + make V=1 -j $1 + make V=1 install -j $1 +fi Index: /issm/trunk/externalpackages/adolc/install-with_ampi.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-with_ampi.sh (revision 25836) +++ /issm/trunk/externalpackages/adolc/install-with_ampi.sh (revision 25836) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + + +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +## Environment +# +export CFLAGS="-O2 -L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi" +export CXXFLAGS="-O2 -std=c++11 -L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz" "ADOL-C.tar.gz" + +# Unpack source +tar -zxvf ADOL-C.tar.gz + +# Configure +cd src +./configure \ + --prefix=${ISSM_DIR}/externalpackages/adolc/install \ + --libdir=${ISSM_DIR}/externalpackages/adolc/install/lib \ + --with-mpi-root=${ISSM_DIR}/externalpackages/petsc/install \ + --enable-ampi \ + --with-ampi=${ISSM_DIR}/externalpackages/adjoinablempi/install \ + --with-soname=adolc \ + --disable-tapedoc-values + +# Clean +make clean + +# Compile +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi + +# Install +make V=1 install Index: sm/trunk/externalpackages/adolc/install-withampi-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi-macosx64.sh (revision 25835) +++ (revision ) @@ -1,35 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install src - -# Keeping the following commented line for potential future use. -#git clone https://gitlab.com/adol-c/adol-c.git src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C' 'ADOL-C.tar.gz' - -#Untar ADOL-C -tar -zxf ADOL-C.tar.gz - -#Compile ADOL-C -export CFLAGS="-O2 -L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich" -export CXXFLAGS="-O2 -L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich" - -cd src -./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ - --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ - --with-mpi-root=$ISSM_DIR/externalpackages/mpich/install \ - --enable-ampi \ - --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ - --with-soname=adolc \ - --disable-tapedoc-values - -make clean -if [ $# -eq 0 ]; then - make V=1 -else - make -j $1 V=1 -fi -make V=1 install Index: sm/trunk/externalpackages/adolc/install-withampi.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi.sh (revision 25835) +++ (revision ) @@ -1,45 +1,0 @@ -#!/bin/bash -set -eu - - -# Keeping the following commented line for potential future use. -#git clone https://gitlab.com/adol-c/adol-c.git src - -## Environment -# -export CFLAGS="-O2 -L${ISSM_DIR}/externalpackages/mpich/install/lib -lmpi" -export CXXFLAGS="-O2 -std=c++11 -L${ISSM_DIR}/externalpackages/mpich/install/lib -lmpi" - -# Cleanup -rm -rf install src -mkdir install src - -# Download source -${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz" "ADOL-C.tar.gz" - -# Unpack source -tar -zxvf ADOL-C.tar.gz - -# Configure -cd src -./configure \ - --prefix=${ISSM_DIR}/externalpackages/adolc/install \ - --libdir=${ISSM_DIR}/externalpackages/adolc/install/lib \ - --with-mpi-root=${ISSM_DIR}/externalpackages/mpich/install \ - --enable-ampi \ - --with-ampi=${ISSM_DIR}/externalpackages/adjoinablempi/install \ - --with-soname=adolc \ - --disable-tapedoc-values - -# Clean -make clean - -# Compile -if [ $# -eq 0 ]; then - make V=1 -else - make -j $1 V=1 -fi - -# Install -make V=1 install Index: /issm/trunk/externalpackages/autotools/install-debian-linux.sh =================================================================== --- /issm/trunk/externalpackages/autotools/install-debian-linux.sh (revision 25835) +++ /issm/trunk/externalpackages/autotools/install-debian-linux.sh (revision 25836) @@ -33,6 +33,11 @@ ./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install" -make -make install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi cd .. @@ -45,6 +50,11 @@ cd src ./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install" -make -make install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi cd .. @@ -57,6 +67,11 @@ cd src ./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install" -make -make install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi cd .. @@ -70,5 +85,10 @@ cd src ./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install" -make -make install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi cd .. Index: /issm/trunk/externalpackages/boost/configs/1.73/boost/math/tools/user.hpp =================================================================== --- /issm/trunk/externalpackages/boost/configs/1.73/boost/math/tools/user.hpp (revision 25836) +++ /issm/trunk/externalpackages/boost/configs/1.73/boost/math/tools/user.hpp (revision 25836) @@ -0,0 +1,105 @@ +// Copyright John Maddock 2007. +// Copyright Paul A. Bristow 2007. + +// Use, modification and distribution are subject to the +// Boost Software License, Version 1.0. +// (See accompanying file LICENSE_1_0.txt +// or copy at http://www.boost.org/LICENSE_1_0.txt) + +#ifndef BOOST_MATH_TOOLS_USER_HPP +#define BOOST_MATH_TOOLS_USER_HPP + +#ifdef _MSC_VER +#pragma once +#endif + +// This file can be modified by the user to change the default policies. +// See "Changing the Policy Defaults" in documentation. + +// define this if the platform has no long double functions, +// or if the long double versions have only double precision: +// +// #define BOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS +// +// Performance tuning options: +// +// #define BOOST_MATH_POLY_METHOD 3 +// #define BOOST_MATH_RATIONAL_METHOD 3 +// +// The maximum order of polynomial that will be evaluated +// via an unrolled specialisation: +// +// #define BOOST_MATH_MAX_POLY_ORDER 17 +// +// decide whether to store constants as integers or reals: +// +// #define BOOST_MATH_INT_TABLE_TYPE(RT, IT) IT + +// +// Default policies follow: +// +// Domain errors: +// +// #define BOOST_MATH_DOMAIN_ERROR_POLICY throw_on_error +// +// Pole errors: +// +// #define BOOST_MATH_POLE_ERROR_POLICY throw_on_error +// +// Overflow Errors: +// +// #define BOOST_MATH_OVERFLOW_ERROR_POLICY throw_on_error +// +// Internal Evaluation Errors: +// +// #define BOOST_MATH_EVALUATION_ERROR_POLICY throw_on_error +// +// Underflow: +// +// #define BOOST_MATH_UNDERFLOW_ERROR_POLICY ignore_error +// +// Denorms: +// +// #define BOOST_MATH_DENORM_ERROR_POLICY ignore_error +// +// Max digits to use for internal calculations: +// +// #define BOOST_MATH_DIGITS10_POLICY 0 +// +// Promote floats to doubles internally? +// +// #define BOOST_MATH_PROMOTE_FLOAT_POLICY true +// +// Promote doubles to long double internally: +// +#define BOOST_MATH_PROMOTE_DOUBLE_POLICY false +// +// What do discrete quantiles return? +// +// #define BOOST_MATH_DISCRETE_QUANTILE_POLICY integer_round_outwards +// +// If a function is mathematically undefined +// (for example the Cauchy distribution has no mean), +// then do we stop the code from compiling? +// +// #define BOOST_MATH_ASSERT_UNDEFINED_POLICY true +// +// Maximum series iterations permitted: +// +// #define BOOST_MATH_MAX_SERIES_ITERATION_POLICY 1000000 +// +// Maximum root finding steps permitted: +// +// define BOOST_MATH_MAX_ROOT_ITERATION_POLICY 200 +// +// Enable use of __float128 in numeric constants: +// +// #define BOOST_MATH_USE_FLOAT128 +// +// Disable use of __float128 in numeric_constants even if the compiler looks to support it: +// +// #define BOOST_MATH_DISABLE_FLOAT128 + +#endif // BOOST_MATH_TOOLS_USER_HPP + + Index: /issm/trunk/externalpackages/boost/install-1.55-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-linux-static.sh (revision 25835) +++ /issm/trunk/externalpackages/boost/install-1.55-linux-static.sh (revision 25836) @@ -10,5 +10,5 @@ # export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" -export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost +export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost # Download source Index: /issm/trunk/externalpackages/boost/install-1.55-linux.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-linux.sh (revision 25835) +++ /issm/trunk/externalpackages/boost/install-1.55-linux.sh (revision 25836) @@ -10,5 +10,5 @@ # export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" -export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost +export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost # Download source Index: /issm/trunk/externalpackages/boost/install-1.55-lonestar.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-lonestar.sh (revision 25835) +++ /issm/trunk/externalpackages/boost/install-1.55-lonestar.sh (revision 25836) @@ -23,4 +23,6 @@ patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch +patch src/boost/iterator/reverse_iterator.hpp ./configs/1.55/reverse_iterator.hpp.patch +patch src/boost/multi_index/ordered_index.hpp ./configs/1.55/ordered_index.hpp.patch #Configure and compile Index: /issm/trunk/externalpackages/boost/install-1.55-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-mac-static.sh (revision 25835) +++ /issm/trunk/externalpackages/boost/install-1.55-mac-static.sh (revision 25836) @@ -39,5 +39,5 @@ # Compile and install -./bjam toolset=darwin link=static install +./bjam link=static install # Copy binary to install directory Index: /issm/trunk/externalpackages/boost/install-1.55-mac.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-mac.sh (revision 25835) +++ /issm/trunk/externalpackages/boost/install-1.55-mac.sh (revision 25836) @@ -39,5 +39,5 @@ # Compile and install -./bjam toolset=darwin install +./bjam install # Copy binary to install directory Index: /issm/trunk/externalpackages/boost/install-1.55-stallo.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-stallo.sh (revision 25835) +++ /issm/trunk/externalpackages/boost/install-1.55-stallo.sh (revision 25836) @@ -24,5 +24,5 @@ patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch -#Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost +#Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost #export PATH="/usr/bin":$PATH export CXXFLAGS='-std=c++98' Index: /issm/trunk/externalpackages/boost/install-1.7-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.7-linux-static.sh (revision 25836) +++ /issm/trunk/externalpackages/boost/install-1.7-linux-static.sh (revision 25836) @@ -0,0 +1,43 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +## Envrionment +# +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source into 'src' directory +mv boost_${VER}/* src/ +rm -rf boost_${VER} + +# Configure +cd src +./bootstrap.sh \ + --prefix="${BOOST_ROOT}/install" \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=static runtime-link=static + +# Remove any dynamic libraries that may have been compiled +# +# TODO: Reconfigure so that dynamic libraries are not compiled at all +# +rm -f $(find ${BOOST_ROOT}/install/lib -name *.so*) Index: /issm/trunk/externalpackages/boost/install-1.7-linux-valgrind.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 25836) +++ /issm/trunk/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 25836) @@ -0,0 +1,40 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +## Envrionment +# +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source into 'src' directory +mv boost_${VER}/* src/ +rm -rf boost_${VER} + +# Copy customized source and config files to 'src' directory +cp ./configs/1.73/boost/math/tools/user.hpp ./src/boost/math/tools/ + +# Configure +cd src +./bootstrap.sh \ + --prefix="${BOOST_ROOT}/install" \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=shared runtime-link=shared Index: /issm/trunk/externalpackages/boost/install-1.7-linux.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.7-linux.sh (revision 25836) +++ /issm/trunk/externalpackages/boost/install-1.7-linux.sh (revision 25836) @@ -0,0 +1,37 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +## Envrionment +# +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source into 'src' directory +mv boost_${VER}/* src/ +rm -rf boost_${VER} + +# Configure +cd src +./bootstrap.sh \ + --prefix="${BOOST_ROOT}/install" \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=shared runtime-link=shared Index: /issm/trunk/externalpackages/boost/install-1.7-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.7-mac-static.sh (revision 25836) +++ /issm/trunk/externalpackages/boost/install-1.7-mac-static.sh (revision 25836) @@ -0,0 +1,43 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +## Environment +# +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source into 'src' directory +mv boost_${VER}/* src/ +rm -rf boost_${VER} + +# Configure +cd src +./bootstrap.sh \ + --prefix="${BOOST_ROOT}/install" \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=static runtime-link=static + +# Remove any dynamic libraries that may have been compiled +# +# TODO: Reconfigure so that dynamic libraries are not compiled at all +# +rm -f $(find ${BOOST_ROOT}/install/lib -name *.dylib) Index: /issm/trunk/externalpackages/boost/install-1.7-mac.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.7-mac.sh (revision 25836) +++ /issm/trunk/externalpackages/boost/install-1.7-mac.sh (revision 25836) @@ -0,0 +1,54 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +## Environment +# +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +export LDFLAGS="-Wl,-headerpad_max_install_names" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source into 'src' directory +mv boost_${VER}/* src/ +rm -rf boost_${VER} + +# Configure +cd src +./bootstrap.sh \ + --prefix=${BOOST_ROOT}/install \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=shared runtime-link=shared + +# Set install_name for all shared libraries +# +# NOTE: The install_name_tool prints an error message on some installations, +# but this is not a shell error, and it does not seem to affect the +# Boost libraries called by ISSM. For now, we are simply redirecting the +# error to null. +# +# TODO: +# - Modify the source to apply absolute paths to the library ids so that +# patching it after the fact with install_name_tool is not necessary. +# +cd ${BOOST_ROOT}/install/lib +for name in *.dylib; do + install_name_tool -id ${BOOST_ROOT}/install/lib/${name} ${name} 2>/dev/null +done Index: sm/trunk/externalpackages/boost/install-1.72-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.72-linux-static.sh (revision 25835) +++ (revision ) @@ -1,48 +1,0 @@ -#!/bin/bash -#set -eu # Do not `run set -eu` because it causes some targets to fail - - -# NOTE: -# - Stop after bootstrap step and run `b2 --debug-configuration` to figure -# out which paths Boost is using to include Python. Make sure that each of -# the listed paths is covered by Python. If not, you must create a symbolic -# link from $ISSM_DIR/externalpackages/python to the location of the file -# that Boost is expecting. There is no way to get the Boost to compile with -# Python otherwise. -# - -## Constants -# -VER="1_72_0" - -## Envrionment -# -#export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost -#export CXXFLAGS='-std=c++11' - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" - -# Unpack source -tar -zxvf boost_${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source into 'src' directory -mv boost_${VER}/* src/ -rm -rf boost_${VER} - -# Configure -cd src -./bootstrap.sh \ - --prefix="${ISSM_DIR}/externalpackages/boost/install" \ - --with-python=python2.7 \ - --with-python-root="${ISSM_DIR}/externalpackages/python/install" - -# Modify project config to enable MPI -printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam - -# Compile and install -./b2 link=static install Index: sm/trunk/externalpackages/boost/install-1.72-linux.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.72-linux.sh (revision 25835) +++ (revision ) @@ -1,48 +1,0 @@ -#!/bin/bash -#set -eu # Do not `run set -eu` because it causes some targets to fail - - -# NOTE: -# - Stop after bootstrap step and run `b2 --debug-configuration` to figure -# out which paths Boost is using to include Python. Make sure that each of -# the listed paths is covered by Python. If not, you must create a symbolic -# link from $ISSM_DIR/externalpackages/python to the location of the file -# that Boost is expecting. There is no way to get the Boost to compile with -# Python otherwise. -# - -## Constants -# -VER="1_72_0" - -## Envrionment -# -#export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost -#export CXXFLAGS='-std=c++11' - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" - -# Unpack source -tar -zxvf boost_${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source into 'src' directory -mv boost_${VER}/* src/ -rm -rf boost_${VER} - -# Configure -cd src -./bootstrap.sh \ - --prefix="${ISSM_DIR}/externalpackages/boost/install" \ - --with-python=python2.7 \ - --with-python-root="${ISSM_DIR}/externalpackages/python/install" - -# Modify project config to enable MPI -printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam - -# Compile and install -./b2 --toolset=gcc install Index: sm/trunk/externalpackages/boost/install-1.72-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.72-mac-static.sh (revision 25835) +++ (revision ) @@ -1,47 +1,0 @@ -#!/bin/bash -#set -eu # Do not `run set -eu` because it causes some targets to fail - - -## Constants -# -VER="1_72_0" - -## Environment -# -export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" - -# Unpack source -tar -zxvf boost_${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source into 'src' directory -mv boost_${VER}/* src/ -rm -rf boost_${VER} - -# Configure -cd src -./bootstrap.sh \ - --prefix=${BOOST_ROOT}/install \ - --with-python=python2.7 - -# Modify project config to enable MPI -printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam - -# Compile and install -./b2 toolset=darwin link=static install - -# Copy binary to install directory -mkdir ${BOOST_ROOT}/install/bin -cp bjam ${BOOST_ROOT}/install/bin - -# Remove any dynamic libraries that may have been compiled -# -# TODO: Reconfigure so that dynamic libraries are not compiled at all -# -rm -f $(ls ${BOOST_ROOT}/install/lib/*.dylib) Index: sm/trunk/externalpackages/boost/install-1.72-mac.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.72-mac.sh (revision 25835) +++ (revision ) @@ -1,47 +1,0 @@ -#!/bin/bash -#set -eu # Do not `run set -eu` because it causes some targets to fail - - -## Constants -# -VER="1_72_0" - -## Environment -# -export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" - -# Unpack source -tar -zxvf boost_${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source into 'src' directory -mv boost_${VER}/* src/ -rm -rf boost_${VER} - -# Configure -cd src -./bootstrap.sh \ - --prefix=${BOOST_ROOT}/install \ - --with-python=python2.7 - -# Modify project config to enable MPI -printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam - -# Compile and install -./b2 toolset=darwin install - -# Copy binary to install directory -mkdir ${BOOST_ROOT}/install/bin -cp bjam ${BOOST_ROOT}/install/bin - -# Set install_name for all shared libraries -cd ${BOOST_ROOT}/install/lib -for name in *.dylib; do - install_name_tool -id ${BOOST_ROOT}/install/lib/${name} ${name} -done Index: /issm/trunk/externalpackages/chaco/patches/Makefile.macosx64-sierra.patch =================================================================== --- /issm/trunk/externalpackages/chaco/patches/Makefile.macosx64-sierra.patch (revision 25835) +++ /issm/trunk/externalpackages/chaco/patches/Makefile.macosx64-sierra.patch (revision 25836) @@ -6,5 +6,5 @@ #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions -CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -+CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/local/include/ ++CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/local/include/ -Wno-implicit-function-declaration #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB OFLAGS = -O2 Index: /issm/trunk/externalpackages/chaco/patches/Makefile.patch =================================================================== --- /issm/trunk/externalpackages/chaco/patches/Makefile.patch (revision 25835) +++ /issm/trunk/externalpackages/chaco/patches/Makefile.patch (revision 25836) @@ -6,5 +6,5 @@ #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions -CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -+CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/include/malloc ++CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/include/malloc -Wno-implicit-function-declaration #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB OFLAGS = -O2 Index: /issm/trunk/externalpackages/curl/install-7-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-7-linux-static.sh (revision 25836) +++ /issm/trunk/externalpackages/curl/install-7-linux-static.sh (revision 25836) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-$VER.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv curl-$VER/* src +rm -rf curl-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --disable-shared \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose \ + --without-libidn2 + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/curl/install-7-linux-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-7-linux-with_tests.sh (revision 25836) +++ /issm/trunk/externalpackages/curl/install-7-linux-with_tests.sh (revision 25836) @@ -0,0 +1,41 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-$VER.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv curl-$VER/* src +rm -rf curl-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --disable-static \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose + +# Compile and install +if [ $# -eq 0 ]; then + make + make test + make install +else + make -j $1 + make -j $1 test + make -j $1 install +fi Index: /issm/trunk/externalpackages/curl/install-7-linux.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-7-linux.sh (revision 25836) +++ /issm/trunk/externalpackages/curl/install-7-linux.sh (revision 25836) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-$VER.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv curl-$VER/* src +rm -rf curl-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --disable-static \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/curl/install-7-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-7-mac-static.sh (revision 25836) +++ /issm/trunk/externalpackages/curl/install-7-mac-static.sh (revision 25836) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +## Environment +# +export MACOSX_DEPLOYMENT_TARGET="10.5" # Allows fall back to older API (source: https://curl.se/docs/install.html) + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-$VER.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv curl-$VER/* src +rm -rf curl-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --disable-shared \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose \ + --without-libidn2 \ + --with-secure-transport + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/curl/install-7-mac.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-7-mac.sh (revision 25836) +++ /issm/trunk/externalpackages/curl/install-7-mac.sh (revision 25836) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +## Environment +# +export MACOSX_DEPLOYMENT_TARGET="10.5" # Allows fall back to older API (source: https://curl.se/docs/install.html) + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-$VER.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv curl-$VER/* src +rm -rf curl-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --disable-static \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose \ + --with-secure-transport + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: sm/trunk/externalpackages/curl/install-7.67-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-7.67-with_tests.sh (revision 25835) +++ (revision ) @@ -1,41 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="7.67.0" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" - -# Unpack source -tar -zxvf curl-$VER.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv curl-$VER/* src -rm -rf curl-$VER - -# Configure -cd src -./configure \ - --prefix="${ISSM_DIR}/externalpackages/curl/install" \ - --disable-manual - -# Compile and install -if [ $# -eq 0 ]; then - make - make test - make install -else - make -j $1 - make -j $1 test - make -j $1 install -fi - -# Return to initial directory -cd ../.. Index: sm/trunk/externalpackages/curl/install-7.67.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-7.67.sh (revision 25835) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="7.67.0" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" - -# Unpack source -tar -zxvf curl-$VER.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv curl-$VER/* src -rm -rf curl-$VER - -# Configure -cd src -./configure \ - --prefix="${ISSM_DIR}/externalpackages/curl/install" \ - --disable-manual \ - --disable-verbose - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Return to initial directory -cd ../.. Index: sm/trunk/externalpackages/curl/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-macosx64.sh (revision 25835) +++ (revision ) @@ -1,32 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src install curl-7.39.0 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/curl-7.39.0.tar.gz' 'curl-7.39.0.tar.gz' - -#Untar -tar -zxvf curl-7.39.0.tar.gz - -#Move curl into src directory -mv curl-7.39.0/* src -rm -rf curl-7.39.0 - -#Configure curl -cd src - -export CFLAGS=" -arch x86_64" - -./configure \ - --prefix="$ISSM_DIR/externalpackages/curl/install" - -#Compile curl -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover20.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover20.patch (revision 25836) +++ /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover20.patch (revision 25836) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/usr/local/intel/2020/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/usr/local/intel/2020/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/include/xtndispatch.h =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/include/xtndispatch.h (revision 25836) +++ /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/include/xtndispatch.h (revision 25836) @@ -0,0 +1,147 @@ +/* This code was computer generated */ + +/* + + These programs construct and manipulate orthogonal +arrays. They were prepared by + + Art Owen + Department of Statistics + Sequoia Hall + Stanford CA 94305 + + They may be freely used and shared. This code comes +with no warranty of any kind. Use it at your own +risk. + + I thank the Semiconductor Research Corporation and +the National Science Foundation for supporting this +work. + +*/ + +/* Fix for C99 */ +extern int ipow(int a, int b); /* primes.c */ + +if( q== ipow(2,2) )xtn = xtn2t2; +if( q== ipow(2,3) )xtn = xtn2t3; +if( q== ipow(2,4) )xtn = xtn2t4; +if( q== ipow(2,5) )xtn = xtn2t5; +if( q== ipow(2,6) )xtn = xtn2t6; +if( q== ipow(2,7) )xtn = xtn2t7; +if( q== ipow(2,8) )xtn = xtn2t8; +if( q== ipow(2,9) )xtn = xtn2t9; +if( q== ipow(2,10) )xtn = xtn2t10; +if( q== ipow(2,11) )xtn = xtn2t11; +if( q== ipow(2,12) )xtn = xtn2t12; +if( q== ipow(2,13) )xtn = xtn2t13; +if( q== ipow(2,14) )xtn = xtn2t14; +if( q== ipow(2,15) )xtn = xtn2t15; +if( q== ipow(2,16) )xtn = xtn2t16; +if( q== ipow(2,17) )xtn = xtn2t17; +if( q== ipow(2,18) )xtn = xtn2t18; +if( q== ipow(2,19) )xtn = xtn2t19; +if( q== ipow(2,20) )xtn = xtn2t20; +if( q== ipow(2,21) )xtn = xtn2t21; +if( q== ipow(2,22) )xtn = xtn2t22; +if( q== ipow(2,23) )xtn = xtn2t23; +if( q== ipow(2,24) )xtn = xtn2t24; +if( q== ipow(2,25) )xtn = xtn2t25; +if( q== ipow(2,26) )xtn = xtn2t26; +if( q== ipow(2,27) )xtn = xtn2t27; +if( q== ipow(2,28) )xtn = xtn2t28; +if( q== ipow(2,29) )xtn = xtn2t29; +if( q== ipow(3,2) )xtn = xtn3t2; +if( q== ipow(3,3) )xtn = xtn3t3; +if( q== ipow(3,4) )xtn = xtn3t4; +if( q== ipow(3,5) )xtn = xtn3t5; +if( q== ipow(3,6) )xtn = xtn3t6; +if( q== ipow(3,7) )xtn = xtn3t7; +if( q== ipow(3,8) )xtn = xtn3t8; +if( q== ipow(3,9) )xtn = xtn3t9; +if( q== ipow(3,10) )xtn = xtn3t10; +if( q== ipow(3,11) )xtn = xtn3t11; +if( q== ipow(3,12) )xtn = xtn3t12; +if( q== ipow(3,13) )xtn = xtn3t13; +if( q== ipow(3,14) )xtn = xtn3t14; +if( q== ipow(3,15) )xtn = xtn3t15; +if( q== ipow(3,16) )xtn = xtn3t16; +if( q== ipow(3,17) )xtn = xtn3t17; +if( q== ipow(3,18) )xtn = xtn3t18; +if( q== ipow(5,2) )xtn = xtn5t2; +if( q== ipow(5,3) )xtn = xtn5t3; +if( q== ipow(5,4) )xtn = xtn5t4; +if( q== ipow(5,5) )xtn = xtn5t5; +if( q== ipow(5,6) )xtn = xtn5t6; +if( q== ipow(5,7) )xtn = xtn5t7; +if( q== ipow(5,8) )xtn = xtn5t8; +if( q== ipow(5,9) )xtn = xtn5t9; +if( q== ipow(5,10) )xtn = xtn5t10; +if( q== ipow(5,11) )xtn = xtn5t11; +if( q== ipow(5,12) )xtn = xtn5t12; +if( q== ipow(7,2) )xtn = xtn7t2; +if( q== ipow(7,3) )xtn = xtn7t3; +if( q== ipow(7,4) )xtn = xtn7t4; +if( q== ipow(7,5) )xtn = xtn7t5; +if( q== ipow(7,6) )xtn = xtn7t6; +if( q== ipow(7,7) )xtn = xtn7t7; +if( q== ipow(7,8) )xtn = xtn7t8; +if( q== ipow(7,9) )xtn = xtn7t9; +if( q== ipow(7,10) )xtn = xtn7t10; +if( q== ipow(11,2) )xtn = xtn11t2; +if( q== ipow(11,3) )xtn = xtn11t3; +if( q== ipow(11,4) )xtn = xtn11t4; +if( q== ipow(11,5) )xtn = xtn11t5; +if( q== ipow(11,6) )xtn = xtn11t6; +if( q== ipow(11,7) )xtn = xtn11t7; +if( q== ipow(11,8) )xtn = xtn11t8; +if( q== ipow(13,2) )xtn = xtn13t2; +if( q== ipow(13,3) )xtn = xtn13t3; +if( q== ipow(13,4) )xtn = xtn13t4; +if( q== ipow(13,5) )xtn = xtn13t5; +if( q== ipow(13,6) )xtn = xtn13t6; +if( q== ipow(13,7) )xtn = xtn13t7; +if( q== ipow(13,8) )xtn = xtn13t8; +if( q== ipow(17,2) )xtn = xtn17t2; +if( q== ipow(17,3) )xtn = xtn17t3; +if( q== ipow(17,4) )xtn = xtn17t4; +if( q== ipow(17,5) )xtn = xtn17t5; +if( q== ipow(17,6) )xtn = xtn17t6; +if( q== ipow(17,7) )xtn = xtn17t7; +if( q== ipow(19,2) )xtn = xtn19t2; +if( q== ipow(19,3) )xtn = xtn19t3; +if( q== ipow(19,4) )xtn = xtn19t4; +if( q== ipow(19,5) )xtn = xtn19t5; +if( q== ipow(19,6) )xtn = xtn19t6; +if( q== ipow(19,7) )xtn = xtn19t7; +if( q== ipow(23,2) )xtn = xtn23t2; +if( q== ipow(23,3) )xtn = xtn23t3; +if( q== ipow(23,4) )xtn = xtn23t4; +if( q== ipow(23,5) )xtn = xtn23t5; +if( q== ipow(23,6) )xtn = xtn23t6; +if( q== ipow(29,2) )xtn = xtn29t2; +if( q== ipow(29,3) )xtn = xtn29t3; +if( q== ipow(29,4) )xtn = xtn29t4; +if( q== ipow(29,5) )xtn = xtn29t5; +if( q== ipow(29,6) )xtn = xtn29t6; +if( q== ipow(31,2) )xtn = xtn31t2; +if( q== ipow(31,3) )xtn = xtn31t3; +if( q== ipow(31,4) )xtn = xtn31t4; +if( q== ipow(31,5) )xtn = xtn31t5; +if( q== ipow(31,6) )xtn = xtn31t6; +if( q== ipow(37,2) )xtn = xtn37t2; +if( q== ipow(37,3) )xtn = xtn37t3; +if( q== ipow(37,4) )xtn = xtn37t4; +if( q== ipow(37,5) )xtn = xtn37t5; +if( q== ipow(41,2) )xtn = xtn41t2; +if( q== ipow(41,3) )xtn = xtn41t3; +if( q== ipow(41,4) )xtn = xtn41t4; +if( q== ipow(41,5) )xtn = xtn41t5; +if( q== ipow(43,2) )xtn = xtn43t2; +if( q== ipow(43,3) )xtn = xtn43t3; +if( q== ipow(43,4) )xtn = xtn43t4; +if( q== ipow(43,5) )xtn = xtn43t5; +if( q== ipow(47,2) )xtn = xtn47t2; +if( q== ipow(47,3) )xtn = xtn47t3; +if( q== ipow(47,4) )xtn = xtn47t4; +if( q== ipow(47,5) )xtn = xtn47t5; Index: /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/boselink.c =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/boselink.c (revision 25836) +++ /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/boselink.c (revision 25836) @@ -0,0 +1,150 @@ +#if defined(HAVE_CONFIG_H) && !defined(DISABLE_DAKOTA_CONFIG_H) + #include "ddace_config.h" +#endif +#include +#include +#include "galois.h" + +/* Fix for C99*/ +extern int bose(struct GF *gf, int **A, int ncol); /* construct.c */ +extern int bush(struct GF *gf, int **A, int str, int ncol); /* construct.c */ +extern void GF_free(struct GF *gf); /* galois.c */ +extern int GF_getfield(int q, struct GF *gf); /* gfields.c */ + +int bose_link( int n, int ninputs, int str, int ***AA ) +{ + int i, nsym, nsamples, **A; + double dtemp, dpower; + struct GF gf; + + if ( n <= 0 ) return -1; + + /* only one method for strength of 3 */ + + if ( str == 3 ) + { + dtemp = (double) n; + dtemp = pow(dtemp, 0.333333334); + nsym = (int) dtemp; + if( ninputs > (nsym+1) ){ + fprintf(stderr,"Only q+1 = %d cols given in Bush design.\n",nsym+1); + fprintf(stderr,"Columns requested was %d.\n",ninputs); + return -1; + } + if( !GF_getfield(nsym, &gf) ) { + fprintf(stderr,"Could not construct the Galois field needed\n"); + fprintf(stderr,"for the strength 3 Bush design.\n"); + GF_free( &gf ); + return -1; + } + nsamples = nsym * nsym * nsym; + A = imatrix( 0, nsamples, 0, ninputs-1 ); + if( !A ) + { + fprintf(stderr,"Could not allocate array for Bush design.\n"); + GF_free( &gf ); + return -1; + } + if( ! bush( &gf, A, 3, ninputs ) ) + { + fprintf(stderr,"Unable to construct the strength 3 "); + fprintf(stderr,"Bush design nsym=%d, ninputs=%d.\n", nsym,ninputs); + GF_free( &gf ); + return -1; + } + else + { + (*AA) = A; + return nsamples; + } + } + + /* only one method for strength greater than 3 */ + + if ( str > 3 ) + { + dtemp = (double) n; + dpower = 1.0 / (double) str + 0.00000001; + dtemp = pow(dtemp, dpower); + nsym = (int) dtemp; + if( ninputs > (nsym+1) ){ + fprintf(stderr,"Only q+1 = %d cols given in Bush design.\n",nsym+1); + fprintf(stderr,"Columns requested was %d.\n",ninputs); + return -1; + } + nsamples = nsym; + for ( i = 1; i < str; i++ ) nsamples = nsamples * nsym; + if( !GF_getfield(nsym, &gf) ){ + fprintf(stderr,"Could not construct the Galois field needed\n"); + fprintf(stderr,"for the strength %d Bush design\n",str); + fprintf(stderr,"on %d levels.\n", nsym); + GF_free( &gf ); + return -1; + } + A = imatrix( 0, nsamples-1, 0, ninputs-1 ); + if( !A ) + { + fprintf(stderr,"Could not allocate array for Bush design.\n"); + GF_free( &gf ); + return -1; + } + if( ! bush( &gf, A, str, ninputs ) ) + { + fprintf(stderr,"Unable to construct the strength %d \n", str); + fprintf(stderr,"Bush design nsym=%d, ninputs=%d.\n", nsym,ninputs); + GF_free( &gf ); + return -1; + } + else + { + (*AA) = A; + GF_free( &gf ); + return nsamples; + } + } + + /* for the cases when strength = 2 */ + + if ( str == 2 ) + { + dtemp = (double) n; + dtemp = pow(dtemp, 0.500001); + nsym = (int) dtemp; + + if ( ninputs > ( nsym + 1 ) ) + { + fprintf(stderr,"Number of samples too small to construct OA.\n"); + fprintf(stderr,"Need at least %d. \n", (ninputs-1)*(ninputs-1)); + return -1; + } + if( !GF_getfield( nsym, &gf) ) + { + fprintf(stderr,"Could not construct Galois field needed\n"); + fprintf(stderr,"for Bose design.\n"); + GF_free( &gf ); + return -1; + } + nsamples = nsym * nsym; + A = imatrix( 0, nsamples-1, 0, ninputs-1 ); + if( !A ) + { + fprintf(stderr,"Could not allocate array for Bose design.\n"); + GF_free( &gf ); + return -1; + } + if( ! bose( &gf, A, ninputs ) ) + { + fprintf(stderr,"Unable to construct Bose design q=%d,",nsym); + fprintf(stderr," ninputs=%d.\n", ninputs); + GF_free( &gf ); + return -1; + } + else + { + (*AA) = A; + GF_free( &gf ); + return nsamples; + } + } +} + Index: /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/construct.c =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/construct.c (revision 25836) +++ /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/construct.c (revision 25836) @@ -0,0 +1,410 @@ +#if defined(HAVE_CONFIG_H) && !defined(DISABLE_DAKOTA_CONFIG_H) + #include "ddace_config.h" +#endif +/* + + These programs construct and manipulate orthogonal +arrays. They were prepared by + + Art Owen + Department of Statistics + Sequoia Hall + Stanford CA 94305 + + They may be freely used and shared. This code comes +with no warranty of any kind. Use it at your own +risk. + + I thank the Semiconductor Research Corporation and +the National Science Foundation for supporting this +work. + +*/ + + +/* Constructions for designs using Galois fields */ + +#include +#include + +#include "galois.h" + +/* Fix for C99 */ +extern int ipow(int a, int b); /* primes.c */ +extern int isprime(int p); /* primes.c */ +extern void free_ivector(int *v, int nl, int nh); /* memory.c */ +extern void free_imatrix(int **m, int nrl, int nrh, int ncl, int nch); /* memory.c */ +extern int akodd(struct GF *gf, int *kay, int *b, int *c, int *k); /* akconst.c */ +extern int akeven(struct GF *gf, int *kay, int *b, int *c, int *k); /* akconst.c */ + +/* Glossary: + + bose: OA( q^2, q+1, q, 2 ) + R.C. Bose (1938) Sankhya Vol 3 pp 323-338 + bosecheck: test input to bose + + bosebush: OA( 2q^2, 2q+1, q, 2 ), only implemented for q=2^n + bosebushcheck: test input to bosebush + + polyeval: evaluate a polynomial with coefficients, argument + and result in a Galois field + +*/ + + +bosecheck( q,ncol ) +int q, ncol; +{ +if( ncol > q+1 ){ + fprintf(stderr,"Bose's design must have ncol <= q+1.\n"); + fprintf(stderr,"Had q=%d and ncol=%d.\n",q,ncol); + return 0; +} +if( ncol <= 0 ){ + fprintf(stderr,"Nonpositive number of columns requested for Bose's design\n"); + return 0; +} +return 1; +} + + +bose( gf, A, ncol ) +struct GF *gf; +int **A, ncol; +{ +int i,j, icol, q=gf->q, irow; + +if( !bosecheck(q,ncol) )return 0; + +irow = 0; +for( i=0; i 1 )A[ irow ][ icol++ ] = j; + for( icol=2; icolplus[j][gf->times[i][icol-1]]; + irow++; +} + + +return 1; +} + +itopoly( n,q,d,coef ) +int n,q,d,*coef; +{ +int i; + +for( i=0; i<=d; i++ ){ + coef[i] = n % q; + n = n/q; +} +} + + +polyeval( gf, d, poly, arg, value ) +/* find value = poly(arg) where poly is a polynomial of degree d + and all the arithmetic takes place in the given Galois field.*/ + +struct GF *gf; +int d, *poly, arg, *value; +{ +int i,ans; + +ans = 0; +for( i= d; i>=0; i-- ) /* Horner's rule */ + ans = gf->plus[ gf->times[ans][arg] ][ poly[i] ]; + +*value = ans; +} + +bushcheck(q,str,ncol) +int q,str,ncol; +{ +if( ncol > q+1 ){ + fprintf(stderr,"Bush designs require ncol <= q+1.\n"); + fprintf(stderr,"Cannot have q = %d and ncol = %d.\n",q,ncol); + return 0; +} +if( str > ncol ){ + fprintf(stderr,"It doesn't make sense to have an array of strength\n"); + fprintf(stderr,"%d with only %d columns.\n",str,ncol); + return 0; +} +if( str >= q+1 ){ + fprintf(stderr,"Bush's (1952) theorem has a condition tq; +if( !bushcheck(q,str,ncol) )return 0; + +coef = ivector( 0,str-1 ); +if( !coef ){ /* Very unlikely */ + fprintf(stderr,"Could not allocate memory for Bush design.\n"); + return 0; +} + +for( i=0; i4 ){ + fprintf(stderr,"This Addelman-Kempthorne OA(2q^2,ncol,q,2) is only\n"); + fprintf(stderr,"available for odd prime powers q and for even prime\n"); + fprintf(stderr,"powers q<=4. q=%d is not available, but a Bose Bush\n",q); + fprintf(stderr,"construction exists for that design.\n"); + return 0; +} + +if( ncol > 2*q+1 ){ + fprintf(stderr,"The Addelman-Kempthorne construction needs ncol <= 2q+1.\n"); + fprintf(stderr,"Can't have ncol = %d with q = %d,\n",ncol,q); + return 0; +} + +if( ncol == 2*q+1 ){ + fprintf(stderr,"\nWarning: The Addelman-Kempthorne construction with ncol = 2q+1\n"); + fprintf(stderr,"has a defect. While it is still an OA(2q^2,2q+1,q,2),\n"); + fprintf(stderr,"there exist some pairs of rows that agree in three columns.\n"); + fprintf(stderr,"The final column in the array is involved in all of these\n"); + fprintf(stderr,"triple coincidences.\n\n\n"); +} +return 1; +} + + +addelkemp( gf, A, ncol ) +/* Implement Addelman and Kempthorne's 1961 A.M.S. method with n=2 */ +struct GF *gf; +int ncol, **A; +{ +int i,j,m,p,q; +int kay,*b,*c,*k; /* A&K notation */ +int row, col, square, ksquare, temp; + +p=gf->p, q=gf->q; + +if( !addelkempcheck( q,p,ncol ) )return 0; + +b = ivector( 0,q-1 ); +c = ivector( 0,q-1 ); +k = ivector( 0,q-1 ); + +for( i=0; itimes[i][i]; + for( j=0; jplus[i][gf->times[m][j]]; + for( m=0; mplus[j][gf->times[m][i]]; + A[row][col++] = gf->plus[temp][square]; /* Rgt cols */ + } + if( coltimes[i][i]; + ksquare = gf->times[kay][square]; + for( j=0; jplus[A[row-q*q][col]][b[m]]; + if( colplus[ksquare][j]; /* q+1 */ + for( m=1; mtimes[i][k[m]]; + temp = gf->plus[ksquare][temp]; + temp = gf->plus[j][temp]; + A[row][col++] = gf->plus[temp][c[m]]; + } + if( col 2*q+1 ){ + fprintf(stderr,"The Bose-Bush construction needs ncol <= 2q+1.\n"); + fprintf(stderr,"Can't have ncol = %d with q = %d,\n",ncol,q); + return 0; +} + +if( ncol == 2*q+1 ){ + fprintf(stderr,"\nWarning: The Bose-Bush construction with ncol = 2q+1\n"); + fprintf(stderr,"has a defect. While it is still an OA(2q^2,2q+1,q,2),\n"); + fprintf(stderr,"there exist some pairs of rows that agree in three columns.\n\n\n"); +} +return 1; +} + +bosebush( gf, B, ncol ) +/* Implement Bose and Bush's 1952 A.M.S. method with p=2, u=1 */ +struct GF *gf; +int **B; +{ +int p,q,s,irow; +int i,j,k,mul; +int **A; + +p=gf->p, /* GF(q) used to generate design with q/2 levels */ +q=gf->q; +s=q/2; /* number of levels in design */ + +if( !bosebushcheck( s,p,ncol ) ) + return 0; + +A = imatrix(0,s-1,0,q-1); +if( !A ){ + fprintf(stderr,"Unable to allocate scratch space for Bose-Bush array.\n"); + return 0; +} + +irow = 0; +for( i=0; itimes[i][j]; + mul = mul % s; + for( k=0; kplus[mul][k];*/ + A[k][j] = gf->plus[mul][k]; + } + for( k=0; k lam*s+1 ){ + fprintf(stderr,"The Bose-Bush construction needs ncol <= lambda*q+1.\n"); + fprintf(stderr,"Can't have ncol = %d with lam = %d and q = %d,\n",ncol,lam,s); + return 0; +} + +if( ncol == lam*s+1 ){ + fprintf(stderr,"\nWarning: The Bose-Bush construction with ncol = lambda*q+1\n"); + fprintf(stderr,"has a defect. While it is still an OA(lambda*q^2,lambda*q+1,q,2),\n"); + fprintf(stderr,"it may have worse coincidence properties than\n"); + fprintf(stderr,"OA(lambda*q^2,lambda*q+1,q,2).\n"); +} +return 1; +} + +bosebushl( gf, lam, B, ncol ) +/* Implement Bose and Bush's 1952 A.M.S. method with given lambda */ +struct GF *gf; +int **B, lam; +{ +int p,q,s,irow; +int i,j,k,mul; +int **A; + +p=gf->p, /* GF(q) used to generate design with q/lam levels */ +q=gf->q; +s=q/lam; /* number of levels in design */ + +if( !bosebushlcheck( s,p,lam,ncol ) ) + return 0; + +A = imatrix(0,s-1,0,q-1); +if( !A ){ + fprintf(stderr,"Unable to allocate scratch space for Bose-Bush array.\n"); + return 0; +} + +irow = 0; +for( i=0; itimes[i][j]; + mul = mul % s; + for( k=0; kplus[mul][k];*/ + A[k][j] = gf->plus[mul][k]; + } + for( k=0; k +#include + +#include "galois.h" + +/* Fix for C99 */ +extern void free_ivector(int v, int nl, int nh); /* memory.c */ +extern void free_imatrix(int m, int nrl, int nrh, int ncl, int nch); /* memory.c */ + +/* Glossary: + + GF_poly_sum Addition in polynomial representation + GF_poly_prod Multiplication in polynomial representation + GF_poly2int Convert polynomial to integer in 0..q-1 + GF_ready Prepare (+,*,^-1) lookup tables + GF_print Print Galois field + GF_free Free storage + +*/ + + +/*---------------------------------------------------------------*/ + +GF_poly_sum( p,n,p1,p2,sum ) +int n,p,*p1,*p2,*sum; +{ +int i; + +for( i=0; in-1; i-- ) +for( j=0; j0; i-- ) + ans = (ans+poly[i])*p; +ans += poly[0]; + +return ans; +} + +/*---------------------------------------------------------------*/ + +#define GFPUNT {fprintf(stderr,"Unable to allocate space for Galois field on %d elements.\n",q);return 0;} + +GF_ready( gf,p,n,xton ) +/* + Make ready the Galois Field +*/ +struct GF *gf; +int n,p,*xton; +{ +int i,j,q,click,*poly; + +poly = ivector(0,n-1); + +gf->n = n; +gf->p = p; +q = 1; +for( i=0; iq = q; +gf->xton = ivector(0,n-1); if( !gf->xton )GFPUNT; +for( i=0; ixton[i] = xton[i]; +gf->plus = imatrix(0,q-1,0,q-1); if( !gf->plus )GFPUNT; +gf->times= imatrix(0,q-1,0,q-1); if( !gf->times )GFPUNT; +gf->inv = ivector(0,q-1); if( !gf->inv )GFPUNT; +gf->neg = ivector(0,q-1); if( !gf->neg )GFPUNT; +gf->root = ivector(0,q-1); if( !gf->root )GFPUNT; +gf->poly = imatrix(0,q-1,0,n-1); if( !gf->poly )GFPUNT; + +for( i=0; ipoly[0][i] = 0; + +for( i=1; ipoly[i-1][click]==(p-1); click++ ) + gf->poly[i][click] = 0; + gf->poly[i][click] = gf->poly[i-1][click]+1; + for( j=click+1; jpoly[i][j] = gf->poly[i-1][j]; +} + +for( i=0; ipoly[i],gf->poly[j],poly ); + gf->plus[i][j] = GF_poly2int( p,n,poly ); + GF_poly_prod( p,n,xton,gf->poly[i],gf->poly[j],poly ); + gf->times[i][j] = GF_poly2int( p,n,poly ); +} + +for( i=0; iinv[i] = -1; + for( j=0; jtimes[i][j]==1 ) + gf->inv[i] = j; + if( i>0 && gf->inv[i] <= 0 ){ + fprintf(stderr,"There is something wrong with the Galois field\n"); + fprintf(stderr,"used for q=%d. Element %d has no reciprocal.\n",q,i); + return 0; + } +} + +for( i=0; ineg[i] = -1; + for( j=0; jplus[i][j]==0 ) + gf->neg[i] = j; + if( i>0 && gf->neg[i] <= 0 ){ + fprintf(stderr,"There is something wrong with the Galois field\n"); + fprintf(stderr,"used for q=%d. Element %d has no negative.\n",q,i); + return 0; + } +} + +for( i=0; iroot[i] = -1; + for( j=0; jtimes[j][j]==i ) + gf->root[i] = j; +} + +/*printf("%d %d %d\n",q,p,n);*/ + +/* Added by J Cramp 07.02.04 to fix memory leak. */ +free_ivector(poly,0,n-1); + +return 1; +} + +/*---------------------------------------------------------------*/ + +GF_print( gf ) + +struct GF *gf; +{ +int i,j,n,p,q; + +n=gf->n, p=gf->p, q=gf->q; + +if( q>999 )fprintf(stderr,"Warning q=%d will overflow print field.\n",q); + +printf("\nFor GF(%d) p=%d n=%d\n",q,p,n); +printf("x**n = ("); +for( i=0; ixton[i]); +printf("%d)\n",gf->xton[n-1]); +printf("\n\nGF(%d) Polynomial coefficients:\n",q); +for( i=0; ipoly[i][j]); + printf("\n"); +} +printf("\n\nGF(%d) Addition Table\n",q); +for( i=0; iplus[i][j]); + printf("\n"); +} +printf("\n\nGF(%d) Multiplication table\n",q); +for( i=0; itimes[i][j]); + printf("\n"); +} +printf("\n\nGF(%d) Reciprocals\n",q); +for( i=1; iinv[i]); + +printf("\n\nGF(%d) Negatives\n",q); +for( i=0; ineg[i]); + +printf("\n\nGF(%d) Square roots\n",q); +for( i=0; iroot[i]); +} + +/*---------------------------------------------------------------*/ + +GF_free( gf ) +/* + Deallocate the Galois Field +*/ +struct GF *gf; +{ +/*int q,p,n; +q = gf->q, p=gf->p, n=gf->n;*/ + +int q,n; +q = gf->q, n=gf->n; /* Shuts lint up */ + +free_imatrix(gf->poly,0,q-1,0,n-1); +free_ivector(gf->root,0,q-1); +free_ivector(gf->neg,0,q-1); +free_ivector(gf->inv,0,q-1); +free_imatrix(gf->times,0,q-1,0,q-1); +free_imatrix(gf->plus,0,q-1,0,q-1); +free_ivector(gf->xton,0,n-1); +} Index: /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/gfields.c =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/gfields.c (revision 25836) +++ /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/gfields.c (revision 25836) @@ -0,0 +1,120 @@ +#if defined(HAVE_CONFIG_H) && !defined(DISABLE_DAKOTA_CONFIG_H) + #include "ddace_config.h" +#endif +/* + + These programs construct and manipulate orthogonal +arrays. They were prepared by + + Art Owen + Department of Statistics + Sequoia Hall + Stanford CA 94305 + + They may be freely used and shared. This code comes +with no warranty of any kind. Use it at your own +risk. + + I thank the Semiconductor Research Corporation and +the National Science Foundation for supporting this +work. + +*/ + + +/* Construction of specific Galois fields. See galois.c + for manipulation of generic Galois fields. + + To add a new Galois field GF(q)=GF(p^n) it is necessary + to find the polynomial representation of x^n, and use it to + include another *xtn--- vector like those used below. + +*/ + +#include +#include + +#include "galois.h" + +/* Fix for C99 */ +extern int isprime(int p); /* primes.c */ +extern void primepow(int q, int *p, int *n, int *isit); /* primes.c */ +extern int GF_ready(struct GF *gf, int p, int n, int *xton); /* galois.c */ + +/* Glossary: + + xtn2t2 Polynomial representation of x^2 in gf2t2 + xtn2t3 Polynomial representation of x^3 in gf2t3 + . . . Polynomial representation of p^n in gfptn + xtn13t2 Polynomial representation of x^2 in gf13t2 + + GF_set_fields Initialize polynomial representations + GF_fields_are_set Indicates initialization done + GF_getfield Construct and return GF(q) if possible +*/ + +#include "xtndeclare.h" +int *xtnpt1; + +int GF_fields_are_set = 0; + +GF_set_fields() +{ +/* Brute force set up of defining vectors, from Carmichael */ + +/* Declare x-to-the-power-n vectors, for GFs p-to-the-n */ + +if( GF_fields_are_set ) + fprintf(stderr,"Warning: Fields being re-initialized. Possible memory waste.\n"); + + +#include "xtnset.h" + +xtnpt1 = ivector(0,0); +xtnpt1[0] = 0; +GF_fields_are_set = 1; +} + + +GF_getfield( q, gf ) +int q; +struct GF *gf; +{ +int *xtn; +int p,n,ispp; + +if( !GF_fields_are_set ) + GF_set_fields(); + +if( q<1 ){ /* Impossible argument */ + fprintf(stderr,"Field must have positive number of elements.\n"); + return 0; } +if( q==1 ){ /* Pointless argument */ + fprintf(stderr,"Field with 1 element was requested.\n"); + return 0; } + +primepow( q,&p,&n,&ispp ); +if( !ispp ){ + fprintf(stderr,"q=%d is not a prime power.\n",q); + return 0; } + +xtn = NULL; + +#include "xtndispatch.h" + +if( isprime(q) )xtn = xtnpt1; /* Could have tested p=q, or n=1 */ + +if( xtn ){ + if( GF_ready( gf,p,n,xtn ) ) + return 1; + else{ + fprintf(stderr,"Construction failed for GF(%d).\n",q); + return 0; + } +} +else { + fprintf(stderr,"GF(%d) = GF(%d^%d) is not included in this program.\n",q,p,n); + fprintf(stderr,"To add it, consider modifying gfields.c.\n"); + return 0; +} +} Index: /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/oa.c =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/oa.c (revision 25836) +++ /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/oa.c (revision 25836) @@ -0,0 +1,664 @@ +#if defined(HAVE_CONFIG_H) && !defined(DISABLE_DAKOTA_CONFIG_H) + #include "ddace_config.h" +#endif +/** + + These programs construct and manipulate orthogonal +arrays. They were prepared by + + Art Owen + Department of Statistics + Sequoia Hall + Stanford CA 94305 + + They may be freely used and shared. This code comes +with no warranty of any kind. Use it at your own +risk. + + I thank the Semiconductor Research Corporation and +the National Science Foundation for supporting this +work. + +*/ + + +#include +/* for exit: */ +#include + +#include "oa.h" + +int **imatrix(), *ivector(); + +/* Fix for C99 */ +extern int grow_imatrix_byrows(int ***imat, int oldrowsize, int newrowsize, int colsize); /* memory.c */ +extern void free_ivector(int *v, int nl, int nh); /* memory.c */ +extern int ipow(int a, int b); /* primes.c */ + +/** + + Glossary: + + OA_put write OA to standard output + OA_fput write OA to stream + OA_get get OA from standard input + OA_fget get OA from stream + + OA_parsein read arguments q,nrow,ncol to OA "filter programs" + OA_strworkcheck warn about large work loads in strength checking programs + +*/ + + +/* OUTPUT OUTPUT OUTPUT OUTPUT OUTPUT OUTPUT OUTPUT */ + +OA_fput( stream,A,n,k,q ) +FILE *stream; +int **A, n, k, q; +{ +int i,j; +char* format; + +format = "%d%s"; +if( q < 1000 )format = "%3d%s"; +if( q < 100 )format = "%2d%s"; +if( q < 10 )format = "%1d%s"; +if( q < 0 )format = "%d%s"; + +for( i=0; i= q ){ + fprintf(stderr,"Invalid array element %d. All elements should be\n", + A[i][j]); + fprintf(stderr,"strictly less than q = %d.\n",q); + return 0; + }else if( A[i][j] <0 ){ + fprintf(stderr,"Invalid array element %d, should be >= 0.\n",A[i][j]); + return 0; + } + +if( eof_assert && fscanf(stream,"%d",&eof_assert) != EOF ){ + fprintf(stderr,"Input has more integers than expected.\n"); + fprintf(stderr,"Perhaps the number of rows and/or columns is incorrect.\n"); + return 0; + } +return 1; +} + +OA_get( A,n,k,q, eof_assert ) +int **A, n, k, q, eof_assert; +{ +return OA_fget( stdin,A,n,k,q,eof_assert ); +} + +/* READ READ READ READ READ READ READ READ READ */ + +/* Read array and determine dimensions. Inspired by approach +taken in Xgobi. */ + +#define MAXK 5000 +#define ROWINC 1000 +int line0[ MAXK ]; + +OA_fread( stream,A,n,k,q ) +FILE *stream; +int ***A, *n, *k, *q; +{ +int i, j; +char c; + +*k = 0; + +while( (c = getc(stream)) != '\n' ){ + if( c=='\t' || c==' ' ) + ; + else{ + ungetc(c,stream); + if( *k >= MAXK ){ + fprintf(stderr,"Error: Input appears to have more than %d columns.\n",*k); + fprintf(stderr,"If such large input is desired, increase MAXK in oa.c\n"); + fprintf(stderr,"and re-install the software.\n"); + return 0; + } + if( fscanf(stream,"%d",&line0[(*k)++]) <= 0 ){ + fprintf(stderr,"Error: no newline character found. Could be empty\n"); + fprintf(stderr,"input or matrix all on one line.\n"); + return 0; + } + } +} + +*A = imatrix( 0,ROWINC-1, 0,*k-1 ); +if( !(*A) ){ + fprintf(stderr,"Unable to allocate memory to read the array.\n"); + return 0; +} + +*n = 0; +for( j=0; j<*k; j++ ) + A[0][*n][j] = line0[j]; + +while( 1 ){ + (*n)++; + if( (*n % ROWINC)==0 ) + if( !grow_imatrix_byrows( A, (*n), (*n)+ROWINC, *k ) ){ + fprintf(stderr,"Unable to allocate extra memory for row %d of the array.\n" + ,*n); + return 0; + } + + if( fscanf(stream,"%d",&(A[0][*n][0])) == EOF ) + break; + + for( j=1; j<*k; j++ ) + if( fscanf(stream,"%d",&(A[0][*n][j])) == EOF ){ + fprintf(stderr,"Unexpected end of input encountered. Row %d only has\n",*n); + fprintf(stderr,"%d elements of %d expected.\n",j,*k); + return 0; + } +} +*q = 0; /* Assume that q = max(A)+1 */ + +for( i=0; i<*n; i++ ) +for( j=0; j<*k; j++ ) + if( A[0][i][j] > *q ) + *q = A[0][i][j]; +*q = *q +1; + +return 1; +} + +OA_read( A,n,k,q ) +int ***A, *n, *k, *q; +{ +return OA_fread( stdin,A,n,k,q ); +} + +/* PARSE PARSE PARSE PARSE PARSE PARSE PARSE PARSE */ + +OA_parsein( argc,argv, q,nrow,ncol, A ) +int argc; +char *argv[]; +int *q, *nrow, *ncol, ***A; +{ +if( argc<=1 ){ + if( !OA_read( A,nrow,ncol,q ) ){ + fprintf(stderr,"Fatal error while reading the array.\n"); + exit(1); + } +} +else if( argc==2 ){ + sscanf(argv[1],"%d",q); + scanf("%d %d",nrow,ncol); +}else if( argc==3 ){ + sscanf(argv[1],"%d",q); + sscanf(argv[2],"%d",nrow); + scanf("%d",ncol); +}else{ + sscanf(argv[1],"%d",q); + sscanf(argv[2],"%d",nrow); + sscanf(argv[3],"%d",ncol); +} + +if( *q<1 ){ + fprintf(stderr,"Array has only %d symbol(s). At least one\n",*q); + fprintf(stderr,"symbol is necessary in an orthogonal array.\n"); + exit(1); +} + +if( *ncol<1 ){ + fprintf(stderr,"Array has only %d column(s). At least one\n",*ncol); + fprintf(stderr,"column is necessary in an orthogonal array.\n"); + exit(1); +} + +if( *nrow<1 ){ + fprintf(stderr,"Array has only %d rows. At least one\n",*nrow); + fprintf(stderr,"row is necessary in an orthogonal array.\n"); + exit(1); +} + + +if( argc >1 ){ + *A = imatrix( 0,*nrow-1,0,*ncol-1 ); + if( !(*A) ){ + fprintf(stderr,"The array is too large (%d by %d) to fit in memory.\n",nrow,ncol); + exit(1); + } + + if( !OA_get( *A,*nrow,*ncol,*q, 1 ) ){/* Read 'em all */ + fprintf(stderr,"Read error getting the orthogonal array.\n"); + exit(1); + } +} +} + + +/* WORK WORK WORK WORK WORK WORK WORK WORK WORK */ + +OA_strworkcheck( work,str ) +double work; +int str; +{ +if( work > BIGWORK ){ + fprintf(stderr,"If the array has strength %d, %g comparisons will\n", + str, work); + fprintf(stderr,"be required to prove it. This might take a long time.\n"); + fprintf(stderr,"This warning is triggered when more than %d comparisons\n", + BIGWORK); + fprintf(stderr,"are required. To avoid this warning increase BIGWORK in\n"); + fprintf(stderr,"oa.h. Intermediate results will be printed.\n\n"); + fflush(stderr); +}else if( work > MEDWORK ){ + fprintf(stderr,"Since more than %d comparisons may be required to\n",MEDWORK); + fprintf(stderr,"to check whether the array has strength %d, intermediate\n", + str); + fprintf(stderr,"results will be printed. To avoid this warning increase\n"); + fprintf(stderr,"MEDWORK in oa.h\n\n"); + fflush(stderr); +} +} + + +/* STRENGTH STRENGTH STRENGTH STRENGTH STRENGTH */ + +/* Check strength 0 */ +OA_str0( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1; + +for( j1=0; j1= q ){ + if( verbose >= 2 ){ + printf("Array is not even of strength 0, that is there are elements\n"); + // BMA 20141204; added q-1 as argument to silence compiler warning + //printf("other than integers 0 through %d inclusive in it.\n"); + printf("other than integers 0 through %d inclusive in it.\n", (q-1)); + printf("The first exception is A[%d][%d] = %d.\n",i,j1,A[i][j1]); + } + return 0; + } +if( verbose >=2 ) + printf("The array has strength (at least) 0.\n"); +return 1; +} + + +/* Check strength 1 */ +OA_str1( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1, q1; +int lambda, count; +double work; + +if( nrow%q ){ + if( verbose >= 2 ){ + printf("The array cannot have strength 1, because the number\n"); + printf("of rows %d is not a multiple of q = %d.\n",nrow,q); + } + return 0; +} + +lambda = nrow/q; +work = nrow * ncol * q * 1.0; +OA_strworkcheck( work,1 ); +for( j1=0; j1= 2 ){ + printf("Array is not of strength 1. The first violation arises for\n"); + printf("the number of times A[,%d] = %d.\n", + j1, q1); + printf("This happened in %d rows, it should have happened in %d rows.\n", + count, lambda); + } + return 0; + } + } +if( work > MEDWORK && verbose > 0 ) + fprintf(stderr,"No violation of strength 1 involves column %d.\n",j1); +} +if( verbose >=2 ) + printf("The array has strength (at least) 1.\n"); +return 1; +} + +/* Check strength 2 */ +OA_str2( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1,j2, q1,q2; +int lambda, count; +double work; + +if( ncol<2 ){ + if( verbose > 0 ){ + fprintf(stderr,"Array has only %d column(s). At least two\n",ncol); + fprintf(stderr,"columns are necessary for strength 2 to make sense.\n"); + } + return 0; +} +if( nrow % (q*q) ){ + if( verbose > 0 ){ + fprintf(stderr,"The array cannot have strength 2, because the number\n"); + fprintf(stderr,"of rows %d is not a multiple of q^2 = %d^2 = %d.\n",nrow,q,q*q); + } + return 0; +} + +lambda = nrow/(q*q); +work = nrow*ncol*(ncol-1.0)*q*q/2.0; +OA_strworkcheck( work,2 ); + +for( j1=0; j1= 2 ){ + printf("Array is not of strength 2. The first violation arises for\n"); + printf("the number of times (A[,%d],A[,%d]) = (%d,%d).\n", + j1,j2, q1,q2 ); + printf("This happened in %d rows, it should have happened in %d rows.\n", + count, lambda); + } + return 0; + } + } +} +if( work > MEDWORK && verbose > 0 ) + fprintf(stderr,"No violation of strength 2 involves column %d.\n",j1); +} + +if( verbose >=2 ) + printf("The array has strength (at least) 2.\n"); +return 1; +} + + + +/* Check strength 3 */ +OA_str3( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1,j2,j3, q1,q2,q3; +int lambda, count; +double work; + +if( ncol<3 ){ + if( verbose > 0 ){ + fprintf(stderr,"Array has only %d column(s). At least three\n",ncol); + fprintf(stderr,"columns are necessary for strength 3 to make sense.\n"); + } + return 0; +} +if( nrow % (q*q*q) ){ + if( verbose > 0 ){ + fprintf(stderr,"The array cannot have strength 3, because the number\n"); + fprintf(stderr,"of rows %d is not a multiple of q^3 = %d^3 = %d.\n",nrow,q,q*q*q); + } + return 0; +} + +lambda = nrow/(q*q*q); +work = nrow*ncol*(ncol-1.0)*(ncol-2.0)*q*q*q/6.0; +OA_strworkcheck( work,3 ); + +for( j1=0; j1= 2 ){ + printf("Array is not of strength 3. The first violation arises for\n"); + printf("the number of times (A[,%d],A[,%d],A[,%d]) = (%d,%d,%d).\n", + j1,j2,j3, q1,q2,q3 ); + printf("This happened in %d rows, it should have happened in %d rows.\n", + count, lambda); + } + return 0; + } + } +} +if( work > MEDWORK && verbose > 0 ) + fprintf(stderr,"No violation of strength 3 involves column %d.\n",j1); +} +if( verbose >=2 ) + printf("The array has strength (at least) 3.\n"); +return 1; +} + + +/* Check strength 4 */ +OA_str4( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1,j2,j3,j4, q1,q2,q3,q4; +int lambda, count; +double work; + +if( ncol<4 ){ + if( verbose > 0 ){ + fprintf(stderr,"Array has only %d column(s). At least four\n",ncol); + fprintf(stderr,"columns are necessary for strength 4 to make sense.\n"); + } + return 0; +} +if( nrow % (q*q*q*q) ){ + if( verbose > 0 ){ + fprintf(stderr,"The array cannot have strength 4, because the number\n"); + fprintf(stderr,"of rows %d is not a multiple of q^4 = %d^4 = %d.\n",nrow,q,q*q*q*q); + } + return 0; +} + +lambda = nrow/(q*q*q*q); +work = nrow*ncol*(ncol-1.0)*(ncol-2.0)*(ncol-3.0)*q*q*q*q/24.0; +OA_strworkcheck( work,4 ); + +for( j1=0; j1= 2 ){ + printf("Array is not of strength 4. The first violation arises for\n"); + printf("the number of times (A[,%d],A[,%d],A[,%d],A[,%d]) = (%d,%d,%d,%d).\n", + j1,j2,j3,j4, q1,q2,q3,q4 ); + printf("This happened in %d rows, it should have happened in %d rows.\n", + count, lambda); + } + return 0; + } + } + } +} +if( work > MEDWORK && verbose > 0 ) + fprintf(stderr,"No violation of strength 4 involves column %d.\n",j1); + +if( verbose >=2 ) + printf("The array has strength (at least) 4.\n"); +return 1; +} + + +/* Check strength t */ +OA_strt( q,nrow,ncol,A,t,verbose ) +int q,nrow,ncol,**A,t,verbose; +{ +int row, i, ic, iq, *clist, *qlist, ctuples, qtuples; +int lambda, count, match; +double work; + +if( t<0 ){ + if( verbose > 0 ){ + fprintf(stderr,"Don't know how to verify strength %d. It doesn't\n",t); + fprintf(stderr,"make sense.\n"); + } + return 0; +} +if( ncol 0 ){ + fprintf(stderr,"Array has only %d column(s). At least %d\n",ncol,t); + fprintf(stderr,"columns are necessary for strength %d to make sense.\n",t); + } + return 0; +} +if( t==0 ) + return OA_str0( q,nrow,ncol,A,verbose ); +if( nrow % ipow(q,t) ){ + if( verbose > 0 ){ + fprintf(stderr,"The array cannot have strength %d, because the number\n",t); + fprintf(stderr,"of rows %d is not a multiple of q^%d = %d^%d = %d.\n", + nrow,t,q,t,ipow(q,t)); + } + return 0; +} + +lambda = nrow/ipow(q,t); +work = nrow*ipow(q,t); +ctuples = 1; + +clist = ivector( 0,t-1 ); +qlist = ivector( 0,t-1 ); + +for( i=0; i= 2 ){ + printf("Array is not of strength %d. The first violation arises for\n",t); + printf("the number of times ("); + for( i=0; i=0; i-- ){ + qlist[i] = (qlist[i]+1) % q; + if( qlist[i] )break; + } + } + + for( i= t-1; i>=0; i-- ){ + clist[i] = (clist[i]+1) % (ncol+i-t+1); + if( clist[i] )break; + } + + if( work > MEDWORK && verbose > 0 && (t==1||t>1 && clist[1]==0) ) + fprintf(stderr,"No violation of strength %d involves column %d.\n", + t,(clist[0]+ncol-1)%ncol); + + for( i=1; i< t; i++ ) + if( clist[i] <= clist[i-1] ) + clist[i] = clist[i-1]+1; +} + +if( verbose >=2 ) + printf("The array has strength (at least) %d.\n",t); + +/* Added by J Cramp on 07.02.04 to + * fix memory leak problems. */ +free_ivector(clist,0,t-1); +free_ivector(qlist,0,t-1); + +return 1; +} + +void OA_strength( q,nrow,ncol,A,str,verbose ) +int q,nrow,ncol,**A,*str, verbose; +/* + Calculate and return the strength of the array A. + +verbose = 0 => No printed output +verbose = 1 => Only stderr output +verbose = 2 => Output to both stdout and stderr + +*/ +{ +*str = -1; + +if( OA_str0( q,nrow,ncol,A,verbose) ) + *str = 0; +else + return; +if( OA_str1( q,nrow,ncol,A,verbose) ) + *str = 1; +else + return; +while( OA_strt( q,nrow,ncol,A,*str+1,verbose ) ) + (*str)++; +return; +} Index: /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr-scanner.c =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr-scanner.c (revision 25836) +++ /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr-scanner.c (revision 25836) @@ -0,0 +1,2063 @@ +/* A lexical scanner generated by flex*/ + +/* Scanner skeleton version: + * $Header: /home/daffy/u0/vern/flex/RCS/flex.skl,v 2.91 96/09/10 16:58:48 vern Exp $ + */ + +#define FLEX_SCANNER +#define YY_FLEX_MAJOR_VERSION 2 +#define YY_FLEX_MINOR_VERSION 5 + +#include + + +/* cfront 1.2 defines "c_plusplus" instead of "__cplusplus" */ +#ifdef c_plusplus +#ifndef __cplusplus +#define __cplusplus +#endif +#endif + + +#ifdef __cplusplus + +#include + +/* Use prototypes in function declarations. */ +#define YY_USE_PROTOS + +/* The "const" storage-class-modifier is valid. */ +#define YY_USE_CONST + +#else /* ! __cplusplus */ + +#if __STDC__ + +#define YY_USE_PROTOS +#define YY_USE_CONST + +#endif /* __STDC__ */ +#endif /* ! __cplusplus */ + +#ifdef __TURBOC__ + #pragma warn -rch + #pragma warn -use +#include +#include +#define YY_USE_CONST +#define YY_USE_PROTOS +#endif + +#ifdef YY_USE_CONST +#define nidrconst const +#else +#define nidrconst +#endif + + +#ifdef YY_USE_PROTOS +#define YY_PROTO(proto) proto +#else +#define YY_PROTO(proto) () +#endif + +/* Returned upon end-of-file. */ +#define YY_NULL 0 + +/* Promotes a possibly negative, possibly signed char to an unsigned + * integer for use as an array index. If the signed char is negative, + * we want to instead treat it as an 8-bit unsigned char, hence the + * double cast. + */ +#define YY_SC_TO_UI(c) ((unsigned int) (unsigned char) c) + +/* Enter a start condition. This macro really ought to take a parameter, + * but we do it the disgusting crufty way forced on us by the ()-less + * definition of BEGIN. + */ +#define BEGIN nidr_start = 1 + 2 * + +/* Translate the current start state into a value that can be later handed + * to BEGIN to return to the state. The YYSTATE alias is for lex + * compatibility. + */ +#define YY_START ((nidr_start - 1) / 2) +#define YYSTATE YY_START + +/* Action number for EOF rule of a given start state. */ +#define YY_STATE_EOF(state) (YY_END_OF_BUFFER + state + 1) + +/* Special action meaning "start processing a new file". */ +#define YY_NEW_FILE nidrrestart( nidrin ) + +#define YY_END_OF_BUFFER_CHAR 0 + +/* Size of default input buffer. */ +#define YY_BUF_SIZE 16384 + +typedef struct nidr_buffer_state *YY_BUFFER_STATE; + +extern int nidrleng; +extern FILE *nidrin, *nidrout; + +#define EOB_ACT_CONTINUE_SCAN 0 +#define EOB_ACT_END_OF_FILE 1 +#define EOB_ACT_LAST_MATCH 2 + +/* The funky do-while in the following #define is used to turn the definition + * int a single C statement (which needs a semi-colon terminator). This + * avoids problems with code like: + * + * if ( condition_holds ) + * nidrless( 5 ); + * else + * do_something_else(); + * + * Prior to using the do-while the compiler would get upset at the + * "else" because it interpreted the "if" statement as being all + * done when it reached the ';' after the nidrless() call. + */ + +/* Return all but the first 'n' matched characters back to the input stream. */ + +#define nidrless(n) \ + do \ + { \ + /* Undo effects of setting up nidrtext. */ \ + *nidr_cp = nidr_hold_char; \ + YY_RESTORE_YY_MORE_OFFSET \ + nidr_c_buf_p = nidr_cp = nidr_bp + n - YY_MORE_ADJ; \ + YY_DO_BEFORE_ACTION; /* set up nidrtext again */ \ + } \ + while ( 0 ) + +#define unput(c) nidrunput( c, nidrtext_ptr ) + +/* Some routines like nidr_flex_realloc() are emitted as static but are + not called by all lexers. This generates warnings in some compilers, + notably GCC. Arrange to suppress these. */ +#ifdef __GNUC__ +#define YY_MAY_BE_UNUSED __attribute__((unused)) +#else +#define YY_MAY_BE_UNUSED +#endif + +/* The following is because we cannot portably get our hands on size_t + * (without autoconf's help, which isn't available because we want + * flex-generated scanners to compile on their own). + */ +typedef unsigned int nidr_size_t; + + +struct nidr_buffer_state + { + FILE *nidr_input_file; + + char *nidr_ch_buf; /* input buffer */ + char *nidr_buf_pos; /* current position in input buffer */ + + /* Size of input buffer in bytes, not including room for EOB + * characters. + */ + nidr_size_t nidr_buf_size; + + /* Number of characters read into nidr_ch_buf, not including EOB + * characters. + */ + int nidr_n_chars; + + /* Whether we "own" the buffer - i.e., we know we created it, + * and can realloc() it to grow it, and should free() it to + * delete it. + */ + int nidr_is_our_buffer; + + /* Whether this is an "interactive" input source; if so, and + * if we're using stdio for input, then we want to use getc() + * instead of fread(), to make sure we stop fetching input after + * each newline. + */ + int nidr_is_interactive; + + /* Whether we're considered to be at the beginning of a line. + * If so, '^' rules will be active on the next match, otherwise + * not. + */ + int nidr_at_bol; + + /* Whether to try to fill the input buffer when we reach the + * end of it. + */ + int nidr_fill_buffer; + + int nidr_buffer_status; +#define YY_BUFFER_NEW 0 +#define YY_BUFFER_NORMAL 1 + /* When an EOF's been seen but there's still some text to process + * then we mark the buffer as YY_EOF_PENDING, to indicate that we + * shouldn't try reading from the input source any more. We might + * still have a bunch of tokens to match, though, because of + * possible backing-up. + * + * When we actually see the EOF, we change the status to "new" + * (via nidrrestart()), so that the user can continue scanning by + * just pointing nidrin at a new input file. + */ +#define YY_BUFFER_EOF_PENDING 2 + }; + +static YY_BUFFER_STATE nidr_current_buffer = 0; + +/* We provide macros for accessing buffer states in case in the + * future we want to put the buffer states in a more general + * "scanner state". + */ +#define YY_CURRENT_BUFFER nidr_current_buffer + + +/* nidr_hold_char holds the character lost when nidrtext is formed. */ +static char nidr_hold_char; + +static int nidr_n_chars; /* number of characters read into nidr_ch_buf */ + + +int nidrleng; + +/* Points to current character in buffer. */ +static char *nidr_c_buf_p = (char *) 0; +static int nidr_init = 1; /* whether we need to initialize */ +static int nidr_start = 0; /* start state number */ + +/* Flag which is used to allow nidrwrap()'s to do buffer switches + * instead of setting up a fresh nidrin. A bit of a hack ... + */ +static int nidr_did_buffer_switch_on_eof; + +void nidrrestart YY_PROTO(( FILE *input_file )); + +void nidr_switch_to_buffer YY_PROTO(( YY_BUFFER_STATE new_buffer )); +void nidr_load_buffer_state YY_PROTO(( void )); +YY_BUFFER_STATE nidr_create_buffer YY_PROTO(( FILE *file, int size )); +void nidr_delete_buffer YY_PROTO(( YY_BUFFER_STATE b )); +void nidr_init_buffer YY_PROTO(( YY_BUFFER_STATE b, FILE *file )); +void nidr_flush_buffer YY_PROTO(( YY_BUFFER_STATE b )); +#define YY_FLUSH_BUFFER nidr_flush_buffer( nidr_current_buffer ) + +YY_BUFFER_STATE nidr_scan_buffer YY_PROTO(( char *base, nidr_size_t size )); +YY_BUFFER_STATE nidr_scan_string YY_PROTO(( nidrconst char *nidr_str )); +YY_BUFFER_STATE nidr_scan_bytes YY_PROTO(( nidrconst char *bytes, int len )); + +static void *nidr_flex_alloc YY_PROTO(( nidr_size_t )); +static void *nidr_flex_realloc YY_PROTO(( void *, nidr_size_t )) YY_MAY_BE_UNUSED; +static void nidr_flex_free YY_PROTO(( void * )); + +#define nidr_new_buffer nidr_create_buffer + +#define nidr_set_interactive(is_interactive) \ + { \ + if ( ! nidr_current_buffer ) \ + nidr_current_buffer = nidr_create_buffer( nidrin, YY_BUF_SIZE ); \ + nidr_current_buffer->nidr_is_interactive = is_interactive; \ + } + +#define nidr_set_bol(at_bol) \ + { \ + if ( ! nidr_current_buffer ) \ + nidr_current_buffer = nidr_create_buffer( nidrin, YY_BUF_SIZE ); \ + nidr_current_buffer->nidr_at_bol = at_bol; \ + } + +#define YY_AT_BOL() (nidr_current_buffer->nidr_at_bol) + +typedef unsigned char YY_CHAR; +FILE *nidrin = (FILE *) 0, *nidrout = (FILE *) 0; +typedef int nidr_state_type; +extern char *nidrtext; +#define nidrtext_ptr nidrtext + +static nidr_state_type nidr_get_previous_state YY_PROTO(( void )); +static nidr_state_type nidr_try_NUL_trans YY_PROTO(( nidr_state_type current_state )); +static int nidr_get_next_buffer YY_PROTO(( void )); +static void nidr_fatal_error YY_PROTO(( nidrconst char msg[] )); + +/* Done after the current pattern has been matched and before the + * corresponding action - sets up nidrtext. + */ +#define YY_DO_BEFORE_ACTION \ + nidrtext_ptr = nidr_bp; \ + nidrtext_ptr -= nidr_more_len; \ + nidrleng = (int) (nidr_cp - nidrtext_ptr); \ + nidr_hold_char = *nidr_cp; \ + *nidr_cp = '\0'; \ + nidr_c_buf_p = nidr_cp; + +#define YY_NUM_RULES 27 +#define YY_END_OF_BUFFER 28 +static nidrconst short int nidr_accept[125] = + { 0, + 0, 0, 0, 0, 21, 21, 18, 18, 28, 6, + 5, 2, 25, 4, 3, 3, 6, 16, 12, 2, + 15, 25, 13, 26, 16, 8, 16, 9, 14, 7, + 11, 11, 11, 16, 21, 21, 22, 22, 21, 21, + 18, 18, 19, 18, 19, 18, 5, 25, 0, 25, + 25, 4, 24, 3, 3, 0, 23, 12, 8, 7, + 0, 9, 0, 0, 10, 9, 9, 9, 7, 11, + 11, 11, 21, 21, 21, 21, 20, 21, 21, 21, + 18, 18, 18, 18, 18, 18, 17, 18, 24, 3, + 0, 0, 10, 10, 9, 10, 9, 9, 10, 10, + + 10, 21, 18, 1, 10, 10, 10, 10, 10, 9, + 10, 11, 0, 10, 10, 11, 0, 11, 0, 11, + 0, 10, 10, 0 + } ; + +static nidrconst int nidr_ec[256] = + { 0, + 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 2, 1, 4, 5, 1, 1, 1, 6, 1, + 1, 7, 8, 9, 10, 11, 1, 12, 12, 12, + 12, 12, 12, 12, 12, 12, 12, 7, 13, 1, + 14, 1, 1, 15, 16, 17, 17, 17, 18, 19, + 17, 17, 20, 17, 17, 17, 17, 21, 17, 17, + 17, 17, 17, 22, 17, 17, 17, 23, 24, 17, + 1, 25, 1, 1, 26, 1, 16, 17, 17, 17, + + 18, 19, 17, 17, 20, 17, 17, 17, 17, 21, + 17, 17, 17, 17, 17, 22, 17, 17, 17, 23, + 24, 17, 1, 1, 1, 15, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1 + } ; + +static nidrconst int nidr_meta[27] = + { 0, + 1, 1, 2, 3, 1, 4, 1, 5, 1, 6, + 6, 6, 1, 1, 7, 6, 6, 6, 6, 6, + 6, 6, 6, 6, 1, 6 + } ; + +static nidrconst short int nidr_base[137] = + { 0, + 0, 0, 26, 0, 51, 75, 99, 123, 263, 264, + 56, 264, 57, 264, 0, 239, 57, 264, 147, 264, + 264, 236, 264, 264, 162, 264, 248, 53, 264, 257, + 0, 237, 241, 64, 0, 67, 264, 252, 59, 71, + 0, 81, 264, 62, 249, 86, 88, 229, 92, 228, + 86, 227, 249, 0, 230, 94, 264, 0, 264, 247, + 236, 96, 226, 230, 91, 233, 98, 107, 242, 0, + 224, 212, 0, 116, 108, 120, 264, 126, 226, 129, + 0, 132, 114, 133, 121, 224, 264, 140, 217, 191, + 193, 178, 169, 150, 168, 126, 155, 167, 166, 157, + + 0, 174, 173, 0, 151, 264, 158, 157, 156, 147, + 143, 133, 132, 138, 135, 125, 120, 76, 63, 51, + 33, 0, 264, 264, 183, 190, 197, 199, 202, 203, + 210, 217, 224, 231, 234, 236 + } ; + +static nidrconst short int nidr_def[137] = + { 0, + 124, 1, 124, 3, 125, 125, 126, 126, 124, 124, + 124, 124, 127, 124, 128, 128, 124, 124, 124, 124, + 124, 127, 124, 124, 124, 124, 124, 129, 124, 124, + 130, 130, 130, 124, 131, 131, 124, 124, 132, 131, + 133, 133, 124, 134, 124, 133, 124, 127, 124, 127, + 127, 127, 124, 128, 128, 124, 124, 19, 124, 124, + 124, 129, 124, 124, 135, 129, 136, 129, 124, 130, + 130, 130, 131, 131, 132, 131, 124, 132, 131, 131, + 133, 133, 134, 133, 134, 133, 124, 133, 124, 128, + 124, 124, 135, 135, 136, 135, 136, 129, 135, 130, + + 130, 131, 133, 128, 124, 124, 135, 135, 135, 136, + 135, 130, 124, 135, 135, 130, 124, 130, 124, 130, + 124, 130, 124, 0, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124 + } ; + +static nidrconst short int nidr_nxt[291] = + { 0, + 10, 11, 12, 10, 13, 10, 10, 10, 10, 10, + 10, 10, 14, 10, 10, 15, 15, 16, 15, 15, + 15, 15, 15, 15, 17, 10, 18, 19, 20, 21, + 22, 23, 24, 25, 26, 25, 27, 28, 29, 30, + 18, 31, 31, 31, 31, 32, 33, 31, 31, 31, + 34, 18, 36, 37, 38, 39, 123, 47, 56, 57, + 48, 51, 50, 67, 62, 56, 57, 50, 74, 52, + 68, 75, 80, 57, 122, 40, 36, 37, 38, 39, + 49, 53, 82, 79, 121, 83, 86, 88, 57, 47, + 51, 76, 48, 56, 57, 56, 57, 120, 52, 40, + + 42, 43, 65, 44, 45, 84, 67, 62, 94, 96, + 53, 50, 49, 68, 98, 97, 98, 74, 99, 50, + 75, 80, 57, 46, 42, 43, 50, 44, 45, 50, + 80, 57, 79, 82, 88, 57, 83, 96, 86, 119, + 76, 88, 57, 109, 118, 86, 115, 46, 58, 115, + 79, 48, 117, 116, 111, 59, 84, 107, 111, 107, + 60, 108, 110, 114, 110, 114, 111, 115, 108, 108, + 113, 49, 61, 62, 103, 102, 112, 99, 99, 124, + 124, 63, 64, 35, 35, 35, 35, 35, 35, 35, + 41, 41, 41, 41, 41, 41, 41, 50, 106, 50, + + 50, 50, 50, 50, 54, 54, 66, 66, 70, 70, + 73, 105, 104, 73, 73, 73, 73, 78, 89, 78, + 78, 78, 78, 78, 81, 103, 81, 102, 81, 81, + 81, 85, 101, 85, 85, 85, 85, 85, 93, 93, + 95, 95, 100, 69, 124, 92, 91, 65, 69, 90, + 89, 53, 53, 53, 87, 77, 72, 71, 69, 65, + 53, 55, 124, 9, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124, 124, 124, 124, 124 + } ; + +static nidrconst short int nidr_chk[291] = + { 0, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, + 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, + 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, + 3, 3, 5, 5, 5, 5, 121, 11, 17, 17, + 11, 13, 39, 28, 28, 34, 34, 44, 36, 13, + 28, 36, 40, 40, 120, 5, 6, 6, 6, 6, + 11, 13, 42, 39, 119, 42, 44, 46, 46, 47, + 51, 36, 47, 49, 49, 56, 56, 118, 51, 6, + + 7, 7, 65, 7, 7, 42, 62, 62, 65, 67, + 51, 75, 47, 62, 68, 67, 68, 74, 68, 83, + 74, 76, 76, 7, 8, 8, 85, 8, 8, 78, + 80, 80, 75, 82, 84, 84, 82, 96, 83, 117, + 74, 88, 88, 96, 116, 85, 115, 8, 19, 114, + 78, 19, 113, 112, 111, 19, 82, 94, 110, 94, + 19, 94, 97, 109, 97, 109, 97, 109, 108, 107, + 105, 19, 25, 25, 103, 102, 100, 99, 98, 95, + 93, 25, 25, 125, 125, 125, 125, 125, 125, 125, + 126, 126, 126, 126, 126, 126, 126, 127, 92, 127, + + 127, 127, 127, 127, 128, 128, 129, 129, 130, 130, + 131, 91, 90, 131, 131, 131, 131, 132, 89, 132, + 132, 132, 132, 132, 133, 86, 133, 79, 133, 133, + 133, 134, 72, 134, 134, 134, 134, 134, 135, 135, + 136, 136, 71, 69, 66, 64, 63, 61, 60, 55, + 53, 52, 50, 48, 45, 38, 33, 32, 30, 27, + 22, 16, 9, 124, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124, 124, 124, 124, 124 + } ; + +static nidr_state_type nidr_last_accepting_state; +static char *nidr_last_accepting_cpos; + +/* The intent behind this definition is that it'll catch + * any uses of REJECT which flex missed. + */ +#define REJECT reject_used_but_not_detected +static int nidr_more_flag = 0; +static int nidr_more_len = 0; +#define nidrmore() (nidr_more_flag = 1) +#define YY_MORE_ADJ nidr_more_len +#define YY_RESTORE_YY_MORE_OFFSET +char *nidrtext; +/* #line 1 "nidrscan.l" */ +#define INITIAL 0 +/* #line 2 "nidrscan.l" */ +/********************************************************************* +Copyright 2008, 2010 Sandia Corporation. Under the terms of Contract +DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government +retains certain rights in this software. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: + +* Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright +notice, this list of conditions and the following disclaimer in the +documentation and/or other materials provided with the distribution. + +* Neither the name of Sandia Corporation nor the names of its +contributors may be used to endorse or promote products derived from +this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +***********************************************************************/ + +#ifndef NIDR_H +#include "nidr.h" +#endif +#ifndef NIDR_PARSER_H +#include "nidr-parser.h" +#endif +#include /* possibly redundant, but necessary for strtod on some systems */ + +static int my_nidr_input(char*, int); +extern char *nidr_KWscopy(const char*); + +#ifdef IDR_DEBUG +static void print_token( char*, char*, char* ); +#else +#define print_token(a,b,c) /*nothing*/ +#endif + + +#define YY_INPUT(buf,result,maxsize) result = my_nidr_input(buf,maxsize) + +int nidrLineNumber = 1; + +extern void nidr_abort(void); +extern void (*nidr_comment)(const char*); +extern KeyWord *(*nidr_identifier)(const char*); +extern KeyWord *nidr_keyword(const char*); +extern const char *nidr_keyword_name(void); +/* Hardwire the now rarely used help text. It truly is something the + application should provide, not NIDR, but had trouble with the + declaration/definition w.r.t. MSVS when building DAKOTA source. + Ultimately would want to pass it into nidr_parse(...) +extern char nidr_please_refer[]; +*/ +char nidr_please_refer[] = + "Please refer to the input specification reference for this application."; +extern void nidr_tolower(char*); +static void bad_number(const char*); +static void unput_string(char *, int); +#define DATA 1 + +#define DQ_STRING 2 + +#define Q_STRING 3 + +/* #line 545 "nidr-scanner.c" */ + +/* Macros after this point can all be overridden by user definitions in + * section 1. + */ + +#ifndef YY_SKIP_YYWRAP +#ifdef __cplusplus +extern "C" int nidrwrap YY_PROTO(( void )); +#else +extern int nidrwrap YY_PROTO(( void )); +#endif +#endif + +#ifndef YY_NO_UNPUT +static void nidrunput YY_PROTO(( int c, char *buf_ptr )); +#endif + +#ifndef nidrtext_ptr +static void nidr_flex_strncpy YY_PROTO(( char *, nidrconst char *, int )); +#endif + +#ifdef YY_NEED_STRLEN +static int nidr_flex_strlen YY_PROTO(( nidrconst char * )); +#endif + +#ifndef YY_NO_INPUT +#ifdef __cplusplus +static int nidrinput YY_PROTO(( void )); +#else +static int input YY_PROTO(( void )); +#endif +#endif + +#if YY_STACK_USED +static int nidr_start_stack_ptr = 0; +static int nidr_start_stack_depth = 0; +static int *nidr_start_stack = 0; +#ifndef YY_NO_PUSH_STATE +static void nidr_push_state YY_PROTO(( int new_state )); +#endif +#ifndef YY_NO_POP_STATE +static void nidr_pop_state YY_PROTO(( void )); +#endif +#ifndef YY_NO_TOP_STATE +static int nidr_top_state YY_PROTO(( void )); +#endif + +#else +#define YY_NO_PUSH_STATE 1 +#define YY_NO_POP_STATE 1 +#define YY_NO_TOP_STATE 1 +#endif + +#ifdef YY_MALLOC_DECL +YY_MALLOC_DECL +#else +#if __STDC__ +#ifndef __cplusplus +#include +#endif +#else +/* Just try to get by without declaring the routines. This will fail + * miserably on non-ANSI systems for which sizeof(size_t) != sizeof(int) + * or sizeof(void*) != sizeof(int). + */ +#endif +#endif + +/* Amount of stuff to slurp up with each read. */ +#ifndef YY_READ_BUF_SIZE +#define YY_READ_BUF_SIZE 8192 +#endif + +/* Copy whatever the last rule matched to the standard output. */ + +#ifndef ECHO +/* This used to be an fputs(), but since the string might contain NUL's, + * we now use fwrite(). + */ +#define ECHO (void) fwrite( nidrtext, nidrleng, 1, nidrout ) +#endif + +/* Gets input and stuffs it into "buf". number of characters read, or YY_NULL, + * is returned in "result". + */ +#ifndef YY_INPUT +#define YY_INPUT(buf,result,max_size) \ + if ( nidr_current_buffer->nidr_is_interactive ) \ + { \ + int c = '*', n; \ + for ( n = 0; n < max_size && \ + (c = getc( nidrin )) != EOF && c != '\n'; ++n ) \ + buf[n] = (char) c; \ + if ( c == '\n' ) \ + buf[n++] = (char) c; \ + if ( c == EOF && ferror( nidrin ) ) \ + YY_FATAL_ERROR( "input in flex scanner failed" ); \ + result = n; \ + } \ + else if ( ((result = fread( buf, 1, max_size, nidrin )) == 0) \ + && ferror( nidrin ) ) \ + YY_FATAL_ERROR( "input in flex scanner failed" ); +#endif + +/* No semi-colon after return; correct usage is to write "nidrterminate();" - + * we don't want an extra ';' after the "return" because that will cause + * some compilers to complain about unreachable statements. + */ +#ifndef nidrterminate +#define nidrterminate() return YY_NULL +#endif + +/* Number of entries by which start-condition stack grows. */ +#ifndef YY_START_STACK_INCR +#define YY_START_STACK_INCR 25 +#endif + +/* Report a fatal error. */ +#ifndef YY_FATAL_ERROR +#define YY_FATAL_ERROR(msg) nidr_fatal_error( msg ) +#endif + +/* Default declaration of generated scanner - a define so the user can + * easily add parameters. + */ +#ifndef YY_DECL +#define YY_DECL int nidrlex YY_PROTO(( void )) +#endif + +/* Code executed at the beginning of each rule, after nidrtext and nidrleng + * have been set up. + */ +#ifndef YY_USER_ACTION +#define YY_USER_ACTION +#endif + +/* Code executed at the end of each rule. */ +#ifndef YY_BREAK +#define YY_BREAK break; +#endif + +#define YY_RULE_SETUP \ + YY_USER_ACTION + +YY_DECL + { + register nidr_state_type nidr_current_state; + register char *nidr_cp = NULL, *nidr_bp = NULL; + register int nidr_act; + +/* #line 85 "nidrscan.l" */ + + + + KeyWord *identifier, *keyword; + char *se; + + +/* #line 704 "nidr-scanner.c" */ + + if ( nidr_init ) + { + nidr_init = 0; + +#ifdef YY_USER_INIT + YY_USER_INIT; +#endif + + if ( ! nidr_start ) + nidr_start = 1; /* first start state */ + + if ( ! nidrin ) + nidrin = stdin; + + if ( ! nidrout ) + nidrout = stdout; + + if ( ! nidr_current_buffer ) + nidr_current_buffer = + nidr_create_buffer( nidrin, YY_BUF_SIZE ); + + nidr_load_buffer_state(); + } + + while ( 1 ) /* loops until end-of-file is reached */ + { + nidr_more_len = 0; + if ( nidr_more_flag ) + { + nidr_more_len = nidr_c_buf_p - nidrtext_ptr; + nidr_more_flag = 0; + } + nidr_cp = nidr_c_buf_p; + + /* Support of nidrtext. */ + *nidr_cp = nidr_hold_char; + + /* nidr_bp points to the position in nidr_ch_buf of the start of + * the current run. + */ + nidr_bp = nidr_cp; + + nidr_current_state = nidr_start; +nidr_match: + do + { + register YY_CHAR nidr_c = nidr_ec[YY_SC_TO_UI(*nidr_cp)]; + if ( nidr_accept[nidr_current_state] ) + { + nidr_last_accepting_state = nidr_current_state; + nidr_last_accepting_cpos = nidr_cp; + } + while ( nidr_chk[nidr_base[nidr_current_state] + nidr_c] != nidr_current_state ) + { + nidr_current_state = (int) nidr_def[nidr_current_state]; + if ( nidr_current_state >= 125 ) + nidr_c = nidr_meta[(unsigned int) nidr_c]; + } + nidr_current_state = nidr_nxt[nidr_base[nidr_current_state] + (unsigned int) nidr_c]; + ++nidr_cp; + } + while ( nidr_base[nidr_current_state] != 264 ); + +nidr_find_action: + nidr_act = nidr_accept[nidr_current_state]; + if ( nidr_act == 0 ) + { /* have to back up */ + nidr_cp = nidr_last_accepting_cpos; + nidr_current_state = nidr_last_accepting_state; + nidr_act = nidr_accept[nidr_current_state]; + } + + YY_DO_BEFORE_ACTION; + + +do_action: /* This label is used only to access EOF actions. */ + + + switch ( nidr_act ) + { /* beginning of action switch */ + case 0: /* must back up */ + /* undo the effects of YY_DO_BEFORE_ACTION */ + *nidr_cp = nidr_hold_char; + nidr_cp = nidr_last_accepting_cpos; + nidr_current_state = nidr_last_accepting_state; + goto nidr_find_action; + +case 1: +YY_RULE_SETUP +/* #line 92 "nidrscan.l" */ +{ + print_token("exit", NULL, "" ); + return 0; + } + YY_BREAK +case 2: +YY_RULE_SETUP +/* #line 97 "nidrscan.l" */ +{ + if (nidr_comment) + nidr_comment(nidrtext); + nidrLineNumber++; + } + YY_BREAK +case 3: +YY_RULE_SETUP +/* #line 103 "nidrscan.l" */ +{ + nidr_tolower(nidrtext); + keyword = nidr_keyword(nidrtext); + + if (keyword) { + print_token( "keyword", (char*) nidrtext, "" ); + if (keyword->kind & KWKind_Dynmult) + return END; + nidrlval.keyword = keyword; + BEGIN DATA; + return KEY_WORD; + } + print_token( "error", (char*) nidrtext, "" ); + nidrlval.string = nidrtext; + return KEYWORDERROR; + } + YY_BREAK +case 4: +YY_RULE_SETUP +/* #line 120 "nidrscan.l" */ +{ + if (*nidrtext == '#') { + if (nidr_comment) + nidr_comment(nidrtext); + } + else { + print_token( "end", NULL, "" ); + return END; + } + } + YY_BREAK +case 5: +YY_RULE_SETUP +/* #line 131 "nidrscan.l" */ +{ print_token( "whitespace", (char*) nidrtext, "" ); } + YY_BREAK +case 6: +YY_RULE_SETUP +/* #line 133 "nidrscan.l" */ +{ + print_token( "word", (char*) nidrtext, "" ); + nidrlval.string = nidr_KWscopy(nidrtext); + return STRING; + } + YY_BREAK +case 7: +YY_RULE_SETUP +/* #line 138 "nidrscan.l" */ +{ + print_token( "equals", NULL, "" ); + return EQUALS; + } + YY_BREAK +case 8: +YY_RULE_SETUP +/* #line 142 "nidrscan.l" */ +{ + print_token( "separator", NULL, "" ); + return SEPARATOR; + } + YY_BREAK +case 9: +YY_RULE_SETUP +/* #line 146 "nidrscan.l" */ +{ + print_token( "integer", (char*) nidrtext, "" ); + /* The following, old way has trouble with */ + /* big floating-point numbers written without */ + /* a decimal point */ + /* nidrlval.integer = (int) atoi( (char*) nidrtext ); */ + /* return INTEGER; */ + nidrlval.real = strtod(nidrtext,&se); + if (*se) + bad_number(nidrtext); + return REAL; + } + YY_BREAK +case 10: +YY_RULE_SETUP +/* #line 158 "nidrscan.l" */ +{ + print_token( "real", (char*) nidrtext, "" ); + nidrlval.real = strtod(nidrtext,&se); + if (*se) + bad_number(nidrtext); + return REAL; + } + YY_BREAK +case 11: +YY_RULE_SETUP +/* #line 165 "nidrscan.l" */ +{ + nidr_tolower(nidrtext); + if (nidr_keyword(nidrtext)) { + unput_string(nidrtext, nidrleng); + BEGIN INITIAL; + return END; + } + identifier = nidr_identifier(nidrtext); + + if (identifier) { + print_token( "identifier", (char*) nidrtext, ""); + + nidrlval.identifier = identifier; + return IDENTIFIER; + } + else { + print_token( "word", (char*) nidrtext, "" ); + fprintf(stderr,"\n\tunrecognized identifier '%s'\n", nidrtext); + fprintf(stderr,"\tinput line %d, within %s keyword.\n", + nidrLineNumber, nidr_keyword_name()); + fprintf(stderr, "%s\n", nidr_please_refer); + nidr_abort(); + nidrlval.string = nidr_KWscopy(nidrtext); + return STRING; + } + } + YY_BREAK +case 12: +YY_RULE_SETUP +/* #line 192 "nidrscan.l" */ +{ print_token( "whitespace", (char*) nidrtext, "" ); } + YY_BREAK +case 13: +YY_RULE_SETUP +/* #line 194 "nidrscan.l" */ +{ + print_token( "opening quote", NULL, "" ); + BEGIN Q_STRING; + } + YY_BREAK +case 14: +YY_RULE_SETUP +/* #line 198 "nidrscan.l" */ +{ + print_token( "end", NULL, "" ); + BEGIN INITIAL; + return END; + } + YY_BREAK +case 15: +YY_RULE_SETUP +/* #line 203 "nidrscan.l" */ +{ + print_token( "double quote", NULL, "" ); + BEGIN DQ_STRING; + } + YY_BREAK +case 16: +YY_RULE_SETUP +/* #line 207 "nidrscan.l" */ +{ + print_token( "word", (char*) nidrtext, "" ); + fprintf(stderr, "Input line %d: '%s' unexpected.\n", + nidrLineNumber, nidrtext); + nidr_abort(); + nidrlval.string = nidr_KWscopy(nidrtext); + return STRING; + } + YY_BREAK +case 17: +YY_RULE_SETUP +/* #line 215 "nidrscan.l" */ +{ + print_token( "q:repeated quote", NULL, "" ); + nidrtext[--nidrleng] = 0; + nidrmore(); + } + YY_BREAK +case 18: +YY_RULE_SETUP +/* #line 220 "nidrscan.l" */ +{ + nidrmore(); + print_token( "q:text", (char*) nidrtext, "" ); + } + YY_BREAK +case 19: +YY_RULE_SETUP +/* #line 224 "nidrscan.l" */ +{ + print_token( "closing quote", NULL, "" ); + if (nidrtext[--nidrleng] == '\n') + unput('\n'); + nidrtext[nidrleng] = 0; + print_token( "quoted string", (char*) nidrtext, "" ); + nidrlval.qstring = nidr_KWscopy(nidrtext); + BEGIN DATA; + return QUOTED_STRING; + } + YY_BREAK +case 20: +YY_RULE_SETUP +/* #line 234 "nidrscan.l" */ +{ + print_token( "q:repeated double quote", NULL, "" ); + nidrtext[--nidrleng] = 0; + nidrmore(); + } + YY_BREAK +case 21: +YY_RULE_SETUP +/* #line 239 "nidrscan.l" */ +{ + nidrmore(); + print_token( "q:text", (char*) nidrtext, "" ); + } + YY_BREAK +case 22: +YY_RULE_SETUP +/* #line 243 "nidrscan.l" */ +{ + print_token( "closing double quote", NULL, "" ); + if (nidrtext[--nidrleng] == '\n') + unput('\n'); + nidrtext[nidrleng] = 0; + print_token( "quoted string", (char*) nidrtext, "" ); + nidrlval.qstring = nidr_KWscopy(nidrtext); + BEGIN DATA; + return QUOTED_STRING; + } + YY_BREAK +case 23: +YY_RULE_SETUP +/* #line 253 "nidrscan.l" */ +{ + print_token( "newline", NULL, NULL ); + if (nidr_comment) + nidr_comment(nidrtext); + nidrLineNumber++; + } + YY_BREAK +case 24: +YY_RULE_SETUP +/* #line 259 "nidrscan.l" */ +{ + if (nidr_comment) + nidr_comment(nidrtext); + print_token( "comment - escaped newline", (char*) nidrtext, "" ); + unput( '\\' ); + } + YY_BREAK +case 25: +YY_RULE_SETUP +/* #line 265 "nidrscan.l" */ +{ + if (nidr_comment) + nidr_comment(nidrtext); + print_token( "comment", (char*) nidrtext, "" ); + } + YY_BREAK +case 26: +YY_RULE_SETUP +/* #line 270 "nidrscan.l" */ +{ return nidrtext[0]; } + YY_BREAK +case 27: +YY_RULE_SETUP +/* #line 272 "nidrscan.l" */ +ECHO; + YY_BREAK +/* #line 1074 "nidr-scanner.c" */ +case YY_STATE_EOF(INITIAL): +case YY_STATE_EOF(DATA): +case YY_STATE_EOF(DQ_STRING): +case YY_STATE_EOF(Q_STRING): + nidrterminate(); + + case YY_END_OF_BUFFER: + { + /* Amount of text matched not including the EOB char. */ + int nidr_amount_of_matched_text = (int) (nidr_cp - nidrtext_ptr) - 1; + + /* Undo the effects of YY_DO_BEFORE_ACTION. */ + *nidr_cp = nidr_hold_char; + YY_RESTORE_YY_MORE_OFFSET + + if ( nidr_current_buffer->nidr_buffer_status == YY_BUFFER_NEW ) + { + /* We're scanning a new file or input source. It's + * possible that this happened because the user + * just pointed nidrin at a new source and called + * nidrlex(). If so, then we have to assure + * consistency between nidr_current_buffer and our + * globals. Here is the right place to do so, because + * this is the first action (other than possibly a + * back-up) that will match for the new input source. + */ + nidr_n_chars = nidr_current_buffer->nidr_n_chars; + nidr_current_buffer->nidr_input_file = nidrin; + nidr_current_buffer->nidr_buffer_status = YY_BUFFER_NORMAL; + } + + /* Note that here we test for nidr_c_buf_p "<=" to the position + * of the first EOB in the buffer, since nidr_c_buf_p will + * already have been incremented past the NUL character + * (since all states make transitions on EOB to the + * end-of-buffer state). Contrast this with the test + * in input(). + */ + if ( nidr_c_buf_p <= &nidr_current_buffer->nidr_ch_buf[nidr_n_chars] ) + { /* This was really a NUL. */ + nidr_state_type nidr_next_state; + + nidr_c_buf_p = nidrtext_ptr + nidr_amount_of_matched_text; + + nidr_current_state = nidr_get_previous_state(); + + /* Okay, we're now positioned to make the NUL + * transition. We couldn't have + * nidr_get_previous_state() go ahead and do it + * for us because it doesn't know how to deal + * with the possibility of jamming (and we don't + * want to build jamming into it because then it + * will run more slowly). + */ + + nidr_next_state = nidr_try_NUL_trans( nidr_current_state ); + + nidr_bp = nidrtext_ptr + YY_MORE_ADJ; + + if ( nidr_next_state ) + { + /* Consume the NUL. */ + nidr_cp = ++nidr_c_buf_p; + nidr_current_state = nidr_next_state; + goto nidr_match; + } + + else + { + nidr_cp = nidr_c_buf_p; + goto nidr_find_action; + } + } + + else switch ( nidr_get_next_buffer() ) + { + case EOB_ACT_END_OF_FILE: + { + nidr_did_buffer_switch_on_eof = 0; + + if ( nidrwrap() ) + { + /* Note: because we've taken care in + * nidr_get_next_buffer() to have set up + * nidrtext, we can now set up + * nidr_c_buf_p so that if some total + * hoser (like flex itself) wants to + * call the scanner after we return the + * YY_NULL, it'll still work - another + * YY_NULL will get returned. + */ + nidr_c_buf_p = nidrtext_ptr + YY_MORE_ADJ; + + nidr_act = YY_STATE_EOF(YY_START); + goto do_action; + } + + else + { + if ( ! nidr_did_buffer_switch_on_eof ) + YY_NEW_FILE; + } + break; + } + + case EOB_ACT_CONTINUE_SCAN: + nidr_c_buf_p = + nidrtext_ptr + nidr_amount_of_matched_text; + + nidr_current_state = nidr_get_previous_state(); + + nidr_cp = nidr_c_buf_p; + nidr_bp = nidrtext_ptr + YY_MORE_ADJ; + goto nidr_match; + + case EOB_ACT_LAST_MATCH: + nidr_c_buf_p = + &nidr_current_buffer->nidr_ch_buf[nidr_n_chars]; + + nidr_current_state = nidr_get_previous_state(); + + nidr_cp = nidr_c_buf_p; + nidr_bp = nidrtext_ptr + YY_MORE_ADJ; + goto nidr_find_action; + } + break; + } + + default: + YY_FATAL_ERROR( + "fatal flex scanner internal error--no action found" ); + } /* end of action switch */ + } /* end of scanning one token */ + } /* end of nidrlex */ + + +/* nidr_get_next_buffer - try to read in a new buffer + * + * Returns a code representing an action: + * EOB_ACT_LAST_MATCH - + * EOB_ACT_CONTINUE_SCAN - continue scanning from current position + * EOB_ACT_END_OF_FILE - end of file + */ + +static int nidr_get_next_buffer() + { + register char *dest = nidr_current_buffer->nidr_ch_buf; + register char *source = nidrtext_ptr; + register int number_to_move, i; + int ret_val; + + if ( nidr_c_buf_p > &nidr_current_buffer->nidr_ch_buf[nidr_n_chars + 1] ) + YY_FATAL_ERROR( + "fatal flex scanner internal error--end of buffer missed" ); + + if ( nidr_current_buffer->nidr_fill_buffer == 0 ) + { /* Don't try to fill the buffer, so this is an EOF. */ + if ( nidr_c_buf_p - nidrtext_ptr - YY_MORE_ADJ == 1 ) + { + /* We matched a single character, the EOB, so + * treat this as a final EOF. + */ + return EOB_ACT_END_OF_FILE; + } + + else + { + /* We matched some text prior to the EOB, first + * process it. + */ + return EOB_ACT_LAST_MATCH; + } + } + + /* Try to read more data. */ + + /* First move last chars to start of buffer. */ + number_to_move = (int) (nidr_c_buf_p - nidrtext_ptr) - 1; + + for ( i = 0; i < number_to_move; ++i ) + *(dest++) = *(source++); + + if ( nidr_current_buffer->nidr_buffer_status == YY_BUFFER_EOF_PENDING ) + /* don't do the read, it's not guaranteed to return an EOF, + * just force an EOF + */ + nidr_current_buffer->nidr_n_chars = nidr_n_chars = 0; + + else + { + int num_to_read = + nidr_current_buffer->nidr_buf_size - number_to_move - 1; + + while ( num_to_read <= 0 ) + { /* Not enough room in the buffer - grow it. */ +#ifdef YY_USES_REJECT + YY_FATAL_ERROR( +"input buffer overflow, can't enlarge buffer because scanner uses REJECT" ); +#else + + /* just a shorter name for the current buffer */ + YY_BUFFER_STATE b = nidr_current_buffer; + + int nidr_c_buf_p_offset = + (int) (nidr_c_buf_p - b->nidr_ch_buf); + + if ( b->nidr_is_our_buffer ) + { + int new_size = b->nidr_buf_size * 2; + + if ( new_size <= 0 ) + b->nidr_buf_size += b->nidr_buf_size / 8; + else + b->nidr_buf_size *= 2; + + b->nidr_ch_buf = (char *) + /* Include room in for 2 EOB chars. */ + nidr_flex_realloc( (void *) b->nidr_ch_buf, + b->nidr_buf_size + 2 ); + } + else + /* Can't grow it, we don't own it. */ + b->nidr_ch_buf = 0; + + if ( ! b->nidr_ch_buf ) + YY_FATAL_ERROR( + "fatal error - scanner input buffer overflow" ); + + nidr_c_buf_p = &b->nidr_ch_buf[nidr_c_buf_p_offset]; + + num_to_read = nidr_current_buffer->nidr_buf_size - + number_to_move - 1; +#endif + } + + if ( num_to_read > YY_READ_BUF_SIZE ) + num_to_read = YY_READ_BUF_SIZE; + + /* Read in more data. */ + YY_INPUT( (&nidr_current_buffer->nidr_ch_buf[number_to_move]), + nidr_n_chars, num_to_read ); + + nidr_current_buffer->nidr_n_chars = nidr_n_chars; + } + + if ( nidr_n_chars == 0 ) + { + if ( number_to_move == YY_MORE_ADJ ) + { + ret_val = EOB_ACT_END_OF_FILE; + nidrrestart( nidrin ); + } + + else + { + ret_val = EOB_ACT_LAST_MATCH; + nidr_current_buffer->nidr_buffer_status = + YY_BUFFER_EOF_PENDING; + } + } + + else + ret_val = EOB_ACT_CONTINUE_SCAN; + + nidr_n_chars += number_to_move; + nidr_current_buffer->nidr_ch_buf[nidr_n_chars] = YY_END_OF_BUFFER_CHAR; + nidr_current_buffer->nidr_ch_buf[nidr_n_chars + 1] = YY_END_OF_BUFFER_CHAR; + + nidrtext_ptr = &nidr_current_buffer->nidr_ch_buf[0]; + + return ret_val; + } + + +/* nidr_get_previous_state - get the state just before the EOB char was reached */ + +static nidr_state_type nidr_get_previous_state() + { + register nidr_state_type nidr_current_state; + register char *nidr_cp; + + nidr_current_state = nidr_start; + + for ( nidr_cp = nidrtext_ptr + YY_MORE_ADJ; nidr_cp < nidr_c_buf_p; ++nidr_cp ) + { + register YY_CHAR nidr_c = (*nidr_cp ? nidr_ec[YY_SC_TO_UI(*nidr_cp)] : 1); + if ( nidr_accept[nidr_current_state] ) + { + nidr_last_accepting_state = nidr_current_state; + nidr_last_accepting_cpos = nidr_cp; + } + while ( nidr_chk[nidr_base[nidr_current_state] + nidr_c] != nidr_current_state ) + { + nidr_current_state = (int) nidr_def[nidr_current_state]; + if ( nidr_current_state >= 125 ) + nidr_c = nidr_meta[(unsigned int) nidr_c]; + } + nidr_current_state = nidr_nxt[nidr_base[nidr_current_state] + (unsigned int) nidr_c]; + } + + return nidr_current_state; + } + + +/* nidr_try_NUL_trans - try to make a transition on the NUL character + * + * synopsis + * next_state = nidr_try_NUL_trans( current_state ); + */ + +#ifdef YY_USE_PROTOS +static nidr_state_type nidr_try_NUL_trans( nidr_state_type nidr_current_state ) +#else +static nidr_state_type nidr_try_NUL_trans( nidr_current_state ) +nidr_state_type nidr_current_state; +#endif + { + register int nidr_is_jam; + register char *nidr_cp = nidr_c_buf_p; + + register YY_CHAR nidr_c = 1; + if ( nidr_accept[nidr_current_state] ) + { + nidr_last_accepting_state = nidr_current_state; + nidr_last_accepting_cpos = nidr_cp; + } + while ( nidr_chk[nidr_base[nidr_current_state] + nidr_c] != nidr_current_state ) + { + nidr_current_state = (int) nidr_def[nidr_current_state]; + if ( nidr_current_state >= 125 ) + nidr_c = nidr_meta[(unsigned int) nidr_c]; + } + nidr_current_state = nidr_nxt[nidr_base[nidr_current_state] + (unsigned int) nidr_c]; + nidr_is_jam = (nidr_current_state == 124); + + return nidr_is_jam ? 0 : nidr_current_state; + } + + +#ifndef YY_NO_UNPUT +#ifdef YY_USE_PROTOS +static void nidrunput( int c, register char *nidr_bp ) +#else +static void nidrunput( c, nidr_bp ) +int c; +register char *nidr_bp; +#endif + { + register char *nidr_cp = nidr_c_buf_p; + + /* undo effects of setting up nidrtext */ + *nidr_cp = nidr_hold_char; + + if ( nidr_cp < nidr_current_buffer->nidr_ch_buf + 2 ) + { /* need to shift things up to make room */ + /* +2 for EOB chars. */ + register int number_to_move = nidr_n_chars + 2; + register char *dest = &nidr_current_buffer->nidr_ch_buf[ + nidr_current_buffer->nidr_buf_size + 2]; + register char *source = + &nidr_current_buffer->nidr_ch_buf[number_to_move]; + + while ( source > nidr_current_buffer->nidr_ch_buf ) + *--dest = *--source; + + nidr_cp += (int) (dest - source); + nidr_bp += (int) (dest - source); + nidr_current_buffer->nidr_n_chars = + nidr_n_chars = nidr_current_buffer->nidr_buf_size; + + if ( nidr_cp < nidr_current_buffer->nidr_ch_buf + 2 ) + YY_FATAL_ERROR( "flex scanner push-back overflow" ); + } + + *--nidr_cp = (char) c; + + + nidrtext_ptr = nidr_bp; + nidr_hold_char = *nidr_cp; + nidr_c_buf_p = nidr_cp; + } +#endif /* ifndef YY_NO_UNPUT */ + + +#ifndef YY_NO_INPUT +#ifdef __cplusplus +static int nidrinput() +#else +static int input() +#endif + { + int c; + + *nidr_c_buf_p = nidr_hold_char; + + if ( *nidr_c_buf_p == YY_END_OF_BUFFER_CHAR ) + { + /* nidr_c_buf_p now points to the character we want to return. + * If this occurs *before* the EOB characters, then it's a + * valid NUL; if not, then we've hit the end of the buffer. + */ + if ( nidr_c_buf_p < &nidr_current_buffer->nidr_ch_buf[nidr_n_chars] ) + /* This was really a NUL. */ + *nidr_c_buf_p = '\0'; + + else + { /* need more input */ + int offset = nidr_c_buf_p - nidrtext_ptr; + ++nidr_c_buf_p; + + switch ( nidr_get_next_buffer() ) + { + case EOB_ACT_LAST_MATCH: + /* This happens because nidr_g_n_b() + * sees that we've accumulated a + * token and flags that we need to + * try matching the token before + * proceeding. But for input(), + * there's no matching to consider. + * So convert the EOB_ACT_LAST_MATCH + * to EOB_ACT_END_OF_FILE. + */ + + /* Reset buffer status. */ + nidrrestart( nidrin ); + + /* fall through */ + + case EOB_ACT_END_OF_FILE: + { + if ( nidrwrap() ) + return EOF; + + if ( ! nidr_did_buffer_switch_on_eof ) + YY_NEW_FILE; +#ifdef __cplusplus + return nidrinput(); +#else + return input(); +#endif + } + + case EOB_ACT_CONTINUE_SCAN: + nidr_c_buf_p = nidrtext_ptr + offset; + break; + } + } + } + + c = *(unsigned char *) nidr_c_buf_p; /* cast for 8-bit char's */ + *nidr_c_buf_p = '\0'; /* preserve nidrtext */ + nidr_hold_char = *++nidr_c_buf_p; + + + return c; + } +#endif /* YY_NO_INPUT */ + +#ifdef YY_USE_PROTOS +void nidrrestart( FILE *input_file ) +#else +void nidrrestart( input_file ) +FILE *input_file; +#endif + { + if ( ! nidr_current_buffer ) + nidr_current_buffer = nidr_create_buffer( nidrin, YY_BUF_SIZE ); + + nidr_init_buffer( nidr_current_buffer, input_file ); + nidr_load_buffer_state(); + } + + +#ifdef YY_USE_PROTOS +void nidr_switch_to_buffer( YY_BUFFER_STATE new_buffer ) +#else +void nidr_switch_to_buffer( new_buffer ) +YY_BUFFER_STATE new_buffer; +#endif + { + if ( nidr_current_buffer == new_buffer ) + return; + + if ( nidr_current_buffer ) + { + /* Flush out information for old buffer. */ + *nidr_c_buf_p = nidr_hold_char; + nidr_current_buffer->nidr_buf_pos = nidr_c_buf_p; + nidr_current_buffer->nidr_n_chars = nidr_n_chars; + } + + nidr_current_buffer = new_buffer; + nidr_load_buffer_state(); + + /* We don't actually know whether we did this switch during + * EOF (nidrwrap()) processing, but the only time this flag + * is looked at is after nidrwrap() is called, so it's safe + * to go ahead and always set it. + */ + nidr_did_buffer_switch_on_eof = 1; + } + + +#ifdef YY_USE_PROTOS +void nidr_load_buffer_state( void ) +#else +void nidr_load_buffer_state() +#endif + { + nidr_n_chars = nidr_current_buffer->nidr_n_chars; + nidrtext_ptr = nidr_c_buf_p = nidr_current_buffer->nidr_buf_pos; + nidrin = nidr_current_buffer->nidr_input_file; + nidr_hold_char = *nidr_c_buf_p; + } + + +#ifdef YY_USE_PROTOS +YY_BUFFER_STATE nidr_create_buffer( FILE *file, int size ) +#else +YY_BUFFER_STATE nidr_create_buffer( file, size ) +FILE *file; +int size; +#endif + { + YY_BUFFER_STATE b; + + b = (YY_BUFFER_STATE) nidr_flex_alloc( sizeof( struct nidr_buffer_state ) ); + if ( ! b ) + YY_FATAL_ERROR( "out of dynamic memory in nidr_create_buffer()" ); + + b->nidr_buf_size = size; + + /* nidr_ch_buf has to be 2 characters longer than the size given because + * we need to put in 2 end-of-buffer characters. + */ + b->nidr_ch_buf = (char *) nidr_flex_alloc( b->nidr_buf_size + 2 ); + if ( ! b->nidr_ch_buf ) + YY_FATAL_ERROR( "out of dynamic memory in nidr_create_buffer()" ); + + b->nidr_is_our_buffer = 1; + + nidr_init_buffer( b, file ); + + return b; + } + + +#ifdef YY_USE_PROTOS +void nidr_delete_buffer( YY_BUFFER_STATE b ) +#else +void nidr_delete_buffer( b ) +YY_BUFFER_STATE b; +#endif + { + if ( ! b ) + return; + + if ( b == nidr_current_buffer ) + nidr_current_buffer = (YY_BUFFER_STATE) 0; + + if ( b->nidr_is_our_buffer ) + nidr_flex_free( (void *) b->nidr_ch_buf ); + + nidr_flex_free( (void *) b ); + } + +/* Fix for C99 */ +#ifndef __cplusplus +extern int isatty(int); +#endif /* __cplusplus */ + +#ifdef YY_USE_PROTOS +void nidr_init_buffer( YY_BUFFER_STATE b, FILE *file ) +#else +void nidr_init_buffer( b, file ) +YY_BUFFER_STATE b; +FILE *file; +#endif + + + { + nidr_flush_buffer( b ); + + b->nidr_input_file = file; + b->nidr_fill_buffer = 1; + +#if YY_ALWAYS_INTERACTIVE + b->nidr_is_interactive = 1; +#else +#if YY_NEVER_INTERACTIVE + b->nidr_is_interactive = 0; +#else + b->nidr_is_interactive = file ? (isatty( fileno(file) ) > 0) : 0; +#endif +#endif + } + + +#ifdef YY_USE_PROTOS +void nidr_flush_buffer( YY_BUFFER_STATE b ) +#else +void nidr_flush_buffer( b ) +YY_BUFFER_STATE b; +#endif + + { + if ( ! b ) + return; + + b->nidr_n_chars = 0; + + /* We always need two end-of-buffer characters. The first causes + * a transition to the end-of-buffer state. The second causes + * a jam in that state. + */ + b->nidr_ch_buf[0] = YY_END_OF_BUFFER_CHAR; + b->nidr_ch_buf[1] = YY_END_OF_BUFFER_CHAR; + + b->nidr_buf_pos = &b->nidr_ch_buf[0]; + + b->nidr_at_bol = 1; + b->nidr_buffer_status = YY_BUFFER_NEW; + + if ( b == nidr_current_buffer ) + nidr_load_buffer_state(); + } + + +#ifndef YY_NO_SCAN_BUFFER +#ifdef YY_USE_PROTOS +YY_BUFFER_STATE nidr_scan_buffer( char *base, nidr_size_t size ) +#else +YY_BUFFER_STATE nidr_scan_buffer( base, size ) +char *base; +nidr_size_t size; +#endif + { + YY_BUFFER_STATE b; + + if ( size < 2 || + base[size-2] != YY_END_OF_BUFFER_CHAR || + base[size-1] != YY_END_OF_BUFFER_CHAR ) + /* They forgot to leave room for the EOB's. */ + return 0; + + b = (YY_BUFFER_STATE) nidr_flex_alloc( sizeof( struct nidr_buffer_state ) ); + if ( ! b ) + YY_FATAL_ERROR( "out of dynamic memory in nidr_scan_buffer()" ); + + b->nidr_buf_size = size - 2; /* "- 2" to take care of EOB's */ + b->nidr_buf_pos = b->nidr_ch_buf = base; + b->nidr_is_our_buffer = 0; + b->nidr_input_file = 0; + b->nidr_n_chars = b->nidr_buf_size; + b->nidr_is_interactive = 0; + b->nidr_at_bol = 1; + b->nidr_fill_buffer = 0; + b->nidr_buffer_status = YY_BUFFER_NEW; + + nidr_switch_to_buffer( b ); + + return b; + } +#endif + + +#ifndef YY_NO_SCAN_STRING +#ifdef YY_USE_PROTOS +YY_BUFFER_STATE nidr_scan_string( nidrconst char *nidr_str ) +#else +YY_BUFFER_STATE nidr_scan_string( nidr_str ) +nidrconst char *nidr_str; +#endif + { + int len; + for ( len = 0; nidr_str[len]; ++len ) + ; + + return nidr_scan_bytes( nidr_str, len ); + } +#endif + + +#ifndef YY_NO_SCAN_BYTES +#ifdef YY_USE_PROTOS +YY_BUFFER_STATE nidr_scan_bytes( nidrconst char *bytes, int len ) +#else +YY_BUFFER_STATE nidr_scan_bytes( bytes, len ) +nidrconst char *bytes; +int len; +#endif + { + YY_BUFFER_STATE b; + char *buf; + nidr_size_t n; + int i; + + /* Get memory for full buffer, including space for trailing EOB's. */ + n = len + 2; + buf = (char *) nidr_flex_alloc( n ); + if ( ! buf ) + YY_FATAL_ERROR( "out of dynamic memory in nidr_scan_bytes()" ); + + for ( i = 0; i < len; ++i ) + buf[i] = bytes[i]; + + buf[len] = buf[len+1] = YY_END_OF_BUFFER_CHAR; + + b = nidr_scan_buffer( buf, n ); + if ( ! b ) + YY_FATAL_ERROR( "bad buffer in nidr_scan_bytes()" ); + + /* It's okay to grow etc. this buffer, and we should throw it + * away when we're done. + */ + b->nidr_is_our_buffer = 1; + + return b; + } +#endif + + +#ifndef YY_NO_PUSH_STATE +#ifdef YY_USE_PROTOS +static void nidr_push_state( int new_state ) +#else +static void nidr_push_state( new_state ) +int new_state; +#endif + { + if ( nidr_start_stack_ptr >= nidr_start_stack_depth ) + { + nidr_size_t new_size; + + nidr_start_stack_depth += YY_START_STACK_INCR; + new_size = nidr_start_stack_depth * sizeof( int ); + + if ( ! nidr_start_stack ) + nidr_start_stack = (int *) nidr_flex_alloc( new_size ); + + else + nidr_start_stack = (int *) nidr_flex_realloc( + (void *) nidr_start_stack, new_size ); + + if ( ! nidr_start_stack ) + YY_FATAL_ERROR( + "out of memory expanding start-condition stack" ); + } + + nidr_start_stack[nidr_start_stack_ptr++] = YY_START; + + BEGIN(new_state); + } +#endif + + +#ifndef YY_NO_POP_STATE +static void nidr_pop_state() + { + if ( --nidr_start_stack_ptr < 0 ) + YY_FATAL_ERROR( "start-condition stack underflow" ); + + BEGIN(nidr_start_stack[nidr_start_stack_ptr]); + } +#endif + + +#ifndef YY_NO_TOP_STATE +static int nidr_top_state() + { + return nidr_start_stack[nidr_start_stack_ptr - 1]; + } +#endif + +#ifndef YY_EXIT_FAILURE +#define YY_EXIT_FAILURE 2 +#endif + +#ifdef YY_USE_PROTOS +static void nidr_fatal_error( nidrconst char msg[] ) +#else +static void nidr_fatal_error( msg ) +char msg[]; +#endif + { + (void) fprintf( stderr, "%s\n", msg ); + exit( YY_EXIT_FAILURE ); + } + + + +/* Redefine nidrless() so it works in section 3 code. */ + +#undef nidrless +#define nidrless(n) \ + do \ + { \ + /* Undo effects of setting up nidrtext. */ \ + nidrtext[nidrleng] = nidr_hold_char; \ + nidr_c_buf_p = nidrtext + n; \ + nidr_hold_char = *nidr_c_buf_p; \ + *nidr_c_buf_p = '\0'; \ + nidrleng = n; \ + } \ + while ( 0 ) + + +/* Internal utility routines. */ + +#ifndef nidrtext_ptr +#ifdef YY_USE_PROTOS +static void nidr_flex_strncpy( char *s1, nidrconst char *s2, int n ) +#else +static void nidr_flex_strncpy( s1, s2, n ) +char *s1; +nidrconst char *s2; +int n; +#endif + { + register int i; + for ( i = 0; i < n; ++i ) + s1[i] = s2[i]; + } +#endif + +#ifdef YY_NEED_STRLEN +#ifdef YY_USE_PROTOS +static int nidr_flex_strlen( nidrconst char *s ) +#else +static int nidr_flex_strlen( s ) +nidrconst char *s; +#endif + { + register int n; + for ( n = 0; s[n]; ++n ) + ; + + return n; + } +#endif + + +#ifdef YY_USE_PROTOS +static void *nidr_flex_alloc( nidr_size_t size ) +#else +static void *nidr_flex_alloc( size ) +nidr_size_t size; +#endif + { + return (void *) malloc( size ); + } + +#ifdef YY_USE_PROTOS +static void *nidr_flex_realloc( void *ptr, nidr_size_t size ) +#else +static void *nidr_flex_realloc( ptr, size ) +void *ptr; +nidr_size_t size; +#endif + { + /* The cast to (char *) in the following accommodates both + * implementations that use char* generic pointers, and those + * that use void* generic pointers. It works with the latter + * because both ANSI C and C++ allow castless assignment from + * any pointer type to void*, and deal with argument conversions + * as though doing an assignment. + */ + return (void *) realloc( (char *) ptr, size ); + } + +#ifdef YY_USE_PROTOS +static void nidr_flex_free( void *ptr ) +#else +static void nidr_flex_free( ptr ) +void *ptr; +#endif + { + free( ptr ); + } + +#if YY_MAIN +int main() + { + nidrlex(); + return 0; + } +#endif +/* #line 272 "nidrscan.l" */ + + + static int nidr_ateof = 0; + static const char *nidr_instring = 0; + + void +bad_number(const char *s) +{ + fprintf(stderr, "\n*** Invalid number \"%s\" on input line %d within " + "%s keyword.\n", s, nidrLineNumber, nidr_keyword_name()); + nidr_abort(); + } + + void +nidr_set_input_string(const char *s) +{ + nidr_instring = s; + } + + static int +my_nidr_input(char *buf, int bmax) +{ + int c, n; + + if (nidr_ateof) + return 0; + n = 0; + if (nidr_instring) { + while(n < bmax && (c = *nidr_instring)) { + ++nidr_instring; + if (c != '\r') + buf[n++] = c; + if (c == '\n') + break; + } + } + else if (nidr_current_buffer->nidr_is_interactive) + while(n < bmax) { + if ((c = getc(nidrin)) == EOF) + break; + if (c != '\r') + buf[n++] = c; + if (c == '\n') + break; + } + else + while(n < bmax) { + if ((c = getc(nidrin)) == EOF) + break; + if (c != '\r') + buf[n++] = c; + } + if (n <= 0) { + nidr_ateof = n = 1; + if (c == EOF) { + fclose(nidrin); + nidrin = NULL; + } + buf[0] = ';'; + } + return n; + } + + void +reset_nidrlex_state(void) +{ + BEGIN INITIAL; + nidr_abort(); + } + + void +unput_string(char *s, int len) +{ + while(--len >= 0) + unput(s[len]); + } + + void +nidr_reinit(void) +{ + nidr_init = 1; + nidr_ateof = 0; + if (nidr_current_buffer) { + free(nidr_current_buffer->nidr_ch_buf); + free(nidr_current_buffer); + nidr_current_buffer = 0; + } + } + + int +nidrwrap(void) +{ return 1; } Index: /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr.c =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr.c (revision 25836) +++ /issm/trunk/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr.c (revision 25836) @@ -0,0 +1,2427 @@ +/********************************************************************* +Copyright 2008, 2010 Sandia Corporation. Under the terms of Contract +DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government +retains certain rights in this software. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: + +* Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright +notice, this list of conditions and the following disclaimer in the +documentation and/or other materials provided with the distribution. + +* Neither the name of Sandia Corporation nor the names of its +contributors may be used to endorse or promote products derived from +this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +***********************************************************************/ + +/* nidr.c */ + +#ifndef NIDR_H /* for $DAKOTA/src/nidr.c */ +#include "nidr.h" +#endif +#include +#include +#include +#include +#include +#include +#include +#include "avltree.h" + +#ifndef NIDR_SQUAWKMAX +#define NIDR_SQUAWKMAX 10 +#endif + +#ifndef NO_NIDR_DYNLIB /*{*/ +typedef KeyWord *(*KW_ADD)(void); +static KeyWord *kwfind(const char *, KeyWord *, int, int *); +static KeyWord *toomany(const char *, KeyWord *, int); +#ifdef _WIN32 /*{{*/ +#include +#define dlopen(x,y) LoadLibrary(x) +#define find_dlsym(a,b,c) (a = (KW_ADD)GetProcAddress((HINSTANCE)(b),c)) +#define dlclose(x) FreeLibrary((HMODULE)x) +#define NO_DLERROR +#else /*}{*/ +#include +#include +#define find_dlsym(a,b,c) (a = (KW_ADD)dlsym(b,c)) +#undef NO_DLERROR +#endif /*}}*/ +#endif /*}*/ + + extern KeyWord Dakota_Keyword_Top; + extern int nidrLineNumber; + static KeyWord* Keyword_Top = &Dakota_Keyword_Top; + static void *KW_g; + void (*nidr_comment)(const char*); + static void nidr_keyword_finish(void); + static Comment *OutsideComment; + static void kw_finish2(void), kw_finish3(void); + static void kw_setup1(KeyWord *); + static FILE *dumpfile; + static KeyWord **ToClear, **ToClear0, **ToClearEnd; + static int dumplev, nsquawk, nparse_errors, primary, strict; + + int NIDR_disallow_missing_start = 1; + + enum {n_KWStack0 = 64}; + + static KWinfo KWStack0[n_KWStack0]; + + static Uint n_KWStack = n_KWStack0; + + static KeyWord *curid, *curkw; + static KWinfo *KWStack = KWStack0, + *KWStackBot = KWStack0, + *KWStackEnd = KWStack0 + n_KWStack0; + + static Values KWval, KWvalmax; + static Real *KWvalbuf; + static Uint nKWvalbuf; + + typedef struct Sbuf Sbuf; + enum { n_KWsbuf = 8192 }; + struct Sbuf { + char buf[n_KWsbuf]; + Sbuf *next; + }; + + typedef struct KWseen KWseen; + + struct +KWseen { + const char *name; + KeyWord *kw; + KWseen *mnext, *mprev; /* for identifiers so far unrequited when kw == 0 */ + /* kw != 0 ==> mprev = first child, and mnext = next sibling */ + KWseen *parent; + KWseen **lcn; /* &mprev field of last child; lcn == 0 when this */ + /* keyword was entered into the AVL tree because */ + /* its parent was seen. */ + Comment *comment; + char **svals; + Real *rvals; + size_t nvals; + }; + + static KWseen *KW_cur; + NIDR_KWlib *NIDR_Libs; + + void +nidr_lib_cleanup(void) +{ + KeyWord *kw; + NIDR_KWlib *L, *L1; + + L1 = NIDR_Libs; + NIDR_Libs = 0; + while((L = L1)) { + if (L->oldtop) + Keyword_Top = L->oldtop; + if ((kw = L->kw0)) { + kw->f.vs = 0; + kw->kind &= ~KWKind_Loaded; + } +#ifndef NO_NIDR_DYNLIB /*{{*/ + dlclose(L->h); +#else /*}{*/ + /* botch("dlclose is NOT SUPPORTED for current configuration"); */ + fprintf(stderr, "\ndlclose is NOT SUPPORTED for current configuration"); +#endif /*}}*/ + L1 = L->next; + free(L); + } + } + + static Sbuf KWsbuf0, *KWsbuf = &KWsbuf0; + static char *KWsbuf1 = KWsbuf0.buf, *KWsbufe = KWsbuf0.buf + n_KWsbuf; + static KWseen *curkws; + static const char *valkind[3] = {"integer","numeric","string"}; + + int +nidr_parse_error(void) +{ + int n; + if ((n = nsquawk - NIDR_SQUAWKMAX) > 0) + fprintf(stderr, "\n%d error message%s suppressed.\n", + n, "s" + (n == 1)); + return nsquawk + nparse_errors; + } + + void +nidr_signal_parse_error(void) +{ ++nparse_errors; } + + void +nidr_tolower(char *s) +{ + for(; *s; ++s) + *s = tolower(*s); + } + + static void +botch(const char *fmt, ...) +{ + va_list ap; + va_start(ap, fmt); + fprintf(stderr, "\nBotch: "); + vfprintf(stderr, fmt, ap); + fputs(".\n", stderr); + va_end(ap); + exit(1); + } + + static void +squawk(const char *fmt, ...) +{ + va_list ap; + if (++nsquawk <= NIDR_SQUAWKMAX) { + fprintf(stderr, "Input line %d: ", nidrLineNumber); + va_start(ap, fmt); + vfprintf(stderr, fmt, ap); + fputs(".\n", stderr); + va_end(ap); + } + } + +#ifdef NIDR_MALLOC_DEBUG + typedef struct MallocDebug MallocDebug; + struct MallocDebug +{ + MallocDebug *next, *prev; + char *where; + int nalloc; + }; + + static MallocDebug MDtop = {&MDtop, &MDtop, 0, 0}; + int MallocDebugCount, MallocDebugCount1; + + static void* +Alloc(const char *where, size_t len) +{ + MallocDebug *md = malloc(len + sizeof(MallocDebug)); + if (!md) { + fprintf(stderr, "malloc(%lu) failure in %s\n", (unsigned long)len, where); + exit(1); + } + (md->next = MDtop.next)->prev = md; + (md->prev = &MDtop)->next = md; + md->where = where; + if ((md->nalloc = ++MallocDebugCount) == MallocDebugCount1) + printf("Hit %d\n", md->nalloc); + return (void*)(md + 1); + } + + static void +MallocDebugFree(void *v) +{ + MallocDebug *md = (MallocDebug *)v - 1; + md->next->prev = md->prev; + md->prev->next = md->next; + free(md); + } +#define free MallocDebugFree + +#else //!NIDR_MALLOC_DEBUG + static void* +Alloc(const char *where, size_t len) +{ + void *rv = malloc(len); + if (!rv) { + fprintf(stderr, "malloc(%lu) failure in %s\n", (unsigned long)len, where); + exit(1); + } + return rv; + } +#endif //NIDR_MALLOC_DEBUG + + const char * +nidr_basename(const char *p) +{ + const char *b; + +#ifdef _WIN32 + if (p[0] && p[1] == ':') + p += 2; + else if (p[0] == '\\' && p[1] == '\\') + for(p += 2; *p; ) + switch(*p++) { + case '/': + case '\\': + goto break2; + } + break2: +#endif + b = p; + while(*p) + switch(*p++) { + case '/': +#ifdef _WIN32 + case '\\': +#endif + b = p; + } + return b; + } + + const char *nidr_exedir; + int nidr_exedir_len = -1; /* allow resetting to -1 for debugging */ + +#ifndef _WIN32 + static int +Is_executable(uid_t myuid, gid_t mygid, struct stat *sb) +{ + if (sb->st_uid == myuid) { + if (sb->st_mode & S_IXUSR) + return 1; + } + else if (sb->st_gid == mygid) { + if (sb->st_mode & S_IXGRP) + return 1; + } + else if (sb->st_mode & S_IXOTH) + return 1; + return 0; + } +#endif + + int +nidr_save_exedir(const char *argv0, int pathadj) +{ + /* pathadj & 1 ==> add exedir to $PATH */ + /* pathadj & 2 ==> add . to $PATH */ + /* (in both cases if not already there) */ + + /* These conditionals don't seem to work (perhaps expected) for Cygwin + binaries run from Windows command prompt as the compile-time is + unix-style, but runtime the path is windows-like. For now comment + out warning when on Cygwin build */ +#ifdef _WIN32 +#define Pathname "Path" +#define Sep ';' +#define Slash '\\' +#define Executable(x) !stat(x,&sb) +#else +#define Pathname "PATH" +#define Sep ':' +#define Slash '/' +#define Executable(x) !stat(x,&sb) && Is_executable(myuid, mygid, &sb) +#endif + char *buf, buf0[4096], *s; + const char *av0, *p, *p0, *p1, *p2; + int dotseen, finaldot, rc; + size_t buflen, L, L1, L2, L3; + struct stat sb; + static const char dotslash[3] = { '.', Slash, 0 }; +#ifdef _WIN32 + int c; + pathadj &= 1; /* . is implicitly in $PATH under _WIN32 */ +#else + gid_t mygid; + uid_t myuid; +#endif + if (nidr_exedir_len != -1) { + fprintf(stderr, "\nIgnoring extra call on nidr_save_argv0()\n"); + return 1; + } + nidr_exedir_len = 0; + if (!(av0 = argv0)) + return 2; + if (!(p = getenv(Pathname))) { + fprintf(stderr, "\nnidr_save_exedir: no $%s\n", Pathname); + return 3; + } + dotseen = finaldot = rc = 0; + buf = buf0; + buflen = sizeof(buf0); + p0 = p2 = p; + p1 = nidr_basename(av0); + if ((L = p1 - av0) > 0) { + memcpy(s = (char*)Alloc("nidr_save_argv0", L+1), av0, L); + s[L] = 0; + nidr_exedir = s; + nidr_exedir_len = (int)L; +#ifdef _WIN32 + for(L1 = 0; L1 < L; ++L1) + if (s[L1] == '/') + s[L1] = '\\'; +#endif + if (!pathadj) + return 0; + if (*p == Sep) + dotseen = 1; + while(*p) { + if (*p == Sep && (p[1] == Sep || p[1] == 0)) { + dotseen = 1; + break; + } + ++p; + } + if (s[0] == '.' && s[1] == Slash && L == 2) { +#ifdef _WIN32 + return 0; +#else + if (!dotseen) + goto dot_add; +#endif + } + L1 = L - 1; + for(p = p0;;) { + while(*p == Sep) + ++p; + if (!*p) + break; + if (!strncmp(p, s, L1)) { +#ifdef _WIN32 + return 0; +#else + if (!(pathadj &= ~1) || *p0 == Sep) + return 0; + for(p = p0;;) { + if (*p == Sep || (*p == '.' && p[1] == Sep)) + return 0; + while(*p != Sep) { + if (!*p) + goto dot_add; + ++p; + } + if (!*++p) + return 0; + } +#endif + } + while(*++p != Sep) + if (!*p) + goto break2; + if (!*++p) { +#ifdef _WIN32 + finaldot = 1; /* leave at 0 for !_WIN32 */ +#endif + break; + } + } + break2: + L1 = strlen(Pathname); + L2 = strlen(p0); + if (!pathadj & 2) + dotseen = 1; + L3 = L1 + L2 + L + 3; + s = (char*)Alloc("nidr_save_argv0", L3); + memcpy(s, Pathname, L1); + s[L1++] = '='; + memcpy(s+L1, p0, L2); + L1 += L2; + if (!finaldot) + s[L1++] = Sep; + memcpy(s+L1, nidr_exedir, --L); + L1 += L; + if (!dotseen) + s[L1++] = Sep; + s[L1] = 0; /* omit final slash */ + putenv(s); + return 0; + } + L = strlen(av0); +#ifdef _WIN32 + if (L < 5 || av0[L-4] != '.' + || ((c = av0[L-3]) != 'e' && c != 'E') + || ((c = av0[L-2]) != 'x' && c != 'X') + || ((c = av0[L-1]) != 'e' && c != 'E')) { + memcpy(s = (char*)Alloc("nidr_save_argv0", L + 5), av0, L); + strcpy(s+L, ".exe"); + L += 4; + av0 = s; + } + if (Executable(av0)) { + /* handle implicit . */ + dotseen = 1; + nidr_exedir = dotslash; + } + else /* do for loop */ +#else + +/* Fix for C99 */ +#ifndef __cplusplus +extern uid_t geteuid(void); +extern uid_t getegid(void); +#endif /* __cplusplus */ + + myuid = geteuid(); + mygid = getegid(); +#endif + for(; *p; p = p2) { + for(p1 = p;; ++p1) { + if (*p1 == Sep) { + p2 = p1 + 1; + if (!*p2) + finaldot = 1; + break; + } + if (!*p1) { + p2 = p1; + break; + } + } + if (p1 == p || (*p == '.' && p1 == p + 1)) { + if (!dotseen) { + dotseen = 1; + if (Executable(av0)) { + nidr_exedir = dotslash; + break; + } + } + } + else { + L1 = p1 - p; + L2 = L + L1 + 2; + if (L2 > buflen) { + if (buf != buf0) + free(buf); + buf = (char*)Alloc("nidr_save_argv0", L2); + buflen = L2; + } + memcpy(buf, p, L1); + buf[L1++] = Slash; + strcpy(buf+L1, av0); + if (Executable(buf)) { + s = (char*)Alloc("nidr_save_argv0", L1+1); + memcpy(s, buf, L1); + s[L1] = 0; + nidr_exedir = s; + nidr_exedir_len = (int)L1; + pathadj &= ~1; + break; + } + } + } + if (dotseen) + pathadj &= ~2; + if (!finaldot && *p2) { + while(p2[1]) + ++p2; + if (*p2 == Sep) + finaldot = 1; + } + if (finaldot && !dotseen && !nidr_exedir) { + dotseen = 1; + if (Executable(av0)) + nidr_exedir = dotslash; + } + if (nidr_exedir == dotslash) + nidr_exedir_len = 2; + else { + if (pathadj & 2 && !finaldot) { +#ifndef _WIN32 + dot_add: +#endif + L = strlen(p0); + L1 = strlen(Pathname); + L2 = L + L1 + 3; + s = (char*)Alloc("nidr_save_argv0", L2); + memcpy(s, Pathname, L1); + s[L1++] = '='; + memcpy(s+L1, p0, L); + s[L += L1] = Sep; + s[L+1] = 0; + putenv(s); + } + if (!nidr_exedir) { +/* Suppress warning for Cygwin and Windows, where path isn't resolved correctly above */ +#if !defined(__CYGWIN__) && !defined(_MSC_VER) + fprintf(stderr, "\nnidr_save_exedir: could not find \"%s\" in $%s\n", + av0, Pathname); +#endif + rc = 4; + } + } + if (buf != buf0) + free(buf); + return rc; + } + + void * +nidr_dlopen(const char *libname) +{ +#ifdef NO_NIDR_DYNLIB /*{{*/ + botch("dlopen for \"%s\" is NOT SUPPORTED", libname); + return (void*)libname; +#else /*}{*/ + char buf0[4096], *buf; + const char *b; + size_t buflen, L, L1; + void *h; + + b = nidr_basename(libname); + if (b > libname) + return dlopen(libname, RTLD_NOW); + buf = buf0; + buflen = sizeof(buf0); + L = strlen(libname); + if (nidr_exedir) { + L1 = L + nidr_exedir_len + 1; + if (L1 > buflen) { + buf = (char*)Alloc("nidr_dlopen", L1); + buflen = L1; + } + memcpy(buf, nidr_exedir, nidr_exedir_len); + strcpy(buf + nidr_exedir_len, libname); + if ((h = dlopen(buf, RTLD_NOW))) + goto ret; + } + if (!(h = dlopen(libname, RTLD_NOW))) { + L1 = L + 3; + if (L1 > buflen) { + buf = (char*)Alloc("nidr_dlopen", L1); + buflen = L1; + } + buf[0] = '.'; + buf[1] = Slash; + strcpy(buf+2, libname); + if (!(h = dlopen(buf, RTLD_NOW))) + h = dlopen(libname, RTLD_NOW); /* for dlerror */ + } + ret: + if (buf != buf0) + free(buf); + return h; +#endif /*}}*/ + } + +#undef Executable +#undef Slash +#undef Sep +#undef Pathname + + + struct +Comment { + int k; /* subscript for comfree */ + size_t avail; /* bytes left (from tnext) */ + char *text; /* text of comment */ + char *tnext; /* null byte at end of comment */ + Comment *fnext; /* next free Comment */ + }; + + enum { Comment_kmax = 7 }; + + static Comment *comfree[Comment_kmax+1]; + static size_t Comment_maxlen[Comment_kmax+1]; + + static void +comment_free(Comment *c) +{ + int k = c->k; + + if (k > Comment_kmax) + free(c); + else { + c->fnext = comfree[k]; + comfree[k] = c; + } + } + + static Comment* +alloc_comment(int k, size_t L) +{ + Comment *c; + + for(; k <= Comment_kmax; ++k) { + if (L <= Comment_maxlen[k]) { + L = Comment_maxlen[k]; + if ((c = comfree[k])) { + comfree[k] = c->fnext; + goto have_c; + } + break; + } + } + c = (Comment*)Alloc("save_comment", L + sizeof(Comment) + 1); + c->k = k; + c->text = (char*)(c+1); + have_c: + c->avail = L; + c->tnext = c->text; + return c; + } + + static void +save_comment(const char *s) +{ + Comment *c, *c1, **cp; + size_t L, L1; + + L = strlen(s); + cp = curid ? &curid->comment : curkws ? &curkws->comment : &OutsideComment; + if ((c = *cp)) { + if (c->avail >= L) + goto cupdate; + L1 = c->tnext - c->text; + c1 = alloc_comment(c->k + 1, L + L1); + memcpy(c1->text, c->text, L1); + c1->tnext = c1->text + L1; + c1->avail -= L1; + comment_free(c); + c = c1; + } + else + c = alloc_comment(0, L); + cupdate: + memcpy(c->tnext, s, L+1); + c->tnext += L; + c->avail -= L; + *cp = c; + } + + static void +comment_setup(void) +{ + int i; + size_t L; + nidr_comment = save_comment; + /* "- 1" to allow for terminating '\0' */ + for(L = 64; L <= sizeof(Comment) - 1; L <<= 1); + for(i = 0; i <= Comment_kmax; ++i, L <<= 1) + Comment_maxlen[i] = L - sizeof(Comment) - 1; + } + + static void +comment_reset(void) +{ + Comment *c, *c1; + int i; + + for(i = 0; i <= Comment_kmax; ++i) { + c1 = comfree[i]; + comfree[i] = 0; + while((c = c1)) { + c1 = c->fnext; + free(c); + } + } + nidr_comment = 0; + } + + static void +dumpcomment(Comment **cp) +{ + Comment *c = *cp; + *cp = 0; + fprintf(dumpfile, "%s", c->text); + comment_free(c); + } + + static void +dumpname(int hasval, KeyWord *kw) +{ + const char *fmt[2] = { "%s", "%s =" }; + int i; + if (OutsideComment) + dumpcomment(&OutsideComment); + if (primary) + kw += kw->paoff; + for(i = 0; i < dumplev; ++i) + putc(' ', dumpfile); + fprintf(dumpfile,fmt[hasval],kw->name); + if (!hasval) { + if (kw->comment) + dumpcomment(&kw->comment); + else if (kw != curkw) + putc('\n', dumpfile); + } + } + + static void +dumpstring(const char *s0) +{ + const char *s; + int c, n1, n2, q; + + n1 = n2 = 0; + for(s = s0;;) + switch(*s++) { + case 0: goto break2; + case '\'': + ++n1; + break; + case '"': + ++n2; + } + break2: + q = '\''; + if (n1 > n2) + q = '"'; + putc(' ', dumpfile); + putc(q, dumpfile); + s = s0; + while((c = *s++)) { + if (c == q) + putc(q, dumpfile); + putc(c, dumpfile); + } + putc(q, dumpfile); + } + + static void +dumpvals0(KeyWord *kw) +{ + Real *r; + const char **sp; + int i, *ip, indent, j, n; + + ip = 0; /* shut up warning of possible use without initialization */ + sp = 0; /* ditto */ + if (!(r = KWval.r) && !(ip = KWval.i) && !(sp = KWval.s)) + return; + n = KWval.n; + putc((indent = n > 1) ? '\n' : ' ', dumpfile); + for(i = 0;;) { + if (indent) { + putc('\t', dumpfile); + for(j = 0; j < dumplev; ++j) + putc(' ', dumpfile); + } + if (r) + fprintf(dumpfile, "%.15g", r[i]); + else if (ip) + fprintf(dumpfile, "%d", ip[i]); + else + dumpstring(sp[i]); + if (++i >= n) + break; + indent = 1; + putc('\n', dumpfile); + } + if (kw->comment) + dumpcomment(&kw->comment); + else + putc('\n', dumpfile); + } + + static void (*dumpvals)(KeyWord *kw) = dumpvals0; + + static void +dumpvals1(KeyWord *kw) +{ + Real *r; + const char **sp; + int i, *ip, n; + + ip = 0; /* shut up warning of possible use without initialization */ + sp = 0; /* ditto */ + if ((r = KWval.r) || (ip = KWval.i) || (sp = KWval.s)) { + n = KWval.n; + for(i = 0; i < n; ++i) { + if (r) + fprintf(dumpfile, " %.15g", r[i]); + else if (ip) + fprintf(dumpfile, " %d", ip[i]); + else + dumpstring(sp[i]); + } + } + if (kw->comment) + dumpcomment(&kw->comment); + else + putc('\n', dumpfile); + } + + char * +nidr_KWscopy(const char *s) +{ + Sbuf *sb; + char *rv; + + size_t L = strlen(s) + 1; + if (L >= n_KWsbuf) + botch("String too long in KWscopy"); + if (KWsbufe - KWsbuf1 < L) { + if (!KWsbuf->next) { + KWsbuf->next = sb = (Sbuf*)Alloc("KWscopy", sizeof(Sbuf)); + sb->next = 0; + } + KWsbuf = KWsbuf->next; + KWsbuf1 = KWsbuf->buf; + KWsbufe = KWsbuf1 + n_KWsbuf; + } + strcpy(KWsbuf1, s); + rv = KWsbuf1; + KWsbuf1 += L; + return rv; + } + + static void +KWvalbuf_inc(void) +{ + Real *r; + Uint n; + + n = nKWvalbuf << 1; + r = (Real*)Alloc("KWvalbuf", n*sizeof(Real)); + memcpy(r, KWvalbuf, nKWvalbuf*sizeof(Real)); + free(KWvalbuf); + KWvalbuf = r; + nKWvalbuf = n; + KWvalmax.n <<= 1; + if (KWval.r) { + KWval.r = r; + KWvalmax.r = r + n; + } + else if (KWval.i) { + KWval.i = (int*) r; + KWvalmax.i = (int*)(r + n); + } + else if (KWval.s) { + KWval.s = (const char**)r; + KWvalmax.s = (const char**)(r + n); + } + else + botch("Unexpected case in KWvalbuf_inc"); + } + +/* KWval.rstate values... + * value form seen + * 0 v + * 1 L:u + * 2 L:s:u + * 3 n*v + * 4 n*L:u + * 5 n*L:s:u + */ + + static void +finish_rexpand(void) +{ + int i, k, n, os; + Real sgn, st, u, v, x; + + os = KWval.rstate; + KWval.rstate = 0; + n = KWval.n; + k = 1; + if (os >= 3) { + KWval.n = n -= os-1; + k = KWval.r[n]; + if (k != KWval.r[n]) { + squawk("Noninteger replication factor %.17g", KWval.r[n]); + return; + } + else if (k < 1) { + squawk("Nonpositive replication factor %d", k); + return; + } + ++n; + os -= 3; + } + else + KWval.n = n -= os + 1; + v = KWval.r[n++]; + u = st = 0.; /* Shut up warning of not being initialized. */ + /* Both will be assigned before being used. */ + switch(os) { + case 0: + n = KWval.n; + for(i = 0; i < k; ++i) { + if (n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.r[n++] = v; + } + KWval.n = n; + return; + case 1: + st = 1; + u = KWval.r[n]; + break; + case 2: + st = KWval.r[n]; + if (st == 0.) { + squawk("Invalid stride == zero."); + return; + } + u = KWval.r[n+1]; + } + sgn = 1.; + if (st < 0.) + sgn = -1.; + if (sgn*(u - v) < 0.) { + squawk("Empty sequence."); + return; + } + n = KWval.n; + do { + for(i = 0; sgn*(u - (x = v + i*st)) >= 0.; ++i) { + if (n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.r[n++] = x; + } + } + while(--k > 0); + KWval.n = n; + } + + static void +rexpand(int state) +{ + int os; + + os = KWval.rstate; + KWval.rstate = 0; + switch(state) { + case 1: /* just saw *v */ + if (os == 0) + KWval.rstate = 3; + else + squawk("Unexpected '*'"); + break; + case 2: /* just saw :v */ + if (os == 2 || os == 5) + squawk("Unexpected ':'"); + else + KWval.rstate = os + 1; + break; + } + } + + static void +nidr_bufr_strict(Real r, int state) +{ + int k, n; + + if (KWval.s) { + squawk("expected a quoted string, but found a number"); + return; + } + if (KWval.rstate && !state) + finish_rexpand(); + if (!KWval.r && !KWval.i) { + squawk("No values may be specified for %s", KWStack->kw->name); + return; + } + if ((n = KWval.n) >= KWvalmax.n) + KWvalbuf_inc(); + if (KWval.r) + KWval.r[n] = r; + else { + k = (int)r; + if (k != r) + squawk("truncating %.17g to %d", r, k); + KWval.i[n] = k; + } + ++KWval.n; + if (state | KWval.rstate) + rexpand(state); + } + + static void +nidr_bufs_strict(const char *s) +{ + if (!KWval.s) { + if (KWval.r) + squawk("Expected a number, but found a quoted string"); + else + squawk("Misplaced quoted string"); + return; + } + if (KWval.n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.s[KWval.n++] = s; + } + + void +nidr_reset(void) +{ + /* Originally did this in case KWKind_Str of kw_setup(), */ + /* but this leads to confusion with erroneous input. */ + if (curkw) + nidr_keyword_finish(); + KWsbuf = &KWsbuf0; + KWsbuf1 = KWsbuf0.buf; + KWsbufe = KWsbuf0.buf + n_KWsbuf; + } + + NIDR_KWlib * +nidr_lib_record(void *h, const char *libname) +{ + NIDR_KWlib *Lib; + size_t L; + + L = strlen(libname) + 1; + Lib = (NIDR_KWlib*)Alloc("NIDR_lib_record", sizeof(NIDR_KWlib) + L); + memset(Lib, 0, sizeof(NIDR_KWlib)); + memcpy(Lib->libname = (char*)(Lib+1), libname, L); + if (!(Lib->next = NIDR_Libs)) + atexit(nidr_lib_cleanup); + NIDR_Libs = Lib; + Lib->h = h; + return Lib; + } + + static KeyWord* +kw_insert(KeyWord *kw, int *tryagain) +{ +#ifdef NO_NIDR_DYNLIB /*{{*/ + botch("Loading library \"%s\" for %s is disallowed", + kw->f.vf, kw->name); +#else /*}{*/ + KW_ADD kwa; + KeyWord *kw0, *kw1, *kw2; + NIDR_KWlib *Lib; + Uint u1, ui; + const char *lname, *s; + int newtop, nmatch; + void *h; + + if (tryagain) + *tryagain = 0; + if (kw->kind & KWKind_Loaded) + return (KeyWord*)kw->f.vs; + h = nidr_dlopen(lname = (const char*)kw->f.vf); + if (!h) { +#ifndef NO_DLERROR + if ((s = dlerror())) + botch("Cannot open library \"%s\" for %s:\n\t%s", + lname, kw->name, s); + else +#endif + botch("Cannot open library \"%s\" for %s", + lname, kw->name); + } + if (!find_dlsym(kwa, h, "keyword_add")) + botch("dlsym(\"keyword_add\") failed for %s", lname); + kw1 = (*kwa)(); + if (!(s = kw1->name)) { + s = ""; + goto namebotch; + } + newtop = 0; + if (strcmp(s, kw->name)) { + if (!KW_cur && !strcmp(s,"KeywordTop") && kw1->kind & KWKind_Dynmult) + newtop = 1; + else if (tryagain && kw1->nkw > 0 + && (kw2 = kwfind(kw->name, kw1->kw, kw1->nkw, &nmatch))) { + if (nmatch > 1) { + toomany(kw->name, kw1, nmatch); + botch("Too many matches in library %s", lname); + } + *tryagain = 1; + } + else + namebotch: + botch("Library %s: expected top keyword to be %s but got %s", + lname, kw->name, s); + } + ui = kw->kind & (KWKind_Mask|KWKind_List); + u1 = kw1->kind & (KWKind_Mask|KWKind_List); + if (ui != u1) + botch("Library %s: expected kind %u for %s, but got %u", + lname, ui, s, u1); + Lib = nidr_lib_record(h, lname); + Lib->kw0 = kw0 = kw; + memcpy(&Lib->kw, kw, sizeof(KeyWord)); + kw = &Lib->kw; + kw->kw = kw1->kw; + kw->nkw = kw1->nkw; + kw->f = kw1->f; + kw0->f.vs = (void*)kw; + kw0->kind |= KWKind_Loaded; + if (newtop) { + Lib->oldtop = Keyword_Top; + Keyword_Top = kw; + kw->kind |= KWKind_Dynmult; + } +#endif /*}}*/ + return kw; + } + + static void +kwnext_setup(KeyWord *kw, Uint n) +{ + KeyWord *kwe; + + if (kw->kwnext || (n <= 1 && kw->name)) + return; +#ifndef NO_NIDR_DYNLIB /*{*/ + if (kw->kind & KWKind_Extended) { + KeyWordx *kx1, *kxe; + for(kx1 = (KeyWordx*)kw; !kx1->kw.name; ++kx1) + kx1->kw.kwnext = (KeyWord*)(kx1 + 1); + for(kxe = kx1 + n - 1; kx1 < kxe; ++kx1) + kx1->kw.kwnext = (KeyWord*)(kx1 + 1); + return; + } +#endif + for(; !kw->name; ++kw) + kw->kwnext = kw + 1; + for(kwe = kw + n - 1; kw < kwe; ++kw) + kw->kwnext = kw + 1; + } + + static void +KWStack_inc(void) +{ + KWinfo *kwi; + Uint nn; + size_t len; + + nn = n_KWStack << 1; + kwi = (KWinfo*)Alloc("kw_setup", len = nn*sizeof(KWinfo)); + memcpy(kwi, KWStackBot, len >> 1); + if (KWStackBot != KWStack0) + free(KWStackBot); + KWStackBot = kwi; + KWStackEnd = kwi + nn; + KWStack = kwi + n_KWStack; + n_KWStack = nn; + } + + static KeyWord* +kw_setup(KeyWord *kw, void *g, const char *name) +{ + KWinfo *kwi; + KeyWord **alt, *kw1, **req; + + Uint k, nalt, nn, nreq; + int *altct, deferred; + size_t len; + + deferred = 0; + if (kw->kind & KWKind_Dynlib) { + if (kw->kw) + deferred = 1; + else + kw = kw_insert(kw, 0); + } + top: + if ((kw1 = kw->kw)) { + kwnext_setup(kw1, kw->nkw); + if (kw->kind & KWKind_Dynmult) + return kw; + while(!kw1->name) { + if (!(kw1->kind & KWKind_Stacked)) { + kw1->kind |= KWKind_Stacked; + kw_setup(kw1, g, name); + } + kw1 = kw1->kwnext; + } + } + if (!curkw) { + KWStack = KWStackBot = KWStack0; + KWStackEnd = KWStack0 + n_KWStack0; + curkw = kw; + } + else if (++KWStack >= KWStackEnd) + KWStack_inc(); + kwi = KWStack; + kwi->name = name; + kwi->kw = kw; + kwi->kw1 = kw1; + nalt = nreq = 0; + if (kw1) + for(; kw1; kw1 = kw1->kwnext) { + if (nalt < kw1->alt) + nalt = kw1->alt; + if (nreq < kw1->req) + nreq = kw1->req; + } + kwi->nalt = nalt; + kwi->nreq = nreq; + alt = req = 0; + altct = 0; + if ((nn = nalt + nreq) > 0) { + nn += 2; + alt = (KeyWord**)Alloc("kw_setup(alt)", + len = nn*sizeof(KeyWord*) + (nalt+1)*sizeof(int)); + memset(alt, 0, len); + req = alt + nalt + 1; + altct = (int*)(req + nreq + 1); + /* altct[0], alt[0] and req[0] = "don't care" slots */ + } + kwi->alt = alt; + kwi->req = req; + kwi->altct = altct; + if (nreq) + for(kw1 = kwi->kw1; kw1; kw1 = kw1->kwnext) + req[kw1->req] = kw1; + if (nalt) + for(kw1 = kwi->kw1; kw1; kw1 = kw1->kwnext) + if (kw1->kind & KWKind_primary) + ++altct[kw1->alt]; + kwi->g = g; + KWval.n = 0; + KWval.i = 0; + KWval.r = 0; + KWval.s = 0; + if ((k = kw->kind & KWKind_Mask)) { + if (!KWvalmax.r) + KWvalbuf = (Real *)Alloc("kw_setup(KWvalbuf)", + (nKWvalbuf = 128)*sizeof(Real)); + switch(k) { + + case KWKind_Int: + KWval.i = (int*)KWvalbuf; + KWvalmax.n = (nKWvalbuf*sizeof(Real))/sizeof(int); + KWvalmax.i = KWval.i + KWvalmax.n; + break; + + case KWKind_Real: + KWval.r = KWvalbuf; + KWvalmax.r = KWvalbuf + (KWvalmax.n = nKWvalbuf); + break; + + case KWKind_Str: + KWval.s = (const char**)KWvalbuf; + KWvalmax.n = (nKWvalbuf*sizeof(Real))/sizeof(char*); + KWvalmax.s = KWval.s + KWvalmax.n; + } + } + if (deferred) { + kw = kw_insert(kw, 0); + deferred = 0; + goto top; + } + if (!(kwi->needstart = kw->kind & KWKind_Mask)) { + if (kw->name) { + if (dumpfile) + dumpname(0, kw); + ++dumplev; + } + if (kw->f.start) + (*kw->f.start)(kw->name, 0, &KWStack->g, kw->f.vs); + } + else if (!kw->f.start && NIDR_disallow_missing_start) + botch("No start routine for %s", kw->name); + return kw; + } + + static KeyWord * +kwfind(const char *name, KeyWord *keywds, int n, int *nmatch) +{ + KeyWord *kn, *kn1; + int k, n0, n1, n2, nn; + size_t L; + + *nmatch = 0; + if (n <= 0) + return 0; + L = strlen(name); + n0 = 0; + nn = n; +#ifndef NO_NIDR_DYNLIB /*{*/ + if (n > 0 && keywds->kind & KWKind_Extended) { + while(n > 0) { + n1 = n >> 1; + kn = (KeyWord*)((KeyWordx*)keywds + n1); + k = strncmp(name, kn->name, L); + if (k < 0) + n = n1; + else if (k > 0) { + n -= ++n1; + n0 += n1; + keywds = (KeyWord*)((KeyWordx*)kn + 1); + } + else { + /* Found -- check for range of matches. */ + /* Here we use linear search, as we expect */ + /* the range to be small. */ + n = n1 + n0; + n2 = n + 1; + if (kn->name[L]) { + for(kn1 = kn; n2 < nn; ++n2) { + kn1 = (KeyWord*)((KeyWordx*)kn1 + 1); + if (strncmp(name, kn1->name, L)) + break; + if (!kn1->name[L]) + goto found1; + } + kn1 = kn; + while(n > 0) { + kn1 = (KeyWord*)((KeyWordx*)kn1 - 1); + if (strncmp(name, kn1->name, L)) + break; + if (!kn1->name[L]) + goto found1; + --n; + kn = kn1; + } + } + *nmatch = n2 - n; + return kn; + } + } + } + else +#endif /*}*/ + while(n > 0) { + n1 = n >> 1; + kn = keywds + n1; + k = strncmp(name, kn->name, L); + if (k < 0) + n = n1; + else if (k > 0) { + n -= ++n1; + n0 += n1; + keywds = kn + 1; + } + else { + /* Found -- check for range of matches. */ + /* Here we use linear search, as we expect */ + /* the range to be small. */ + n = n1 + n0; + n2 = n + 1; + if (kn->name[L]) { + for(kn1 = kn; n2 < nn; ++n2) { + ++kn1; + if (strncmp(name, kn1->name, L)) + break; + if (!kn1->name[L]) + goto found1; + } + kn1 = kn; + while(n > 0) { + --kn1; + if (strncmp(name, kn1->name, L)) + break; + if (!kn1->name[L]) { + found1: + *nmatch = 1; + return kn1; + } + --n; + kn = kn1; + } + } + *nmatch = n2 - n; + return kn; + } + } + return 0; /* not found */ + } + + static KeyWord * +toomany(const char *name, KeyWord *kw, int nmatch) +{ + int i; + squawk("\"%s\" is ambiguous; possible matches..", name); + if (nsquawk <= NIDR_SQUAWKMAX) + for(i = 0; i < nmatch; i++, kw++) + fprintf(stderr, "\t%s\n", kw->name); + return 0; + } + + KeyWord * +nidr_keyword(const char *name) +{ + int nmatch; + KeyWord *kw, *kw1; + + kw = kwfind(name, Keyword_Top->kw, Keyword_Top->nkw, &nmatch); + if (nmatch > 1) + return toomany(name, kw, nmatch); + else if (kw) { + if (!(kw1 = curkw)) { + kw = kw_setup(kw, KW_g, name); + if (kw->kind & KWKind_Dynmult) + return kw; + } + if (!strict) { + if (kw1) + nidr_keyword_finish(); + kw_setup1(kw); + } + } + return kw; + } + + static void +valcheck(KeyWord *kw) +{ + Real *r; + int *z; + int i, k, n; + + n = KWval.n; + switch(k = kw->kind & KWKind_Mask) { + case KWKind_Int: + z = KWval.i; + if (kw->kind & KWKind_strictLb) { + for(i = 0; i < n; ++i) + if (z[i] <= kw->Lb) { + squawk("%s must be > %.0f", kw->name, kw->Lb); + break; + } + } + else if (kw->kind & KWKind_caneqLb) { + for(i = 0; i < n; ++i) + if (z[i] < kw->Lb) { + squawk("%s must be >= %.0f", kw->name, kw->Lb); + break; + } + } + if (kw->kind & KWKind_strictUb) { + for(i = 0; i < n; ++i) + if (z[i] >= kw->Ub) { + squawk("%s must be < %.0f", kw->name, kw->Ub); + break; + } + } + else if (kw->kind & KWKind_caneqUb) { + for(i = 0; i < n; ++i) + if (z[i] > kw->Ub) { + squawk("%s must be >= %.0f", kw->name, kw->Ub); + break; + } + } + break; + case KWKind_Real: + r = KWval.r; + if (kw->kind & KWKind_strictLb) { + for(i = 0; i < n; ++i) + if (r[i] <= kw->Lb) { + squawk("%s must be > %g", kw->name, kw->Lb); + break; + } + } + else if (kw->kind & KWKind_caneqLb) { + for(i = 0; i < n; ++i) + if (r[i] < kw->Lb) { + squawk("%s must be >= %g", kw->name, kw->Lb); + break; + } + } + if (kw->kind & KWKind_strictUb) { + for(i = 0; i < n; ++i) + if (r[i] >= kw->Ub) { + squawk("%s must be < %g", kw->name, kw->Ub); + break; + } + } + else if (kw->kind & KWKind_caneqUb) { + for(i = 0; i < n; ++i) + if (r[i] > kw->Ub) { + squawk("%s must be >= %g", kw->name, kw->Ub); + break; + } + } + break; + default: + botch("Bug: unexpected (kw->kind & KWKind_Mask) = %d in valcheck",n); + } + } + + static void +read_lib(const char *libname, KeyWord *kw) +{ +#ifdef NO_NIDR_DYNLIB /*{{*/ + botch("LIBNAME is disallowed: cannot read \"%s\"", libname); +#else /*}{*/ + KeyWord *kw1; + KW_ADD kwa; + NIDR_KWlib *Lib; + void *h; + + h = nidr_dlopen(libname); + if (!h) { +#ifndef NO_DLERROR + const char *s; + if ((s = dlerror())) + botch("Cannot open library \"%s\":\n\t%s", libname, s); + else +#endif + botch("Cannot open library \"%s\"", libname); + } + if (!find_dlsym(kwa, h, "keyword_add")) + botch("dlsym(\"keyword_add\") failed for %s", libname); + kw1 = (*kwa)(); + Lib = nidr_lib_record(h, libname); + kw->nkw = kw1->nkw; + kw->kw = kw1->kw; + kw->f = kw1->f; + kw->kind |= KWKind_Loaded; +#endif /*}}*/ + } + + static void +nidr_id_strict_finish(KWinfo *kwi, KeyWord *kw, const char *name) +{ + KeyWord *kw1; + int n; + + if (kw->alt) { + if ((kw1 = kwi->alt[n = kw->alt])) { + if (strcmp(kw1->name, name)) + squawk("%s and %s are mutually exclusive", + kw1->name, name); + else + squawk("%s was already specified", name); + } + else + kwi->alt[n] = kw; + } + if (kw->req) { + if (kwi->req[n = kw->req]) + kwi->req[n] = 0; + else if (!kw->alt) + squawk("%s specified more than once", name); + } + } + + static KWinfo * +dispatch_val(KWinfo *kwi) +{ + KeyWord *kw = kwi->kw; + + kwi->needstart = 0; + if (KWval.n) { + if (KWval.rstate) + finish_rexpand(); + if (dumpfile) { + dumpname(1, kw); + dumpvals(kw); + } + if (kw->kind & (KWKind_Lb|KWKind_Ub)) + valcheck(kw); + if (kw->f.start) + (*kw->f.start)(kw->name, &KWval, &kwi->g, kw->f.vs); + else if ((kw->kind & (KWKind_Libname | KWKind_Loaded)) == KWKind_Libname) { + read_lib(KWval.s[0], kw); + kw = kw_setup(kw, kwi->g, kw->name); + if (kw->f.start) + (*kw->f.start)(kw->name, &KWval, &kwi->g, kw->f.vs); + if (kw == kwi->kw) { + *kwi = *KWStack; + --KWStack; + } + else + kwi = KWStack; + } + KWval.n = 0; + } + else if ((kw->kind & (KWKind_Libname|KWKind_Loaded)) + != (KWKind_Libname|KWKind_Loaded)) + squawk("expected %sone %s value for %s", + kw->kind & KWKind_List ? "at least " : "", + valkind[(kw->kind & KWKind_Mask)-1], kw->name); + ++dumplev; + return kwi; + } + + static void +oneof(KeyWord *kw, int alt, int n) +{ + KeyWord *kw1; + + squawk("One of the following %d entities\nmust be specified for %s..", + n, kw->name); + for(kw1 = kw->kw; !kw1->name; kw1 = kw1->kwnext); + for(; kw1; kw1 = kw1->kwnext) + if (kw1->alt == alt && kw1->kind & KWKind_primary) + fprintf(stderr, "\t%s\n", kw1->name); + } + + static void +missing_chk(KeyWord *kw1, KWinfo *kwi) +{ + KeyWord *kw0, *kw2, **req; + Uint a; + char seen0[1024], *seen; + const char *kwname; + int n; + size_t nreq; + + /* only issue one error message per missing keyword */ + + nreq = 0; + for(kw0 = kw1; kw1; kw1 = kw1->kwnext) + if (nreq < kw1->req) + nreq = kw1->req; + seen = seen0; + if (++nreq > sizeof(seen0)) + seen = (char*)Alloc("missing_chk", nreq); + memset(seen, 0, nreq); + req = kwi->req; + for(kw1 = kw0; kw1; kw1 = kw1->kwnext) { + if (kw1->req && req[kw1->req] && !seen[kw1->req] && kw1->kind & KWKind_primary) { + seen[kw1->req] = 1; + a = -1; + if (!kw1->alt || (n = kwi->altct[a = kw1->alt]) <= 1) { + if (!(kwname = kwi->name)) + kwname = ""; + for(kw2 = kw1;;) { + if (kw2->alt == a && kw2->kind & KWKind_primary) + break; + if (!(kw2 = kw2->kwnext)) + botch("Bug in missing_chk"); + } + squawk("%s must be specified for %s", + kw2->name, kwname); + } + else + oneof(kwi->kw, kw1->alt, n); + } + } + if (seen != seen0) + free(seen); + } + + static void +finalize(KWinfo *kwi) +{ + KeyWord *kw, *kw1, **req; + + kw = kwi->kw; + kw->kind &= ~KWKind_Stacked; + if (kwi->needstart) + kwi = dispatch_val(kwi); + if (kw->name) + --dumplev; + if (kw->f.final) + (*kw->f.final)(kw->name, 0, &kwi->g, kw->f.vf); + if (kwi->alt) { + if (kwi->nreq) { + req = kwi->req; + for(kw1 = kwi->kw1; kw1; kw1 = kw1->kwnext) + if (kw1->req && req[kw1->req]) { + missing_chk(kw1, kwi); + break; + } + } + free(kwi->alt); + } + } + + static KeyWord * +nidr_identifier_strict(const char *name) +{ + KWinfo *kwi, *kwi1; + KeyWord *kw, *kw1; + int nmatch; + size_t height; + + if (!curkw) + botch("curkw = 0 in nidr_identifier"); + kwi = KWStack; + if (kwi->needstart) + kwi = dispatch_val(kwi); + for(kwi1 = kwi;;) { + kw1 = kwi->kw; + if ((kw = kwfind(name, kwi->kw1, kw1->nkw, &nmatch))) + break; + if (kwi == KWStackBot) + return 0; + if ((--kwi)->kw->name && !(kwi->kw->kind & KWKind_Loaded)) + kwi1 = kwi; + } + if (nmatch > 1) + return toomany(name, kw, nmatch); + while(KWStack > kwi1) + finalize(KWStack--); + if ((kw->kind & (KWKind_Libname | KWKind_Loaded)) == KWKind_Libname) { + nidr_id_strict_finish(kwi, kw, name); + if (!KWvalmax.r) + KWvalbuf = (Real *)Alloc("nidr_identifier_strict", + (nKWvalbuf = 128)*sizeof(Real)); + if (++KWStack >= KWStackEnd) + KWStack_inc(); + kwi = KWStack; + kwi->kw = kw; + kwi->needstart = 1; + KWval.s = (const char**)KWvalbuf; + KWvalmax.n = (nKWvalbuf*sizeof(Real))/sizeof(char*); + KWvalmax.s = KWval.s + KWvalmax.n; + } + else { + height = kwi - KWStackBot; + kw = kw_setup(kw, kwi->g, name); + kwi = KWStackBot + height; /* in case kw_setup reallocated KWStack */ + nidr_id_strict_finish(kwi, kw, name); + } + return kw; + } + + static void +nidr_keyword_finish(void) +{ + if (!strict) + kw_finish2(); + for(;;--KWStack) { + finalize(KWStack); + if (KWStack == KWStackBot) + break; + } + if (!strict) + kw_finish3(); + curid = curkw = 0; + } + + const char* +nidr_keyword_name(void) +{ return curkw ? curkw->name : ""; } + +/* Some of the above assumes strict nesting according to dakota.input.nspec. */ +/* Code here is meant to relax this assumption, allowing more flexibility in */ +/* the order of identifiers within a DAKOTA "keyword". */ + + typedef struct KWpair KWpair; + typedef struct KWmblk KWmblk; + + struct +KWmblk { + KWmblk *next; + size_t len; + /* memory of length len immediately follows */ + }; + + struct +KWpair { + KeyWord *kw; + KWseen *kws; + }; + + enum{ KWmblk_gulp = 32000 }; + + static AVL_Tree *AVLT, *AVLKWP; + static KWseen **KW_p, **KW_pe, KWmissing, *KWs0; + static KWmblk *KWmblk0, *KWmblk1; + static const char *KWmem0, *KWmem1; + + typedef struct +AVLCmpInfo { + KWseen **found[2]; + int nfound; + int inexact; + } AVLCmpInfo; + + static int +avlcmp(void *v, KWseen **a, KWseen **b) +{ + AVLCmpInfo *AI = (AVLCmpInfo*)v; + KWseen *ksa, *ksb; + const char *s, *t; + + s = (ksa = *a)->name; + t = (ksb = *b)->name; + for(; *s == *t; ++s, ++t) + if (!*s) + return 0; + if ((!*s && !ksa->kw && ksb->kw) + ||(!*t && !ksb->kw && ksa->kw)) { + /* inexact match */ + if (AI->nfound == 0 + || (AI->nfound == 1 && AI->found[0] != b)) + AI->found[AI->nfound++] = b; + return AI->inexact; + } + return *s - *t; + } + + static int +kwpcmp(void *v, KWpair *a, KWpair *b) +{ + if (a->kw == b->kw) + return 0; + return a->kw > b->kw ? 1 : -1; + } + + static void +KWmeminit(void) +{ + KWmblk0 = KWmblk1 = (KWmblk*)Alloc("KWmeminit", + sizeof(KWmblk) + KWmblk_gulp); + KWmem0 = (char*)(KWmblk0 + 1); + KWmem1 = KWmem0 + KWmblk_gulp; + KWmblk0->len = KWmblk_gulp; + KWmblk0->next = 0; + KWmissing.mnext = KWmissing.mprev = &KWmissing; + KW_cur = 0; + memset(&KWval, 0, sizeof(KWval)); + KWvalbuf = (Real *)Alloc("kw_setup(KWValbuf)", (nKWvalbuf = 128)*sizeof(Real)); + ToClear = ToClear0 = (KeyWord**)Alloc("kw_setup(ToClear)", 256*sizeof(KeyWord*)); + ToClearEnd = ToClear0 + 256; + } + + static void +KWmembump(size_t L) +{ + KWmblk *mb, *mb1; + size_t L1; + + for(L1 = KWmblk_gulp; L1 < L; L1 <<= 1); + if ((mb = mb1 = KWmblk1->next) && L1 <= mb->len) + L1 = mb->len; + else { + KWmblk1->next = mb = (KWmblk*)Alloc("KWmembump", L1 + sizeof(KWmblk)); + mb->len = L1; + mb->next = mb1; + } + KWmblk1 = mb; + KWmem0 = (char*)(mb+1); + KWmem1 = KWmem0 + L1; + } + + static void * +KWgetmem(size_t L) /* for aligned memory */ +{ + void *rv; + + L = (L + sizeof(Real) - 1) & ~(sizeof(Real) - 1); + if (KWmem1 - KWmem0 < L) + KWmembump(L); + rv = (void*)KWmem0; + KWmem0 += L; + return rv; + } + + static KWseen ** +KWhash(const char *s, KeyWord *kw) +{ + AVLCmpInfo AI; + KWseen KW0, *KW0p, *kws, **kwsp; + char **ps; + const char *sa, *sb; + + AI.nfound = 0; + AI.inexact = -1; + AVL_setv(AVLT, &AI); + KW0.name = s; + KW0.kw = kw; + KW0p = &KW0; + curkws = 0; + if ((kwsp = (KWseen**)AVL_find((const Element*)&KW0p, AVLT))) + return kwsp; + if (AI.nfound) { + if (AI.nfound == 1) { + AI.inexact = 1; + AVL_find((const Element*)&KW0p, AVLT); + if (AI.nfound == 1) { + if (kw && (kw->kind & (KWKind_Libname | KWKind_Loaded)) + == KWKind_Libname + && (ps = (*AI.found[0])->svals)) + read_lib(ps[0], kw); + return AI.found[0]; + } + } + sa = (*AI.found[0])->name; + sb = (*AI.found[1])->name; + if (kw) + squawk("Both '%s' and '%s' match '%s'", + sa, sb, s); + else + squawk("'%s' is ambiguous:\n\tit matches both '%s' and '%s'", + s, sa, sb); + return AI.found[0]; + } + kws = (KWseen*)KWgetmem(sizeof(KWseen)); + memset(kws, 0, sizeof(KWseen)); + if ((kws->kw = kw)) + s = kw->name; + else { + curkws = kws; + kws->mnext = &KWmissing; + KWmissing.mprev = (kws->mprev = KWmissing.mprev)->mnext = kws; + s = nidr_KWscopy(s); + } + kws->name = s; + if (KW_p >= KW_pe) { + KW_p = (KWseen**)KWgetmem(32*sizeof(KWseen*)); + KW_pe = KW_p + 32; + } + *(kwsp = KW_p++) = kws; + AVL_insert((const Element*)kwsp, AVLT); + return kwsp; + } + + static void +mixed_squawk(void) +{ + squawk("values for %s cannot be both strings and numbers", + KW_cur->name); + } + + static void +nidr_bufr_relaxed(Real r, int state) +{ + int n; + + if (KWval.rstate && !state) + finish_rexpand(); + if (!(n = KWval.n)) { + KWval.r = KWvalbuf; + KWvalmax.r = KWvalbuf + (KWvalmax.n = nKWvalbuf); + } + else if (KWval.s) { + mixed_squawk(); + return; + } + if (n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.r[KWval.n++] = r; + if (state | KWval.rstate) + rexpand(state); + } + + static void +nidr_bufs_relaxed(const char *s) +{ + int n; + + if (!(n = KWval.n)) { + KWval.s = (const char**)KWvalbuf; + KWvalmax.n = (nKWvalbuf*sizeof(Real))/sizeof(char*); + KWvalmax.s = KWval.s + KWvalmax.n; + } + else if (KWval.r) { + mixed_squawk(); + return; + } + if (n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.s[KWval.n++] = s; + } + + static void kw_setup2(KWseen*); + + static void +kw_finish1(KWseen *kws) +{ + KeyWord *kw; + int n; + size_t L; + + if (KWval.rstate) + finish_rexpand(); + kws->nvals = n = KWval.n; + KWval.n = 0; + if (KWval.r) { + L = n*sizeof(Real); + memcpy(kws->rvals = (Real*)KWgetmem(L), KWval.r, L); + KWval.r = 0; + } + else if (KWval.s) { + L = n*sizeof(char*); + memcpy(kws->svals = (char**)KWgetmem(L), KWval.s, L); + if ((kw = kws->kw) && kw->kind & KWKind_Libname) { + read_lib(KWval.s[0], kw); + if (kw->kw) + kw_setup2(kws); + } + KWval.s = 0; + } + } + + static void* +Alloc1(size_t len) +{ + void *rv = malloc(len); + if (!rv) { + fprintf(stderr, "malloc(%lu) failure in Alloc1\n", (unsigned long)len); + exit(1); + } + return rv; + } + + static void +AVL_Clear(void) +{ + while(ToClear > ToClear0) + (*--ToClear)->kind &= ~KWKind_Hashed; + AVL_Tree_free(&AVLT); + if (AVLKWP) + AVL_Tree_free(&AVLKWP); + } + + static void +kw_setup1(KeyWord *kw) +{ + KWseen *kws, *kws1; + KeyWord *kw1; + + if ((kw1 = kw->kw)) + kwnext_setup(kw1, kw->nkw); + if (!KWmblk0) + KWmeminit(); + if (AVLT) + AVL_Clear(); + AVLT = AVL_Tree_alloc(0, (AVL_Elcomp)avlcmp, Alloc1); + KW_cur = KWs0 = kws = (KWseen*)KWgetmem(sizeof(KWseen)); + memset(kws, 0, sizeof(KWseen)); + kws->name = kw->name; + kws->kw = kw; + kws->lcn = &kws->mprev; + if (kw1) { + while(!kw1->name) + kw1 = kw1->kwnext; + for(; kw1; kw1 = kw1->kwnext) { + kws1 = *KWhash(kw1->name, kw1); + kws1->parent = kws; + } + } + } + + static KWseen** +kw_setup3(KWseen **kwtodo1, KWseen *kws, KeyWord *kw) +{ + KWseen *kws1, **kwsp; + + for(; kw; kw = kw->kwnext) { + kwsp = KWhash(kw->name, kw); + kws1 = *kwsp; + if (kws1->comment) { + kw->comment = kws1->comment; + kws1->comment = 0; + } + if (kws1->parent) { + kws1 = (KWseen*)KWgetmem(sizeof(KWseen)); + memset(kws1, 0, sizeof(KWseen)); + kws1->kw = kw; + kws1->name = kw->name; + *kwsp = kws1; + } + kws1->parent = kws; + if (!kws1->kw) { + kws1->mprev->mnext = kws1->mnext; + kws1->mnext->mprev = kws1->mprev; + *kwtodo1 = kws1; + kwtodo1 = kws1->lcn = &kws1->mprev; + *kws->lcn = kws1; + kws->lcn = &kws1->mnext; + } + kws1->kw = kw; + } + return kwtodo1; + } + + static void +bumpToClear(void) +{ + KeyWord **ntc; + size_t L, L1; + + L = ToClearEnd - ToClear0; + L1 = L << 1; + ntc = (KeyWord**)Alloc("bumpToClear", L1*sizeof(KeyWord*)); + memcpy(ntc, ToClear0, L*sizeof(KeyWord*)); + free(ToClear0); + ToClear0 = ntc; + ToClear = ntc + L; + ToClearEnd = ntc + L1; + } + + static void +kw_setup2(KWseen *kws) +{ + KWpair kwp, *pkwp; + KWseen *kws1, *kws2, *kws3, *kwtodo, **kwtodo1, **pkws; + KeyWord *kw, *kw1; + + kwtodo1 = &kwtodo; + for(;;) { + kw = kws->kw; + if ((kw1 = kw->kw)) { + kwnext_setup(kw1, kw->nkw); + kws2 = kws; + while(!kw1->name) { + if (!AVLKWP) + AVLKWP = AVL_Tree_alloc(0, (AVL_Elcomp)kwpcmp, Alloc1); + if (kw1->kind & KWKind_Hashed) { + kwp.kw = kw1->kw; + kwp.kws = 0; + pkwp = (KWpair*)AVL_find((const Element*)&kwp, AVLKWP); + kws2 = pkwp->kws; + } + else { + if (ToClear >= ToClearEnd) + bumpToClear(); + *ToClear++ = kw1; + kw1->kind |= KWKind_Hashed; + pkwp = (KWpair*)KWgetmem(sizeof(KWpair) + sizeof(KWseen)); + kws1 = (KWseen*)(pkwp + 1); + pkwp->kw = kw1->kw; + pkwp->kws = kws1; + memset(kws1, 0, sizeof(KWseen)); + kws1->kw = kw1; + kws1->name = kws->name; + kws1->lcn = &kws1->mprev; + kws1->parent = kws2; + *kws2->lcn = 0; + for(pkws = &kws2->mprev; + (kws3 = *pkws) && !kws3->name; + pkws = &kws3->mnext); + kws1->mnext = *pkws; + if (pkws == kws2->lcn) + kws2->lcn = &kws1->mnext; + kws2 = *pkws = kws1; + kwnext_setup(kw1->kw, kw1->nkw); + kwtodo1 = kw_setup3(kwtodo1, kws1, kw1->kw); + AVL_insert((const Element*)pkwp, AVLKWP); + } + kw1 = kw1->kwnext; + } + if (kw->nkw) + kwtodo1 = kw_setup3(kwtodo1, kws2, kw1); + } + *kwtodo1 = 0; + if (!kwtodo) + break; + kws = kwtodo; + kw = kws->kw; + if (!(kwtodo = kwtodo->mprev)) + kwtodo1 = &kwtodo; + } + } + + static KeyWord * +nidr_identifier_relaxed(const char *name) +{ + KWseen *kws, *kws1; + KeyWord *kw; + int tryagain; + + kw_finish1(KW_cur); + top: + KW_cur = kws = *KWhash(name, 0); + if ((kw = kws->kw)) { + curid = kw; + if (kws->lcn) + squawk("'%s' already seen", kw->name); + else { + if (kws->comment) { + kw->comment = kws->comment; + kws->comment = 0; + } + kws->lcn = &kws->mprev; + kws1 = kws->parent; + *kws1->lcn = kws; + kws1->lcn = &kws->mnext; + if (kw->kw) + kw_setup2(kws); + if (kw->kind & KWKind_Dynlib) { + kw = kw_insert(kw, &tryagain); + if (kw->kw) { + kws->kw = kw; + kw_setup2(kws); + } + if (tryagain) + goto top; + } + } + } + return (KeyWord*)kws; /* just needs to be nonzero; won't be dereferenced */ + } + + static void +num_expected(KeyWord *kw, int n) +{ + squawk("expected numerical value%s for %s, not quoted strings", + "s" + (n == 1), kw->name); + } + + static void +kw_process(KWseen *kws) +{ + KWseen *kws1; + KeyWord *kw; + Real *r; + Uint k; + int i, n; + + kw = kws->kw; + if (kw->name) { + if (kws != KWs0 && !nidr_identifier_strict(kw->name)) + botch("nidr_identifier_strict did not find \"%s\"", kw->name); + if ((n = KWval.n = kws->nvals)) { + KWval.i = 0; + KWval.r = 0; + KWval.s = 0; + KWval.rstate = 0; + switch(k = kw->kind & KWKind_Mask) { + case 0: + squawk("No values may be specified for %s", kw->name); + break; + + case KWKind_Int: + if (!(r = kws->rvals)) { + num_expected(kw,n); + break; + } + KWval.i = (int*)KWvalbuf; + for(i = 0; i < n; i++) + KWval.i[i] = (int)r[i]; + break; + + case KWKind_Real: + if (!(r = kws->rvals)) { + num_expected(kw,n); + break; + } + KWval.r = r; + break; + + case KWKind_Str: + if (!(KWval.s = (const char **)kws->svals)) + squawk("expected string value%s for %s", + "s" + (n == 1), kw->name); + } + } + } + *kws->lcn = 0; + for(kws1 = kws->mprev; kws1; kws1 = kws1->mnext) + kw_process(kws1); + } + + static void +kw_finish2(void) +{ + KWseen *kws, *kwe; + + kw_finish1(KW_cur); + kwe = &KWmissing; + for(kws = KWmissing.mnext; kws != kwe; kws = kws->mnext) { + squawk("unrecognized identifier '%s'", kws->name); + } + KWmissing.mnext = KWmissing.mprev = &KWmissing; + kw_process(KWs0); + KWs0 = 0; + AVL_Clear(); + } + + static void +kw_finish3(void) +{ + KWmblk1 = KWmblk0; + KWmem0 = (char*)(KWmblk0 + 1); + KWmem1 = KWmem0 + KWmblk_gulp; + KW_p = KW_pe = 0; + } + + void (*nidr_bufr)(Real,int) = nidr_bufr_relaxed; + void (*nidr_bufs)(const char*) = nidr_bufs_relaxed; + KeyWord *(*nidr_identifier)(const char*) = nidr_identifier_relaxed; + + void +nidr_set_strict(int n) +{ + if ((strict = n)) { + nidr_bufr = nidr_bufr_strict; + nidr_bufs = nidr_bufs_strict; + nidr_identifier = nidr_identifier_strict; + } + else { + nidr_bufr = nidr_bufr_relaxed; + nidr_bufs = nidr_bufs_relaxed; + nidr_identifier = nidr_identifier_relaxed; + } + } + + int +nidr_cleanup(void) +{ + KWmblk *mb, *mb1; + Sbuf *sb, *sb1; + + if (curkw) + nidr_keyword_finish(); + if (dumpfile) { + if (OutsideComment) + dumpcomment(&OutsideComment); + if (dumpfile != stdout) { + fclose(dumpfile); + dumpfile = 0; + } + if (nidr_comment) + comment_reset(); + } + if (ToClear0) { + free(ToClear0); + ToClear = ToClear0 = 0; + } + if ((mb1 = KWmblk0)) { + KWmblk0 = 0; + do { + mb = mb1; + mb1 = mb->next; + free(mb); + } while(mb1); + } + if (KWvalbuf) { + free(KWvalbuf); + KWvalbuf = 0; + } + if ((sb1 = KWsbuf0.next)) { + KWsbuf0.next = 0; + do { + sb = sb1; + sb1 = sb->next; + free(sb); + } while(sb1); + } + if (AVLT) + AVL_Clear(); + return nidr_parse_error(); + } + + void +nidr_setup(const char *parser, FILE *df) +{ + const char *s; + int comkeep, oneline; + + if (!(s = parser)) + return; + if (!strncmp(s,"nidr",4)) + s += 4; + if (!strncmp(parser,"strict",6)) { + nidr_set_strict(1); + s += 6; + } + comkeep = oneline = 0; + if (*s == '-') for(;;) { + switch(*++s) { + case '1': + ++oneline; + continue; + case 'p': + ++primary; + continue; + case 'c': + ++comkeep; + continue; + } + break; + } + if (df) + dumpfile = df; + else if (s[0] == ':' && s[1]) { + if (s[1] == '-' && !s[2]) + dumpfile = df = stdout; + else { + dumpfile = df = fopen(++s,"w"); + if (!dumpfile) { + fprintf(stderr, "Cannot open \"%s\"\n", s); + exit(1); + } + } + } + if (df) { + if (oneline) + dumpvals = dumpvals1; + if (comkeep) + comment_setup(); + } + } Index: sm/trunk/externalpackages/dakota/install-6.2-aurora.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-aurora.sh (revision 25835) +++ (revision ) @@ -1,58 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf build -rm -rf install -mkdir src build install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' - -#Untar -tar -zxvf dakota-6.2-public-src.tar.gz - -#Move Dakota to src directory -mv dakota-6.2.0.src/* src -rm -rf dakota-6.2.0.src - -#Set up Dakota cmake variables and config -export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src -export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build -export MPIHOME=$ISSM_DIR/externalpackages/mpich/install -cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake -patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.aurora.patch -patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch -patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.aurora.patch - -#Apply patches -patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch -patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch -patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch - -#Configure dakota -cd $DAK_BUILD - -cmake -D CMAKE_C_COMPILER=/opt/intel/impi/4.1.3/intel64/bin/mpicc \ - -D CMAKE_CXX_COMPILER=/opt/intel/impi/4.1.3/intel64/bin/mpicxx \ - -D CMAKE_Fortran_COMPILER=/usr/bin/gfortran \ - -DHAVE_ACRO=off \ - -DHAVE_JEGA=off \ - -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ - -C $DAK_SRC/cmake/DakotaDev.cmake \ - $DAK_SRC -cd .. - -#Compile and install dakota -cd $DAK_BUILD -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-intel20-discover.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-intel20-discover.sh (revision 25836) +++ /issm/trunk/externalpackages/dakota/install-6.2-intel20-discover.sh (revision 25836) @@ -0,0 +1,58 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.discover.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.discover20.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=mpicc \ + -D CMAKE_CXX_COMPILER=mpicxx \ + -D CMAKE_Fortran_COMPILER=/usr/bin/gfortran \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-linux-static.sh (revision 25835) +++ /issm/trunk/externalpackages/dakota/install-6.2-linux-static.sh (revision 25836) @@ -12,9 +12,9 @@ export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install -export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost (absolutely necessary for this version) -#export CXXFLAGS='-std=c++11' +export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version) export DAK_BUILD=${DAK_ROOT}/build export DAK_INSTALL=${DAK_ROOT}/install export DAK_SRC=${DAK_ROOT}/src +export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it @@ -23,5 +23,5 @@ mkdir build install src -#Download from ISSM server +# Download source ${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" @@ -55,6 +55,9 @@ -DCMAKE_CXX_FLAGS="-fPIC" \ -DCMAKE_Fortran_FLAGS="-fPIC" \ + -DBoost_NO_BOOST_CMAKE=TRUE \ -DHAVE_ACRO=OFF \ -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ -C${DAK_SRC}/cmake/DakotaDev.cmake \ Index: /issm/trunk/externalpackages/dakota/install-6.2-linux.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-linux.sh (revision 25835) +++ /issm/trunk/externalpackages/dakota/install-6.2-linux.sh (revision 25836) @@ -12,9 +12,10 @@ export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install -export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost (absolutely necessary for this version) +export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version) #export CXXFLAGS='-std=c++11' export DAK_BUILD=${DAK_ROOT}/build export DAK_INSTALL=${DAK_ROOT}/install export DAK_SRC=${DAK_ROOT}/src +export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it @@ -52,6 +53,9 @@ -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \ -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \ + -DBoost_NO_BOOST_CMAKE=TRUE \ -DHAVE_ACRO=OFF \ -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ -C${DAK_SRC}/cmake/DakotaDev.cmake \ Index: /issm/trunk/externalpackages/dakota/install-6.2-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-mac-static.sh (revision 25835) +++ /issm/trunk/externalpackages/dakota/install-6.2-mac-static.sh (revision 25836) @@ -10,10 +10,25 @@ ## Environment # -export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libgfortran.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libquadmath.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin15/9.3.0/libgcc.a" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it + +# Find libgfortran and libgcc so we do not have to hardcode them. +# +# Should retrieve a copy of gfortran that is compiled from source before +# returning one that is installed via package manager. +# +# TODO: +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. +# +LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | grep -n libgcc.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) + +export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install export DAK_BUILD=${DAK_ROOT}/build export DAK_INSTALL=${DAK_ROOT}/install export DAK_SRC=${DAK_ROOT}/src -export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libgfortran.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libquadmath.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin15/9.3.0/libgcc.a" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install +export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it # Cleanup @@ -41,5 +56,18 @@ cp configs/${VER}/mac/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake cp configs/${VER}/mac/cmake/DakotaDev.cmake ${DAK_SRC}/cmake +cp configs/${VER}/mac/cmake/InstallDarwinDylibs.cmake ${DAK_SRC}/cmake cp configs/${VER}/mac/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src + +# Uncomment to copy the following customized source files if using C99 or later +# standard. If uncommented, adding -Wno-error=implicit-function-declaration +# option to CFLAGS is not needed. +# cp configs/${VER}/mac/static/packages/DDACE/include/xtndispatch.h ${DAK_SRC}/packages/DDACE/include +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/Boselink.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/construct.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/galois.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/gfields.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/oa.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/nidr/nidr.c ${DAK_SRC}/packages/nidr +# cp configs/${VER}/mac/static/packages/nidr/nidr-scanner.c ${DAK_SRC}/packages/nidr # Configure @@ -51,5 +79,5 @@ -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \ -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \ - -DCMAKE_C_FLAGS="-fPIC" \ + -DCMAKE_C_FLAGS="-fPIC -Wno-error=implicit-function-declaration" \ -DCMAKE_CXX_FLAGS="-fPIC -fdelayed-template-parsing" \ -DCMAKE_Fortran_FLAGS="-fPIC" \ @@ -57,4 +85,6 @@ -DHAVE_ACRO=OFF \ -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ -C${DAK_SRC}/cmake/DakotaDev.cmake \ Index: /issm/trunk/externalpackages/dakota/install-6.2-mac.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-mac.sh (revision 25835) +++ /issm/trunk/externalpackages/dakota/install-6.2-mac.sh (revision 25836) @@ -10,10 +10,20 @@ ## Environment # -export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/local/Cellar/gcc/9.3.0/lib/gcc/9 -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it + +# Find libgfortran so that we do not have to hardcode it. +# +# Should retrieve a copy of gfortran that is compiled from source before +# returning one that is installed via package manager. +# +LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} + +export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install export DAK_BUILD=${DAK_ROOT}/build export DAK_INSTALL=${DAK_ROOT}/install export DAK_SRC=${DAK_ROOT}/src -export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/local/Cellar/gcc/9.3.0/lib/gcc/9 -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install +export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it # Cleanup @@ -56,4 +66,6 @@ -DHAVE_ACRO=OFF \ -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ -C${DAK_SRC}/cmake/DakotaDev.cmake \ Index: /issm/trunk/externalpackages/dakota/install-6.2-macosx64-catalina.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-catalina.sh (revision 25836) +++ /issm/trunk/externalpackages/dakota/install-6.2-macosx64-catalina.sh (revision 25836) @@ -0,0 +1,76 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#GSL: +export GSL_HOME=$HOME/externalpackages/gsl/install + +#Set up Dakota cmake variables and config +export DAK_SRC=$HOME/externalpackages/dakota/src +export DAK_BUILD=$HOME/externalpackages/dakota/build +export MPIHOME=$HOME/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.mac.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch +patch src/packages/VPISparseGrid/src/sandia_rules.cpp configs/6.2/sandia_rules.cpp.patch + +export BOOST_ROOT=$HOME/externalpackages/boost/install + + +#Configure dakota +# Set your local gcc compiler here +cd $DAK_BUILD +cmake -DBoost_NO_BOOST_CMAKE=TRUE \ + -DBoost_NO_SYSTEM_PATHS=TRUE \ + -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ + -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \ + -D CMAKE_C_COMPILER=$HOME/externalpackages/mpich/install/bin/mpicc \ + -D CMAKE_CXX_COMPILER=$HOME/externalpackages/mpich/install/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=$HOME/externalpackages/mpich/install/bin/mpif77 \ + -D CMAKE_CXX_FLAGS=-fdelayed-template-parsing \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -DDAKOTA_HAVE_GSL=on \ + -DHAVE_QUESO=on \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +# Snowleopard: Mpi should be made with these compilers +#-DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CC_COMPILER=/usr/bin/gcc \ +#-DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran \ + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: sm/trunk/externalpackages/dakota/install-6.2-macosx64-static.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-static.sh (revision 25835) +++ (revision ) @@ -1,80 +1,0 @@ -#!/bin/bash -set -eu - -# Constants -DAK_VER="6.2" - -# Some cleanup -rm -rf build -rm -rf install -rm -rf tests -rm -rf src -mkdir build install src - -# Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${DAK_VER}-public.src.tar.gz" "dakota-${DAK_VER}-public-src.tar.gz" - -# Untar -tar -zxvf dakota-${DAK_VER}-public-src.tar.gz - -# Move Dakota to src directory -mv dakota-${DAK_VER}.0.src/* src -rm -rf dakota-${DAK_VER}.0.src - -# Set up Dakota and CMake variables -DAK_PATH=$ISSM_DIR/externalpackages/dakota - -export DAK_BUILD=$DAK_PATH/build -export DAK_INSTALL=$DAK_PATH/install -export DAK_SRC=$DAK_PATH/src -export MPIHOME=$ISSM_DIR/externalpackages/mpich/install - - -# Apply patches -cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake -patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/$DAK_VER/BuildDakotaCustom.cmake.mac.patch -patch $DAK_SRC/cmake/DakotaDev.cmake configs/$DAK_VER/DakotaDev.cmake.patch -patch $DAK_SRC/cmake/InstallDarwinDylibs.cmake configs/$DAK_VER/InstallDarwinDylibs.cmake.patch -patch $DAK_SRC/CMakeLists.txt configs/$DAK_VER/CMakeLists.txt.patch -patch src/src/NonDSampling.cpp configs/$DAK_VER/NonDSampling.cpp.patch -patch src/src/NonDLocalReliability.cpp configs/$DAK_VER/NonDLocalReliability.cpp.patch -patch src/packages/pecos/src/pecos_global_defs.hpp configs/$DAK_VER/pecos_global_defs.hpp.patch - -# Configure and build Dakota -cd $DAK_BUILD -cmake \ - -C$DAK_SRC/cmake/BuildDakotaCustom.cmake \ - -C$DAK_SRC/cmake/DakotaDev.cmake \ - -DBUILD_STATIC_LIBS=ON \ - -DBUILD_SHARED_LIBS=OFF \ - -DBOOST_ROOT=$BOOST_ROOT \ - -DBoost_LIBRARY_DIRS=$BOOST_ROOT/lib \ - -DBoost_NO_BOOST_CMAKE=TRUE \ - -DBoost_NO_SYSTEM_PATHS=TRUE \ - -DCMAKE_INSTALL_PREFIX=$DAK_INSTALL \ - -DCMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ - -DCMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ - -DCMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ - -DCMAKE_CXX_FLAGS=-fdelayed-template-parsing \ - -DHAVE_ACRO=off \ - -DHAVE_JEGA=off \ - $DAK_SRC - -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Set paths and library paths -export PATH=$DAK_INSTALL/bin:$DAK_INSTALL/test:$PATH - -if [ -z ${DYLD_LIBRARY_PATH+x} ] -then - export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin -else - export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin:$DYLD_LIBRARY_PATH -fi Index: sm/trunk/externalpackages/dakota/install-6.2-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64.sh (revision 25835) +++ (revision ) @@ -1,78 +1,0 @@ -#!/bin/bash -set -eu - -# Constants -DAK_VER="6.2" - -# Some cleanup -rm -rf build -rm -rf install -rm -rf tests -rm -rf src -mkdir build install src - -# Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${DAK_VER}-public.src.tar.gz" "dakota-${DAK_VER}-public-src.tar.gz" - -# Untar -tar -zxvf dakota-${DAK_VER}-public-src.tar.gz - -# Move Dakota to src directory -mv dakota-${DAK_VER}.0.src/* src -rm -rf dakota-${DAK_VER}.0.src - -# Set up Dakota and CMake variables -DAK_PATH=$ISSM_DIR/externalpackages/dakota - -export DAK_BUILD=$DAK_PATH/build -export DAK_INSTALL=$DAK_PATH/install -export DAK_SRC=$DAK_PATH/src -export MPIHOME=$ISSM_DIR/externalpackages/mpich/install -export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install - -# Apply patches -cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake -patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/$DAK_VER/BuildDakotaCustom.cmake.mac.patch -patch $DAK_SRC/cmake/DakotaDev.cmake configs/$DAK_VER/DakotaDev.cmake.patch -patch $DAK_SRC/cmake/InstallDarwinDylibs.cmake configs/$DAK_VER/InstallDarwinDylibs.cmake.patch -patch $DAK_SRC/CMakeLists.txt configs/$DAK_VER/CMakeLists.txt.patch -patch src/src/NonDSampling.cpp configs/$DAK_VER/NonDSampling.cpp.patch -patch src/src/NonDLocalReliability.cpp configs/$DAK_VER/NonDLocalReliability.cpp.patch -patch src/packages/pecos/src/pecos_global_defs.hpp configs/$DAK_VER/pecos_global_defs.hpp.patch - -# Configure and build Dakota -cd $DAK_BUILD -cmake \ - -C$DAK_SRC/cmake/BuildDakotaCustom.cmake \ - -C$DAK_SRC/cmake/DakotaDev.cmake \ - -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ - -DBoost_NO_BOOST_CMAKE=TRUE \ - -DBoost_NO_SYSTEM_PATHS=TRUE \ - -DBoost_LIBRARY_DIRS:FILEPATH=$BOOST_ROOT/lib \ - -DCMAKE_INSTALL_PREFIX=$DAK_INSTALL \ - -DCMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ - -DCMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ - -DCMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ - -DCMAKE_CXX_FLAGS=-fdelayed-template-parsing \ - -DHAVE_ACRO=off \ - -DHAVE_JEGA=off \ - $DAK_SRC - -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Set paths and library paths -export PATH=$DAK_INSTALL/bin:$DAK_INSTALL/test:$PATH - -if [ -z ${DYLD_LIBRARY_PATH+x} ] -then - export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin -else - export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin:$DYLD_LIBRARY_PATH -fi Index: /issm/trunk/externalpackages/doxygen/install.sh =================================================================== --- /issm/trunk/externalpackages/doxygen/install.sh (revision 25835) +++ /issm/trunk/externalpackages/doxygen/install.sh (revision 25836) @@ -7,8 +7,11 @@ #Download latest version -svn co https://svn.code.sf.net/p/doxygen/code/trunk src +git clone https://github.com/doxygen/doxygen.git install #Configure doxygen -cd src && ./configure --prefix "$ISSM_DIR/externalpackages/doxygen/install" +cd install +mkdir build +cd build +cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/doxygen/install" .. if [ $# -eq 0 ]; then make @@ -17,5 +20,3 @@ fi -#Install doxygen make install -make install_docs Index: /issm/trunk/externalpackages/esmf/install.sh =================================================================== --- /issm/trunk/externalpackages/esmf/install.sh (revision 25835) +++ /issm/trunk/externalpackages/esmf/install.sh (revision 25836) @@ -2,25 +2,15 @@ set -eu +#DOC: https://earthsystemmodeling.org/docs/nightly/develop/ESMC_crefdoc/node5.html#SECTION05063000000000000000 +# https://cpp.hotexamples.com/examples/-/-/ESMC_MeshAddNodes/cpp-esmc_meshaddnodes-function-examples.html + +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/ESMF_8_0_1.tar.gz" "ESMF_8_0_1.tar.gz" +tar -zxvf ESMF_8_0_1.tar.gz +mv ESMF_8_0_1 esmf export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf export ESMF_INSTALL_PREFIX=$ISSM_DIR/externalpackages/esmf/install -export ESMF_COMPILER=gfortran -export ESMF_COMM=mpich2 - -#Some cleanup -rm -rf esmf_6_3_0rp1 -rm -rf esmf - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/esmf_6_3_0rp1_src.tar.gz' 'esmf_6_3_0rp1_src.tar.gz' -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/docs/ESMF_refdoc.pdf' 'ESMF_refdoc.pdf' -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/docs/ESMF_usrdoc.pdf' 'ESMF_usrdoc.pdf' - -#Untar -tar -zxvf esmf_6_3_0rp1_src.tar.gz - -#Configure esmf -cd esmf #Compile and install esmf +cd esmf if [ $# -eq 0 ]; then make Index: /issm/trunk/externalpackages/gdal/install-3-netcdf-static.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3-netcdf-static.sh (revision 25836) +++ /issm/trunk/externalpackages/gdal/install-3-netcdf-static.sh (revision 25836) @@ -0,0 +1,63 @@ +#!/bin/bash +set -eu + + +# TODO +# - May want to supply path to Python instead of, effectively, using result of +# `which python` +# + +## Constants +# +VER="3.1.1" + +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install" +PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +## Environment +# +export CC=mpicc +export CXX=mpicxx +export LDFLAGS="-L${HDF5_ROOT}/lib" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time +export LIBS="-lhdf5_hl -lhdf5" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-$VER.tar.gz + +# Move source into 'src' directory +mv gdal-$VER/* src +rm -rf gdal-$VER + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --disable-shared \ + --without-ld-shared \ + --enable-static \ + --with-pic \ + --with-libz="${ZLIB_ROOT}" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-proj="${PROJ_ROOT}" \ + --with-pg=no + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gdal/install-3-netcdf.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3-netcdf.sh (revision 25836) +++ /issm/trunk/externalpackages/gdal/install-3-netcdf.sh (revision 25836) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="3.1.1" + +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install" +PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +## Environment +# +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-$VER.tar.gz + +# Move source into 'src' directory +mv gdal-$VER/* src +rm -rf gdal-$VER + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --with-libz="${ZLIB_ROOT}" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-proj="${PROJ_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gdal/install-3-python-netcdf-static.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3-python-netcdf-static.sh (revision 25836) +++ /issm/trunk/externalpackages/gdal/install-3-python-netcdf-static.sh (revision 25836) @@ -0,0 +1,64 @@ +#!/bin/bash +set -eu + + +# TODO +# - May want to supply path to Python instead of, effectively, using result of +# `which python` +# + +## Constants +# +VER="3.1.1" + +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install" +PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +## Environment +# +export CC=mpicc +export CXX=mpicxx +export LDFLAGS="-L${HDF5_ROOT}/lib" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time +export LIBS="-lhdf5_hl -lhdf5" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-$VER.tar.gz + +# Move source into 'src' directory +mv gdal-$VER/* src +rm -rf gdal-$VER + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --disable-shared \ + --without-ld-shared \ + --enable-static \ + --with-pic \ + --with-python \ + --with-libz="${ZLIB_ROOT}" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-proj="${PROJ_ROOT}" \ + --with-pg=no + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gdal/install-3-python-netcdf.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3-python-netcdf.sh (revision 25836) +++ /issm/trunk/externalpackages/gdal/install-3-python-netcdf.sh (revision 25836) @@ -0,0 +1,54 @@ +#!/bin/bash +set -eu + + +## TODO +# - May want to supply path to Python instead of, effectively, using result of `which python` +# + +## Constants +# +VER="3.1.1" + +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install" +PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +## Environment +# +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build) + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-$VER.tar.gz + +# Move source into 'src' directory +mv gdal-$VER/* src +rm -rf gdal-$VER + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --with-python \ + --with-libz="${ZLIB_ROOT}" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-proj="${PROJ_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gdal/install-3-python.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3-python.sh (revision 25836) +++ /issm/trunk/externalpackages/gdal/install-3-python.sh (revision 25836) @@ -0,0 +1,50 @@ +#!/bin/bash +set -eu + + +## TODO +# - May want to supply path to Python instead of, effectively, using result of `which python` +# + +## Constants +# +VER="3.1.1" + +PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" + +## Environment +# +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build) + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-$VER.tar.gz + +# Move source into 'src' directory +mv gdal-$VER/* src +rm -rf gdal-$VER + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --with-python \ + --without-hdf5 \ + --without-netcdf \ + --with-proj="${PROJ_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: sm/trunk/externalpackages/gdal/install-3.0-netcdf.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3.0-netcdf.sh (revision 25835) +++ (revision ) @@ -1,44 +1,0 @@ -#!/bin/bash -set -eu - - -# Constants -# -VER="3.0.2" -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -NETCDF_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" - -# Cleanup -rm -rf install src -mkdir install src - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" - -# Unpack source -tar -zxvf gdal-$VER.tar.gz - -# Move source into 'src' directory -mv gdal-$VER/* src -rm -rf gdal-$VER - -# Configure -cd src -./configure \ - --prefix="${ISSM_DIR}/externalpackages/gdal/install" \ - --with-hdf5="${HDF5_ROOT}" \ - --with-netcdf="${NETCDF_ROOT}" \ - --with-proj="${PROJ_ROOT}" - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Return to initial directory -cd .. Index: sm/trunk/externalpackages/gdal/install-3.0-python-netcdf.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3.0-python-netcdf.sh (revision 25835) +++ (revision ) @@ -1,49 +1,0 @@ -#!/bin/bash -set -eu - - -## TODO -# - May want to supply path to Python instead of, effectively, using result of `which python` -# - -## Constants -# -VER="3.0.2" -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -NETCDF_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" - -# Cleanup -rm -rf install src -mkdir install src - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" - -# Unpack source -tar -zxvf gdal-$VER.tar.gz - -# Move source into 'src' directory -mv gdal-$VER/* src -rm -rf gdal-$VER - -# Configure -cd src -./configure \ - --prefix="${ISSM_DIR}/externalpackages/gdal/install" \ - --with-python \ - --with-hdf5="${HDF5_ROOT}" \ - --with-netcdf="${NETCDF_ROOT}" \ - --with-proj="${PROJ_ROOT}" - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Return to initial directory -cd .. Index: sm/trunk/externalpackages/gdal/install-3.0-python.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3.0-python.sh (revision 25835) +++ (revision ) @@ -1,47 +1,0 @@ -#!/bin/bash -set -eu - - -## TODO -# - May want to supply path to Python instead of, effectively, using result of `which python` -# - -## Constants -# -VER="3.0.2" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" - -# Cleanup -rm -rf install src -mkdir install src - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" - -# Unpack source -tar -zxvf gdal-$VER.tar.gz - -# Move source into 'src' directory -mv gdal-$VER/* src -rm -rf gdal-$VER - -# Configure -cd src -./configure \ - --prefix="${ISSM_DIR}/externalpackages/gdal/install" \ - --with-python \ - --without-hdf5 \ - --without-netcdf \ - --with-proj="${PROJ_ROOT}" - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Return to initial directory -cd .. Index: sm/trunk/externalpackages/gdal/install-3.0.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3.0.sh (revision 25835) +++ (revision ) @@ -1,42 +1,0 @@ -#!/bin/bash -set -eu - - -# Constants -# -VER="3.0.2" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" - -# Cleanup -rm -rf install src -mkdir install src - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" - -# Unpack source -tar -zxvf gdal-${VER}.tar.gz - -# Move source into 'src' directory -mv gdal-$VER/* src -rm -rf gdal-$VER - -# Configure -cd src -./configure \ - --prefix="${ISSM_DIR}/externalpackages/gdal/install" \ - --without-hdf5 \ - --without-netcdf \ - --with-proj="${PROJ_ROOT}" - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Return to initial directory -cd .. Index: /issm/trunk/externalpackages/gdal/install-3.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3.sh (revision 25836) +++ /issm/trunk/externalpackages/gdal/install-3.sh (revision 25836) @@ -0,0 +1,48 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="3.1.1" + +PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" + +## Environment +# +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-${VER}.tar.gz + +# Move source into 'src' directory +mv gdal-$VER/* src +rm -rf gdal-$VER + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --without-hdf5 \ + --without-netcdf \ + --with-proj="${PROJ_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Return to initial directory +cd .. Index: /issm/trunk/externalpackages/geocode/geoCode.m =================================================================== --- /issm/trunk/externalpackages/geocode/geoCode.m (revision 25836) +++ /issm/trunk/externalpackages/geocode/geoCode.m (revision 25836) @@ -0,0 +1,180 @@ +function [c] = geoCode(address, service, key) +%GEOCODE look up the latitude and longitude of a an address +% +% COORDS = GEOCODE( ADDRESS ) returns the geocoded latitude and longitude +% of the input address. +% +% COORDS = GEOCODE( ADDRESS, SERVICE) performs the look up using the +% specified SERVICE. Valid services are +% google - Google Maps (default service) +% osm - OpenStreetMap +% yahoo - Yahoo! Place Finder +% +% COORDS = GEOCODE( ..., SERVICE, APIKEY) allows the specifcation of an AppId +% API key if needed. + +% Copyright(c) 2012, Stuart P. Layton +% http://stuartlayton.com +% +% Revision History +% 2012/08/20 - Initial Release +% 2012/08/20 - Simplified XML parsing code + + +% Validate the input arguments + +% Check to see if address is a valid string +if isempty(address) || ~ischar(address) || ~isvector(address) + error('Invalid address provided, must be a string'); +end + +% if no service is specified or an empty service is specified use google +if nargin<2 || isempty(service) + service = 'google'; +end + +% if no key is specified then set it to empty, also check to see if char array +if nargin<3 + key = []; +end + +%replace white spaces in the address with '+' +address = regexprep(address, ' ', '+'); + +% Switch on the specified service, construct the Query URL, and specify the +% function that will be used to parse the resulting XML +switch lower(service) + case('google') + SERVER_URL = 'http://maps.google.com'; + queryUrl = sprintf('%s/maps/geo?output=xml&q=%s',SERVER_URL, address); + parseFcn = @parseGoogleMapsXML; + + case('yahoo') + + SERVER_URL = 'http://where.yahooapis.com/geocode'; + queryUrl = sprintf('%s?location=%s',SERVER_URL, address); + +% The Yahoo docs say that an AppID is required although +% it appears that responses are given without a valid appid +% If an AppId is provided include it in the URL + if ~isempty(key) + queryUrl = sprintf('%s&appid=%s', queryUrl, key); + end + + parseFcn = @parseYahooLocalXML; + + + case {'osm', 'openstreetmaps', 'open street maps'} + + SERVER_URL = 'https://nominatim.openstreetmap.org/search'; + queryUrl = sprintf('%s?format=xml&q=%s', SERVER_URL, address); + parseFcn = @parseOpenStreetMapXML; + + otherwise + error('Invalid geocoding service specified:%s', service); +end + + try + docNode = xmlread(queryUrl); + catch %#ok + error('Error, could not reach %s, is it a valid URL?', SERVER_URL); + end + + c = parseFcn(docNode); +end + +% Function to parse the XML response from Google Maps +function [c] = parseGoogleMapsXML(docNode) + + %check the response code to see if we got a valid response + codeEl = docNode.getElementsByTagName('code'); + errCode = str2double( char( codeEl.item(0).getTextContent ) ); + % code 200 is associated with a valid geocode xml file + if errCode~=200 + fprintf('No data received from server! Received code:%d\n', errCode) + c = nan(2,1); + return; + end + + %get the 'coordinates' element from the document + cordEl = docNode.getElementsByTagName('coordinates'); + + %make sure the xml actually included a coordinates tag + if cordEl.length<1 + c = nan(2,1); + warning('No coordinates returned for the specified address'); + return; + end + + % get the coordinates from the first node, convert them to numbers + coords = cellfun(@str2double, regexp( char( cordEl.item(0).getTextContent), ',', 'split')); + + c = coords([2, 1]); % return the latitude and longitude +end + +% Function to parse the XML response from Yahoo Local +function [c] = parseYahooLocalXML(docNode) + + %check the response code to see if we got a valid response + codeEl = docNode.getElementsByTagName('Error'); + errCode = str2double( char( codeEl.item(0).getTextContent ) ); + + % code 0 is associated with a valid geocode xml file + if errCode~=0 + fprintf('No data received from server! Received code:%d\n', errCode) + c = nan(2,1); + return; + end + + %check to see if a location was actually found + foundEl = docNode.getElementsByTagName('Found'); + found = str2double( char( foundEl.item(0).getTextContent) ); + % + if found<1 + disp('A location with that address was not found!'); + c = nan(2,1); + return; + end + + + latEl = docNode.getElementsByTagName('latitude'); + lonEl = docNode.getElementsByTagName('longitude'); + + %make sure the xml actually included latitude and longitude tags + if latEl.length==0 || lonEl.length==0 + c = nan(2,1); + disp('No coordinates were found for that address'); + return; + end + + c(1) = str2double( char( latEl.item(0).getTextContent) ); + c(2) = str2double( char( lonEl.item(0).getTextContent) ); + +end + +% Function to parse the XML response from OpenStreetMap +function [c] = parseOpenStreetMapXML(docNode) + + serverResponse = docNode.getElementsByTagName('searchresults').item(0); + placeTag = serverResponse.getElementsByTagName('place').item(0); + + if isempty(placeTag) + disp('OpenStreeMap returned no data for that address');%#ok + c = nan(2,1); + return; + end + + c(1) = str2double( char( placeTag.getAttribute('lat') ) ); + c(2) = str2double( char( placeTag.getAttribute('lon') ) ); + +end + + +function elementText = GetElementText(resultNode,elementName) +% GETELEMENTTEXT given a result node and an element name +% returns the text within that node as a Matlab CHAR array + +elementText = ... + char( resultNode.getElementsByTagName(elementName).item(0).getTextContent ); + +end Index: /issm/trunk/externalpackages/geocode/license.txt =================================================================== --- /issm/trunk/externalpackages/geocode/license.txt (revision 25836) +++ /issm/trunk/externalpackages/geocode/license.txt (revision 25836) @@ -0,0 +1,24 @@ +Copyright (c) 2012, Stuart Layton +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/trunk/externalpackages/gmsh/configs/4.5.6/mac/static/CMakeLists.txt =================================================================== --- /issm/trunk/externalpackages/gmsh/configs/4.5.6/mac/static/CMakeLists.txt (revision 25836) +++ /issm/trunk/externalpackages/gmsh/configs/4.5.6/mac/static/CMakeLists.txt (revision 25836) @@ -0,0 +1,2141 @@ +# Gmsh - Copyright (C) 1997-2020 C. Geuzaine, J.-F. Remacle +# +# See the LICENSE.txt file for license information. Please report all +# issues on https://gitlab.onelab.info/gmsh/gmsh/issues. + +cmake_minimum_required(VERSION 2.8 FATAL_ERROR) + +# do not warn about non-definition of WIN32 on Cygwin +set(CMAKE_LEGACY_CYGWIN_WIN32 0) + +# if CMAKE_BUILD_TYPE is specified use it; otherwise set the default +# build type to "RelWithDebInfo" ("-O2 -g" with gcc) prior to calling +# project() +if(DEFINED CMAKE_BUILD_TYPE) + set(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Choose build type") +else() + set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose build type") +endif() + +project(gmsh CXX C) + +# this variable controls the default value of the options which are normally set +# to ON (useful if you want to configure a minimal version of Gmsh: e.g. "cmake +# -DDEFAULT=0 -DENABLE_POST=1 -DENABLE_PARSER=1") +set(DEFAULT ON CACHE INTERNAL "Default value for enabled-by-default options") + +macro(opt OPTION HELP VALUE) + option(ENABLE_${OPTION} ${HELP} ${VALUE}) + set(OPT_TEXI "${OPT_TEXI}\n@item ENABLE_${OPTION}\n${HELP} (default: ${VALUE})") +endmacro() + +opt(3M "Enable proprietary 3M extension" OFF) +opt(ACIS "Enable ACIS geometrical models (experimental)" ${DEFAULT}) +opt(ALGLIB "Enable ALGLIB (used by some mesh optimizers)" ${DEFAULT}) +opt(ANN "Enable ANN (used for fast point search in mesh/post)" ${DEFAULT}) +opt(BAMG "Enable Bamg 2D anisotropic mesh generator" ${DEFAULT}) +opt(BLAS_LAPACK "Enable BLAS/Lapack for linear algebra (required for meshing)" ON) +opt(BLOSSOM "Enable Blossom algorithm (needed for full quad meshing)" ${DEFAULT}) +opt(BUILD_LIB "Enable 'lib' target for building static Gmsh library" OFF) +opt(BUILD_SHARED "Enable 'shared' target for building shared Gmsh library" OFF) +opt(BUILD_DYNAMIC "Enable dynamic Gmsh executable (linked with shared library)" OFF) +opt(BUILD_ANDROID "Enable Android NDK library target (experimental)" OFF) +opt(BUILD_IOS "Enable iOS library target (experimental)" OFF) +opt(CGNS "Enable CGNS import/export (experimental)" ${DEFAULT}) +opt(CGNS_CPEX0045 "Enable high-order CGNS import/export following CPEX0045 (experimental)" OFF) +opt(CAIRO "Enable Cairo to render fonts (experimental)" ${DEFAULT}) +opt(CXX11 "Enable C++11" ON) +opt(C99 "Enable C99" ON) +opt(PROFILE "Enable profiling compiler flags" OFF) +opt(DINTEGRATION "Enable discrete integration (needed for levelsets)" ${DEFAULT}) +opt(DOMHEX "Enable experimental DOMHEX code" ${DEFAULT}) +opt(FLTK "Enable FLTK graphical user interface (requires mesh/post)" ${DEFAULT}) +opt(GETDP "Enable GetDP solver (linked as a library, experimental)" ${DEFAULT}) +opt(GMM "Enable GMM linear solvers (simple alternative to PETSc)" ${DEFAULT}) +opt(GMP "Enable GMP for Kbipack (advanced)" ON) +opt(GRAPHICS "Enable building graphics lib even without GUI (advanced)" OFF) +opt(HXT "Enable HXT library (for reparametrization and meshing)" ${DEFAULT}) +opt(KBIPACK "Enable Kbipack (neeeded by homology solver)" ${DEFAULT}) +opt(MATHEX "Enable Mathex expression parser (used by plugins and options)" ${DEFAULT}) +opt(MED "Enable MED mesh and post file formats" ${DEFAULT}) +opt(MESH "Enable mesh module (required by GUI)" ${DEFAULT}) +opt(METIS "Enable Metis mesh partitioner" ${DEFAULT}) +opt(MMG3D "Enable MMG3D 3D anisotropic mesh refinement" ${DEFAULT}) +opt(MPEG_ENCODE "Enable built-in MPEG movie encoder" ${DEFAULT}) +opt(MPI "Enable MPI (experimental, not used for meshing)" OFF) +opt(MSVC_STATIC_RUNTIME "Enable static Visual C++ runtime" OFF) +opt(MUMPS "Enable MUMPS sparse direct linear solver" OFF) +opt(NETGEN "Enable Netgen 3D frontal mesh generator" ${DEFAULT}) +opt(NUMPY "Enable fullMatrix and numpy array conversion for private API" OFF) +opt(PETSC4PY "Enable petsc4py wrappers for petsc matrices for private API" OFF) +opt(OCC "Enable OpenCASCADE CAD kernel" ${DEFAULT}) +opt(OCC_CAF "Enable OpenCASCADE CAF module (for STEP/IGES attributes)" ${DEFAULT}) +opt(OCC_STATIC "Link OpenCASCADE static instead of dynamic libraries (requires ENABLE_OCC)" OFF) +opt(OCC_TBB "Add TBB libraries in list of OCC libraries" OFF) +opt(ONELAB "Enable ONELAB solver interface" ${DEFAULT}) +opt(ONELAB_METAMODEL "Enable ONELAB metamodels (experimental)" ${DEFAULT}) +opt(OPENACC "Enable OpenACC" OFF) +opt(OPENMP "Enable OpenMP" OFF) +opt(OPTHOM "Enable high-order mesh optimization tools" ${DEFAULT}) +opt(OS_SPECIFIC_INSTALL "Enable OS-specific (e.g. app bundle) installation" OFF) +opt(OSMESA "Enable OSMesa for offscreen rendering (experimental)" OFF) +opt(P4EST "Enable p4est for enabling automatic mesh size firld (experimental)" OFF) +opt(PACKAGE_STRIP "Strip symbols in install packages to reduce install size" ON) +opt(PARSER "Enable GEO file parser (required for .geo/.pos files)" ${DEFAULT}) +opt(PETSC "Enable PETSc linear solvers (required for SLEPc)" OFF) +opt(PLUGINS "Enable post-processing plugins" ${DEFAULT}) +opt(POST "Enable post-processing module (required by GUI)" ${DEFAULT}) +opt(POPPLER "Enable Poppler for displaying PDF documents (experimental)" OFF) +opt(PRIVATE_API "Enable private API" OFF) +opt(QUADTRI "Enable QuadTri structured meshing extensions" ${DEFAULT}) +opt(REVOROPT "Enable Revoropt (used for CVT remeshing)" OFF) +opt(SLEPC "Enable SLEPc eigensolvers" OFF) +opt(SOLVER "Enable built-in finite element solvers (required for compounds)" ${DEFAULT}) +opt(SYSTEM_CONTRIB "Use system versions of contrib libraries, when possible" OFF) +opt(TCMALLOC "Enable libtcmalloc (fast malloc that does not release memory)" OFF) +opt(TOUCHBAR "Enable Apple Touch bar" ${DEFAULT}) +opt(VISUDEV "Enable additional visualization capabilities for development purposes" OFF) +opt(VOROPP "Enable voro++ (for hex meshing, experimental)" ${DEFAULT}) +opt(WRAP_JAVA "Enable generation of Java wrappers for private API" OFF) +opt(WRAP_PYTHON "Enable generation of Python wrappers for private API" OFF) +opt(ZIPPER "Enable Zip file compression/decompression" OFF) + +set(GMSH_MAJOR_VERSION 4) +set(GMSH_MINOR_VERSION 5) +set(GMSH_PATCH_VERSION 6) +set(GMSH_EXTRA_VERSION "") +set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION}") + +if(NOT GMSH_RELEASE) + find_package(Git) + if(GIT_FOUND) + execute_process(COMMAND ${GIT_EXECUTABLE} log -1 --format=%h + WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} ERROR_QUIET + OUTPUT_VARIABLE GIT_COMMIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE) + endif() + if(GIT_COMMIT_HASH) + set(GMSH_EXTRA_VERSION "${GMSH_EXTRA_VERSION}-git-${GIT_COMMIT_HASH}") + endif() + set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION_TEXI} (development version)") +endif() + +set(GMSH_VERSION "${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}") +set(GMSH_VERSION "${GMSH_VERSION}.${GMSH_PATCH_VERSION}${GMSH_EXTRA_VERSION}") +set(GMSH_SHORT_LICENSE "GNU General Public License") + +set(GMSH_API api/gmsh.h api/gmshc.h api/gmsh.h_cwrap) + +if(ENABLE_PRIVATE_API) + message(WARNING "The private API is unsupported and undocumented. It is meant " + "for expert Gmsh developers, not for regular Gmsh users, who should rely " + "on the stable public API (gmsh/api) instead. If you are repackaging Gmsh, " + "e.g. for a Linux distribution, please DO NOT distribute the private API " + "(i.e. all the internal headers) and ship the stable public API instead " + "(i.e. only the headers and modules in gmsh/api).") + file(GLOB_RECURSE HEADERS Common/*.h Numeric/*.h Geo/*.h Mesh/*.h Solver/*.h + Post/*.h Graphics/*.h contrib/kbipack/*.h contrib/DiscreteIntegration/*.h + contrib/HighOrderMeshOptimizer/*.h contrib/MeshOptimizer/*.h + contrib/MeshQualityOptimizer/*.h) + set(GMSH_PRIVATE_API ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h ${HEADERS}) + get_property(IAMCHILD DIRECTORY PROPERTY PARENT_DIRECTORY) + if(IAMCHILD) + set(GMSH_PRIVATE_API ${GMSH_PRIVATE_API} PARENT_SCOPE) + endif() +endif() + +set(ONELAB_PY contrib/onelab/python/onelab.py) +set(GMSH_PY api/gmsh.py) +set(GMSH_JL api/gmsh.jl) + +if(${CMAKE_MAJOR_VERSION} GREATER 2) + string(TIMESTAMP DATE "%Y%m%d") +else() + execute_process(COMMAND date "+%Y%m%d" OUTPUT_VARIABLE DATE + OUTPUT_STRIP_TRAILING_WHITESPACE) +endif() + +if(NOT DATE) + set(DATE "unknown") +endif() +set(GMSH_DATE "${DATE}") + +if(NOT GMSH_HOST) + execute_process(COMMAND hostname OUTPUT_VARIABLE HOSTNAME + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT HOSTNAME) + set(HOSTNAME "unknown") + endif() + set(GMSH_HOST "${HOSTNAME}") +endif() + +if(NOT GMSH_PACKAGER) + execute_process(COMMAND whoami OUTPUT_VARIABLE PACKAGER + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT PACKAGER) + set(PACKAGER "unknown") + endif() + string(REPLACE "\\" " " PACKAGER ${PACKAGER}) + set(GMSH_PACKAGER "${PACKAGER}") +endif() + +if(APPLE) + set(GMSH_OS "MacOSX") +elseif(CYGWIN OR MSYS) + # detect if we use the MinGW compilers on Cygwin - if we do, handle the build + # as a pure Windows build + if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpmachine + OUTPUT_VARIABLE CXX_COMPILER_MACHINE + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(CXX_COMPILER_MACHINE MATCHES "mingw") + set(GMSH_OS "Windows") + set(WIN32 1) + add_definitions(-DWIN32) + endif() + endif() +else() + set(GMSH_OS "${CMAKE_SYSTEM_NAME}") +endif() + +include(CheckTypeSize) +include(CheckFunctionExists) +include(CheckIncludeFile) +include(CheckCXXCompilerFlag) +include(CheckCCompilerFlag) + +macro(set_config_option VARNAME STRING) + set(${VARNAME} TRUE) + list(APPEND CONFIG_OPTIONS ${STRING}) + message(STATUS "Found " ${STRING}) +endmacro() + +# check if the machine is 64 bits (this is more reliable than using +# CMAKE_SIZEOF_VOID_P, which does not seem to work e.g. on some Suse +# machines) +check_type_size("void*" SIZEOF_VOID_P) +if(SIZEOF_VOID_P EQUAL 8) + set_config_option(HAVE_64BIT_SIZE_T "64Bit") +endif() + +# append 32/64 to the build name on Linux and Windows +if(NOT APPLE) + if(HAVE_64BIT_SIZE_T) + set(GMSH_OS "${GMSH_OS}64") + else() + set(GMSH_OS "${GMSH_OS}32") + endif() +endif() + +if(NOT ENABLE_BUILD_SHARED) + if(ENABLE_WRAP_PYTHON OR ENABLE_WRAP_JAVA) + set(ENABLE_BUILD_DYNAMIC ON) + endif() +endif() + +if(ENABLE_BUILD_DYNAMIC) + set(GMSH_OS "${GMSH_OS}-sdk") +endif() + +if(APPLE) + # FIXME: change this once we understand rpaths - the options below do not work + set(CMAKE_MACOSX_RPATH 0) +else() + # make sure that dynamic libraries can be found when installing/ displacing the + # binaries: from https://gitlab.kitware.com/cmake/community/wikis/doc/cmake/ + # RPATH-handling: + + # use, i.e. don't skip the full RPATH for the build tree + set(CMAKE_SKIP_BUILD_RPATH FALSE) + + # when building, don't use the install RPATH already (but later on when + # installing) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") + + # add the automatically determined parts of the RPATH which point to + # directories outside the build tree to the install RPATH + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + + # the RPATH to be used when installing, but only if it's not a system directory + list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" + isSystemDir) + if("${isSystemDir}" STREQUAL "-1") + set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../lib") + endif() +endif() + +if(MSVC) + # remove annoying warning about bool/int cast performance + set(GMSH_CONFIG_PRAGMAS "#pragma warning(disable:4800 4244 4267)") + foreach(VAR + CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE + CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO + CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE + CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO) + if(ENABLE_MSVC_STATIC_RUNTIME AND ${VAR} MATCHES "/MD") + string(REGEX REPLACE "/MD" "/MT" ${VAR} "${${VAR}}") + endif() + if(NOT ${VAR} MATCHES "/MP") # enable parallel compilation + set(${VAR} "${${VAR}} /MP") + endif() + endforeach() + if(ENABLE_PRIVATE_API) + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + # automatically export .def file with all symbols (requires CMake 3.4); + # depending on the compiling options this might lead to more than 64k export + # symbols; just trim the .def file to keep the ones you need + set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + endif() + endif() +endif() + +if(ENABLE_OPENMP) + find_package(OpenMP) + if(OpenMP_FOUND) + set_config_option(HAVE_OPENMP "OpenMP") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + elseif(APPLE AND EXISTS "/opt/local/lib/libomp") + # just for testing the official Apple compiler with macports' libomp + set_config_option(HAVE_OPENMP "OpenMP[MacPorts]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + list(APPEND EXTERNAL_LIBRARIES "-L/opt/local/lib/libomp -lomp") + elseif(APPLE AND EXISTS "/usr/local/lib/libomp.dylib") + set_config_option(HAVE_OPENMP "OpenMP[usr/local]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp") + list(APPEND EXTERNAL_LIBRARIES "-lomp") + endif() +endif() + +if(ENABLE_OPENACC) + find_package(OpenACC) + if(OpenACC_C_FOUND AND OpenACC_CXX_FOUND) + set_config_option(HAVE_OPENACC "OpenACC") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenACC_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenACC_CXX_FLAGS}") + endif() +endif() + +if(ENABLE_CXX11) + # in recent cmake versions we could do e.g. set(CMAKE_CXX_STANDARD 11) + check_cxx_compiler_flag("-std=c++11" STDCXX11) + if(STDCXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() +endif() + +if(ENABLE_C99) + # in recent cmake versions we could do e.g. set(CMAKE_C_STANDARD 99) + check_c_compiler_flag("-std=c99" STDC99) + if(STDC99) + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99") + endif() +endif() + +if(ENABLE_PROFILE) + # Using the perf set of profiling tools doesn't work without the frame + # pointer and a common optimisation is to remove it + check_cxx_compiler_flag("-fno-omit-frame-pointer" FNOFP) + if(FNOFP) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer") + endif() +endif() + +macro(append_gmsh_src DIRNAME FILES) + foreach(FILE ${FILES}) + list(APPEND LIST ${DIRNAME}/${FILE}) + endforeach() + set(GMSH_SRC ${GMSH_SRC};${LIST} PARENT_SCOPE) + set(GMSH_DIRS ${GMSH_DIRS};${DIRNAME} PARENT_SCOPE) +endmacro() + +macro(find_all_libraries VARNAME LISTNAME PATH SUFFIX) + set(${VARNAME}) + list(LENGTH ${LISTNAME} NUM_LIST) + foreach(LIB ${${LISTNAME}}) + if("${PATH}" STREQUAL "") + find_library(FOUND_LIB ${LIB} PATH_SUFFIXES ${SUFFIX}) + else() + find_library(FOUND_LIB ${LIB} PATHS ${PATH} NO_DEFAULT_PATH) + endif() + if(FOUND_LIB) + list(APPEND ${VARNAME} ${FOUND_LIB}) + endif() + unset(FOUND_LIB CACHE) + endforeach() + list(LENGTH ${VARNAME} NUM_FOUND_LIBRARIES) + if(NUM_FOUND_LIBRARIES LESS NUM_LIST) + set(${VARNAME}) + endif() +endmacro() + +macro(set_compile_flags LISTNAME FLAGS) + foreach(FILE ${${LISTNAME}}) + get_source_file_property(PROP ${FILE} COMPILE_FLAGS) + if(PROP) + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${PROP} ${FLAGS}") + else() + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${FLAGS}") + endif() + endforeach() +endmacro() + +if(ENABLE_BLAS_LAPACK) + if(BLAS_LAPACK_LIBRARIES) + # use libs as specified in the BLAS_LAPACK_LIBRARIES variable + set_config_option(HAVE_BLAS "Blas[custom]") + set_config_option(HAVE_LAPACK "Lapack[custom]") + set(LAPACK_LIBRARIES ${BLAS_LAPACK_LIBRARIES}) + else() + if(MSVC) + # on Windows with Visual C++ try really hard to find blas/lapack *without* + # requiring a Fortran compiler: 1) try to find the Intel MKL libs using + # the standard search path; if not found 2) try to get the reference + # blas/lapack libs (useful for users with no Fortran compiler and no MKL + # license, who can just download our precompiled "gmsh-dep" package) + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH em64t/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_lp64 mkl_intel_thread mkl_core) + else() + set(MKL_PATH ia32/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_c mkl_intel_thread mkl_core) + endif() + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + set(REFLAPACK_LIBS_REQUIRED lapack blas g2c gcc) + find_all_libraries(LAPACK_LIBRARIES REFLAPACK_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[ref]") + set_config_option(HAVE_LAPACK "Lapack[ref]") + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + # on Linux try to find the Intel MKL without a Fortran compiler + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH lib/em64t) + else() + set(MKL_PATH lib/32) + endif() + set(MKL_LIBS_REQUIRED mkl_gf_lp64 iomp5 mkl_gnu_thread mkl_core guide pthread) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(NOT LAPACK_LIBRARIES) + # match lapack 9.0 on 64bit + set(MKL_LIBS_REQUIRED mkl_lapack mkl_em64t guide) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + endif() + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + # on Linux also try to find ATLAS without a Fortran compiler, because + # cmake ships with a buggy FindBLAS e.g. on Ubuntu Lucid Lynx + set(ATLAS_LIBS_REQUIRED lapack f77blas cblas atlas) + find_all_libraries(LAPACK_LIBRARIES ATLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[atlas]") + set_config_option(HAVE_LAPACK "Lapack[atlas]") + else() + # try with generic names + set(GENERIC_LIBS_REQUIRED lapack blas pthread) + find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[generic]") + set_config_option(HAVE_LAPACK "Lapack[generic]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "SunOS") + # on SunOS we know blas and lapack are available in sunperf + set(LAPACK_LIBRARIES -library=sunperf) + set_config_option(HAVE_BLAS "Blas[sunperf]") + set_config_option(HAVE_LAPACK "Lapack[sunperf]") + elseif(APPLE) + # on Mac we also know that blas and lapack are available + set(LAPACK_LIBRARIES "-llapack -lblas") + set_config_option(HAVE_BLAS "Blas[veclib]") + set_config_option(HAVE_LAPACK "Lapack[veclib]") + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we haven't found blas and lapack check for OpenBlas + set(OPENBLAS_LIBS_REQUIRED openblas) + find_all_libraries(LAPACK_LIBRARIES OPENBLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[openblas]") + set_config_option(HAVE_LAPACK "Lapack[openblas]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we still haven't found blas and lapack, use the standard cmake tests, + # which require a working Fortran compiler + enable_language(Fortran) + find_package(BLAS) + if(BLAS_FOUND) + set_config_option(HAVE_BLAS "Blas") + find_package(LAPACK) + if(LAPACK_FOUND) + set_config_option(HAVE_LAPACK "Lapack") + else() + set(LAPACK_LIBRARIES ${BLAS_LIBRARIES}) + endif() + if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU") + if(CMAKE_Fortran_COMPILER MATCHES "gfortran") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "f95") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "g77") + list(APPEND LAPACK_LIBRARIES g2c) + endif() + elseif(CMAKE_Fortran_COMPILER MATCHES "pgi") + list(APPEND LAPACK_LIBRARIES -pgf77libs) + endif() + endif() + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + message(WARNING "Could not find Blas or Lapack: most meshing algorithms " + "will not be functional") + endif() + + endif() +endif() + +if(ENABLE_TCMALLOC) + find_library(TCMALLOC tcmalloc) + if(TCMALLOC) + set_config_option(HAVE_TCMALLOC "TCMalloc") + list(APPEND EXTERNAL_LIBRARIES ${TCMALLOC}) + endif() +endif() + +add_subdirectory(Common) +add_subdirectory(Numeric) +add_subdirectory(Geo) + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh AND ENABLE_MESH) + add_subdirectory(Mesh) + set_config_option(HAVE_MESH "Mesh") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Solver AND ENABLE_SOLVER) + add_subdirectory(Solver) + set_config_option(HAVE_SOLVER "Solver") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Post AND ENABLE_POST) + add_subdirectory(Post) + set_config_option(HAVE_POST "Post") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Plugin AND ENABLE_PLUGINS) + add_subdirectory(Plugin) + set_config_option(HAVE_PLUGINS "Plugins") + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Parser AND ENABLE_PARSER) + add_subdirectory(Parser) + set_config_option(HAVE_PARSER "Parser") +endif() + +if(ENABLE_VISUDEV) + set_config_option(HAVE_VISUDEV "VisuDev") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Fltk AND ENABLE_FLTK) + # first, try to use fltk-config for fltk >= 1.3 (FindFLTK is buggy on Unix, + # where e.g. xft and xinerama options are not dealt with) + find_program(FLTK_CONFIG_SCRIPT fltk-config) + if(FLTK_CONFIG_SCRIPT) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --api-version + OUTPUT_VARIABLE FLTK_VERSION) + string(STRIP "${FLTK_VERSION}" FLTK_VERSION) + if(FLTK_VERSION VERSION_GREATER 1.1) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + message(STATUS "Using fltk-config script for Fltk " ${FLTK_VERSION}) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --includedir + OUTPUT_VARIABLE FLTK_INCLUDE_DIR) + string(STRIP ${FLTK_INCLUDE_DIR} FLTK_INCLUDE_DIR) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # On linux (at least OpenSuSE) the following directories are + # not existing (everything is in /usr/include). To avoid warnings + # check existance of these directories before adding them + if(EXISTS ${FLTK_INCLUDE_DIR}/FL/images) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/FL/images) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/jpeg) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/jpeg) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/zlib) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/zlib) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/png) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/png) + endif() + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --ldflags + OUTPUT_VARIABLE FLTK_LIBRARIES) + string(STRIP ${FLTK_LIBRARIES} FLTK_LIBRARIES) + string(REGEX MATCH "fltk[_ ]jpeg" FLTK_JPEG ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]z" FLTK_Z ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]png" FLTK_PNG ${FLTK_LIBRARIES}) + endif() + endif() + # then try the built-in FindFLTK module + if(NOT HAVE_FLTK) + set(FLTK_SKIP_FORMS TRUE) + set(FLTK_SKIP_FLUID TRUE) + find_package(FLTK) + if(FLTK_FOUND) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # find fltk jpeg + find_library(FLTK_JPEG NAMES fltk_jpeg fltkjpeg) + if(FLTK_JPEG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_JPEG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/jpeg) + endforeach() + endif() + # find fltk zlib + find_library(FLTK_Z NAMES fltk_z fltkz) + if(FLTK_Z) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_Z}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/zlib) + endforeach() + endif() + # find fltk png + find_library(FLTK_PNG NAMES fltk_png fltkpng) + if(FLTK_PNG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_PNG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/png) + endforeach() + endif() + endif() + endif() + # workaround for Fedora/Suse messing up fltk-config (see issue #417) + if(HAVE_FLTK AND ${CMAKE_SYSTEM_NAME} MATCHES "Linux") + string(REGEX MATCH "X11" FLTK_X11 ${FLTK_LIBRARIES}) + if(NOT FLTK_X11) + find_package(X11) + if(X11_FOUND) + list(APPEND EXTERNAL_INCLUDES ${X11_INCLUDE_DIR}) + list(APPEND EXTERNAL_LIBRARIES ${X11_LIBRARIES}) + endif() + endif() + endif() +endif() + +if(APPLE AND HAVE_FLTK AND ENABLE_TOUCHBAR) + if(CMAKE_OSX_DEPLOYMENT_TARGET) + if(${CMAKE_OSX_DEPLOYMENT_TARGET} VERSION_GREATER 10.11) + set(GMSH_SRC ${GMSH_SRC};Fltk/touchBar.mm) + set_config_option(HAVE_TOUCHBAR "TouchBar") + endif() + endif() +endif() + +if(ENABLE_ONELAB) + set_config_option(HAVE_ONELAB "ONELAB") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/onelab) + if(ENABLE_ONELAB_METAMODEL) + add_subdirectory(contrib/onelab) + include_directories(contrib/onelab) + set_config_option(HAVE_ONELAB_METAMODEL "ONELABMetamodel") + endif() + file(COPY ${ONELAB_PY} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + endif() +endif() + +if(ENABLE_BUILD_IOS) + find_file(CMAKE_TOOLCHAIN_FILE "ios.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for iOS without a toolchain") + endif() + add_definitions(-DBUILD_IOS) +endif() + +if(HAVE_FLTK OR ENABLE_GRAPHICS) + if(NOT HAVE_MESH OR NOT HAVE_POST OR NOT HAVE_PLUGINS OR NOT HAVE_ONELAB) + message(SEND_ERROR "Cannot compile GUI without Mesh, Post, Plugin and ONELAB") + endif() + + if(FLTK_JPEG) + set_config_option(HAVE_LIBJPEG "Jpeg[fltk]") + else() + find_package(JPEG) + if(JPEG_FOUND) + set_config_option(HAVE_LIBJPEG "Jpeg") + list(APPEND EXTERNAL_LIBRARIES ${JPEG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${JPEG_INCLUDE_DIR}) + endif() + endif() + + if(FLTK_Z) + set_config_option(HAVE_LIBZ "Zlib[fltk]") + else() + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + + if(HAVE_LIBZ) + if(FLTK_PNG) + set_config_option(HAVE_LIBPNG "Png[fltk]") + else() + find_package(PNG) + if(PNG_FOUND) + set_config_option(HAVE_LIBPNG "Png") + list(APPEND EXTERNAL_LIBRARIES ${PNG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${PNG_INCLUDE_DIR}) + endif() + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/mpeg_encode AND + ENABLE_MPEG_ENCODE) + add_subdirectory(contrib/mpeg_encode) + include_directories(contrib/mpeg_encode/headers) + set_config_option(HAVE_MPEG_ENCODE "Mpeg") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/3M AND ENABLE_3M) + add_subdirectory(contrib/3M) + include_directories(contrib/3M) + set_config_option(HAVE_3M "3M") + endif() + + if(ENABLE_OSMESA) + find_library(OSMESA_LIB OSMesa) + if(OSMESA_LIB) + set_config_option(HAVE_OSMESA "OSMesa") + list(APPEND EXTERNAL_LIBRARIES ${OSMESA_LIB}) + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Graphics) + set(OpenGL_GL_PREFERENCE "LEGACY") + find_package(OpenGL REQUIRED) + if(OPENGL_GLU_FOUND AND OPENGL_FOUND) + add_subdirectory(Graphics) + set_config_option(HAVE_OPENGL "OpenGL") + else() + message(SEND_ERROR "Could not find GLU: disabling OpenGL support") + endif() + endif() +endif() + +if(ENABLE_ANN) + find_library(ANN_LIB ANN PATH_SUFFIXES lib) + find_path(ANN_INC "ANN.h" PATH_SUFFIXES src include ANN) + if(ENABLE_SYSTEM_CONTRIB AND ANN_LIB AND ANN_INC) + message(STATUS "Using system version of ANN") + list(APPEND EXTERNAL_LIBRARIES ${ANN_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ANN_INC}) + set_config_option(HAVE_ANN "Ann[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ANN) + add_subdirectory(contrib/ANN) + include_directories(contrib/ANN/include) + set_config_option(HAVE_ANN "Ann") + endif() +endif() + +if(ENABLE_ALGLIB) + find_library(ALGLIB_LIB alglib PATH_SUFFIXES lib) + find_path(ALGLIB_INC "stdafx.h" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND ALGLIB_LIB AND ALGLIB_INC) + list(APPEND EXTERNAL_LIBRARIES ${ALGLIB_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ALGLIB_INC}) + set_config_option(HAVE_ALGLIB "ALGLIB[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ALGLIB) + add_subdirectory(contrib/ALGLIB) + include_directories(contrib/ALGLIB) + set_config_option(HAVE_ALGLIB "ALGLIB") + endif() +endif() + +if(HAVE_FLTK AND ENABLE_CAIRO) + find_library(CAIRO_LIB cairo) + find_path(CAIRO_INC "cairo/cairo.h" PATH_SUFFIXES include) + if(CAIRO_INC AND CAIRO_LIB) + set_config_option(HAVE_CAIRO "Cairo") + list(APPEND EXTERNAL_LIBRARIES ${CAIRO_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CAIRO_INC}) + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/DiscreteIntegration AND + ENABLE_DINTEGRATION) + add_subdirectory(contrib/DiscreteIntegration) + include_directories(contrib/DiscreteIntegration) + set_config_option(HAVE_DINTEGRATION "DIntegration") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/HighOrderMeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshQualityOptimizer AND + ENABLE_OPTHOM AND HAVE_MESH) + add_subdirectory(contrib/HighOrderMeshOptimizer) + include_directories(contrib/HighOrderMeshOptimizer) + add_subdirectory(contrib/MeshOptimizer) + include_directories(contrib/MeshOptimizer) + include_directories(${CMAKE_CURRENT_BINARY_DIR}/contrib/MeshOptimizer) + add_subdirectory(contrib/MeshQualityOptimizer) + include_directories(contrib/MeshQualityOptimizer) + set_config_option(HAVE_OPTHOM "OptHom") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/domhex AND + ENABLE_DOMHEX AND HAVE_MESH) + add_subdirectory(contrib/domhex) + include_directories(contrib/domhex) + set_config_option(HAVE_DOMHEX "DomHex") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/QuadTri AND + ENABLE_QUADTRI AND HAVE_MESH) + add_subdirectory(contrib/QuadTri) + include_directories(contrib/QuadTri) + set_config_option(HAVE_QUADTRI "QuadTri") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/kbipack AND ENABLE_KBIPACK) + set_config_option(HAVE_KBIPACK "Kbipack") + add_subdirectory(contrib/kbipack) + include_directories(contrib/kbipack) + if(ENABLE_GMP) + find_library(GMP_LIB libgmp.a) + find_path(GMP_INC "gmp.h" PATH_SUFFIXES src include) + endif() + if(GMP_LIB AND GMP_INC) + set_config_option(HAVE_GMP "GMP") + list(APPEND EXTERNAL_LIBRARIES ${GMP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GMP_INC}) + else() + message(STATUS "GMP not found: Kbipack uses long int") + endif() +endif() + +if(ENABLE_MATHEX) + find_library(MATHEX_LIB mathex PATH_SUFFIXES lib) + find_path(MATHEX_INC "mathex.h" PATH_SUFFIXES src include) + if(ENABLE_SYSTEM_CONTRIB AND MATHEX_LIB AND MATHEX_INC) + list(APPEND EXTERNAL_LIBRARIES ${MATHEX_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MATHEX_INC}) + set_config_option(HAVE_MATHEX "MathEx[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MathEx) + add_subdirectory(contrib/MathEx) + include_directories(contrib/MathEx) + set_config_option(HAVE_MATHEX "MathEx") + endif() +endif() + +if(ENABLE_MPI) + find_package(MPI) + if(MPI_FOUND) + set_config_option(HAVE_MPI "MPI") + list(APPEND EXTERNAL_INCLUDES ${MPI_CXX_INCLUDE_PATH}) + list(APPEND EXTERNAL_LIBRARIES ${MPI_CXX_LIBRARIES}) + set(CMAKE_C_COMPILER ${MPI_C_COMPILER}) + set(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER}) + set(CMAKE_Fortran_COMPILER ${MPI_Fortran_COMPILER}) + endif() +endif() + +if(ENABLE_POPPLER) + find_library(POPPLER_LIB poppler) + find_library(POPPLER_CPP_LIB poppler-cpp) + find_path(POPPLER_INC "poppler/cpp/poppler-document.h" PATH_SUFFIXES src include) + if(POPPLER_LIB AND POPPLER_INC) + set_config_option(HAVE_POPPLER "Poppler") + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_LIB}) + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_CPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${POPPLER_INC}) + endif() +endif() + +if(ENABLE_P4EST) + find_library(P4EST_LIB p4est) + find_path(P4EST_INC "p4est.h" PATH_SUFFIXES src) + find_library(SC_LIB sc) + if(P4EST_LIB AND P4EST_INC AND SC_LIB) + set_config_option(HAVE_P4EST "P4est") + list(APPEND EXTERNAL_LIBRARIES ${P4EST_LIB} ${SC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${P4EST_INC}) + endif() +endif() + +if(HAVE_MESH OR HAVE_SOLVER) + if(ENABLE_METIS) + if(METIS_ROOT) + find_library(METIS_LIB metis PATHS ${METIS_ROOT} PATH_SUFFIXES lib) + find_path(METIS_INC "metis.h" PATHS ${METIS_ROOT} PATH_SUFFIXES include) + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis") + else() + find_library(METIS_LIB metis PATH_SUFFIXES lib) + find_path(METIS_INC "metis.h" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC) + message(STATUS "Using system version of METIS") + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/metis) + add_definitions(-DUSE_GKREGEX) + add_subdirectory(contrib/metis) + include_directories(contrib/metis/include contrib/metis/libmetis + contrib/metis/GKlib) + set_config_option(HAVE_METIS "Metis") + endif() + endif() + endif() +endif() + +if(HAVE_MESH) + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh/tetgenBR.cxx) + set_config_option(HAVE_TETGENBR "TetGen/BR") + endif() + + if(ENABLE_VOROPP) + find_library(VOROPP_LIB voro++ PATH_SUFFIXES lib) + find_path(VOROPP_INC "voro++.hh" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND VOROPP_LIB AND VOROPP_INC) + message(STATUS "Using system version of voro++") + list(APPEND EXTERNAL_LIBRARIES ${VOROPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${VOROPP_INC}) + set_config_option(HAVE_VOROPP "Voro++[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++) + add_subdirectory(contrib/voro++) + include_directories(contrib/voro++/src) + set_config_option(HAVE_VOROPP "Voro++") + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/blossom AND ENABLE_BLOSSOM) + add_subdirectory(contrib/blossom) + include_directories(contrib/blossom/MATCH contrib/blossom/concorde97 + contrib/blossom/concorde97/INCLUDE) + set_config_option(HAVE_BLOSSOM "Blossom") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/Netgen AND ENABLE_NETGEN) + add_subdirectory(contrib/Netgen) + include_directories(contrib/Netgen contrib/Netgen/libsrc/include + contrib/Netgen/nglib) + set_config_option(HAVE_NETGEN "Netgen") + add_definitions(-DNO_PARALLEL_THREADS -DNOTCL) + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/bamg AND ENABLE_BAMG) + add_subdirectory(contrib/bamg) + include_directories(contrib/bamg contrib/bamg/bamglib) + set_config_option(HAVE_BAMG "Bamg") + endif() + + if(ENABLE_MMG3D) + find_library(MMG3D_LIB mmg3d PATH_SUFFIXES lib) + find_path(MMG3D_INC "libmmg3d.h" PATH_SUFFIXES src include) + if(ENABLE_SYSTEM_CONTRIB AND MMG3D_LIB AND MMG3D_INC) + list(APPEND EXTERNAL_LIBRARIES ${MMG3D_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MMG3D_INC}) + set_config_option(HAVE_MMG3D "Mmg3d[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/mmg3d) + add_subdirectory(contrib/mmg3d) + include_directories(contrib/mmg3d/build/sources) + set_config_option(HAVE_MMG3D "Mmg3d") + endif() + endif() +endif() + +if(ENABLE_MED OR ENABLE_CGNS) + find_package(HDF5) + if(HDF5_FOUND) + set(HDF5_LIB "${HDF5_C_LIBRARIES}") + list(APPEND EXTERNAL_INCLUDES ${HDF5_INCLUDE_DIRS}) + if(ENABLE_MED) + find_library(MED_LIB medC) + if(MED_LIB) + set_config_option(HAVE_MED "Med") + list(APPEND EXTERNAL_LIBRARIES ${MED_LIB}) + endif() + endif() + if(ENABLE_CGNS) + find_library(CGNS_LIB cgns HINTS ENV CGNS_ROOT PATH_SUFFIXES lib) + find_path(CGNS_INC "cgnslib.h" HINTS ENV CGNS_ROOT PATH_SUFFIXES include) + if(CGNS_LIB AND CGNS_INC) + set_config_option(HAVE_LIBCGNS "Cgns") + list(APPEND EXTERNAL_LIBRARIES ${CGNS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CGNS_INC}) + if(ENABLE_CGNS_CPEX0045) + set_config_option(HAVE_LIBCGNS_CPEX0045 "Cgns_CPEX0045") + endif() + endif() + endif() + if(MED_LIB OR CGNS_LIB) + list(APPEND EXTERNAL_LIBRARIES ${HDF5_LIB}) + find_library(SZ_LIB NAMES szlib sz) + if(SZ_LIB) + list(APPEND EXTERNAL_LIBRARIES ${SZ_LIB}) + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + endif() + endif() + endif() + else() + message(STATUS "HDF5 not found") + endif() +endif() + +if(HAVE_SOLVER) + if(ENABLE_GMM) + find_path(GMM_INC "gmm.h" PATH_SUFFIXES src include include/gmm) + if(ENABLE_SYSTEM_CONTRIB AND GMM_INC) + message(STATUS "Using system version of GMM") + list(APPEND EXTERNAL_INCLUDES ${GMM_INC}) + set_config_option(HAVE_GMM "Gmm[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/gmm) + include_directories(contrib/gmm) + set_config_option(HAVE_GMM "Gmm") + endif() + endif() + + if(ENABLE_PETSC) + if(PETSC_DIR) + set(ENV_PETSC_DIR ${PETSC_DIR}) + else() + set(ENV_PETSC_DIR $ENV{PETSC_DIR}) + endif() + if(PETSC_ARCH) + set(ENV_PETSC_ARCH ${PETSC_ARCH}) + else() + set(ENV_PETSC_ARCH $ENV{PETSC_ARCH}) + endif() + set(PETSC_POSSIBLE_CONF_FILES + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc-conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc/conf/petscvariables) + foreach(FILE ${PETSC_POSSIBLE_CONF_FILES}) + if(EXISTS ${FILE}) + # old-style PETSc installations (using PETSC_DIR and PETSC_ARCH) + message(STATUS "Using PETSc dir: ${ENV_PETSC_DIR}") + message(STATUS "Using PETSc arch: ${ENV_PETSC_ARCH}") + # find includes by parsing the petscvariables file + file(STRINGS ${FILE} PETSC_VARIABLES NEWLINE_CONSUME) + endif() + endforeach() + if(PETSC_VARIABLES) + # try to find PETSC_CC_INCLUDES for PETSc >= 3.4 + string(REGEX MATCH "PETSC_CC_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "PETSC_CC_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + else() + # try to find PETSC_PACKAGES_INCLUDES in older versions + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/include) + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/include) + string(REGEX MATCH "PACKAGES_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + string(REPLACE "PACKAGES_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + endif() + if(PETSC_PACKAGES_INCLUDES) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "-I" "" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + string(REPLACE " " ";" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + foreach(VAR ${PETSC_PACKAGES_INCLUDES}) + # seem to include unexisting directories (/usr/include/lib64) + # check to avoid warnings + if(EXISTS ${VAR}) + list(APPEND EXTERNAL_INCLUDES ${VAR}) + endif() + endforeach() + endif() + endif() + # find libraries (<= 3.0) + set(PETSC_LIBS_REQUIRED petscksp petscdm petscmat petscvec petsc) + find_all_libraries(PETSC_LIBS PETSC_LIBS_REQUIRED + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib "") + # petsc 3.1 creates only one library (libpetsc) + if(NOT PETSC_LIBS) + find_library(PETSC_LIBS petsc PATHS ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + endif() + if(PETSC_LIBS) + set_config_option(HAVE_PETSC "PETSc") + if(NOT HAVE_BLAS) + set_config_option(HAVE_BLAS "Blas[petsc]") + endif() + if(NOT HAVE_LAPACK) + set_config_option(HAVE_LAPACK "Lapack[petsc]") + endif() + endif() + # find slepc (needs to be linked in before petsc) + if(ENABLE_SLEPC) + if(SLEPC_DIR) + set(ENV_SLEPC_DIR ${SLEPC_DIR}) + else() + set(ENV_SLEPC_DIR $ENV{SLEPC_DIR}) + endif() + find_library(SLEPC_LIB slepc PATHS ${ENV_SLEPC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + if(SLEPC_LIB) + find_path(SLEPC_INC "slepc.h" PATHS ${ENV_SLEPC_DIR} PATH_SUFFIXES include + ${ENV_PETSC_ARCH}/include include/slepc NO_DEFAULT_PATH) + if(SLEPC_INC) + message(STATUS "Using SLEPc dir: ${ENV_SLEPC_DIR}") + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + find_path(SLEPC_INC2 "slepcconf.h" PATHS ${ENV_SLEPC_DIR} + PATH_SUFFIXES ${ENV_PETSC_ARCH}/include NO_DEFAULT_PATH) + if(SLEPC_INC2) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC2}) + endif() + endif() + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + # find additional libraries to link with + string(REGEX MATCH "PACKAGES_LIBS = [^\n\r]*" PLIBS ${PETSC_VARIABLES}) + if(PLIBS) + string(REPLACE "PACKAGES_LIBS = " "" PLIBS ${PLIBS}) + string(STRIP ${PLIBS} PLIBS) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS}") + endif() + string(REGEX MATCH "PETSC_EXTERNAL_LIB_BASIC = [^\n\r]*" PLIBS_BASIC ${PETSC_VARIABLES}) + if(PLIBS_BASIC) + string(REPLACE "PETSC_EXTERNAL_LIB_BASIC = " "" PLIBS_BASIC ${PLIBS_BASIC}) + string(STRIP ${PLIBS_BASIC} PLIBS_BASIC) + separate_arguments(PLIBS_BASIC) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS_BASIC}") + endif() + string(REGEX MATCH "PCC_LINKER_LIBS = [^\n\r]*" LLIBS ${PETSC_VARIABLES}) + if(LLIBS) + string(REPLACE "PCC_LINKER_LIBS = " "" LLIBS ${LLIBS}) + string(STRIP ${LLIBS} LLIBS) + list(APPEND EXTERNAL_LIBRARIES "${LLIBS}") + endif() + else() + # new-style PETSc installations (in standard system directories) + find_library(PETSC_LIBS petsc) + find_path(PETSC_INC "petsc.h" PATH_SUFFIXES include/petsc) + if(PETSC_LIBS AND PETSC_INC) + set_config_option(HAVE_PETSC "PETSc") + if(ENABLE_SLEPC) + find_library(SLEPC_LIB slepc) + find_path(SLEPC_INC "slepc.h" PATH_SUFFIXES include/slepc) + if(SLEPC_LIB AND SLEPC_INC) + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${PETSC_INC}) + endif() + endif() + endif() + + if(ENABLE_MUMPS AND HAVE_BLAS AND HAVE_LAPACK) + set(MUMPS_LIBS_REQUIRED smumps dmumps cmumps zmumps mumps_common pord) + if(NOT ENABLE_MPI) + list(APPEND MUMPS_LIBS_REQUIRED mpiseq) + endif() + find_all_libraries(MUMPS_LIBRARIES MUMPS_LIBS_REQUIRED "" "lib") + find_path(SMUMPS_INC "smumps_c.h" PATH_SUFFIXES src include) + find_path(DMUMPS_INC "dmumps_c.h" PATH_SUFFIXES src include) + find_path(CMUMPS_INC "cmumps_c.h" PATH_SUFFIXES src include) + find_path(ZMUMPS_INC "zmumps_c.h" PATH_SUFFIXES src include) + if(MUMPS_LIBRARIES AND SMUMPS_INC AND DMUMPS_INC AND CMUMPS_INC AND ZMUMPS_INC) + set_config_option(HAVE_MUMPS "MUMPS") + list(APPEND EXTERNAL_LIBRARIES ${MUMPS_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${SMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${DMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${CMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${ZMUMPS_INC}) + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND EXTERNAL_LIBRARIES ${GFORTRAN_LIB}) + endif() + if(ENABLE_GMM) # use GMM/MUMPS interface + add_definitions(-DGMM_USES_MUMPS) + endif() + endif() + endif() + + if(ENABLE_GETDP) + find_library(GETDP_LIB GetDP) + find_path(GETDP_INC "GetDP.h" PATH_SUFFIXES getdp) + if(GETDP_LIB AND GETDP_INC) + set_config_option(HAVE_GETDP "GetDP") + list(APPEND EXTERNAL_LIBRARIES ${GETDP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GETDP_INC}) + endif() + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt AND + ENABLE_HXT AND HAVE_METIS) + set_config_option(HAVE_HXT "Hxt") + add_subdirectory(contrib/hxt) + include_directories(BEFORE contrib/hxt) + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/hxt_tetDelaunay.c) + set_config_option(HAVE_HXT3D "Hxt3D") + endif() + if(MSVC) + # Visual C++ does not support C99 - force compilation as C++ code + file(GLOB_RECURSE HXT_SRC contrib/hxt/*.c) + set_compile_flags(HXT_SRC "/TP") + endif() + check_include_file("immintrin.h" HAVE_IMMINTRIN_H) + if(NOT HAVE_IMMINTRIN_H) + add_definitions(-DHAVE_NO_IMMINTRIN_H) + endif() + if(HAVE_PETSC) + add_definitions(-DHXT_HAVE_PETSC) + endif() + if(CMAKE_C_COMPILER MATCHES "pgi") + add_definitions(-DHAVE_NO_OPENMP_SIMD) + endif() +endif() + +if(ENABLE_OCC) + set(OCC_MINIMAL_VERSION "6.9.1") + if(WIN32) + if(HAVE_64BIT_SIZE_T) + set(OCC_SYS_NAME win64) + else() + set(OCC_SYS_NAME win32) + endif() + else() + set(OCC_SYS_NAME ${CMAKE_SYSTEM_NAME}) + endif() + find_path(OCC_INC "Standard_Version.hxx" HINTS ENV CASROOT PATH_SUFFIXES + inc include include/oce opencascade include/opencascade + occt include/occt) + if(OCC_INC) + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAJOR REGEX "#define OCC_VERSION_MAJOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MINOR REGEX "#define OCC_VERSION_MINOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAINT REGEX "#define OCC_VERSION_MAINTENANCE.*") + if(OCC_MAJOR AND OCC_MINOR AND OCC_MAINT) + string(REGEX MATCH "[0-9]+" OCC_MAJOR "${OCC_MAJOR}") + string(REGEX MATCH "[0-9]+" OCC_MINOR "${OCC_MINOR}") + string(REGEX MATCH "[0-9]+" OCC_MAINT "${OCC_MAINT}") + set(OCC_VERSION "${OCC_MAJOR}.${OCC_MINOR}.${OCC_MAINT}") + message(STATUS "Found OpenCASCADE version ${OCC_VERSION} in ${OCC_INC}") + endif() + endif() + if(OCC_VERSION AND OCC_VERSION STRLESS ${OCC_MINIMAL_VERSION}) + message(WARNING "Gmsh requires OpenCASCADE >= ${OCC_MINIMAL_VERSION}. " + "Use CMAKE_PREFIX_PATH or the CASROOT environment variable " + "to explicitely specify the installation path of OpenCASCADE") + elseif(OCC_INC) + set(OCC_LIBS_REQUIRED + # subset of DataExchange + TKSTEP TKSTEP209 TKSTEPAttr TKSTEPBase TKIGES TKXSBase + # ModelingAlgorithms + TKOffset TKFeat TKFillet TKBool TKMesh TKHLR TKBO TKPrim TKShHealing + TKTopAlgo TKGeomAlgo + # ModelingData + TKBRep TKGeomBase TKG3d TKG2d + # FoundationClasses + TKMath TKernel) + if(ENABLE_OCC_TBB) + list(APPEND OCC_LIBS_REQUIRED tbb tbbmalloc) + endif() + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS_REQUIRED) + if(OCC_LIBS) + message(STATUS "OCC libraries specified explicitly: " ${OCC_LIBS}) + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS) + else() + set(OCC_LIBS) + foreach(OCC ${OCC_LIBS_REQUIRED}) + if(ENABLE_OCC_STATIC) + set(LIBNAME lib${OCC}.a) + else() + set(LIBNAME ${OCC}) + endif() + find_library(OCC_LIB ${LIBNAME} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib) + if(OCC_LIB) + list(APPEND OCC_LIBS ${OCC_LIB}) + else() + message(STATUS "OCC lib " ${LIBNAME} " not Found") + endif() + unset(OCC_LIB CACHE) + endforeach() + list(LENGTH OCC_LIBS NUM_OCC_LIBS) + endif() + endif() + + # additional OCC libraries to handle reading of STEP/IGES attributes. Oh my... + if(ENABLE_OCC_CAF) + find_package(Freetype) + if(FREETYPE_FOUND) + set(OCC_CAF_LIBS_REQUIRED + TKXDESTEP TKXDEIGES TKXCAF TKLCAF TKVCAF TKCAF TKV3d TKService TKCDF) + list(LENGTH OCC_CAF_LIBS_REQUIRED NUM_OCC_CAF_LIBS_REQUIRED) + set(OCC_CAF_LIBS) + foreach(OCC ${OCC_CAF_LIBS_REQUIRED}) + find_library(OCC_CAF_LIB ${OCC} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib) + if(OCC_CAF_LIB) + list(APPEND OCC_CAF_LIBS ${OCC_CAF_LIB}) + else() + message(STATUS "OCC CAF lib " ${OCC} " not Found") + endif() + unset(OCC_CAF_LIB CACHE) + endforeach() + list(LENGTH OCC_CAF_LIBS NUM_OCC_CAF_LIBS) + endif() + endif() + + # append OCC CAF libraries first... + if(NUM_OCC_CAF_LIBS EQUAL NUM_OCC_CAF_LIBS_REQUIRED) + set_config_option(HAVE_OCC_CAF "OpenCASCADE-CAF") + list(APPEND EXTERNAL_LIBRARIES ${OCC_CAF_LIBS} ${FREETYPE_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${FREETYPE_INCLUDE_DIRS}) + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "windowscodecs") + list(APPEND EXTERNAL_LIBRARIES "ole32") + endif() + endif() + + # then append OCC libraries + if(NUM_OCC_LIBS EQUAL NUM_OCC_LIBS_REQUIRED) + set_config_option(HAVE_OCC "OpenCASCADE") + list(APPEND EXTERNAL_LIBRARIES ${OCC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${OCC_INC}) + if(HAVE_64BIT_SIZE_T) + add_definitions(-D_OCC64) + endif() + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "winspool") + add_definitions(-DOCC_CONVERT_SIGNALS) + elseif(MSVC) + add_definitions(-DWNT) + endif() + endif() +endif() + +if(ENABLE_ACIS) + find_library(ACIS_LIB SpaACIS PATH_SUFFIXES bin/maci386) + if(ACIS_LIB) + find_path(ACIS_INC "kernapi.hxx" PATH_SUFFIXES include) + if(ACIS_INC) + set_config_option(HAVE_ACIS "Acis") + list(APPEND EXTERNAL_LIBRARIES ${ACIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ACIS_INC}) + endif() + endif() +endif() + +if(ENABLE_ZIPPER) + if(ENABLE_BUILD_IOS) + set_config_option(HAVE_LIBZ "Zlib") + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/zipper AND HAVE_LIBZ) + add_subdirectory(contrib/zipper) + include_directories(contrib/zipper) + set_config_option(HAVE_ZIPPER "Zipper") + endif() +endif() + +if(ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON) + find_package(SWIG REQUIRED) + include(${SWIG_USE_FILE}) + find_package(PythonLibs) + if(SWIG_FOUND AND PYTHONLIBS_FOUND) + message(STATUS "Found SWIG version " ${SWIG_VERSION}) + find_package(PythonInterp) + string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION) + if(SWIG_MAJOR_VERSION EQUAL 1) + message(WARNING "Python bindings require SWIG >= 2: disabling Python") + else() + set_config_option(HAVE_PYTHON "Python") + mark_as_advanced(CLEAR PYTHON_LIBRARY PYTHON_INCLUDE_DIR) + if(ENABLE_NUMPY) + if (NOT NUMPY_INC) + EXEC_PROGRAM (${PYTHON_EXECUTABLE} + ARGS "-c \"import numpy; print(numpy.get_include())\"" + OUTPUT_VARIABLE NUMPY_INC + RETURN_VALUE NUMPY_NOT_FOUND) + endif() + if(NUMPY_INC) + list(APPEND EXTERNAL_INCLUDES ${NUMPY_INC}) + set_config_option(HAVE_NUMPY "Numpy") + endif() + endif() + if(HAVE_PETSC) + if(ENABLE_PETSC4PY) + EXECUTE_PROCESS( + COMMAND ${PYTHON_EXECUTABLE} -c "import petsc4py; print(petsc4py.get_include())" + OUTPUT_VARIABLE PETSC4PY_INC + RESULT_VARIABLE PETSC4PY_NOT_FOUND + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(PETSC4PY_INC) + list(APPEND EXTERNAL_INCLUDES ${PETSC4PY_INC}) + set_config_option(HAVE_PETSC4PY "PETSc4py") + endif() + endif() + endif() + endif() + endif() +endif() + +check_function_exists(vsnprintf HAVE_VSNPRINTF) +if(NOT HAVE_VSNPRINTF AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_VSNPRINTF "NoVsnprintf") +endif() + +check_include_file(sys/socket.h HAVE_SYS_SOCKET_H) +if(HAVE_SYS_SOCKET_H) + set(CMAKE_EXTRA_INCLUDE_FILES sys/socket.h) +endif() +check_type_size(socklen_t SOCKLEN_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT SOCKLEN_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_SOCKLEN_T "NoSocklenT") +endif() + +check_include_file(stdint.h HAVE_STDINT_H) +if(HAVE_STDINT_H) + set(CMAKE_EXTRA_INCLUDE_FILES stdint.h) +else() + set_config_option(HAVE_NO_STDINT_H "NoStdintH") +endif() +check_type_size(intptr_t INTPTR_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT INTPTR_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_INTPTR_T "NoIntptrT") +endif() + +check_include_file(dlfcn.h DLFCN_H) +if(DLFCN_H) + set_config_option(HAVE_DLOPEN "Dlopen") + list(APPEND EXTERNAL_LIBRARIES ${CMAKE_DL_LIBS}) +endif() + +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + check_include_file(linux/joystick.h LINUX_JOYSTICK_H) + if(LINUX_JOYSTICK_H) + set_config_option(HAVE_LINUX_JOYSTICK "LinuxJoystick") + endif() +endif() + +if(WIN32) + add_definitions(-D_USE_MATH_DEFINES) + list(APPEND EXTERNAL_LIBRARIES winmm wsock32 ws2_32 psapi) +endif() + +if(MSVC) + add_definitions(-DNOMINMAX -D_CRT_SECURE_NO_DEPRECATE -D_SCL_SECURE_NO_DEPRECATE) +endif() + +# add C functions API +set(GMSH_SRC ${GMSH_SRC};api/gmshc.cpp) + +# force full warnings to encourage everybody to write clean(er) code +check_cxx_compiler_flag("-Wall" WALL) +if(WALL AND NOT MSVC) + file(GLOB_RECURSE WALL_SRC Common/*.cpp Fltk/*.cpp FunctionSpace/*.cpp + Geo/*.cpp Graphics/*.cpp Mesh/*.cpp Numeric/*.cpp Parser/*.cpp + Plugin/*.cpp Post/*.cpp Solver/*.cpp) + set(WF "-Wall") + check_cxx_compiler_flag("-Wint-to-void-pointer-cast" WCAST) + if(WCAST) + set(WF "${WF} -Wno-int-to-void-pointer-cast") + endif() + check_cxx_compiler_flag("-Wdeprecated-declarations" WDEPREC) + if(WDEPREC) + # FIXME: remove this when we have fixed the deprecated GLU code for OpenGL3 + set(WF "${WF} -Wno-deprecated-declarations") + endif() + check_cxx_compiler_flag("-Wmisleading-indentation" WIND) + if(WIND) + set(WF "${WF} -Wno-misleading-indentation") + endif() + set_compile_flags(WALL_SRC ${WF}) +endif() + +# don't issue warnings for contributed libraries +check_cxx_compiler_flag("-w" NOWARN) +if(NOWARN) + file(GLOB_RECURSE NOWARN_SRC contrib/*.cpp contrib/*.cc contrib/*.cxx contrib/*.c) + set_compile_flags(NOWARN_SRC "-w") +endif() + +# disable compile optimization on some known problematic files +check_cxx_compiler_flag("-O0" NOOPT) +if(NOOPT OR ENABLE_BUILD_IOS) + if(ENABLE_BUILD_IOS) # optimized iOS 10 64 bits screws somewhere in Geo + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Geo/G*.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* Mesh/Background*) + else() + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* contrib/bamg/* Mesh/Background*) + endif() + set_compile_flags(NOOPT_SRC "-O0") +endif() + +# do not use arithmetic contraction in predicates.cpp +# if("${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "/fp:strict") +# elseif(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fno-unsafe-math-optimizations -ffp-contract=off") +# elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fp-model strict") +# endif() + +# enable Revoropt and set compile flags for the corresponding plugin +if(ENABLE_REVOROPT) + find_path(EIGEN3_INC "eigen3/Eigen/Dense") + if(EIGEN3_INC AND HAVE_MESH AND HAVE_PLUGINS AND HAVE_ANN AND HAVE_ALGLIB) + list(APPEND EXTERNAL_INCLUDES ${EIGEN3_INC} contrib/Revoropt/include) + message(STATUS "using contrib/Revoropt") + set_config_option(HAVE_REVOROPT "Revoropt") + add_definitions(-DUSE_ANN) + get_source_file_property(PROP Plugin/CVTRemesh.cpp COMPILE_FLAGS) + if(PROP) + set_source_files_properties(Plugin/CVTRemesh.cpp PROPERTIES + COMPILE_FLAGS "${PROP} -std=c++11") + else() + set_source_files_properties(Plugin/CVTRemesh.cpp PROPERTIES + COMPILE_FLAGS "-std=c++11") + endif() + else() + message(WARNING "Revoropt requires Eigen3, Mesh, Plugins, ANN and ALGLIB") + endif() +endif() + +list(SORT CONFIG_OPTIONS) +set(GMSH_CONFIG_OPTIONS "") +foreach(OPT ${CONFIG_OPTIONS}) + set(GMSH_CONFIG_OPTIONS "${GMSH_CONFIG_OPTIONS} ${OPT}") +endforeach() + +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshConfig.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshVersion.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h) + +# the texi version file is modified in the source directory (not ideal, but +# since git tracks the contents of the file this is acceptable as it will only +# change when the actual version is changed - not for each git hash) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi.in + ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi) + +file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/version.txt + ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION}) + +# process cmake environment variables so we can append them to the -I include +# commands. This is not recommended (we should only use the cache variables) but +# it is very convenient: otherwise we have to remember providing the +# -D... options to cmake for each new build. +set(ENV_CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH}) +set(ENV_CMAKE_INCLUDE_PATH $ENV{CMAKE_INCLUDE_PATH}) +if(UNIX) + if(ENV_CMAKE_PREFIX_PATH) + string(REPLACE ":" ";" ENV_CMAKE_PREFIX_PATH ${ENV_CMAKE_PREFIX_PATH}) + endif() + if(ENV_CMAKE_INCLUDE_PATH) + string(REPLACE ":" ";" ENV_CMAKE_INCLUDE_PATH ${ENV_CMAKE_INCLUDE_PATH}) + endif() +endif() +list(APPEND EXTERNAL_INCLUDES ${CMAKE_INCLUDE_PATH} ${ENV_CMAKE_INCLUDE_PATH}) +list(APPEND EXTERNAL_INCLUDES ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) +foreach(DIR ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/include) +endforeach() + +if(EXTERNAL_INCLUDES) + list(REMOVE_DUPLICATES EXTERNAL_INCLUDES) +endif() + +if(HAVE_FLTK) + set(LINK_LIBRARIES ${FLTK_LIBRARIES} ${EXTERNAL_LIBRARIES} + ${OPENGL_LIBRARIES} ${LAPACK_LIBRARIES}) +elseif(HAVE_OPENGL) + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${OPENGL_LIBRARIES} + ${LAPACK_LIBRARIES}) +else() + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) +endif() + +# try to use static gfortran on static builds (cannot do this on dynamic builds +# as e.g. Debian compiles libgfortran.a without -fPIC: sigh...) +if(NOT ENABLE_BUILD_DYNAMIC AND NOT ENABLE_BUILD_SHARED) + find_library(GFORTRAN_STATIC libgfortran.a) + if(GFORTRAN_STATIC) + set(CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES) + message(STATUS "Using static libgfortran") + foreach(STR ${LINK_LIBRARIES}) + string(REPLACE "-lgfortran" ${GFORTRAN_STATIC} STR2 ${STR}) + list(APPEND LINK_LIBRARIES2 ${STR2}) + endforeach() + set(LINK_LIBRARIES ${LINK_LIBRARIES2}) + endif() +endif() + +# Linux-specific linking +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + if(HAVE_OCC) + find_library(RT_LIB rt) + if(RT_LIB) + list(APPEND LINK_LIBRARIES ${RT_LIB}) + endif() + endif() + if(CMAKE_C_COMPILER_ID MATCHES "GNU" OR CMAKE_C_COMPILER_ID MATCHES "Intel") + add_definitions(-fPIC) + endif() +endif() + +# we could specify include dirs more selectively, but this is simpler +include_directories(Common Fltk Geo Graphics Mesh Solver Numeric Parser + Plugin Post api ${EXTERNAL_INCLUDES} ${CMAKE_CURRENT_BINARY_DIR}/Common) + +# set this for external codes that might include this CMakeList file +set(GMSH_EXTERNAL_INCLUDE_DIRS ${EXTERNAL_INCLUDES} CACHE + STRING "External include directories" FORCE) +set(GMSH_EXTERNAL_LIBRARIES ${LINK_LIBRARIES} CACHE + STRING "External libraries" FORCE) + +# group sources for easier navigation in IDEs +foreach(DIR ${GMSH_DIRS}) + string(REGEX REPLACE "\\+" "\\\\+" DIR ${DIR}) + source_group(${DIR} REGULAR_EXPRESSION ${DIR}/.*) +endforeach() + +# static library target +if(ENABLE_BUILD_LIB) + add_library(lib STATIC ${GMSH_SRC}) + set_target_properties(lib PROPERTIES OUTPUT_NAME gmsh) + if(MSVC) + set_target_properties(lib PROPERTIES DEBUG_POSTFIX d) + if(ENABLE_MSVC_STATIC_RUNTIME) + set_target_properties(lib PROPERTIES LINK_FLAGS_RELEASE "/nodefaultlib:LIBCMT") + endif() + endif() +endif() + +# shared library target +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + add_library(shared SHARED ${GMSH_SRC}) + set_target_properties(shared PROPERTIES OUTPUT_NAME gmsh + VERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION} + SOVERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}) + if(WIN32) + set_target_properties(shared PROPERTIES PREFIX "" IMPORT_PREFIX "" + IMPORT_SUFFIX ".lib" COMPILE_FLAGS "-DGMSH_DLL -DGMSH_DLL_EXPORT") + endif() + target_link_libraries(shared ${LINK_LIBRARIES}) + if(MSVC AND ENABLE_MSVC_STATIC_RUNTIME) + message(STATUS "Note: By enabling ENABLE_MSVC_STATIC_RUNTIME, shared library " + "won't link. In MSVC change /MT to /MD in the shared project properties") + endif() +endif() + +# binary targets +if(HAVE_FLTK) + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh WIN32 Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh WIN32 Common/Main.cpp ${GMSH_SRC}) + endif() + # we could add this to create a minimal app bundle even without install + # if(APPLE AND NOT ENABLE_OS_SPECIFIC_INSTALL) + # set_target_properties(gmsh PROPERTIES MACOSX_BUNDLE ON + # MACOSX_BUNDLE_INFO_PLIST ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_dev.plist) + # endif() +else() + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh Common/Main.cpp ${GMSH_SRC}) + endif() +endif() +target_link_libraries(gmsh ${LINK_LIBRARIES}) + +# Windows specific linker options +if(WIN32 AND NOT MSVC) + set(FLAGS "-Wl,--stack,16777216 -mwindows") + if(HAVE_64BIT_SIZE_T) + set(FLAGS "${FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win64Icon.res") + else() + set(FLAGS "${FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win32Icon.res") + endif() + set_target_properties(gmsh PROPERTIES LINK_FLAGS "${FLAGS} -static") + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + set_target_properties(shared PROPERTIES LINK_FLAGS -static) + endif() + # remove -Wl,-Bdynamic flags + set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) + set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS) +elseif(MSVC) + set_target_properties(gmsh PROPERTIES LINK_FLAGS "/STACK:16777216 /SAFESEH:NO") +endif() + +# android target +if(ENABLE_BUILD_ANDROID) + find_file(CMAKE_TOOLCHAIN_FILE "android.toolchain.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for android without android-cmake") + endif() + add_definitions(-D_GLIBCXX_USE_C99_MATH=1) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + set(CMAKE_BUILD_TYPE Release) + set(LIBRARY_OUTPUT_PATH_ROOT ${CMAKE_CURRENT_BINARY_DIR}) + set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_BINARY_DIR}/libs/) + add_definitions(-DBUILD_ANDROID) + add_definitions(-DPICOJSON_USE_LOCALE=0) + add_library(androidGmsh SHARED ${GMSH_SRC}) + set_target_properties(androidGmsh PROPERTIES OUTPUT_NAME gmsh) + target_link_libraries(androidGmsh ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) + add_custom_command(TARGET androidGmsh POST_BUILD COMMAND + ${CMAKE_STRIP} ${LIBRARY_OUTPUT_PATH}/libgmsh.so) +endif() + +# parser target +find_program(BISON bison) +find_program(FLEX flex) +if(BISON AND FLEX) + add_custom_target(parser + COMMAND ${BISON} -p gmsh_yy --output Gmsh.tab.cpp -d Gmsh.y + COMMAND ${FLEX} -P gmsh_yy -o Gmsh.yy.cpp Gmsh.l + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Parser) +endif() + +if(UNIX) + # cannot use cmake's file search functions here (they would only find files + # existing at configuration time) + add_custom_target(purge + COMMAND rm -f `find . -name *~ -o -name *~~` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + add_custom_target(etags + COMMAND etags `find . -name *.cpp -o -name *.h -o -name *.y` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion + OUTPUT_VARIABLE CXX_COMPILER_VERSION + OUTPUT_STRIP_TRAILING_WHITESPACE) +else() + set(CXX_COMPILER_VERSION "Unknown") +endif() + +set(WELCOME_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/WELCOME.txt) +set(SDK_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/SDK.txt) +set(LICENSE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE.txt) +set(CREDITS_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CREDITS.txt) +set(CHANGELOG_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.txt) +file(GLOB TUTORIAL_GEO_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/?*.*) +file(GLOB TUTORIAL_CPP_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c++/?*.*) +file(GLOB TUTORIAL_C_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c/?*.*) +file(GLOB TUTORIAL_PY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/python/?*.*) +file(GLOB TUTORIAL_JL_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/julia/?*.*) +file(GLOB DEMOS ${CMAKE_CURRENT_SOURCE_DIR}/demos/*) +foreach(SUBDIR ${DEMOS}) + if(IS_DIRECTORY ${SUBDIR}) + list(APPEND DEMOS_DIRS ${SUBDIR}) + endif() +endforeach() +set(TEX_DIR ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo) +file(GLOB TEX_SRC ${TEX_DIR}/*.texi) +set(TEX_OBJ ${TEX_DIR}/gmsh.aux ${TEX_DIR}/gmsh.cp ${TEX_DIR}/gmsh.cps + ${TEX_DIR}/gmsh.fn ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.ky + ${TEX_DIR}/gmsh.log ${TEX_DIR}/gmsh.pdf ${TEX_DIR}/gmsh.pg ${TEX_DIR}/gmsh.toc + ${TEX_DIR}/gmsh.tp ${TEX_DIR}/gmsh.tps ${TEX_DIR}/gmsh.txt ${TEX_DIR}/gmsh.vr) + +macro(unix2dos VARNAME) + file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/unix2dos) + set(UNIX2DOS_FILES) + foreach(FILE ${${VARNAME}}) + file(READ ${FILE} F0) + get_filename_component(N ${FILE} NAME) + if(CYGWIN) + string(REGEX REPLACE "\n" "\r\n" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F1}") + else() # if not in Cygwin, cmake adds '\r's automatically + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F0}") + endif() + list(APPEND UNIX2DOS_FILES ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N}) + endforeach() + set(${VARNAME} ${UNIX2DOS_FILES}) +endmacro() + +if(WIN32) + if(ENABLE_OS_SPECIFIC_INSTALL) + set(GMSH_BIN .) + set(GMSH_LIB .) + set(GMSH_DOC .) + set(GMSH_MAN .) + set(GMSH_INC .) + else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) + endif() + if(CYGWIN) + unix2dos(GMSH_API) + if(ENABLE_PRIVATE_API) + unix2dos(GMSH_PRIVATE_API) + endif() + unix2dos(WELCOME_FILE) + unix2dos(SDK_FILE) + unix2dos(LICENSE_FILE) + unix2dos(CREDITS_FILE) + unix2dos(CHANGELOG_FILE) + unix2dos(TUTORIAL_GEO_FILES) + unix2dos(TUTORIAL_CPP_FILES) + unix2dos(TUTORIAL_C_FILES) + unix2dos(TUTORIAL_PY_FILES) + unix2dos(TUTORIAL_JL_FILES) + foreach(DIR ${DEMOS_DIRS}) + file(GLOB DEMO_FILES ${DIR}/?*.*) + unix2dos(DEMO_FILES) + endforeach() + endif() +elseif(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + # set these so that the files get installed nicely in the MacOSX + # .app bundle + set(GMSH_BIN ../MacOS) + set(GMSH_LIB ../MacOS) + set(GMSH_DOC ../../..) + set(GMSH_MAN ../../..) + set(GMSH_INC ../MacOS) +else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) +endif() + +# FIXME: change this once we understand rpaths +if(APPLE) + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + set_target_properties(shared PROPERTIES INSTALL_NAME_DIR + ${CMAKE_INSTALL_PREFIX}/${GMSH_LIB}) + endif() +endif() + +# mark targets as optional so we can install them separately if needed +# (e.g. "make lib" or "make shared" followed by "make install/fast") +install(TARGETS gmsh DESTINATION ${GMSH_BIN} OPTIONAL) +if(ENABLE_BUILD_LIB) + install(TARGETS lib DESTINATION ${GMSH_LIB} OPTIONAL) +endif() +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(TARGETS shared DESTINATION ${GMSH_LIB} OPTIONAL) +endif() + +if(ENABLE_ONELAB) + install(FILES ${ONELAB_PY} DESTINATION ${GMSH_BIN}) +endif() +if(ENABLE_BUILD_LIB OR ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(FILES ${GMSH_API} DESTINATION ${GMSH_INC}) + install(FILES ${GMSH_PY} DESTINATION ${GMSH_LIB}) + install(FILES ${GMSH_JL} DESTINATION ${GMSH_LIB}) + if(ENABLE_PRIVATE_API) + install(FILES ${GMSH_PRIVATE_API} DESTINATION ${GMSH_INC}/gmsh) + endif() +endif() +if(INSTALL_SDK_README) + configure_file(${SDK_FILE} ${CMAKE_CURRENT_BINARY_DIR}/README.txt) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/README.txt DESTINATION .) +endif() +install(FILES ${WELCOME_FILE} DESTINATION ${GMSH_DOC} RENAME README.txt) +install(FILES ${LICENSE_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CREDITS_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CHANGELOG_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${TUTORIAL_GEO_FILES} DESTINATION ${GMSH_DOC}/tutorial) +install(FILES ${TUTORIAL_CPP_FILES} DESTINATION ${GMSH_DOC}/tutorial/c++) +install(FILES ${TUTORIAL_C_FILES} DESTINATION ${GMSH_DOC}/tutorial/c) +install(FILES ${TUTORIAL_PY_FILES} DESTINATION ${GMSH_DOC}/tutorial/python) +install(FILES ${TUTORIAL_JL_FILES} DESTINATION ${GMSH_DOC}/tutorial/julia) +foreach(DIR ${DEMOS_DIRS}) + get_filename_component(DEMOS_DIR_NAME ${DIR} NAME) + file(GLOB DEMO_FILES ${DIR}/?*.*) + install(FILES ${DEMO_FILES} DESTINATION ${GMSH_DOC}/demos/${DEMOS_DIR_NAME}) +endforeach() +if(UNIX AND NOT CYGWIN) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/doc/gmsh.1 DESTINATION ${GMSH_MAN}) +endif() + +add_custom_target(get_headers + COMMAND ${CMAKE_COMMAND} -E make_directory Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +foreach(FILE ${GMSH_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endforeach() +if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/gmsh/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() +endif() + +find_program(MAKEINFO makeinfo) +if(MAKEINFO) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.info DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --split-size 1000000 + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(info DEPENDS ${TEX_DIR}/gmsh.info) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.txt DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --plaintext -o gmsh.txt + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(txt DEPENDS ${TEX_DIR}/gmsh.txt) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.html DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --html --css-ref=http://gmsh.info/gmsh.css + --no-split --set-customization-variable + EXTRA_HEAD='' + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(html DEPENDS ${TEX_DIR}/gmsh.html) + install(FILES ${TEX_DIR}/gmsh.html DESTINATION ${GMSH_DOC} OPTIONAL) +else() + add_custom_target(html COMMAND ${CMAKE_COMMAND} -E touch ${TEX_DIR}/gmsh.html) +endif() + +find_program(TEXI2PDF texi2pdf) +if(TEXI2PDF) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.pdf DEPENDS ${TEX_SRC} + COMMAND ${TEXI2PDF} ARGS gmsh.texi + WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(pdf DEPENDS ${TEX_DIR}/gmsh.pdf) + install(FILES ${TEX_DIR}/gmsh.pdf DESTINATION ${GMSH_DOC} OPTIONAL) +endif() + +execute_process(COMMAND ${CMAKE_COMMAND} -E echo + "@c This file was generated by cmake: do not edit manually!\n${OPT_TEXI}" + OUTPUT_FILE cmake_options.texi) + +if(MAKEINFO AND TEXI2PDF) + add_custom_target(doc COMMAND ${CMAKE_COMMAND} -E tar zcf + ${CMAKE_CURRENT_BINARY_DIR}/gmsh-${GMSH_VERSION}-doc.tgz + CREDITS.txt LICENSE.txt CHANGELOG.txt + doc/gmsh.1 doc/texinfo/gmsh.html doc/texinfo/gmsh.info + doc/texinfo/gmsh.pdf doc/texinfo/gmsh.txt + COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ} + DEPENDS ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.txt + ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.pdf + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(MAKEINFO OR TEXI2PDF) + add_custom_target(clean_doc COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ}) +endif() + +if(APPLE AND ENABLE_BUILD_LIB) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_framework.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info_framework.plist "${F1}") + get_target_property(LIBNAME lib LOCATION) # depracated + #set(LIBNAME $) # FIXME: use this in the future + add_custom_target(framework DEPENDS lib + COMMAND ${CMAKE_COMMAND} -E remove_directory gmsh.framework + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Headers + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Resources + COMMAND ${CMAKE_COMMAND} -E copy ${LIBNAME} gmsh.framework/gmsh + COMMAND ${CMAKE_COMMAND} -E copy Info_framework.plist + gmsh.framework/Resources/Info.plist + COMMAND ${CMAKE_COMMAND} -E create_symlink . gmsh.framework/Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + foreach(FILE ${GMSH_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + endif() +endif() + +set(CPACK_PACKAGE_VENDOR "Christophe Geuzaine and Jean-Francois Remacle") +set(CPACK_PACKAGE_VERSION_MAJOR ${GMSH_MAJOR_VERSION}) +set(CPACK_PACKAGE_VERSION_MINOR ${GMSH_MINOR_VERSION}) +set(CPACK_PACKAGE_VERSION_PATCH ${GMSH_PATCH_VERSION}) +set(CPACK_PACKAGE_DESCRIPTION_FILE ${WELCOME_FILE}) +set(CPACK_PACKAGE_DESCRIPTION_SUMMARY + "3D finite element mesh generator with built-in CAD engine and post-processor") +if(GMSH_EXTRA_VERSION MATCHES "-git.*") # so that we'll overwrite the archives + set(CPACK_PACKAGE_FILE_NAME gmsh-git-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh-git-source) +else() + set(CPACK_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-source) +endif() +set(CPACK_PACKAGE_INSTALL_DIRECTORY "gmsh") +set(CPACK_RESOURCE_FILE_LICENSE ${LICENSE_FILE}) +set(CPACK_RESOURCE_FILE_README ${WELCOME_FILE}) +set(CPACK_RESOURCE_FILE_WELCOME ${WELCOME_FILE}) +set(CPACK_PACKAGE_EXECUTABLE "gmsh") +if(ENABLE_PACKAGE_STRIP) + set(CPACK_STRIP_FILES TRUE) +else() + set(CPACK_STRIP_FILES FALSE) +endif() +set(CPACK_SOURCE_GENERATOR TGZ) +set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR}" "/CVS/" "/.svn" "/.git" + "~$" "DS_Store$" "GmshConfig.h$" "GmshVersion.h$" "/benchmarks/" "/tmp/" + "/bin/" "/lib/" "/nightly/" "GPATH" "GRTAGS" "GSYMS" "GTAGS" "/HTML/" + "/contrib/3M/" "/contrib/Parasolid/") + +if(UNIX) + # make sure we remove previous installs before doing the next one (on Mac for + # example "make package; make package_source" would lead to huge file lists + # getting generated due to the 'Applications' symlink in the bundle) + set(CPACK_INSTALL_COMMANDS "rm -rf ${CMAKE_CURRENT_BINARY_DIR}/_CPack_Packages") +endif() + +if(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + set(CPACK_GENERATOR Bundle) + set(CPACK_BUNDLE_NAME Gmsh) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_app.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info.plist "${F1}") + set(CPACK_BUNDLE_PLIST ${CMAKE_CURRENT_BINARY_DIR}/Info.plist) + set(CPACK_BUNDLE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) + if(PACKAGER STREQUAL "geuzaine - removed: we sign on a separate machine") + # codesigning requires CMake >= 3.2 + set(CPACK_BUNDLE_APPLE_CERT_APP "Developer ID Application: Christophe Geuzaine") + endif() + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsGeo.icns DESTINATION . + RENAME GmshGeo.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsMsh.icns DESTINATION . + RENAME GmshMsh.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsSol.icns DESTINATION . + RENAME GmshSol.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsPos.icns DESTINATION . + RENAME GmshPos.icns) + set(CPACK_PACKAGE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) +elseif(WIN32) + set(CPACK_GENERATOR ZIP) +else() + set(CPACK_GENERATOR TGZ) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/gmshpy AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON AND HAVE_PYTHON) + add_subdirectory(utils/wrappers/gmshpy) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/java AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_JAVA) + add_subdirectory(utils/wrappers/java) +endif() + +include(CPack) + +if(NOT DISABLE_GMSH_TESTS) + # disabling tests is useful when including this CMakeLists in an external project + include(CTest) + file(GLOB_RECURSE TESTFILES + tutorial/*.geo demos/*.geo benchmarks/?d/*.geo benchmarks/extrude/*.geo + benchmarks/occ/*.geo) + # disable this test for now on our Linux32 machine - the current config + # crashes on the OCC STL generation + if(${GMSH_OS} MATCHES "Linux32") + list(REMOVE_ITEM TESTFILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/t18.geo) + endif() + foreach(TESTFILE ${TESTFILES}) + # use relative path for Cygwin/MinGW (the pure win exe built with the MinGW + # compilers does not understand a full Cygwin-style path) + FILE(RELATIVE_PATH TEST ${CMAKE_CURRENT_BINARY_DIR} ${TESTFILE}) + if(HAVE_OCC OR NOT ${TEST} MATCHES "boolean" OR NOT ${TEST} MATCHES "occ") + add_test(${TEST} ./gmsh ${TEST} -3 -nopopup -o ./tmp.msh) + endif() + endforeach() + # test c++ api tutorials with dynamic builds (except on 32 bit windows for + # now: our win32 setup does not currently handle exceptions) + if(ENABLE_BUILD_DYNAMIC AND NOT ${GMSH_OS} MATCHES "Windows32") + file(GLOB_RECURSE TESTFILES tutorial/c++/*.cpp) + foreach(TESTFILE ${TESTFILES}) + get_filename_component(TEST ${TESTFILE} NAME_WE) + add_executable(${TEST} WIN32 ${TESTFILE}) + target_link_libraries(${TEST} shared) + if(WIN32 AND NOT MSVC) + set_target_properties(${TEST} PROPERTIES LINK_FLAGS "-mwindows -static") + endif() + add_test(${TEST}_cpp ${TEST}) + endforeach() + endif() +endif() + +message(STATUS "") +message(STATUS "Gmsh ${GMSH_VERSION} has been configured for ${GMSH_OS}") +message(STATUS "") +message(STATUS " * Build options:" ${GMSH_CONFIG_OPTIONS}) +message(STATUS " * Build type: " ${CMAKE_BUILD_TYPE}) +message(STATUS " * C compiler: " ${CMAKE_C_COMPILER}) +message(STATUS " * C++ compiler: " ${CMAKE_CXX_COMPILER}) +message(STATUS " * Install prefix: " ${CMAKE_INSTALL_PREFIX}) +message(STATUS "") + +mark_as_advanced(GMSH_EXTRA_VERSION + ACIS_LIB ANN_INC ANN_LIB CAIRO_LIB CAIRO_INC CGNS_INC GMM_INC + GMP_INC GMP_LIB MMG3D_INC MMG3D_LIB HDF5_LIB + MED_LIB OCC_INC SZ_LIB + PETSC_LIBS SLEPC_INC SLEPC_INC2 SLEPC_LIB + BISON FLEX MAKEINFO TEXI2PDF FLTK_CONFIG_SCRIPT + GMSH_EXTERNAL_INCLUDE_DIRS GMSH_EXTERNAL_LIBRARIES) Index: /issm/trunk/externalpackages/gmsh/configs/4.5.6/static/CMakeLists.txt =================================================================== --- /issm/trunk/externalpackages/gmsh/configs/4.5.6/static/CMakeLists.txt (revision 25836) +++ /issm/trunk/externalpackages/gmsh/configs/4.5.6/static/CMakeLists.txt (revision 25836) @@ -0,0 +1,2141 @@ +# Gmsh - Copyright (C) 1997-2020 C. Geuzaine, J.-F. Remacle +# +# See the LICENSE.txt file for license information. Please report all +# issues on https://gitlab.onelab.info/gmsh/gmsh/issues. + +cmake_minimum_required(VERSION 2.8 FATAL_ERROR) + +# do not warn about non-definition of WIN32 on Cygwin +set(CMAKE_LEGACY_CYGWIN_WIN32 0) + +# if CMAKE_BUILD_TYPE is specified use it; otherwise set the default +# build type to "RelWithDebInfo" ("-O2 -g" with gcc) prior to calling +# project() +if(DEFINED CMAKE_BUILD_TYPE) + set(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Choose build type") +else() + set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose build type") +endif() + +project(gmsh CXX C) + +# this variable controls the default value of the options which are normally set +# to ON (useful if you want to configure a minimal version of Gmsh: e.g. "cmake +# -DDEFAULT=0 -DENABLE_POST=1 -DENABLE_PARSER=1") +set(DEFAULT ON CACHE INTERNAL "Default value for enabled-by-default options") + +macro(opt OPTION HELP VALUE) + option(ENABLE_${OPTION} ${HELP} ${VALUE}) + set(OPT_TEXI "${OPT_TEXI}\n@item ENABLE_${OPTION}\n${HELP} (default: ${VALUE})") +endmacro() + +opt(3M "Enable proprietary 3M extension" OFF) +opt(ACIS "Enable ACIS geometrical models (experimental)" ${DEFAULT}) +opt(ALGLIB "Enable ALGLIB (used by some mesh optimizers)" ${DEFAULT}) +opt(ANN "Enable ANN (used for fast point search in mesh/post)" ${DEFAULT}) +opt(BAMG "Enable Bamg 2D anisotropic mesh generator" ${DEFAULT}) +opt(BLAS_LAPACK "Enable BLAS/Lapack for linear algebra (required for meshing)" ON) +opt(BLOSSOM "Enable Blossom algorithm (needed for full quad meshing)" ${DEFAULT}) +opt(BUILD_LIB "Enable 'lib' target for building static Gmsh library" OFF) +opt(BUILD_SHARED "Enable 'shared' target for building shared Gmsh library" OFF) +opt(BUILD_DYNAMIC "Enable dynamic Gmsh executable (linked with shared library)" OFF) +opt(BUILD_ANDROID "Enable Android NDK library target (experimental)" OFF) +opt(BUILD_IOS "Enable iOS library target (experimental)" OFF) +opt(CGNS "Enable CGNS import/export (experimental)" ${DEFAULT}) +opt(CGNS_CPEX0045 "Enable high-order CGNS import/export following CPEX0045 (experimental)" OFF) +opt(CAIRO "Enable Cairo to render fonts (experimental)" ${DEFAULT}) +opt(CXX11 "Enable C++11" ON) +opt(C99 "Enable C99" ON) +opt(PROFILE "Enable profiling compiler flags" OFF) +opt(DINTEGRATION "Enable discrete integration (needed for levelsets)" ${DEFAULT}) +opt(DOMHEX "Enable experimental DOMHEX code" ${DEFAULT}) +opt(FLTK "Enable FLTK graphical user interface (requires mesh/post)" ${DEFAULT}) +opt(GETDP "Enable GetDP solver (linked as a library, experimental)" ${DEFAULT}) +opt(GMM "Enable GMM linear solvers (simple alternative to PETSc)" ${DEFAULT}) +opt(GMP "Enable GMP for Kbipack (advanced)" ON) +opt(GRAPHICS "Enable building graphics lib even without GUI (advanced)" OFF) +opt(HXT "Enable HXT library (for reparametrization and meshing)" ${DEFAULT}) +opt(KBIPACK "Enable Kbipack (neeeded by homology solver)" ${DEFAULT}) +opt(MATHEX "Enable Mathex expression parser (used by plugins and options)" ${DEFAULT}) +opt(MED "Enable MED mesh and post file formats" ${DEFAULT}) +opt(MESH "Enable mesh module (required by GUI)" ${DEFAULT}) +opt(METIS "Enable Metis mesh partitioner" ${DEFAULT}) +opt(MMG3D "Enable MMG3D 3D anisotropic mesh refinement" ${DEFAULT}) +opt(MPEG_ENCODE "Enable built-in MPEG movie encoder" ${DEFAULT}) +opt(MPI "Enable MPI (experimental, not used for meshing)" OFF) +opt(MSVC_STATIC_RUNTIME "Enable static Visual C++ runtime" OFF) +opt(MUMPS "Enable MUMPS sparse direct linear solver" OFF) +opt(NETGEN "Enable Netgen 3D frontal mesh generator" ${DEFAULT}) +opt(NUMPY "Enable fullMatrix and numpy array conversion for private API" OFF) +opt(PETSC4PY "Enable petsc4py wrappers for petsc matrices for private API" OFF) +opt(OCC "Enable OpenCASCADE CAD kernel" ${DEFAULT}) +opt(OCC_CAF "Enable OpenCASCADE CAF module (for STEP/IGES attributes)" ${DEFAULT}) +opt(OCC_STATIC "Link OpenCASCADE static instead of dynamic libraries (requires ENABLE_OCC)" OFF) +opt(OCC_TBB "Add TBB libraries in list of OCC libraries" OFF) +opt(ONELAB "Enable ONELAB solver interface" ${DEFAULT}) +opt(ONELAB_METAMODEL "Enable ONELAB metamodels (experimental)" ${DEFAULT}) +opt(OPENACC "Enable OpenACC" OFF) +opt(OPENMP "Enable OpenMP" OFF) +opt(OPTHOM "Enable high-order mesh optimization tools" ${DEFAULT}) +opt(OS_SPECIFIC_INSTALL "Enable OS-specific (e.g. app bundle) installation" OFF) +opt(OSMESA "Enable OSMesa for offscreen rendering (experimental)" OFF) +opt(P4EST "Enable p4est for enabling automatic mesh size firld (experimental)" OFF) +opt(PACKAGE_STRIP "Strip symbols in install packages to reduce install size" ON) +opt(PARSER "Enable GEO file parser (required for .geo/.pos files)" ${DEFAULT}) +opt(PETSC "Enable PETSc linear solvers (required for SLEPc)" OFF) +opt(PLUGINS "Enable post-processing plugins" ${DEFAULT}) +opt(POST "Enable post-processing module (required by GUI)" ${DEFAULT}) +opt(POPPLER "Enable Poppler for displaying PDF documents (experimental)" OFF) +opt(PRIVATE_API "Enable private API" OFF) +opt(QUADTRI "Enable QuadTri structured meshing extensions" ${DEFAULT}) +opt(REVOROPT "Enable Revoropt (used for CVT remeshing)" OFF) +opt(SLEPC "Enable SLEPc eigensolvers" OFF) +opt(SOLVER "Enable built-in finite element solvers (required for compounds)" ${DEFAULT}) +opt(SYSTEM_CONTRIB "Use system versions of contrib libraries, when possible" OFF) +opt(TCMALLOC "Enable libtcmalloc (fast malloc that does not release memory)" OFF) +opt(TOUCHBAR "Enable Apple Touch bar" ${DEFAULT}) +opt(VISUDEV "Enable additional visualization capabilities for development purposes" OFF) +opt(VOROPP "Enable voro++ (for hex meshing, experimental)" ${DEFAULT}) +opt(WRAP_JAVA "Enable generation of Java wrappers for private API" OFF) +opt(WRAP_PYTHON "Enable generation of Python wrappers for private API" OFF) +opt(ZIPPER "Enable Zip file compression/decompression" OFF) + +set(GMSH_MAJOR_VERSION 4) +set(GMSH_MINOR_VERSION 5) +set(GMSH_PATCH_VERSION 6) +set(GMSH_EXTRA_VERSION "") +set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION}") + +if(NOT GMSH_RELEASE) + find_package(Git) + if(GIT_FOUND) + execute_process(COMMAND ${GIT_EXECUTABLE} log -1 --format=%h + WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} ERROR_QUIET + OUTPUT_VARIABLE GIT_COMMIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE) + endif() + if(GIT_COMMIT_HASH) + set(GMSH_EXTRA_VERSION "${GMSH_EXTRA_VERSION}-git-${GIT_COMMIT_HASH}") + endif() + set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION_TEXI} (development version)") +endif() + +set(GMSH_VERSION "${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}") +set(GMSH_VERSION "${GMSH_VERSION}.${GMSH_PATCH_VERSION}${GMSH_EXTRA_VERSION}") +set(GMSH_SHORT_LICENSE "GNU General Public License") + +set(GMSH_API api/gmsh.h api/gmshc.h api/gmsh.h_cwrap) + +if(ENABLE_PRIVATE_API) + message(WARNING "The private API is unsupported and undocumented. It is meant " + "for expert Gmsh developers, not for regular Gmsh users, who should rely " + "on the stable public API (gmsh/api) instead. If you are repackaging Gmsh, " + "e.g. for a Linux distribution, please DO NOT distribute the private API " + "(i.e. all the internal headers) and ship the stable public API instead " + "(i.e. only the headers and modules in gmsh/api).") + file(GLOB_RECURSE HEADERS Common/*.h Numeric/*.h Geo/*.h Mesh/*.h Solver/*.h + Post/*.h Graphics/*.h contrib/kbipack/*.h contrib/DiscreteIntegration/*.h + contrib/HighOrderMeshOptimizer/*.h contrib/MeshOptimizer/*.h + contrib/MeshQualityOptimizer/*.h) + set(GMSH_PRIVATE_API ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h ${HEADERS}) + get_property(IAMCHILD DIRECTORY PROPERTY PARENT_DIRECTORY) + if(IAMCHILD) + set(GMSH_PRIVATE_API ${GMSH_PRIVATE_API} PARENT_SCOPE) + endif() +endif() + +set(ONELAB_PY contrib/onelab/python/onelab.py) +set(GMSH_PY api/gmsh.py) +set(GMSH_JL api/gmsh.jl) + +if(${CMAKE_MAJOR_VERSION} GREATER 2) + string(TIMESTAMP DATE "%Y%m%d") +else() + execute_process(COMMAND date "+%Y%m%d" OUTPUT_VARIABLE DATE + OUTPUT_STRIP_TRAILING_WHITESPACE) +endif() + +if(NOT DATE) + set(DATE "unknown") +endif() +set(GMSH_DATE "${DATE}") + +if(NOT GMSH_HOST) + execute_process(COMMAND hostname OUTPUT_VARIABLE HOSTNAME + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT HOSTNAME) + set(HOSTNAME "unknown") + endif() + set(GMSH_HOST "${HOSTNAME}") +endif() + +if(NOT GMSH_PACKAGER) + execute_process(COMMAND whoami OUTPUT_VARIABLE PACKAGER + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT PACKAGER) + set(PACKAGER "unknown") + endif() + string(REPLACE "\\" " " PACKAGER ${PACKAGER}) + set(GMSH_PACKAGER "${PACKAGER}") +endif() + +if(APPLE) + set(GMSH_OS "MacOSX") +elseif(CYGWIN OR MSYS) + # detect if we use the MinGW compilers on Cygwin - if we do, handle the build + # as a pure Windows build + if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpmachine + OUTPUT_VARIABLE CXX_COMPILER_MACHINE + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(CXX_COMPILER_MACHINE MATCHES "mingw") + set(GMSH_OS "Windows") + set(WIN32 1) + add_definitions(-DWIN32) + endif() + endif() +else() + set(GMSH_OS "${CMAKE_SYSTEM_NAME}") +endif() + +include(CheckTypeSize) +include(CheckFunctionExists) +include(CheckIncludeFile) +include(CheckCXXCompilerFlag) +include(CheckCCompilerFlag) + +macro(set_config_option VARNAME STRING) + set(${VARNAME} TRUE) + list(APPEND CONFIG_OPTIONS ${STRING}) + message(STATUS "Found " ${STRING}) +endmacro() + +# check if the machine is 64 bits (this is more reliable than using +# CMAKE_SIZEOF_VOID_P, which does not seem to work e.g. on some Suse +# machines) +check_type_size("void*" SIZEOF_VOID_P) +if(SIZEOF_VOID_P EQUAL 8) + set_config_option(HAVE_64BIT_SIZE_T "64Bit") +endif() + +# append 32/64 to the build name on Linux and Windows +if(NOT APPLE) + if(HAVE_64BIT_SIZE_T) + set(GMSH_OS "${GMSH_OS}64") + else() + set(GMSH_OS "${GMSH_OS}32") + endif() +endif() + +if(NOT ENABLE_BUILD_SHARED) + if(ENABLE_WRAP_PYTHON OR ENABLE_WRAP_JAVA) + set(ENABLE_BUILD_DYNAMIC ON) + endif() +endif() + +if(ENABLE_BUILD_DYNAMIC) + set(GMSH_OS "${GMSH_OS}-sdk") +endif() + +if(APPLE) + # FIXME: change this once we understand rpaths - the options below do not work + set(CMAKE_MACOSX_RPATH 0) +else() + # make sure that dynamic libraries can be found when installing/ displacing the + # binaries: from https://gitlab.kitware.com/cmake/community/wikis/doc/cmake/ + # RPATH-handling: + + # use, i.e. don't skip the full RPATH for the build tree + set(CMAKE_SKIP_BUILD_RPATH FALSE) + + # when building, don't use the install RPATH already (but later on when + # installing) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") + + # add the automatically determined parts of the RPATH which point to + # directories outside the build tree to the install RPATH + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + + # the RPATH to be used when installing, but only if it's not a system directory + list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" + isSystemDir) + if("${isSystemDir}" STREQUAL "-1") + set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../lib") + endif() +endif() + +if(MSVC) + # remove annoying warning about bool/int cast performance + set(GMSH_CONFIG_PRAGMAS "#pragma warning(disable:4800 4244 4267)") + foreach(VAR + CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE + CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO + CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE + CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO) + if(ENABLE_MSVC_STATIC_RUNTIME AND ${VAR} MATCHES "/MD") + string(REGEX REPLACE "/MD" "/MT" ${VAR} "${${VAR}}") + endif() + if(NOT ${VAR} MATCHES "/MP") # enable parallel compilation + set(${VAR} "${${VAR}} /MP") + endif() + endforeach() + if(ENABLE_PRIVATE_API) + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + # automatically export .def file with all symbols (requires CMake 3.4); + # depending on the compiling options this might lead to more than 64k export + # symbols; just trim the .def file to keep the ones you need + set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + endif() + endif() +endif() + +if(ENABLE_OPENMP) + find_package(OpenMP) + if(OpenMP_FOUND) + set_config_option(HAVE_OPENMP "OpenMP") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + elseif(APPLE AND EXISTS "/opt/local/lib/libomp") + # just for testing the official Apple compiler with macports' libomp + set_config_option(HAVE_OPENMP "OpenMP[MacPorts]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + list(APPEND EXTERNAL_LIBRARIES "-L/opt/local/lib/libomp -lomp") + elseif(APPLE AND EXISTS "/usr/local/lib/libomp.dylib") + set_config_option(HAVE_OPENMP "OpenMP[usr/local]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp") + list(APPEND EXTERNAL_LIBRARIES "-lomp") + endif() +endif() + +if(ENABLE_OPENACC) + find_package(OpenACC) + if(OpenACC_C_FOUND AND OpenACC_CXX_FOUND) + set_config_option(HAVE_OPENACC "OpenACC") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenACC_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenACC_CXX_FLAGS}") + endif() +endif() + +if(ENABLE_CXX11) + # in recent cmake versions we could do e.g. set(CMAKE_CXX_STANDARD 11) + check_cxx_compiler_flag("-std=c++11" STDCXX11) + if(STDCXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() +endif() + +if(ENABLE_C99) + # in recent cmake versions we could do e.g. set(CMAKE_C_STANDARD 99) + check_c_compiler_flag("-std=c99" STDC99) + if(STDC99) + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99") + endif() +endif() + +if(ENABLE_PROFILE) + # Using the perf set of profiling tools doesn't work without the frame + # pointer and a common optimisation is to remove it + check_cxx_compiler_flag("-fno-omit-frame-pointer" FNOFP) + if(FNOFP) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer") + endif() +endif() + +macro(append_gmsh_src DIRNAME FILES) + foreach(FILE ${FILES}) + list(APPEND LIST ${DIRNAME}/${FILE}) + endforeach() + set(GMSH_SRC ${GMSH_SRC};${LIST} PARENT_SCOPE) + set(GMSH_DIRS ${GMSH_DIRS};${DIRNAME} PARENT_SCOPE) +endmacro() + +macro(find_all_libraries VARNAME LISTNAME PATH SUFFIX) + set(${VARNAME}) + list(LENGTH ${LISTNAME} NUM_LIST) + foreach(LIB ${${LISTNAME}}) + if("${PATH}" STREQUAL "") + find_library(FOUND_LIB ${LIB} PATH_SUFFIXES ${SUFFIX}) + else() + find_library(FOUND_LIB ${LIB} PATHS ${PATH} NO_DEFAULT_PATH) + endif() + if(FOUND_LIB) + list(APPEND ${VARNAME} ${FOUND_LIB}) + endif() + unset(FOUND_LIB CACHE) + endforeach() + list(LENGTH ${VARNAME} NUM_FOUND_LIBRARIES) + if(NUM_FOUND_LIBRARIES LESS NUM_LIST) + set(${VARNAME}) + endif() +endmacro() + +macro(set_compile_flags LISTNAME FLAGS) + foreach(FILE ${${LISTNAME}}) + get_source_file_property(PROP ${FILE} COMPILE_FLAGS) + if(PROP) + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${PROP} ${FLAGS}") + else() + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${FLAGS}") + endif() + endforeach() +endmacro() + +if(ENABLE_BLAS_LAPACK) + if(BLAS_LAPACK_LIBRARIES) + # use libs as specified in the BLAS_LAPACK_LIBRARIES variable + set_config_option(HAVE_BLAS "Blas[custom]") + set_config_option(HAVE_LAPACK "Lapack[custom]") + set(LAPACK_LIBRARIES ${BLAS_LAPACK_LIBRARIES}) + else() + if(MSVC) + # on Windows with Visual C++ try really hard to find blas/lapack *without* + # requiring a Fortran compiler: 1) try to find the Intel MKL libs using + # the standard search path; if not found 2) try to get the reference + # blas/lapack libs (useful for users with no Fortran compiler and no MKL + # license, who can just download our precompiled "gmsh-dep" package) + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH em64t/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_lp64 mkl_intel_thread mkl_core) + else() + set(MKL_PATH ia32/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_c mkl_intel_thread mkl_core) + endif() + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + set(REFLAPACK_LIBS_REQUIRED lapack blas g2c gcc) + find_all_libraries(LAPACK_LIBRARIES REFLAPACK_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[ref]") + set_config_option(HAVE_LAPACK "Lapack[ref]") + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + # on Linux try to find the Intel MKL without a Fortran compiler + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH lib/em64t) + else() + set(MKL_PATH lib/32) + endif() + set(MKL_LIBS_REQUIRED mkl_gf_lp64 iomp5 mkl_gnu_thread mkl_core guide pthread) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(NOT LAPACK_LIBRARIES) + # match lapack 9.0 on 64bit + set(MKL_LIBS_REQUIRED mkl_lapack mkl_em64t guide) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + endif() + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + # on Linux also try to find ATLAS without a Fortran compiler, because + # cmake ships with a buggy FindBLAS e.g. on Ubuntu Lucid Lynx + set(ATLAS_LIBS_REQUIRED lapack f77blas cblas atlas) + find_all_libraries(LAPACK_LIBRARIES ATLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[atlas]") + set_config_option(HAVE_LAPACK "Lapack[atlas]") + else() + # try with generic names + set(GENERIC_LIBS_REQUIRED lapack blas pthread) + find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[generic]") + set_config_option(HAVE_LAPACK "Lapack[generic]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "SunOS") + # on SunOS we know blas and lapack are available in sunperf + set(LAPACK_LIBRARIES -library=sunperf) + set_config_option(HAVE_BLAS "Blas[sunperf]") + set_config_option(HAVE_LAPACK "Lapack[sunperf]") + elseif(APPLE) + # on Mac we also know that blas and lapack are available + set(LAPACK_LIBRARIES "-llapack -lblas") + set_config_option(HAVE_BLAS "Blas[veclib]") + set_config_option(HAVE_LAPACK "Lapack[veclib]") + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we haven't found blas and lapack check for OpenBlas + set(OPENBLAS_LIBS_REQUIRED openblas) + find_all_libraries(LAPACK_LIBRARIES OPENBLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[openblas]") + set_config_option(HAVE_LAPACK "Lapack[openblas]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we still haven't found blas and lapack, use the standard cmake tests, + # which require a working Fortran compiler + enable_language(Fortran) + find_package(BLAS) + if(BLAS_FOUND) + set_config_option(HAVE_BLAS "Blas") + find_package(LAPACK) + if(LAPACK_FOUND) + set_config_option(HAVE_LAPACK "Lapack") + else() + set(LAPACK_LIBRARIES ${BLAS_LIBRARIES}) + endif() + if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU") + if(CMAKE_Fortran_COMPILER MATCHES "gfortran") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "f95") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "g77") + list(APPEND LAPACK_LIBRARIES g2c) + endif() + elseif(CMAKE_Fortran_COMPILER MATCHES "pgi") + list(APPEND LAPACK_LIBRARIES -pgf77libs) + endif() + endif() + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + message(WARNING "Could not find Blas or Lapack: most meshing algorithms " + "will not be functional") + endif() + + endif() +endif() + +if(ENABLE_TCMALLOC) + find_library(TCMALLOC tcmalloc) + if(TCMALLOC) + set_config_option(HAVE_TCMALLOC "TCMalloc") + list(APPEND EXTERNAL_LIBRARIES ${TCMALLOC}) + endif() +endif() + +add_subdirectory(Common) +add_subdirectory(Numeric) +add_subdirectory(Geo) + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh AND ENABLE_MESH) + add_subdirectory(Mesh) + set_config_option(HAVE_MESH "Mesh") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Solver AND ENABLE_SOLVER) + add_subdirectory(Solver) + set_config_option(HAVE_SOLVER "Solver") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Post AND ENABLE_POST) + add_subdirectory(Post) + set_config_option(HAVE_POST "Post") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Plugin AND ENABLE_PLUGINS) + add_subdirectory(Plugin) + set_config_option(HAVE_PLUGINS "Plugins") + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Parser AND ENABLE_PARSER) + add_subdirectory(Parser) + set_config_option(HAVE_PARSER "Parser") +endif() + +if(ENABLE_VISUDEV) + set_config_option(HAVE_VISUDEV "VisuDev") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Fltk AND ENABLE_FLTK) + # first, try to use fltk-config for fltk >= 1.3 (FindFLTK is buggy on Unix, + # where e.g. xft and xinerama options are not dealt with) + find_program(FLTK_CONFIG_SCRIPT fltk-config) + if(FLTK_CONFIG_SCRIPT) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --api-version + OUTPUT_VARIABLE FLTK_VERSION) + string(STRIP "${FLTK_VERSION}" FLTK_VERSION) + if(FLTK_VERSION VERSION_GREATER 1.1) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + message(STATUS "Using fltk-config script for Fltk " ${FLTK_VERSION}) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --includedir + OUTPUT_VARIABLE FLTK_INCLUDE_DIR) + string(STRIP ${FLTK_INCLUDE_DIR} FLTK_INCLUDE_DIR) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # On linux (at least OpenSuSE) the following directories are + # not existing (everything is in /usr/include). To avoid warnings + # check existance of these directories before adding them + if(EXISTS ${FLTK_INCLUDE_DIR}/FL/images) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/FL/images) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/jpeg) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/jpeg) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/zlib) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/zlib) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/png) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/png) + endif() + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --ldflags + OUTPUT_VARIABLE FLTK_LIBRARIES) + string(STRIP ${FLTK_LIBRARIES} FLTK_LIBRARIES) + string(REGEX MATCH "fltk[_ ]jpeg" FLTK_JPEG ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]z" FLTK_Z ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]png" FLTK_PNG ${FLTK_LIBRARIES}) + endif() + endif() + # then try the built-in FindFLTK module + if(NOT HAVE_FLTK) + set(FLTK_SKIP_FORMS TRUE) + set(FLTK_SKIP_FLUID TRUE) + find_package(FLTK) + if(FLTK_FOUND) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # find fltk jpeg + find_library(FLTK_JPEG NAMES fltk_jpeg fltkjpeg) + if(FLTK_JPEG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_JPEG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/jpeg) + endforeach() + endif() + # find fltk zlib + find_library(FLTK_Z NAMES fltk_z fltkz) + if(FLTK_Z) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_Z}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/zlib) + endforeach() + endif() + # find fltk png + find_library(FLTK_PNG NAMES fltk_png fltkpng) + if(FLTK_PNG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_PNG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/png) + endforeach() + endif() + endif() + endif() + # workaround for Fedora/Suse messing up fltk-config (see issue #417) + if(HAVE_FLTK AND ${CMAKE_SYSTEM_NAME} MATCHES "Linux") + string(REGEX MATCH "X11" FLTK_X11 ${FLTK_LIBRARIES}) + if(NOT FLTK_X11) + find_package(X11) + if(X11_FOUND) + list(APPEND EXTERNAL_INCLUDES ${X11_INCLUDE_DIR}) + list(APPEND EXTERNAL_LIBRARIES ${X11_LIBRARIES}) + endif() + endif() + endif() +endif() + +if(APPLE AND HAVE_FLTK AND ENABLE_TOUCHBAR) + if(CMAKE_OSX_DEPLOYMENT_TARGET) + if(${CMAKE_OSX_DEPLOYMENT_TARGET} VERSION_GREATER 10.11) + set(GMSH_SRC ${GMSH_SRC};Fltk/touchBar.mm) + set_config_option(HAVE_TOUCHBAR "TouchBar") + endif() + endif() +endif() + +if(ENABLE_ONELAB) + set_config_option(HAVE_ONELAB "ONELAB") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/onelab) + if(ENABLE_ONELAB_METAMODEL) + add_subdirectory(contrib/onelab) + include_directories(contrib/onelab) + set_config_option(HAVE_ONELAB_METAMODEL "ONELABMetamodel") + endif() + file(COPY ${ONELAB_PY} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + endif() +endif() + +if(ENABLE_BUILD_IOS) + find_file(CMAKE_TOOLCHAIN_FILE "ios.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for iOS without a toolchain") + endif() + add_definitions(-DBUILD_IOS) +endif() + +if(HAVE_FLTK OR ENABLE_GRAPHICS) + if(NOT HAVE_MESH OR NOT HAVE_POST OR NOT HAVE_PLUGINS OR NOT HAVE_ONELAB) + message(SEND_ERROR "Cannot compile GUI without Mesh, Post, Plugin and ONELAB") + endif() + + if(FLTK_JPEG) + set_config_option(HAVE_LIBJPEG "Jpeg[fltk]") + else() + find_package(JPEG) + if(JPEG_FOUND) + set_config_option(HAVE_LIBJPEG "Jpeg") + list(APPEND EXTERNAL_LIBRARIES ${JPEG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${JPEG_INCLUDE_DIR}) + endif() + endif() + + if(FLTK_Z) + set_config_option(HAVE_LIBZ "Zlib[fltk]") + else() + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + + if(HAVE_LIBZ) + if(FLTK_PNG) + set_config_option(HAVE_LIBPNG "Png[fltk]") + else() + find_package(PNG) + if(PNG_FOUND) + set_config_option(HAVE_LIBPNG "Png") + list(APPEND EXTERNAL_LIBRARIES ${PNG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${PNG_INCLUDE_DIR}) + endif() + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/mpeg_encode AND + ENABLE_MPEG_ENCODE) + add_subdirectory(contrib/mpeg_encode) + include_directories(contrib/mpeg_encode/headers) + set_config_option(HAVE_MPEG_ENCODE "Mpeg") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/3M AND ENABLE_3M) + add_subdirectory(contrib/3M) + include_directories(contrib/3M) + set_config_option(HAVE_3M "3M") + endif() + + if(ENABLE_OSMESA) + find_library(OSMESA_LIB OSMesa) + if(OSMESA_LIB) + set_config_option(HAVE_OSMESA "OSMesa") + list(APPEND EXTERNAL_LIBRARIES ${OSMESA_LIB}) + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Graphics) + set(OpenGL_GL_PREFERENCE "LEGACY") + find_package(OpenGL REQUIRED) + if(OPENGL_GLU_FOUND AND OPENGL_FOUND) + add_subdirectory(Graphics) + set_config_option(HAVE_OPENGL "OpenGL") + else() + message(SEND_ERROR "Could not find GLU: disabling OpenGL support") + endif() + endif() +endif() + +if(ENABLE_ANN) + find_library(ANN_LIB ANN PATH_SUFFIXES lib) + find_path(ANN_INC "ANN.h" PATH_SUFFIXES src include ANN) + if(ENABLE_SYSTEM_CONTRIB AND ANN_LIB AND ANN_INC) + message(STATUS "Using system version of ANN") + list(APPEND EXTERNAL_LIBRARIES ${ANN_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ANN_INC}) + set_config_option(HAVE_ANN "Ann[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ANN) + add_subdirectory(contrib/ANN) + include_directories(contrib/ANN/include) + set_config_option(HAVE_ANN "Ann") + endif() +endif() + +if(ENABLE_ALGLIB) + find_library(ALGLIB_LIB alglib PATH_SUFFIXES lib) + find_path(ALGLIB_INC "stdafx.h" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND ALGLIB_LIB AND ALGLIB_INC) + list(APPEND EXTERNAL_LIBRARIES ${ALGLIB_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ALGLIB_INC}) + set_config_option(HAVE_ALGLIB "ALGLIB[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ALGLIB) + add_subdirectory(contrib/ALGLIB) + include_directories(contrib/ALGLIB) + set_config_option(HAVE_ALGLIB "ALGLIB") + endif() +endif() + +if(HAVE_FLTK AND ENABLE_CAIRO) + find_library(CAIRO_LIB cairo) + find_path(CAIRO_INC "cairo/cairo.h" PATH_SUFFIXES include) + if(CAIRO_INC AND CAIRO_LIB) + set_config_option(HAVE_CAIRO "Cairo") + list(APPEND EXTERNAL_LIBRARIES ${CAIRO_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CAIRO_INC}) + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/DiscreteIntegration AND + ENABLE_DINTEGRATION) + add_subdirectory(contrib/DiscreteIntegration) + include_directories(contrib/DiscreteIntegration) + set_config_option(HAVE_DINTEGRATION "DIntegration") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/HighOrderMeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshQualityOptimizer AND + ENABLE_OPTHOM AND HAVE_MESH) + add_subdirectory(contrib/HighOrderMeshOptimizer) + include_directories(contrib/HighOrderMeshOptimizer) + add_subdirectory(contrib/MeshOptimizer) + include_directories(contrib/MeshOptimizer) + include_directories(${CMAKE_CURRENT_BINARY_DIR}/contrib/MeshOptimizer) + add_subdirectory(contrib/MeshQualityOptimizer) + include_directories(contrib/MeshQualityOptimizer) + set_config_option(HAVE_OPTHOM "OptHom") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/domhex AND + ENABLE_DOMHEX AND HAVE_MESH) + add_subdirectory(contrib/domhex) + include_directories(contrib/domhex) + set_config_option(HAVE_DOMHEX "DomHex") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/QuadTri AND + ENABLE_QUADTRI AND HAVE_MESH) + add_subdirectory(contrib/QuadTri) + include_directories(contrib/QuadTri) + set_config_option(HAVE_QUADTRI "QuadTri") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/kbipack AND ENABLE_KBIPACK) + set_config_option(HAVE_KBIPACK "Kbipack") + add_subdirectory(contrib/kbipack) + include_directories(contrib/kbipack) + if(ENABLE_GMP) + find_library(GMP_LIB libgmp.a) + find_path(GMP_INC "gmp.h" PATH_SUFFIXES src include) + endif() + if(GMP_LIB AND GMP_INC) + set_config_option(HAVE_GMP "GMP") + list(APPEND EXTERNAL_LIBRARIES ${GMP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GMP_INC}) + else() + message(STATUS "GMP not found: Kbipack uses long int") + endif() +endif() + +if(ENABLE_MATHEX) + find_library(MATHEX_LIB mathex PATH_SUFFIXES lib) + find_path(MATHEX_INC "mathex.h" PATH_SUFFIXES src include) + if(ENABLE_SYSTEM_CONTRIB AND MATHEX_LIB AND MATHEX_INC) + list(APPEND EXTERNAL_LIBRARIES ${MATHEX_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MATHEX_INC}) + set_config_option(HAVE_MATHEX "MathEx[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MathEx) + add_subdirectory(contrib/MathEx) + include_directories(contrib/MathEx) + set_config_option(HAVE_MATHEX "MathEx") + endif() +endif() + +if(ENABLE_MPI) + find_package(MPI) + if(MPI_FOUND) + set_config_option(HAVE_MPI "MPI") + list(APPEND EXTERNAL_INCLUDES ${MPI_CXX_INCLUDE_PATH}) + list(APPEND EXTERNAL_LIBRARIES ${MPI_CXX_LIBRARIES}) + set(CMAKE_C_COMPILER ${MPI_C_COMPILER}) + set(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER}) + set(CMAKE_Fortran_COMPILER ${MPI_Fortran_COMPILER}) + endif() +endif() + +if(ENABLE_POPPLER) + find_library(POPPLER_LIB poppler) + find_library(POPPLER_CPP_LIB poppler-cpp) + find_path(POPPLER_INC "poppler/cpp/poppler-document.h" PATH_SUFFIXES src include) + if(POPPLER_LIB AND POPPLER_INC) + set_config_option(HAVE_POPPLER "Poppler") + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_LIB}) + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_CPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${POPPLER_INC}) + endif() +endif() + +if(ENABLE_P4EST) + find_library(P4EST_LIB p4est) + find_path(P4EST_INC "p4est.h" PATH_SUFFIXES src) + find_library(SC_LIB sc) + if(P4EST_LIB AND P4EST_INC AND SC_LIB) + set_config_option(HAVE_P4EST "P4est") + list(APPEND EXTERNAL_LIBRARIES ${P4EST_LIB} ${SC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${P4EST_INC}) + endif() +endif() + +if(HAVE_MESH OR HAVE_SOLVER) + if(ENABLE_METIS) + if(METIS_ROOT) + find_library(METIS_LIB metis PATHS ${METIS_ROOT} PATH_SUFFIXES lib) + find_path(METIS_INC "metis.h" PATHS ${METIS_ROOT} PATH_SUFFIXES include) + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis") + else() + find_library(METIS_LIB metis PATH_SUFFIXES lib) + find_path(METIS_INC "metis.h" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC) + message(STATUS "Using system version of METIS") + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/metis) + add_definitions(-DUSE_GKREGEX) + add_subdirectory(contrib/metis) + include_directories(contrib/metis/include contrib/metis/libmetis + contrib/metis/GKlib) + set_config_option(HAVE_METIS "Metis") + endif() + endif() + endif() +endif() + +if(HAVE_MESH) + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh/tetgenBR.cxx) + set_config_option(HAVE_TETGENBR "TetGen/BR") + endif() + + if(ENABLE_VOROPP) + find_library(VOROPP_LIB voro++ PATH_SUFFIXES lib) + find_path(VOROPP_INC "voro++.hh" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND VOROPP_LIB AND VOROPP_INC) + message(STATUS "Using system version of voro++") + list(APPEND EXTERNAL_LIBRARIES ${VOROPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${VOROPP_INC}) + set_config_option(HAVE_VOROPP "Voro++[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++) + add_subdirectory(contrib/voro++) + include_directories(contrib/voro++/src) + set_config_option(HAVE_VOROPP "Voro++") + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/blossom AND ENABLE_BLOSSOM) + add_subdirectory(contrib/blossom) + include_directories(contrib/blossom/MATCH contrib/blossom/concorde97 + contrib/blossom/concorde97/INCLUDE) + set_config_option(HAVE_BLOSSOM "Blossom") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/Netgen AND ENABLE_NETGEN) + add_subdirectory(contrib/Netgen) + include_directories(contrib/Netgen contrib/Netgen/libsrc/include + contrib/Netgen/nglib) + set_config_option(HAVE_NETGEN "Netgen") + add_definitions(-DNO_PARALLEL_THREADS -DNOTCL) + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/bamg AND ENABLE_BAMG) + add_subdirectory(contrib/bamg) + include_directories(contrib/bamg contrib/bamg/bamglib) + set_config_option(HAVE_BAMG "Bamg") + endif() + + if(ENABLE_MMG3D) + find_library(MMG3D_LIB mmg3d PATH_SUFFIXES lib) + find_path(MMG3D_INC "libmmg3d.h" PATH_SUFFIXES src include) + if(ENABLE_SYSTEM_CONTRIB AND MMG3D_LIB AND MMG3D_INC) + list(APPEND EXTERNAL_LIBRARIES ${MMG3D_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MMG3D_INC}) + set_config_option(HAVE_MMG3D "Mmg3d[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/mmg3d) + add_subdirectory(contrib/mmg3d) + include_directories(contrib/mmg3d/build/sources) + set_config_option(HAVE_MMG3D "Mmg3d") + endif() + endif() +endif() + +if(ENABLE_MED OR ENABLE_CGNS) + find_package(HDF5) + if(HDF5_FOUND) + set(HDF5_LIB "${HDF5_C_LIBRARIES}") + list(APPEND EXTERNAL_INCLUDES ${HDF5_INCLUDE_DIRS}) + if(ENABLE_MED) + find_library(MED_LIB medC) + if(MED_LIB) + set_config_option(HAVE_MED "Med") + list(APPEND EXTERNAL_LIBRARIES ${MED_LIB}) + endif() + endif() + if(ENABLE_CGNS) + find_library(CGNS_LIB cgns HINTS ENV CGNS_ROOT PATH_SUFFIXES lib) + find_path(CGNS_INC "cgnslib.h" HINTS ENV CGNS_ROOT PATH_SUFFIXES include) + if(CGNS_LIB AND CGNS_INC) + set_config_option(HAVE_LIBCGNS "Cgns") + list(APPEND EXTERNAL_LIBRARIES ${CGNS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CGNS_INC}) + if(ENABLE_CGNS_CPEX0045) + set_config_option(HAVE_LIBCGNS_CPEX0045 "Cgns_CPEX0045") + endif() + endif() + endif() + if(MED_LIB OR CGNS_LIB) + list(APPEND EXTERNAL_LIBRARIES ${HDF5_LIB}) + find_library(SZ_LIB NAMES szlib sz) + if(SZ_LIB) + list(APPEND EXTERNAL_LIBRARIES ${SZ_LIB}) + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + endif() + endif() + endif() + else() + message(STATUS "HDF5 not found") + endif() +endif() + +if(HAVE_SOLVER) + if(ENABLE_GMM) + find_path(GMM_INC "gmm.h" PATH_SUFFIXES src include include/gmm) + if(ENABLE_SYSTEM_CONTRIB AND GMM_INC) + message(STATUS "Using system version of GMM") + list(APPEND EXTERNAL_INCLUDES ${GMM_INC}) + set_config_option(HAVE_GMM "Gmm[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/gmm) + include_directories(contrib/gmm) + set_config_option(HAVE_GMM "Gmm") + endif() + endif() + + if(ENABLE_PETSC) + if(PETSC_DIR) + set(ENV_PETSC_DIR ${PETSC_DIR}) + else() + set(ENV_PETSC_DIR $ENV{PETSC_DIR}) + endif() + if(PETSC_ARCH) + set(ENV_PETSC_ARCH ${PETSC_ARCH}) + else() + set(ENV_PETSC_ARCH $ENV{PETSC_ARCH}) + endif() + set(PETSC_POSSIBLE_CONF_FILES + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc-conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc/conf/petscvariables) + foreach(FILE ${PETSC_POSSIBLE_CONF_FILES}) + if(EXISTS ${FILE}) + # old-style PETSc installations (using PETSC_DIR and PETSC_ARCH) + message(STATUS "Using PETSc dir: ${ENV_PETSC_DIR}") + message(STATUS "Using PETSc arch: ${ENV_PETSC_ARCH}") + # find includes by parsing the petscvariables file + file(STRINGS ${FILE} PETSC_VARIABLES NEWLINE_CONSUME) + endif() + endforeach() + if(PETSC_VARIABLES) + # try to find PETSC_CC_INCLUDES for PETSc >= 3.4 + string(REGEX MATCH "PETSC_CC_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "PETSC_CC_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + else() + # try to find PETSC_PACKAGES_INCLUDES in older versions + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/include) + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/include) + string(REGEX MATCH "PACKAGES_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + string(REPLACE "PACKAGES_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + endif() + if(PETSC_PACKAGES_INCLUDES) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "-I" "" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + string(REPLACE " " ";" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + foreach(VAR ${PETSC_PACKAGES_INCLUDES}) + # seem to include unexisting directories (/usr/include/lib64) + # check to avoid warnings + if(EXISTS ${VAR}) + list(APPEND EXTERNAL_INCLUDES ${VAR}) + endif() + endforeach() + endif() + endif() + # find libraries (<= 3.0) + set(PETSC_LIBS_REQUIRED petscksp petscdm petscmat petscvec petsc) + find_all_libraries(PETSC_LIBS PETSC_LIBS_REQUIRED + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib "") + # petsc 3.1 creates only one library (libpetsc) + if(NOT PETSC_LIBS) + find_library(PETSC_LIBS petsc PATHS ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + endif() + if(PETSC_LIBS) + set_config_option(HAVE_PETSC "PETSc") + if(NOT HAVE_BLAS) + set_config_option(HAVE_BLAS "Blas[petsc]") + endif() + if(NOT HAVE_LAPACK) + set_config_option(HAVE_LAPACK "Lapack[petsc]") + endif() + endif() + # find slepc (needs to be linked in before petsc) + if(ENABLE_SLEPC) + if(SLEPC_DIR) + set(ENV_SLEPC_DIR ${SLEPC_DIR}) + else() + set(ENV_SLEPC_DIR $ENV{SLEPC_DIR}) + endif() + find_library(SLEPC_LIB slepc PATHS ${ENV_SLEPC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + if(SLEPC_LIB) + find_path(SLEPC_INC "slepc.h" PATHS ${ENV_SLEPC_DIR} PATH_SUFFIXES include + ${ENV_PETSC_ARCH}/include include/slepc NO_DEFAULT_PATH) + if(SLEPC_INC) + message(STATUS "Using SLEPc dir: ${ENV_SLEPC_DIR}") + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + find_path(SLEPC_INC2 "slepcconf.h" PATHS ${ENV_SLEPC_DIR} + PATH_SUFFIXES ${ENV_PETSC_ARCH}/include NO_DEFAULT_PATH) + if(SLEPC_INC2) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC2}) + endif() + endif() + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + # find additional libraries to link with + string(REGEX MATCH "PACKAGES_LIBS = [^\n\r]*" PLIBS ${PETSC_VARIABLES}) + if(PLIBS) + string(REPLACE "PACKAGES_LIBS = " "" PLIBS ${PLIBS}) + string(STRIP ${PLIBS} PLIBS) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS}") + endif() + string(REGEX MATCH "PETSC_EXTERNAL_LIB_BASIC = [^\n\r]*" PLIBS_BASIC ${PETSC_VARIABLES}) + if(PLIBS_BASIC) + string(REPLACE "PETSC_EXTERNAL_LIB_BASIC = " "" PLIBS_BASIC ${PLIBS_BASIC}) + string(STRIP ${PLIBS_BASIC} PLIBS_BASIC) + separate_arguments(PLIBS_BASIC) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS_BASIC}") + endif() + string(REGEX MATCH "PCC_LINKER_LIBS = [^\n\r]*" LLIBS ${PETSC_VARIABLES}) + if(LLIBS) + string(REPLACE "PCC_LINKER_LIBS = " "" LLIBS ${LLIBS}) + string(STRIP ${LLIBS} LLIBS) + list(APPEND EXTERNAL_LIBRARIES "${LLIBS}") + endif() + else() + # new-style PETSc installations (in standard system directories) + find_library(PETSC_LIBS petsc) + find_path(PETSC_INC "petsc.h" PATH_SUFFIXES include/petsc) + if(PETSC_LIBS AND PETSC_INC) + set_config_option(HAVE_PETSC "PETSc") + if(ENABLE_SLEPC) + find_library(SLEPC_LIB slepc) + find_path(SLEPC_INC "slepc.h" PATH_SUFFIXES include/slepc) + if(SLEPC_LIB AND SLEPC_INC) + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${PETSC_INC}) + endif() + endif() + endif() + + if(ENABLE_MUMPS AND HAVE_BLAS AND HAVE_LAPACK) + set(MUMPS_LIBS_REQUIRED smumps dmumps cmumps zmumps mumps_common pord) + if(NOT ENABLE_MPI) + list(APPEND MUMPS_LIBS_REQUIRED mpiseq) + endif() + find_all_libraries(MUMPS_LIBRARIES MUMPS_LIBS_REQUIRED "" "lib") + find_path(SMUMPS_INC "smumps_c.h" PATH_SUFFIXES src include) + find_path(DMUMPS_INC "dmumps_c.h" PATH_SUFFIXES src include) + find_path(CMUMPS_INC "cmumps_c.h" PATH_SUFFIXES src include) + find_path(ZMUMPS_INC "zmumps_c.h" PATH_SUFFIXES src include) + if(MUMPS_LIBRARIES AND SMUMPS_INC AND DMUMPS_INC AND CMUMPS_INC AND ZMUMPS_INC) + set_config_option(HAVE_MUMPS "MUMPS") + list(APPEND EXTERNAL_LIBRARIES ${MUMPS_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${SMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${DMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${CMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${ZMUMPS_INC}) + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND EXTERNAL_LIBRARIES ${GFORTRAN_LIB}) + endif() + if(ENABLE_GMM) # use GMM/MUMPS interface + add_definitions(-DGMM_USES_MUMPS) + endif() + endif() + endif() + + if(ENABLE_GETDP) + find_library(GETDP_LIB GetDP) + find_path(GETDP_INC "GetDP.h" PATH_SUFFIXES getdp) + if(GETDP_LIB AND GETDP_INC) + set_config_option(HAVE_GETDP "GetDP") + list(APPEND EXTERNAL_LIBRARIES ${GETDP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GETDP_INC}) + endif() + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt AND + ENABLE_HXT AND HAVE_METIS) + set_config_option(HAVE_HXT "Hxt") + add_subdirectory(contrib/hxt) + include_directories(BEFORE contrib/hxt) + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/hxt_tetDelaunay.c) + set_config_option(HAVE_HXT3D "Hxt3D") + endif() + if(MSVC) + # Visual C++ does not support C99 - force compilation as C++ code + file(GLOB_RECURSE HXT_SRC contrib/hxt/*.c) + set_compile_flags(HXT_SRC "/TP") + endif() + check_include_file("immintrin.h" HAVE_IMMINTRIN_H) + if(NOT HAVE_IMMINTRIN_H) + add_definitions(-DHAVE_NO_IMMINTRIN_H) + endif() + if(HAVE_PETSC) + add_definitions(-DHXT_HAVE_PETSC) + endif() + if(CMAKE_C_COMPILER MATCHES "pgi") + add_definitions(-DHAVE_NO_OPENMP_SIMD) + endif() +endif() + +if(ENABLE_OCC) + set(OCC_MINIMAL_VERSION "6.9.1") + if(WIN32) + if(HAVE_64BIT_SIZE_T) + set(OCC_SYS_NAME win64) + else() + set(OCC_SYS_NAME win32) + endif() + else() + set(OCC_SYS_NAME ${CMAKE_SYSTEM_NAME}) + endif() + find_path(OCC_INC "Standard_Version.hxx" HINTS ENV CASROOT PATH_SUFFIXES + inc include include/oce opencascade include/opencascade + occt include/occt) + if(OCC_INC) + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAJOR REGEX "#define OCC_VERSION_MAJOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MINOR REGEX "#define OCC_VERSION_MINOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAINT REGEX "#define OCC_VERSION_MAINTENANCE.*") + if(OCC_MAJOR AND OCC_MINOR AND OCC_MAINT) + string(REGEX MATCH "[0-9]+" OCC_MAJOR "${OCC_MAJOR}") + string(REGEX MATCH "[0-9]+" OCC_MINOR "${OCC_MINOR}") + string(REGEX MATCH "[0-9]+" OCC_MAINT "${OCC_MAINT}") + set(OCC_VERSION "${OCC_MAJOR}.${OCC_MINOR}.${OCC_MAINT}") + message(STATUS "Found OpenCASCADE version ${OCC_VERSION} in ${OCC_INC}") + endif() + endif() + if(OCC_VERSION AND OCC_VERSION STRLESS ${OCC_MINIMAL_VERSION}) + message(WARNING "Gmsh requires OpenCASCADE >= ${OCC_MINIMAL_VERSION}. " + "Use CMAKE_PREFIX_PATH or the CASROOT environment variable " + "to explicitely specify the installation path of OpenCASCADE") + elseif(OCC_INC) + set(OCC_LIBS_REQUIRED + # subset of DataExchange + TKSTEP TKSTEP209 TKSTEPAttr TKSTEPBase TKIGES TKXSBase + # ModelingAlgorithms + TKOffset TKFeat TKFillet TKBool TKMesh TKHLR TKBO TKPrim TKShHealing + TKTopAlgo TKGeomAlgo + # ModelingData + TKBRep TKGeomBase TKG3d TKG2d + # FoundationClasses + TKMath TKernel) + if(ENABLE_OCC_TBB) + list(APPEND OCC_LIBS_REQUIRED tbb tbbmalloc) + endif() + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS_REQUIRED) + if(OCC_LIBS) + message(STATUS "OCC libraries specified explicitly: " ${OCC_LIBS}) + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS) + else() + set(OCC_LIBS) + foreach(OCC ${OCC_LIBS_REQUIRED}) + if(ENABLE_OCC_STATIC) + set(LIBNAME lib${OCC}.a) + else() + set(LIBNAME ${OCC}) + endif() + find_library(OCC_LIB ${LIBNAME} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib) + if(OCC_LIB) + list(APPEND OCC_LIBS ${OCC_LIB}) + else() + message(STATUS "OCC lib " ${LIBNAME} " not Found") + endif() + unset(OCC_LIB CACHE) + endforeach() + list(LENGTH OCC_LIBS NUM_OCC_LIBS) + endif() + endif() + + # additional OCC libraries to handle reading of STEP/IGES attributes. Oh my... + if(ENABLE_OCC_CAF) + find_package(Freetype) + if(FREETYPE_FOUND) + set(OCC_CAF_LIBS_REQUIRED + TKXDESTEP TKXDEIGES TKXCAF TKLCAF TKVCAF TKCAF TKV3d TKService TKCDF) + list(LENGTH OCC_CAF_LIBS_REQUIRED NUM_OCC_CAF_LIBS_REQUIRED) + set(OCC_CAF_LIBS) + foreach(OCC ${OCC_CAF_LIBS_REQUIRED}) + find_library(OCC_CAF_LIB ${OCC} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib) + if(OCC_CAF_LIB) + list(APPEND OCC_CAF_LIBS ${OCC_CAF_LIB}) + else() + message(STATUS "OCC CAF lib " ${OCC} " not Found") + endif() + unset(OCC_CAF_LIB CACHE) + endforeach() + list(LENGTH OCC_CAF_LIBS NUM_OCC_CAF_LIBS) + endif() + endif() + + # append OCC CAF libraries first... + if(NUM_OCC_CAF_LIBS EQUAL NUM_OCC_CAF_LIBS_REQUIRED) + set_config_option(HAVE_OCC_CAF "OpenCASCADE-CAF") + list(APPEND EXTERNAL_LIBRARIES ${OCC_CAF_LIBS} ${FREETYPE_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${FREETYPE_INCLUDE_DIRS}) + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "windowscodecs") + list(APPEND EXTERNAL_LIBRARIES "ole32") + endif() + endif() + + # then append OCC libraries + if(NUM_OCC_LIBS EQUAL NUM_OCC_LIBS_REQUIRED) + set_config_option(HAVE_OCC "OpenCASCADE") + list(APPEND EXTERNAL_LIBRARIES ${OCC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${OCC_INC}) + if(HAVE_64BIT_SIZE_T) + add_definitions(-D_OCC64) + endif() + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "winspool") + add_definitions(-DOCC_CONVERT_SIGNALS) + elseif(MSVC) + add_definitions(-DWNT) + endif() + endif() +endif() + +if(ENABLE_ACIS) + find_library(ACIS_LIB SpaACIS PATH_SUFFIXES bin/maci386) + if(ACIS_LIB) + find_path(ACIS_INC "kernapi.hxx" PATH_SUFFIXES include) + if(ACIS_INC) + set_config_option(HAVE_ACIS "Acis") + list(APPEND EXTERNAL_LIBRARIES ${ACIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ACIS_INC}) + endif() + endif() +endif() + +if(ENABLE_ZIPPER) + if(ENABLE_BUILD_IOS) + set_config_option(HAVE_LIBZ "Zlib") + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/zipper AND HAVE_LIBZ) + add_subdirectory(contrib/zipper) + include_directories(contrib/zipper) + set_config_option(HAVE_ZIPPER "Zipper") + endif() +endif() + +if(ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON) + find_package(SWIG REQUIRED) + include(${SWIG_USE_FILE}) + find_package(PythonLibs) + if(SWIG_FOUND AND PYTHONLIBS_FOUND) + message(STATUS "Found SWIG version " ${SWIG_VERSION}) + find_package(PythonInterp) + string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION) + if(SWIG_MAJOR_VERSION EQUAL 1) + message(WARNING "Python bindings require SWIG >= 2: disabling Python") + else() + set_config_option(HAVE_PYTHON "Python") + mark_as_advanced(CLEAR PYTHON_LIBRARY PYTHON_INCLUDE_DIR) + if(ENABLE_NUMPY) + if (NOT NUMPY_INC) + EXEC_PROGRAM (${PYTHON_EXECUTABLE} + ARGS "-c \"import numpy; print(numpy.get_include())\"" + OUTPUT_VARIABLE NUMPY_INC + RETURN_VALUE NUMPY_NOT_FOUND) + endif() + if(NUMPY_INC) + list(APPEND EXTERNAL_INCLUDES ${NUMPY_INC}) + set_config_option(HAVE_NUMPY "Numpy") + endif() + endif() + if(HAVE_PETSC) + if(ENABLE_PETSC4PY) + EXECUTE_PROCESS( + COMMAND ${PYTHON_EXECUTABLE} -c "import petsc4py; print(petsc4py.get_include())" + OUTPUT_VARIABLE PETSC4PY_INC + RESULT_VARIABLE PETSC4PY_NOT_FOUND + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(PETSC4PY_INC) + list(APPEND EXTERNAL_INCLUDES ${PETSC4PY_INC}) + set_config_option(HAVE_PETSC4PY "PETSc4py") + endif() + endif() + endif() + endif() + endif() +endif() + +check_function_exists(vsnprintf HAVE_VSNPRINTF) +if(NOT HAVE_VSNPRINTF AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_VSNPRINTF "NoVsnprintf") +endif() + +check_include_file(sys/socket.h HAVE_SYS_SOCKET_H) +if(HAVE_SYS_SOCKET_H) + set(CMAKE_EXTRA_INCLUDE_FILES sys/socket.h) +endif() +check_type_size(socklen_t SOCKLEN_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT SOCKLEN_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_SOCKLEN_T "NoSocklenT") +endif() + +check_include_file(stdint.h HAVE_STDINT_H) +if(HAVE_STDINT_H) + set(CMAKE_EXTRA_INCLUDE_FILES stdint.h) +else() + set_config_option(HAVE_NO_STDINT_H "NoStdintH") +endif() +check_type_size(intptr_t INTPTR_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT INTPTR_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_INTPTR_T "NoIntptrT") +endif() + +check_include_file(dlfcn.h DLFCN_H) +if(DLFCN_H) + set_config_option(HAVE_DLOPEN "Dlopen") + list(APPEND EXTERNAL_LIBRARIES ${CMAKE_DL_LIBS}) +endif() + +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + check_include_file(linux/joystick.h LINUX_JOYSTICK_H) + if(LINUX_JOYSTICK_H) + set_config_option(HAVE_LINUX_JOYSTICK "LinuxJoystick") + endif() +endif() + +if(WIN32) + add_definitions(-D_USE_MATH_DEFINES) + list(APPEND EXTERNAL_LIBRARIES winmm wsock32 ws2_32 psapi) +endif() + +if(MSVC) + add_definitions(-DNOMINMAX -D_CRT_SECURE_NO_DEPRECATE -D_SCL_SECURE_NO_DEPRECATE) +endif() + +# add C functions API +set(GMSH_SRC ${GMSH_SRC};api/gmshc.cpp) + +# force full warnings to encourage everybody to write clean(er) code +check_cxx_compiler_flag("-Wall" WALL) +if(WALL AND NOT MSVC) + file(GLOB_RECURSE WALL_SRC Common/*.cpp Fltk/*.cpp FunctionSpace/*.cpp + Geo/*.cpp Graphics/*.cpp Mesh/*.cpp Numeric/*.cpp Parser/*.cpp + Plugin/*.cpp Post/*.cpp Solver/*.cpp) + set(WF "-Wall") + check_cxx_compiler_flag("-Wint-to-void-pointer-cast" WCAST) + if(WCAST) + set(WF "${WF} -Wno-int-to-void-pointer-cast") + endif() + check_cxx_compiler_flag("-Wdeprecated-declarations" WDEPREC) + if(WDEPREC) + # FIXME: remove this when we have fixed the deprecated GLU code for OpenGL3 + set(WF "${WF} -Wno-deprecated-declarations") + endif() + check_cxx_compiler_flag("-Wmisleading-indentation" WIND) + if(WIND) + set(WF "${WF} -Wno-misleading-indentation") + endif() + set_compile_flags(WALL_SRC ${WF}) +endif() + +# don't issue warnings for contributed libraries +check_cxx_compiler_flag("-w" NOWARN) +if(NOWARN) + file(GLOB_RECURSE NOWARN_SRC contrib/*.cpp contrib/*.cc contrib/*.cxx contrib/*.c) + set_compile_flags(NOWARN_SRC "-w") +endif() + +# disable compile optimization on some known problematic files +check_cxx_compiler_flag("-O0" NOOPT) +if(NOOPT OR ENABLE_BUILD_IOS) + if(ENABLE_BUILD_IOS) # optimized iOS 10 64 bits screws somewhere in Geo + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Geo/G*.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* Mesh/Background*) + else() + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* contrib/bamg/* Mesh/Background*) + endif() + set_compile_flags(NOOPT_SRC "-O0") +endif() + +# do not use arithmetic contraction in predicates.cpp +# if("${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "/fp:strict") +# elseif(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fno-unsafe-math-optimizations -ffp-contract=off") +# elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fp-model strict") +# endif() + +# enable Revoropt and set compile flags for the corresponding plugin +if(ENABLE_REVOROPT) + find_path(EIGEN3_INC "eigen3/Eigen/Dense") + if(EIGEN3_INC AND HAVE_MESH AND HAVE_PLUGINS AND HAVE_ANN AND HAVE_ALGLIB) + list(APPEND EXTERNAL_INCLUDES ${EIGEN3_INC} contrib/Revoropt/include) + message(STATUS "using contrib/Revoropt") + set_config_option(HAVE_REVOROPT "Revoropt") + add_definitions(-DUSE_ANN) + get_source_file_property(PROP Plugin/CVTRemesh.cpp COMPILE_FLAGS) + if(PROP) + set_source_files_properties(Plugin/CVTRemesh.cpp PROPERTIES + COMPILE_FLAGS "${PROP} -std=c++11") + else() + set_source_files_properties(Plugin/CVTRemesh.cpp PROPERTIES + COMPILE_FLAGS "-std=c++11") + endif() + else() + message(WARNING "Revoropt requires Eigen3, Mesh, Plugins, ANN and ALGLIB") + endif() +endif() + +list(SORT CONFIG_OPTIONS) +set(GMSH_CONFIG_OPTIONS "") +foreach(OPT ${CONFIG_OPTIONS}) + set(GMSH_CONFIG_OPTIONS "${GMSH_CONFIG_OPTIONS} ${OPT}") +endforeach() + +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshConfig.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshVersion.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h) + +# the texi version file is modified in the source directory (not ideal, but +# since git tracks the contents of the file this is acceptable as it will only +# change when the actual version is changed - not for each git hash) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi.in + ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi) + +file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/version.txt + ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION}) + +# process cmake environment variables so we can append them to the -I include +# commands. This is not recommended (we should only use the cache variables) but +# it is very convenient: otherwise we have to remember providing the +# -D... options to cmake for each new build. +set(ENV_CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH}) +set(ENV_CMAKE_INCLUDE_PATH $ENV{CMAKE_INCLUDE_PATH}) +if(UNIX) + if(ENV_CMAKE_PREFIX_PATH) + string(REPLACE ":" ";" ENV_CMAKE_PREFIX_PATH ${ENV_CMAKE_PREFIX_PATH}) + endif() + if(ENV_CMAKE_INCLUDE_PATH) + string(REPLACE ":" ";" ENV_CMAKE_INCLUDE_PATH ${ENV_CMAKE_INCLUDE_PATH}) + endif() +endif() +list(APPEND EXTERNAL_INCLUDES ${CMAKE_INCLUDE_PATH} ${ENV_CMAKE_INCLUDE_PATH}) +list(APPEND EXTERNAL_INCLUDES ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) +foreach(DIR ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/include) +endforeach() + +if(EXTERNAL_INCLUDES) + list(REMOVE_DUPLICATES EXTERNAL_INCLUDES) +endif() + +if(HAVE_FLTK) + set(LINK_LIBRARIES ${FLTK_LIBRARIES} ${EXTERNAL_LIBRARIES} + ${OPENGL_LIBRARIES} ${LAPACK_LIBRARIES}) +elseif(HAVE_OPENGL) + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${OPENGL_LIBRARIES} + ${LAPACK_LIBRARIES}) +else() + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) +endif() + +# try to use static gfortran on static builds (cannot do this on dynamic builds +# as e.g. Debian compiles libgfortran.a without -fPIC: sigh...) +if(NOT ENABLE_BUILD_DYNAMIC AND NOT ENABLE_BUILD_SHARED) + find_library(GFORTRAN_STATIC libgfortran.a) + if(GFORTRAN_STATIC) + set(CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES) + message(STATUS "Using static libgfortran") + foreach(STR ${LINK_LIBRARIES}) + string(REPLACE "-lgfortran" ${GFORTRAN_STATIC} STR2 ${STR}) + list(APPEND LINK_LIBRARIES2 ${STR2}) + endforeach() + set(LINK_LIBRARIES ${LINK_LIBRARIES2}) + endif() +endif() + +# Linux-specific linking +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + if(HAVE_OCC) + find_library(RT_LIB rt) + if(RT_LIB) + list(APPEND LINK_LIBRARIES ${RT_LIB}) + endif() + endif() + if(CMAKE_C_COMPILER_ID MATCHES "GNU" OR CMAKE_C_COMPILER_ID MATCHES "Intel") + add_definitions(-fPIC) + endif() +endif() + +# we could specify include dirs more selectively, but this is simpler +include_directories(Common Fltk Geo Graphics Mesh Solver Numeric Parser + Plugin Post api ${EXTERNAL_INCLUDES} ${CMAKE_CURRENT_BINARY_DIR}/Common) + +# set this for external codes that might include this CMakeList file +set(GMSH_EXTERNAL_INCLUDE_DIRS ${EXTERNAL_INCLUDES} CACHE + STRING "External include directories" FORCE) +set(GMSH_EXTERNAL_LIBRARIES ${LINK_LIBRARIES} CACHE + STRING "External libraries" FORCE) + +# group sources for easier navigation in IDEs +foreach(DIR ${GMSH_DIRS}) + string(REGEX REPLACE "\\+" "\\\\+" DIR ${DIR}) + source_group(${DIR} REGULAR_EXPRESSION ${DIR}/.*) +endforeach() + +# static library target +if(ENABLE_BUILD_LIB) + add_library(lib STATIC ${GMSH_SRC}) + set_target_properties(lib PROPERTIES OUTPUT_NAME gmsh) + if(MSVC) + set_target_properties(lib PROPERTIES DEBUG_POSTFIX d) + if(ENABLE_MSVC_STATIC_RUNTIME) + set_target_properties(lib PROPERTIES LINK_FLAGS_RELEASE "/nodefaultlib:LIBCMT") + endif() + endif() +endif() + +# shared library target +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + add_library(shared SHARED ${GMSH_SRC}) + set_target_properties(shared PROPERTIES OUTPUT_NAME gmsh + VERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION} + SOVERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}) + if(WIN32) + set_target_properties(shared PROPERTIES PREFIX "" IMPORT_PREFIX "" + IMPORT_SUFFIX ".lib" COMPILE_FLAGS "-DGMSH_DLL -DGMSH_DLL_EXPORT") + endif() + target_link_libraries(shared ${LINK_LIBRARIES}) + if(MSVC AND ENABLE_MSVC_STATIC_RUNTIME) + message(STATUS "Note: By enabling ENABLE_MSVC_STATIC_RUNTIME, shared library " + "won't link. In MSVC change /MT to /MD in the shared project properties") + endif() +endif() + +# binary targets +if(HAVE_FLTK) + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh WIN32 Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh WIN32 Common/Main.cpp ${GMSH_SRC}) + endif() + # we could add this to create a minimal app bundle even without install + # if(APPLE AND NOT ENABLE_OS_SPECIFIC_INSTALL) + # set_target_properties(gmsh PROPERTIES MACOSX_BUNDLE ON + # MACOSX_BUNDLE_INFO_PLIST ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_dev.plist) + # endif() +else() + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh Common/Main.cpp ${GMSH_SRC}) + endif() +endif() +target_link_libraries(gmsh ${LINK_LIBRARIES}) + +# Windows specific linker options +if(WIN32 AND NOT MSVC) + set(FLAGS "-Wl,--stack,16777216 -mwindows") + if(HAVE_64BIT_SIZE_T) + set(FLAGS "${FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win64Icon.res") + else() + set(FLAGS "${FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win32Icon.res") + endif() + set_target_properties(gmsh PROPERTIES LINK_FLAGS "${FLAGS} -static") + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + set_target_properties(shared PROPERTIES LINK_FLAGS -static) + endif() + # remove -Wl,-Bdynamic flags + set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) + set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS) +elseif(MSVC) + set_target_properties(gmsh PROPERTIES LINK_FLAGS "/STACK:16777216 /SAFESEH:NO") +endif() + +# android target +if(ENABLE_BUILD_ANDROID) + find_file(CMAKE_TOOLCHAIN_FILE "android.toolchain.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for android without android-cmake") + endif() + add_definitions(-D_GLIBCXX_USE_C99_MATH=1) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + set(CMAKE_BUILD_TYPE Release) + set(LIBRARY_OUTPUT_PATH_ROOT ${CMAKE_CURRENT_BINARY_DIR}) + set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_BINARY_DIR}/libs/) + add_definitions(-DBUILD_ANDROID) + add_definitions(-DPICOJSON_USE_LOCALE=0) + add_library(androidGmsh SHARED ${GMSH_SRC}) + set_target_properties(androidGmsh PROPERTIES OUTPUT_NAME gmsh) + target_link_libraries(androidGmsh ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) + add_custom_command(TARGET androidGmsh POST_BUILD COMMAND + ${CMAKE_STRIP} ${LIBRARY_OUTPUT_PATH}/libgmsh.so) +endif() + +# parser target +find_program(BISON bison) +find_program(FLEX flex) +if(BISON AND FLEX) + add_custom_target(parser + COMMAND ${BISON} -p gmsh_yy --output Gmsh.tab.cpp -d Gmsh.y + COMMAND ${FLEX} -P gmsh_yy -o Gmsh.yy.cpp Gmsh.l + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Parser) +endif() + +if(UNIX) + # cannot use cmake's file search functions here (they would only find files + # existing at configuration time) + add_custom_target(purge + COMMAND rm -f `find . -name *~ -o -name *~~` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + add_custom_target(etags + COMMAND etags `find . -name *.cpp -o -name *.h -o -name *.y` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion + OUTPUT_VARIABLE CXX_COMPILER_VERSION + OUTPUT_STRIP_TRAILING_WHITESPACE) +else() + set(CXX_COMPILER_VERSION "Unknown") +endif() + +set(WELCOME_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/WELCOME.txt) +set(SDK_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/SDK.txt) +set(LICENSE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE.txt) +set(CREDITS_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CREDITS.txt) +set(CHANGELOG_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.txt) +file(GLOB TUTORIAL_GEO_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/?*.*) +file(GLOB TUTORIAL_CPP_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c++/?*.*) +file(GLOB TUTORIAL_C_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c/?*.*) +file(GLOB TUTORIAL_PY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/python/?*.*) +file(GLOB TUTORIAL_JL_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/julia/?*.*) +file(GLOB DEMOS ${CMAKE_CURRENT_SOURCE_DIR}/demos/*) +foreach(SUBDIR ${DEMOS}) + if(IS_DIRECTORY ${SUBDIR}) + list(APPEND DEMOS_DIRS ${SUBDIR}) + endif() +endforeach() +set(TEX_DIR ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo) +file(GLOB TEX_SRC ${TEX_DIR}/*.texi) +set(TEX_OBJ ${TEX_DIR}/gmsh.aux ${TEX_DIR}/gmsh.cp ${TEX_DIR}/gmsh.cps + ${TEX_DIR}/gmsh.fn ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.ky + ${TEX_DIR}/gmsh.log ${TEX_DIR}/gmsh.pdf ${TEX_DIR}/gmsh.pg ${TEX_DIR}/gmsh.toc + ${TEX_DIR}/gmsh.tp ${TEX_DIR}/gmsh.tps ${TEX_DIR}/gmsh.txt ${TEX_DIR}/gmsh.vr) + +macro(unix2dos VARNAME) + file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/unix2dos) + set(UNIX2DOS_FILES) + foreach(FILE ${${VARNAME}}) + file(READ ${FILE} F0) + get_filename_component(N ${FILE} NAME) + if(CYGWIN) + string(REGEX REPLACE "\n" "\r\n" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F1}") + else() # if not in Cygwin, cmake adds '\r's automatically + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F0}") + endif() + list(APPEND UNIX2DOS_FILES ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N}) + endforeach() + set(${VARNAME} ${UNIX2DOS_FILES}) +endmacro() + +if(WIN32) + if(ENABLE_OS_SPECIFIC_INSTALL) + set(GMSH_BIN .) + set(GMSH_LIB .) + set(GMSH_DOC .) + set(GMSH_MAN .) + set(GMSH_INC .) + else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) + endif() + if(CYGWIN) + unix2dos(GMSH_API) + if(ENABLE_PRIVATE_API) + unix2dos(GMSH_PRIVATE_API) + endif() + unix2dos(WELCOME_FILE) + unix2dos(SDK_FILE) + unix2dos(LICENSE_FILE) + unix2dos(CREDITS_FILE) + unix2dos(CHANGELOG_FILE) + unix2dos(TUTORIAL_GEO_FILES) + unix2dos(TUTORIAL_CPP_FILES) + unix2dos(TUTORIAL_C_FILES) + unix2dos(TUTORIAL_PY_FILES) + unix2dos(TUTORIAL_JL_FILES) + foreach(DIR ${DEMOS_DIRS}) + file(GLOB DEMO_FILES ${DIR}/?*.*) + unix2dos(DEMO_FILES) + endforeach() + endif() +elseif(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + # set these so that the files get installed nicely in the MacOSX + # .app bundle + set(GMSH_BIN ../MacOS) + set(GMSH_LIB ../MacOS) + set(GMSH_DOC ../../..) + set(GMSH_MAN ../../..) + set(GMSH_INC ../MacOS) +else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) +endif() + +# FIXME: change this once we understand rpaths +if(APPLE) + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + set_target_properties(shared PROPERTIES INSTALL_NAME_DIR + ${CMAKE_INSTALL_PREFIX}/${GMSH_LIB}) + endif() +endif() + +# mark targets as optional so we can install them separately if needed +# (e.g. "make lib" or "make shared" followed by "make install/fast") +install(TARGETS gmsh DESTINATION ${GMSH_BIN} OPTIONAL) +if(ENABLE_BUILD_LIB) + install(TARGETS lib DESTINATION ${GMSH_LIB} OPTIONAL) +endif() +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(TARGETS shared DESTINATION ${GMSH_LIB} OPTIONAL) +endif() + +if(ENABLE_ONELAB) + install(FILES ${ONELAB_PY} DESTINATION ${GMSH_BIN}) +endif() +if(ENABLE_BUILD_LIB OR ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(FILES ${GMSH_API} DESTINATION ${GMSH_INC}) + install(FILES ${GMSH_PY} DESTINATION ${GMSH_LIB}) + install(FILES ${GMSH_JL} DESTINATION ${GMSH_LIB}) + if(ENABLE_PRIVATE_API) + install(FILES ${GMSH_PRIVATE_API} DESTINATION ${GMSH_INC}/gmsh) + endif() +endif() +if(INSTALL_SDK_README) + configure_file(${SDK_FILE} ${CMAKE_CURRENT_BINARY_DIR}/README.txt) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/README.txt DESTINATION .) +endif() +install(FILES ${WELCOME_FILE} DESTINATION ${GMSH_DOC} RENAME README.txt) +install(FILES ${LICENSE_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CREDITS_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CHANGELOG_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${TUTORIAL_GEO_FILES} DESTINATION ${GMSH_DOC}/tutorial) +install(FILES ${TUTORIAL_CPP_FILES} DESTINATION ${GMSH_DOC}/tutorial/c++) +install(FILES ${TUTORIAL_C_FILES} DESTINATION ${GMSH_DOC}/tutorial/c) +install(FILES ${TUTORIAL_PY_FILES} DESTINATION ${GMSH_DOC}/tutorial/python) +install(FILES ${TUTORIAL_JL_FILES} DESTINATION ${GMSH_DOC}/tutorial/julia) +foreach(DIR ${DEMOS_DIRS}) + get_filename_component(DEMOS_DIR_NAME ${DIR} NAME) + file(GLOB DEMO_FILES ${DIR}/?*.*) + install(FILES ${DEMO_FILES} DESTINATION ${GMSH_DOC}/demos/${DEMOS_DIR_NAME}) +endforeach() +if(UNIX AND NOT CYGWIN) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/doc/gmsh.1 DESTINATION ${GMSH_MAN}) +endif() + +add_custom_target(get_headers + COMMAND ${CMAKE_COMMAND} -E make_directory Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +foreach(FILE ${GMSH_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endforeach() +if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/gmsh/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() +endif() + +find_program(MAKEINFO makeinfo) +if(MAKEINFO) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.info DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --split-size 1000000 + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(info DEPENDS ${TEX_DIR}/gmsh.info) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.txt DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --plaintext -o gmsh.txt + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(txt DEPENDS ${TEX_DIR}/gmsh.txt) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.html DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --html --css-ref=http://gmsh.info/gmsh.css + --no-split --set-customization-variable + EXTRA_HEAD='' + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(html DEPENDS ${TEX_DIR}/gmsh.html) + install(FILES ${TEX_DIR}/gmsh.html DESTINATION ${GMSH_DOC} OPTIONAL) +else() + add_custom_target(html COMMAND ${CMAKE_COMMAND} -E touch ${TEX_DIR}/gmsh.html) +endif() + +find_program(TEXI2PDF texi2pdf) +if(TEXI2PDF) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.pdf DEPENDS ${TEX_SRC} + COMMAND ${TEXI2PDF} ARGS gmsh.texi + WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(pdf DEPENDS ${TEX_DIR}/gmsh.pdf) + install(FILES ${TEX_DIR}/gmsh.pdf DESTINATION ${GMSH_DOC} OPTIONAL) +endif() + +execute_process(COMMAND ${CMAKE_COMMAND} -E echo + "@c This file was generated by cmake: do not edit manually!\n${OPT_TEXI}" + OUTPUT_FILE cmake_options.texi) + +if(MAKEINFO AND TEXI2PDF) + add_custom_target(doc COMMAND ${CMAKE_COMMAND} -E tar zcf + ${CMAKE_CURRENT_BINARY_DIR}/gmsh-${GMSH_VERSION}-doc.tgz + CREDITS.txt LICENSE.txt CHANGELOG.txt + doc/gmsh.1 doc/texinfo/gmsh.html doc/texinfo/gmsh.info + doc/texinfo/gmsh.pdf doc/texinfo/gmsh.txt + COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ} + DEPENDS ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.txt + ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.pdf + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(MAKEINFO OR TEXI2PDF) + add_custom_target(clean_doc COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ}) +endif() + +if(APPLE AND ENABLE_BUILD_LIB) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_framework.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info_framework.plist "${F1}") + get_target_property(LIBNAME lib LOCATION) # depracated + #set(LIBNAME $) # FIXME: use this in the future + add_custom_target(framework DEPENDS lib + COMMAND ${CMAKE_COMMAND} -E remove_directory gmsh.framework + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Headers + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Resources + COMMAND ${CMAKE_COMMAND} -E copy ${LIBNAME} gmsh.framework/gmsh + COMMAND ${CMAKE_COMMAND} -E copy Info_framework.plist + gmsh.framework/Resources/Info.plist + COMMAND ${CMAKE_COMMAND} -E create_symlink . gmsh.framework/Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + foreach(FILE ${GMSH_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + endif() +endif() + +set(CPACK_PACKAGE_VENDOR "Christophe Geuzaine and Jean-Francois Remacle") +set(CPACK_PACKAGE_VERSION_MAJOR ${GMSH_MAJOR_VERSION}) +set(CPACK_PACKAGE_VERSION_MINOR ${GMSH_MINOR_VERSION}) +set(CPACK_PACKAGE_VERSION_PATCH ${GMSH_PATCH_VERSION}) +set(CPACK_PACKAGE_DESCRIPTION_FILE ${WELCOME_FILE}) +set(CPACK_PACKAGE_DESCRIPTION_SUMMARY + "3D finite element mesh generator with built-in CAD engine and post-processor") +if(GMSH_EXTRA_VERSION MATCHES "-git.*") # so that we'll overwrite the archives + set(CPACK_PACKAGE_FILE_NAME gmsh-git-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh-git-source) +else() + set(CPACK_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-source) +endif() +set(CPACK_PACKAGE_INSTALL_DIRECTORY "gmsh") +set(CPACK_RESOURCE_FILE_LICENSE ${LICENSE_FILE}) +set(CPACK_RESOURCE_FILE_README ${WELCOME_FILE}) +set(CPACK_RESOURCE_FILE_WELCOME ${WELCOME_FILE}) +set(CPACK_PACKAGE_EXECUTABLE "gmsh") +if(ENABLE_PACKAGE_STRIP) + set(CPACK_STRIP_FILES TRUE) +else() + set(CPACK_STRIP_FILES FALSE) +endif() +set(CPACK_SOURCE_GENERATOR TGZ) +set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR}" "/CVS/" "/.svn" "/.git" + "~$" "DS_Store$" "GmshConfig.h$" "GmshVersion.h$" "/benchmarks/" "/tmp/" + "/bin/" "/lib/" "/nightly/" "GPATH" "GRTAGS" "GSYMS" "GTAGS" "/HTML/" + "/contrib/3M/" "/contrib/Parasolid/") + +if(UNIX) + # make sure we remove previous installs before doing the next one (on Mac for + # example "make package; make package_source" would lead to huge file lists + # getting generated due to the 'Applications' symlink in the bundle) + set(CPACK_INSTALL_COMMANDS "rm -rf ${CMAKE_CURRENT_BINARY_DIR}/_CPack_Packages") +endif() + +if(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + set(CPACK_GENERATOR Bundle) + set(CPACK_BUNDLE_NAME Gmsh) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_app.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info.plist "${F1}") + set(CPACK_BUNDLE_PLIST ${CMAKE_CURRENT_BINARY_DIR}/Info.plist) + set(CPACK_BUNDLE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) + if(PACKAGER STREQUAL "geuzaine - removed: we sign on a separate machine") + # codesigning requires CMake >= 3.2 + set(CPACK_BUNDLE_APPLE_CERT_APP "Developer ID Application: Christophe Geuzaine") + endif() + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsGeo.icns DESTINATION . + RENAME GmshGeo.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsMsh.icns DESTINATION . + RENAME GmshMsh.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsSol.icns DESTINATION . + RENAME GmshSol.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsPos.icns DESTINATION . + RENAME GmshPos.icns) + set(CPACK_PACKAGE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) +elseif(WIN32) + set(CPACK_GENERATOR ZIP) +else() + set(CPACK_GENERATOR TGZ) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/gmshpy AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON AND HAVE_PYTHON) + add_subdirectory(utils/wrappers/gmshpy) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/java AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_JAVA) + add_subdirectory(utils/wrappers/java) +endif() + +include(CPack) + +if(NOT DISABLE_GMSH_TESTS) + # disabling tests is useful when including this CMakeLists in an external project + include(CTest) + file(GLOB_RECURSE TESTFILES + tutorial/*.geo demos/*.geo benchmarks/?d/*.geo benchmarks/extrude/*.geo + benchmarks/occ/*.geo) + # disable this test for now on our Linux32 machine - the current config + # crashes on the OCC STL generation + if(${GMSH_OS} MATCHES "Linux32") + list(REMOVE_ITEM TESTFILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/t18.geo) + endif() + foreach(TESTFILE ${TESTFILES}) + # use relative path for Cygwin/MinGW (the pure win exe built with the MinGW + # compilers does not understand a full Cygwin-style path) + FILE(RELATIVE_PATH TEST ${CMAKE_CURRENT_BINARY_DIR} ${TESTFILE}) + if(HAVE_OCC OR NOT ${TEST} MATCHES "boolean" OR NOT ${TEST} MATCHES "occ") + add_test(${TEST} ./gmsh ${TEST} -3 -nopopup -o ./tmp.msh) + endif() + endforeach() + # test c++ api tutorials with dynamic builds (except on 32 bit windows for + # now: our win32 setup does not currently handle exceptions) + if(ENABLE_BUILD_DYNAMIC AND NOT ${GMSH_OS} MATCHES "Windows32") + file(GLOB_RECURSE TESTFILES tutorial/c++/*.cpp) + foreach(TESTFILE ${TESTFILES}) + get_filename_component(TEST ${TESTFILE} NAME_WE) + add_executable(${TEST} WIN32 ${TESTFILE}) + target_link_libraries(${TEST} shared) + if(WIN32 AND NOT MSVC) + set_target_properties(${TEST} PROPERTIES LINK_FLAGS "-mwindows -static") + endif() + add_test(${TEST}_cpp ${TEST}) + endforeach() + endif() +endif() + +message(STATUS "") +message(STATUS "Gmsh ${GMSH_VERSION} has been configured for ${GMSH_OS}") +message(STATUS "") +message(STATUS " * Build options:" ${GMSH_CONFIG_OPTIONS}) +message(STATUS " * Build type: " ${CMAKE_BUILD_TYPE}) +message(STATUS " * C compiler: " ${CMAKE_C_COMPILER}) +message(STATUS " * C++ compiler: " ${CMAKE_CXX_COMPILER}) +message(STATUS " * Install prefix: " ${CMAKE_INSTALL_PREFIX}) +message(STATUS "") + +mark_as_advanced(GMSH_EXTRA_VERSION + ACIS_LIB ANN_INC ANN_LIB CAIRO_LIB CAIRO_INC CGNS_INC GMM_INC + GMP_INC GMP_LIB MMG3D_INC MMG3D_LIB HDF5_LIB + MED_LIB OCC_INC SZ_LIB + PETSC_LIBS SLEPC_INC SLEPC_INC2 SLEPC_LIB + BISON FLEX MAKEINFO TEXI2PDF FLTK_CONFIG_SCRIPT + GMSH_EXTERNAL_INCLUDE_DIRS GMSH_EXTERNAL_LIBRARIES) Index: /issm/trunk/externalpackages/gmsh/configs/4.7.0/mac/static/CMakeLists.txt =================================================================== --- /issm/trunk/externalpackages/gmsh/configs/4.7.0/mac/static/CMakeLists.txt (revision 25836) +++ /issm/trunk/externalpackages/gmsh/configs/4.7.0/mac/static/CMakeLists.txt (revision 25836) @@ -0,0 +1,2191 @@ +# Gmsh - Copyright (C) 1997-2020 C. Geuzaine, J.-F. Remacle +# +# See the LICENSE.txt file for license information. Please report all +# issues on https://gitlab.onelab.info/gmsh/gmsh/issues. + +cmake_minimum_required(VERSION 3.1 FATAL_ERROR) + +# if CMAKE_BUILD_TYPE is specified use it; otherwise set the default +# build type to "RelWithDebInfo" ("-O2 -g" with gcc) prior to calling +# project() +if(DEFINED CMAKE_BUILD_TYPE) + set(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Choose build type") +else() + set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose build type") +endif() + +project(gmsh CXX C) + +# require C++11 and request C99 +set(CMAKE_CXX_STANDARD 11) +set(CMAKE_CXX_STANDARD_REQUIRED ON) +set(CMAKE_C_STANDARD 99) + +# this variable controls the default value of the options which are normally set +# to ON (useful if you want to configure a minimal version of Gmsh: e.g. "cmake +# -DDEFAULT=0 -DENABLE_POST=1 -DENABLE_PARSER=1") +set(DEFAULT ON CACHE INTERNAL "Default value for enabled-by-default options") + +macro(opt OPTION HELP VALUE) + option(ENABLE_${OPTION} ${HELP} ${VALUE}) + set(OPT_TEXI "${OPT_TEXI}\n@item ENABLE_${OPTION}\n${HELP} (default: ${VALUE})") +endmacro() + +opt(3M "Enable proprietary 3M extension" OFF) +opt(ALGLIB "Enable ALGLIB (used by some mesh optimizers)" ${DEFAULT}) +opt(ANN "Enable ANN (used for fast point search in mesh/post)" ${DEFAULT}) +opt(BAMG "Enable Bamg 2D anisotropic mesh generator" ${DEFAULT}) +opt(BLAS_LAPACK "Enable BLAS/Lapack for linear algebra (if Eigen if disabled)" OFF) +opt(BLOSSOM "Enable Blossom algorithm (needed for full quad meshing)" ${DEFAULT}) +opt(BUILD_LIB "Enable 'lib' target for building static Gmsh library" OFF) +opt(BUILD_SHARED "Enable 'shared' target for building shared Gmsh library" OFF) +opt(BUILD_DYNAMIC "Enable dynamic Gmsh executable (linked with shared library)" OFF) +opt(BUILD_ANDROID "Enable Android NDK library target (experimental)" OFF) +opt(BUILD_IOS "Enable iOS library target (experimental)" OFF) +opt(CGNS "Enable CGNS import/export (experimental)" ${DEFAULT}) +opt(CGNS_CPEX0045 "Enable high-order CGNS import/export following CPEX0045 (experimental)" OFF) +opt(CAIRO "Enable Cairo to render fonts (experimental)" ${DEFAULT}) +opt(PROFILE "Enable profiling compiler flags" OFF) +opt(DINTEGRATION "Enable discrete integration (needed for levelsets)" ${DEFAULT}) +opt(DOMHEX "Enable experimental DOMHEX code" ${DEFAULT}) +opt(EIGEN "Enable Eigen for linear algebra (instead of Blas/Lapack)" ON) +opt(FLTK "Enable FLTK graphical user interface (requires mesh/post)" ${DEFAULT}) +opt(GETDP "Enable GetDP solver (linked as a library, experimental)" ${DEFAULT}) +opt(GMM "Enable GMM linear solvers (simple alternative to PETSc)" ${DEFAULT}) +opt(GMP "Enable GMP for Kbipack (advanced)" ON) +opt(GRAPHICS "Enable building graphics lib even without GUI (advanced)" OFF) +opt(HXT "Enable HXT library (for reparametrization and meshing)" ${DEFAULT}) +opt(KBIPACK "Enable Kbipack (neeeded by homology solver)" ${DEFAULT}) +opt(MATHEX "Enable Mathex expression parser (used by plugins and options)" ${DEFAULT}) +opt(MED "Enable MED mesh and post file formats" ${DEFAULT}) +opt(MESH "Enable mesh module (required by GUI)" ${DEFAULT}) +opt(METIS "Enable Metis mesh partitioner" ${DEFAULT}) +opt(MMG "Enable Mmg mesh adaptation interface" ${DEFAULT}) +opt(MPEG_ENCODE "Enable built-in MPEG movie encoder" ${DEFAULT}) +opt(MPI "Enable MPI (experimental, not used for meshing)" OFF) +opt(MSVC_STATIC_RUNTIME "Enable static Visual C++ runtime" OFF) +opt(MUMPS "Enable MUMPS sparse direct linear solver" OFF) +opt(NETGEN "Enable Netgen 3D frontal mesh generator" ${DEFAULT}) +opt(NUMPY "Enable fullMatrix and numpy array conversion for private API" OFF) +opt(PETSC4PY "Enable petsc4py wrappers for petsc matrices for private API" OFF) +opt(OCC "Enable OpenCASCADE CAD kernel" ${DEFAULT}) +opt(OCC_CAF "Enable OpenCASCADE CAF module (for STEP/IGES attributes)" ${DEFAULT}) +opt(OCC_STATIC "Link OpenCASCADE static instead of dynamic libraries (requires ENABLE_OCC)" OFF) +opt(OCC_TBB "Add TBB libraries in list of OCC libraries" OFF) +opt(ONELAB "Enable ONELAB solver interface" ${DEFAULT}) +opt(ONELAB_METAMODEL "Enable ONELAB metamodels (experimental)" ${DEFAULT}) +opt(OPENACC "Enable OpenACC" OFF) +opt(OPENMP "Enable OpenMP" OFF) +opt(OPTHOM "Enable high-order mesh optimization tools" ${DEFAULT}) +opt(OS_SPECIFIC_INSTALL "Enable OS-specific (e.g. app bundle) installation" OFF) +opt(OSMESA "Enable OSMesa for offscreen rendering (experimental)" OFF) +opt(P4EST "Enable p4est for enabling automatic mesh size field (experimental)" OFF) +opt(PACKAGE_STRIP "Strip symbols in install packages to reduce install size" ON) +opt(PARSER "Enable GEO file parser (required for .geo/.pos scripts)" ${DEFAULT}) +opt(PETSC "Enable PETSc linear solvers (required for SLEPc)" OFF) +opt(PLUGINS "Enable post-processing plugins" ${DEFAULT}) +opt(POST "Enable post-processing module (required by GUI)" ${DEFAULT}) +opt(POPPLER "Enable Poppler for displaying PDF documents (experimental)" OFF) +opt(PRIVATE_API "Enable private API" OFF) +opt(PRO "Enable PRO extensions" ${DEFAULT}) +opt(QUADTRI "Enable QuadTri structured meshing extensions" ${DEFAULT}) +opt(REVOROPT "Enable Revoropt (used for CVT remeshing)" OFF) +opt(RPATH "Use RPATH in dynamically linked targets" ON) +opt(SLEPC "Enable SLEPc eigensolvers" OFF) +opt(SOLVER "Enable built-in finite element solvers (required for reparametrization)" ${DEFAULT}) +opt(SYSTEM_CONTRIB "Use system versions of contrib libraries, when possible" OFF) +opt(TCMALLOC "Enable libtcmalloc (fast malloc that does not release memory)" OFF) +opt(TOUCHBAR "Enable Apple Touch bar" ${DEFAULT}) +opt(VISUDEV "Enable additional visualization capabilities for development purposes" OFF) +opt(VOROPP "Enable voro++ (for hex meshing, experimental)" ${DEFAULT}) +opt(WRAP_JAVA "Generate SWIG Java wrappers for private API" OFF) +opt(WRAP_PYTHON "Generate SWIG Python wrappers for private API (not used by public API)" OFF) +opt(ZIPPER "Enable Zip file compression/decompression" OFF) + +set(GMSH_MAJOR_VERSION 4) +set(GMSH_MINOR_VERSION 7) +set(GMSH_PATCH_VERSION 0) +if(NOT GMSH_EXTRA_VERSION) + set(GMSH_EXTRA_VERSION "") +endif() +set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION}") +set(GMSH_EXTRA_VERSION_ORIG ${GMSH_EXTRA_VERSION}) + +if(NOT GMSH_RELEASE) + find_package(Git) + if(GIT_FOUND) + execute_process(COMMAND ${GIT_EXECUTABLE} log -1 --format=%h + WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} ERROR_QUIET + OUTPUT_VARIABLE GIT_COMMIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE) + endif() + if(GIT_COMMIT_HASH) + set(GMSH_EXTRA_VERSION "${GMSH_EXTRA_VERSION}-git-${GIT_COMMIT_HASH}") + endif() + set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION_TEXI} (development version)") +endif() + +set(GMSH_SHORT_VERSION + "${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION}") +set(GMSH_VERSION "${GMSH_SHORT_VERSION}${GMSH_EXTRA_VERSION}") +set(GMSH_SHORT_LICENSE "GNU General Public License") + +set(GMSH_GITLAB_PREFIX "https://gitlab.onelab.info/gmsh/gmsh") +if(GMSH_RELEASE) + set(GMSH_GITLAB_PREFIX "${GMSH_GITLAB_PREFIX}/blob/gmsh_${GMSH_SHORT_VERSION}") +else() + set(GMSH_GITLAB_PREFIX "${GMSH_GITLAB_PREFIX}/blob/master") +endif() + +set(GMSH_API api/gmsh.h api/gmshc.h api/gmsh.h_cwrap) + +if(ENABLE_PRIVATE_API) + message(WARNING "The private API is unsupported and undocumented. It is meant " + "for expert Gmsh developers, not for regular Gmsh users, who should rely " + "on the stable public API (gmsh/api) instead.") + file(GLOB_RECURSE HEADERS Common/*.h Numeric/*.h Geo/*.h Mesh/*.h Solver/*.h + Post/*.h Plugin/*.h Graphics/*.h contrib/kbipack/*.h + contrib/DiscreteIntegration/*.h contrib/HighOrderMeshOptimizer/*.h + contrib/MeshOptimizer/*.h contrib/MeshQualityOptimizer/*.h) + set(GMSH_PRIVATE_API ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h ${HEADERS}) + get_property(IAMCHILD DIRECTORY PROPERTY PARENT_DIRECTORY) + if(IAMCHILD) + set(GMSH_PRIVATE_API ${GMSH_PRIVATE_API} PARENT_SCOPE) + endif() + if(ENABLE_WRAP_PYTHON OR ENABLE_WRAP_JAVA) + set(ENABLE_BUILD_DYNAMIC ON) + message(WARNING "SWIG wrappers for the private API are unsupported and " + "undocumented. The stable public Python API does not required SWIG.") + endif() +endif() + +set(ONELAB_PY contrib/onelab/python/onelab.py) +set(GMSH_PY api/gmsh.py) +set(GMSH_JL api/gmsh.jl) + +if(${CMAKE_MAJOR_VERSION} GREATER 2) + string(TIMESTAMP DATE "%Y%m%d") +else() + execute_process(COMMAND date "+%Y%m%d" OUTPUT_VARIABLE DATE + OUTPUT_STRIP_TRAILING_WHITESPACE) +endif() + +if(NOT DATE) + set(DATE "unknown") +endif() +set(GMSH_DATE "${DATE}") + +if(NOT GMSH_HOST) + execute_process(COMMAND hostname OUTPUT_VARIABLE HOST + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT HOST) + set(HOST "unknown") + endif() + set(GMSH_HOST "${HOST}") +endif() + +if(NOT GMSH_PACKAGER) + execute_process(COMMAND whoami OUTPUT_VARIABLE PACKAGER + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT PACKAGER) + set(PACKAGER "unknown") + endif() + string(REPLACE "\\" " " PACKAGER ${PACKAGER}) + set(GMSH_PACKAGER "${PACKAGER}") +endif() + +if(APPLE) + set(GMSH_OS "MacOSX") +elseif(CYGWIN OR MSYS) + # detect if we use the MinGW compilers on Cygwin - if we do, handle the build + # as a pure Windows build and make cmake find pure Windows import libraries + # (.lib) + if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpmachine + OUTPUT_VARIABLE CXX_COMPILER_MACHINE + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(CXX_COMPILER_MACHINE MATCHES "mingw") + set(GMSH_OS "Windows") + set(WIN32 1) + add_definitions(-DWIN32) + set(CMAKE_FIND_LIBRARY_PREFIXES "lib" "") + set(CMAKE_FIND_LIBRARY_SUFFIXES ".a" ".so" ".lib" ".LIB" ".dll" ".DLL" ".dll.a") + endif() + endif() +else() + set(GMSH_OS "${CMAKE_SYSTEM_NAME}") +endif() + +include(CheckTypeSize) +include(CheckFunctionExists) +include(CheckIncludeFile) +include(CheckCXXCompilerFlag) +include(CheckCCompilerFlag) + +macro(set_config_option VARNAME STRING) + set(${VARNAME} TRUE) + list(APPEND CONFIG_OPTIONS ${STRING}) + message(STATUS "Found " ${STRING}) +endmacro() + +# check the size of size_t +check_type_size("size_t" SIZEOF_SIZE_T) +if(SIZEOF_SIZE_T EQUAL 8) + set_config_option(HAVE_64BIT_SIZE_T "64Bit") +endif() + +# append 32/64 to the build name on Linux and Windows +if(NOT APPLE) + if(HAVE_64BIT_SIZE_T) + set(GMSH_OS "${GMSH_OS}64") + else() + set(GMSH_OS "${GMSH_OS}32") + endif() +endif() + +if(ENABLE_BUILD_DYNAMIC) + set(GMSH_OS "${GMSH_OS}-sdk") +endif() + +if(ENABLE_RPATH) + set(CMAKE_MACOSX_RPATH 1) + + # make sure that dynamic libraries can be found when installing/ displacing + # the binaries: from https://gitlab.kitware.com/cmake/community/wikis/doc/ + # cmake/RPATH-handling: + + # use, i.e. don't skip the full RPATH for the build tree + set(CMAKE_SKIP_BUILD_RPATH FALSE) + + # when building, don't use the install RPATH already (but later on when + # installing) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") + + # add the automatically determined parts of the RPATH which point to + # directories outside the build tree to the install RPATH + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + + # the RPATH to be used when installing, but only if it's not a system directory + list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" + isSystemDir) + if("${isSystemDir}" STREQUAL "-1") + if(APPLE) + set(CMAKE_INSTALL_RPATH "@executable_path/../lib") + else() + set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../lib") + endif() + endif() +else() + set(CMAKE_MACOSX_RPATH 0) + set(CMAKE_SKIP_BUILD_RPATH TRUE) +endif() + +if(MSVC) + # remove annoying warning about bool/int cast performance + set(GMSH_CONFIG_PRAGMAS "#pragma warning(disable:4800 4244 4267)") + foreach(VAR + CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE + CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO + CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE + CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO) + if(ENABLE_MSVC_STATIC_RUNTIME AND ${VAR} MATCHES "/MD") + string(REGEX REPLACE "/MD" "/MT" ${VAR} "${${VAR}}") + endif() + if(NOT ${VAR} MATCHES "/MP") # enable parallel compilation + set(${VAR} "${${VAR}} /MP") + endif() + endforeach() + if(ENABLE_PRIVATE_API) + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + # automatically export .def file with all symbols (requires CMake 3.4); + # depending on the compiling options this might lead to more than 64k export + # symbols; just trim the .def file to keep the ones you need + set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + endif() + endif() +endif() + +# reduce memory usage of GCC on 32 bit systems +if(NOT HAVE_64BIT_SIZE_T AND CMAKE_CXX_COMPILER_ID MATCHES "GNU") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} --param ggc-min-expand=1 --param ggc-min-heapsize=512000") +endif() + +if(ENABLE_OPENMP) + find_package(OpenMP) + if(OpenMP_FOUND OR OPENMP_FOUND) + set_config_option(HAVE_OPENMP "OpenMP") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + elseif(APPLE AND EXISTS "/opt/local/lib/libomp") + # official Apple compiler with macports' libomp + set_config_option(HAVE_OPENMP "OpenMP[MacPorts]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + list(APPEND EXTERNAL_LIBRARIES "-L/opt/local/lib/libomp -lomp") + elseif(APPLE AND EXISTS "/usr/local/lib/libomp.dylib") + # official Apple compiler with homebrew's libomp + set_config_option(HAVE_OPENMP "OpenMP[Homebrew]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp") + list(APPEND EXTERNAL_LIBRARIES "-L/usr/local/lib -lomp") + endif() +endif() + +if(ENABLE_OPENACC) + find_package(OpenACC) + if(OpenACC_C_FOUND AND OpenACC_CXX_FOUND) + set_config_option(HAVE_OPENACC "OpenACC") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenACC_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenACC_CXX_FLAGS}") + endif() +endif() + +if(ENABLE_PROFILE) + # Using the perf set of profiling tools doesn't work without the frame + # pointer and a common optimisation is to remove it + check_cxx_compiler_flag("-fno-omit-frame-pointer" FNOFP) + if(FNOFP) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer") + endif() +endif() + +macro(append_gmsh_src DIRNAME FILES) + foreach(FILE ${FILES}) + list(APPEND LIST ${DIRNAME}/${FILE}) + endforeach() + set(GMSH_SRC ${GMSH_SRC};${LIST} PARENT_SCOPE) + set(GMSH_DIRS ${GMSH_DIRS};${DIRNAME} PARENT_SCOPE) +endmacro() + +macro(find_all_libraries VARNAME LISTNAME PATH SUFFIX) + set(${VARNAME}) + list(LENGTH ${LISTNAME} NUM_LIST) + foreach(LIB ${${LISTNAME}}) + if("${PATH}" STREQUAL "") + find_library(FOUND_LIB ${LIB} PATH_SUFFIXES ${SUFFIX}) + else() + find_library(FOUND_LIB ${LIB} PATHS ${PATH} NO_DEFAULT_PATH) + endif() + if(FOUND_LIB) + list(APPEND ${VARNAME} ${FOUND_LIB}) + endif() + unset(FOUND_LIB CACHE) + endforeach() + list(LENGTH ${VARNAME} NUM_FOUND_LIBRARIES) + if(NUM_FOUND_LIBRARIES LESS NUM_LIST) + set(${VARNAME}) + endif() +endmacro() + +macro(set_compile_flags LISTNAME FLAGS) + foreach(FILE ${${LISTNAME}}) + get_source_file_property(PROP ${FILE} COMPILE_FLAGS) + if(PROP) + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${PROP} ${FLAGS}") + else() + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${FLAGS}") + endif() + endforeach() +endmacro() + +if(ENABLE_EIGEN) + if(ENABLE_SYSTEM_CONTRIB) + find_path(EIGEN_INC "Eigen/Dense" HINTS eigen3) + if(EIGEN_INC) + include_directories(${EIGEN_INC}) + set_config_option(HAVE_EIGEN "Eigen[system]") + endif() + endif() + if(NOT HAVE_EIGEN) + include_directories(contrib/eigen) + set_config_option(HAVE_EIGEN "Eigen") + endif() + # We could also add an option to use BLAS with Eigen + # add_definitions(-DEIGEN_USE_BLAS) +elseif(ENABLE_BLAS_LAPACK) + if(BLAS_LAPACK_LIBRARIES) + # use libs as specified in the BLAS_LAPACK_LIBRARIES variable + set_config_option(HAVE_BLAS "Blas[custom]") + set_config_option(HAVE_LAPACK "Lapack[custom]") + set(LAPACK_LIBRARIES ${BLAS_LAPACK_LIBRARIES}) + else() + if(MSVC) + # on Windows with Visual C++ try really hard to find blas/lapack *without* + # requiring a Fortran compiler: 1) try to find the Intel MKL libs using + # the standard search path; if not found 2) try to get the reference + # blas/lapack libs (useful for users with no Fortran compiler and no MKL + # license, who can just download our precompiled "gmsh-dep" package) + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH em64t/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_lp64 mkl_intel_thread mkl_core) + else() + set(MKL_PATH ia32/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_c mkl_intel_thread mkl_core) + endif() + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + set(REFLAPACK_LIBS_REQUIRED lapack blas g2c gcc) + find_all_libraries(LAPACK_LIBRARIES REFLAPACK_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[ref]") + set_config_option(HAVE_LAPACK "Lapack[ref]") + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + # on Linux try to find the Intel MKL without a Fortran compiler + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH lib/em64t) + else() + set(MKL_PATH lib/32) + endif() + set(MKL_LIBS_REQUIRED mkl_gf_lp64 iomp5 mkl_gnu_thread mkl_core guide pthread) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(NOT LAPACK_LIBRARIES) + # match lapack 9.0 on 64bit + set(MKL_LIBS_REQUIRED mkl_lapack mkl_em64t guide) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + endif() + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + # on Linux also try to find ATLAS without a Fortran compiler, because + # cmake ships with a buggy FindBLAS e.g. on Ubuntu Lucid Lynx + set(ATLAS_LIBS_REQUIRED lapack f77blas cblas atlas) + find_all_libraries(LAPACK_LIBRARIES ATLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[atlas]") + set_config_option(HAVE_LAPACK "Lapack[atlas]") + else() + # try with generic names + set(GENERIC_LIBS_REQUIRED lapack blas pthread) + find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[generic]") + set_config_option(HAVE_LAPACK "Lapack[generic]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "SunOS") + # on SunOS we know blas and lapack are available in sunperf + set(LAPACK_LIBRARIES -library=sunperf) + set_config_option(HAVE_BLAS "Blas[sunperf]") + set_config_option(HAVE_LAPACK "Lapack[sunperf]") + elseif(APPLE) + # on Mac we also know that blas and lapack are available + set(LAPACK_LIBRARIES "-llapack -lblas") + set_config_option(HAVE_BLAS "Blas[veclib]") + set_config_option(HAVE_LAPACK "Lapack[veclib]") + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we haven't found blas and lapack check for OpenBlas + set(OPENBLAS_LIBS_REQUIRED openblas) + find_all_libraries(LAPACK_LIBRARIES OPENBLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[openblas]") + set_config_option(HAVE_LAPACK "Lapack[openblas]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we still haven't found blas and lapack, use the standard cmake tests, + # which require a working Fortran compiler + enable_language(Fortran) + find_package(BLAS) + if(BLAS_FOUND) + set_config_option(HAVE_BLAS "Blas") + find_package(LAPACK) + if(LAPACK_FOUND) + set_config_option(HAVE_LAPACK "Lapack") + else() + set(LAPACK_LIBRARIES ${BLAS_LIBRARIES}) + endif() + if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU") + if(CMAKE_Fortran_COMPILER MATCHES "gfortran") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "f95") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "g77") + list(APPEND LAPACK_LIBRARIES g2c) + endif() + elseif(CMAKE_Fortran_COMPILER MATCHES "pgi") + list(APPEND LAPACK_LIBRARIES -pgf77libs) + endif() + endif() + endif() + endif() +endif() + +if(ENABLE_TCMALLOC) + find_library(TCMALLOC tcmalloc) + if(TCMALLOC) + set_config_option(HAVE_TCMALLOC "TCMalloc") + list(APPEND EXTERNAL_LIBRARIES ${TCMALLOC}) + endif() +endif() + +add_subdirectory(Common) +add_subdirectory(Numeric) +add_subdirectory(Geo) + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh AND ENABLE_MESH) + add_subdirectory(Mesh) + set_config_option(HAVE_MESH "Mesh") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Solver AND ENABLE_SOLVER) + add_subdirectory(Solver) + set_config_option(HAVE_SOLVER "Solver") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Post AND ENABLE_POST) + add_subdirectory(Post) + set_config_option(HAVE_POST "Post") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Plugin AND ENABLE_PLUGINS) + add_subdirectory(Plugin) + set_config_option(HAVE_PLUGINS "Plugins") + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Parser AND ENABLE_PARSER) + add_subdirectory(Parser) + set_config_option(HAVE_PARSER "Parser") +endif() + +if(ENABLE_VISUDEV) + set_config_option(HAVE_VISUDEV "VisuDev") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Fltk AND ENABLE_FLTK) + # first, try to use fltk-config for fltk >= 1.3 (FindFLTK is buggy on Unix, + # where e.g. xft and xinerama options are not dealt with) + find_program(FLTK_CONFIG_SCRIPT fltk-config) + if(FLTK_CONFIG_SCRIPT) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --api-version + OUTPUT_VARIABLE FLTK_VERSION) + string(STRIP "${FLTK_VERSION}" FLTK_VERSION) + if(FLTK_VERSION VERSION_GREATER 1.1) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + message(STATUS "Using fltk-config script for Fltk " ${FLTK_VERSION}) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --includedir + OUTPUT_VARIABLE FLTK_INCLUDE_DIR) + string(STRIP ${FLTK_INCLUDE_DIR} FLTK_INCLUDE_DIR) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # On linux (at least OpenSuSE) the following directories are + # not existing (everything is in /usr/include). To avoid warnings + # check existance of these directories before adding them + if(EXISTS ${FLTK_INCLUDE_DIR}/FL/images) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/FL/images) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/jpeg) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/jpeg) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/zlib) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/zlib) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/png) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/png) + endif() + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --ldflags + OUTPUT_VARIABLE FLTK_LIBRARIES) + string(STRIP ${FLTK_LIBRARIES} FLTK_LIBRARIES) + string(REGEX MATCH "fltk[_ ]jpeg" FLTK_JPEG ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]z" FLTK_Z ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]png" FLTK_PNG ${FLTK_LIBRARIES}) + endif() + endif() + # then try the built-in FindFLTK module + if(NOT HAVE_FLTK) + set(FLTK_SKIP_FORMS TRUE) + set(FLTK_SKIP_FLUID TRUE) + find_package(FLTK) + if(FLTK_FOUND) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # find fltk jpeg + find_library(FLTK_JPEG NAMES fltk_jpeg fltkjpeg) + if(FLTK_JPEG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_JPEG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/jpeg) + endforeach() + endif() + # find fltk zlib + find_library(FLTK_Z NAMES fltk_z fltkz) + if(FLTK_Z) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_Z}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/zlib) + endforeach() + endif() + # find fltk png + find_library(FLTK_PNG NAMES fltk_png fltkpng) + if(FLTK_PNG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_PNG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/png) + endforeach() + endif() + endif() + endif() + # workaround for Fedora/Suse messing up fltk-config (see issue #417) + if(HAVE_FLTK AND ${CMAKE_SYSTEM_NAME} MATCHES "Linux") + string(REGEX MATCH "X11" FLTK_X11 ${FLTK_LIBRARIES}) + if(NOT FLTK_X11) + find_package(X11) + if(X11_FOUND) + list(APPEND EXTERNAL_INCLUDES ${X11_INCLUDE_DIR}) + list(APPEND EXTERNAL_LIBRARIES ${X11_LIBRARIES}) + endif() + endif() + endif() +endif() + +if(APPLE AND HAVE_FLTK AND ENABLE_TOUCHBAR) + STRING(REGEX MATCH "([0-9]+.[0-9]+)" OSX_SDK_VERSION "${CMAKE_OSX_SYSROOT}") + if(OSX_SDK_VERSION) + if(${OSX_SDK_VERSION} VERSION_GREATER 10.11) + set(GMSH_SRC ${GMSH_SRC};Fltk/touchBar.mm) + set_config_option(HAVE_TOUCHBAR "TouchBar") + endif() + endif() +endif() + +if(ENABLE_ONELAB) + set_config_option(HAVE_ONELAB "ONELAB") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/onelab) + if(ENABLE_ONELAB_METAMODEL) + add_subdirectory(contrib/onelab) + include_directories(contrib/onelab) + set_config_option(HAVE_ONELAB_METAMODEL "ONELABMetamodel") + endif() + file(COPY ${ONELAB_PY} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + endif() +endif() + +if(ENABLE_BUILD_IOS) + find_file(CMAKE_TOOLCHAIN_FILE "ios.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for iOS without a toolchain") + endif() + add_definitions(-DBUILD_IOS) +endif() + +if(HAVE_FLTK OR ENABLE_GRAPHICS) + if(NOT HAVE_MESH OR NOT HAVE_POST OR NOT HAVE_PLUGINS OR NOT HAVE_ONELAB) + message(SEND_ERROR "Cannot compile GUI without Mesh, Post, Plugin and ONELAB") + endif() + + if(FLTK_JPEG) + set_config_option(HAVE_LIBJPEG "Jpeg[fltk]") + else() + find_package(JPEG) + if(JPEG_FOUND) + set_config_option(HAVE_LIBJPEG "Jpeg") + list(APPEND EXTERNAL_LIBRARIES ${JPEG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${JPEG_INCLUDE_DIR}) + endif() + endif() + + if(FLTK_Z) + set_config_option(HAVE_LIBZ "Zlib[fltk]") + else() + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + + if(HAVE_LIBZ) + if(FLTK_PNG) + set_config_option(HAVE_LIBPNG "Png[fltk]") + else() + find_package(PNG) + if(PNG_FOUND) + set_config_option(HAVE_LIBPNG "Png") + list(APPEND EXTERNAL_LIBRARIES ${PNG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${PNG_INCLUDE_DIR}) + endif() + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/mpeg_encode AND + ENABLE_MPEG_ENCODE) + add_subdirectory(contrib/mpeg_encode) + include_directories(contrib/mpeg_encode/headers) + set_config_option(HAVE_MPEG_ENCODE "Mpeg") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/3M AND ENABLE_3M) + add_subdirectory(contrib/3M) + include_directories(contrib/3M) + set_config_option(HAVE_3M "3M") + endif() + + if(ENABLE_OSMESA) + find_library(OSMESA_LIB OSMesa) + if(OSMESA_LIB) + set_config_option(HAVE_OSMESA "OSMesa") + list(APPEND EXTERNAL_LIBRARIES ${OSMESA_LIB}) + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Graphics) + set(OpenGL_GL_PREFERENCE "LEGACY") + find_package(OpenGL REQUIRED) + if(OPENGL_GLU_FOUND AND OPENGL_FOUND) + add_subdirectory(Graphics) + set_config_option(HAVE_OPENGL "OpenGL") + else() + message(SEND_ERROR "Could not find GLU: disabling OpenGL support") + endif() + endif() +endif() + +if(ENABLE_ANN) + find_library(ANN_LIB ANN PATH_SUFFIXES lib) + find_path(ANN_INC "ANN.h" PATH_SUFFIXES src include ANN) + if(ENABLE_SYSTEM_CONTRIB AND ANN_LIB AND ANN_INC) + message(STATUS "Using system version of ANN") + list(APPEND EXTERNAL_LIBRARIES ${ANN_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ANN_INC}) + set_config_option(HAVE_ANN "ANN[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ANN) + add_subdirectory(contrib/ANN) + include_directories(contrib/ANN/include) + set_config_option(HAVE_ANN "ANN") + endif() +endif() + +if(ENABLE_ALGLIB) + find_library(ALGLIB_LIB alglib) + find_path(ALGLIB_INC "stdafx.h" PATH_SUFFIXES libalglib) + if(ENABLE_SYSTEM_CONTRIB AND ALGLIB_LIB AND ALGLIB_INC) + list(APPEND EXTERNAL_LIBRARIES ${ALGLIB_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ALGLIB_INC}) + set_config_option(HAVE_ALGLIB "ALGLIB[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ALGLIB) + add_subdirectory(contrib/ALGLIB) + include_directories(contrib/ALGLIB) + set_config_option(HAVE_ALGLIB "ALGLIB") + endif() +endif() + +if(HAVE_FLTK AND ENABLE_CAIRO) + find_library(CAIRO_LIB cairo) + find_path(CAIRO_INC "cairo/cairo.h" PATH_SUFFIXES include) + if(CAIRO_INC AND CAIRO_LIB) + set_config_option(HAVE_CAIRO "Cairo") + list(APPEND EXTERNAL_LIBRARIES ${CAIRO_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CAIRO_INC}) + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/DiscreteIntegration AND + ENABLE_DINTEGRATION) + add_subdirectory(contrib/DiscreteIntegration) + include_directories(contrib/DiscreteIntegration) + set_config_option(HAVE_DINTEGRATION "DIntegration") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/HighOrderMeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshQualityOptimizer AND + ENABLE_OPTHOM AND HAVE_MESH) + add_subdirectory(contrib/HighOrderMeshOptimizer) + include_directories(contrib/HighOrderMeshOptimizer) + add_subdirectory(contrib/MeshOptimizer) + include_directories(contrib/MeshOptimizer) + include_directories(${CMAKE_CURRENT_BINARY_DIR}/contrib/MeshOptimizer) + add_subdirectory(contrib/MeshQualityOptimizer) + include_directories(contrib/MeshQualityOptimizer) + set_config_option(HAVE_OPTHOM "OptHom") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/domhex AND + ENABLE_DOMHEX AND HAVE_MESH) + add_subdirectory(contrib/domhex) + include_directories(contrib/domhex) + set_config_option(HAVE_DOMHEX "DomHex") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/QuadTri AND + ENABLE_QUADTRI AND HAVE_MESH) + add_subdirectory(contrib/QuadTri) + include_directories(contrib/QuadTri) + set_config_option(HAVE_QUADTRI "QuadTri") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/kbipack AND ENABLE_KBIPACK) + set_config_option(HAVE_KBIPACK "Kbipack") + add_subdirectory(contrib/kbipack) + include_directories(contrib/kbipack) + if(ENABLE_GMP) + find_library(GMP_LIB libgmp.a) + find_path(GMP_INC "gmp.h" PATH_SUFFIXES src include) + endif() + if(GMP_LIB AND GMP_INC) + set_config_option(HAVE_GMP "GMP") + list(APPEND EXTERNAL_LIBRARIES ${GMP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GMP_INC}) + else() + message(STATUS "GMP not found: Kbipack uses long int") + endif() +endif() + +if(ENABLE_MATHEX) + find_library(MATHEX_LIB mathex PATH_SUFFIXES lib) + find_path(MATHEX_INC "mathex.h" PATH_SUFFIXES src include) + if(ENABLE_SYSTEM_CONTRIB AND MATHEX_LIB AND MATHEX_INC) + list(APPEND EXTERNAL_LIBRARIES ${MATHEX_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MATHEX_INC}) + set_config_option(HAVE_MATHEX "MathEx[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MathEx) + add_subdirectory(contrib/MathEx) + include_directories(contrib/MathEx) + set_config_option(HAVE_MATHEX "MathEx") + endif() +endif() + +if(ENABLE_MPI) + find_package(MPI) + if(MPI_FOUND) + set_config_option(HAVE_MPI "MPI") + list(APPEND EXTERNAL_INCLUDES ${MPI_CXX_INCLUDE_PATH}) + list(APPEND EXTERNAL_LIBRARIES ${MPI_CXX_LIBRARIES}) + set(CMAKE_C_COMPILER ${MPI_C_COMPILER}) + set(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER}) + set(CMAKE_Fortran_COMPILER ${MPI_Fortran_COMPILER}) + endif() +endif() + +if(ENABLE_POPPLER) + find_library(POPPLER_LIB poppler) + find_library(POPPLER_CPP_LIB poppler-cpp) + find_path(POPPLER_INC "poppler/cpp/poppler-document.h" PATH_SUFFIXES src include) + if(POPPLER_LIB AND POPPLER_INC) + set_config_option(HAVE_POPPLER "Poppler") + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_LIB}) + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_CPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${POPPLER_INC}) + endif() +endif() + +if(ENABLE_P4EST) + find_library(P4EST_LIB p4est) + find_path(P4EST_INC "p4est.h" PATH_SUFFIXES src) + find_library(SC_LIB sc) + if(P4EST_LIB AND P4EST_INC AND SC_LIB) + set_config_option(HAVE_P4EST "P4est") + list(APPEND EXTERNAL_LIBRARIES ${P4EST_LIB} ${SC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${P4EST_INC}) + endif() +endif() + +if(HAVE_MESH OR HAVE_SOLVER) + if(ENABLE_METIS) + if(METIS_LIB AND METIS_INC) + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis") + else() + find_library(METIS_LIB metis PATH_SUFFIXES lib) + find_path(METIS_INC "metis.h" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC) + message(STATUS "Using system version of METIS") + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/metis) + add_definitions(-DUSE_GKREGEX) + add_subdirectory(contrib/metis) + include_directories(contrib/metis/include contrib/metis/libmetis + contrib/metis/GKlib) + set_config_option(HAVE_METIS "Metis") + endif() + endif() + endif() +endif() + +if(HAVE_MESH) + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh/tetgenBR.cxx) + set_config_option(HAVE_TETGENBR "TetGen/BR") + endif() + + if(ENABLE_VOROPP) + find_library(VOROPP_LIB voro++) + find_path(VOROPP_INC "voro++.hh" PATH_SUFFIXES voro++) + if(ENABLE_SYSTEM_CONTRIB AND VOROPP_LIB AND VOROPP_INC) + message(STATUS "Using system version of voro++") + list(APPEND EXTERNAL_LIBRARIES ${VOROPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${VOROPP_INC}) + set_config_option(HAVE_VOROPP "Voro++[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++) + add_subdirectory(contrib/voro++) + include_directories(contrib/voro++/src) + set_config_option(HAVE_VOROPP "Voro++") + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/blossom AND ENABLE_BLOSSOM) + add_subdirectory(contrib/blossom) + include_directories(contrib/blossom/MATCH contrib/blossom/concorde97 + contrib/blossom/concorde97/INCLUDE) + set_config_option(HAVE_BLOSSOM "Blossom") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/Netgen AND ENABLE_NETGEN) + add_subdirectory(contrib/Netgen) + include_directories(contrib/Netgen contrib/Netgen/libsrc/include + contrib/Netgen/nglib) + set_config_option(HAVE_NETGEN "Netgen") + add_definitions(-DNO_PARALLEL_THREADS -DNOTCL) + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/bamg AND ENABLE_BAMG) + add_subdirectory(contrib/bamg) + include_directories(contrib/bamg contrib/bamg/bamglib) + set_config_option(HAVE_BAMG "Bamg") + endif() + + if(ENABLE_MMG) + find_library(MMG_LIB NAMES Mmg mmg) + find_path(MMG_INC "libmmg.h" PATH_SUFFIXES mmg) + if(MMG_LIB AND MMG_INC) + list(APPEND EXTERNAL_LIBRARIES ${MMG_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MMG_INC}) + set_config_option(HAVE_MMG "Mmg") + endif() + endif() +endif() + +if(ENABLE_MED OR ENABLE_CGNS) + find_package(HDF5) + if(HDF5_FOUND) + set(HDF5_LIB "${HDF5_C_LIBRARIES}") + list(APPEND EXTERNAL_INCLUDES ${HDF5_INCLUDE_DIRS}) + if(ENABLE_MED) + find_library(MED_LIB medC) + if(MED_LIB) + set_config_option(HAVE_MED "Med") + list(APPEND EXTERNAL_LIBRARIES ${MED_LIB}) + endif() + endif() + if(ENABLE_CGNS) + find_library(CGNS_LIB cgns HINTS ENV CGNS_ROOT PATH_SUFFIXES lib) + find_path(CGNS_INC "cgnslib.h" HINTS ENV CGNS_ROOT PATH_SUFFIXES include) + if(CGNS_LIB AND CGNS_INC) + set_config_option(HAVE_LIBCGNS "Cgns") + list(APPEND EXTERNAL_LIBRARIES ${CGNS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CGNS_INC}) + if(ENABLE_CGNS_CPEX0045) + set_config_option(HAVE_LIBCGNS_CPEX0045 "Cgns_CPEX0045") + endif() + endif() + endif() + if(MED_LIB OR CGNS_LIB) + list(APPEND EXTERNAL_LIBRARIES ${HDF5_LIB}) + find_library(SZ_LIB NAMES szlib sz) + if(SZ_LIB) + list(APPEND EXTERNAL_LIBRARIES ${SZ_LIB}) + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + endif() + endif() + endif() + else() + message(STATUS "HDF5 not found") + endif() +endif() + +if(HAVE_SOLVER) + if(ENABLE_GMM) + find_path(GMM_INC "gmm.h" PATH_SUFFIXES src include include/gmm) + if(ENABLE_SYSTEM_CONTRIB AND GMM_INC) + message(STATUS "Using system version of GMM") + list(APPEND EXTERNAL_INCLUDES ${GMM_INC}) + set_config_option(HAVE_GMM "Gmm[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/gmm) + include_directories(contrib/gmm) + set_config_option(HAVE_GMM "Gmm") + endif() + endif() + + if(ENABLE_PETSC) + if(PETSC_DIR) + set(ENV_PETSC_DIR ${PETSC_DIR}) + else() + set(ENV_PETSC_DIR $ENV{PETSC_DIR}) + endif() + if(PETSC_ARCH) + set(ENV_PETSC_ARCH ${PETSC_ARCH}) + else() + set(ENV_PETSC_ARCH $ENV{PETSC_ARCH}) + endif() + set(PETSC_POSSIBLE_CONF_FILES + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc-conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc/conf/petscvariables) + foreach(FILE ${PETSC_POSSIBLE_CONF_FILES}) + if(EXISTS ${FILE}) + # old-style PETSc installations (using PETSC_DIR and PETSC_ARCH) + message(STATUS "Using PETSc dir: ${ENV_PETSC_DIR}") + message(STATUS "Using PETSc arch: ${ENV_PETSC_ARCH}") + # find includes by parsing the petscvariables file + file(STRINGS ${FILE} PETSC_VARIABLES NEWLINE_CONSUME) + endif() + endforeach() + if(PETSC_VARIABLES) + # try to find PETSC_CC_INCLUDES for PETSc >= 3.4 + string(REGEX MATCH "PETSC_CC_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "PETSC_CC_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + else() + # try to find PETSC_PACKAGES_INCLUDES in older versions + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/include) + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/include) + string(REGEX MATCH "PACKAGES_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + string(REPLACE "PACKAGES_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + endif() + if(PETSC_PACKAGES_INCLUDES) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "-I" "" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + string(REPLACE " " ";" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + foreach(VAR ${PETSC_PACKAGES_INCLUDES}) + # seem to include unexisting directories (/usr/include/lib64) + # check to avoid warnings + if(EXISTS ${VAR}) + list(APPEND EXTERNAL_INCLUDES ${VAR}) + endif() + endforeach() + endif() + endif() + # find libraries (<= 3.0) + set(PETSC_LIBS_REQUIRED petscksp petscdm petscmat petscvec petsc) + find_all_libraries(PETSC_LIBS PETSC_LIBS_REQUIRED + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib "") + # petsc 3.1 creates only one library (libpetsc) + if(NOT PETSC_LIBS) + find_library(PETSC_LIBS petsc PATHS ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + endif() + if(PETSC_LIBS) + set_config_option(HAVE_PETSC "PETSc") + if(NOT HAVE_BLAS) + set_config_option(HAVE_BLAS "Blas[petsc]") + endif() + if(NOT HAVE_LAPACK) + set_config_option(HAVE_LAPACK "Lapack[petsc]") + endif() + endif() + # find slepc (needs to be linked in before petsc) + if(ENABLE_SLEPC) + if(SLEPC_DIR) + set(ENV_SLEPC_DIR ${SLEPC_DIR}) + else() + set(ENV_SLEPC_DIR $ENV{SLEPC_DIR}) + endif() + find_library(SLEPC_LIB slepc PATHS ${ENV_SLEPC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + if(SLEPC_LIB) + find_path(SLEPC_INC "slepc.h" PATHS ${ENV_SLEPC_DIR} PATH_SUFFIXES include + ${ENV_PETSC_ARCH}/include include/slepc NO_DEFAULT_PATH) + if(SLEPC_INC) + message(STATUS "Using SLEPc dir: ${ENV_SLEPC_DIR}") + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + find_path(SLEPC_INC2 "slepcconf.h" PATHS ${ENV_SLEPC_DIR} + PATH_SUFFIXES ${ENV_PETSC_ARCH}/include NO_DEFAULT_PATH) + if(SLEPC_INC2) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC2}) + endif() + endif() + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + # find additional libraries to link with + string(REGEX MATCH "PACKAGES_LIBS = [^\n\r]*" PLIBS ${PETSC_VARIABLES}) + if(PLIBS) + string(REPLACE "PACKAGES_LIBS = " "" PLIBS ${PLIBS}) + string(STRIP ${PLIBS} PLIBS) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS}") + endif() + string(REGEX MATCH "PETSC_EXTERNAL_LIB_BASIC = [^\n\r]*" PLIBS_BASIC ${PETSC_VARIABLES}) + if(PLIBS_BASIC) + string(REPLACE "PETSC_EXTERNAL_LIB_BASIC = " "" PLIBS_BASIC ${PLIBS_BASIC}) + string(STRIP ${PLIBS_BASIC} PLIBS_BASIC) + separate_arguments(PLIBS_BASIC) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS_BASIC}") + endif() + string(REGEX MATCH "PCC_LINKER_LIBS = [^\n\r]*" LLIBS ${PETSC_VARIABLES}) + if(LLIBS) + string(REPLACE "PCC_LINKER_LIBS = " "" LLIBS ${LLIBS}) + string(STRIP ${LLIBS} LLIBS) + list(APPEND EXTERNAL_LIBRARIES "${LLIBS}") + endif() + else() + # new-style PETSc installations (in standard system directories) + find_library(PETSC_LIBS petsc) + find_path(PETSC_INC "petsc.h" PATH_SUFFIXES include/petsc) + if(PETSC_LIBS AND PETSC_INC) + set_config_option(HAVE_PETSC "PETSc") + if(ENABLE_SLEPC) + find_library(SLEPC_LIB slepc) + find_path(SLEPC_INC "slepc.h" PATH_SUFFIXES include/slepc) + if(SLEPC_LIB AND SLEPC_INC) + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${PETSC_INC}) + endif() + endif() + endif() + + if(ENABLE_MUMPS AND HAVE_BLAS AND HAVE_LAPACK) + set(MUMPS_LIBS_REQUIRED smumps dmumps cmumps zmumps mumps_common pord) + if(NOT ENABLE_MPI) + list(APPEND MUMPS_LIBS_REQUIRED mpiseq) + endif() + find_all_libraries(MUMPS_LIBRARIES MUMPS_LIBS_REQUIRED "" "lib") + find_path(SMUMPS_INC "smumps_c.h" PATH_SUFFIXES src include) + find_path(DMUMPS_INC "dmumps_c.h" PATH_SUFFIXES src include) + find_path(CMUMPS_INC "cmumps_c.h" PATH_SUFFIXES src include) + find_path(ZMUMPS_INC "zmumps_c.h" PATH_SUFFIXES src include) + if(MUMPS_LIBRARIES AND SMUMPS_INC AND DMUMPS_INC AND CMUMPS_INC AND ZMUMPS_INC) + set_config_option(HAVE_MUMPS "MUMPS") + list(APPEND EXTERNAL_LIBRARIES ${MUMPS_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${SMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${DMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${CMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${ZMUMPS_INC}) + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND EXTERNAL_LIBRARIES ${GFORTRAN_LIB}) + endif() + if(ENABLE_GMM) # use GMM/MUMPS interface + add_definitions(-DGMM_USES_MUMPS) + endif() + endif() + endif() + + if(ENABLE_GETDP) + find_library(GETDP_LIB GetDP) + find_path(GETDP_INC "GetDP.h" PATH_SUFFIXES getdp) + if(GETDP_LIB AND GETDP_INC) + set_config_option(HAVE_GETDP "GetDP") + list(APPEND EXTERNAL_LIBRARIES ${GETDP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GETDP_INC}) + endif() + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt AND ENABLE_HXT) + add_subdirectory(contrib/hxt) + include_directories(BEFORE ${HXT_INC_DIRS}) + set_config_option(HAVE_HXT "Hxt") + # do not use arithmetic contraction in predicates.c + if(MSVC OR (CMAKE_C_COMPILER_ID STREQUAL "Intel" AND WIN32)) + set_source_files_properties( + "${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/predicates/src/predicates.c" + PROPERTIES COMPILE_FLAGS "/fp:strict") + elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel") + set_source_files_properties( + "${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/predicates/src/predicates.c" + PROPERTIES COMPILE_FLAGS "-fp-model strict") + elseif(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang") + set_source_files_properties( + "${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/predicates/src/predicates.c" + PROPERTIES COMPILE_FLAGS "-fno-unsafe-math-optimizations -ffp-contract=off") + else() + message(WARNING + "Unsupported compiler ! + Make sure compiled functions from predicates.c + do NOT use extended double precision and follow IEEE754 standard. + It is crucial for the robustness of geometric predicates.") + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/pro AND ENABLE_PRO) + add_subdirectory(pro) +endif() + +if(ENABLE_OCC) + set(OCC_MINIMAL_VERSION "6.9.1") + if(WIN32) + if(HAVE_64BIT_SIZE_T) + set(OCC_SYS_NAME win64) + else() + set(OCC_SYS_NAME win32) + endif() + else() + set(OCC_SYS_NAME ${CMAKE_SYSTEM_NAME}) + endif() + find_path(OCC_INC "Standard_Version.hxx" HINTS ENV CASROOT PATH_SUFFIXES + inc include include/oce opencascade include/opencascade + occt include/occt) + if(OCC_INC) + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAJOR REGEX "#define OCC_VERSION_MAJOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MINOR REGEX "#define OCC_VERSION_MINOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAINT REGEX "#define OCC_VERSION_MAINTENANCE.*") + if(OCC_MAJOR AND OCC_MINOR AND OCC_MAINT) + string(REGEX MATCH "[0-9]+" OCC_MAJOR "${OCC_MAJOR}") + string(REGEX MATCH "[0-9]+" OCC_MINOR "${OCC_MINOR}") + string(REGEX MATCH "[0-9]+" OCC_MAINT "${OCC_MAINT}") + set(OCC_VERSION "${OCC_MAJOR}.${OCC_MINOR}.${OCC_MAINT}") + message(STATUS "Found OpenCASCADE version ${OCC_VERSION} in ${OCC_INC}") + endif() + endif() + if(OCC_VERSION AND OCC_VERSION STRLESS ${OCC_MINIMAL_VERSION}) + message(WARNING "Gmsh requires OpenCASCADE >= ${OCC_MINIMAL_VERSION}. " + "Use CMAKE_PREFIX_PATH or the CASROOT environment variable " + "to explicitely specify the installation path of OpenCASCADE") + elseif(OCC_INC) + set(OCC_LIBS_REQUIRED + # subset of DataExchange + TKSTEP TKSTEP209 TKSTEPAttr TKSTEPBase TKIGES TKXSBase + # ModelingAlgorithms + TKOffset TKFeat TKFillet TKBool TKMesh TKHLR TKBO TKPrim TKShHealing + TKTopAlgo TKGeomAlgo + # ModelingData + TKBRep TKGeomBase TKG3d TKG2d + # FoundationClasses + TKMath TKernel) + if(ENABLE_OCC_TBB) + list(APPEND OCC_LIBS_REQUIRED tbb tbbmalloc) + endif() + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS_REQUIRED) + if(OCC_LIBS) + message(STATUS "OCC libraries specified explicitly: " ${OCC_LIBS}) + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS) + else() + set(OCC_LIBS) + foreach(OCC ${OCC_LIBS_REQUIRED}) + find_library(OCC_LIB ${OCC} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib + ${OCC_SYS_NAME}/gcc/lib ${OCC_SYS_NAME}/gcc/bin) + if(OCC_LIB) + list(APPEND OCC_LIBS ${OCC_LIB}) + else() + message(STATUS "OCC lib " ${OCC} " not Found") + endif() + unset(OCC_LIB CACHE) + endforeach() + list(LENGTH OCC_LIBS NUM_OCC_LIBS) + endif() + endif() + + # additional OCC libraries to handle reading of STEP/IGES attributes. Oh my... + if(ENABLE_OCC_CAF) + find_package(Freetype) + if(FREETYPE_FOUND) + set(OCC_CAF_LIBS_REQUIRED + TKXDESTEP TKXDEIGES TKXCAF TKLCAF TKVCAF TKCAF TKV3d TKService TKCDF) + list(LENGTH OCC_CAF_LIBS_REQUIRED NUM_OCC_CAF_LIBS_REQUIRED) + set(OCC_CAF_LIBS) + foreach(OCC ${OCC_CAF_LIBS_REQUIRED}) + find_library(OCC_CAF_LIB ${OCC} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib + ${OCC_SYS_NAME}/gcc/lib ${OCC_SYS_NAME}/gcc/bin) + if(OCC_CAF_LIB) + list(APPEND OCC_CAF_LIBS ${OCC_CAF_LIB}) + else() + message(STATUS "OCC CAF lib " ${OCC} " not Found") + endif() + unset(OCC_CAF_LIB CACHE) + endforeach() + list(LENGTH OCC_CAF_LIBS NUM_OCC_CAF_LIBS) + endif() + endif() + + if(NUM_OCC_LIBS EQUAL NUM_OCC_LIBS_REQUIRED) + # append OCC CAF libraries first... + if(NUM_OCC_CAF_LIBS EQUAL NUM_OCC_CAF_LIBS_REQUIRED) + set_config_option(HAVE_OCC_CAF "OpenCASCADE-CAF") + list(APPEND EXTERNAL_LIBRARIES ${OCC_CAF_LIBS} ${FREETYPE_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${FREETYPE_INCLUDE_DIRS}) + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "windowscodecs") + list(APPEND EXTERNAL_LIBRARIES "ole32") + endif() + endif() + # then append OCC libraries + set_config_option(HAVE_OCC "OpenCASCADE") + list(APPEND EXTERNAL_LIBRARIES ${OCC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${OCC_INC}) + if(HAVE_64BIT_SIZE_T) + add_definitions(-D_OCC64) + endif() + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "winspool") + add_definitions(-DOCC_CONVERT_SIGNALS) + elseif(MSVC) + add_definitions(-DWNT) + endif() + endif() +endif() + +if(ENABLE_ZIPPER) + if(ENABLE_BUILD_IOS) + set_config_option(HAVE_LIBZ "Zlib") + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/zipper AND HAVE_LIBZ) + add_subdirectory(contrib/zipper) + include_directories(contrib/zipper) + set_config_option(HAVE_ZIPPER "Zipper") + endif() +endif() + +if(ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON) + find_package(SWIG REQUIRED) + include(${SWIG_USE_FILE}) + find_package(PythonLibs) + if(SWIG_FOUND AND PYTHONLIBS_FOUND) + message(STATUS "Found SWIG version " ${SWIG_VERSION}) + find_package(PythonInterp) + string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION) + if(SWIG_MAJOR_VERSION EQUAL 1) + message(WARNING "Python bindings require SWIG >= 2: disabling Python") + else() + set_config_option(HAVE_PYTHON "Python") + mark_as_advanced(CLEAR PYTHON_LIBRARY PYTHON_INCLUDE_DIR) + if(ENABLE_NUMPY) + if (NOT NUMPY_INC) + EXEC_PROGRAM (${PYTHON_EXECUTABLE} + ARGS "-c \"import numpy; print(numpy.get_include())\"" + OUTPUT_VARIABLE NUMPY_INC + RETURN_VALUE NUMPY_NOT_FOUND) + endif() + if(NUMPY_INC) + list(APPEND EXTERNAL_INCLUDES ${NUMPY_INC}) + set_config_option(HAVE_NUMPY "Numpy") + endif() + endif() + if(HAVE_PETSC) + if(ENABLE_PETSC4PY) + EXECUTE_PROCESS( + COMMAND ${PYTHON_EXECUTABLE} -c "import petsc4py; print(petsc4py.get_include())" + OUTPUT_VARIABLE PETSC4PY_INC + RESULT_VARIABLE PETSC4PY_NOT_FOUND + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(PETSC4PY_INC) + list(APPEND EXTERNAL_INCLUDES ${PETSC4PY_INC}) + set_config_option(HAVE_PETSC4PY "PETSc4py") + endif() + endif() + endif() + endif() + endif() +endif() + +check_function_exists(vsnprintf HAVE_VSNPRINTF) +if(NOT HAVE_VSNPRINTF AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_VSNPRINTF "NoVsnprintf") +endif() + +check_include_file(sys/socket.h HAVE_SYS_SOCKET_H) +if(HAVE_SYS_SOCKET_H) + set(CMAKE_EXTRA_INCLUDE_FILES sys/socket.h) +endif() +check_type_size(socklen_t SOCKLEN_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT SOCKLEN_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_SOCKLEN_T "NoSocklenT") +endif() + +check_include_file(stdint.h HAVE_STDINT_H) +if(HAVE_STDINT_H) + set(CMAKE_EXTRA_INCLUDE_FILES stdint.h) +else() + set_config_option(HAVE_NO_STDINT_H "NoStdintH") +endif() +check_type_size(intptr_t INTPTR_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT INTPTR_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_INTPTR_T "NoIntptrT") +endif() + +check_include_file(dlfcn.h DLFCN_H) +if(DLFCN_H) + set_config_option(HAVE_DLOPEN "Dlopen") + list(APPEND EXTERNAL_LIBRARIES ${CMAKE_DL_LIBS}) +endif() + +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + check_include_file(linux/joystick.h LINUX_JOYSTICK_H) + if(LINUX_JOYSTICK_H) + set_config_option(HAVE_LINUX_JOYSTICK "LinuxJoystick") + endif() +endif() + +if(WIN32) + add_definitions(-D_USE_MATH_DEFINES) + list(APPEND EXTERNAL_LIBRARIES winmm wsock32 ws2_32 psapi) +endif() + +if(MSVC) + add_definitions(-DNOMINMAX -D_CRT_SECURE_NO_DEPRECATE -D_SCL_SECURE_NO_DEPRECATE) +endif() + +# add C functions API +set(GMSH_SRC ${GMSH_SRC};api/gmshc.cpp) + +# force full warnings to encourage everybody to write clean(er) code +check_cxx_compiler_flag("-Wall" WALL) +if(WALL AND NOT MSVC) + file(GLOB_RECURSE WALL_SRC Common/*.cpp Fltk/*.cpp FunctionSpace/*.cpp + Geo/*.cpp Graphics/*.cpp Mesh/*.cpp Numeric/*.cpp Parser/*.cpp + Plugin/*.cpp Post/*.cpp Solver/*.cpp) + set(WF "-Wall") + check_cxx_compiler_flag("-Wint-to-void-pointer-cast" WCAST) + if(WCAST) + set(WF "${WF} -Wno-int-to-void-pointer-cast") + endif() + check_cxx_compiler_flag("-Wdeprecated-declarations" WDEPREC) + if(WDEPREC) + # FIXME: remove this when we have fixed the deprecated GLU code for OpenGL3 + set(WF "${WF} -Wno-deprecated-declarations") + endif() + check_cxx_compiler_flag("-Wmisleading-indentation" WIND) + if(WIND) + set(WF "${WF} -Wno-misleading-indentation") + endif() + check_cxx_compiler_flag("-Wno-attributes" WATTR) + if(WATTR) + # FIXME: remove this when GCC behaves more intelligently + set(WF "${WF} -Wno-attributes") + endif() + set_compile_flags(WALL_SRC ${WF}) +endif() + +# don't issue warnings for contributed libraries +check_cxx_compiler_flag("-w" NOWARN) +if(NOWARN) + file(GLOB_RECURSE NOWARN_SRC contrib/*.cpp contrib/*.cc contrib/*.cxx contrib/*.c) + set_compile_flags(NOWARN_SRC "-w") +endif() + +# disable compile optimization on some known problematic files +check_cxx_compiler_flag("-O0" NOOPT) +if(NOOPT OR ENABLE_BUILD_IOS) + if(ENABLE_BUILD_IOS) # optimized iOS 10 64 bits screws somewhere in Geo + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Geo/G*.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* Mesh/Background*) + else() + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* contrib/bamg/* Mesh/Background*) + endif() + set_compile_flags(NOOPT_SRC "-O0") +endif() + +# do not use arithmetic contraction in predicates.cpp +# if("${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "/fp:strict") +# elseif(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fno-unsafe-math-optimizations -ffp-contract=off") +# elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fp-model strict") +# endif() + +# enable Revoropt and set compile flags for the corresponding plugin +if(ENABLE_REVOROPT) + if(HAVE_EIGEN AND HAVE_MESH AND HAVE_PLUGINS AND HAVE_ANN AND HAVE_ALGLIB) + list(APPEND EXTERNAL_INCLUDES contrib/Revoropt/include) + set_config_option(HAVE_REVOROPT "Revoropt") + add_definitions(-DUSE_ANN) + else() + message(WARNING "Revoropt requires Eigen, Mesh, Plugins, ANN and ALGLIB") + endif() +endif() + +if(HAVE_MESH AND NOT HAVE_EIGEN AND NOT HAVE_LAPACK) + message(WARNING "Most meshing algorithms will not be functional without " + "Eigen or Lapack") +endif() + +list(SORT CONFIG_OPTIONS) +set(GMSH_CONFIG_OPTIONS "") +foreach(OPT ${CONFIG_OPTIONS}) + set(GMSH_CONFIG_OPTIONS "${GMSH_CONFIG_OPTIONS} ${OPT}") +endforeach() + +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshConfig.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshVersion.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h) + +# the texi and pypi version files are modified in the source directory (not +# ideal for version.texi, but since git tracks the contents of the file this is +# acceptable as it will only change when the actual version is changed - not for +# each git hash; setup.py is not under version control) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi.in + ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh/setup.py.in + ${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh/setup.py) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh-dev/setup.py.in + ${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh-dev/setup.py) + +file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/version.txt ${GMSH_SHORT_VERSION}) + +# process cmake environment variables so we can append them to the -I include +# commands. This is not recommended (we should only use the cache variables) but +# it is very convenient: otherwise we have to remember providing the +# -D... options to cmake for each new build. +set(ENV_CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH}) +set(ENV_CMAKE_INCLUDE_PATH $ENV{CMAKE_INCLUDE_PATH}) +if(UNIX) + if(ENV_CMAKE_PREFIX_PATH) + string(REPLACE ":" ";" ENV_CMAKE_PREFIX_PATH ${ENV_CMAKE_PREFIX_PATH}) + endif() + if(ENV_CMAKE_INCLUDE_PATH) + string(REPLACE ":" ";" ENV_CMAKE_INCLUDE_PATH ${ENV_CMAKE_INCLUDE_PATH}) + endif() +endif() +list(APPEND EXTERNAL_INCLUDES ${CMAKE_INCLUDE_PATH} ${ENV_CMAKE_INCLUDE_PATH}) +list(APPEND EXTERNAL_INCLUDES ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) +foreach(DIR ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/include) +endforeach() + +if(EXTERNAL_INCLUDES) + list(REMOVE_DUPLICATES EXTERNAL_INCLUDES) +endif() + +if(HAVE_FLTK) + set(LINK_LIBRARIES ${FLTK_LIBRARIES} ${EXTERNAL_LIBRARIES} + ${OPENGL_LIBRARIES} ${LAPACK_LIBRARIES}) +elseif(HAVE_OPENGL) + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${OPENGL_LIBRARIES} + ${LAPACK_LIBRARIES}) +else() + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) +endif() + +# try to use static gfortran on static builds (cannot do this on dynamic builds +# as e.g. Debian compiles libgfortran.a without -fPIC: sigh...) +if(NOT ENABLE_BUILD_DYNAMIC AND NOT ENABLE_BUILD_SHARED) + find_library(GFORTRAN_STATIC libgfortran.a) + if(GFORTRAN_STATIC) + set(CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES) + message(STATUS "Using static libgfortran") + foreach(STR ${LINK_LIBRARIES}) + string(REPLACE "-lgfortran" ${GFORTRAN_STATIC} STR2 ${STR}) + list(APPEND LINK_LIBRARIES2 ${STR2}) + endforeach() + set(LINK_LIBRARIES ${LINK_LIBRARIES2}) + endif() +endif() + +# Linux-specific linker options +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + if(HAVE_OCC) + find_library(RT_LIB rt) + if(RT_LIB) + list(APPEND LINK_LIBRARIES ${RT_LIB}) + endif() + endif() + if(CMAKE_C_COMPILER_ID MATCHES "GNU" OR CMAKE_C_COMPILER_ID MATCHES "Intel") + add_definitions(-fPIC) + endif() +endif() + +# we could specify include dirs more selectively, but this is simpler +include_directories(Common Fltk Geo Graphics Mesh Solver Numeric Parser + Plugin Post api ${EXTERNAL_INCLUDES} ${CMAKE_CURRENT_BINARY_DIR}/Common) + +# set this for external codes that might include this CMakeList file +set(GMSH_EXTERNAL_INCLUDE_DIRS ${EXTERNAL_INCLUDES} CACHE + STRING "External include directories" FORCE) +set(GMSH_EXTERNAL_LIBRARIES ${LINK_LIBRARIES} CACHE + STRING "External libraries" FORCE) + +# group sources for easier navigation in IDEs +foreach(DIR ${GMSH_DIRS}) + string(REGEX REPLACE "\\+" "\\\\+" DIR ${DIR}) + source_group(${DIR} REGULAR_EXPRESSION ${DIR}/.*) +endforeach() + +# static library target +if(ENABLE_BUILD_LIB) + add_library(lib STATIC ${GMSH_SRC}) + set_target_properties(lib PROPERTIES OUTPUT_NAME gmsh) + if(MSVC) + set_target_properties(lib PROPERTIES DEBUG_POSTFIX d) + if(ENABLE_MSVC_STATIC_RUNTIME) + set_target_properties(lib PROPERTIES LINK_FLAGS_RELEASE "/nodefaultlib:LIBCMT") + endif() + endif() +endif() + +# shared library target +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + add_library(shared SHARED ${GMSH_SRC}) + set_target_properties(shared PROPERTIES OUTPUT_NAME gmsh + VERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION} + SOVERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}) + if(WIN32) + set_target_properties(shared PROPERTIES PREFIX "" IMPORT_PREFIX "" + IMPORT_SUFFIX ".lib" COMPILE_FLAGS "-DGMSH_DLL -DGMSH_DLL_EXPORT") + endif() + target_link_libraries(shared ${LINK_LIBRARIES}) + # don't define LC_RPATH in dylib for development, to not get endless warnings + # about code signing + if(APPLE AND NOT GMSH_RELEASE) + set_target_properties(shared PROPERTIES INSTALL_RPATH "") + endif() + if(MSVC AND ENABLE_MSVC_STATIC_RUNTIME) + message(STATUS "Note: By enabling ENABLE_MSVC_STATIC_RUNTIME, shared library " + "won't link. In MSVC change /MT to /MD in the shared project properties") + endif() +endif() + +# binary targets +if(HAVE_FLTK) + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh WIN32 Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh WIN32 Common/Main.cpp ${GMSH_SRC}) + endif() + # we could add this to create a minimal app bundle even without install + # if(APPLE AND NOT ENABLE_OS_SPECIFIC_INSTALL) + # set_target_properties(gmsh PROPERTIES MACOSX_BUNDLE ON + # MACOSX_BUNDLE_INFO_PLIST ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_dev.plist) + # endif() +else() + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh Common/Main.cpp ${GMSH_SRC}) + endif() +endif() +target_link_libraries(gmsh ${LINK_LIBRARIES}) + +# Windows specific linker options +if(WIN32 AND NOT MSVC) + set(FLAGS "-Wl,--stack,16777216 -static -municode") + if(HAVE_FLTK) + set(FLAGS "${FLAGS} -mwindows") + else() + set(FLAGS "${FLAGS} -mconsole") + endif() + if(HAVE_64BIT_SIZE_T) + set(FLAGS "${FLAGS} \"${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win64Icon.res\"") + else() + set(FLAGS "${FLAGS} \"${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win32Icon.res\"") + endif() + set_target_properties(gmsh PROPERTIES LINK_FLAGS "${FLAGS}") + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + set_target_properties(shared PROPERTIES LINK_FLAGS -static) + endif() + # remove -Wl,-Bdynamic flags + set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) + set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS) +elseif(MSVC) + set_target_properties(gmsh PROPERTIES LINK_FLAGS "/STACK:16777216 /SAFESEH:NO") +endif() + +# android target +if(ENABLE_BUILD_ANDROID) + find_file(CMAKE_TOOLCHAIN_FILE "android.toolchain.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for android without android-cmake") + endif() + add_definitions(-D_GLIBCXX_USE_C99_MATH=1) + set(CMAKE_BUILD_TYPE Release) + set(LIBRARY_OUTPUT_PATH_ROOT ${CMAKE_CURRENT_BINARY_DIR}) + set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_BINARY_DIR}/libs/) + add_definitions(-DBUILD_ANDROID) + add_definitions(-DPICOJSON_USE_LOCALE=0) + add_library(androidGmsh SHARED ${GMSH_SRC}) + set_target_properties(androidGmsh PROPERTIES OUTPUT_NAME gmsh) + target_link_libraries(androidGmsh ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) + add_custom_command(TARGET androidGmsh POST_BUILD COMMAND + ${CMAKE_STRIP} ${LIBRARY_OUTPUT_PATH}/libgmsh.so) +endif() + +# parser target +find_program(BISON bison) +find_program(FLEX flex) +if(BISON AND FLEX) + add_custom_target(parser + COMMAND ${BISON} -p gmsh_yy --output Gmsh.tab.cpp -d Gmsh.y + COMMAND ${FLEX} -P gmsh_yy -o Gmsh.yy.cpp Gmsh.l + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Parser) +endif() + +if(UNIX) + # cannot use cmake's file search functions here (they would only find files + # existing at configuration time) + add_custom_target(purge + COMMAND rm -f `find . -name *~ -o -name *~~` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + add_custom_target(etags + COMMAND etags `find . -name *.cpp -o -name *.h -o -name *.y` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion + OUTPUT_VARIABLE CXX_COMPILER_VERSION + OUTPUT_STRIP_TRAILING_WHITESPACE) +else() + set(CXX_COMPILER_VERSION "Unknown") +endif() + +set(WELCOME_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/WELCOME.txt) +set(SDK_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/SDK.txt) +set(LICENSE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE.txt) +set(CREDITS_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CREDITS.txt) +set(CHANGELOG_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.txt) +file(GLOB TUTORIAL_GEO_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/?*.*) +file(GLOB TUTORIAL_CPP_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c++/?*.*) +file(GLOB TUTORIAL_C_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c/?*.*) +file(GLOB TUTORIAL_PY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/python/?*.*) +file(GLOB TUTORIAL_JL_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/julia/?*.*) +file(GLOB DEMOS ${CMAKE_CURRENT_SOURCE_DIR}/demos/*) +foreach(SUBDIR ${DEMOS}) + if(IS_DIRECTORY ${SUBDIR}) + list(APPEND DEMOS_DIRS ${SUBDIR}) + endif() +endforeach() +set(TEX_DIR ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo) +file(GLOB TEX_SRC ${TEX_DIR}/*.texi) +set(TEX_OBJ ${TEX_DIR}/gmsh.aux ${TEX_DIR}/gmsh.cp ${TEX_DIR}/gmsh.cps + ${TEX_DIR}/gmsh.fn ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.ky + ${TEX_DIR}/gmsh.log ${TEX_DIR}/gmsh.pdf ${TEX_DIR}/gmsh.pg ${TEX_DIR}/gmsh.toc + ${TEX_DIR}/gmsh.tp ${TEX_DIR}/gmsh.tps ${TEX_DIR}/gmsh.txt ${TEX_DIR}/gmsh.vr) + +macro(unix2dos VARNAME) + file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/unix2dos) + set(UNIX2DOS_FILES) + foreach(FILE ${${VARNAME}}) + file(READ ${FILE} F0) + get_filename_component(N ${FILE} NAME) + if(CYGWIN) + string(REGEX REPLACE "\n" "\r\n" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F1}") + else() # if not in Cygwin, cmake adds '\r's automatically + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F0}") + endif() + list(APPEND UNIX2DOS_FILES ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N}) + endforeach() + set(${VARNAME} ${UNIX2DOS_FILES}) +endmacro() + +if(WIN32) + if(ENABLE_OS_SPECIFIC_INSTALL) + set(GMSH_BIN .) + set(GMSH_LIB .) + set(GMSH_DOC .) + set(GMSH_MAN .) + set(GMSH_INC .) + else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) + endif() + if(CYGWIN) + unix2dos(GMSH_API) + if(ENABLE_PRIVATE_API) + unix2dos(GMSH_PRIVATE_API) + endif() + unix2dos(WELCOME_FILE) + unix2dos(SDK_FILE) + unix2dos(LICENSE_FILE) + unix2dos(CREDITS_FILE) + unix2dos(CHANGELOG_FILE) + unix2dos(TUTORIAL_GEO_FILES) + unix2dos(TUTORIAL_CPP_FILES) + unix2dos(TUTORIAL_C_FILES) + unix2dos(TUTORIAL_PY_FILES) + unix2dos(TUTORIAL_JL_FILES) + foreach(DIR ${DEMOS_DIRS}) + file(GLOB DEMO_FILES ${DIR}/?*.*) + unix2dos(DEMO_FILES) + endforeach() + endif() +elseif(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + # set these so that the files get installed nicely in the MacOSX + # .app bundle + set(GMSH_BIN ../MacOS) + set(GMSH_LIB ../MacOS) + set(GMSH_DOC ../../..) + set(GMSH_MAN ../../..) + set(GMSH_INC ../MacOS) +else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) +endif() + +# mark targets as optional so we can install them separately if needed +# (e.g. "make lib" or "make shared" followed by "make install/fast") +install(TARGETS gmsh DESTINATION ${GMSH_BIN} OPTIONAL) +if(ENABLE_BUILD_LIB) + install(TARGETS lib DESTINATION ${GMSH_LIB} OPTIONAL) +endif() +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(TARGETS shared DESTINATION ${GMSH_LIB} OPTIONAL) +endif() + +if(ENABLE_ONELAB) + install(FILES ${ONELAB_PY} DESTINATION ${GMSH_BIN}) +endif() +if(ENABLE_BUILD_LIB OR ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(FILES ${GMSH_API} DESTINATION ${GMSH_INC}) + install(FILES ${GMSH_PY} DESTINATION ${GMSH_LIB}) + install(FILES ${GMSH_JL} DESTINATION ${GMSH_LIB}) + if(ENABLE_PRIVATE_API) + install(FILES ${GMSH_PRIVATE_API} DESTINATION ${GMSH_INC}/gmsh) + endif() +endif() +if(INSTALL_SDK_README) + configure_file(${SDK_FILE} ${CMAKE_CURRENT_BINARY_DIR}/README.txt) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/README.txt DESTINATION .) +endif() +install(FILES ${WELCOME_FILE} DESTINATION ${GMSH_DOC} RENAME README.txt) +install(FILES ${LICENSE_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CREDITS_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CHANGELOG_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${TUTORIAL_GEO_FILES} DESTINATION ${GMSH_DOC}/tutorial) +install(FILES ${TUTORIAL_CPP_FILES} DESTINATION ${GMSH_DOC}/tutorial/c++) +install(FILES ${TUTORIAL_C_FILES} DESTINATION ${GMSH_DOC}/tutorial/c) +install(FILES ${TUTORIAL_PY_FILES} DESTINATION ${GMSH_DOC}/tutorial/python) +install(FILES ${TUTORIAL_JL_FILES} DESTINATION ${GMSH_DOC}/tutorial/julia) +foreach(DIR ${DEMOS_DIRS}) + get_filename_component(DEMOS_DIR_NAME ${DIR} NAME) + file(GLOB DEMO_FILES ${DIR}/?*.*) + install(FILES ${DEMO_FILES} DESTINATION ${GMSH_DOC}/demos/${DEMOS_DIR_NAME}) +endforeach() +if(UNIX AND NOT CYGWIN) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/doc/gmsh.1 DESTINATION ${GMSH_MAN}) +endif() + +add_custom_target(get_headers + COMMAND ${CMAKE_COMMAND} -E make_directory Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +foreach(FILE ${GMSH_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endforeach() +if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/gmsh/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() +endif() + +find_program(MAKEINFO makeinfo) +if(MAKEINFO) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.info DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --split-size 1000000 + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(info DEPENDS ${TEX_DIR}/gmsh.info) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.txt DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --plaintext -o gmsh.txt + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(txt DEPENDS ${TEX_DIR}/gmsh.txt) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.html DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --html --css-ref=/gmsh.css + --no-split --set-customization-variable + EXTRA_HEAD='' + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(html DEPENDS ${TEX_DIR}/gmsh.html) + install(FILES ${TEX_DIR}/gmsh.html DESTINATION ${GMSH_DOC} OPTIONAL) +else() + add_custom_target(html COMMAND ${CMAKE_COMMAND} -E touch ${TEX_DIR}/gmsh.html) +endif() + +find_program(TEXI2PDF texi2pdf) +if(TEXI2PDF) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.pdf DEPENDS ${TEX_SRC} + COMMAND ${TEXI2PDF} ARGS gmsh.texi + WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(pdf DEPENDS ${TEX_DIR}/gmsh.pdf) + install(FILES ${TEX_DIR}/gmsh.pdf DESTINATION ${GMSH_DOC} OPTIONAL) +endif() + +execute_process(COMMAND ${CMAKE_COMMAND} -E echo + "@c This file was generated by cmake: do not edit manually!\n${OPT_TEXI}" + OUTPUT_FILE cmake_options.texi) + +if(MAKEINFO AND TEXI2PDF) + add_custom_target(doc COMMAND ${CMAKE_COMMAND} -E tar zcf + ${CMAKE_CURRENT_BINARY_DIR}/gmsh-${GMSH_VERSION}-doc.tgz + CREDITS.txt LICENSE.txt CHANGELOG.txt + doc/gmsh.1 doc/texinfo/gmsh.html doc/texinfo/gmsh.info + doc/texinfo/gmsh.pdf doc/texinfo/gmsh.txt + COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ} + DEPENDS ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.txt + ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.pdf + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(MAKEINFO OR TEXI2PDF) + add_custom_target(clean_doc COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ}) +endif() + +if(APPLE AND ENABLE_BUILD_LIB) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_framework.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info_framework.plist "${F1}") + set(LIBNAME $) + add_custom_target(framework DEPENDS lib + COMMAND ${CMAKE_COMMAND} -E remove_directory gmsh.framework + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Headers + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Resources + COMMAND ${CMAKE_COMMAND} -E copy ${LIBNAME} gmsh.framework/gmsh + COMMAND ${CMAKE_COMMAND} -E copy Info_framework.plist + gmsh.framework/Resources/Info.plist + COMMAND ${CMAKE_COMMAND} -E create_symlink . gmsh.framework/Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + foreach(FILE ${GMSH_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + endif() +endif() + +set(CPACK_PACKAGE_VENDOR "Christophe Geuzaine and Jean-Francois Remacle") +set(CPACK_PACKAGE_VERSION_MAJOR ${GMSH_MAJOR_VERSION}) +set(CPACK_PACKAGE_VERSION_MINOR ${GMSH_MINOR_VERSION}) +set(CPACK_PACKAGE_VERSION_PATCH ${GMSH_PATCH_VERSION}) +set(CPACK_PACKAGE_DESCRIPTION_FILE ${WELCOME_FILE}) +set(CPACK_PACKAGE_DESCRIPTION_SUMMARY + "3D finite element mesh generator with built-in CAD engine and post-processor") +if(GMSH_EXTRA_VERSION MATCHES "-git.*") # so that we'll overwrite the archives + set(CPACK_PACKAGE_FILE_NAME gmsh${GMSH_EXTRA_VERSION_ORIG}-git-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh${GMSH_EXTRA_VERSION_ORIG}-git-source) +else() + set(CPACK_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-source) +endif() +set(CPACK_PACKAGE_INSTALL_DIRECTORY "gmsh") +set(CPACK_RESOURCE_FILE_LICENSE ${LICENSE_FILE}) +set(CPACK_RESOURCE_FILE_README ${WELCOME_FILE}) +set(CPACK_RESOURCE_FILE_WELCOME ${WELCOME_FILE}) +set(CPACK_PACKAGE_EXECUTABLE "gmsh") +if(ENABLE_PACKAGE_STRIP) + set(CPACK_STRIP_FILES TRUE) +else() + set(CPACK_STRIP_FILES FALSE) +endif() +set(CPACK_SOURCE_GENERATOR TGZ) +set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR}" "/CVS/" "/.svn" "/.git" + "~$" "DS_Store$" "GmshConfig.h$" "GmshVersion.h$" "/benchmarks/" "/tmp/" + "/bin/" "/lib/" "/nightly/" "GPATH" "GRTAGS" "GSYMS" "GTAGS" "/HTML/" + "/contrib/3M/" "/contrib/Parasolid/") + +if(UNIX) + # make sure we remove previous installs before doing the next one (on Mac for + # example "make package; make package_source" would lead to huge file lists + # getting generated due to the 'Applications' symlink in the bundle) + set(CPACK_INSTALL_COMMANDS "rm -rf ${CMAKE_CURRENT_BINARY_DIR}/_CPack_Packages") +endif() + +if(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + set(CPACK_GENERATOR Bundle) + set(CPACK_BUNDLE_NAME Gmsh) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_app.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info.plist "${F1}") + set(CPACK_BUNDLE_PLIST ${CMAKE_CURRENT_BINARY_DIR}/Info.plist) + set(CPACK_BUNDLE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) + if(PACKAGER STREQUAL "geuzaine - removed: we sign on a separate machine") + # codesigning requires CMake >= 3.2 + set(CPACK_BUNDLE_APPLE_CERT_APP "Developer ID Application: Christophe Geuzaine") + endif() + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsGeo.icns DESTINATION . + RENAME GmshGeo.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsMsh.icns DESTINATION . + RENAME GmshMsh.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsSol.icns DESTINATION . + RENAME GmshSol.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsPos.icns DESTINATION . + RENAME GmshPos.icns) + set(CPACK_PACKAGE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) +elseif(WIN32) + set(CPACK_GENERATOR ZIP) +else() + set(CPACK_GENERATOR TGZ) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/gmshpy AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON AND HAVE_PYTHON) + add_subdirectory(utils/wrappers/gmshpy) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/java AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_JAVA) + add_subdirectory(utils/wrappers/java) +endif() + +include(CPack) + +macro(filter_tests IN OUT) + unset(${OUT}) + foreach(FILE ${IN}) + unset(BAD1) + unset(BAD2) + unset(BAD3) + # OS-specific + if(${GMSH_OS} MATCHES "Linux32") + # OCC STL generation crashes on our Linux32 docker + string(REGEX MATCH "t18" BAD1 ${FILE}) + endif() + # OpenCASCADE + if(NOT HAVE_OCC AND NOT BAD1 AND NOT BAD2 AND NOT BAD3) + file(STRINGS ${FILE} BAD1 REGEX "^SetFactory.*OpenCASCADE.*") + file(STRINGS ${FILE} BAD2 REGEX ".*occ\\.synchronize.*") + file(STRINGS ${FILE} BAD3 REGEX ".*occ::synchronize.*") + endif() + # Metis + if(NOT HAVE_METIS AND NOT BAD1 AND NOT BAD2 AND NOT BAD3) + file(STRINGS ${FILE} BAD1 REGEX ".*PartitionMesh.*") + file(STRINGS ${FILE} BAD2 REGEX ".*mesh\\.partition.*") + file(STRINGS ${FILE} BAD3 REGEX ".*mesh::partition.*") + endif() + if(BAD1 OR BAD2 OR BAD3) + message("Skipping test " ${FILE}) + else() + list(APPEND ${OUT} ${FILE}) + endif() + endforeach() +endmacro() + +if(NOT DISABLE_GMSH_TESTS) + # disabling tests is useful when including this CMakeLists in an external project + include(CTest) + file(GLOB_RECURSE ALLFILES + tutorial/*.geo demos/*.geo benchmarks/?d/*.geo benchmarks/extrude/*.geo + benchmarks/occ/*.geo) + filter_tests("${ALLFILES}" TESTFILES) + foreach(TESTFILE ${TESTFILES}) + # use relative path for Cygwin/MinGW (the pure win exe built with the MinGW + # compilers does not understand a full Cygwin-style path) + FILE(RELATIVE_PATH TEST ${CMAKE_CURRENT_BINARY_DIR} ${TESTFILE}) + add_test(${TEST} ./gmsh ${TEST} -3 -nopopup -o ./tmp.msh) + endforeach() + # test c++ api tutorials with dynamic builds (except on 32 bit windows for + # now: our win32 setup does not currently handle exceptions) + if(ENABLE_BUILD_DYNAMIC AND NOT ${GMSH_OS} MATCHES "Windows32") + file(GLOB_RECURSE ALLFILES tutorial/c++/*.cpp) + filter_tests("${ALLFILES}" TESTFILES) + foreach(TESTFILE ${TESTFILES}) + get_filename_component(TEST ${TESTFILE} NAME_WE) + add_executable(${TEST} WIN32 ${TESTFILE}) + target_link_libraries(${TEST} shared) + if(WIN32 AND NOT MSVC) + set(FLAGS "-static") + if(HAVE_FLTK) + set(FLAGS "${FLAGS} -mwindows") + else() + set(FLAGS "${FLAGS} -mconsole") + endif() + set_target_properties(${TEST} PROPERTIES LINK_FLAGS "${FLAGS}") + endif() + add_test(${TEST}_cpp ${TEST} -nopopup) + endforeach() + endif() + # enable this once we have worked out the path issues on the build machines + if(0 AND ENABLE_BUILD_DYNAMIC) + find_package(PythonInterp) + if(PYTHONINTERP_FOUND) + file(GLOB_RECURSE ALLFILES tutorial/python/*.py demos/api/*.py) + filter_tests("${ALLFILES}" TESTFILES) + foreach(TESTFILE ${TESTFILES}) + get_filename_component(TEST ${TESTFILE} NAME_WE) + add_test(NAME ${TEST}_py COMMAND ${PYTHON_EXECUTABLE} ${TESTFILE} -nopopup) + set_property(TEST ${TEST}_py APPEND PROPERTY ENVIRONMENT + "PYTHONPATH=${CMAKE_SOURCE_DIR}/api") + set_property(TEST ${TEST}_py APPEND PROPERTY ENVIRONMENT + "LD_LIBRARY_PATH=${CMAKE_CURRENT_BINARY_DIR}") + endforeach() + endif() + endif() +endif() + +message(STATUS "") +message(STATUS "Gmsh ${GMSH_VERSION} has been configured for ${GMSH_OS}") +message(STATUS "") +message(STATUS " * Build options:" ${GMSH_CONFIG_OPTIONS}) +message(STATUS " * Build type: " ${CMAKE_BUILD_TYPE}) +message(STATUS " * C compiler: " ${CMAKE_C_COMPILER}) +message(STATUS " * C++ compiler: " ${CMAKE_CXX_COMPILER}) +message(STATUS " * Install prefix: " ${CMAKE_INSTALL_PREFIX}) +message(STATUS "") + +mark_as_advanced(ANN_INC ANN_LIB CAIRO_LIB CAIRO_INC CGNS_INC GMM_INC + GMP_INC GMP_LIB MMG_INC MMG_LIB HDF5_LIB + MED_LIB OCC_INC SZ_LIB + PETSC_LIBS SLEPC_INC SLEPC_INC2 SLEPC_LIB + BISON FLEX MAKEINFO TEXI2PDF FLTK_CONFIG_SCRIPT + GMSH_EXTERNAL_INCLUDE_DIRS GMSH_EXTERNAL_LIBRARIES) Index: /issm/trunk/externalpackages/gmsh/configs/4.7.0/static/CMakeLists.txt =================================================================== --- /issm/trunk/externalpackages/gmsh/configs/4.7.0/static/CMakeLists.txt (revision 25836) +++ /issm/trunk/externalpackages/gmsh/configs/4.7.0/static/CMakeLists.txt (revision 25836) @@ -0,0 +1,2191 @@ +# Gmsh - Copyright (C) 1997-2020 C. Geuzaine, J.-F. Remacle +# +# See the LICENSE.txt file for license information. Please report all +# issues on https://gitlab.onelab.info/gmsh/gmsh/issues. + +cmake_minimum_required(VERSION 3.1 FATAL_ERROR) + +# if CMAKE_BUILD_TYPE is specified use it; otherwise set the default +# build type to "RelWithDebInfo" ("-O2 -g" with gcc) prior to calling +# project() +if(DEFINED CMAKE_BUILD_TYPE) + set(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Choose build type") +else() + set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose build type") +endif() + +project(gmsh CXX C) + +# require C++11 and request C99 +set(CMAKE_CXX_STANDARD 11) +set(CMAKE_CXX_STANDARD_REQUIRED ON) +set(CMAKE_C_STANDARD 99) + +# this variable controls the default value of the options which are normally set +# to ON (useful if you want to configure a minimal version of Gmsh: e.g. "cmake +# -DDEFAULT=0 -DENABLE_POST=1 -DENABLE_PARSER=1") +set(DEFAULT ON CACHE INTERNAL "Default value for enabled-by-default options") + +macro(opt OPTION HELP VALUE) + option(ENABLE_${OPTION} ${HELP} ${VALUE}) + set(OPT_TEXI "${OPT_TEXI}\n@item ENABLE_${OPTION}\n${HELP} (default: ${VALUE})") +endmacro() + +opt(3M "Enable proprietary 3M extension" OFF) +opt(ALGLIB "Enable ALGLIB (used by some mesh optimizers)" ${DEFAULT}) +opt(ANN "Enable ANN (used for fast point search in mesh/post)" ${DEFAULT}) +opt(BAMG "Enable Bamg 2D anisotropic mesh generator" ${DEFAULT}) +opt(BLAS_LAPACK "Enable BLAS/Lapack for linear algebra (if Eigen if disabled)" OFF) +opt(BLOSSOM "Enable Blossom algorithm (needed for full quad meshing)" ${DEFAULT}) +opt(BUILD_LIB "Enable 'lib' target for building static Gmsh library" OFF) +opt(BUILD_SHARED "Enable 'shared' target for building shared Gmsh library" OFF) +opt(BUILD_DYNAMIC "Enable dynamic Gmsh executable (linked with shared library)" OFF) +opt(BUILD_ANDROID "Enable Android NDK library target (experimental)" OFF) +opt(BUILD_IOS "Enable iOS library target (experimental)" OFF) +opt(CGNS "Enable CGNS import/export (experimental)" ${DEFAULT}) +opt(CGNS_CPEX0045 "Enable high-order CGNS import/export following CPEX0045 (experimental)" OFF) +opt(CAIRO "Enable Cairo to render fonts (experimental)" ${DEFAULT}) +opt(PROFILE "Enable profiling compiler flags" OFF) +opt(DINTEGRATION "Enable discrete integration (needed for levelsets)" ${DEFAULT}) +opt(DOMHEX "Enable experimental DOMHEX code" ${DEFAULT}) +opt(EIGEN "Enable Eigen for linear algebra (instead of Blas/Lapack)" ON) +opt(FLTK "Enable FLTK graphical user interface (requires mesh/post)" ${DEFAULT}) +opt(GETDP "Enable GetDP solver (linked as a library, experimental)" ${DEFAULT}) +opt(GMM "Enable GMM linear solvers (simple alternative to PETSc)" ${DEFAULT}) +opt(GMP "Enable GMP for Kbipack (advanced)" ON) +opt(GRAPHICS "Enable building graphics lib even without GUI (advanced)" OFF) +opt(HXT "Enable HXT library (for reparametrization and meshing)" ${DEFAULT}) +opt(KBIPACK "Enable Kbipack (neeeded by homology solver)" ${DEFAULT}) +opt(MATHEX "Enable Mathex expression parser (used by plugins and options)" ${DEFAULT}) +opt(MED "Enable MED mesh and post file formats" ${DEFAULT}) +opt(MESH "Enable mesh module (required by GUI)" ${DEFAULT}) +opt(METIS "Enable Metis mesh partitioner" ${DEFAULT}) +opt(MMG "Enable Mmg mesh adaptation interface" ${DEFAULT}) +opt(MPEG_ENCODE "Enable built-in MPEG movie encoder" ${DEFAULT}) +opt(MPI "Enable MPI (experimental, not used for meshing)" OFF) +opt(MSVC_STATIC_RUNTIME "Enable static Visual C++ runtime" OFF) +opt(MUMPS "Enable MUMPS sparse direct linear solver" OFF) +opt(NETGEN "Enable Netgen 3D frontal mesh generator" ${DEFAULT}) +opt(NUMPY "Enable fullMatrix and numpy array conversion for private API" OFF) +opt(PETSC4PY "Enable petsc4py wrappers for petsc matrices for private API" OFF) +opt(OCC "Enable OpenCASCADE CAD kernel" ${DEFAULT}) +opt(OCC_CAF "Enable OpenCASCADE CAF module (for STEP/IGES attributes)" ${DEFAULT}) +opt(OCC_STATIC "Link OpenCASCADE static instead of dynamic libraries (requires ENABLE_OCC)" OFF) +opt(OCC_TBB "Add TBB libraries in list of OCC libraries" OFF) +opt(ONELAB "Enable ONELAB solver interface" ${DEFAULT}) +opt(ONELAB_METAMODEL "Enable ONELAB metamodels (experimental)" ${DEFAULT}) +opt(OPENACC "Enable OpenACC" OFF) +opt(OPENMP "Enable OpenMP" OFF) +opt(OPTHOM "Enable high-order mesh optimization tools" ${DEFAULT}) +opt(OS_SPECIFIC_INSTALL "Enable OS-specific (e.g. app bundle) installation" OFF) +opt(OSMESA "Enable OSMesa for offscreen rendering (experimental)" OFF) +opt(P4EST "Enable p4est for enabling automatic mesh size field (experimental)" OFF) +opt(PACKAGE_STRIP "Strip symbols in install packages to reduce install size" ON) +opt(PARSER "Enable GEO file parser (required for .geo/.pos scripts)" ${DEFAULT}) +opt(PETSC "Enable PETSc linear solvers (required for SLEPc)" OFF) +opt(PLUGINS "Enable post-processing plugins" ${DEFAULT}) +opt(POST "Enable post-processing module (required by GUI)" ${DEFAULT}) +opt(POPPLER "Enable Poppler for displaying PDF documents (experimental)" OFF) +opt(PRIVATE_API "Enable private API" OFF) +opt(PRO "Enable PRO extensions" ${DEFAULT}) +opt(QUADTRI "Enable QuadTri structured meshing extensions" ${DEFAULT}) +opt(REVOROPT "Enable Revoropt (used for CVT remeshing)" OFF) +opt(RPATH "Use RPATH in dynamically linked targets" ON) +opt(SLEPC "Enable SLEPc eigensolvers" OFF) +opt(SOLVER "Enable built-in finite element solvers (required for reparametrization)" ${DEFAULT}) +opt(SYSTEM_CONTRIB "Use system versions of contrib libraries, when possible" OFF) +opt(TCMALLOC "Enable libtcmalloc (fast malloc that does not release memory)" OFF) +opt(TOUCHBAR "Enable Apple Touch bar" ${DEFAULT}) +opt(VISUDEV "Enable additional visualization capabilities for development purposes" OFF) +opt(VOROPP "Enable voro++ (for hex meshing, experimental)" ${DEFAULT}) +opt(WRAP_JAVA "Generate SWIG Java wrappers for private API" OFF) +opt(WRAP_PYTHON "Generate SWIG Python wrappers for private API (not used by public API)" OFF) +opt(ZIPPER "Enable Zip file compression/decompression" OFF) + +set(GMSH_MAJOR_VERSION 4) +set(GMSH_MINOR_VERSION 7) +set(GMSH_PATCH_VERSION 0) +if(NOT GMSH_EXTRA_VERSION) + set(GMSH_EXTRA_VERSION "") +endif() +set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION}") +set(GMSH_EXTRA_VERSION_ORIG ${GMSH_EXTRA_VERSION}) + +if(NOT GMSH_RELEASE) + find_package(Git) + if(GIT_FOUND) + execute_process(COMMAND ${GIT_EXECUTABLE} log -1 --format=%h + WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} ERROR_QUIET + OUTPUT_VARIABLE GIT_COMMIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE) + endif() + if(GIT_COMMIT_HASH) + set(GMSH_EXTRA_VERSION "${GMSH_EXTRA_VERSION}-git-${GIT_COMMIT_HASH}") + endif() + set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION_TEXI} (development version)") +endif() + +set(GMSH_SHORT_VERSION + "${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION}") +set(GMSH_VERSION "${GMSH_SHORT_VERSION}${GMSH_EXTRA_VERSION}") +set(GMSH_SHORT_LICENSE "GNU General Public License") + +set(GMSH_GITLAB_PREFIX "https://gitlab.onelab.info/gmsh/gmsh") +if(GMSH_RELEASE) + set(GMSH_GITLAB_PREFIX "${GMSH_GITLAB_PREFIX}/blob/gmsh_${GMSH_SHORT_VERSION}") +else() + set(GMSH_GITLAB_PREFIX "${GMSH_GITLAB_PREFIX}/blob/master") +endif() + +set(GMSH_API api/gmsh.h api/gmshc.h api/gmsh.h_cwrap) + +if(ENABLE_PRIVATE_API) + message(WARNING "The private API is unsupported and undocumented. It is meant " + "for expert Gmsh developers, not for regular Gmsh users, who should rely " + "on the stable public API (gmsh/api) instead.") + file(GLOB_RECURSE HEADERS Common/*.h Numeric/*.h Geo/*.h Mesh/*.h Solver/*.h + Post/*.h Plugin/*.h Graphics/*.h contrib/kbipack/*.h + contrib/DiscreteIntegration/*.h contrib/HighOrderMeshOptimizer/*.h + contrib/MeshOptimizer/*.h contrib/MeshQualityOptimizer/*.h) + set(GMSH_PRIVATE_API ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h ${HEADERS}) + get_property(IAMCHILD DIRECTORY PROPERTY PARENT_DIRECTORY) + if(IAMCHILD) + set(GMSH_PRIVATE_API ${GMSH_PRIVATE_API} PARENT_SCOPE) + endif() + if(ENABLE_WRAP_PYTHON OR ENABLE_WRAP_JAVA) + set(ENABLE_BUILD_DYNAMIC ON) + message(WARNING "SWIG wrappers for the private API are unsupported and " + "undocumented. The stable public Python API does not required SWIG.") + endif() +endif() + +set(ONELAB_PY contrib/onelab/python/onelab.py) +set(GMSH_PY api/gmsh.py) +set(GMSH_JL api/gmsh.jl) + +if(${CMAKE_MAJOR_VERSION} GREATER 2) + string(TIMESTAMP DATE "%Y%m%d") +else() + execute_process(COMMAND date "+%Y%m%d" OUTPUT_VARIABLE DATE + OUTPUT_STRIP_TRAILING_WHITESPACE) +endif() + +if(NOT DATE) + set(DATE "unknown") +endif() +set(GMSH_DATE "${DATE}") + +if(NOT GMSH_HOST) + execute_process(COMMAND hostname OUTPUT_VARIABLE HOST + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT HOST) + set(HOST "unknown") + endif() + set(GMSH_HOST "${HOST}") +endif() + +if(NOT GMSH_PACKAGER) + execute_process(COMMAND whoami OUTPUT_VARIABLE PACKAGER + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT PACKAGER) + set(PACKAGER "unknown") + endif() + string(REPLACE "\\" " " PACKAGER ${PACKAGER}) + set(GMSH_PACKAGER "${PACKAGER}") +endif() + +if(APPLE) + set(GMSH_OS "MacOSX") +elseif(CYGWIN OR MSYS) + # detect if we use the MinGW compilers on Cygwin - if we do, handle the build + # as a pure Windows build and make cmake find pure Windows import libraries + # (.lib) + if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpmachine + OUTPUT_VARIABLE CXX_COMPILER_MACHINE + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(CXX_COMPILER_MACHINE MATCHES "mingw") + set(GMSH_OS "Windows") + set(WIN32 1) + add_definitions(-DWIN32) + set(CMAKE_FIND_LIBRARY_PREFIXES "lib" "") + set(CMAKE_FIND_LIBRARY_SUFFIXES ".a" ".so" ".lib" ".LIB" ".dll" ".DLL" ".dll.a") + endif() + endif() +else() + set(GMSH_OS "${CMAKE_SYSTEM_NAME}") +endif() + +include(CheckTypeSize) +include(CheckFunctionExists) +include(CheckIncludeFile) +include(CheckCXXCompilerFlag) +include(CheckCCompilerFlag) + +macro(set_config_option VARNAME STRING) + set(${VARNAME} TRUE) + list(APPEND CONFIG_OPTIONS ${STRING}) + message(STATUS "Found " ${STRING}) +endmacro() + +# check the size of size_t +check_type_size("size_t" SIZEOF_SIZE_T) +if(SIZEOF_SIZE_T EQUAL 8) + set_config_option(HAVE_64BIT_SIZE_T "64Bit") +endif() + +# append 32/64 to the build name on Linux and Windows +if(NOT APPLE) + if(HAVE_64BIT_SIZE_T) + set(GMSH_OS "${GMSH_OS}64") + else() + set(GMSH_OS "${GMSH_OS}32") + endif() +endif() + +if(ENABLE_BUILD_DYNAMIC) + set(GMSH_OS "${GMSH_OS}-sdk") +endif() + +if(ENABLE_RPATH) + set(CMAKE_MACOSX_RPATH 1) + + # make sure that dynamic libraries can be found when installing/ displacing + # the binaries: from https://gitlab.kitware.com/cmake/community/wikis/doc/ + # cmake/RPATH-handling: + + # use, i.e. don't skip the full RPATH for the build tree + set(CMAKE_SKIP_BUILD_RPATH FALSE) + + # when building, don't use the install RPATH already (but later on when + # installing) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") + + # add the automatically determined parts of the RPATH which point to + # directories outside the build tree to the install RPATH + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + + # the RPATH to be used when installing, but only if it's not a system directory + list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" + isSystemDir) + if("${isSystemDir}" STREQUAL "-1") + if(APPLE) + set(CMAKE_INSTALL_RPATH "@executable_path/../lib") + else() + set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../lib") + endif() + endif() +else() + set(CMAKE_MACOSX_RPATH 0) + set(CMAKE_SKIP_BUILD_RPATH TRUE) +endif() + +if(MSVC) + # remove annoying warning about bool/int cast performance + set(GMSH_CONFIG_PRAGMAS "#pragma warning(disable:4800 4244 4267)") + foreach(VAR + CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE + CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO + CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE + CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO) + if(ENABLE_MSVC_STATIC_RUNTIME AND ${VAR} MATCHES "/MD") + string(REGEX REPLACE "/MD" "/MT" ${VAR} "${${VAR}}") + endif() + if(NOT ${VAR} MATCHES "/MP") # enable parallel compilation + set(${VAR} "${${VAR}} /MP") + endif() + endforeach() + if(ENABLE_PRIVATE_API) + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + # automatically export .def file with all symbols (requires CMake 3.4); + # depending on the compiling options this might lead to more than 64k export + # symbols; just trim the .def file to keep the ones you need + set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + endif() + endif() +endif() + +# reduce memory usage of GCC on 32 bit systems +if(NOT HAVE_64BIT_SIZE_T AND CMAKE_CXX_COMPILER_ID MATCHES "GNU") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} --param ggc-min-expand=1 --param ggc-min-heapsize=512000") +endif() + +if(ENABLE_OPENMP) + find_package(OpenMP) + if(OpenMP_FOUND OR OPENMP_FOUND) + set_config_option(HAVE_OPENMP "OpenMP") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + elseif(APPLE AND EXISTS "/opt/local/lib/libomp") + # official Apple compiler with macports' libomp + set_config_option(HAVE_OPENMP "OpenMP[MacPorts]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + list(APPEND EXTERNAL_LIBRARIES "-L/opt/local/lib/libomp -lomp") + elseif(APPLE AND EXISTS "/usr/local/lib/libomp.dylib") + # official Apple compiler with homebrew's libomp + set_config_option(HAVE_OPENMP "OpenMP[Homebrew]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp") + list(APPEND EXTERNAL_LIBRARIES "-L/usr/local/lib -lomp") + endif() +endif() + +if(ENABLE_OPENACC) + find_package(OpenACC) + if(OpenACC_C_FOUND AND OpenACC_CXX_FOUND) + set_config_option(HAVE_OPENACC "OpenACC") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenACC_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenACC_CXX_FLAGS}") + endif() +endif() + +if(ENABLE_PROFILE) + # Using the perf set of profiling tools doesn't work without the frame + # pointer and a common optimisation is to remove it + check_cxx_compiler_flag("-fno-omit-frame-pointer" FNOFP) + if(FNOFP) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer") + endif() +endif() + +macro(append_gmsh_src DIRNAME FILES) + foreach(FILE ${FILES}) + list(APPEND LIST ${DIRNAME}/${FILE}) + endforeach() + set(GMSH_SRC ${GMSH_SRC};${LIST} PARENT_SCOPE) + set(GMSH_DIRS ${GMSH_DIRS};${DIRNAME} PARENT_SCOPE) +endmacro() + +macro(find_all_libraries VARNAME LISTNAME PATH SUFFIX) + set(${VARNAME}) + list(LENGTH ${LISTNAME} NUM_LIST) + foreach(LIB ${${LISTNAME}}) + if("${PATH}" STREQUAL "") + find_library(FOUND_LIB ${LIB} PATH_SUFFIXES ${SUFFIX}) + else() + find_library(FOUND_LIB ${LIB} PATHS ${PATH} NO_DEFAULT_PATH) + endif() + if(FOUND_LIB) + list(APPEND ${VARNAME} ${FOUND_LIB}) + endif() + unset(FOUND_LIB CACHE) + endforeach() + list(LENGTH ${VARNAME} NUM_FOUND_LIBRARIES) + if(NUM_FOUND_LIBRARIES LESS NUM_LIST) + set(${VARNAME}) + endif() +endmacro() + +macro(set_compile_flags LISTNAME FLAGS) + foreach(FILE ${${LISTNAME}}) + get_source_file_property(PROP ${FILE} COMPILE_FLAGS) + if(PROP) + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${PROP} ${FLAGS}") + else() + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${FLAGS}") + endif() + endforeach() +endmacro() + +if(ENABLE_EIGEN) + if(ENABLE_SYSTEM_CONTRIB) + find_path(EIGEN_INC "Eigen/Dense" HINTS eigen3) + if(EIGEN_INC) + include_directories(${EIGEN_INC}) + set_config_option(HAVE_EIGEN "Eigen[system]") + endif() + endif() + if(NOT HAVE_EIGEN) + include_directories(contrib/eigen) + set_config_option(HAVE_EIGEN "Eigen") + endif() + # We could also add an option to use BLAS with Eigen + # add_definitions(-DEIGEN_USE_BLAS) +elseif(ENABLE_BLAS_LAPACK) + if(BLAS_LAPACK_LIBRARIES) + # use libs as specified in the BLAS_LAPACK_LIBRARIES variable + set_config_option(HAVE_BLAS "Blas[custom]") + set_config_option(HAVE_LAPACK "Lapack[custom]") + set(LAPACK_LIBRARIES ${BLAS_LAPACK_LIBRARIES}) + else() + if(MSVC) + # on Windows with Visual C++ try really hard to find blas/lapack *without* + # requiring a Fortran compiler: 1) try to find the Intel MKL libs using + # the standard search path; if not found 2) try to get the reference + # blas/lapack libs (useful for users with no Fortran compiler and no MKL + # license, who can just download our precompiled "gmsh-dep" package) + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH em64t/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_lp64 mkl_intel_thread mkl_core) + else() + set(MKL_PATH ia32/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_c mkl_intel_thread mkl_core) + endif() + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + set(REFLAPACK_LIBS_REQUIRED lapack blas g2c gcc) + find_all_libraries(LAPACK_LIBRARIES REFLAPACK_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[ref]") + set_config_option(HAVE_LAPACK "Lapack[ref]") + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + # on Linux try to find the Intel MKL without a Fortran compiler + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH lib/em64t) + else() + set(MKL_PATH lib/32) + endif() + set(MKL_LIBS_REQUIRED mkl_gf_lp64 iomp5 mkl_gnu_thread mkl_core guide pthread) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(NOT LAPACK_LIBRARIES) + # match lapack 9.0 on 64bit + set(MKL_LIBS_REQUIRED mkl_lapack mkl_em64t guide) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + endif() + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + # on Linux also try to find ATLAS without a Fortran compiler, because + # cmake ships with a buggy FindBLAS e.g. on Ubuntu Lucid Lynx + set(ATLAS_LIBS_REQUIRED lapack f77blas cblas atlas) + find_all_libraries(LAPACK_LIBRARIES ATLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[atlas]") + set_config_option(HAVE_LAPACK "Lapack[atlas]") + else() + # try with generic names + set(GENERIC_LIBS_REQUIRED lapack blas pthread) + find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[generic]") + set_config_option(HAVE_LAPACK "Lapack[generic]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "SunOS") + # on SunOS we know blas and lapack are available in sunperf + set(LAPACK_LIBRARIES -library=sunperf) + set_config_option(HAVE_BLAS "Blas[sunperf]") + set_config_option(HAVE_LAPACK "Lapack[sunperf]") + elseif(APPLE) + # on Mac we also know that blas and lapack are available + set(LAPACK_LIBRARIES "-llapack -lblas") + set_config_option(HAVE_BLAS "Blas[veclib]") + set_config_option(HAVE_LAPACK "Lapack[veclib]") + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we haven't found blas and lapack check for OpenBlas + set(OPENBLAS_LIBS_REQUIRED openblas) + find_all_libraries(LAPACK_LIBRARIES OPENBLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[openblas]") + set_config_option(HAVE_LAPACK "Lapack[openblas]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we still haven't found blas and lapack, use the standard cmake tests, + # which require a working Fortran compiler + enable_language(Fortran) + find_package(BLAS) + if(BLAS_FOUND) + set_config_option(HAVE_BLAS "Blas") + find_package(LAPACK) + if(LAPACK_FOUND) + set_config_option(HAVE_LAPACK "Lapack") + else() + set(LAPACK_LIBRARIES ${BLAS_LIBRARIES}) + endif() + if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU") + if(CMAKE_Fortran_COMPILER MATCHES "gfortran") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "f95") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "g77") + list(APPEND LAPACK_LIBRARIES g2c) + endif() + elseif(CMAKE_Fortran_COMPILER MATCHES "pgi") + list(APPEND LAPACK_LIBRARIES -pgf77libs) + endif() + endif() + endif() + endif() +endif() + +if(ENABLE_TCMALLOC) + find_library(TCMALLOC tcmalloc) + if(TCMALLOC) + set_config_option(HAVE_TCMALLOC "TCMalloc") + list(APPEND EXTERNAL_LIBRARIES ${TCMALLOC}) + endif() +endif() + +add_subdirectory(Common) +add_subdirectory(Numeric) +add_subdirectory(Geo) + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh AND ENABLE_MESH) + add_subdirectory(Mesh) + set_config_option(HAVE_MESH "Mesh") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Solver AND ENABLE_SOLVER) + add_subdirectory(Solver) + set_config_option(HAVE_SOLVER "Solver") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Post AND ENABLE_POST) + add_subdirectory(Post) + set_config_option(HAVE_POST "Post") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Plugin AND ENABLE_PLUGINS) + add_subdirectory(Plugin) + set_config_option(HAVE_PLUGINS "Plugins") + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Parser AND ENABLE_PARSER) + add_subdirectory(Parser) + set_config_option(HAVE_PARSER "Parser") +endif() + +if(ENABLE_VISUDEV) + set_config_option(HAVE_VISUDEV "VisuDev") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Fltk AND ENABLE_FLTK) + # first, try to use fltk-config for fltk >= 1.3 (FindFLTK is buggy on Unix, + # where e.g. xft and xinerama options are not dealt with) + find_program(FLTK_CONFIG_SCRIPT fltk-config) + if(FLTK_CONFIG_SCRIPT) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --api-version + OUTPUT_VARIABLE FLTK_VERSION) + string(STRIP "${FLTK_VERSION}" FLTK_VERSION) + if(FLTK_VERSION VERSION_GREATER 1.1) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + message(STATUS "Using fltk-config script for Fltk " ${FLTK_VERSION}) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --includedir + OUTPUT_VARIABLE FLTK_INCLUDE_DIR) + string(STRIP ${FLTK_INCLUDE_DIR} FLTK_INCLUDE_DIR) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # On linux (at least OpenSuSE) the following directories are + # not existing (everything is in /usr/include). To avoid warnings + # check existance of these directories before adding them + if(EXISTS ${FLTK_INCLUDE_DIR}/FL/images) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/FL/images) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/jpeg) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/jpeg) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/zlib) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/zlib) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/png) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/png) + endif() + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --ldflags + OUTPUT_VARIABLE FLTK_LIBRARIES) + string(STRIP ${FLTK_LIBRARIES} FLTK_LIBRARIES) + string(REGEX MATCH "fltk[_ ]jpeg" FLTK_JPEG ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]z" FLTK_Z ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]png" FLTK_PNG ${FLTK_LIBRARIES}) + endif() + endif() + # then try the built-in FindFLTK module + if(NOT HAVE_FLTK) + set(FLTK_SKIP_FORMS TRUE) + set(FLTK_SKIP_FLUID TRUE) + find_package(FLTK) + if(FLTK_FOUND) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # find fltk jpeg + find_library(FLTK_JPEG NAMES fltk_jpeg fltkjpeg) + if(FLTK_JPEG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_JPEG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/jpeg) + endforeach() + endif() + # find fltk zlib + find_library(FLTK_Z NAMES fltk_z fltkz) + if(FLTK_Z) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_Z}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/zlib) + endforeach() + endif() + # find fltk png + find_library(FLTK_PNG NAMES fltk_png fltkpng) + if(FLTK_PNG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_PNG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/png) + endforeach() + endif() + endif() + endif() + # workaround for Fedora/Suse messing up fltk-config (see issue #417) + if(HAVE_FLTK AND ${CMAKE_SYSTEM_NAME} MATCHES "Linux") + string(REGEX MATCH "X11" FLTK_X11 ${FLTK_LIBRARIES}) + if(NOT FLTK_X11) + find_package(X11) + if(X11_FOUND) + list(APPEND EXTERNAL_INCLUDES ${X11_INCLUDE_DIR}) + list(APPEND EXTERNAL_LIBRARIES ${X11_LIBRARIES}) + endif() + endif() + endif() +endif() + +if(APPLE AND HAVE_FLTK AND ENABLE_TOUCHBAR) + STRING(REGEX MATCH "([0-9]+.[0-9]+)" OSX_SDK_VERSION "${CMAKE_OSX_SYSROOT}") + if(OSX_SDK_VERSION) + if(${OSX_SDK_VERSION} VERSION_GREATER 10.11) + set(GMSH_SRC ${GMSH_SRC};Fltk/touchBar.mm) + set_config_option(HAVE_TOUCHBAR "TouchBar") + endif() + endif() +endif() + +if(ENABLE_ONELAB) + set_config_option(HAVE_ONELAB "ONELAB") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/onelab) + if(ENABLE_ONELAB_METAMODEL) + add_subdirectory(contrib/onelab) + include_directories(contrib/onelab) + set_config_option(HAVE_ONELAB_METAMODEL "ONELABMetamodel") + endif() + file(COPY ${ONELAB_PY} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + endif() +endif() + +if(ENABLE_BUILD_IOS) + find_file(CMAKE_TOOLCHAIN_FILE "ios.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for iOS without a toolchain") + endif() + add_definitions(-DBUILD_IOS) +endif() + +if(HAVE_FLTK OR ENABLE_GRAPHICS) + if(NOT HAVE_MESH OR NOT HAVE_POST OR NOT HAVE_PLUGINS OR NOT HAVE_ONELAB) + message(SEND_ERROR "Cannot compile GUI without Mesh, Post, Plugin and ONELAB") + endif() + + if(FLTK_JPEG) + set_config_option(HAVE_LIBJPEG "Jpeg[fltk]") + else() + find_package(JPEG) + if(JPEG_FOUND) + set_config_option(HAVE_LIBJPEG "Jpeg") + list(APPEND EXTERNAL_LIBRARIES ${JPEG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${JPEG_INCLUDE_DIR}) + endif() + endif() + + if(FLTK_Z) + set_config_option(HAVE_LIBZ "Zlib[fltk]") + else() + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + + if(HAVE_LIBZ) + if(FLTK_PNG) + set_config_option(HAVE_LIBPNG "Png[fltk]") + else() + find_package(PNG) + if(PNG_FOUND) + set_config_option(HAVE_LIBPNG "Png") + list(APPEND EXTERNAL_LIBRARIES ${PNG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${PNG_INCLUDE_DIR}) + endif() + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/mpeg_encode AND + ENABLE_MPEG_ENCODE) + add_subdirectory(contrib/mpeg_encode) + include_directories(contrib/mpeg_encode/headers) + set_config_option(HAVE_MPEG_ENCODE "Mpeg") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/3M AND ENABLE_3M) + add_subdirectory(contrib/3M) + include_directories(contrib/3M) + set_config_option(HAVE_3M "3M") + endif() + + if(ENABLE_OSMESA) + find_library(OSMESA_LIB OSMesa) + if(OSMESA_LIB) + set_config_option(HAVE_OSMESA "OSMesa") + list(APPEND EXTERNAL_LIBRARIES ${OSMESA_LIB}) + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Graphics) + set(OpenGL_GL_PREFERENCE "LEGACY") + find_package(OpenGL REQUIRED) + if(OPENGL_GLU_FOUND AND OPENGL_FOUND) + add_subdirectory(Graphics) + set_config_option(HAVE_OPENGL "OpenGL") + else() + message(SEND_ERROR "Could not find GLU: disabling OpenGL support") + endif() + endif() +endif() + +if(ENABLE_ANN) + find_library(ANN_LIB ANN PATH_SUFFIXES lib) + find_path(ANN_INC "ANN.h" PATH_SUFFIXES src include ANN) + if(ENABLE_SYSTEM_CONTRIB AND ANN_LIB AND ANN_INC) + message(STATUS "Using system version of ANN") + list(APPEND EXTERNAL_LIBRARIES ${ANN_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ANN_INC}) + set_config_option(HAVE_ANN "ANN[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ANN) + add_subdirectory(contrib/ANN) + include_directories(contrib/ANN/include) + set_config_option(HAVE_ANN "ANN") + endif() +endif() + +if(ENABLE_ALGLIB) + find_library(ALGLIB_LIB alglib) + find_path(ALGLIB_INC "stdafx.h" PATH_SUFFIXES libalglib) + if(ENABLE_SYSTEM_CONTRIB AND ALGLIB_LIB AND ALGLIB_INC) + list(APPEND EXTERNAL_LIBRARIES ${ALGLIB_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ALGLIB_INC}) + set_config_option(HAVE_ALGLIB "ALGLIB[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ALGLIB) + add_subdirectory(contrib/ALGLIB) + include_directories(contrib/ALGLIB) + set_config_option(HAVE_ALGLIB "ALGLIB") + endif() +endif() + +if(HAVE_FLTK AND ENABLE_CAIRO) + find_library(CAIRO_LIB cairo) + find_path(CAIRO_INC "cairo/cairo.h" PATH_SUFFIXES include) + if(CAIRO_INC AND CAIRO_LIB) + set_config_option(HAVE_CAIRO "Cairo") + list(APPEND EXTERNAL_LIBRARIES ${CAIRO_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CAIRO_INC}) + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/DiscreteIntegration AND + ENABLE_DINTEGRATION) + add_subdirectory(contrib/DiscreteIntegration) + include_directories(contrib/DiscreteIntegration) + set_config_option(HAVE_DINTEGRATION "DIntegration") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/HighOrderMeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshQualityOptimizer AND + ENABLE_OPTHOM AND HAVE_MESH) + add_subdirectory(contrib/HighOrderMeshOptimizer) + include_directories(contrib/HighOrderMeshOptimizer) + add_subdirectory(contrib/MeshOptimizer) + include_directories(contrib/MeshOptimizer) + include_directories(${CMAKE_CURRENT_BINARY_DIR}/contrib/MeshOptimizer) + add_subdirectory(contrib/MeshQualityOptimizer) + include_directories(contrib/MeshQualityOptimizer) + set_config_option(HAVE_OPTHOM "OptHom") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/domhex AND + ENABLE_DOMHEX AND HAVE_MESH) + add_subdirectory(contrib/domhex) + include_directories(contrib/domhex) + set_config_option(HAVE_DOMHEX "DomHex") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/QuadTri AND + ENABLE_QUADTRI AND HAVE_MESH) + add_subdirectory(contrib/QuadTri) + include_directories(contrib/QuadTri) + set_config_option(HAVE_QUADTRI "QuadTri") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/kbipack AND ENABLE_KBIPACK) + set_config_option(HAVE_KBIPACK "Kbipack") + add_subdirectory(contrib/kbipack) + include_directories(contrib/kbipack) + if(ENABLE_GMP) + find_library(GMP_LIB libgmp.a) + find_path(GMP_INC "gmp.h" PATH_SUFFIXES src include) + endif() + if(GMP_LIB AND GMP_INC) + set_config_option(HAVE_GMP "GMP") + list(APPEND EXTERNAL_LIBRARIES ${GMP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GMP_INC}) + else() + message(STATUS "GMP not found: Kbipack uses long int") + endif() +endif() + +if(ENABLE_MATHEX) + find_library(MATHEX_LIB mathex PATH_SUFFIXES lib) + find_path(MATHEX_INC "mathex.h" PATH_SUFFIXES src include) + if(ENABLE_SYSTEM_CONTRIB AND MATHEX_LIB AND MATHEX_INC) + list(APPEND EXTERNAL_LIBRARIES ${MATHEX_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MATHEX_INC}) + set_config_option(HAVE_MATHEX "MathEx[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MathEx) + add_subdirectory(contrib/MathEx) + include_directories(contrib/MathEx) + set_config_option(HAVE_MATHEX "MathEx") + endif() +endif() + +if(ENABLE_MPI) + find_package(MPI) + if(MPI_FOUND) + set_config_option(HAVE_MPI "MPI") + list(APPEND EXTERNAL_INCLUDES ${MPI_CXX_INCLUDE_PATH}) + list(APPEND EXTERNAL_LIBRARIES ${MPI_CXX_LIBRARIES}) + set(CMAKE_C_COMPILER ${MPI_C_COMPILER}) + set(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER}) + set(CMAKE_Fortran_COMPILER ${MPI_Fortran_COMPILER}) + endif() +endif() + +if(ENABLE_POPPLER) + find_library(POPPLER_LIB poppler) + find_library(POPPLER_CPP_LIB poppler-cpp) + find_path(POPPLER_INC "poppler/cpp/poppler-document.h" PATH_SUFFIXES src include) + if(POPPLER_LIB AND POPPLER_INC) + set_config_option(HAVE_POPPLER "Poppler") + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_LIB}) + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_CPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${POPPLER_INC}) + endif() +endif() + +if(ENABLE_P4EST) + find_library(P4EST_LIB p4est) + find_path(P4EST_INC "p4est.h" PATH_SUFFIXES src) + find_library(SC_LIB sc) + if(P4EST_LIB AND P4EST_INC AND SC_LIB) + set_config_option(HAVE_P4EST "P4est") + list(APPEND EXTERNAL_LIBRARIES ${P4EST_LIB} ${SC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${P4EST_INC}) + endif() +endif() + +if(HAVE_MESH OR HAVE_SOLVER) + if(ENABLE_METIS) + if(METIS_LIB AND METIS_INC) + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis") + else() + find_library(METIS_LIB metis PATH_SUFFIXES lib) + find_path(METIS_INC "metis.h" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC) + message(STATUS "Using system version of METIS") + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/metis) + add_definitions(-DUSE_GKREGEX) + add_subdirectory(contrib/metis) + include_directories(contrib/metis/include contrib/metis/libmetis + contrib/metis/GKlib) + set_config_option(HAVE_METIS "Metis") + endif() + endif() + endif() +endif() + +if(HAVE_MESH) + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh/tetgenBR.cxx) + set_config_option(HAVE_TETGENBR "TetGen/BR") + endif() + + if(ENABLE_VOROPP) + find_library(VOROPP_LIB voro++) + find_path(VOROPP_INC "voro++.hh" PATH_SUFFIXES voro++) + if(ENABLE_SYSTEM_CONTRIB AND VOROPP_LIB AND VOROPP_INC) + message(STATUS "Using system version of voro++") + list(APPEND EXTERNAL_LIBRARIES ${VOROPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${VOROPP_INC}) + set_config_option(HAVE_VOROPP "Voro++[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++) + add_subdirectory(contrib/voro++) + include_directories(contrib/voro++/src) + set_config_option(HAVE_VOROPP "Voro++") + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/blossom AND ENABLE_BLOSSOM) + add_subdirectory(contrib/blossom) + include_directories(contrib/blossom/MATCH contrib/blossom/concorde97 + contrib/blossom/concorde97/INCLUDE) + set_config_option(HAVE_BLOSSOM "Blossom") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/Netgen AND ENABLE_NETGEN) + add_subdirectory(contrib/Netgen) + include_directories(contrib/Netgen contrib/Netgen/libsrc/include + contrib/Netgen/nglib) + set_config_option(HAVE_NETGEN "Netgen") + add_definitions(-DNO_PARALLEL_THREADS -DNOTCL) + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/bamg AND ENABLE_BAMG) + add_subdirectory(contrib/bamg) + include_directories(contrib/bamg contrib/bamg/bamglib) + set_config_option(HAVE_BAMG "Bamg") + endif() + + if(ENABLE_MMG) + find_library(MMG_LIB NAMES Mmg mmg) + find_path(MMG_INC "libmmg.h" PATH_SUFFIXES mmg) + if(MMG_LIB AND MMG_INC) + list(APPEND EXTERNAL_LIBRARIES ${MMG_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MMG_INC}) + set_config_option(HAVE_MMG "Mmg") + endif() + endif() +endif() + +if(ENABLE_MED OR ENABLE_CGNS) + find_package(HDF5) + if(HDF5_FOUND) + set(HDF5_LIB "${HDF5_C_LIBRARIES}") + list(APPEND EXTERNAL_INCLUDES ${HDF5_INCLUDE_DIRS}) + if(ENABLE_MED) + find_library(MED_LIB medC) + if(MED_LIB) + set_config_option(HAVE_MED "Med") + list(APPEND EXTERNAL_LIBRARIES ${MED_LIB}) + endif() + endif() + if(ENABLE_CGNS) + find_library(CGNS_LIB cgns HINTS ENV CGNS_ROOT PATH_SUFFIXES lib) + find_path(CGNS_INC "cgnslib.h" HINTS ENV CGNS_ROOT PATH_SUFFIXES include) + if(CGNS_LIB AND CGNS_INC) + set_config_option(HAVE_LIBCGNS "Cgns") + list(APPEND EXTERNAL_LIBRARIES ${CGNS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CGNS_INC}) + if(ENABLE_CGNS_CPEX0045) + set_config_option(HAVE_LIBCGNS_CPEX0045 "Cgns_CPEX0045") + endif() + endif() + endif() + if(MED_LIB OR CGNS_LIB) + list(APPEND EXTERNAL_LIBRARIES ${HDF5_LIB}) + find_library(SZ_LIB NAMES szlib sz) + if(SZ_LIB) + list(APPEND EXTERNAL_LIBRARIES ${SZ_LIB}) + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + endif() + endif() + endif() + else() + message(STATUS "HDF5 not found") + endif() +endif() + +if(HAVE_SOLVER) + if(ENABLE_GMM) + find_path(GMM_INC "gmm.h" PATH_SUFFIXES src include include/gmm) + if(ENABLE_SYSTEM_CONTRIB AND GMM_INC) + message(STATUS "Using system version of GMM") + list(APPEND EXTERNAL_INCLUDES ${GMM_INC}) + set_config_option(HAVE_GMM "Gmm[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/gmm) + include_directories(contrib/gmm) + set_config_option(HAVE_GMM "Gmm") + endif() + endif() + + if(ENABLE_PETSC) + if(PETSC_DIR) + set(ENV_PETSC_DIR ${PETSC_DIR}) + else() + set(ENV_PETSC_DIR $ENV{PETSC_DIR}) + endif() + if(PETSC_ARCH) + set(ENV_PETSC_ARCH ${PETSC_ARCH}) + else() + set(ENV_PETSC_ARCH $ENV{PETSC_ARCH}) + endif() + set(PETSC_POSSIBLE_CONF_FILES + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc-conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc/conf/petscvariables) + foreach(FILE ${PETSC_POSSIBLE_CONF_FILES}) + if(EXISTS ${FILE}) + # old-style PETSc installations (using PETSC_DIR and PETSC_ARCH) + message(STATUS "Using PETSc dir: ${ENV_PETSC_DIR}") + message(STATUS "Using PETSc arch: ${ENV_PETSC_ARCH}") + # find includes by parsing the petscvariables file + file(STRINGS ${FILE} PETSC_VARIABLES NEWLINE_CONSUME) + endif() + endforeach() + if(PETSC_VARIABLES) + # try to find PETSC_CC_INCLUDES for PETSc >= 3.4 + string(REGEX MATCH "PETSC_CC_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "PETSC_CC_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + else() + # try to find PETSC_PACKAGES_INCLUDES in older versions + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/include) + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/include) + string(REGEX MATCH "PACKAGES_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + string(REPLACE "PACKAGES_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + endif() + if(PETSC_PACKAGES_INCLUDES) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "-I" "" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + string(REPLACE " " ";" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + foreach(VAR ${PETSC_PACKAGES_INCLUDES}) + # seem to include unexisting directories (/usr/include/lib64) + # check to avoid warnings + if(EXISTS ${VAR}) + list(APPEND EXTERNAL_INCLUDES ${VAR}) + endif() + endforeach() + endif() + endif() + # find libraries (<= 3.0) + set(PETSC_LIBS_REQUIRED petscksp petscdm petscmat petscvec petsc) + find_all_libraries(PETSC_LIBS PETSC_LIBS_REQUIRED + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib "") + # petsc 3.1 creates only one library (libpetsc) + if(NOT PETSC_LIBS) + find_library(PETSC_LIBS petsc PATHS ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + endif() + if(PETSC_LIBS) + set_config_option(HAVE_PETSC "PETSc") + if(NOT HAVE_BLAS) + set_config_option(HAVE_BLAS "Blas[petsc]") + endif() + if(NOT HAVE_LAPACK) + set_config_option(HAVE_LAPACK "Lapack[petsc]") + endif() + endif() + # find slepc (needs to be linked in before petsc) + if(ENABLE_SLEPC) + if(SLEPC_DIR) + set(ENV_SLEPC_DIR ${SLEPC_DIR}) + else() + set(ENV_SLEPC_DIR $ENV{SLEPC_DIR}) + endif() + find_library(SLEPC_LIB slepc PATHS ${ENV_SLEPC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + if(SLEPC_LIB) + find_path(SLEPC_INC "slepc.h" PATHS ${ENV_SLEPC_DIR} PATH_SUFFIXES include + ${ENV_PETSC_ARCH}/include include/slepc NO_DEFAULT_PATH) + if(SLEPC_INC) + message(STATUS "Using SLEPc dir: ${ENV_SLEPC_DIR}") + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + find_path(SLEPC_INC2 "slepcconf.h" PATHS ${ENV_SLEPC_DIR} + PATH_SUFFIXES ${ENV_PETSC_ARCH}/include NO_DEFAULT_PATH) + if(SLEPC_INC2) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC2}) + endif() + endif() + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + # find additional libraries to link with + string(REGEX MATCH "PACKAGES_LIBS = [^\n\r]*" PLIBS ${PETSC_VARIABLES}) + if(PLIBS) + string(REPLACE "PACKAGES_LIBS = " "" PLIBS ${PLIBS}) + string(STRIP ${PLIBS} PLIBS) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS}") + endif() + string(REGEX MATCH "PETSC_EXTERNAL_LIB_BASIC = [^\n\r]*" PLIBS_BASIC ${PETSC_VARIABLES}) + if(PLIBS_BASIC) + string(REPLACE "PETSC_EXTERNAL_LIB_BASIC = " "" PLIBS_BASIC ${PLIBS_BASIC}) + string(STRIP ${PLIBS_BASIC} PLIBS_BASIC) + separate_arguments(PLIBS_BASIC) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS_BASIC}") + endif() + string(REGEX MATCH "PCC_LINKER_LIBS = [^\n\r]*" LLIBS ${PETSC_VARIABLES}) + if(LLIBS) + string(REPLACE "PCC_LINKER_LIBS = " "" LLIBS ${LLIBS}) + string(STRIP ${LLIBS} LLIBS) + list(APPEND EXTERNAL_LIBRARIES "${LLIBS}") + endif() + else() + # new-style PETSc installations (in standard system directories) + find_library(PETSC_LIBS petsc) + find_path(PETSC_INC "petsc.h" PATH_SUFFIXES include/petsc) + if(PETSC_LIBS AND PETSC_INC) + set_config_option(HAVE_PETSC "PETSc") + if(ENABLE_SLEPC) + find_library(SLEPC_LIB slepc) + find_path(SLEPC_INC "slepc.h" PATH_SUFFIXES include/slepc) + if(SLEPC_LIB AND SLEPC_INC) + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${PETSC_INC}) + endif() + endif() + endif() + + if(ENABLE_MUMPS AND HAVE_BLAS AND HAVE_LAPACK) + set(MUMPS_LIBS_REQUIRED smumps dmumps cmumps zmumps mumps_common pord) + if(NOT ENABLE_MPI) + list(APPEND MUMPS_LIBS_REQUIRED mpiseq) + endif() + find_all_libraries(MUMPS_LIBRARIES MUMPS_LIBS_REQUIRED "" "lib") + find_path(SMUMPS_INC "smumps_c.h" PATH_SUFFIXES src include) + find_path(DMUMPS_INC "dmumps_c.h" PATH_SUFFIXES src include) + find_path(CMUMPS_INC "cmumps_c.h" PATH_SUFFIXES src include) + find_path(ZMUMPS_INC "zmumps_c.h" PATH_SUFFIXES src include) + if(MUMPS_LIBRARIES AND SMUMPS_INC AND DMUMPS_INC AND CMUMPS_INC AND ZMUMPS_INC) + set_config_option(HAVE_MUMPS "MUMPS") + list(APPEND EXTERNAL_LIBRARIES ${MUMPS_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${SMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${DMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${CMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${ZMUMPS_INC}) + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND EXTERNAL_LIBRARIES ${GFORTRAN_LIB}) + endif() + if(ENABLE_GMM) # use GMM/MUMPS interface + add_definitions(-DGMM_USES_MUMPS) + endif() + endif() + endif() + + if(ENABLE_GETDP) + find_library(GETDP_LIB GetDP) + find_path(GETDP_INC "GetDP.h" PATH_SUFFIXES getdp) + if(GETDP_LIB AND GETDP_INC) + set_config_option(HAVE_GETDP "GetDP") + list(APPEND EXTERNAL_LIBRARIES ${GETDP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GETDP_INC}) + endif() + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt AND ENABLE_HXT) + add_subdirectory(contrib/hxt) + include_directories(BEFORE ${HXT_INC_DIRS}) + set_config_option(HAVE_HXT "Hxt") + # do not use arithmetic contraction in predicates.c + if(MSVC OR (CMAKE_C_COMPILER_ID STREQUAL "Intel" AND WIN32)) + set_source_files_properties( + "${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/predicates/src/predicates.c" + PROPERTIES COMPILE_FLAGS "/fp:strict") + elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel") + set_source_files_properties( + "${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/predicates/src/predicates.c" + PROPERTIES COMPILE_FLAGS "-fp-model strict") + elseif(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang") + set_source_files_properties( + "${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/predicates/src/predicates.c" + PROPERTIES COMPILE_FLAGS "-fno-unsafe-math-optimizations -ffp-contract=off") + else() + message(WARNING + "Unsupported compiler ! + Make sure compiled functions from predicates.c + do NOT use extended double precision and follow IEEE754 standard. + It is crucial for the robustness of geometric predicates.") + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/pro AND ENABLE_PRO) + add_subdirectory(pro) +endif() + +if(ENABLE_OCC) + set(OCC_MINIMAL_VERSION "6.9.1") + if(WIN32) + if(HAVE_64BIT_SIZE_T) + set(OCC_SYS_NAME win64) + else() + set(OCC_SYS_NAME win32) + endif() + else() + set(OCC_SYS_NAME ${CMAKE_SYSTEM_NAME}) + endif() + find_path(OCC_INC "Standard_Version.hxx" HINTS ENV CASROOT PATH_SUFFIXES + inc include include/oce opencascade include/opencascade + occt include/occt) + if(OCC_INC) + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAJOR REGEX "#define OCC_VERSION_MAJOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MINOR REGEX "#define OCC_VERSION_MINOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAINT REGEX "#define OCC_VERSION_MAINTENANCE.*") + if(OCC_MAJOR AND OCC_MINOR AND OCC_MAINT) + string(REGEX MATCH "[0-9]+" OCC_MAJOR "${OCC_MAJOR}") + string(REGEX MATCH "[0-9]+" OCC_MINOR "${OCC_MINOR}") + string(REGEX MATCH "[0-9]+" OCC_MAINT "${OCC_MAINT}") + set(OCC_VERSION "${OCC_MAJOR}.${OCC_MINOR}.${OCC_MAINT}") + message(STATUS "Found OpenCASCADE version ${OCC_VERSION} in ${OCC_INC}") + endif() + endif() + if(OCC_VERSION AND OCC_VERSION STRLESS ${OCC_MINIMAL_VERSION}) + message(WARNING "Gmsh requires OpenCASCADE >= ${OCC_MINIMAL_VERSION}. " + "Use CMAKE_PREFIX_PATH or the CASROOT environment variable " + "to explicitely specify the installation path of OpenCASCADE") + elseif(OCC_INC) + set(OCC_LIBS_REQUIRED + # subset of DataExchange + TKSTEP TKSTEP209 TKSTEPAttr TKSTEPBase TKIGES TKXSBase + # ModelingAlgorithms + TKOffset TKFeat TKFillet TKBool TKMesh TKHLR TKBO TKPrim TKShHealing + TKTopAlgo TKGeomAlgo + # ModelingData + TKBRep TKGeomBase TKG3d TKG2d + # FoundationClasses + TKMath TKernel) + if(ENABLE_OCC_TBB) + list(APPEND OCC_LIBS_REQUIRED tbb tbbmalloc) + endif() + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS_REQUIRED) + if(OCC_LIBS) + message(STATUS "OCC libraries specified explicitly: " ${OCC_LIBS}) + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS) + else() + set(OCC_LIBS) + foreach(OCC ${OCC_LIBS_REQUIRED}) + find_library(OCC_LIB ${OCC} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib + ${OCC_SYS_NAME}/gcc/lib ${OCC_SYS_NAME}/gcc/bin) + if(OCC_LIB) + list(APPEND OCC_LIBS ${OCC_LIB}) + else() + message(STATUS "OCC lib " ${OCC} " not Found") + endif() + unset(OCC_LIB CACHE) + endforeach() + list(LENGTH OCC_LIBS NUM_OCC_LIBS) + endif() + endif() + + # additional OCC libraries to handle reading of STEP/IGES attributes. Oh my... + if(ENABLE_OCC_CAF) + find_package(Freetype) + if(FREETYPE_FOUND) + set(OCC_CAF_LIBS_REQUIRED + TKXDESTEP TKXDEIGES TKXCAF TKLCAF TKVCAF TKCAF TKV3d TKService TKCDF) + list(LENGTH OCC_CAF_LIBS_REQUIRED NUM_OCC_CAF_LIBS_REQUIRED) + set(OCC_CAF_LIBS) + foreach(OCC ${OCC_CAF_LIBS_REQUIRED}) + find_library(OCC_CAF_LIB ${OCC} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib + ${OCC_SYS_NAME}/gcc/lib ${OCC_SYS_NAME}/gcc/bin) + if(OCC_CAF_LIB) + list(APPEND OCC_CAF_LIBS ${OCC_CAF_LIB}) + else() + message(STATUS "OCC CAF lib " ${OCC} " not Found") + endif() + unset(OCC_CAF_LIB CACHE) + endforeach() + list(LENGTH OCC_CAF_LIBS NUM_OCC_CAF_LIBS) + endif() + endif() + + if(NUM_OCC_LIBS EQUAL NUM_OCC_LIBS_REQUIRED) + # append OCC CAF libraries first... + if(NUM_OCC_CAF_LIBS EQUAL NUM_OCC_CAF_LIBS_REQUIRED) + set_config_option(HAVE_OCC_CAF "OpenCASCADE-CAF") + list(APPEND EXTERNAL_LIBRARIES ${OCC_CAF_LIBS} ${FREETYPE_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${FREETYPE_INCLUDE_DIRS}) + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "windowscodecs") + list(APPEND EXTERNAL_LIBRARIES "ole32") + endif() + endif() + # then append OCC libraries + set_config_option(HAVE_OCC "OpenCASCADE") + list(APPEND EXTERNAL_LIBRARIES ${OCC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${OCC_INC}) + if(HAVE_64BIT_SIZE_T) + add_definitions(-D_OCC64) + endif() + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "winspool") + add_definitions(-DOCC_CONVERT_SIGNALS) + elseif(MSVC) + add_definitions(-DWNT) + endif() + endif() +endif() + +if(ENABLE_ZIPPER) + if(ENABLE_BUILD_IOS) + set_config_option(HAVE_LIBZ "Zlib") + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/zipper AND HAVE_LIBZ) + add_subdirectory(contrib/zipper) + include_directories(contrib/zipper) + set_config_option(HAVE_ZIPPER "Zipper") + endif() +endif() + +if(ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON) + find_package(SWIG REQUIRED) + include(${SWIG_USE_FILE}) + find_package(PythonLibs) + if(SWIG_FOUND AND PYTHONLIBS_FOUND) + message(STATUS "Found SWIG version " ${SWIG_VERSION}) + find_package(PythonInterp) + string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION) + if(SWIG_MAJOR_VERSION EQUAL 1) + message(WARNING "Python bindings require SWIG >= 2: disabling Python") + else() + set_config_option(HAVE_PYTHON "Python") + mark_as_advanced(CLEAR PYTHON_LIBRARY PYTHON_INCLUDE_DIR) + if(ENABLE_NUMPY) + if (NOT NUMPY_INC) + EXEC_PROGRAM (${PYTHON_EXECUTABLE} + ARGS "-c \"import numpy; print(numpy.get_include())\"" + OUTPUT_VARIABLE NUMPY_INC + RETURN_VALUE NUMPY_NOT_FOUND) + endif() + if(NUMPY_INC) + list(APPEND EXTERNAL_INCLUDES ${NUMPY_INC}) + set_config_option(HAVE_NUMPY "Numpy") + endif() + endif() + if(HAVE_PETSC) + if(ENABLE_PETSC4PY) + EXECUTE_PROCESS( + COMMAND ${PYTHON_EXECUTABLE} -c "import petsc4py; print(petsc4py.get_include())" + OUTPUT_VARIABLE PETSC4PY_INC + RESULT_VARIABLE PETSC4PY_NOT_FOUND + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(PETSC4PY_INC) + list(APPEND EXTERNAL_INCLUDES ${PETSC4PY_INC}) + set_config_option(HAVE_PETSC4PY "PETSc4py") + endif() + endif() + endif() + endif() + endif() +endif() + +check_function_exists(vsnprintf HAVE_VSNPRINTF) +if(NOT HAVE_VSNPRINTF AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_VSNPRINTF "NoVsnprintf") +endif() + +check_include_file(sys/socket.h HAVE_SYS_SOCKET_H) +if(HAVE_SYS_SOCKET_H) + set(CMAKE_EXTRA_INCLUDE_FILES sys/socket.h) +endif() +check_type_size(socklen_t SOCKLEN_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT SOCKLEN_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_SOCKLEN_T "NoSocklenT") +endif() + +check_include_file(stdint.h HAVE_STDINT_H) +if(HAVE_STDINT_H) + set(CMAKE_EXTRA_INCLUDE_FILES stdint.h) +else() + set_config_option(HAVE_NO_STDINT_H "NoStdintH") +endif() +check_type_size(intptr_t INTPTR_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT INTPTR_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_INTPTR_T "NoIntptrT") +endif() + +check_include_file(dlfcn.h DLFCN_H) +if(DLFCN_H) + set_config_option(HAVE_DLOPEN "Dlopen") + list(APPEND EXTERNAL_LIBRARIES ${CMAKE_DL_LIBS}) +endif() + +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + check_include_file(linux/joystick.h LINUX_JOYSTICK_H) + if(LINUX_JOYSTICK_H) + set_config_option(HAVE_LINUX_JOYSTICK "LinuxJoystick") + endif() +endif() + +if(WIN32) + add_definitions(-D_USE_MATH_DEFINES) + list(APPEND EXTERNAL_LIBRARIES winmm wsock32 ws2_32 psapi) +endif() + +if(MSVC) + add_definitions(-DNOMINMAX -D_CRT_SECURE_NO_DEPRECATE -D_SCL_SECURE_NO_DEPRECATE) +endif() + +# add C functions API +set(GMSH_SRC ${GMSH_SRC};api/gmshc.cpp) + +# force full warnings to encourage everybody to write clean(er) code +check_cxx_compiler_flag("-Wall" WALL) +if(WALL AND NOT MSVC) + file(GLOB_RECURSE WALL_SRC Common/*.cpp Fltk/*.cpp FunctionSpace/*.cpp + Geo/*.cpp Graphics/*.cpp Mesh/*.cpp Numeric/*.cpp Parser/*.cpp + Plugin/*.cpp Post/*.cpp Solver/*.cpp) + set(WF "-Wall") + check_cxx_compiler_flag("-Wint-to-void-pointer-cast" WCAST) + if(WCAST) + set(WF "${WF} -Wno-int-to-void-pointer-cast") + endif() + check_cxx_compiler_flag("-Wdeprecated-declarations" WDEPREC) + if(WDEPREC) + # FIXME: remove this when we have fixed the deprecated GLU code for OpenGL3 + set(WF "${WF} -Wno-deprecated-declarations") + endif() + check_cxx_compiler_flag("-Wmisleading-indentation" WIND) + if(WIND) + set(WF "${WF} -Wno-misleading-indentation") + endif() + check_cxx_compiler_flag("-Wno-attributes" WATTR) + if(WATTR) + # FIXME: remove this when GCC behaves more intelligently + set(WF "${WF} -Wno-attributes") + endif() + set_compile_flags(WALL_SRC ${WF}) +endif() + +# don't issue warnings for contributed libraries +check_cxx_compiler_flag("-w" NOWARN) +if(NOWARN) + file(GLOB_RECURSE NOWARN_SRC contrib/*.cpp contrib/*.cc contrib/*.cxx contrib/*.c) + set_compile_flags(NOWARN_SRC "-w") +endif() + +# disable compile optimization on some known problematic files +check_cxx_compiler_flag("-O0" NOOPT) +if(NOOPT OR ENABLE_BUILD_IOS) + if(ENABLE_BUILD_IOS) # optimized iOS 10 64 bits screws somewhere in Geo + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Geo/G*.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* Mesh/Background*) + else() + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* contrib/bamg/* Mesh/Background*) + endif() + set_compile_flags(NOOPT_SRC "-O0") +endif() + +# do not use arithmetic contraction in predicates.cpp +# if("${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "/fp:strict") +# elseif(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fno-unsafe-math-optimizations -ffp-contract=off") +# elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fp-model strict") +# endif() + +# enable Revoropt and set compile flags for the corresponding plugin +if(ENABLE_REVOROPT) + if(HAVE_EIGEN AND HAVE_MESH AND HAVE_PLUGINS AND HAVE_ANN AND HAVE_ALGLIB) + list(APPEND EXTERNAL_INCLUDES contrib/Revoropt/include) + set_config_option(HAVE_REVOROPT "Revoropt") + add_definitions(-DUSE_ANN) + else() + message(WARNING "Revoropt requires Eigen, Mesh, Plugins, ANN and ALGLIB") + endif() +endif() + +if(HAVE_MESH AND NOT HAVE_EIGEN AND NOT HAVE_LAPACK) + message(WARNING "Most meshing algorithms will not be functional without " + "Eigen or Lapack") +endif() + +list(SORT CONFIG_OPTIONS) +set(GMSH_CONFIG_OPTIONS "") +foreach(OPT ${CONFIG_OPTIONS}) + set(GMSH_CONFIG_OPTIONS "${GMSH_CONFIG_OPTIONS} ${OPT}") +endforeach() + +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshConfig.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshVersion.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h) + +# the texi and pypi version files are modified in the source directory (not +# ideal for version.texi, but since git tracks the contents of the file this is +# acceptable as it will only change when the actual version is changed - not for +# each git hash; setup.py is not under version control) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi.in + ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh/setup.py.in + ${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh/setup.py) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh-dev/setup.py.in + ${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh-dev/setup.py) + +file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/version.txt ${GMSH_SHORT_VERSION}) + +# process cmake environment variables so we can append them to the -I include +# commands. This is not recommended (we should only use the cache variables) but +# it is very convenient: otherwise we have to remember providing the +# -D... options to cmake for each new build. +set(ENV_CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH}) +set(ENV_CMAKE_INCLUDE_PATH $ENV{CMAKE_INCLUDE_PATH}) +if(UNIX) + if(ENV_CMAKE_PREFIX_PATH) + string(REPLACE ":" ";" ENV_CMAKE_PREFIX_PATH ${ENV_CMAKE_PREFIX_PATH}) + endif() + if(ENV_CMAKE_INCLUDE_PATH) + string(REPLACE ":" ";" ENV_CMAKE_INCLUDE_PATH ${ENV_CMAKE_INCLUDE_PATH}) + endif() +endif() +list(APPEND EXTERNAL_INCLUDES ${CMAKE_INCLUDE_PATH} ${ENV_CMAKE_INCLUDE_PATH}) +list(APPEND EXTERNAL_INCLUDES ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) +foreach(DIR ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/include) +endforeach() + +if(EXTERNAL_INCLUDES) + list(REMOVE_DUPLICATES EXTERNAL_INCLUDES) +endif() + +if(HAVE_FLTK) + set(LINK_LIBRARIES ${FLTK_LIBRARIES} ${EXTERNAL_LIBRARIES} + ${OPENGL_LIBRARIES} ${LAPACK_LIBRARIES}) +elseif(HAVE_OPENGL) + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${OPENGL_LIBRARIES} + ${LAPACK_LIBRARIES}) +else() + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) +endif() + +# try to use static gfortran on static builds (cannot do this on dynamic builds +# as e.g. Debian compiles libgfortran.a without -fPIC: sigh...) +if(NOT ENABLE_BUILD_DYNAMIC AND NOT ENABLE_BUILD_SHARED) + find_library(GFORTRAN_STATIC libgfortran.a) + if(GFORTRAN_STATIC) + set(CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES) + message(STATUS "Using static libgfortran") + foreach(STR ${LINK_LIBRARIES}) + string(REPLACE "-lgfortran" ${GFORTRAN_STATIC} STR2 ${STR}) + list(APPEND LINK_LIBRARIES2 ${STR2}) + endforeach() + set(LINK_LIBRARIES ${LINK_LIBRARIES2}) + endif() +endif() + +# Linux-specific linker options +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + if(HAVE_OCC) + find_library(RT_LIB rt) + if(RT_LIB) + list(APPEND LINK_LIBRARIES ${RT_LIB}) + endif() + endif() + if(CMAKE_C_COMPILER_ID MATCHES "GNU" OR CMAKE_C_COMPILER_ID MATCHES "Intel") + add_definitions(-fPIC) + endif() +endif() + +# we could specify include dirs more selectively, but this is simpler +include_directories(Common Fltk Geo Graphics Mesh Solver Numeric Parser + Plugin Post api ${EXTERNAL_INCLUDES} ${CMAKE_CURRENT_BINARY_DIR}/Common) + +# set this for external codes that might include this CMakeList file +set(GMSH_EXTERNAL_INCLUDE_DIRS ${EXTERNAL_INCLUDES} CACHE + STRING "External include directories" FORCE) +set(GMSH_EXTERNAL_LIBRARIES ${LINK_LIBRARIES} CACHE + STRING "External libraries" FORCE) + +# group sources for easier navigation in IDEs +foreach(DIR ${GMSH_DIRS}) + string(REGEX REPLACE "\\+" "\\\\+" DIR ${DIR}) + source_group(${DIR} REGULAR_EXPRESSION ${DIR}/.*) +endforeach() + +# static library target +if(ENABLE_BUILD_LIB) + add_library(lib STATIC ${GMSH_SRC}) + set_target_properties(lib PROPERTIES OUTPUT_NAME gmsh) + if(MSVC) + set_target_properties(lib PROPERTIES DEBUG_POSTFIX d) + if(ENABLE_MSVC_STATIC_RUNTIME) + set_target_properties(lib PROPERTIES LINK_FLAGS_RELEASE "/nodefaultlib:LIBCMT") + endif() + endif() +endif() + +# shared library target +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + add_library(shared SHARED ${GMSH_SRC}) + set_target_properties(shared PROPERTIES OUTPUT_NAME gmsh + VERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION} + SOVERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}) + if(WIN32) + set_target_properties(shared PROPERTIES PREFIX "" IMPORT_PREFIX "" + IMPORT_SUFFIX ".lib" COMPILE_FLAGS "-DGMSH_DLL -DGMSH_DLL_EXPORT") + endif() + target_link_libraries(shared ${LINK_LIBRARIES}) + # don't define LC_RPATH in dylib for development, to not get endless warnings + # about code signing + if(APPLE AND NOT GMSH_RELEASE) + set_target_properties(shared PROPERTIES INSTALL_RPATH "") + endif() + if(MSVC AND ENABLE_MSVC_STATIC_RUNTIME) + message(STATUS "Note: By enabling ENABLE_MSVC_STATIC_RUNTIME, shared library " + "won't link. In MSVC change /MT to /MD in the shared project properties") + endif() +endif() + +# binary targets +if(HAVE_FLTK) + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh WIN32 Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh WIN32 Common/Main.cpp ${GMSH_SRC}) + endif() + # we could add this to create a minimal app bundle even without install + # if(APPLE AND NOT ENABLE_OS_SPECIFIC_INSTALL) + # set_target_properties(gmsh PROPERTIES MACOSX_BUNDLE ON + # MACOSX_BUNDLE_INFO_PLIST ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_dev.plist) + # endif() +else() + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh Common/Main.cpp ${GMSH_SRC}) + endif() +endif() +target_link_libraries(gmsh ${LINK_LIBRARIES}) + +# Windows specific linker options +if(WIN32 AND NOT MSVC) + set(FLAGS "-Wl,--stack,16777216 -static -municode") + if(HAVE_FLTK) + set(FLAGS "${FLAGS} -mwindows") + else() + set(FLAGS "${FLAGS} -mconsole") + endif() + if(HAVE_64BIT_SIZE_T) + set(FLAGS "${FLAGS} \"${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win64Icon.res\"") + else() + set(FLAGS "${FLAGS} \"${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win32Icon.res\"") + endif() + set_target_properties(gmsh PROPERTIES LINK_FLAGS "${FLAGS}") + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + set_target_properties(shared PROPERTIES LINK_FLAGS -static) + endif() + # remove -Wl,-Bdynamic flags + set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) + set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS) +elseif(MSVC) + set_target_properties(gmsh PROPERTIES LINK_FLAGS "/STACK:16777216 /SAFESEH:NO") +endif() + +# android target +if(ENABLE_BUILD_ANDROID) + find_file(CMAKE_TOOLCHAIN_FILE "android.toolchain.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for android without android-cmake") + endif() + add_definitions(-D_GLIBCXX_USE_C99_MATH=1) + set(CMAKE_BUILD_TYPE Release) + set(LIBRARY_OUTPUT_PATH_ROOT ${CMAKE_CURRENT_BINARY_DIR}) + set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_BINARY_DIR}/libs/) + add_definitions(-DBUILD_ANDROID) + add_definitions(-DPICOJSON_USE_LOCALE=0) + add_library(androidGmsh SHARED ${GMSH_SRC}) + set_target_properties(androidGmsh PROPERTIES OUTPUT_NAME gmsh) + target_link_libraries(androidGmsh ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) + add_custom_command(TARGET androidGmsh POST_BUILD COMMAND + ${CMAKE_STRIP} ${LIBRARY_OUTPUT_PATH}/libgmsh.so) +endif() + +# parser target +find_program(BISON bison) +find_program(FLEX flex) +if(BISON AND FLEX) + add_custom_target(parser + COMMAND ${BISON} -p gmsh_yy --output Gmsh.tab.cpp -d Gmsh.y + COMMAND ${FLEX} -P gmsh_yy -o Gmsh.yy.cpp Gmsh.l + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Parser) +endif() + +if(UNIX) + # cannot use cmake's file search functions here (they would only find files + # existing at configuration time) + add_custom_target(purge + COMMAND rm -f `find . -name *~ -o -name *~~` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + add_custom_target(etags + COMMAND etags `find . -name *.cpp -o -name *.h -o -name *.y` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion + OUTPUT_VARIABLE CXX_COMPILER_VERSION + OUTPUT_STRIP_TRAILING_WHITESPACE) +else() + set(CXX_COMPILER_VERSION "Unknown") +endif() + +set(WELCOME_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/WELCOME.txt) +set(SDK_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/SDK.txt) +set(LICENSE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE.txt) +set(CREDITS_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CREDITS.txt) +set(CHANGELOG_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.txt) +file(GLOB TUTORIAL_GEO_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/?*.*) +file(GLOB TUTORIAL_CPP_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c++/?*.*) +file(GLOB TUTORIAL_C_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c/?*.*) +file(GLOB TUTORIAL_PY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/python/?*.*) +file(GLOB TUTORIAL_JL_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/julia/?*.*) +file(GLOB DEMOS ${CMAKE_CURRENT_SOURCE_DIR}/demos/*) +foreach(SUBDIR ${DEMOS}) + if(IS_DIRECTORY ${SUBDIR}) + list(APPEND DEMOS_DIRS ${SUBDIR}) + endif() +endforeach() +set(TEX_DIR ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo) +file(GLOB TEX_SRC ${TEX_DIR}/*.texi) +set(TEX_OBJ ${TEX_DIR}/gmsh.aux ${TEX_DIR}/gmsh.cp ${TEX_DIR}/gmsh.cps + ${TEX_DIR}/gmsh.fn ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.ky + ${TEX_DIR}/gmsh.log ${TEX_DIR}/gmsh.pdf ${TEX_DIR}/gmsh.pg ${TEX_DIR}/gmsh.toc + ${TEX_DIR}/gmsh.tp ${TEX_DIR}/gmsh.tps ${TEX_DIR}/gmsh.txt ${TEX_DIR}/gmsh.vr) + +macro(unix2dos VARNAME) + file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/unix2dos) + set(UNIX2DOS_FILES) + foreach(FILE ${${VARNAME}}) + file(READ ${FILE} F0) + get_filename_component(N ${FILE} NAME) + if(CYGWIN) + string(REGEX REPLACE "\n" "\r\n" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F1}") + else() # if not in Cygwin, cmake adds '\r's automatically + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F0}") + endif() + list(APPEND UNIX2DOS_FILES ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N}) + endforeach() + set(${VARNAME} ${UNIX2DOS_FILES}) +endmacro() + +if(WIN32) + if(ENABLE_OS_SPECIFIC_INSTALL) + set(GMSH_BIN .) + set(GMSH_LIB .) + set(GMSH_DOC .) + set(GMSH_MAN .) + set(GMSH_INC .) + else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) + endif() + if(CYGWIN) + unix2dos(GMSH_API) + if(ENABLE_PRIVATE_API) + unix2dos(GMSH_PRIVATE_API) + endif() + unix2dos(WELCOME_FILE) + unix2dos(SDK_FILE) + unix2dos(LICENSE_FILE) + unix2dos(CREDITS_FILE) + unix2dos(CHANGELOG_FILE) + unix2dos(TUTORIAL_GEO_FILES) + unix2dos(TUTORIAL_CPP_FILES) + unix2dos(TUTORIAL_C_FILES) + unix2dos(TUTORIAL_PY_FILES) + unix2dos(TUTORIAL_JL_FILES) + foreach(DIR ${DEMOS_DIRS}) + file(GLOB DEMO_FILES ${DIR}/?*.*) + unix2dos(DEMO_FILES) + endforeach() + endif() +elseif(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + # set these so that the files get installed nicely in the MacOSX + # .app bundle + set(GMSH_BIN ../MacOS) + set(GMSH_LIB ../MacOS) + set(GMSH_DOC ../../..) + set(GMSH_MAN ../../..) + set(GMSH_INC ../MacOS) +else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) +endif() + +# mark targets as optional so we can install them separately if needed +# (e.g. "make lib" or "make shared" followed by "make install/fast") +install(TARGETS gmsh DESTINATION ${GMSH_BIN} OPTIONAL) +if(ENABLE_BUILD_LIB) + install(TARGETS lib DESTINATION ${GMSH_LIB} OPTIONAL) +endif() +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(TARGETS shared DESTINATION ${GMSH_LIB} OPTIONAL) +endif() + +if(ENABLE_ONELAB) + install(FILES ${ONELAB_PY} DESTINATION ${GMSH_BIN}) +endif() +if(ENABLE_BUILD_LIB OR ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(FILES ${GMSH_API} DESTINATION ${GMSH_INC}) + install(FILES ${GMSH_PY} DESTINATION ${GMSH_LIB}) + install(FILES ${GMSH_JL} DESTINATION ${GMSH_LIB}) + if(ENABLE_PRIVATE_API) + install(FILES ${GMSH_PRIVATE_API} DESTINATION ${GMSH_INC}/gmsh) + endif() +endif() +if(INSTALL_SDK_README) + configure_file(${SDK_FILE} ${CMAKE_CURRENT_BINARY_DIR}/README.txt) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/README.txt DESTINATION .) +endif() +install(FILES ${WELCOME_FILE} DESTINATION ${GMSH_DOC} RENAME README.txt) +install(FILES ${LICENSE_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CREDITS_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CHANGELOG_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${TUTORIAL_GEO_FILES} DESTINATION ${GMSH_DOC}/tutorial) +install(FILES ${TUTORIAL_CPP_FILES} DESTINATION ${GMSH_DOC}/tutorial/c++) +install(FILES ${TUTORIAL_C_FILES} DESTINATION ${GMSH_DOC}/tutorial/c) +install(FILES ${TUTORIAL_PY_FILES} DESTINATION ${GMSH_DOC}/tutorial/python) +install(FILES ${TUTORIAL_JL_FILES} DESTINATION ${GMSH_DOC}/tutorial/julia) +foreach(DIR ${DEMOS_DIRS}) + get_filename_component(DEMOS_DIR_NAME ${DIR} NAME) + file(GLOB DEMO_FILES ${DIR}/?*.*) + install(FILES ${DEMO_FILES} DESTINATION ${GMSH_DOC}/demos/${DEMOS_DIR_NAME}) +endforeach() +if(UNIX AND NOT CYGWIN) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/doc/gmsh.1 DESTINATION ${GMSH_MAN}) +endif() + +add_custom_target(get_headers + COMMAND ${CMAKE_COMMAND} -E make_directory Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +foreach(FILE ${GMSH_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endforeach() +if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/gmsh/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() +endif() + +find_program(MAKEINFO makeinfo) +if(MAKEINFO) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.info DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --split-size 1000000 + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(info DEPENDS ${TEX_DIR}/gmsh.info) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.txt DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --plaintext -o gmsh.txt + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(txt DEPENDS ${TEX_DIR}/gmsh.txt) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.html DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --html --css-ref=/gmsh.css + --no-split --set-customization-variable + EXTRA_HEAD='' + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(html DEPENDS ${TEX_DIR}/gmsh.html) + install(FILES ${TEX_DIR}/gmsh.html DESTINATION ${GMSH_DOC} OPTIONAL) +else() + add_custom_target(html COMMAND ${CMAKE_COMMAND} -E touch ${TEX_DIR}/gmsh.html) +endif() + +find_program(TEXI2PDF texi2pdf) +if(TEXI2PDF) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.pdf DEPENDS ${TEX_SRC} + COMMAND ${TEXI2PDF} ARGS gmsh.texi + WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(pdf DEPENDS ${TEX_DIR}/gmsh.pdf) + install(FILES ${TEX_DIR}/gmsh.pdf DESTINATION ${GMSH_DOC} OPTIONAL) +endif() + +execute_process(COMMAND ${CMAKE_COMMAND} -E echo + "@c This file was generated by cmake: do not edit manually!\n${OPT_TEXI}" + OUTPUT_FILE cmake_options.texi) + +if(MAKEINFO AND TEXI2PDF) + add_custom_target(doc COMMAND ${CMAKE_COMMAND} -E tar zcf + ${CMAKE_CURRENT_BINARY_DIR}/gmsh-${GMSH_VERSION}-doc.tgz + CREDITS.txt LICENSE.txt CHANGELOG.txt + doc/gmsh.1 doc/texinfo/gmsh.html doc/texinfo/gmsh.info + doc/texinfo/gmsh.pdf doc/texinfo/gmsh.txt + COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ} + DEPENDS ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.txt + ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.pdf + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(MAKEINFO OR TEXI2PDF) + add_custom_target(clean_doc COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ}) +endif() + +if(APPLE AND ENABLE_BUILD_LIB) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_framework.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info_framework.plist "${F1}") + set(LIBNAME $) + add_custom_target(framework DEPENDS lib + COMMAND ${CMAKE_COMMAND} -E remove_directory gmsh.framework + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Headers + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Resources + COMMAND ${CMAKE_COMMAND} -E copy ${LIBNAME} gmsh.framework/gmsh + COMMAND ${CMAKE_COMMAND} -E copy Info_framework.plist + gmsh.framework/Resources/Info.plist + COMMAND ${CMAKE_COMMAND} -E create_symlink . gmsh.framework/Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + foreach(FILE ${GMSH_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + endif() +endif() + +set(CPACK_PACKAGE_VENDOR "Christophe Geuzaine and Jean-Francois Remacle") +set(CPACK_PACKAGE_VERSION_MAJOR ${GMSH_MAJOR_VERSION}) +set(CPACK_PACKAGE_VERSION_MINOR ${GMSH_MINOR_VERSION}) +set(CPACK_PACKAGE_VERSION_PATCH ${GMSH_PATCH_VERSION}) +set(CPACK_PACKAGE_DESCRIPTION_FILE ${WELCOME_FILE}) +set(CPACK_PACKAGE_DESCRIPTION_SUMMARY + "3D finite element mesh generator with built-in CAD engine and post-processor") +if(GMSH_EXTRA_VERSION MATCHES "-git.*") # so that we'll overwrite the archives + set(CPACK_PACKAGE_FILE_NAME gmsh${GMSH_EXTRA_VERSION_ORIG}-git-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh${GMSH_EXTRA_VERSION_ORIG}-git-source) +else() + set(CPACK_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-source) +endif() +set(CPACK_PACKAGE_INSTALL_DIRECTORY "gmsh") +set(CPACK_RESOURCE_FILE_LICENSE ${LICENSE_FILE}) +set(CPACK_RESOURCE_FILE_README ${WELCOME_FILE}) +set(CPACK_RESOURCE_FILE_WELCOME ${WELCOME_FILE}) +set(CPACK_PACKAGE_EXECUTABLE "gmsh") +if(ENABLE_PACKAGE_STRIP) + set(CPACK_STRIP_FILES TRUE) +else() + set(CPACK_STRIP_FILES FALSE) +endif() +set(CPACK_SOURCE_GENERATOR TGZ) +set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR}" "/CVS/" "/.svn" "/.git" + "~$" "DS_Store$" "GmshConfig.h$" "GmshVersion.h$" "/benchmarks/" "/tmp/" + "/bin/" "/lib/" "/nightly/" "GPATH" "GRTAGS" "GSYMS" "GTAGS" "/HTML/" + "/contrib/3M/" "/contrib/Parasolid/") + +if(UNIX) + # make sure we remove previous installs before doing the next one (on Mac for + # example "make package; make package_source" would lead to huge file lists + # getting generated due to the 'Applications' symlink in the bundle) + set(CPACK_INSTALL_COMMANDS "rm -rf ${CMAKE_CURRENT_BINARY_DIR}/_CPack_Packages") +endif() + +if(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + set(CPACK_GENERATOR Bundle) + set(CPACK_BUNDLE_NAME Gmsh) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_app.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info.plist "${F1}") + set(CPACK_BUNDLE_PLIST ${CMAKE_CURRENT_BINARY_DIR}/Info.plist) + set(CPACK_BUNDLE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) + if(PACKAGER STREQUAL "geuzaine - removed: we sign on a separate machine") + # codesigning requires CMake >= 3.2 + set(CPACK_BUNDLE_APPLE_CERT_APP "Developer ID Application: Christophe Geuzaine") + endif() + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsGeo.icns DESTINATION . + RENAME GmshGeo.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsMsh.icns DESTINATION . + RENAME GmshMsh.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsSol.icns DESTINATION . + RENAME GmshSol.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsPos.icns DESTINATION . + RENAME GmshPos.icns) + set(CPACK_PACKAGE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) +elseif(WIN32) + set(CPACK_GENERATOR ZIP) +else() + set(CPACK_GENERATOR TGZ) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/gmshpy AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON AND HAVE_PYTHON) + add_subdirectory(utils/wrappers/gmshpy) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/java AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_JAVA) + add_subdirectory(utils/wrappers/java) +endif() + +include(CPack) + +macro(filter_tests IN OUT) + unset(${OUT}) + foreach(FILE ${IN}) + unset(BAD1) + unset(BAD2) + unset(BAD3) + # OS-specific + if(${GMSH_OS} MATCHES "Linux32") + # OCC STL generation crashes on our Linux32 docker + string(REGEX MATCH "t18" BAD1 ${FILE}) + endif() + # OpenCASCADE + if(NOT HAVE_OCC AND NOT BAD1 AND NOT BAD2 AND NOT BAD3) + file(STRINGS ${FILE} BAD1 REGEX "^SetFactory.*OpenCASCADE.*") + file(STRINGS ${FILE} BAD2 REGEX ".*occ\\.synchronize.*") + file(STRINGS ${FILE} BAD3 REGEX ".*occ::synchronize.*") + endif() + # Metis + if(NOT HAVE_METIS AND NOT BAD1 AND NOT BAD2 AND NOT BAD3) + file(STRINGS ${FILE} BAD1 REGEX ".*PartitionMesh.*") + file(STRINGS ${FILE} BAD2 REGEX ".*mesh\\.partition.*") + file(STRINGS ${FILE} BAD3 REGEX ".*mesh::partition.*") + endif() + if(BAD1 OR BAD2 OR BAD3) + message("Skipping test " ${FILE}) + else() + list(APPEND ${OUT} ${FILE}) + endif() + endforeach() +endmacro() + +if(NOT DISABLE_GMSH_TESTS) + # disabling tests is useful when including this CMakeLists in an external project + include(CTest) + file(GLOB_RECURSE ALLFILES + tutorial/*.geo demos/*.geo benchmarks/?d/*.geo benchmarks/extrude/*.geo + benchmarks/occ/*.geo) + filter_tests("${ALLFILES}" TESTFILES) + foreach(TESTFILE ${TESTFILES}) + # use relative path for Cygwin/MinGW (the pure win exe built with the MinGW + # compilers does not understand a full Cygwin-style path) + FILE(RELATIVE_PATH TEST ${CMAKE_CURRENT_BINARY_DIR} ${TESTFILE}) + add_test(${TEST} ./gmsh ${TEST} -3 -nopopup -o ./tmp.msh) + endforeach() + # test c++ api tutorials with dynamic builds (except on 32 bit windows for + # now: our win32 setup does not currently handle exceptions) + if(ENABLE_BUILD_DYNAMIC AND NOT ${GMSH_OS} MATCHES "Windows32") + file(GLOB_RECURSE ALLFILES tutorial/c++/*.cpp) + filter_tests("${ALLFILES}" TESTFILES) + foreach(TESTFILE ${TESTFILES}) + get_filename_component(TEST ${TESTFILE} NAME_WE) + add_executable(${TEST} WIN32 ${TESTFILE}) + target_link_libraries(${TEST} shared) + if(WIN32 AND NOT MSVC) + set(FLAGS "-static") + if(HAVE_FLTK) + set(FLAGS "${FLAGS} -mwindows") + else() + set(FLAGS "${FLAGS} -mconsole") + endif() + set_target_properties(${TEST} PROPERTIES LINK_FLAGS "${FLAGS}") + endif() + add_test(${TEST}_cpp ${TEST} -nopopup) + endforeach() + endif() + # enable this once we have worked out the path issues on the build machines + if(0 AND ENABLE_BUILD_DYNAMIC) + find_package(PythonInterp) + if(PYTHONINTERP_FOUND) + file(GLOB_RECURSE ALLFILES tutorial/python/*.py demos/api/*.py) + filter_tests("${ALLFILES}" TESTFILES) + foreach(TESTFILE ${TESTFILES}) + get_filename_component(TEST ${TESTFILE} NAME_WE) + add_test(NAME ${TEST}_py COMMAND ${PYTHON_EXECUTABLE} ${TESTFILE} -nopopup) + set_property(TEST ${TEST}_py APPEND PROPERTY ENVIRONMENT + "PYTHONPATH=${CMAKE_SOURCE_DIR}/api") + set_property(TEST ${TEST}_py APPEND PROPERTY ENVIRONMENT + "LD_LIBRARY_PATH=${CMAKE_CURRENT_BINARY_DIR}") + endforeach() + endif() + endif() +endif() + +message(STATUS "") +message(STATUS "Gmsh ${GMSH_VERSION} has been configured for ${GMSH_OS}") +message(STATUS "") +message(STATUS " * Build options:" ${GMSH_CONFIG_OPTIONS}) +message(STATUS " * Build type: " ${CMAKE_BUILD_TYPE}) +message(STATUS " * C compiler: " ${CMAKE_C_COMPILER}) +message(STATUS " * C++ compiler: " ${CMAKE_CXX_COMPILER}) +message(STATUS " * Install prefix: " ${CMAKE_INSTALL_PREFIX}) +message(STATUS "") + +mark_as_advanced(ANN_INC ANN_LIB CAIRO_LIB CAIRO_INC CGNS_INC GMM_INC + GMP_INC GMP_LIB MMG_INC MMG_LIB HDF5_LIB + MED_LIB OCC_INC SZ_LIB + PETSC_LIBS SLEPC_INC SLEPC_INC2 SLEPC_LIB + BISON FLEX MAKEINFO TEXI2PDF FLTK_CONFIG_SCRIPT + GMSH_EXTERNAL_INCLUDE_DIRS GMSH_EXTERNAL_LIBRARIES) Index: /issm/trunk/externalpackages/gmsh/install-3.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-3.sh (revision 25836) +++ /issm/trunk/externalpackages/gmsh/install-3.sh (revision 25836) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.0.5" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Configure +cd install +cmake ../src \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_MPI=1 \ + -DENABLE_BUILD_DYNAMIC=1 \ + -DENABLE_BUILD_SHARED=1 + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gmsh/install-4-linux-python-static.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-4-linux-python-static.sh (revision 25836) +++ /issm/trunk/externalpackages/gmsh/install-4-linux-python-static.sh (revision 25836) @@ -0,0 +1,67 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Add support for, +# - BLAS_LAPACK +# - MUMPS +# - NUMPY +# - PETSC4PY +# - PETSC +# (see configs/4/linux/static/CMakeLists.txt) +# + +## Constants +# +VER="4.5.6" + +PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Copy customized source and config files to 'src' directory +cp configs/${VER}/static/CMakeLists.txt src + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we +# do not need to support Apple Touch bar. +# +cd install +cmake ../src \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_BUILD_LIB=1 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DMETIS_ROOT="${PETSC_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gmsh/install-4-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-4-linux-static.sh (revision 25836) +++ /issm/trunk/externalpackages/gmsh/install-4-linux-static.sh (revision 25836) @@ -0,0 +1,63 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Add support for, +# - BLAS_LAPACK +# - MUMPS +# - PETSC +# (see configs/4/linux/static/CMakeLists.txt) +# + +## Constants +# +VER="4.5.6" + +PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Copy customized source and config files to 'src' directory +cp configs/${VER}/static/CMakeLists.txt src + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# +cd install +cmake ../src \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_BUILD_LIB=1 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DMETIS_ROOT="${PETSC_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gmsh/install-4-mac-python-static.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-4-mac-python-static.sh (revision 25836) +++ /issm/trunk/externalpackages/gmsh/install-4-mac-python-static.sh (revision 25836) @@ -0,0 +1,68 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Add support for, +# - BLAS_LAPACK +# - MUMPS +# - NUMPY +# - PETSC4PY +# - PETSC +# (see configs/4/mac/static/CMakeLists.txt) +# + +## Constants +# +VER="4.5.6" + +PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Copy customized source and config files to 'src' directory +cp configs/${VER}/mac/static/CMakeLists.txt src + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we +# do not need to support Apple Touch bar. +# +cd install +cmake ../src \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_BUILD_LIB=1 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DENABLE_TOUCHBAR=0 \ + -DMETIS_ROOT="${PETSC_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gmsh/install-4-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-4-mac-static.sh (revision 25836) +++ /issm/trunk/externalpackages/gmsh/install-4-mac-static.sh (revision 25836) @@ -0,0 +1,65 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Add support for, +# - BLAS_LAPACK +# - MUMPS +# - PETSC +# (see configs/4/mac/static/CMakeLists.txt) +# + +## Constants +# +VER="4.5.6" + +PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Copy customized source and config files to 'src' directory +cp configs/${VER}/mac/static/CMakeLists.txt src + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we +# do not need to support Apple Touch bar. +# +cd install +cmake ../src \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_BUILD_LIB=1 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DENABLE_TOUCHBAR=0 \ + -DMETIS_ROOT="${PETSC_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gmsh/install-4.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-4.sh (revision 25836) +++ /issm/trunk/externalpackages/gmsh/install-4.sh (revision 25836) @@ -0,0 +1,55 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="4.5.6" + +PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we +# do not need to support Apple Touch bar. +# +cd install +cmake ../src \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_BUILD_DYNAMIC=1 \ + -DENABLE_BUILD_SHARED=1 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DENABLE_TOUCHBAR=0 \ + -DMETIS_ROOT="${PETSC_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: sm/trunk/externalpackages/gmsh/install-static.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-static.sh (revision 25835) +++ (revision ) @@ -1,37 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install src -mkdir install - -#Download latest version -#svn co --username gmsh --password gmsh https://geuz.org/svn/gmsh/trunk src -#git clone http://gitlab.onelab.info/gmsh/gmsh.git src - -#Set gmsh version -GMSH_VER="3.0.5" - -#Remove tarball if it exists -rm -f gmsh-$GMSH_VER-source.tgz - -#Download last stable version that we know works -wget http://gmsh.info/src/gmsh-$GMSH_VER-source.tgz - -#Untar gmsh -tar -xvzf gmsh-$GMSH_VER-source.tgz - -#Rename gmsh source directory -mv gmsh-$GMSH_VER-source src - -#Configure -cd install -cmake ../src -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/gmsh/install" -DENABLE_METIS=0 - -#Compile and install -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk/externalpackages/gmsh/install.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install.sh (revision 25835) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.0.5" - -# Cleanup -rm -rf install src -mkdir install src - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" - -# Untar source -tar -xvzf gmsh-${VER}-source.tgz - -# Move source to 'src' directory -mv gmsh-${VER}-source/* src -rm -rf gmsh-${VER}-source - -# Configure -cd install -cmake ../src \ - -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ - -DENABLE_MPI=1 - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: /issm/trunk/externalpackages/gmt/configs/6/cmake/ConfigUser.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/cmake/ConfigUser.cmake (revision 25836) +++ /issm/trunk/externalpackages/gmt/configs/6/cmake/ConfigUser.cmake (revision 25836) @@ -0,0 +1,308 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License +# for more details. +# +# Contact info: www.generic-mapping-tools.org +# ---------------------------------------------------------------------------- + +# Use this file to override variables in 'ConfigDefault.cmake' on a per-user +# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then +# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled +# (currently listed in .gitignore). +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## Section 1: Installation paths +## + +# ============================================================================ +# Basic setup begins here. All settings are optional. In most cases, setting +# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with +# reasonable defaults enabled. Note: If you need to specify directory names +# with spaces (e.g., on Windows) then you must put them in quotes. +# ============================================================================ + +# Installation path (usually defaults to /usr/local) [auto]: +set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") + +# Set install name suffix used for directories and gmt executables +# [undefined]: +#set (GMT_INSTALL_NAME_SUFFIX "suffix") + +# Install into traditional directory structure. Disable to install a +# distribution type directory structure (doc and share separated) [on]: +#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) + +# Install convenience links for GMT modules. Disable to install only the main +# gmt program and access modules as "gmt modulename options" [TRUE]: +#set (GMT_INSTALL_MODULE_LINKS FALSE) + +# Make executables relocatable on supported platforms (relative RPATH) [FALSE]: +set (GMT_INSTALL_RELOCATABLE TRUE) + +# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE] +#set (GMT_EXCLUDE_GDAL TRUE) +#set (GMT_EXCLUDE_PCRE TRUE) +#set (GMT_EXCLUDE_PCRE2 TRUE) +#set (GMT_EXCLUDE_FFTW3 TRUE) +#set (GMT_EXCLUDE_LAPACK TRUE) +#set (GMT_EXCLUDE_BLAS TRUE) +#set (GMT_EXCLUDE_ZLIB TRUE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set URL to GMT Data server [auto]: +#set (GMT_DATA_SERVER "data_server_url") + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") + +# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]: +#set (COPY_GSHHG TRUE) + +# Set path to DCW Digital Chart of the World for GMT [auto]: +#set (DCW_ROOT "dcw-gmt_path") + +# Copy DCW files to ${GMT_DATADIR}/dcw [FALSE]: +#set (COPY_DCW TRUE) + +# Copy GDAL's 'data' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (GDAL_DATA_PATH C:/programs/compa_libs/gdal_GIT/compileds/VC14_64/data) + +# Copy PROJ4's 'share' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (PROJ_DATA_PATH C:/programs/compa_libs/proj5_GIT/compileds/VC14_64/share/proj) + +# FOR WINDOWS ONLY +# Set path to location of Ghostscript binaries (optional install) +#set (GHOST_DATA_PATH C:/programs/compa_libs/ghostscript/bin) + +# FOR WINDOWS ONLY +# Set path to location where the gmtmex is located. +#set (GMTMEX_PATH "C:/progs_cygw/GMTdev/gmtmex/${GMTver}") + +# Set location of NetCDF (can be root directory, path to header file or path +# to nc-config) [auto]: +set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/netcdf/install") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") +# Alternatively, set location of PCRE2 (can be root directory, path to header file or path to +# pcre2-config) [auto]: +#set (PCRE2_ROOT "pcre2_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +set (ZLIB_ROOT "$ENV{ISSM_DIR}/externalpackages/petsc/install") + +# Set location of CURL (can be root directory or path to header file) [auto]: +#set (CURL_ROOT "curl_install_prefix") + +# Set location of GLIB component gthread [auto]. This is an optional (and +# experimental) option which you need to enable: +#set (GMT_USE_THREADS TRUE) +# If pkg-config is not installed (e.g. on Windows) you need to specify these: +#set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0) +#set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib) + +# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically +set (LAPACK_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lflapack") +set (BLAS_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lfblas") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Allow building of OpenMP if compiler supports it +# set (GMT_ENABLE_OPENMP TRUE) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# Enable building of shared libraries [TRUE] (disable to use static libraries; +# not recommended; on non-x86 architectures uncomment the next option as well): +#set (BUILD_SHARED_LIBS FALSE) + +# Create position independent code on all targets [auto] (needed for static +# build on non-x86): +#set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) + +# Build GMT shared lib with supplemental modules [TRUE]: +#set (BUILD_SUPPLEMENTS FALSE) + +# Build/Install GMT Developer include files [TRUE]: +# This installs the extra include files and configured files needed by 3rd-party +# developers. Until we build a separate gmt-devel we include them in the main +# Distribution. +#set (BUILD_DEVELOPER FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#set (DO_EXAMPLES TRUE) +#set (DO_TESTS TRUE) +#set (DO_ANIMATIONS TRUE) +# Number of parallel test jobs with "make check": +#set (N_TEST_JOBS 4) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmt-custom project). +#set (EXTRA_BUILD_DIRS apidemo) +# Uncomment the following line to enable running low-level C tests of the API +#set (DO_API_TESTS ON) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel +# [Release]: +#set (CMAKE_BUILD_TYPE Debug) + +# Extra debugging for developers: +#if ( CMAKE_GENERATOR STREQUAL "Xcode" ) +## So Xcode can find the supplemental plug-ins during debug sessions +# add_definitions(-DXCODER) +# add_definitions(-DDEBUG_MODERN) # To set PPID == 0 during Xcode test +# message("Add Xcode definition for GMT") +#endif() +#add_definitions(-DDEBUG) +#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info +#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies +if (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions") # check uninitialized variables +else (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +endif (HAVE_OPENMP) + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +#set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +# WARNING: if using this option it is mandatory that the suffix starts with an underscore. +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) Index: /issm/trunk/externalpackages/gmt/configs/6/static/cmake/ConfigUser.static.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/cmake/ConfigUser.static.cmake (revision 25836) +++ /issm/trunk/externalpackages/gmt/configs/6/static/cmake/ConfigUser.static.cmake (revision 25836) @@ -0,0 +1,308 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License +# for more details. +# +# Contact info: www.generic-mapping-tools.org +# ---------------------------------------------------------------------------- + +# Use this file to override variables in 'ConfigDefault.cmake' on a per-user +# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then +# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled +# (currently listed in .gitignore). +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## Section 1: Installation paths +## + +# ============================================================================ +# Basic setup begins here. All settings are optional. In most cases, setting +# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with +# reasonable defaults enabled. Note: If you need to specify directory names +# with spaces (e.g., on Windows) then you must put them in quotes. +# ============================================================================ + +# Installation path (usually defaults to /usr/local) [auto]: +set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") + +# Set install name suffix used for directories and gmt executables +# [undefined]: +#set (GMT_INSTALL_NAME_SUFFIX "suffix") + +# Install into traditional directory structure. Disable to install a +# distribution type directory structure (doc and share separated) [on]: +#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) + +# Install convenience links for GMT modules. Disable to install only the main +# gmt program and access modules as "gmt modulename options" [TRUE]: +#set (GMT_INSTALL_MODULE_LINKS FALSE) + +# Make executables relocatable on supported platforms (relative RPATH) [FALSE]: +set (GMT_INSTALL_RELOCATABLE TRUE) + +# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE] +#set (GMT_EXCLUDE_GDAL TRUE) +#set (GMT_EXCLUDE_PCRE TRUE) +#set (GMT_EXCLUDE_PCRE2 TRUE) +#set (GMT_EXCLUDE_FFTW3 TRUE) +#set (GMT_EXCLUDE_LAPACK TRUE) +#set (GMT_EXCLUDE_BLAS TRUE) +#set (GMT_EXCLUDE_ZLIB TRUE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set URL to GMT Data server [auto]: +#set (GMT_DATA_SERVER "data_server_url") + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") + +# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]: +#set (COPY_GSHHG TRUE) + +# Set path to DCW Digital Chart of the World for GMT [auto]: +#set (DCW_ROOT "dcw-gmt_path") + +# Copy DCW files to ${GMT_DATADIR}/dcw [FALSE]: +#set (COPY_DCW TRUE) + +# Copy GDAL's 'data' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (GDAL_DATA_PATH C:/programs/compa_libs/gdal_GIT/compileds/VC14_64/data) + +# Copy PROJ4's 'share' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (PROJ_DATA_PATH C:/programs/compa_libs/proj5_GIT/compileds/VC14_64/share/proj) + +# FOR WINDOWS ONLY +# Set path to location of Ghostscript binaries (optional install) +#set (GHOST_DATA_PATH C:/programs/compa_libs/ghostscript/bin) + +# FOR WINDOWS ONLY +# Set path to location where the gmtmex is located. +#set (GMTMEX_PATH "C:/progs_cygw/GMTdev/gmtmex/${GMTver}") + +# Set location of NetCDF (can be root directory, path to header file or path +# to nc-config) [auto]: +set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/netcdf/install") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") +# Alternatively, set location of PCRE2 (can be root directory, path to header file or path to +# pcre2-config) [auto]: +#set (PCRE2_ROOT "pcre2_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +set (ZLIB_ROOT "$ENV{ISSM_DIR}/externalpackages/petsc/install") + +# Set location of CURL (can be root directory or path to header file) [auto]: +set (CURL_ROOT "$ENV{ISSM_DIR}/externalpackages/curl/install") + +# Set location of GLIB component gthread [auto]. This is an optional (and +# experimental) option which you need to enable: +#set (GMT_USE_THREADS TRUE) +# If pkg-config is not installed (e.g. on Windows) you need to specify these: +#set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0) +#set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib) + +# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically +#set (LAPACK_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lflapack") +#set (BLAS_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lfblas") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Allow building of OpenMP if compiler supports it +# set (GMT_ENABLE_OPENMP TRUE) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# Enable building of shared libraries [TRUE] (disable to use static libraries; +# not recommended; on non-x86 architectures uncomment the next option as well): +set (BUILD_SHARED_LIBS FALSE) + +# Create position independent code on all targets [auto] (needed for static +# build on non-x86): +set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) + +# Build GMT shared lib with supplemental modules [TRUE]: +set (BUILD_SUPPLEMENTS FALSE) + +# Build/Install GMT Developer include files [TRUE]: +# This installs the extra include files and configured files needed by 3rd-party +# developers. Until we build a separate gmt-devel we include them in the main +# Distribution. +#set (BUILD_DEVELOPER FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#set (DO_EXAMPLES TRUE) +#set (DO_TESTS TRUE) +#set (DO_ANIMATIONS TRUE) +# Number of parallel test jobs with "make check": +#set (N_TEST_JOBS 4) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmt-custom project). +#set (EXTRA_BUILD_DIRS apidemo) +# Uncomment the following line to enable running low-level C tests of the API +#set (DO_API_TESTS ON) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel +# [Release]: +#set (CMAKE_BUILD_TYPE Debug) + +# Extra debugging for developers: +#if ( CMAKE_GENERATOR STREQUAL "Xcode" ) +## So Xcode can find the supplemental plug-ins during debug sessions +# add_definitions(-DXCODER) +# add_definitions(-DDEBUG_MODERN) # To set PPID == 0 during Xcode test +# message("Add Xcode definition for GMT") +#endif() +#add_definitions(-DDEBUG) +#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info +#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies +if (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions") # check uninitialized variables +else (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +endif (HAVE_OPENMP) + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +# WARNING: if using this option it is mandatory that the suffix starts with an underscore. +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) Index: /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake (revision 25836) +++ /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake (revision 25836) @@ -0,0 +1,187 @@ +# +# +# Locate gdal +# +# This module accepts the following environment variables: +# +# GDAL_DIR or GDAL_ROOT - Specify the location of GDAL +# +# This module defines the following CMake variables: +# +# GDAL_FOUND - True if libgdal is found +# GDAL_LIBRARY - A variable pointing to the GDAL library +# GDAL_INCLUDE_DIR - Where to find the headers + +#============================================================================= +# Copyright 2007-2009 Kitware, Inc. +# +# Distributed under the OSI-approved BSD License (the "License"); +# see accompanying file Copyright.txt for details. +# +# This software is distributed WITHOUT ANY WARRANTY; without even the +# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See COPYING-CMAKE-SCRIPTS for more information. +#============================================================================= +# Note: this file is not an exact copy of the original file from Kitware. +# It has been modified for the needs of GMT. + +# +# $GDAL_DIR is an environment variable that would +# correspond to the ./configure --prefix=$GDAL_DIR +# used in building gdal. +# +# Created by Eric Wing. I'm not a gdal user, but OpenSceneGraph uses it +# for osgTerrain so I whipped this module together for completeness. +# I actually don't know the conventions or where files are typically +# placed in distros. +# Any real gdal users are encouraged to correct this (but please don't +# break the OS X framework stuff when doing so which is what usually seems +# to happen). + +# This makes the presumption that you are include gdal.h like +# +#include "gdal.h" + +if (DEFINED GDAL_ROOT AND NOT GDAL_ROOT) + set (GDAL_LIBRARY "" CACHE INTERNAL "") + set (GDAL_INCLUDE_DIR "" CACHE INTERNAL "") + return() +endif (DEFINED GDAL_ROOT AND NOT GDAL_ROOT) + +if (UNIX AND NOT GDAL_FOUND) + # Use gdal-config to obtain the library version (this should hopefully + # allow us to -lgdal1.x.y where x.y are correct version) + # For some reason, libgdal development packages do not contain + # libgdal.so... + find_program (GDAL_CONFIG gdal-config + HINTS + ${GDAL_DIR} + ${GDAL_ROOT} + $ENV{GDAL_DIR} + $ENV{GDAL_ROOT} + PATH_SUFFIXES bin + PATHS + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local + ) + + if (GDAL_CONFIG) + execute_process (COMMAND ${GDAL_CONFIG} --cflags + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE GDAL_CONFIG_CFLAGS) + if (GDAL_CONFIG_CFLAGS) + string (REGEX MATCHALL "-I[^ ]+" _gdal_dashI ${GDAL_CONFIG_CFLAGS}) + string (REGEX REPLACE "-I" "" _gdal_includepath "${_gdal_dashI}") + string (REGEX REPLACE "-I[^ ]+" "" _gdal_cflags_other ${GDAL_CONFIG_CFLAGS}) + endif (GDAL_CONFIG_CFLAGS) + execute_process (COMMAND ${GDAL_CONFIG} --libs + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE GDAL_CONFIG_LIBS) + if (GDAL_CONFIG_LIBS) + string (REGEX MATCHALL "-l[^ ]+" _gdal_dashl ${GDAL_CONFIG_LIBS}) + string (REGEX REPLACE "-l" "" _gdal_lib "${_gdal_dashl}") + string (REGEX MATCHALL "-L[^ ]+" _gdal_dashL ${GDAL_CONFIG_LIBS}) + string (REGEX REPLACE "-L" "" _gdal_libpath "${_gdal_dashL}") + endif (GDAL_CONFIG_LIBS) + execute_process (COMMAND ${GDAL_CONFIG} --dep-libs + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE GDAL_CONFIG_DEP_LIBS) + if (GDAL_CONFIG_DEP_LIBS) + string (REGEX MATCHALL "-l[^ ]+" _gdal_dashl ${GDAL_CONFIG_DEP_LIBS}) + string (REGEX REPLACE "-l" "" _gdal_dep_lib "${_gdal_dashl}") + string (REGEX MATCHALL "-L[^ ]+" _gdal_dashL ${GDAL_CONFIG_DEP_LIBS}) + string (REGEX REPLACE "-L" "" _gdal_dep_libpath "${_gdal_dashL}") + endif (GDAL_CONFIG_DEP_LIBS) + endif (GDAL_CONFIG) + if (_gdal_dep_lib) + list (REMOVE_DUPLICATES _gdal_dep_lib) + list (REMOVE_ITEM _gdal_dep_lib gdal) + endif (_gdal_dep_lib) +endif (UNIX AND NOT GDAL_FOUND) + +find_path (GDAL_INCLUDE_DIR gdal.h + HINTS + ${_gdal_includepath} + ${GDAL_DIR} + ${GDAL_ROOT} + $ENV{GDAL_DIR} + $ENV{GDAL_ROOT} + PATH_SUFFIXES + include/gdal + include/GDAL + include + PATHS + ~/Library/Frameworks/gdal.framework/Headers + /Library/Frameworks/gdal.framework/Headers + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local +) + +find_library (GDAL_LIBRARY + NAMES ${_gdal_lib} gdal gdal_i gdal1.5.0 gdal1.4.0 gdal1.3.2 GDAL + HINTS + ${GDAL_DIR} + ${GDAL_ROOT} + $ENV{GDAL_DIR} + $ENV{GDAL_ROOT} + ${_gdal_libpath} + PATH_SUFFIXES lib + PATHS + ~/Library/Frameworks/gdal.framework + /Library/Frameworks/gdal.framework + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local +) + +# find all libs that gdal-config --dep-libs reports +foreach (_extralib ${_gdal_dep_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + HINTS + ${HDF5_ROOT} + $ENV{HDF5_ROOT} + ${ZLIB_ROOT} + $ENV{ZLIB_ROOT} + ${CURL_ROOT} + $ENV{CURL_ROOT} + PATH_SUFFIXES lib + PATHS + ${_gdal_dep_libpath} + ) + list (APPEND GDAL_LIBRARY ${_found_lib_${_extralib}}) +endforeach (_extralib) + +# append manually-supplied libs +# find all manually-supplied libs +if (GDAL_EXTRA_LIBS) + # Ensure -l is precedeced by whitespace to not match + # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' + string (REGEX MATCHALL "(^| )-l[^ ]+" _gdal_extra_lib_dashl ${GDAL_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-l" "" _gdal_extra_lib "${_gdal_extra_lib_dashl}") + string (REGEX MATCHALL "(^| )-L[^ ]+" _gdal_extra_lib_dashL ${GDAL_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-L" "" _gdal_extra_libpath "${_gdal_extra_lib_dashL}") + foreach (_extralib ${_gdal_extra_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + PATH_SUFFIXES lib + PATHS + ${_gdal_extra_libpath} + ) + list (APPEND GDAL_LIBRARY ${_found_lib_${_extralib}}) + endforeach (_extralib) +endif (GDAL_EXTRA_LIBS) + +include (FindPackageHandleStandardArgs) +find_package_handle_standard_args (GDAL DEFAULT_MSG GDAL_LIBRARY GDAL_INCLUDE_DIR) + +set (GDAL_LIBRARIES ${GDAL_LIBRARY}) +set (GDAL_INCLUDE_DIRS ${GDAL_INCLUDE_DIR}) Index: /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGSHHG.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGSHHG.cmake (revision 25836) +++ /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGSHHG.cmake (revision 25836) @@ -0,0 +1,95 @@ +# +# +# Locate GSHHG shorelines +# +# This module accepts the following environment variables: +# +# GSHHG_ROOT, GSHHGDIR - Specify the location of GSHHG +# +# This module defines the following CMake variables: +# +# GSHHG_FOUND - True if GSHHG is found +# GSHHG_PATH - A variable pointing to the GSHHG path +# GSHHG_VERSION - String of the GSHHG version found +# GSHHG_MIN_REQUIRED_VERSION_{MAJOR, MINOR, PATCH} +# - Major, minor, and patch version required + +# get GSHHG path +find_path (GSHHG_PATH + NAMES binned_GSHHS_c.nc + HINTS ${GSHHG_ROOT} $ENV{GSHHG_ROOT} $ENV{GSHHGDIR} + PATH_SUFFIXES + gmt-gshhg + gshhg + gshhg-gmt + gshhg-gmt-nc4 + share/gmt/gshhg + share/gmt-gshhg + share/gshhg + share/gshhg-gmt + share/gshhg-gmt-nc4 + PATHS + ${CMAKE_SOURCE_DIR} + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local + DOC "Global Self-consistent Hierarchical High-resolution Geography" +) + +# get GSHHG file +if (GSHHG_PATH) + find_file (_GSHHG_FILE + NAMES binned_GSHHS_c.nc + HINTS ${GSHHG_PATH}) +endif (GSHHG_PATH) + +# The minimum required GSHHG version +set (GSHHG_MIN_REQUIRED_VERSION_MAJOR 2 CACHE INTERNAL "GSHHG required version major") +set (GSHHG_MIN_REQUIRED_VERSION_MINOR 2 CACHE INTERNAL "GSHHG required version minor") +set (GSHHG_MIN_REQUIRED_VERSION_PATCH 0 CACHE INTERNAL "GSHHG required version patch") +set (GSHHG_MIN_REQUIRED_VERSION + "${GSHHG_MIN_REQUIRED_VERSION_MAJOR}.${GSHHG_MIN_REQUIRED_VERSION_MINOR}.${GSHHG_MIN_REQUIRED_VERSION_PATCH}") + +# Temporary hack to bypass failure of compilation of code to find GSHHG +set (GSHHG_FOUND TRUE) +set (GSHHG_VERSION "2.3.4" CACHE INTERNAL "GSHHG version") + +# check GSHHG version +if (_GSHHG_FILE AND NOT GSHHG_FOUND) + try_run (_EXIT_GSHHG_VERSION _COMPILED_GSHHG_VERSION + ${CMAKE_BINARY_DIR}/CMakeTmp + ${CMAKE_CURRENT_SOURCE_DIR}/gshhg_version.c + CMAKE_FLAGS + -DINCLUDE_DIRECTORIES=${NETCDF_INCLUDE_DIR} + -DLINK_LIBRARIES=${NETCDF_LIBRARIES} + COMPILE_DEFINITIONS -DSTANDALONE + COMPILE_OUTPUT_VARIABLE _GSHHG_VERSION_COMPILE_OUT + RUN_OUTPUT_VARIABLE _GSHHG_VERSION_STRING + ARGS \"${_GSHHG_FILE}\" ${GSHHG_MIN_REQUIRED_VERSION}) + + if (NOT _COMPILED_GSHHG_VERSION OR _EXIT_GSHHG_VERSION STREQUAL FAILED_TO_RUN) + message(FATAL_ERROR "Cannot determine GSHHG version:\n + ${_GSHHG_VERSION_COMPILE_OUT}\n + ${_GSHHG_VERSION_STRING}") + endif () + + # check version string + if (_COMPILED_GSHHG_VERSION) + # strip whitespace + string (STRIP ${_GSHHG_VERSION_STRING} GSHHG_VERSION) + if (_EXIT_GSHHG_VERSION EQUAL 0) + # found GSHHG of required version or higher + set (GSHHG_VERSION ${GSHHG_VERSION} CACHE INTERNAL "GSHHG version") + elseif (_EXIT_GSHHG_VERSION EQUAL -1) + # found GSHHG but version is too old + message (WARNING "GSHHG found but it is too old (${GSHHG_VERSION}). " + "Need at least ${GSHHG_MIN_REQUIRED_VERSION}.") + endif (_EXIT_GSHHG_VERSION EQUAL 0) + endif (_COMPILED_GSHHG_VERSION) +endif (_GSHHG_FILE AND NOT GSHHG_FOUND) + +include (FindPackageHandleStandardArgs) +find_package_handle_standard_args (GSHHG DEFAULT_MSG + GSHHG_PATH GSHHG_VERSION) Index: /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake (revision 25836) +++ /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake (revision 25836) @@ -0,0 +1,181 @@ +# +# +# Locate netcdf +# +# This module accepts the following environment variables: +# +# NETCDF_DIR or NETCDF_ROOT - Specify the location of NetCDF +# +# This module defines the following CMake variables: +# +# NETCDF_FOUND - True if libnetcdf is found +# NETCDF_LIBRARY - A variable pointing to the NetCDF library +# NETCDF_INCLUDE_DIR - Where to find the headers +# NETCDF_INCLUDE_DIRS - Where to find the headers +# NETCDF_DEFINITIONS - Extra compiler flags + +#============================================================================= +# Inspired by FindGDAL +# +# Distributed under the OSI-approved bsd license (the "License") +# +# This software is distributed WITHOUT ANY WARRANTY; without even the +# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See COPYING-CMAKE-SCRIPTS for more information. +#============================================================================= + +# This makes the presumption that you are include netcdf.h like +# +#include "netcdf.h" + +if (UNIX AND NOT NETCDF_FOUND) + # Use nc-config to obtain the libraries + find_program (NETCDF_CONFIG nc-config + HINTS + ${NETCDF_DIR} + ${NETCDF_ROOT} + $ENV{NETCDF_DIR} + $ENV{NETCDF_ROOT} + PATH_SUFFIXES bin + PATHS + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local + ) + + if (NETCDF_CONFIG) + execute_process (COMMAND ${NETCDF_CONFIG} --cflags + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE NETCDF_CONFIG_CFLAGS) + if (NETCDF_CONFIG_CFLAGS) + string (REGEX MATCHALL "(^| )-I[^ ]+" _netcdf_dashI ${NETCDF_CONFIG_CFLAGS}) + string (REGEX REPLACE "(^| )-I" "" _netcdf_includepath "${_netcdf_dashI}") + string (REGEX REPLACE "(^| )-I[^ ]+" "" _netcdf_cflags_other ${NETCDF_CONFIG_CFLAGS}) + endif (NETCDF_CONFIG_CFLAGS) + execute_process (COMMAND ${NETCDF_CONFIG} --libs + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE NETCDF_CONFIG_LIBS) + if (NETCDF_CONFIG_LIBS) + # Ensure -l is precedeced by whitespace to not match + # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' + string (REGEX MATCHALL "(^| )-l[^ ]+" _netcdf_dashl ${NETCDF_CONFIG_LIBS}) + string (REGEX REPLACE "(^| )-l" "" _netcdf_lib "${_netcdf_dashl}") + string (REGEX MATCHALL "(^| )-L[^ ]+" _netcdf_dashL ${NETCDF_CONFIG_LIBS}) + string (REGEX REPLACE "(^| )-L" "" _netcdf_libpath "${_netcdf_dashL}") + endif (NETCDF_CONFIG_LIBS) + endif (NETCDF_CONFIG) + if (_netcdf_lib) + list (REMOVE_DUPLICATES _netcdf_lib) + list (REMOVE_ITEM _netcdf_lib netcdf) + endif (_netcdf_lib) +endif (UNIX AND NOT NETCDF_FOUND) + +find_path (NETCDF_INCLUDE_DIR netcdf.h + HINTS + ${_netcdf_includepath} + ${NETCDF_DIR} + ${NETCDF_ROOT} + $ENV{NETCDF_DIR} + $ENV{NETCDF_ROOT} + PATH_SUFFIXES + include/netcdf + include/netcdf-4 + include/netcdf-3 + include + PATHS + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local +) + +find_library (NETCDF_LIBRARY + NAMES netcdf + HINTS + ${_netcdf_libpath} + ${NETCDF_DIR} + ${NETCDF_ROOT} + $ENV{NETCDF_DIR} + $ENV{NETCDF_ROOT} + PATH_SUFFIXES lib + PATHS + /sw + /opt/local + /opt/csw + /opt + /usr/local +) + +# find all libs that nc-config reports +foreach (_extralib ${_netcdf_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + HINTS + ${HDF5_ROOT} + $ENV{HDF5_ROOT} + ${ZLIB_ROOT} + $ENV{ZLIB_ROOT} + ${CURL_ROOT} + $ENV{CURL_ROOT} + PATH_SUFFIXES lib + PATHS + ${_netcdf_libpath} + ) + list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) +endforeach (_extralib) + +# find all manually-supplied libs +if (NETCDF_EXTRA_LIBS) + # Ensure -l is precedeced by whitespace to not match + # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' + string (REGEX MATCHALL "(^| )-l[^ ]+" _netcdf_extra_lib_dashl ${NETCDF_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-l" "" _netcdf_extra_shared_lib "${_netcdf_extra_lib_dashl}") + string (REGEX MATCHALL "(^| )-L[^ ]+" _netcdf_extra_lib_dashL ${NETCDF_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-L" "" _netcdf_extra_libpath "${_netcdf_extra_lib_dashL}") + foreach (_extralib ${_netcdf_extra_shared_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + PATH_SUFFIXES lib + PATHS + ${_netcdf_extra_libpath} + ) + list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) + endforeach (_extralib) + # Retrieve static library names + string(REGEX MATCHALL "[a-zA-Z0-9]+\\.a" _netcdf_extra_static_lib "${NETCDF_EXTRA_LIBS}") + foreach (_extralib ${_netcdf_extra_static_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + PATH_SUFFIXES lib + PATHS + ${_netcdf_extra_libpath} + ) + list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) + endforeach (_extralib) +endif (NETCDF_EXTRA_LIBS) + +if (NETCDF_LIBRARY AND NETCDF_INCLUDE_DIR AND NOT HAVE_NETCDF4) + # Ensure that NetCDF with version 4 extensions is installed + include (CMakePushCheckState) + include (CheckSymbolExists) + cmake_push_check_state() # save state of CMAKE_REQUIRED_* + set (CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${NETCDF_INCLUDE_DIR}) + set (CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES} ${NETCDF_LIBRARY}) + set (HAVE_NETCDF4 HAVE_NETCDF4) # to force check_symbol_exists again + check_symbol_exists (nc_def_var_deflate netcdf.h HAVE_NETCDF4) + cmake_pop_check_state() # restore state of CMAKE_REQUIRED_* + if (NOT HAVE_NETCDF4) + message (SEND_ERROR "Library found but netCDF-4/HDF5 format unsupported. Do not configure netCDF-4 with --disable-netcdf-4.") + endif (NOT HAVE_NETCDF4) +endif (NETCDF_LIBRARY AND NETCDF_INCLUDE_DIR AND NOT HAVE_NETCDF4) + +include (FindPackageHandleStandardArgs) +find_package_handle_standard_args (NETCDF + DEFAULT_MSG NETCDF_LIBRARY NETCDF_INCLUDE_DIR HAVE_NETCDF4) + +set (NETCDF_LIBRARIES ${NETCDF_LIBRARY}) +set (NETCDF_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR}) +string (REPLACE "-DNDEBUG" "" NETCDF_DEFINITIONS "${_netcdf_cflags_other}") Index: /issm/trunk/externalpackages/gmt/configs/6/static/src/CMakeLists.txt =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/src/CMakeLists.txt (revision 25836) +++ /issm/trunk/externalpackages/gmt/configs/6/static/src/CMakeLists.txt (revision 25836) @@ -0,0 +1,730 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# Contact info: www.generic-mapping-tools.org +#------------------------------------------------------------------------------- +# +# To modify the cmake process: Edit your cmake/ConfigUser.cmake file +# +# src/CMakeLists.txt +# + +include (ManageString) +include (GmtHelperMacros) + +if (UNIX AND NOT APPLE) + set (LINUX TRUE) +else (UNIX AND NOT APPLE) + set (LINUX FALSE) +endif (UNIX AND NOT APPLE) + +# On Windows do not prefix the DLLs with the 'lib' prefix +if (WIN32) + set(LIB_PREFIX "") +else (WIN32) + set(LIB_PREFIX "lib") +endif (WIN32) + +# Include CREATE_DEBUG_SYM macro and set DEBUG_BUILD +include (CreateDebugSym) + +# Find executable needed by gmt +find_program (OGR2OGR ogr2ogr) +if (NOT OGR2OGR) + message (WARNING "Cannot find program ogr2ogr - gmt will be unable to convert Shapefiles to GMT/OGR format") + set (GMT_CONFIG_OGR2OGR_MESSAGE "no" CACHE INTERNAL "OGR2OGR config message") +else (NOT OGR2OGR) + execute_process(COMMAND ogr2ogr --version OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + string (REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" answer "${answer}") + set (GMT_CONFIG_OGR2OGR_MESSAGE "yes (${answer})" CACHE INTERNAL "OGR2OGR config message") +endif (NOT OGR2OGR) + +# Find executable needed by psconvert +find_program (GDAL_TRANSLATE gdal_translate) +if (NOT GDAL_TRANSLATE) + message (WARNING "Cannot find program gdal_translate - psconvert will be unable to convert TIFF to GeoTIFF") + set (GMT_CONFIG_GDAL_TRANSLATE_MESSAGE "no" CACHE INTERNAL "GDAL_TRANSLATE config message") +else (NOT GDAL_TRANSLATE) + execute_process(COMMAND gdal_translate --version OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + string (REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" answer "${answer}") + set (GMT_CONFIG_GDAL_TRANSLATE_MESSAGE "yes (${answer})" CACHE INTERNAL "GDAL_TRANSLATE config message") +endif (NOT GDAL_TRANSLATE) + +# Find executables needed by movie +find_program (GM gm) +if (NOT GM) + message (WARNING "Cannot find GraphicsMagick program gm - gmt movie will be unable to make animated GIFs") + set (GMT_CONFIG_GM_MESSAGE "no" CACHE INTERNAL "GM config message") +else (NOT GM) + execute_process(COMMAND gm help OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + string (REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" answer "${answer}") + set (GMT_CONFIG_GM_MESSAGE "yes (${answer})" CACHE INTERNAL "GM config message") +endif (NOT GM) + +find_program (FFMPEG ffmpeg) +if (NOT FFMPEG) + message (WARNING "Cannot find ffmpeg - gmt movie will be unable to make movies from frames") + set (GMT_CONFIG_FFMPEG_MESSAGE "no" CACHE INTERNAL "FFMPEG config message") +else (NOT FFMPEG) + execute_process(COMMAND ffmpeg -version OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + string (REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" answer "${answer}") + set (GMT_CONFIG_FFMPEG_MESSAGE "yes (${answer})" CACHE INTERNAL "FFMPEG config message") +endif (NOT FFMPEG) + +# Find executable needed by docs +if (LINUX) + find_program (XDGOPEN xdg-open) + if (NOT XDGOPEN) + message (WARNING "Cannot find program xdg-open - gmt docs will be unable to open the documentation") + set (GMT_CONFIG_OPEN_MESSAGE "no" CACHE INTERNAL "OPEN config message") + else (NOT XDGOPEN) + set (GMT_CONFIG_OPEN_MESSAGE "yes" CACHE INTERNAL "OPEN config message") + endif (NOT XDGOPEN) +else (LINUX) + set (GMT_CONFIG_OPEN_MESSAGE "yes" CACHE INTERNAL "OPEN config message") +endif (LINUX) + +# Find executable needed by psconvert +if (WIN32) + set (GMT_CONFIG_GS_MESSAGE "yes" CACHE INTERNAL "GS config message") +else (WIN32) + find_program (GS gs) + if (NOT GS) + message (WARNING "Cannot find ghostscript program gs - gmt psconvert will be unable to convert PostScript to other formats") + set (GMT_CONFIG_GS_MESSAGE "no" CACHE INTERNAL "GS config message") + else (NOT GS) + execute_process(COMMAND gs --version OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + set (GMT_CONFIG_GS_MESSAGE "yes (${answer})" CACHE INTERNAL "GS config message") + endif (NOT GS) +endif (WIN32) + +# Find libraries +message (STATUS "Searching dependent libraries. This may take a few minutes...") +# NetCDF is required +find_package (NETCDF REQUIRED) +include_directories (${NETCDF_INCLUDE_DIR}) + +# libcurl is required since 5.4 +include_directories ($ENV{CURL_INCLUDE_DIRS}) +list (APPEND GMT_OPTIONAL_LIBRARIES $ENV{CURL_LIBRARIES}) + +if (NOT DEFINED GMT_EXCLUDE_GDAL) + find_package (GDAL) +endif (NOT DEFINED GMT_EXCLUDE_GDAL) +if (GDAL_FOUND) + set (HAVE_GDAL TRUE CACHE INTERNAL "System has GDAL") + include_directories (${GDAL_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${GDAL_LIBRARIES}) +endif (GDAL_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_PCRE) + find_package (PCRE) +endif (NOT DEFINED GMT_EXCLUDE_PCRE) +if (NOT PCRE_FOUND AND NOT DEFINED GMT_EXCLUDE_PCRE2) + find_package (PCRE2) +endif (NOT PCRE_FOUND AND NOT DEFINED GMT_EXCLUDE_PCRE2) +if (PCRE_FOUND) + set (HAVE_PCRE TRUE CACHE INTERNAL "System has PCRE") + set (GMT_CONFIG_REGEX_MESSAGE "PCRE (${PCRE_LIBRARIES})" + CACHE INTERNAL "Regex config message") + include_directories (${PCRE_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${PCRE_LIBRARIES}) +elseif (PCRE2_FOUND) + set (HAVE_PCRE2 TRUE CACHE INTERNAL "System has PCRE2") + set (GMT_CONFIG_REGEX_MESSAGE "PCRE2 (${PCRE2_LIBRARIES})" + CACHE INTERNAL "Regex config message") + include_directories (${PCRE2_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${PCRE2_LIBRARIES}) +else (PCRE_FOUND) + find_package (REGEX) + if (REGEX_FOUND) + set (HAVE_POSIX_ERE TRUE CACHE INTERNAL "System has regex.h") + set (GMT_CONFIG_REGEX_MESSAGE "POSIX Regex (${REGEX_INCLUDE_DIR}/regex.h)" + CACHE INTERNAL "Regex config message") + include_directories (${REGEX_INCLUDE_DIR}) + # I don't think its needed but just in case: + list (APPEND GMT_OPTIONAL_LIBRARIES ${REGEX_LIBRARIES}) + else (REGEX_FOUND) + set (GMT_CONFIG_REGEX_MESSAGE "unsupported" + CACHE INTERNAL "Regex config message") + endif (REGEX_FOUND) +endif (PCRE_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_FFTW3) + find_package (FFTW3) +endif (NOT DEFINED GMT_EXCLUDE_FFTW3) +if (FFTW3_FOUND) + set (HAVE_FFTW3F TRUE CACHE INTERNAL "System has single precision FFTW") + if (FFTW3F_THREADS_LIBRARY) + set (HAVE_FFTW3F_THREADS TRUE CACHE INTERNAL "System has single precision threaded FFTW") + endif (FFTW3F_THREADS_LIBRARY) + include_directories (${FFTW3_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${FFTW3F_LIBRARIES}) +endif (FFTW3_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_LAPACK) + find_package (LAPACK) +endif (NOT DEFINED GMT_EXCLUDE_LAPACK) +if (LAPACK_FOUND) + set (HAVE_LAPACK TRUE CACHE INTERNAL "System has LAPACK") + set (GMT_CONFIG_LAPACK_MESSAGE "yes" CACHE INTERNAL "LAPACK config message") + include_directories (${LAPACK_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${LAPACK_LIBRARIES}) +else (LAPACK_FOUND) + if (LAPACK_LIBRARY) + # Set in ConfigUser.cmake + set (HAVE_LAPACK TRUE CACHE INTERNAL "System has LAPACK") + set (GMT_CONFIG_LAPACK_MESSAGE "yes" CACHE INTERNAL "LAPACK config message") + list (APPEND GMT_OPTIONAL_LIBRARIES ${LAPACK_LIBRARY}) + else (LAPACK_LIBRARY) + set (GMT_CONFIG_LAPACK_MESSAGE "no" CACHE INTERNAL "LAPACK config message") + endif (LAPACK_LIBRARY) +endif (LAPACK_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_BLAS) + find_package (BLAS) +endif (NOT DEFINED GMT_EXCLUDE_BLAS) +if (BLAS_FOUND) + set (HAVE_BLAS TRUE CACHE INTERNAL "System has BLAS") + set (GMT_CONFIG_BLAS_MESSAGE "yes" CACHE INTERNAL "BLAS config message") + include_directories (${BLAS_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${BLAS_LIBRARIES}) +else (BLAS_FOUND) + if (BLAS_LIBRARY) + # Set in ConfigUser.cmake + set (HAVE_BLAS TRUE CACHE INTERNAL "System has BLAS") + set (GMT_CONFIG_BLAS_MESSAGE "yes" CACHE INTERNAL "BLAS config message") + list (APPEND GMT_OPTIONAL_LIBRARIES ${BLAS_LIBRARY}) + else (BLAS_LIBRARY) + set (GMT_CONFIG_BLAS_MESSAGE "no" CACHE INTERNAL "BLAS config message") + endif (BLAS_LIBRARY) +endif (BLAS_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_ZLIB) + find_package (ZLIB) +endif (NOT DEFINED GMT_EXCLUDE_ZLIB) +if (ZLIB_FOUND) + set (HAVE_ZLIB TRUE CACHE INTERNAL "System has ZLIB") + include_directories (${ZLIB_INCLUDE_DIRS}) +endif (ZLIB_FOUND) + + +if (APPLE) + # Accelerate framework + find_library (ACCELERATE_FRAMEWORK Accelerate) + mark_as_advanced (ACCELERATE_FRAMEWORK) + list (APPEND GMT_OPTIONAL_LIBRARIES ${ACCELERATE_FRAMEWORK}) +endif (APPLE) + +if (DEFINED GMT_ENABLE_OPENMP) + set (GMT_OPENMP TRUE CACHE INTERNAL "Turn on GMT OpenMP") +endif (DEFINED GMT_ENABLE_OPENMP) +find_package (OpenMP) +if (OPENMP_FOUND AND GMT_OPENMP) + set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}") + set (CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS}") + set (HAVE_OPENMP TRUE CACHE INTERNAL "OpenMP enabled." FORCE) + set (GMT_CONFIG_OPENMP_MESSAGE "enabled" + CACHE INTERNAL "OPENMP config message") + if (WIN32 AND OMP_DLL_LOC) + # UGLY AND RISKY PATCH FOR THE CPACK BUG OF NOT COPYING THE OMP DLL. THIS PATCH RELIES + # ON THE SETTING OF THE OMP_DLL_LOC VARIABLE IN ConfigUser.cmake. MINE HAS: + # set (OMP_DLL_LOC "C:/Program Files (x86)/Microsoft Visual Studio 12.0/VC/redist/x64/Microsoft.VC120.OPENMP/vcomp120.dll") + install(FILES ${OMP_DLL_LOC} DESTINATION bin COMPONENT Libraries) + endif (WIN32 AND OMP_DLL_LOC) +else (OPENMP_FOUND AND GMT_OPENMP) + set (HAVE_OPENMP FALSE CACHE INTERNAL "OpenMP disabled." FORCE) + set (GMT_CONFIG_OPENMP_MESSAGE "disabled" + CACHE INTERNAL "OPENMP config message") +endif (OPENMP_FOUND AND GMT_OPENMP) +if (OPENMP_FOUND AND NOT GMT_OPENMP) + message (STATUS "User variable GMT_OPENMP not set: disabling OpenMP.") + set (GMT_CONFIG_OPENMP_MESSAGE "disabled (GMT_OPENMP not set)" + CACHE INTERNAL "OPENMP config message") +endif (OPENMP_FOUND AND NOT GMT_OPENMP) + +find_package(GLIB COMPONENTS gthread) +if (GLIB_FOUND AND GMT_USE_THREADS) + set (HAVE_GLIB_GTHREAD TRUE CACHE INTERNAL "System has GLIB component gthread") + include_directories (${GLIB_INCLUDE_DIRS}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${GLIB_LIBRARIES}) + set (GMT_CONFIG_GTHREAD_MESSAGE "enabled" + CACHE INTERNAL "GTHREAD config message") +endif (GLIB_FOUND AND GMT_USE_THREADS) +if (GLIB_FOUND AND NOT GMT_USE_THREADS) + set (HAVE_GLIB_GTHREAD FALSE CACHE INTERNAL "User disabled threads") + message (STATUS "User variable GMT_USE_THREADS not set: disabling GThread.") + set (GMT_CONFIG_GTHREAD_MESSAGE "disabled" + CACHE INTERNAL "GTHREAD config message") +endif (GLIB_FOUND AND NOT GMT_USE_THREADS) +if (GMT_USE_THREADS AND NOT GLIB_FOUND) + message (FATAL_ERROR "User variable GMT_USE_THREADS set but GLIB component gthread not found.") + set (GMT_CONFIG_GTHREAD_MESSAGE "unavailable" + CACHE INTERNAL "GTHREAD config message") +endif (GMT_USE_THREADS AND NOT GLIB_FOUND) + +# check for math and POSIX functions +include(ConfigureChecks) + +include_directories (${GMT_SOURCE_DIR}/src) +include_directories (${CMAKE_CURRENT_BINARY_DIR}) +set(CMAKE_INCLUDE_CURRENT_DIR TRUE) + +# Examples and tests depend on Shorelines +find_package (GSHHG) +if (DO_EXAMPLES OR DO_TESTS AND NOT GSHHG_FOUND) + message (FATAL_ERROR "Cannot proceed without GSHHG Shorelines. " + "Need to either set GSHHG_ROOT or disable tests.") +endif (DO_EXAMPLES OR DO_TESTS AND NOT GSHHG_FOUND) + +# Examples and tests depend on DCW +find_package (DCW) +if (DO_EXAMPLES OR DO_TESTS AND NOT DCW_FOUND) + message (FATAL_ERROR "Cannot proceed without DCW polygons. " + "Need to either set DCW_ROOT or disable tests." + "Obtain dcw-gmt-.tar.gz or dcw-gmt-.zip from ftp://ftp.soest.hawaii.edu/gmt and make DCW_ROOT variable point to the directory where you unarchived the files") +endif (DO_EXAMPLES OR DO_TESTS AND NOT DCW_FOUND) + +if (DO_API_TESTS) + # These lines are temporarily here for the beta release - comment to avoid in the build + set (GMT_DEMOS_SRCS testapi.c testpsl.c testgmt.c testgmtshell.c testgmtio.c testgrdio.c testio.c + testapiconv.c example1.c testapi_matrix.c testapi_matrix_plot.c testapi_vector.c test_JL.c testapi_mixmatrix.c + test_walter.c testapi_usergrid.c testapi_userdataset.c testapi_uservectors.c) +endif (DO_API_TESTS) + +if (NOT LICENSE_RESTRICTED) # off + # enable Shewchuk's triangle routine + set (GMT_TRIANGULATE "Shewchuk" PARENT_SCOPE) + set (GMT_TRIANGLE_SRCS triangle.c triangle.h) + list (APPEND GMT_EXTRA_LICENSE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.TRIANGLE) + set (GMT_EXTRA_LICENSE_FILES ${GMT_EXTRA_LICENSE_FILES} PARENT_SCOPE) +else (NOT LICENSE_RESTRICTED) # on + # disable Shewchuk's triangle routine + set (GMT_TRIANGULATE "Watson" PARENT_SCOPE) +endif (NOT LICENSE_RESTRICTED) + +# Note: Developers can set EXTRA_MODULES in ConfigUser.cmake to test new modules +set (GMT_PROGS_SRCS blockmean.c blockmedian.c blockmode.c docs.c dimfilter.c filter1d.c grd2kml.c + fitcircle.c gmt2kml.c gmtconvert.c gmtlogo.c gmtmath.c gmtselect.c gmtsimplify.c + gmtspatial.c gmtconnect.c gmtregress.c gmtvector.c gmtwhich.c grd2cpt.c + grd2xyz.c grdblend.c grdclip.c grdcut.c grdedit.c grdfft.c grdfill.c grdfilter.c + grdgradient.c grdhisteq.c grdinfo.c grdlandmask.c grdmask.c grdmath.c + grdpaste.c grdproject.c grdsample.c grdconvert.c grdtrack.c movie.c + grdtrend.c grdvolume.c greenspline.c kml2gmt.c makecpt.c mapproject.c + gmtinfo.c nearneighbor.c project.c psconvert.c sample1d.c spectrum1d.c + sph2grd.c sphdistance.c sphinterpolate.c sphtriangulate.c splitxyz.c + surface.c trend1d.c trend2d.c triangulate.c xyz2grd.c gmtdefaults.c gmtget.c + gmtset.c grdcontour.c grdimage.c grdvector.c grdview.c psbasemap.c psclip.c + pscoast.c pscontour.c psevents.c pshistogram.c psimage.c psmask.c psrose.c psscale.c + pssolar.c psternary.c pstext.c pswiggle.c psxy.c psxyz.c pslegend.c ${EXTRA_MODULES}) + +# Legacy modules for which to install compatibility links via +# install_module_symlink +set (GMT_COMPAT_MODULES minmax gmt2rgb gmtstitch gmtdp grdreformat ps2raster) + +# libpslib +set (GMT_PSL_SRCS postscriptlight.c declspec.h psl_config.h PSL_Standard+.h + PSL_Standard.h PSL_ISOLatin1+.h PSL_ISOLatin1.h PSL_ISO-8859-1.h + PSL_ISO-8859-2.h PSL_ISO-8859-3.h PSL_ISO-8859-4.h PSL_ISO-8859-5.h + PSL_ISO-8859-6.h PSL_ISO-8859-7.h PSL_ISO-8859-8.h PSL_ISO-8859-9.h + PSL_ISO-8859-10.h PSL_ISO-8859-13.h PSL_ISO-8859-14.h PSL_ISO-8859-15.h + PSL_strings.h PSL_patterns.h) + +set (GMT_MBSYSTEM_SRCS gmt_mbsystem_module.c gmt_mbsystem_module.h) + +# libgmt +set (GMT_LIB_SRCS block_subs.h common_byteswap.h common_math.h + common_runpath.h common_sighandler.c common_string.h clear.c begin.c + gmt_color_rgb.h gmt_colornames.h + gmt_modern.c end.c declspec.h gmt_hidden.h gmt_remote.h gmt_remote.c + figure.c gmt_dev.h gmt_common.h gmt_constants.h compat/qsort.h + gmt_contour.h gmt_customio.h gmt_datums.h gmt_dcw.h gmt_decorate.h gmt_defaults.h + gmt_ellipsoids.h gmt_error.h gmt_gdalread.h gmt_glib.h gmt_grd.h gmt_grdio.h gmt_hash.h + gmt_internals.h gmt_io.h gmt_macros.h gmt_media_name.h gmt_modern.h + gmt_media_size.h gmt_mgg_header2.h gmt_sharedlibs.h gmt_memory.h gmt_mb.h + gmt_core_module.h gmt_nan.h gmt_notposix.h gmt_pennames.h gmt_enum_dict.h + gmt_plot.h gmt_project.h gmt_prototypes.h gmt_psl.h gmt_shore.h gmt_gsformats.h + gmt_symbol.h gmt_synopsis.h gmt_texture.h gmt_time.h gmt_cpt_masters.h + gmt_types.h gmt_unique.h gmt_version.h gshhg_version.h postscriptlight.h + s_rint.h triangle.h gmt.h gmt_resources.h gmt_private.h subplot.c + gmt_error_codes.h gmt_api.c gmt_bcr.c gmt_calclock.c gmt_cdf.c gmt_compat.c + gmt_customio.c gmt_dcw.c gmt_error.c gmt_fft.c gmt_grdio.c gmt_io.c + gmt_memory.c gmt_nc.c gmt_notposix.c gmt_proj.c gmt_shore.c gmt_sph.c + gmt_stat.c gmt_support.c gmt_regexp.c gmt_vector.c gmt_parse.c inset.c + gmt_error_codes.c gshhg_version.c gmtread.c gmtwrite.c common_math.c + common_runpath.c common_sighandler.c common_string.c compat/qsort.c + gmt_sharedlibs.c gmt_core_module.c gmt_init.c gmt_map.c gmt_plot.c + kiss_fft/_kiss_fft_guts.h kiss_fft/kiss_fft.c kiss_fft/kiss_fft.h + kiss_fft/kiss_fftnd.c kiss_fft/kiss_fftnd.h + ${GMT_TRIANGLE_SRCS} ${GMT_MBSYSTEM_SRCS}) + +if (BUILD_SUPPLEMENTS) + # Needed in supplib, + supplements themselves + set (GMT_SUPPL_SRCS gmt_modern.c gmt_supplements_module.h gmt_supplements_module.c) +endif (BUILD_SUPPLEMENTS) + +# dependencies on generated files +set (GMT_GEN_HDRS gmt_keycases.h + gmt_keywords.h gmt_config.h + gmt_dimensions.h + CACHE INTERNAL "Autogenerated GMT headers") + +# Add commands to create header files + +add_custom_command (OUTPUT gmt_keycases.h gmt_keywords.h + COMMAND ${CMAKE_COMMAND} + -D GENERATE_COMMAND=gen_gmt_keywords_h + -D CMAKE_MODULE_PATH=${CMAKE_MODULE_PATH} + -D GMT_SRC=${GMT_SOURCE_DIR} + -P ${CMAKE_MODULE_PATH}/GmtGenExtraHeaders.cmake + DEPENDS gmt_keywords.txt gmt_keywords.d) + +add_custom_command (OUTPUT gmt_dimensions.h + COMMAND ${CMAKE_COMMAND} + -D GENERATE_COMMAND=gen_gmt_dimensions_h + -D CMAKE_MODULE_PATH=${CMAKE_MODULE_PATH} + -D GMT_SRC=${GMT_SOURCE_DIR} + -P ${CMAKE_MODULE_PATH}/GmtGenExtraHeaders.cmake + DEPENDS gmt_media_name.h gmt_pennames.h gmt_unique.h gmt_cpt_masters.h + gmt_keycases.h) + # depends on cached line numbers from these generated files: + +# autogenerated files target +add_custom_target (gen_gmt_headers DEPENDS ${GMT_GEN_HDRS}) + +# Configure header files to pass some of the CMake settings to the source code +configure_file (gmt_config.h.in gmt_config.h) +configure_file (psl_config.h.in psl_config.h) +configure_file (gmt_version.h.in gmt_version.h) +configure_file (isogmt.in isogmt${GMT_INSTALL_NAME_SUFFIX} @ONLY) +configure_file (gmt-config.in gmt-config${GMT_INSTALL_NAME_SUFFIX} @ONLY) + +# gmtprogram +set (GMT_PROGRAM ${GMT_SOURCE_DIR}/src/gmtprogram.c) + +# extra ugly definitions for triangle +set_source_files_properties (triangle.c + PROPERTIES + COMPILE_DEFINITIONS "NO_TIMER;TRILIBRARY;REDUCED;CDT_ONLY;ANSI_DECLARATORS") + +# libpslib +add_library (pslib + ${GMT_GEN_HDRS} + ${GMT_PSL_SRCS}) + +add_dependencies (pslib gen_gmt_headers) # make pslib after gen_gmt_headers + +if (HAVE_M_LIBRARY) + # link the math library + target_link_libraries (pslib m) +endif (HAVE_M_LIBRARY) + +if (HAVE_ZLIB) + # for DEFLATE encoding + target_link_libraries (pslib ${ZLIB_LIBRARIES}) +endif (HAVE_ZLIB) + +# set the build version (VERSION) and the API version (SOVERSION) +set_target_properties (pslib + PROPERTIES + OUTPUT_NAME postscriptlight + PREFIX "${LIB_PREFIX}" + IMPORT_PREFIX "${LIB_PREFIX}" + VERSION ${GMT_LIB_VERSION} + SOVERSION ${GMT_LIB_SOVERSION} + DEFINE_SYMBOL "LIBRARY_EXPORTS") + +# If a renaming of the gmtpslpsl dll has been set in ConfigUser.cmake +if (WIN32 AND PSL_DLL_RENAME) + set_target_properties (pslib PROPERTIES RUNTIME_OUTPUT_NAME ${PSL_DLL_RENAME}) +endif (WIN32 AND PSL_DLL_RENAME) + +if (BUILD_SUPPLEMENTS) + # supplement directories (only those, which are to be included in gmtlib) + # EXTRA_BUILD_DIRS are for testing new supplements that are not yet in + # subversion. See cmake/ConfigUserTemplate.cmake for setting this parameter. + set (GMT_SUPPL_DIRS geodesy gshhg img mgd77 potential segy seis + spotter x2sys ${EXTRA_BUILD_DIRS}) +endif (BUILD_SUPPLEMENTS) + +# path to all binary dirs (used to set PATH in test scripts) +set (GMT_BINARY_DIR_PATH "${CMAKE_CURRENT_BINARY_DIR}/\${CMAKE_CONFIG_TYPE:-.}") + +if (BUILD_SUPPLEMENTS) + # process supplement directories + if (UNIX) + set (CMAKE_SHARED_MODULE_SUFFIX .so) + endif (UNIX) + foreach (_dir ${GMT_SUPPL_DIRS}) + add_subdirectory (${_dir}) + list (APPEND GMT_BINARY_DIR_PATH + "${CMAKE_CURRENT_BINARY_DIR}/${_dir}/\${CMAKE_CONFIG_TYPE:-.}") + endforeach (_dir) + # supplement library files + get_subdir_var_files (GMT_SUPPL_LIB_SRCS LIB_SRCS ${GMT_SUPPL_DIRS}) + + # include supplement directories + foreach (_dir ${GMT_SUPPL_DIRS}) + include_directories (${CMAKE_CURRENT_BINARY_DIR}/${_dir}) + endforeach (_dir) + # libgmtsuppl + if (WIN32) + add_library (supplib + ${GMT_GEN_HDRS} + ${GMT_SUPPL_SRCS} + ${GMT_SUPPL_LIB_SRCS}) + else (WIN32) + add_library (supplib MODULE + ${GMT_GEN_HDRS} + ${GMT_SUPPL_SRCS} + ${GMT_SUPPL_LIB_SRCS}) + endif (WIN32) + + add_dependencies (supplib gen_gmt_headers) # make supplib after gen_gmt_headers + add_dependencies (supplib pslib) # make supplib after pslib + add_dependencies (supplib gmtlib) # make supplib after pslib + + # No SOVERSION & VERSION for a MODULE, only for SHARED libs + target_link_libraries (supplib + gmtlib + pslib) + + # Include any extra files that are listed in EXTRA_INCLUDE_GMTSUPPL defined in ConfigUser.cmake + # This include(s) will add new modules to the official GMT supplements + if (EXTRA_INCLUDE_GMTSUPPL) + foreach (_f ${EXTRA_INCLUDE_GMTSUPPL}) + include (${_f}) + endforeach(_f) + endif (EXTRA_INCLUDE_GMTSUPPL) + + set_target_properties (supplib + PROPERTIES + OUTPUT_NAME supplements + RUNTIME_OUTPUT_NAME supplements + LIBRARY_OUTPUT_DIRECTORY plugins + RUNTIME_OUTPUT_DIRECTORY plugins + PREFIX "" + LINK_FLAGS "${USER_GMTLIB_LINK_FLAGS}" + DEFINE_SYMBOL "LIBRARY_EXPORTS") + + if (WIN32 AND SUPP_DLL_RENAME) + set_target_properties (supplib PROPERTIES RUNTIME_OUTPUT_NAME ${SUPP_DLL_RENAME}) + endif (WIN32 AND SUPP_DLL_RENAME) + + if (HAVE_DLADDR AND HAVE_LIBDL) + # link the dynamic linking loader library + target_link_libraries (supplib dl) + endif (HAVE_DLADDR AND HAVE_LIBDL) + + if (HAVE_M_LIBRARY) + # link the math library + target_link_libraries (supplib m) + endif (HAVE_M_LIBRARY) + + # install target + install (TARGETS supplib + LIBRARY DESTINATION ${GMT_LIBDIR}/gmt${GMT_INSTALL_NAME_SUFFIX}/plugins # UNIX + COMPONENT Runtime + RUNTIME DESTINATION ${GMT_BINDIR}/gmt_plugins # Windows + COMPONENT Runtime) +endif (BUILD_SUPPLEMENTS) + +# Include any extra files that are listed in EXTRA_INCLUDE_NEWSUPPL defined in ConfigUser.cmake +# This include(s) will create new pluggins +if (EXTRA_INCLUDE_NEWSUPPL) + foreach (_f ${EXTRA_INCLUDE_NEWSUPPL}) + include (${_f}) + endforeach(_f) +endif (EXTRA_INCLUDE_NEWSUPPL) + + +# make UNIX PATH variable +string (REPLACE ";" ":" GMT_BINARY_DIR_PATH "${GMT_BINARY_DIR_PATH}") +set (GMT_BINARY_DIR_PATH ${GMT_BINARY_DIR_PATH} CACHE INTERNAL + "UNIX PATH to all binary dirs") + +# libgmt +add_library (gmtlib + ${GMT_GEN_HDRS} + ${GMT_LIB_SRCS} + ${GMT_PROGS_SRCS}) + +add_dependencies (gmtlib gen_gmt_headers) # make gmtlib after gen_gmt_headers +add_dependencies (gmtlib pslib) # make gmtlib after pslib + +target_link_libraries (gmtlib + ${NETCDF_LIBRARIES} + ${GMT_OPTIONAL_LIBRARIES} + pslib) + +if (HAVE_M_LIBRARY) + # link the math library + target_link_libraries (gmtlib m) +endif (HAVE_M_LIBRARY) + +# set the build version (VERSION) and the API version (SOVERSION) +set_target_properties (gmtlib + PROPERTIES + OUTPUT_NAME gmt + PREFIX "${LIB_PREFIX}" + IMPORT_PREFIX "${LIB_PREFIX}" + VERSION ${GMT_LIB_VERSION} + SOVERSION ${GMT_LIB_SOVERSION} + LINK_FLAGS "${USER_GMTLIB_LINK_FLAGS}" + DEFINE_SYMBOL "LIBRARY_EXPORTS") + +# If a renaming of the gmt dll has been set in ConfigUser.cmake +if (WIN32 AND GMT_DLL_RENAME) + set_target_properties (gmtlib PROPERTIES RUNTIME_OUTPUT_NAME ${GMT_DLL_RENAME}) +endif (WIN32 AND GMT_DLL_RENAME) + +if (HAVE_DLADDR AND HAVE_LIBDL) + # link the dynamic linking loader library + target_link_libraries (pslib dl) + target_link_libraries (gmtlib dl) +endif (HAVE_DLADDR AND HAVE_LIBDL) + +if (MSVC AND FFTW3_FOUND) + target_link_libraries (gmtlib ws2_32) +endif (MSVC AND FFTW3_FOUND) + +# build targets for standalone gmt target and demos +string (REPLACE ".c" "" _gmt_progs "gmt.c;${GMT_DEMOS_SRCS}") +foreach (_gmt_prog ${_gmt_progs}) + add_executable (${_gmt_prog} ${_gmt_prog}.c) + target_link_libraries (${_gmt_prog} gmtlib) +endforeach (_gmt_prog) + +add_executable (psldemo psldemo.h psldemo.c) +target_link_libraries (psldemo pslib) + +# Rename gmt target to prevent version clash +set_target_properties (gmt PROPERTIES OUTPUT_NAME gmt${GMT_INSTALL_NAME_SUFFIX}) + +# generate and install Mac/Windows debugging symbols +create_debug_sym (${GMT_BINDIR} gmt) +if (WIN32) + create_debug_sym (${GMT_BINDIR} gmtlib pslib) + create_debug_sym (${GMT_BINDIR}/gmt_plugins supplib) +else (WIN32) + create_debug_sym (${GMT_LIBDIR} gmtlib pslib) + create_debug_sym (${GMT_LIBDIR}/gmt${GMT_INSTALL_NAME_SUFFIX}/plugins supplib) +endif (WIN32) + +# gshhg_version +add_executable (gshhg_version gshhg_version.h gshhg_version.c) +set_target_properties (gshhg_version + PROPERTIES COMPILE_DEFINITIONS "STANDALONE") +target_link_libraries (gshhg_version ${NETCDF_LIBRARIES}) + +# script2verbatim for removing svn keywords, comments etc. from example scripts +add_executable (script2verbatim script2verbatim.c) + +if (BUILD_SUPPLEMENTS) + # Tests depend on GMT progs and supplements: + add_dependencies (check ${_gmt_progs} psldemo supplib) +else (BUILD_SUPPLEMENTS) + # Tests depend on GMT progs and supplements: + add_dependencies (check ${_gmt_progs} psldemo) +endif (BUILD_SUPPLEMENTS) + +if (MSVC) + # Disable automatic manifest generation + string(REGEX REPLACE "/MANIFEST[^ ]*( |$)" "" + CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}") + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /MANIFEST:NO") + + # To expand the command line arguments in Windows, see: + # http://msdn.microsoft.com/en-us/library/8bch7bkk.aspx + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} setargv.obj") +endif (MSVC) + +# add the install targets +install (TARGETS gmtlib pslib gmt + ARCHIVE DESTINATION ${GMT_LIBDIR} + COMPONENT Runtime + LIBRARY DESTINATION ${GMT_LIBDIR} + COMPONENT Runtime + RUNTIME DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) + +string (REPLACE ".c" "" _gmt_modules "${GMT_PROGS_SRCS}") +install_module_symlink (${_gmt_modules} ${GMT_COMPAT_MODULES}) + +# Install public headers +install (FILES gmt.h gmt_resources.h declspec.h + DESTINATION ${GMT_INCLUDEDIR} + COMPONENT Runtime) + +if (BUILD_DEVELOPER) + # Install Developer headers [These are clean and have no #define HAVE_* configuration] + install (FILES postscriptlight.h common_math.h common_string.h gmt_common.h gmt_constants.h gmt_contour.h + gmt_dcw.h gmt_decorate.h gmt_defaults.h gmt_error.h gmt_error_codes.h gmt_fft.h gmt_gdalread.h gmt_grd.h + gmt_grdio.h gmt_hash.h gmt_io.h gmt_macros.h gmt_memory.h gmt_modern.h gmt_nan.h gmt_notposix.h gmt_plot.h + gmt_private.h gmt_project.h gmt_prototypes.h gmt_psl.h gmt_shore.h gmt_symbol.h gmt_synopsis.h + gmt_texture.h gmt_time.h gmt_types.h gmt_dev.h gmt_customio.h gmt_hidden.h gmt_mb.h + gmt_core_module.h gmt_supplements_module.h compat/qsort.h + DESTINATION ${GMT_INCLUDEDIR} + COMPONENT Runtime) + install (FILES compat/qsort.h + DESTINATION ${GMT_INCLUDEDIR}/compat + COMPONENT Runtime) + # Install Configured Developer headers [These are produced by cmake from *.h.in files] + install (FILES ${PROJECT_BINARY_DIR}/src/config.h ${PROJECT_BINARY_DIR}/src/gmt_config.h + ${PROJECT_BINARY_DIR}/src/gmt_dimensions.h ${PROJECT_BINARY_DIR}/src/gmt_version.h + ${PROJECT_BINARY_DIR}/src/psl_config.h + DESTINATION ${GMT_INCLUDEDIR} + COMPONENT Runtime) +endif (BUILD_DEVELOPER) + +# symlink to gmt-wrapper in bindir and libdir: +if (UNIX AND GMT_INSTALL_NAME_SUFFIX) + get_target_property(_gmt_wrapper_name gmt OUTPUT_NAME) + install (CODE " + execute_process ( + COMMAND ${CMAKE_COMMAND} -E create_symlink + \"${_gmt_wrapper_name}\" \"\$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/${GMT_BINDIR}/gmt\") + ") +endif (UNIX AND GMT_INSTALL_NAME_SUFFIX) + +# install extra files +install (PROGRAMS + ${CMAKE_CURRENT_BINARY_DIR}/isogmt${GMT_INSTALL_NAME_SUFFIX} + ${CMAKE_CURRENT_BINARY_DIR}/gmt-config${GMT_INSTALL_NAME_SUFFIX} + DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) + +install (PROGRAMS gmtswitch + RENAME gmtswitch${GMT_INSTALL_NAME_SUFFIX} + DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) + +install (PROGRAMS gmt_shell_functions.sh + RENAME gmt_shell_functions${GMT_INSTALL_NAME_SUFFIX}.sh + DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) + +if (WIN32) + install (PROGRAMS + gmtswitch.bat + DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) +endif (WIN32) + +# this prints out the final version of the compiler/linker flags +string (TOUPPER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_UPPER) +string(REGEX REPLACE "[ ]+" " " _using_cflags ${CMAKE_C_FLAGS} " " + ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE_UPPER}}) +message (STATUS "Using CFLAGS = '${_using_cflags}'") Index: sm/trunk/externalpackages/gmt/configs/ConfigUser.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/ConfigUser.cmake (revision 25835) +++ (revision ) @@ -1,240 +1,0 @@ -# -# $Id: ConfigUserTemplate.cmake 12904 2014-02-17 20:52:35Z fwobbe $ -# -# Copyright (c) 1991-2014 by P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis and F. Wobbe -# See LICENSE.TXT file for copying and redistribution conditions. -# -# This program is free software; you can redistribute it and/or modify it -# under the terms of the GNU Lesser General Public License as published by the -# Free Software Foundation; version 3 or any later version. -# -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or -# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License -# for more details. -# -# Contact info: gmt.soest.hawaii.edu -# ---------------------------------------------------------------------------- - -# Use this file to override variables in 'ConfigDefault.cmake' on a per-user -# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then -# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled -# (currently listed in svn:ignore property) -# -# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string -# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so -# "False", "off", "no", and "something-NotFound" are all false). Other values -# are true. Thus it does not matter whether you use TRUE and FALSE, ON and -# OFF, or YES and NO for your booleans. - -## -## Section 1: Installation paths -## - -# ============================================================================ -# Basic setup begins here. All settings are optional. In most cases, setting -# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with -# reasonable defaults enabled. -# ============================================================================ - -# Installation path (usually defaults to /usr/local) [auto]: -set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") - -# Set install name suffix used for directories and gmt executables -# [undefined]: -#set (GMT_INSTALL_NAME_SUFFIX "suffix") - -# Install into traditional directory structure. Disable to install a -# distribution type directory structure (doc and share separated) [on]: -#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) - -# Install convenience links for GMT modules. Disable to install only the main -# gmt program and access modules as "gmt modulename options" [TRUE]: -#set (GMT_INSTALL_MODULE_LINKS FALSE) - -# Make executables relocatable on supported platforms (relative RPATH) [TRUE]: -#set (GMT_INSTALL_RELOCATABLE FALSE) - -# ============================================================================ -# Advanced configuration begins here. Usually it is not necessary to edit any -# settings below. You should know what you are doing if you do though. Note: -# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute -# path is given. -# ============================================================================ - -# Set binary installation path [bin]: -#set (GMT_BINDIR "bin") - -# Set library installation path [lib or lib64]: -#set (GMT_LIBDIR "lib") - -# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: -#set (GMT_INCLUDEDIR "include/gmt") - -# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: -#set (GMT_DATADIR "share/gmt") - -# Set doc installation path [share/doc or -# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: -#set (GMT_DOCDIR "share/doc/gmt") - -# Set manpage installation path [share/man or -# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: -#set (GMT_MANDIR "share/doc/gmt/man") - -# Install documentation files from this external location instead of creating -# new PDF and HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: -#set (GMT_INSTALL_EXTERNAL_DOC OFF) - -# Install manual pages from this external location instead of creating the -# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: -#set (GMT_INSTALL_EXTERNAL_MAN OFF) - -## -## Section 2: Build dependencies (should only be needed if CMake cannot -## automatically detect the rights version or path.) -## - -# Set path to GSHHG Shoreline Database [auto]: -set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") - -# Copy GSHHG files to $/coast [FALSE]: -#set (COPY_GSHHG TRUE) - -# Set path to DCW Digital Chart of the World for GMT [auto]: -#set (DCW_ROOT "$ENV{ISSM_DIR}/externalpackages/dcw/install") - -# Copy DCW files to $/dcw [FALSE]: -#set (COPY_DCW TRUE) - -# Set location of NetCDF (can be root directory, path to header file or path -# to nc-config) [auto]: -set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/netcdf/install") - -# Set location of GDAL (can be root directory, path to header file or path to -# gdal-config) [auto]: -set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") - -# Set location of PCRE (can be root directory, path to header file or path to -# pcre-config) [auto]: -#set (PCRE_ROOT "pcre_install_prefix") - -# Set location of single precision FFTW (can be root directory or path to -# header file) [auto]: -#set (FFTW3_ROOT "fftw_install_prefix") - -# Set location of ZLIB (can be root directory or path to header file) [auto]: -#set (ZLIB_ROOT "zlib_install_prefix") - -## -## Section 3: GMT features -## - -# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be -# redistributed under the terms of the GPL or LGPL such as Shewchuk's -# triangulation (valid values are GPL, LGPL and off) [off]: -#set (LICENSE_RESTRICTED GPL) - -# Configure default units (possible values are SI and US) [SI]: -#set (UNITS "US") - -# Enable building of shared libraries [TRUE] (disable to use static libraries; -# not recommended): -#set (BUILD_SHARED_LIBS TRUE) - -# Build GMT shared lib with supplemental modules [TRUE]: -#set (BUILD_SUPPLEMENTS TRUE) - -## -## Section 4: Advanced tweaking -## - -# -# Testing and development -# - -# Enable running examples/tests with "ctest" or "make check" (out-of-source). -# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following -# line. -#enable_testing() -#set (DO_EXAMPLES TRUE) -#set (DO_TESTS TRUE) -# Number of parallel test jobs with "make check": -#set (N_TEST_JOBS 4) - -# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without -# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required -# for testing [OFF]: -#set (SUPPORT_EXEC_IN_BINARY_DIR ON) - -# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes -# that link against the full gmt libs (not just the API; for building codes -# that only need the GMT API, see the gmtextension project). -#set (EXTRA_BUILD_DIRS apidemo) - -# Directory in which to install the release sources per default -# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: -#set (GMT_RELEASE_PREFIX "release-src-prefix") - -# If set to false, image conversion from PS images to PNG and PDF does -# not depend on the gmt binary target. Note: "make gmt" is then required -# before docs_depends [TRUE]. -#set (GMT_DOCS_DEPEND_ON_GMT FALSE) - -# -# Debugging -# - -# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel -# [Release]: -#set (CMAKE_BUILD_TYPE Debug) - -# Extra debugging for developers: -#add_definitions(-DDEBUG) -#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info -#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build -#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings -#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols -#set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables -#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies - -# -# System specific tweaks -# - -# This is for GCC on Solaris to avoid "relocations remain against allocatable -# but non-writable sections" problems: -#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) - -# This may be needed to enable strdup and extended math functions with GCC and -# Suncc on Solaris: -#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") - -# Do not warn when building with Windows SDK or Visual Studio Express: -#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) - -# Manually select runtime library when compiling with Windows SDK or Visual -# Studio Express: -#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) - -# If your NetCDF library is static (not recommended, applies to Windows only) -#set (NETCDF_STATIC TRUE) - -# If want to rename the DLLs to something else than the default (e.g. to -# append the bitness - Windows only) -#if (WIN32) -# set (BITAGE 32) -# # Detect if we are building a 32 or 64 bits version -# if (CMAKE_SIZEOF_VOID_P EQUAL 8) -# set (BITAGE 64) -# endif () -# set (GMT_DLL_RENAME gmt_w${BITAGE}) -# set (PSL_DLL_RENAME psl_w${BITAGE}) -#endif(WIN32) - -# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build -#if(MSVC11) -# add_definitions(/D_ALLOW_KEYWORD_MACROS) -#endif(MSVC11) - -# vim: textwidth=78 noexpandtab tabstop=2 softtabstop=2 shiftwidth=2 Index: sm/trunk/externalpackages/gmt/configs/ConfigUser.cmake-static =================================================================== --- /issm/trunk/externalpackages/gmt/configs/ConfigUser.cmake-static (revision 25835) +++ (revision ) @@ -1,240 +1,0 @@ -# -# $Id: ConfigUserTemplate.cmake 12904 2014-02-17 20:52:35Z fwobbe $ -# -# Copyright (c) 1991-2014 by P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis and F. Wobbe -# See LICENSE.TXT file for copying and redistribution conditions. -# -# This program is free software; you can redistribute it and/or modify it -# under the terms of the GNU Lesser General Public License as published by the -# Free Software Foundation; version 3 or any later version. -# -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or -# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License -# for more details. -# -# Contact info: gmt.soest.hawaii.edu -# ---------------------------------------------------------------------------- - -# Use this file to override variables in 'ConfigDefault.cmake' on a per-user -# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then -# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled -# (currently listed in svn:ignore property) -# -# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string -# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so -# "False", "off", "no", and "something-NotFound" are all false). Other values -# are true. Thus it does not matter whether you use TRUE and FALSE, ON and -# OFF, or YES and NO for your booleans. - -## -## Section 1: Installation paths -## - -# ============================================================================ -# Basic setup begins here. All settings are optional. In most cases, setting -# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with -# reasonable defaults enabled. -# ============================================================================ - -# Installation path (usually defaults to /usr/local) [auto]: -set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") - -# Set install name suffix used for directories and gmt executables -# [undefined]: -#set (GMT_INSTALL_NAME_SUFFIX "suffix") - -# Install into traditional directory structure. Disable to install a -# distribution type directory structure (doc and share separated) [on]: -#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) - -# Install convenience links for GMT modules. Disable to install only the main -# gmt program and access modules as "gmt modulename options" [TRUE]: -#set (GMT_INSTALL_MODULE_LINKS FALSE) - -# Make executables relocatable on supported platforms (relative RPATH) [TRUE]: -#set (GMT_INSTALL_RELOCATABLE FALSE) - -# ============================================================================ -# Advanced configuration begins here. Usually it is not necessary to edit any -# settings below. You should know what you are doing if you do though. Note: -# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute -# path is given. -# ============================================================================ - -# Set binary installation path [bin]: -#set (GMT_BINDIR "bin") - -# Set library installation path [lib or lib64]: -#set (GMT_LIBDIR "lib") - -# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: -#set (GMT_INCLUDEDIR "include/gmt") - -# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: -#set (GMT_DATADIR "share/gmt") - -# Set doc installation path [share/doc or -# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: -#set (GMT_DOCDIR "share/doc/gmt") - -# Set manpage installation path [share/man or -# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: -#set (GMT_MANDIR "share/doc/gmt/man") - -# Install documentation files from this external location instead of creating -# new PDF and HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: -#set (GMT_INSTALL_EXTERNAL_DOC OFF) - -# Install manual pages from this external location instead of creating the -# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: -#set (GMT_INSTALL_EXTERNAL_MAN OFF) - -## -## Section 2: Build dependencies (should only be needed if CMake cannot -## automatically detect the rights version or path.) -## - -# Set path to GSHHG Shoreline Database [auto]: -set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") - -# Copy GSHHG files to $/coast [FALSE]: -#set (COPY_GSHHG TRUE) - -# Set path to DCW Digital Chart of the World for GMT [auto]: -#set (DCW_ROOT "dcw-gmt_path") - -# Copy DCW files to $/dcw [FALSE]: -#set (COPY_DCW TRUE) - -# Set location of NetCDF (can be root directory, path to header file or path -# to nc-config) [auto]: -set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/netcdf/install") - -# Set location of GDAL (can be root directory, path to header file or path to -# gdal-config) [auto]: -set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") - -# Set location of PCRE (can be root directory, path to header file or path to -# pcre-config) [auto]: -#set (PCRE_ROOT "pcre_install_prefix") - -# Set location of single precision FFTW (can be root directory or path to -# header file) [auto]: -#set (FFTW3_ROOT "fftw_install_prefix") - -# Set location of ZLIB (can be root directory or path to header file) [auto]: -#set (ZLIB_ROOT "zlib_install_prefix") - -## -## Section 3: GMT features -## - -# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be -# redistributed under the terms of the GPL or LGPL such as Shewchuk's -# triangulation (valid values are GPL, LGPL and off) [off]: -#set (LICENSE_RESTRICTED GPL) - -# Configure default units (possible values are SI and US) [SI]: -#set (UNITS "US") - -# Enable building of shared libraries [TRUE] (disable to use static libraries; -# not recommended): -set (BUILD_SHARED_LIBS FALSE) - -# Build GMT shared lib with supplemental modules [TRUE]: -#set (BUILD_SUPPLEMENTS FALSE) - -## -## Section 4: Advanced tweaking -## - -# -# Testing and development -# - -# Enable running examples/tests with "ctest" or "make check" (out-of-source). -# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following -# line. -#enable_testing() -#set (DO_EXAMPLES TRUE) -#set (DO_TESTS TRUE) -# Number of parallel test jobs with "make check": -#set (N_TEST_JOBS 4) - -# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without -# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required -# for testing [OFF]: -#set (SUPPORT_EXEC_IN_BINARY_DIR ON) - -# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes -# that link against the full gmt libs (not just the API; for building codes -# that only need the GMT API, see the gmtextension project). -#set (EXTRA_BUILD_DIRS apidemo) - -# Directory in which to install the release sources per default -# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: -#set (GMT_RELEASE_PREFIX "release-src-prefix") - -# If set to false, image conversion from PS images to PNG and PDF does -# not depend on the gmt binary target. Note: "make gmt" is then required -# before docs_depends [TRUE]. -#set (GMT_DOCS_DEPEND_ON_GMT FALSE) - -# -# Debugging -# - -# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel -# [Release]: -#set (CMAKE_BUILD_TYPE Debug) - -# Extra debugging for developers: -#add_definitions(-DDEBUG) -#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info -#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build -#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings -#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols -#set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables -#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies - -# -# System specific tweaks -# - -# This is for GCC on Solaris to avoid "relocations remain against allocatable -# but non-writable sections" problems: -#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) - -# This may be needed to enable strdup and extended math functions with GCC and -# Suncc on Solaris: -#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") - -# Do not warn when building with Windows SDK or Visual Studio Express: -#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) - -# Manually select runtime library when compiling with Windows SDK or Visual -# Studio Express: -#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) - -# If your NetCDF library is static (not recommended, applies to Windows only) -set (NETCDF_STATIC TRUE) - -# If want to rename the DLLs to something else than the default (e.g. to -# append the bitness - Windows only) -#if (WIN32) -# set (BITAGE 32) -# # Detect if we are building a 32 or 64 bits version -# if (CMAKE_SIZEOF_VOID_P EQUAL 8) -# set (BITAGE 64) -# endif () -# set (GMT_DLL_RENAME gmt_w${BITAGE}) -# set (PSL_DLL_RENAME psl_w${BITAGE}) -#endif(WIN32) - -# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build -#if(MSVC11) -# add_definitions(/D_ALLOW_KEYWORD_MACROS) -#endif(MSVC11) - -# vim: textwidth=78 noexpandtab tabstop=2 softtabstop=2 shiftwidth=2 Index: sm/trunk/externalpackages/gmt/install-5.1-linux.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-5.1-linux.sh (revision 25835) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - - -# Constants -# -VER="5.1.1" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" - -# Unpack source -tar -zxvf gmt-$VER.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv gmt-$VER/* src -rm -rf gmt-$VER - -# Copy source customizations -cp configs/5.1/linux/cmake/ConfigUser.cmake src/cmake - -# Configure -cd src -mkdir build -cd build -cmake .. - -# Install -if [ $# -eq 0 ]; then - make install -else - make -j $1 install -fi - -# Return to initial directory -cd ../.. Index: /issm/trunk/externalpackages/gmt/install-6-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-6-linux-static.sh (revision 25836) +++ /issm/trunk/externalpackages/gmt/install-6-linux-static.sh (revision 25836) @@ -0,0 +1,86 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.0.0" + +CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" +PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +BLASLAPACK_ROOT="${PETSC_ROOT}" +HDF5_ROOT="${PETSC_ROOT}" + +# Find libgfortran and libgcc so we do not have to hardcode them +# +# NOTE: For now, paths are hardcoded. +# +# TODO: +# - Figure out how to find and grep for single result like we do with mdfind +# under macOS. +# +LIBGFORTRAN="/usr/lib/gcc/x86_64-linux-gnu/8/libgfortran.a" +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC="/usr/lib/gcc/x86_64-linux-gnu/8/libgcc.a" + +CURL_INCLUDE_DIRS="${CURL_ROOT}/include" \ +CURL_LIBRARIES="${CURL_ROOT}/lib/libcurl.a;/usr/lib/x86_64-linux-gnu/libssl.a;/usr/lib/x86_64-linux-gnu/libcrypto.a" \ +GDAL_EXTRA_LIBS="-lstdc++" # Determined by running `$GDAL_ROOT/bin/gdal-config --dep-libs` then removing duplicate libs +NETCDF_EXTRA_LIBS="-lm -ldl -lz" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6.0/static/cmake/modules/FindNETCDF.cmake) + +# Environment +# +export CC=mpicc +export CURL_INCLUDE_DIRS=${CURL_INCLUDE_DIRS} +export CURL_LIBRARIES=${CURL_LIBRARIES} + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gmt-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv gmt-${VER}/* src +rm -rf gmt-${VER} + +# Copy custom configuration files +cp ./configs/6/static/cmake/ConfigUser.static.cmake ./src/cmake/ConfigUser.cmake +cp ./configs/6/static/cmake/modules/FindGDAL.cmake ./src/cmake/modules +cp ./configs/6/static/cmake/modules/FindGSHHG.cmake ./src/cmake/modules +cp ./configs/6/static/cmake/modules/FindNETCDF.cmake ./src/cmake/modules +cp ./configs/6/static/src/CMakeLists.txt ./src/src + +# Configure +cd src +mkdir build +cd build + +# NOTE: +# - The CMake modules used to find and probe the BLAS and LAPACK libraries do +# not seem to handle the situation where BLAS_LIBRARY and LAPACK_LIBRARY are +# set but we are working with static libraries +# (see customized ConfigUser.static.cmake). Using BLAS_LIBRARIES and +# LAPACK_LIBRARIES is a workaround. +# +cmake \ + -DBLAS_LIBRARIES="${BLASLAPACK_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \ + -DHDF5_ROOT="${HDF5_ROOT}" \ + -DLAPACK_LIBRARIES="${BLASLAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gmt/install-6-linux.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-6-linux.sh (revision 25836) +++ /issm/trunk/externalpackages/gmt/install-6-linux.sh (revision 25836) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.0.0" + +CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" + +# Environment +# +export CC=mpicc + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gmt-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv gmt-${VER}/* src +rm -rf gmt-${VER} + +# Copy custom configuration files +cp ./configs/6/cmake/ConfigUser.cmake ./src/cmake + +# Configure +cd src +mkdir build +cd build + +# NOTE: +# - There is a CMake variable named CURL_ROOT in src/cmake/ConfigUser.cmake +# that, ostensibly, allows for supplying the path to curl when it is in a +# non-standard location. That said, newer versions of CMake will ignore said +# variable and instead try to find curl itself. Passing in the two options +# below overrides this behavior. +# +cmake \ + -DCURL_LIBRARY="${CURL_ROOT}/lib" \ + -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gmt/install-6-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-6-mac-static.sh (revision 25836) +++ /issm/trunk/externalpackages/gmt/install-6-mac-static.sh (revision 25836) @@ -0,0 +1,73 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.0.0" + +PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +BLASLAPACK_ROOT="${PETSC_ROOT}" +HDF5_ROOT="${PETSC_ROOT}" + +# Find libgfortran and libgcc so we do not have to hardcode them +# +# Should retrieve a copy of gfortran that is compiled from source before returning one that is installed via package manager +# +# TODO: +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. +# +LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | grep -n libgcc.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) + +GDAL_EXTRA_LIBS="-lc++" # `$GDAL_ROOT/bin/gdal-config --dep-libs` does not report need to link to libc++ (see also customized configuration file ./configs/6.0/static/cmake/modules/FindGDAL.cmake) +NETCDF_EXTRA_LIBS="-lsqlite3 -lpthread -ldl -liconv" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6.0/static/cmake/modules/FindNETCDF.cmake) + +# Environment +# +export CC=mpicc + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gmt-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv gmt-${VER}/* src +rm -rf gmt-${VER} + +# Copy custom configuration files +cp ./configs/6/static/cmake/ConfigUser.static.cmake ./src/cmake/ConfigUser.cmake +cp ./configs/6/static/cmake/modules/FindGDAL.cmake ./src/cmake/modules +cp ./configs/6/static/cmake/modules/FindGSHHG.cmake ./src/cmake/modules +cp ./configs/6/static/cmake/modules/FindNETCDF.cmake ./src/cmake/modules + +# Configure +cd src +mkdir build +cd build + +cmake \ + -DBLAS_LIBRARIES="${BLASLAPACK_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \ + -DHDF5_ROOT="${HDF5_ROOT}" \ + -DLAPACK_LIBRARIES="${BLASLAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gmt/install-6-mac.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-6-mac.sh (revision 25836) +++ /issm/trunk/externalpackages/gmt/install-6-mac.sh (revision 25836) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.0.0" + +CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" + +# Environment +# +export CC=mpicc + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gmt-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv gmt-${VER}/* src +rm -rf gmt-${VER} + +# Copy custom configuration files +cp ./configs/6/cmake/ConfigUser.cmake ./src/cmake + +# Configure +cd src +mkdir build +cd build + +# NOTE: +# - There is a CMake variable named CURL_ROOT in src/cmake/ConfigUser.cmake +# that, ostensibly, allows for supplying the path to curl when it is in a +# non-standard location. That said, newer versions of CMake will ignore said +# variable and instead try to find curl itself. Passing in the two options +# below overrides this behavior. +# +cmake \ + -DCURL_LIBRARY="${CURL_ROOT}/lib" \ + -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: sm/trunk/externalpackages/gmt/install-6.0-linux.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-6.0-linux.sh (revision 25835) +++ (revision ) @@ -1,52 +1,0 @@ -#!/bin/bash -set -eu - - -## Environment -# -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" - -## Constants -# -VER="6.0.0" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" - -# Unpack source -tar -zxvf gmt-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv gmt-${VER}/* src -rm -rf gmt-${VER} - -# Copy custom configuration files -cp ./configs/6.0/linux/cmake/ConfigUser.cmake ./src/cmake - -# Configure -cd src -mkdir build -cd build - -# NOTE: There is a CMake variable named CURL_ROOT in src/cmake/ConfigUser.cmake -# that, ostensibly, allows for supplying the path to curl when it is in a -# a non-standard location. That said, newer versions of CMake will -# ignore said variable and instead try to find curl itself. Passing in -# the two options below overrides this behavior. -cmake \ - -DCURL_LIBRARY="${CURL_ROOT}/lib" \ - -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \ - .. - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: sm/trunk/externalpackages/gmt/install-jenkins.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-jenkins.sh (revision 25835) +++ (revision ) @@ -1,32 +1,0 @@ -#!/bin/bash -set -eu - -#Erase install -rm -rf install src gmt - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gmt-5.1.1.tar.gz' 'gmt-5.1.1.tar.gz' - -#install directory -mkdir src -tar -zxvf gmt-5.1.1.tar.gz -mv gmt-5.1.1/* src -rm -rf gmt-5.1.1 - -#configure: -cp configs/ConfigUser.cmake-jenkins ./src/cmake/ConfigUser.cmake - -cd src -mkdir build -cd build -cmake ../ - -#compile -if [ $# -eq 0 ]; then - make install -else - make -j $1 install -fi - -#come back: -cd ../../ Index: sm/trunk/externalpackages/gmt/install-static.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-static.sh (revision 25835) +++ (revision ) @@ -1,32 +1,0 @@ -#!/bin/bash -set -eu - -#Erase install -rm -rf install src gmt - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gmt-5.1.1.tar.gz' 'gmt-5.1.1.tar.gz' - -#install directory -mkdir src -tar -zxvf gmt-5.1.1.tar.gz -mv gmt-5.1.1/* src -rm -rf gmt-5.1.1 - -#configure: -cp configs/ConfigUser.cmake-static ./src/cmake/ConfigUser.cmake - -cd src -mkdir build -cd build -cmake ../ - -#compile -if [ $# -eq 0 ]; then - make install -else - make -j $1 install -fi - -#come back: -cd ../../ Index: sm/trunk/externalpackages/gmt/install.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install.sh (revision 25835) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - - -# Constants -# -VER="5.1.1" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" - -# Unpack source -tar -zxvf gmt-$VER.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv gmt-$VER/* src -rm -rf gmt-$VER - -# Copy source customizations -cp configs/ConfigUser.cmake src/cmake - -# Configure -cd src -mkdir build -cd build -cmake .. - -# Install -if [ $# -eq 0 ]; then - make install -else - make -j $1 install -fi - -# Return to initial directory -cd ../.. Index: sm/trunk/externalpackages/gsl/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-linux64.sh (revision 25835) +++ (revision ) @@ -1,30 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src install gsl-1.15 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' - -#Untar -tar -zxvf gsl-1.15.tar.gz - -#Move gsl into src directory -mv gsl-1.15/* src -rm -rf gsl-1.15 - -#Configure gsl -cd src - -./configure \ - --prefix="$ISSM_DIR/externalpackages/gsl/install" - -#Compile gsl -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk/externalpackages/gsl/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-macosx64.sh (revision 25835) +++ (revision ) @@ -1,32 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src install gsl-1.15 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' - -#Untar -tar -zxvf gsl-1.15.tar.gz - -#Move gsl into src directory -mv gsl-1.15/* src -rm -rf gsl-1.15 - -#Configure gsl -cd src - -export CFLAGS=" -arch x86_64" - -./configure \ - --prefix="$ISSM_DIR/externalpackages/gsl/install" - -#Compile gsl -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk/externalpackages/gsl/install-static.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-static.sh (revision 25836) +++ /issm/trunk/externalpackages/gsl/install-static.sh (revision 25836) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + + +# Constants +# +GSL_ROOT=${ISSM_DIR}/externalpackages/gsl +VER="1.15" + +# Cleanup= +rm -rf install src +mkdir install src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gsl-${VER}.tar.gz" "gsl-${VER}.tar.gz" + +# Unpack source +tar -zxvf gsl-${VER}.tar.gz + +# Move source to 'src' directory +mv gsl-${VER}/* src +rm -rf gsl-${VER} + +# Configure +cd src +./configure \ + --prefix="${GSL_ROOT}/install" \ + --disable-shared \ + --with-pic + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/gsl/install.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install.sh (revision 25836) +++ /issm/trunk/externalpackages/gsl/install.sh (revision 25836) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + + +# Constants +# +GSL_ROOT=${ISSM_DIR}/externalpackages/gsl +VER="1.15" + +# Cleanup= +rm -rf install src +mkdir install src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gsl-${VER}.tar.gz" "gsl-${VER}.tar.gz" + +# Unpack source +tar -zxvf gsl-${VER}.tar.gz + +# Move source to 'src' directory +mv gsl-${VER}/* src +rm -rf gsl-${VER} + +# Configure +cd src +./configure \ + --prefix="${GSL_ROOT}/install" \ + --disable-static + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/m1qn3/install-maui.sh =================================================================== --- /issm/trunk/externalpackages/m1qn3/install-maui.sh (revision 25836) +++ /issm/trunk/externalpackages/m1qn3/install-maui.sh (revision 25836) @@ -0,0 +1,55 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src m1qn3-3.3-distrib +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/m1qn3-3.3-distrib.tgz' 'm1qn3-3.3-distrib.tgz' + +#Untar +tar -xzf m1qn3-3.3-distrib.tgz +mv m1qn3-3.3-distrib src + +FC="ftn" + +#Compile m1qn3 +cd src/src/ +( +cat << EOF +LIB_EXT=a +FC=$FC +install: libm1qn3.\$(LIB_EXT) + cp libm1qn3.\$(LIB_EXT) ../../install/ +OBJECTS= m1qn3.o +libm1qn3.\$(LIB_EXT): \$(OBJECTS) + ar -r libm1qn3.\$(LIB_EXT) \$(OBJECTS) + ranlib libm1qn3.\$(LIB_EXT) +%.o: %.f + \$(FC) \$(FFLAGS) -fPIC -c $< -o \$@ +clean: + rm -rf *.o *.\$(LIB_EXT) +EOF +) > Makefile +make + +#compile ddot +cd ../blas +( +cat << EOF +LIB_EXT=a +FC=$FC +install: libddot.\$(LIB_EXT) + cp libddot.\$(LIB_EXT) ../../install/ +OBJECTS= ddot.o +libddot.\$(LIB_EXT): \$(OBJECTS) + ar -r libddot.\$(LIB_EXT) \$(OBJECTS) + ranlib libddot.\$(LIB_EXT) +%.o: %.f + \$(FC) \$(FFLAGS) -fPIC -c $< -o \$@ +clean: + rm -rf *.o *.\$(LIB_EXT) +EOF +) > Makefile +make Index: /issm/trunk/externalpackages/mealpix/help/alm2pix_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/alm2pix_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/alm2pix_help.m (revision 25836) @@ -0,0 +1,33 @@ +%% alm2pix +% Evaluate function, expressed as spherical harmonic expansion +% coefficients, on HEALPix pixel centers + +%% Syntax +% v = alm2pix( nSide, alm, 'Param1', Value1, 'Param2', Value2, ...) + +%% Input Arguments +% nSide HEALPix resolution parameter (power of 2) +% alm Spherical harmonic expansion coefficients +% +% Param Value +% 'lmax' max order of harmonic to calculate (default floor2*nSide/3) +% 'nest' (true | {false}) + +%% Return Arguments +% v Function values at pixels in either ring or nest indexing + +%% Example +% Shows the gibbs-like error at the poles +nSide = 2^4; +alm = pix2alm(ones(1,12*nSide^2)); +v = alm2pix(nSide,alm); +hp3d(v-1); + +%% See also +% pix2alm + +%% Requires +% ylm + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/alm2spec_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/alm2spec_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/alm2spec_help.m (revision 25836) @@ -0,0 +1,39 @@ +%% alm2spec +% Evaluate angular power spectral density + +%% Syntax +% cL = alm2spec(alm) +% cL = alm2spec(alm, lMax) + +%% Input Arguments +% alm real valued coefficients +% lMax max order of harmonic to calculate (default 20) + +%% Return Arguments +% cL angular power spectrum + +%% Description +% The angular power spectrum of the function f, +% +% $$f(\theta,\phi) = \sum a_{\ell m}Y_{\ell m}(\theta,\phi)$$ +% +% are the coefficients +% +% $$c_{\ell} = \frac{\sum_{m=-\ell}^\ell |a_{\ell m}|^2}{2*\ell+1}$$ + +%% Example +% Find power spectrum coefficients of dummy data set +nSide = 2^4; +nPix = nSide2nPix(nSide); +pix = 3*(ylm(nSide,4,2) + ylm(nSide,4,1)) + sqrt(17)*ylm(nSide,8,-4) ... + + rand(1,nPix); +lMax = 10; +alm = pix2alm(pix,lMax); +cL = alm2spec(alm,lMax); +stem(0:lMax,cL); + +%% See also +% pix2alm, alm2pix + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/ang2pix_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/ang2pix_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/ang2pix_help.m (revision 25836) @@ -0,0 +1,40 @@ +%% ang2pix +% Convert spherical coordinate location to HEALPix pixel number + +%% Syntax +% pix = ang2pix(nSide, v); +% pix = ang2pix(nSide, v, nest); + +%% Input Arguments +% nSide HEALPix resolution parameter +% v (theta, phi) pairs in radians as either [2,n] or as cellarray +% of [2,1] +% nest (optional) nested pixel number scheme (true | {false}) + +%% Return Arguments +% pix array of pix numbers: +% v on input output +% iscell(v) size(v) cell array of pixel numbers +% isnumeric(v) size(v,1) numeric array of pixel numbers +% +% Note that Matlab numbers pixels from 1 + +%% Example +vTheta = acos(2*rand(3,5)-1); +vPhi = 2*pi*rand(3,5); +vc = arrayfun(@(x,y)([x;y]),vTheta,vPhi,'UniformOutput',false); +va = reshape(cell2mat(vc),[2,3,5]); +nSide = 8; +size(vc) +size(va) +pix = ang2pix(nSide,vc) +pix = ang2pix(nSide,va) + +%% See also +% vec2pix, pix2ang, pix2vec + +%% Requires +% ring2nest + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/ang2vec_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/ang2vec_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/ang2vec_help.m (revision 25836) @@ -0,0 +1,26 @@ +%% ang2vec +% Convert from spherical to cartesian coordinates + +%% Syntax +% xyz = ang2vec(tp) + +%% Input Arguments +% tp cell of [2,1] angular locations (theta; phi) + +%% Return Arguments +% xyz size(tp) celll array of [3,1] vectors + +%% Example +tp = [acos(2*rand(1,12)-1); 2*pi*rand(1,12)]; +tp = mat2cell(tp,2,ones(12,1)); +tp = reshape(tp,3,4); +xyz = ang2vec(tp); +xyz{2,3}' +tp23 = tp{2,3}; +[sin(tp23(1))*cos(tp23(2)),sin(tp23(1))*sin(tp23(2)),cos(tp23(1))] + +%% See also +% vec2ang + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/angDist_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/angDist_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/angDist_help.m (revision 25836) @@ -0,0 +1,66 @@ +%% angDist +% Compute angular distance between pixel centers or points on the sphere + +%% Syntax +% rad = angDist(v0,v1,'Param1',Value1,'Param2',Value2,...) + +%% Input Arguments +% v0, v1 (numerical or cell) array of points on sphere +% +% Param Value +% 'nSide' HEALPix resolution parameter (integer power 2) +% 'nest' nested indexing (true | {false}) + +%% Return Arguments +% rad array of angular distances (radians) + +%% Description +% angDist computes the angular distances between points on the sphere. +% Points may be specified as MEALPix pixel numbers, spherical coordinate +% location vectors, or cartesian coordinate vectors. Cartesian coordinate +% input vectors need not be normalized. +% +% Either or both of v0, v1 may be a scalar; otherwise they must both be +% the same size. When one is a scalar than the distance is computed between +% that point and all the points specified in the complementary argument. +% When pix0 and pix1 are arrays then the distances are returned between the +% corresponding points in the two arrays. +% +% If any location is specified as a pixel number than nSide must be +% specified. The indexing scheme for pixels center locations defaults to +% ring; to specify nested indexing set the 'nest' parameter to true. + +%% v0 or v1 specified as numeric arrays +% If all points in v0 are pixel numbers then v0 may be specified as a +% numeric array (similarly v1, mutatis mundis). then nSide must be specified. +% Pixels numbers may be specified in ring indexing or nested indexing. For +% nested indexing the nest flag must be specified as true. + +%% pix0 or pix1 specified as cell arrays +% Either or both pix0 or pix1 may be specified as a cell array, in which +% case each cell specifies a location on the sphere as either a pixel +% number, a two-component ([theta; phi]) spherical coordinate vector, or a +% three component ([x;y;z]) cartesian vector. nSide must be specified if +% any location is identified as a pixel center. + +%% Example + % angular distance from pole to equator: + v0 = {[0;0;1]}; % north pole + v1 = {[1;0;0]}; % point on equator + rad = angDist(v0, v1); + + % angular distance from pole to pixels 1, 17, 33 for nSide = 4: + v0 = {[0;0;1]}; + rad = angDist([1, 17, 33], v0, 'nSide', 4) + + % angular distance from pixels 1 to 4, 2 to 5, and 3 to 6 for nSide = 8: + rad = angDist([1, 2, 3], [4, 5, 6],'nSide',8) + +%% See also +% queryDisc + +%% Requires +% pix2vec, ang2vec + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/corners_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/corners_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/corners_help.m (revision 25836) @@ -0,0 +1,37 @@ +%% corners +% Find pixel corners + +%% Syntax +% xyz = corners(nSide,nPix,'Param1',Value1,...); + +%% Input Arguments +% nSide HEALPix resolution parameter +% nPix (optional) pixel list. Default all pixels. +% +% Param Value +% 'nest' nested indexing (true | {false}) + +%% Return Arguments +% xyz size(nPix) cell array of [3,1] cartesian vector pixel corner +% locations + +%% Example: +nSide = 2^2; +% Corners for all 48 nSide=4 pixels in ring-indexed order +xyzR = corners(nSide); +size(xyzR) +xyzR{1} +xyzR{end-1} + +nPix = randi(nSide2nPix(nSide), 3, 4); +% Corners for an assortment of pixels in nested index order +xyzN = corners(nSide,nPix,'nest',true); +% Convert to pixel list to ring indexing +r = xyzR{nest2ring(nSide,nPix(2,3))} +% Corners for same pixels requested via ring indexing +n = xyzN{2,3} +% Compare +all(r == n) + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/helpfuncalpha.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/helpfuncalpha.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/helpfuncalpha.m (revision 25836) @@ -0,0 +1,30 @@ +%% Function Alphabetical List +% * - Evaluate spherical harmonic function expansion on HEALPix pixels +% * - valuate angular power spectral density +% * - Convert spherical coordinate location to HEALPix pixel number +% * - Convert from spherical to cartesian coordinates +% * - Computes angular distance on the unit sphere +% * - Find pixel corners +% * - Plots a HEALPix dataset on a 3D sphere +% * - Compute descriptive statistics of a pixel value list +% * - return pixels in ring or ring section +% * - Convert number of pixels to number of facet side subdivisions +% * - Convert resolution parameter to number of pixels +% * - Calculates angular resolution of a HEALPix map in arcsec +% * - Convert MEALPix pixel numbers from nest to ring indexing +% * - Find spherical harmonic decomposition of function on sphere +% * - Find spherical coordinate location of HEALPix pixels +% * - convert HEALPix pixel numbers to (x,y,z) unit vector +% * - Find pixel cartesian face coordinates +% * - Find all pixels whose centers are within a specified disc +% * - Finds minimum base pixel sub-division for required resolution +% * - Convert MEALPix pixel numbers from ring to nest indexing +% * - Find HEALPix ring number corresponding to a given z coordinate +% * - Convert cartesian direction vector to position angle on sphere +% * - Convert cartesian direction vectors to MEALPix pixel numbers +% * - Find pixel number from face and coordinates in face +% * - Return spherical harmonic basis function $Y_L^M$ on the HEALPix sphere +% * - Find HEALPix ring numbers from direction vector z coordinate + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/helpfuncbycat.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/helpfuncbycat.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/helpfuncbycat.m (revision 25836) @@ -0,0 +1,49 @@ +%% Functions by Category +% MEALPix Toolbox +% Version 3.0 +% 21 February 2011 + +%% Coordinate Conversions +% * - Convert from spherical to cartesian coordinates +% * - Convert cartesian direction vector to position angle on sphere + +%% Coordinate-Pixel Conversions +% * - Convert spherical coordinate location to HEALPix pixel number +% * - Find spherical coordinate location of HEALPix pixels +% * - Convert HEALPix pixel numbers to (x,y,z) unit vector +% * - Find HEALPix ring number corresponding to a given z coordinate +% * - Convert cartesian direction vectors to MEALPix pixel numbers +% * - Find HEALPix ring numbers from direction vector z coordinate + +%% Functions on the sphere +% * - Evaluate spherical harmonic function expansion on HEALPix pixels +% * - Computes angular distance on the unit sphere +% * - Find spherical harmonic decomposition of function on sphere +% * - returns spherical harmonic basis $Y_L^M$ on the HEALPix sphere + +%% Map Statistics +% * - valuate angular power spectral density +% * - Compute descriptive statistics of a pixel value list + +%% Pixel Indexing Conversions +% * - Convert MEALPix pixel numbers from nest to ring indexing +% * - Convert MEALPix pixel numbers from ring to nest indexing + +%% Pixel Topology +% * - Find pixel corners +% * - return pixels in ring or ring section +% * - Find pixel cartesian face coordinates +% * - Find all pixels whose centers are within a specified disc +% * - gives the pixel number ipix (NESTED) of ix, iy and face_num + +%% Plotting +% * - Plots a HEALPix dataset on a 3D sphere + +%% Resolution Relations +% * - Convert number of pixels to number of facet side subdivisions +% * - Convert resolution parameter to number of pixels +% * - Calculates angular resolution of a HEALPix map in arcsec +% * - Finds minimum base pixel sub-division for required resolution + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/helptoc.xml =================================================================== --- /issm/trunk/externalpackages/mealpix/help/helptoc.xml (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/helptoc.xml (revision 25836) @@ -0,0 +1,119 @@ + + + + + + MEALPix Toolbox + + + + + + + + + + + + Getting Started with the MEALPix Toolbox + Overview + System Requirements + Installation + MEALPix for the HEALPix User + Reporting problems + References + Notices + + + + + + Function Reference + + Coordinate Conversions + + ang2vec + vec2ang + + Coordinate-Pixel Conversions + ang2pix + pix2ang + pix2vec + ring2z + vec2pix + z2ring + + Functions on the sphere + alm2pix + angDist + pix2alm + ylm + + Map Statistics + alm2spec + hpStat + + Pixel Indexing Conversions + + nest2ring + ring2nest + + + Pixel Topology + corners + inRing + pix2xy + queryDisc + + xy2pix + + Plotting + + hp3d + + + Resolution relations + nPix2nSide + nSide2nPix + nSide2res + res2nSide + + + + + + + + + + MEALPix Toolbox Web Site + + + Index: /issm/trunk/externalpackages/mealpix/help/hp3d_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/hp3d_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/hp3d_help.m (revision 25836) @@ -0,0 +1,31 @@ +%% hp3d +% Plot a HEALPix dataset on a 3D sphere + +%% Syntax +% h = hp3d(vPix,'Param1',Value1,'Param2',Value2,...); + +%% Input Arguments +% vPix vector of values at HEALPix pixels +% +% Param Value +% 'nest' vPix in nest index order (true | {false}) + +%% Return Arguments +% h (optional) array of patch handles for the sphere + +%% Description +% Let $f$ be a (real-valued) function on the sphere and vPix be a vector of +% function values at pixel $k$, $k=1\ldots12n_{\textrm{side}}^2$. +% hp3d(vPix,'nest',nest) plots the function on a sphere. The parameter nest +% indicates whether the values vPix are given in nested index order (true) +% or ring index order (false and default). + +%% Example +% plot nested pixel numbers on a sphere +hp3d(1:768,'nest',true); + +%% Requires +% corners, nPix2nSide + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/hpStat_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/hpStat_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/hpStat_help.m (revision 25836) @@ -0,0 +1,30 @@ +%% hpStat +% Compute descriptive statistics of a pixel value list + +%% Syntax +% stats = hpStat(v) + +%% Input Arguments +% v array of HEALPix pixel values + +%% Output Arguments +% stats struct +% field contents +% ntot total number of data points +% nvalid number n of valid data points +% mind minimum of valid data +% maxd maximum of valid data +% average average of valid points +% absdev absolute deviation +% var variance +% stddev standard deviation +% skew skewness factor +% kurt kurtosis factor + +%% Example +% display stats of Y_3^1 +v = ylm(32,3,1,'real',true); +stats = hpStat(abs(v)) + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/html/alm2pix_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/alm2pix_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/alm2pix_help.html (revision 25836) @@ -0,0 +1,106 @@ + + + + + alm2pix

alm2pix

Evaluate function, expressed as spherical harmonic expansion coefficients, on HEALPix pixel centers

Contents

Syntax

v = alm2pix( nSide, alm, 'Param1', Value1, 'Param2', Value2, ...)

Input Arguments

nSide HEALPix resolution parameter (power of 2) alm Spherical harmonic expansion coefficients

Param Value 'lmax' max order of harmonic to calculate (default floor2*nSide/3) 'nest' (true | {false})

Return Arguments

v       Function values at pixels in either ring or nest indexing

Example

Shows the gibbs-like error at the poles

nSide = 2^4;
+alm = pix2alm(ones(1,12*nSide^2));
+v = alm2pix(nSide,alm);
+hp3d(v-1);
+

See also

pix2alm

Requires

ylm

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/alm2spec_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/alm2spec_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/alm2spec_help.html (revision 25836) @@ -0,0 +1,117 @@ + + + + + alm2spec

alm2spec

Evaluate angular power spectral density

Contents

Syntax

cL = alm2spec(alm)
+cL = alm2spec(alm, lMax)

Input Arguments

alm real valued coefficients lMax max order of harmonic to calculate (default 20)

Return Arguments

cL      angular power spectrum

Description

The angular power spectrum of the function f,

$$f(\theta,\phi) = \sum a_{\ell m}Y_{\ell m}(\theta,\phi)$$

are the coefficients

$$c_{\ell} = \frac{\sum_{m=-\ell}^\ell |a_{\ell m}|^2}{2*\ell+1}$$

Example

Find power spectrum coefficients of dummy data set

nSide = 2^4;
+nPix = nSide2nPix(nSide);
+pix = 3*(ylm(nSide,4,2) + ylm(nSide,4,1)) + sqrt(17)*ylm(nSide,8,-4) ...
+  + rand(1,nPix);
+lMax = 10;
+alm = pix2alm(pix,lMax);
+cL = alm2spec(alm,lMax);
+stem(0:lMax,cL);
+

See also

pix2alm, alm2pix

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/ang2pix_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/ang2pix_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/ang2pix_help.html (revision 25836) @@ -0,0 +1,149 @@ + + + + + ang2pix

ang2pix

Convert spherical coordinate location to HEALPix pixel number

Contents

Syntax

pix = ang2pix(nSide, v);
+pix = ang2pix(nSide, v, nest);

Input Arguments

nSide      HEALPix resolution parameter
+v          (theta, phi) pairs in radians as either [2,n] or as cellarray
+           of [2,1]
+nest       (optional) nested pixel number scheme (true | {false})

Return Arguments

pix             array of pix numbers:
+               v on input     output
+               iscell(v)      size(v) cell array of pixel numbers
+               isnumeric(v)   size(v,1) numeric array of pixel numbers

Note that Matlab numbers pixels from 1

Example

vTheta = acos(2*rand(3,5)-1);
+vPhi = 2*pi*rand(3,5);
+vc = arrayfun(@(x,y)([x;y]),vTheta,vPhi,'UniformOutput',false);
+va = reshape(cell2mat(vc),[2,3,5]);
+nSide = 8;
+size(vc)
+size(va)
+pix = ang2pix(nSide,vc)
+pix = ang2pix(nSide,va)
+
+ans =
+
+     3     5
+
+
+ans =
+
+     2     3     5
+
+
+pix =
+
+   710   602   719   648   504
+   527   167   488    78   610
+   598   437   175   542   152
+
+
+pix =
+
+   710   602   719   648   504
+   527   167   488    78   610
+   598   437   175   542   152
+
+

See also

vec2pix, pix2ang, pix2vec

Requires

ring2nest

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/ang2vec_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/ang2vec_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/ang2vec_help.html (revision 25836) @@ -0,0 +1,112 @@ + + + + + ang2vec

ang2vec

Convert from spherical to cartesian coordinates

Contents

Syntax

xyz = ang2vec(tp)

Input Arguments

tp        cell of [2,1] angular locations (theta; phi)

Return Arguments

xyz       size(tp) celll array of [3,1] vectors

Example

tp = [acos(2*rand(1,12)-1); 2*pi*rand(1,12)];
+tp = mat2cell(tp,2,ones(12,1));
+tp = reshape(tp,3,4);
+xyz = ang2vec(tp);
+xyz{2,3}'
+tp23 = tp{2,3};
+[sin(tp23(1))*cos(tp23(2)),sin(tp23(1))*sin(tp23(2)),cos(tp23(1))]
+
+ans =
+
+   -0.1868    0.1304    0.9737
+
+
+ans =
+
+   -0.1868    0.1304    0.9737
+
+

See also

vec2ang

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/angDist_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/angDist_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/angDist_help.html (revision 25836) @@ -0,0 +1,158 @@ + + + + + angDist

angDist

Compute angular distance between pixel centers or points on the sphere

Contents

Syntax

 rad = angDist(v0,v1,'Param1',Value1,'Param2',Value2,...)

Input Arguments

v0, v1      (numerical or cell) array of points on sphere
Param       Value
+'nSide'     HEALPix resolution parameter (integer power 2)
+'nest'      nested indexing (true | {false})

Return Arguments

 rad     array of angular distances (radians)

Description

angDist computes the angular distances between points on the sphere. Points may be specified as MEALPix pixel numbers, spherical coordinate location vectors, or cartesian coordinate vectors. Cartesian coordinate input vectors need not be normalized.

Either or both of v0, v1 may be a scalar; otherwise they must both be the same size. When one is a scalar than the distance is computed between that point and all the points specified in the complementary argument. When pix0 and pix1 are arrays then the distances are returned between the corresponding points in the two arrays.

If any location is specified as a pixel number than nSide must be specified. The indexing scheme for pixels center locations defaults to ring; to specify nested indexing set the 'nest' parameter to true.

v0 or v1 specified as numeric arrays

If all points in v0 are pixel numbers then v0 may be specified as a numeric array (similarly v1, mutatis mundis). then nSide must be specified. Pixels numbers may be specified in ring indexing or nested indexing. For nested indexing the nest flag must be specified as true.

pix0 or pix1 specified as cell arrays

Either or both pix0 or pix1 may be specified as a cell array, in which case each cell specifies a location on the sphere as either a pixel number, a two-component ([theta; phi]) spherical coordinate vector, or a three component ([x;y;z]) cartesian vector. nSide must be specified if any location is identified as a pixel center.

Example

 % angular distance from pole to equator:
+ v0 = {[0;0;1]}; % north pole
+ v1 = {[1;0;0]}; % point on equator
+ rad = angDist(v0, v1);
+
+ % angular distance from pole to pixels 1, 17, 33 for nSide = 4:
+ v0 = {[0;0;1]};
+ rad = angDist([1, 17, 33], v0, 'nSide', 4)
+
+ % angular distance from pixels 1 to 4, 2 to 5, and 3 to 6 for nSide = 8:
+ rad = angDist([1, 2, 3], [4, 5, 6],'nSide',8)
+
+rad =
+
+    0.2045    0.6224    0.8411
+
+
+rad =
+
+    0.1443    0.2609    0.3013
+
+

See also

queryDisc

Requires

pix2vec, ang2vec

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/corners_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/corners_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/corners_help.html (revision 25836) @@ -0,0 +1,163 @@ + + + + + corners

corners

Find pixel corners

Contents

Syntax

xyz = corners(nSide,nPix,'Param1',Value1,...);

Input Arguments

nSide    HEALPix resolution parameter
+nPix     (optional) pixel list. Default all pixels.
Param    Value
+'nest'   nested indexing (true | {false})

Return Arguments

xyz    size(nPix) cell array of [3,1] cartesian vector pixel corner
+       locations

Example:

nSide = 2^2;
+% Corners for all 48 nSide=4 pixels in ring-indexed order
+xyzR = corners(nSide);
+size(xyzR)
+xyzR{1}
+xyzR{end-1}
+
+nPix = randi(nSide2nPix(nSide), 3, 4);
+% Corners for an assortment of pixels in nested index order
+xyzN = corners(nSide,nPix,'nest',true);
+% Convert to pixel list to ring indexing
+r = xyzR{nest2ring(nSide,nPix(2,3))}
+% Corners for same pixels requested via ring indexing
+n = xyzN{2,3}
+% Compare
+all(r == n)
+
+ans =
+
+     1   192
+
+
+ans =
+
+         0    0.2031    0.2826    0.0000
+         0         0    0.2826    0.2031
+    1.0000    0.9792    0.9167    0.9792
+
+
+ans =
+
+   -0.2826   -0.2031         0   -0.0000
+   -0.2826    0.0000         0   -0.2031
+   -0.9167   -0.9792   -1.0000   -0.9792
+
+
+r =
+
+    0.5478    0.7071    0.5478    0.3827
+    0.8198    0.7071    0.8198    0.9239
+    0.1667         0   -0.1667         0
+
+
+n =
+
+    0.5478    0.7071    0.5478    0.3827
+    0.8198    0.7071    0.8198    0.9239
+    0.1667         0   -0.1667         0
+
+
+ans =
+
+     1     1     1     1
+
+

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/helpfuncalpha.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/helpfuncalpha.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/helpfuncalpha.html (revision 25836) @@ -0,0 +1,100 @@ + + + + + Function Alphabetical List

Function Alphabetical List

  • alm2pix - Evaluate spherical harmonic function expansion on HEALPix pixels
  • alm2spec - valuate angular power spectral density
  • ang2pix - Convert spherical coordinate location to HEALPix pixel number
  • ang2vec - Convert from spherical to cartesian coordinates
  • angDist - Computes angular distance on the unit sphere
  • corners - Find pixel corners
  • hp3d - Plots a HEALPix dataset on a 3D sphere
  • hpStat - Compute descriptive statistics of a pixel value list
  • inRing - return pixels in ring or ring section
  • nPix2nSide - Convert number of pixels to number of facet side subdivisions
  • nSide2nPix - Convert resolution parameter to number of pixels
  • nSide2res - Calculates angular resolution of a HEALPix map in arcsec
  • nest2ring - Convert MEALPix pixel numbers from nest to ring indexing
  • pix2alm - Find spherical harmonic decomposition of function on sphere
  • pix2ang - Find spherical coordinate location of HEALPix pixels
  • pix2vec - convert HEALPix pixel numbers to (x,y,z) unit vector
  • pix2xy - Find pixel cartesian face coordinates
  • queryDisc - Find all pixels whose centers are within a specified disc
  • res2nSide - Finds minimum base pixel sub-division for required resolution
  • ring2nest - Convert MEALPix pixel numbers from ring to nest indexing
  • ring2z - Find HEALPix ring number corresponding to a given z coordinate
  • vec2ang - Convert cartesian direction vector to position angle on sphere
  • vec2pix - Convert cartesian direction vectors to MEALPix pixel numbers
  • xy2pix - Find pixel number from face and coordinates in face
  • ylm - Return spherical harmonic basis function $Y_L^M$ on the HEALPix sphere
  • z2ring - Find HEALPix ring numbers from direction vector z coordinate

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/helpfuncbycat.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/helpfuncbycat.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/helpfuncbycat.html (revision 25836) @@ -0,0 +1,119 @@ + + + + + Functions by Category

Functions by Category

MEALPix Toolbox Version 3.0 21 February 2011

Contents

Coordinate Conversions

  • ang2vec - Convert from spherical to cartesian coordinates
  • vec2ang - Convert cartesian direction vector to position angle on sphere

Coordinate-Pixel Conversions

  • ang2pix - Convert spherical coordinate location to HEALPix pixel number
  • pix2ang - Find spherical coordinate location of HEALPix pixels
  • pix2vec - Convert HEALPix pixel numbers to (x,y,z) unit vector
  • ring2z - Find HEALPix ring number corresponding to a given z coordinate
  • vec2pix - Convert cartesian direction vectors to MEALPix pixel numbers
  • z2ring - Find HEALPix ring numbers from direction vector z coordinate

Functions on the sphere

  • alm2pix - Evaluate spherical harmonic function expansion on HEALPix pixels
  • angDist - Computes angular distance on the unit sphere
  • pix2alm - Find spherical harmonic decomposition of function on sphere
  • ylm - returns spherical harmonic basis $Y_L^M$ on the HEALPix sphere

Map Statistics

  • alm2spec - valuate angular power spectral density
  • hpStat - Compute descriptive statistics of a pixel value list

Pixel Indexing Conversions

  • nest2ring - Convert MEALPix pixel numbers from nest to ring indexing
  • ring2nest - Convert MEALPix pixel numbers from ring to nest indexing

Pixel Topology

  • corners - Find pixel corners
  • inRing - return pixels in ring or ring section
  • pix2xy - Find pixel cartesian face coordinates
  • queryDisc - Find all pixels whose centers are within a specified disc
  • xy2pix - gives the pixel number ipix (NESTED) of ix, iy and face_num

Plotting

  • hp3d - Plots a HEALPix dataset on a 3D sphere

Resolution Relations

  • nPix2nSide - Convert number of pixels to number of facet side subdivisions
  • nSide2nPix - Convert resolution parameter to number of pixels
  • nSide2res - Calculates angular resolution of a HEALPix map in arcsec
  • res2nSide - Finds minimum base pixel sub-division for required resolution

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/hp3d_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/hp3d_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/hp3d_help.html (revision 25836) @@ -0,0 +1,102 @@ + + + + + hp3d

hp3d

Plot a HEALPix dataset on a 3D sphere

Contents

Syntax

h = hp3d(vPix,'Param1',Value1,'Param2',Value2,...);

Input Arguments

vPix   vector of values at HEALPix pixels
Param      Value
+'nest'     vPix in nest index order (true | {false})

Return Arguments

h      (optional) array of patch handles for the sphere

Description

Let $f$ be a (real-valued) function on the sphere and vPix be a vector of function values at pixel $k$, $k=1\ldots12n_{\textrm{side}}^2$. hp3d(vPix,'nest',nest) plots the function on a sphere. The parameter nest indicates whether the values vPix are given in nested index order (true) or ring index order (false and default).

Example

plot nested pixel numbers on a sphere

hp3d(1:768,'nest',true);
+

Requires

corners, nPix2nSide

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/hpStat_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/hpStat_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/hpStat_help.html (revision 25836) @@ -0,0 +1,126 @@ + + + + + hpStat

hpStat

Compute descriptive statistics of a pixel value list

Contents

Syntax

stats = hpStat(v)

Input Arguments

v         array of HEALPix pixel values

Output Arguments

stats     struct
+          field     contents
+          ntot      total number of data points
+          nvalid    number n of valid data points
+          mind      minimum of valid data
+          maxd      maximum of valid data
+          average   average of valid points
+          absdev    absolute deviation
+          var       variance
+          stddev    standard deviation
+          skew      skewness factor
+          kurt      kurtosis factor

Example

display stats of Y_3^1

v = ylm(32,3,1,'real',true);
+stats = hpStat(abs(v))
+
+stats = 
+
+      ntot: 12288
+    nValid: 12288
+      mind: 1.0813e-18
+      maxd: 0.6289
+      mean: 0.2272
+    absdev: 0.1421
+       var: 0.0280
+    stddev: 0.1673
+      skew: 0.5111
+      kurt: 2.2410
+
+

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/inRing_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/inRing_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/inRing_help.html (revision 25836) @@ -0,0 +1,189 @@ + + + + + inRing

inRing

Return list of pixels in a ring or ring section

Contents

Syntax

pixList = inRing(nSide, nRing, phi0, dPhi, 'Param1', Value1, ...);

Input Arguments

nSide       HEALPix resolution parameter
+nRing       Ring number (1 <= nRing <= 4*nSide-1)
+phi0, dPhi  (optional) Ring section longitudes [phi-dPhi,phi+dPhi]
Param       Value
+'nest'      return pixels with nested indexing (true | {false})
+'strict'    return only pixels whose center is in longitude range
+            (true | {false})

Return Arguments

pixList     size(nRing) cell array of pixels in ring defined by nRing,
+            phi0, dPhi

Description

nRing may be a numeric array, in which case phi0, dPhi and nest may each
+be either scalar or a size(nRing) array. If strict is false (default)
+then all pixels intersected by longitude range are included in pixList.

Example

% All pixels in ring 2 of nSide = 4 pixelization (ring indexed)
+pix = inRing(4,2);
+pix{:}
+
+% Same, but nested indexing
+pix = inRing(4,2,'nest',true);
+pix{:}
+nest2ring(4,pix{:})
+
+% Pixels in rings [2,4;8,10;12,14] and the longitude band
+% [7*pi/4,9*pi/4]
+nRing = [2,3;5,12;13,14];
+pix = inRing(4,nRing,2*pi,pi/4);
+pix{1}
+pix{end}
+
+% Same, with strict selection
+pix = inRing(4,nRing,2*pi,pi/4,'strict',true);
+pix{1}
+pix{end}
+
+ans =
+
+     5     6     7     8     9    10    11    12
+
+
+ans =
+
+    65    16    15    32    31    48    47    64
+
+
+ans =
+
+   137     1     5     2     7     3     9     4
+
+
+ans =
+
+    12     5     6
+
+
+ans =
+
+   188   181   182
+
+
+ans =
+
+    12     5
+
+
+ans =
+
+   188   181
+
+

See also

ringNum

Requires

ring2z, pix2vec

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/mealpix_bugreport.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/mealpix_bugreport.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/mealpix_bugreport.html (revision 25836) @@ -0,0 +1,79 @@ + + + + + Reporting bugs

Reporting bugs

MEALPix software distributed on an "as is" basis, without warranties or conditions of any kind, and without promise of support. Nevertheless, the Gravitational Wave Astronomy Group makes extensive use of MEALPix and welcomes any and all bug reports via e-mail to our request-tracking system rt-mealpix@gwastro.org. Bugs reports will be investigated and addressed on a best effort basis.

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/mealpix_gs_top.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/mealpix_gs_top.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/mealpix_gs_top.html (revision 25836) @@ -0,0 +1,80 @@ + + + + + Getting Started with MEALPix

Getting Started with MEALPix

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/mealpix_healpix.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/mealpix_healpix.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/mealpix_healpix.html (revision 25836) @@ -0,0 +1,90 @@ + + + + + MEALPix for the HEALPix User

MEALPix for the HEALPix User

Contents

MEALPix function names are derived from their HEALPix counterparts.

MEALPix functions are typically camel-cased (e.g., angDist, or nSide2nPix). Underscores in HEALPix names are dropped in the conversion to MEALPix names.

MEALPix functions accept array arguments

MEALPix functions exploit Matlab(tm)'s vectorization facilities to allow for the processing of arrays of pixels, direction vectors and position angle vectors via a single function call. For example, the MEALPix implementation of angDist accepts mixed arrays of cartesian direction vectors, angular position vectors, and ring or nest indexed pixels for either argument.

MEALPix indexes pixels from 1

HEALPix pixels are indexed from 0. In keeping with the Matlab standard MEALPix pixels are indexed from 1. MEALPix pixels are indexed from 1: i.e., MEALPix pixel number n corresponds to HEALPix pixel number n-1.

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/mealpix_install.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/mealpix_install.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/mealpix_install.html (revision 25836) @@ -0,0 +1,85 @@ + + + + + Installation

Installation

  • Download MEALPix, which is provided as a gzipped tar file. Un-tar the file and place the MEALPix directory in some appropriate location. Hereafter we will refer to the fully-qualified path to MEALPix as $MEALPIX.
  • Add the MEALPix directory tree to your Matlab™ path using, e.g., the Matlab™ command addpath(genpath('$MEALPIX')). You may wish to add this command to your matlab/startup.m file, in which case MEALPix will be available whenever you start-up Matlab™.

The MEALPix Toolbox includes documentation that will appear in the Matlab Documentation browser when Matlab™ starts-up with MEALPix in its path.

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/mealpix_notices.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/mealpix_notices.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/mealpix_notices.html (revision 25836) @@ -0,0 +1,86 @@ + + + + + Notices

Notices

MEALPix is based on HEALPix. HEALPix is distributed under the terms of the GNU General Public License ("GPL") as published by the Free Software Foundation; either version 2 of the GPL, or (at your option) any later version.

This Matlab™ expression of HEALPix is Copyright 2010-2011 by Lee Samuel Finn. It is licensed under the Apache License, Version 2.0 (the "License"); you may not use MEALPix except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, MEALPix software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/mealpix_overview.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/mealpix_overview.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/mealpix_overview.html (revision 25836) @@ -0,0 +1,101 @@ + + + + + Product Overview

Product Overview

MEALPix is a native Matlab implementation of a substantial subset of the HEALPix subroutine library. It supports the fast and accurate statistical and astrophysical analysis of massive full-sky data sets. HEALPix is supported by NASA and ESO, used extensively by the WMAP and PLANCK missions, and is part of the official FITS World Coordinate System.

MEALPix provides fully vectorized functions for

  • Conversion between position angles, cartesian direction vectors, and HEALPix ring and nest pixel indexing schemes;
  • Spherical harmonic resolution and analysis of functions on the sphere;
  • Nearest pixel identification (pixels within a given disc, pixels in a ring, pixels in a HEALPix face).

MEALPix was created from the Fortran90 implementation HEALPix via a combination of hand coding and machine assisted conversion of the HEALPix F90 source code. Some routines were hand-coded based on the documented functionality of the F90 subroutines on which they were based. Other routines were hand-coded via inspection of the HEALPix F90 implementation source. Still other routines were machine converted from F90 to Matlab™ using f2matlab. In this latter case the resulting Matlab™ source was then hand-modified to vectorize the computations and take advantage of Matlab™ data types and other functions.

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/mealpix_product_page.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/mealpix_product_page.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/mealpix_product_page.html (revision 25836) @@ -0,0 +1,100 @@ + + + + + mealpix_product_page

+Gravitational Wave Astronomy Group Logo +

MEALPix Toolbox

+

Contents

The MEALPix Toolbox is a native Matlab™ implementation of the Hierarchical Equal Area isoLatitude Pixelization of the sphere (HEALPix). It is derived from the HEALPix package, originally developed by ESO and currently supported by JPL and ESO.

Functions

Getting Started

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/mealpix_references.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/mealpix_references.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/mealpix_references.html (revision 25836) @@ -0,0 +1,102 @@ + + + + + References

References

K. M. Gorski et al. 2005. HEALPix: A Framework for High-Resolution Discretization and Fast Analysis of Data Distributed on the Sphere. The Astrophysical Journal 622 759

K. M. Gorski et al. 1999. The HEALPix Primer. arXiv:astro-ph/9905275

K. M. Gorski et al. 2002. HEALPix - a Framework for High Resolution, Fast Analysis on the Sphere. In Astronomical Data Analysis Software and Systems XI, Bohlender, D. A. et al. ed. ASP Conference Series Vol 281, pp. 107-111

Mark R. Calabrettal and Boudewijn F. Roukema. 2007. Mapping on the HEALPix grid. Monthly Notices of the Royal Astronomical Society 381:2 pp. 865 - 872.

W. O'Mullane et al. 2001. Splitting the Sky - HTM and HEALPix. In Mining The Sky. Anthony Banday et al., Ed. Anthony ESO Astrophysics Symposia 2001, 638 - 648.

L. Nicastro and Calderone, G. 2008. Indexing Astronomical Database Tables using HTM and HEALPix. In Astronomical Data Analysis Software and Systems (ADASS) XVII. A. W. Argle et. al, ed. Astronomical Society of the Pacific Conference Series vol. 394 pp. 486-490.

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/mealpix_reqts.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/mealpix_reqts.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/mealpix_reqts.html (revision 25836) @@ -0,0 +1,93 @@ + + + + + System Requirements

System Requirements

MEALPix is a native Matlab™ implementation of HEALPix: neither a HEALPix installation nor any third-party java or mex files are required to make use of the basic HEALPix functionality.

Contents

Matlab™ requirements

MEALPix was developed and tested using Matlab™ R2010a. It should work with any later version.

MEALPix does not require any Mathworks™ Toolboxes or add-ons. MEALPix will make use of the capabilities of the Parallel Computing Toolbox, should it be present.

Third-party software requirements

MEALPix also includes functions not found in HEALPix. Some of these additional functions require other toolboxes:

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/nPix2nSide_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/nPix2nSide_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/nPix2nSide_help.html (revision 25836) @@ -0,0 +1,98 @@ + + + + + nPix2nSide

nPix2nSide

Finds number of HEALPix facet side subdivisions from number of pixels on sphere

Contents

Syntax

nSide = nPix2nSide(nPix);

Input Arguments

nPix     number of pixels on sphere

Return Arguments

nSide    sub-divisions of HEALPix facet side

Example

nPix = 12*[1:4].^2;
+nSide = nPix2nSide(nPix)
+
+nSide =
+
+     1     2     3     4
+
+

See also

nSide2nPix

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/nSide2nPix_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/nSide2nPix_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/nSide2nPix_help.html (revision 25836) @@ -0,0 +1,101 @@ + + + + + nSide2nPix

nSide2nPix

Convert HEALPix resolution parameter to number of pixels on sphere

Contents

Syntax

nPix = nSide2nPix(nSide)

Input Arguments

nSide    sub-divisions of facet sides. May be an array.

Return Arguments

nPix     size(nSide) number of pixels on sphere corresponding to nSide

Description

HEALPix divides the sphere into 12 basic facets. Each facet is further divided into nSide sub-divisions for a total of 12*nSide^2 pixels.

Example

nSide = 2.^[1:4];
+nPix = nSide2nPix(nSide)
+
+nPix =
+
+          48         192         768        3072
+
+

See also

nPix2nSide

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/nSide2res_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/nSide2res_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/nSide2res_help.html (revision 25836) @@ -0,0 +1,97 @@ + + + + + nSide2res

nSide2res

Determine angular resolution of a HEALPix map

Contents

Syntax

angres = nSide2res(nSide)

Input Arguments

nSide   HEALPix resolution parameter (may be an array)

Return Arguments

angres  Angular resolution in arcsec

Example

nSide = 2.^(8:12);
+nSide2res(nSide)
+
+ans =
+
+  824.5167  412.2584  206.1292  103.0646   51.5323
+
+

See also

res2nSide

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/nest2ring_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/nest2ring_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/nest2ring_help.html (revision 25836) @@ -0,0 +1,106 @@ + + + + + nest2ring

nest2ring

Convert MEALPix pixel numbers from nest to ring indexing

Contents

Syntax

rPix = nest2ring(nSide,nPix)

Input Arguments

nSide     HEALPix resolution parameters
+nPix      numeric array of MEALPix nest indexed pixel numbers

Return Arguments

rPix      size(nPix) numeric array of ring indexed pixel numbers

Example

nPix = 1:10;
+rPix = nest2ring(2,nPix)
+nPix = ring2nest(2,rPix)
+
+rPix =
+
+    14     6     5     1    16     8     7     2    18    10
+
+
+nPix =
+
+     1     2     3     4     5     6     7     8     9    10
+
+

See also

ring2nest

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/pix2alm_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/pix2alm_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/pix2alm_help.html (revision 25836) @@ -0,0 +1,132 @@ + + + + + pix2alm

pix2alm

Find spherical harmonic decomposition of function on sphere

Contents

Syntax

alm = pix2alm(v)
+alm = pix2alm(v, lmax)

Input Arguments

v       array of pixel values
+lMax    (optional) max order of harmonic to calculate
nPix = numel(v), with nPix = 12*nSide^2 for nSide a power of 2.
+lMax defaults to 2*floor(nSide/3)

Return Arguments

alm     coefficients of spherical harmonic expansion

Description

Let $x_k$ denote the location of pixel $k$ and $v_k$ the function value at $x_k$. Then

$$alm(j) = \frac{4\pi}{N}\sum_{k=0}^{N-1} Y_{LM}^{\dagger}(x_k) v_k$$

where $j=(L+1)^2+M-L$ and $N$ is the number of pixels (12*nSide^2)

Example

estimate alm of dummy data

ns = 2^4;
+np = 12*ns^2;
+v = ylm(ns,1,1) + ylm(ns,2,-2) + ylm(ns,3,0) + rand(1,np)/10;
+lMax = 4;
+alm = pix2alm(v,lMax);
+for L = 0:3
+  fprintf('L = %d: ',L);
+  fprintf('%7.3f ',abs(alm((L+1)^2+(-L:L)-L)));
+  fprintf('\n');
+end
+
L = 0:   0.176 
+L = 1:   0.001   0.002   1.000 
+L = 2:   1.001   0.002   0.001   0.002   0.003 
+L = 3:   0.003   0.003   0.002   0.998   0.002   0.003   0.003 
+

See also

alm2pix

Requires

ylm

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/pix2ang_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/pix2ang_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/pix2ang_help.html (revision 25836) @@ -0,0 +1,135 @@ + + + + + pix2ang

pix2ang

Find spherical coordinate location of HEALPix pixels

Contents

Syntax

tp = pix2ang(nSide,pix,'Param1',Value1,...)

Input Arguments

nSide    HEALPix resolution parameter (positive integer power of 2)
+pix      (optional) array of pixel values to find coordinates of
Param    Values
+'nest'   pixels are given in nested indexing (true | {false})

Return Arguments

tp       cell array of [theta; phi] pixel locations (radians)

Example

Return [theta; phi] postion angles for all pix of nSide=4, nest scheme

nSide = 4;
+tp = pix2ang(nSide,'nest',true);
+size(tp)
+tp{1}
+% Return position angles for a random assortment of pixels
+pix = randi(nSide2nPix(nSide),3,4);
+tp = pix2ang(nSide,pix);
+size(tp)
+tp{1}
+
+ans =
+
+     1   192
+
+
+ans =
+
+    1.4033
+    0.7854
+
+
+ans =
+
+     3     4
+
+
+ans =
+
+    1.5708
+    6.0868
+
+

See also

See also ang2pix, pix2vec, vec2pix

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/pix2vec_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/pix2vec_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/pix2vec_help.html (revision 25836) @@ -0,0 +1,144 @@ + + + + + pix2vec

pix2vec

Convert MEALPix pixel numbers to cartesian location vectors

Contents

Syntax

[x,y,z] = pix2vec(nSide,pix,'Param1',Value1,...)
+xyz = pix2vec(nSide,pix,'Param1',Value1,...)

Input Arguments

nSide       HEALPix resolution parameter
+pix         (optional) numeric array of pixel numbers
Param       Value
+'nest'      indexing scheme is nested (true | {false})

Return Arguments

x,y,z       size(pix) size(pix) numeric array of unit vector coordinate
+            components corresponding to pixels pix
+xyz         size(pix) size(pix) cell array of cartesian unit vectors
+            corresponding to pixels pix

Example

nSide = 2^4;
+nPix = nSide2nPix(nSide);
+pix0 = reshape(1:6,3,2);
+pix1 = reshape(nPix+(-5:0),3,2);
+pix = [pix0,pix1];
+xyz = pix2vec(nSide,pix);
+xyzn = pix2vec(nSide,pix,'nest',true);
+size(xyz)
+[xyz{1},xyz{end}]
+[xyzn{1},xyzn{end}]
+
+ans =
+
+     3     4
+
+
+ans =
+
+    0.0361    0.0361
+    0.0361   -0.0361
+    0.9987   -0.9987
+
+
+ans =
+
+    0.7065    0.7065
+    0.7065   -0.7065
+    0.0417   -0.0417
+
+

See also

ang2pix, pix2ang, vec2pix

Requires

nest2ring

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/pix2xy_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/pix2xy_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/pix2xy_help.html (revision 25836) @@ -0,0 +1,107 @@ + + + + + pix2xy

pix2xy

Find pixel cartesian face coordinates

Contents

Syntax

xy = pix2xy(nSide,nPix)

Input Arguments

nSide     HEALPix resolution parameter
+nPix      nested indexing pixel numbers to find coordinates of

Return Arguments

xy        size(nPix) cell array of pixel coordinates on face

Example

nPix = reshape(1:24,[4,3,2]);
+xy = pix2xy(2,nPix)
+
+xy(:,:,1) = 
+
+    [2x1 double]    [2x1 double]    [2x1 double]
+    [2x1 double]    [2x1 double]    [2x1 double]
+    [2x1 double]    [2x1 double]    [2x1 double]
+    [2x1 double]    [2x1 double]    [2x1 double]
+
+
+xy(:,:,2) = 
+
+    [2x1 double]    [2x1 double]    [2x1 double]
+    [2x1 double]    [2x1 double]    [2x1 double]
+    [2x1 double]    [2x1 double]    [2x1 double]
+    [2x1 double]    [2x1 double]    [2x1 double]
+
+

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/queryDisc_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/queryDisc_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/queryDisc_help.html (revision 25836) @@ -0,0 +1,145 @@ + + + + + queryDisc

queryDisc

Find all pixels whose centers are within a specified disc

Contents

Syntax

pix = queryDisc(nSide,c0,r,'Param1',Value1,...)

Input Arguments

nSide     HEALPix resolution parameter
+c0        disc center. May be specified as a pixel number, spherical
+          coordinate location [theta, phi] in rads, or as a cartesian
+          unit vector [x;y;z].
+r         disc radius (radians)
Param     Value
+'nest'    pixels are returned using nested indexing (true | {false})

Return Arguments

pix      list of pixels in disc

Example

nSide=32;
+% Pixels within pi/10 radians of north pole
+pix = queryDisc(nSide,[0;0;1],pi/10);
+numel(pix)
+nSide2nPix(nSide)*((pi/10)/(4*pi))
+% Pixels within pi/10 radians of south pole
+pix = queryDisc(nSide,[0;0;-1],pi/10);
+numel(pix)
+% Pixels within pi/10 radians of 0 long, lat
+pix = queryDisc(nSide,[1;0;0],pi/10);
+numel(pix)
+
+ans =
+
+   312
+
+
+ans =
+
+  307.2000
+
+
+ans =
+
+   312
+
+
+ans =
+
+   302
+
+

See also

queryPolygon, queryStrip, queryTriangle

Requires

pix2vec, ang2vec, angDist

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/res2nSide_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/res2nSide_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/res2nSide_help.html (revision 25836) @@ -0,0 +1,99 @@ + + + + + res2nSide

res2nSide

Find minimum HEALPix resolution parameter yielding required resolution

Contents

Syntax

nSide = res2nSide(r)

Input Arguments

r        angular resolution (arc seconds)

Return Arguments

nSide    minimum base pixel sub-divisions corresponding to resolution r

Example

r = 100*rand(3,4);
+nSide = res2nSide(r)
+
+nSide =
+
+        8192        4096        4096        4096
+       16384        4096       16384       16384
+        8192        8192        4096       32768
+
+

See also

nSide2res

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/ring2nest_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/ring2nest_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/ring2nest_help.html (revision 25836) @@ -0,0 +1,106 @@ + + + + + ring2nest

ring2nest

Convert MEALPix pixel numbers from ring to nest indexing

Contents

Syntax

nPix = ring2nest(nSide,rPix)

Input Arguments

nSide      HEALPix resolution parameter
+rPix       ring indexed MEALPix pixel numbers

Return Arguments

nPix       next indexed MEALPix pixel numbers

Example

nPix = ring2nest(4,reshape(1:6,2,3))
+rPix = nest2ring(4,nPix)
+
+nPix =
+
+    16    48    15
+    32    64    14
+
+
+rPix =
+
+     1     3     5
+     2     4     6
+
+

See also

nest2ring

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/ring2z_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/ring2z_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/ring2z_help.html (revision 25836) @@ -0,0 +1,108 @@ + + + + + ring2z

ring2z

Find HEALPix ring number corresponding to a given z coordinate

Contents

Syntax

z = ring2z(nSide,nRing)

Input Arguments

nSide    HEALPix resolution parameter
+nRing    numeric array of ring numbers (in range [1,4*nSide-1])

Return Arguments

z        size(nRing) numeric array of pixel center z coordinates

Example

nRing = reshape(1:15,3,5)
+z = ring2z(4,nRing)
+
+nRing =
+
+     1     4     7    10    13
+     2     5     8    11    14
+     3     6     9    12    15
+
+
+z =
+
+    0.9792    0.6667    0.1667   -0.3333   -0.8125
+    0.9167    0.5000         0   -0.5000   -0.9167
+    0.8125    0.3333   -0.1667   -0.6667   -0.9792
+
+

See also

z2ring

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/ringNum_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/ringNum_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/ringNum_help.html (revision 25836) @@ -0,0 +1,145 @@ + + + + + ringNum

ringNum

Find pixel ring numbers

Contents

Syntax

nRing = ringNum(nSide,pix)

Input Arguments

nSide      HEALPix resolution parameter
+pix        (optional) MEALPix pixel number array (ring indexing).
+           Defaults to all pixels

Return Arguments

nRing      size(pix) array of ring numbers

Description

Algorithm Notes

Example

ringNum(2)
+
Undefined function or method 'ringNum' for input arguments of type 'double'.
+
+Error in ==> ringNum_help at 20
+ringNum(2)
+

See also

inRing

Requires

pix2vec, z2ring

References

K. M. Gorski et al. 2005. HEALPix: A Framework for High-Resolution Discretization and Fast Analysis of Data Distributed on the Sphere. The Astrophysical Journal 622 759

K. M. Gorski et al. 1999. The HEALPix Primer. arXiv:astro-ph/9905275

K. M. Gorski et al. 2002. HEALPix - a Framework for High Resolution, Fast Analysis on the Sphere. In Astronomical Data Analysis Software and Systems XI, Bohlender, D. A. et al. ed. ASP Conference Series Vol 281, pp. 107-111

Mark R. Calabrettal and Boudewijn F. Roukema. 2007. Mapping on the HEALPix grid. Monthly Notices of the Royal Astronomical Society 381:2 pp. 865 - 872.

W. O'Mullane et al. 2001. Splitting the Sky - HTM and HEALPix. In Mining The Sky. Anthony Banday et al., Ed. Anthony ESO Astrophysics Symposia 2001, 638 - 648.

L. Nicastro and Calderone, G. 2008. Indexing Astronomical Database Tables using HTM and HEALPix. In Astronomical Data Analysis Software and Systems (ADASS) XVII. A. W. Argle et. al, ed. Astronomical Society of the Pacific Conference Series vol. 394 pp. 486-490.

Notices

Copyright 2010-2011 Lee Samuel Finn Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.nSideWarn(nSide,mfilename);


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/synopsis.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/synopsis.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/synopsis.html (revision 25836) @@ -0,0 +1,127 @@ + + + + + Synopsis

Synopsis

 alm2pix    - Evaluate spherical harmonic function expansion on HEALPix pixels
+ alm2spec   - valuate angular power spectral density
+ ang2pix    - Convert spherical coordinate location to HEALPix pixel number
+ ang2vec    - Convert from spherical to cartesian coordinates
+ angDist    - Computes angular distance on the unit sphere
+ corners    - Find pixel corners
+ hp3d       - Plots a HEALPix dataset on a 3D sphere
+ hpInterp   - Interpolate data on sphere to MEALPix pixels
+ hpStat     - Compute descriptive statistics of a pixel value list
+ inRing     - return pixels in ring or ring section
+ nPix2nSide - Convert number of pixels to number of facet side subdivisions
+ nSide2nPix - Convert resolution parameter to number of pixels
+ nSide2res  - Calculates angular resolution of a HEALPix map in arcsec
+ nest2ring  - Convert MEALPix pixel numbers from nest to ring indexing
+ pix2alm    - Find spherical harmonic decomposition of function on sphere
+ pix2ang    - Find spherical coordinate location of HEALPix pixels
+ pix2vec    - convert HEALPix pixel numbers to (x,y,z) unit vector
+ pix2xy     - PIX2XY
+ queryDisc  - Find all pixels whose centers are within a specified disc
+ res2nSide  - Finds minimum base pixel sub-division for required resolution
+ ring2nest  - Convert MEALPix pixel numbers from ring to nest indexing
+ ring2z     - Find HEALPix ring number corresponding to a given z coordinate
+ vec2ang    - Convert cartesian direction vector to position angle on sphere
+ vec2pix    - Convert cartesian direction vectors to MEALPix pixel numbers
+ xy2pix     - gives the pixel number ipix (NESTED) of ix, iy and face_num
+ ylm        - returns spherical harmonic basis Y_L^M on the HEALPix sphere
+ z2ring     - Find HEALPix ring numbers from direction vector z coordinate

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/template_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/template_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/template_help.html (revision 25836) @@ -0,0 +1,133 @@ + + + + + NAME

NAME

short descr

Contents

Syntax

Input Arguments

Return Arguments

Description

Algorithm Notes

Example

See also

Requires

References

K. M. Gorski et al. 2005. HEALPix: A Framework for High-Resolution Discretization and Fast Analysis of Data Distributed on the Sphere. The Astrophysical Journal 622 759

K. M. Gorski et al. 1999. The HEALPix Primer. arXiv:astro-ph/9905275

K. M. Gorski et al. 2002. HEALPix - a Framework for High Resolution, Fast Analysis on the Sphere. In Astronomical Data Analysis Software and Systems XI, Bohlender, D. A. et al. ed. ASP Conference Series Vol 281, pp. 107-111

Mark R. Calabrettal and Boudewijn F. Roukema. 2007. Mapping on the HEALPix grid. Monthly Notices of the Royal Astronomical Society 381:2 pp. 865 - 872.

W. O'Mullane et al. 2001. Splitting the Sky - HTM and HEALPix. In Mining The Sky. Anthony Banday et al., Ed. Anthony ESO Astrophysics Symposia 2001, 638 - 648.

L. Nicastro and Calderone, G. 2008. Indexing Astronomical Database Tables using HTM and HEALPix. In Astronomical Data Analysis Software and Systems (ADASS) XVII. A. W. Argle et. al, ed. Astronomical Society of the Pacific Conference Series vol. 394 pp. 486-490.

Notices

Copyright 2010-2011 Lee Samuel Finn Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/vec2ang_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/vec2ang_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/vec2ang_help.html (revision 25836) @@ -0,0 +1,135 @@ + + + + + vec2ang

vec2ang

Convert from cartesian direction vector to position angle on sphere

Contents

Syntax

tp = vec2ang(xyz)

Input Arguments

xyz    cell array of [3,1] cartesian coordinate direction vectors

The direction vectors need not be normalized.

Return Arguments

tp     cell array of [2,1] position angles ([theta, phi]) on sphere

Example

Create a [3,4] cell array of position angles and manually convert to cartesian direction vectors. Use vec2ang to convert back to position angles and compare with originals

% angular position vectors
+z = 2*rand(3,4)-1;
+th = acos(z);
+ph = 2*pi*rand(3,4)-pi;
+
+% convert to cartesian coordinate vectors
+x = sqrt(1-z.^2).*cos(ph);
+y = sqrt(1-z.^2).*sin(ph);
+xyz = arrayfun(@(x,y,z)([x,y,z]),x,y,z,'UniformOutput',false);
+
+% use vec2ang to convert cartesian coordinate vectors to angular position
+% vectors
+tp = vec2ang(xyz);
+
+% Compare original vectors with final vectors
+tp0 = arrayfun(@(t,p)([t;p]),th,ph,'UniformOutput',false);
+tf = cellfun(@(x,y)(any(abs(x-y)>4*eps)),tp,tp0)
+
+tf =
+
+     0     0     0     0
+     0     0     0     0
+     0     0     0     0
+
+

See also

ang2vec

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/vec2pix_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/vec2pix_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/vec2pix_help.html (revision 25836) @@ -0,0 +1,133 @@ + + + + + vec2pix

vec2pix

Convert cartesian direction vectors to MEALPix pixel numbers

Contents

Syntax

nPix = vec2pix(nSide,xyz,'Param1',Value1,...);

Input Arguments

nSide     HEALPix resolution parameter
+xyz       cell array of [3,1] cartesian direction vectors
Param     Value
+'nest'    use nested indexing (true | {false})

Return Arguments

nPix      size(xyz) pixel number array

Example

Find pixels corresponding to a [4,5] set of (unnormalized) cartesian vectors:

nSide = 4;
+xyz0 = squeeze(num2cell(2*rand(3,4,5)-1,1));
+nPix = vec2pix(nSide,xyz0)
+
+% Find the normalized vectors corresponding to the pixels
+xyz1 = pix2vec(nSide,nPix);
+
+% Find angular distance from vectors to pixels
+d = angDist(xyz0,xyz1)
+
+nPix =
+
+    28   157     2   112    58
+   120    37    44   140   153
+    82   121    68   127    25
+   165    29    51   140    42
+
+
+d =
+
+    0.1107    0.0752    0.1586    0.0250    0.1124
+    0.0695    0.1483    0.1005    0.1260    0.1347
+    0.0588    0.0572    0.0838    0.1210    0.0761
+    0.1156    0.1455    0.1688    0.0376    0.1256
+
+

See also

ang2pix, pix2ang, pix2vec

Requires

ring2nest

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/xy2pix_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/xy2pix_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/xy2pix_help.html (revision 25836) @@ -0,0 +1,119 @@ + + + + + xy2pix

xy2pix

Find (nest indexed) MEALPix pixel number corresponding to a pixel index on a HEALPix face

Contents

Syntax

ipix = xy2pix(nSide, ix, iy, nFace)

Input Arguments

nside     HEALPix resolution parameter (power of 2)
+ix,iy     integer pixel location on face (1 <= ix, iy <= nSide)
+nFace     HEALPix face  number (1 <= nFace <= 12)

One or both ix and iy may be scalars. If neither is a scalar both must have the same size.

Return Arguments

ipix      NESTED pixel index for given x,y on the face

Description

At lowest resolution HEALPix divides the sphere into 12 faces, each with its own coordinate system. Each face is further subdivided in a regular fashion as the resolution parameter is increased. Given a face number (from 1 to 12), a resolution parameter, and a location on the face XY2PIX identifies the pixel number (in the nested indexing scheme).

Example

nSide = 4;
+nFace = 3;
+ix = [1 2; 1 2];
+iy = [1 1; 2 2];
+nPix = xy2pix(nSide,ix,iy,nFace)
+
+nPix =
+
+    49    50
+    51    52
+
+

See also

pix2xy

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/ylm_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/ylm_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/ylm_help.html (revision 25836) @@ -0,0 +1,103 @@ + + + + + ylm

ylm

Evaluate spherical harmonic basis functions $Y_{LM}$ at pixel centers

Contents

Syntax

v = ylm(nSide,L,M,'Param1',Value1,'Param2',Value2,...);

Input Arguments

nSide    HEALPix resolution parameter (power of 2)
+L        spherical harmonic degree (0 <= L)
+M        spherical harmonic order (-M <= L <= M)
Param    Value
+'real'   return real values (true | {false})
+'nest'   nested indexing flag (true | {false})

Return Arguments

v       spherical harmonics evaluated at pixel centers

Example

Plot Ylm for (L,M) = (4,2) on nSide = 16 HEALPix sphere

pix = ylm(16,4,2);
+hp3d(pix);
+

Requires

pix2ang

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/html/z2ring_help.html =================================================================== --- /issm/trunk/externalpackages/mealpix/help/html/z2ring_help.html (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/html/z2ring_help.html (revision 25836) @@ -0,0 +1,106 @@ + + + + + z2ring

z2ring

Return HEALPix ring number for a given z

Contents

Syntax

zNum = z2ring(nSide,z)

Input Arguments

nSide      HEALPix resolution parameter
+z          numeric array of z values

Return Arguments

nRing      size(z) numeric array of ring numbers

Description

HEALPix pixels centers are arranged in rings of constant z. Each ring spans a given range of z. z2ring returns the ring numbers that cover the input z values.

Example

nSide = 4;
+zNum = z2ring(nSide,reshape((-7:7)*2/15,3,5))
+
+zNum =
+
+    14    11     9     6     4
+    13    10     8     6     3
+    12    10     7     5     2
+
+

See also

ring2z

Copyright 2010-2011 Lee Samuel Finn. Terms of Use.


+ Published with MATLAB® 7.12

Index: /issm/trunk/externalpackages/mealpix/help/inRing_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/inRing_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/inRing_help.m (revision 25836) @@ -0,0 +1,57 @@ +%% inRing +% Return list of pixels in a ring or ring section + +%% Syntax +% pixList = inRing(nSide, nRing, phi0, dPhi, 'Param1', Value1, ...); + +%% Input Arguments +% nSide HEALPix resolution parameter +% nRing Ring number (1 <= nRing <= 4*nSide-1) +% phi0, dPhi (optional) Ring section longitudes [phi-dPhi,phi+dPhi] +% +% Param Value +% 'nest' return pixels with nested indexing (true | {false}) +% 'strict' return only pixels whose center is in longitude range +% (true | {false}) + +%% Return Arguments +% pixList size(nRing) cell array of pixels in ring defined by nRing, +% phi0, dPhi + +%% Description +% nRing may be a numeric array, in which case phi0, dPhi and nest may each +% be either scalar or a size(nRing) array. If strict is false (default) +% then all pixels intersected by longitude range are included in pixList. + +%% Example + +% All pixels in ring 2 of nSide = 4 pixelization (ring indexed) +pix = inRing(4,2); +pix{:} + +% Same, but nested indexing +pix = inRing(4,2,'nest',true); +pix{:} +nest2ring(4,pix{:}) + +% Pixels in rings [2,4;8,10;12,14] and the longitude band +% [7*pi/4,9*pi/4] +nRing = [2,3;5,12;13,14]; +pix = inRing(4,nRing,2*pi,pi/4); +pix{1} +pix{end} + +% Same, with strict selection +pix = inRing(4,nRing,2*pi,pi/4,'strict',true); +pix{1} +pix{end} + + +%% See also +% ringNum + +%% Requires +% ring2z, pix2vec + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/mealpix_bugreport.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/mealpix_bugreport.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/mealpix_bugreport.m (revision 25836) @@ -0,0 +1,10 @@ +%% Reporting bugs +% MEALPix software distributed on an "as is" basis, without warranties +% or conditions of any kind, and without promise of support. Nevertheless, +% the makes +% extensive use of MEALPix and welcomes any and all bug reports via e-mail +% to our request-tracking system rt-mealpix@gwastro.org. Reported bugs +% will be investigated and addressed on a best effort basis. + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/mealpix_gs_top.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/mealpix_gs_top.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/mealpix_gs_top.m (revision 25836) @@ -0,0 +1,11 @@ +%% Getting Started with MEALPix +% * +% * +% * +% * +% * +% * +% * + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/mealpix_healpix.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/mealpix_healpix.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/mealpix_healpix.m (revision 25836) @@ -0,0 +1,21 @@ +%% MEALPix for the HEALPix User +%% MEALPix function names are derived from their HEALPix counterparts. +% MEALPix functions are typically camel-cased (e.g., , or ). Underscores in HEALPix +% names are dropped in the conversion to MEALPix names. + +%% MEALPix functions accept array arguments +% MEALPix functions exploit Matlab(tm)'s vectorization facilities to +% allow for the processing of arrays of pixels, direction vectors and +% position angle vectors via a single function call. For example, the +% MEALPix implementation of accepts mixed arrays of +% cartesian direction vectors, angular position vectors, and ring or nest +% indexed pixels for either argument. + +%% MEALPix indexes pixels from 1 +% HEALPix pixels are indexed from 0. In keeping with the Matlab standard +% MEALPix pixels are indexed from 1. MEALPix pixels are indexed from 1: +% i.e., MEALPix pixel number n corresponds to HEALPix pixel number n-1. + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/mealpix_install.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/mealpix_install.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/mealpix_install.m (revision 25836) @@ -0,0 +1,16 @@ +%% Installation +% * Download MEALPix, which is provided as a gzipped tar file. Un-tar the +% file and place the MEALPix directory in some appropriate location. +% Hereafter we will refer to the fully-qualified path to MEALPix as +% |$MEALPIX|. +% +% * Add the MEALPix directory tree to your Matlab(TM) path using, e.g., the +% Matlab(TM) command |addpath(genpath('$MEALPIX'))|. You may wish to add +% this command to your matlab/startup.m file, in which case MEALPix will be +% available whenever you start-up Matlab(TM). +% +% The MEALPix Toolbox includes documentation that will appear in the Matlab +% Documentation browser when Matlab(TM) starts-up with MEALPix in its path. + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/mealpix_notices.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/mealpix_notices.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/mealpix_notices.m (revision 25836) @@ -0,0 +1,17 @@ +%% Notices +% MEALPix is based on HEALPix. HEALPix is distributed under the terms of +% the ("GPL") as published by the Free Software Foundation; +% either version 2 of the GPL, or (at your option) any later version. +% +% This Matlab(TM) expression of HEALPix is Copyright 2010-2011 by Lee +% Samuel Finn. It is licensed under the Apache License, Version 2.0 (the +% "License"); you may not use MEALPix except in compliance with the +% License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. Index: /issm/trunk/externalpackages/mealpix/help/mealpix_overview.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/mealpix_overview.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/mealpix_overview.m (revision 25836) @@ -0,0 +1,32 @@ +%% Product Overview +% MEALPix is a native Matlab implementation of a substantial subset of the +% subroutine library. It supports +% the fast and accurate statistical and astrophysical analysis of massive +% full-sky data sets. HEALPix is supported by NASA and ESO, used +% extensively by the WMAP and PLANCK missions, and is part of the official +% FITS World Coordinate System. +% +% MEALPix provides fully vectorized functions for +% +% * Conversion between position angles, cartesian direction vectors, and +% HEALPix ring and nest pixel indexing schemes; +% +% * Spherical harmonic resolution and analysis of functions on the sphere; +% +% * Nearest pixel identification (pixels within a given disc, pixels in a +% ring, pixels in a HEALPix face). +% +% MEALPix was created from the Fortran90 implementation +% via a combination of hand coding +% and machine assisted conversion of the HEALPix F90 source code. Some +% routines were hand-coded based on the documented functionality of the F90 +% subroutines on which they were based. Other routines were hand-coded via +% inspection of the HEALPix F90 implementation source. Still other routines +% were machine converted from F90 to Matlab(TM) using +% . In +% this latter case the resulting Matlab(TM) source was then hand-modified +% to vectorize the computations and take advantage of Matlab(TM) data types +% and other functions. + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/mealpix_product_page.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/mealpix_product_page.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/mealpix_product_page.m (revision 25836) @@ -0,0 +1,27 @@ +%% +% +% Gravitational Wave Astronomy Group Logo +%

MEALPix Toolbox

+% + +%% +% The MEALPix Toolbox is a native Matlab(TM) implementation of the +% Hierarchical Equal Area isoLatitude Pixelization of the sphere (HEALPix). +% It is derived from the package, +% originally developed by ESO and currently supported by JPL and ESO. + +%% Functions +% * +% * + +%% Getting Started +% * +% * +% * +% * +% * +% * + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/mealpix_references.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/mealpix_references.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/mealpix_references.m (revision 25836) @@ -0,0 +1,32 @@ +%% References +% K. M. Gorski et al. 2005. . The Astrophysical Journal 622 759 +% +% K. M. Gorski et al. 1999. . arXiv:astro-ph/9905275 +% +% K. M. Gorski et al. 2002. +% . +% In Astronomical Data Analysis Software and Systems XI, Bohlender, D. A. +% et al. ed. ASP Conference Series Vol 281, pp. 107-111 +% +% Mark R. Calabrettal and Boudewijn F. Roukema. 2007. +% . Monthly Notices of the Royal Astronomical Society 381:2 +% pp. 865 - 872. +% +% W. O'Mullane et al. 2001. . In Mining The Sky. Anthony Banday +% et al., Ed. Anthony ESO Astrophysics Symposia 2001, 638 - 648. +% +% L. Nicastro and Calderone, G. 2008. +% . In Astronomical Data +% Analysis Software and Systems (ADASS) XVII. A. W. Argle et. al, ed. +% Astronomical Society of the Pacific Conference Series vol. 394 pp. +% 486-490. + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/mealpix_reqts.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/mealpix_reqts.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/mealpix_reqts.m (revision 25836) @@ -0,0 +1,23 @@ +%% System Requirements +% MEALPix is a native Matlab(TM) implementation of HEALPix: neither a +% HEALPix installation nor any third-party java or mex files are required +% to make use of the basic HEALPix functionality. + +%% Matlab(TM) requirements +% MEALPix was developed and tested using Matlab(TM) R2010a. It should work +% with any later version. +% +% MEALPix does not require any Mathworks(TM) Toolboxes or add-ons. MEALPix +% will make use of the capabilities of the +% , should it be present. + +%% Third-party software requirements +% MEALPix also includes functions not found in HEALPix. Some of these +% additional functions require other toolboxes: +% +% * requires the +% Toolbox. + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/nPix2nSide_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/nPix2nSide_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/nPix2nSide_help.m (revision 25836) @@ -0,0 +1,22 @@ +%% nPix2nSide +% Finds number of HEALPix facet side subdivisions from number of pixels on +% sphere + +%% Syntax +% nSide = nPix2nSide(nPix); + +%% Input Arguments +% nPix number of pixels on sphere + +%% Return Arguments +% nSide sub-divisions of HEALPix facet side + +%% Example +nPix = 12*[1:4].^2; +nSide = nPix2nSide(nPix) + +%% See also +% nSide2nPix + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/nSide2nPix_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/nSide2nPix_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/nSide2nPix_help.m (revision 25836) @@ -0,0 +1,25 @@ +%% nSide2nPix +% Convert HEALPix resolution parameter to number of pixels on sphere + +%% Syntax +% nPix = nSide2nPix(nSide) + +%% Input Arguments +% nSide sub-divisions of facet sides. May be an array. + +%% Return Arguments +% nPix size(nSide) number of pixels on sphere corresponding to nSide + +%% Description +% HEALPix divides the sphere into 12 basic facets. Each facet is further +% divided into nSide sub-divisions for a total of 12*nSide^2 pixels. + +%% Example +nSide = 2.^[1:4]; +nPix = nSide2nPix(nSide) + +%% See also +% nPix2nSide + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/nSide2res_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/nSide2res_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/nSide2res_help.m (revision 25836) @@ -0,0 +1,21 @@ +%% nSide2res +% Determine angular resolution of a HEALPix map + +%% Syntax +% angres = nSide2res(nSide) + +%% Input Arguments +% nSide HEALPix resolution parameter (may be an array) + +%% Return Arguments +% angres Angular resolution in arcsec + +%% Example +nSide = 2.^(8:12); +nSide2res(nSide) + +%% See also +% res2nSide + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/nest2ring_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/nest2ring_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/nest2ring_help.m (revision 25836) @@ -0,0 +1,23 @@ +%% nest2ring +% Convert MEALPix pixel numbers from nest to ring indexing + +%% Syntax +% rPix = nest2ring(nSide,nPix) + +%% Input Arguments +% nSide HEALPix resolution parameters +% nPix numeric array of MEALPix nest indexed pixel numbers + +%% Return Arguments +% rPix size(nPix) numeric array of ring indexed pixel numbers + +%% Example +nPix = 1:10; +rPix = nest2ring(2,nPix) +nPix = ring2nest(2,rPix) + +%% See also +% ring2nest + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/pix2alm_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/pix2alm_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/pix2alm_help.m (revision 25836) @@ -0,0 +1,46 @@ +%% pix2alm +% Find spherical harmonic decomposition of function on sphere + +%% Syntax +% alm = pix2alm(v) +% alm = pix2alm(v, lmax) + +%% Input Arguments +% v array of pixel values +% lMax (optional) max order of harmonic to calculate +% +% nPix = numel(v), with nPix = 12*nSide^2 for nSide a power of 2. +% lMax defaults to 2*floor(nSide/3) + +%% Return Arguments +% alm coefficients of spherical harmonic expansion + +%% Description +% Let $x_k$ denote the location of pixel $k$ and $v_k$ the function value +% at $x_k$. Then +% +% $$alm(j) = \frac{4\pi}{N}\sum_{k=0}^{N-1} Y_{LM}^{\dagger}(x_k) v_k$$ +% +% where $j=(L+1)^2+M-L$ and $N$ is the number of pixels (12*nSide^2) + +%% Example +% estimate alm of dummy data +ns = 2^4; +np = 12*ns^2; +v = ylm(ns,1,1) + ylm(ns,2,-2) + ylm(ns,3,0) + rand(1,np)/10; +lMax = 4; +alm = pix2alm(v,lMax); +for L = 0:3 + fprintf('L = %d: ',L); + fprintf('%7.3f ',abs(alm((L+1)^2+(-L:L)-L))); + fprintf('\n'); +end + +%% See also +% alm2pix + +%% Requires +% ylm + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/pix2ang_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/pix2ang_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/pix2ang_help.m (revision 25836) @@ -0,0 +1,33 @@ +%% pix2ang +% Find spherical coordinate location of HEALPix pixels + +%% Syntax +% tp = pix2ang(nSide,pix,'Param1',Value1,...) + +%% Input Arguments +% nSide HEALPix resolution parameter (positive integer power of 2) +% pix (optional) array of pixel values to find coordinates of +% +% Param Values +% 'nest' pixels are given in nested indexing (true | {false}) + +%% Return Arguments +% tp cell array of [theta; phi] pixel locations (radians) + +%% Example +% Return [theta; phi] postion angles for all pix of nSide=4, nest scheme +nSide = 4; +tp = pix2ang(nSide,'nest',true); +size(tp) +tp{1} +% Return position angles for a random assortment of pixels +pix = randi(nSide2nPix(nSide),3,4); +tp = pix2ang(nSide,pix); +size(tp) +tp{1} + +%% See also +% See also ang2pix, pix2vec, vec2pix + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/pix2vec_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/pix2vec_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/pix2vec_help.m (revision 25836) @@ -0,0 +1,40 @@ +%% pix2vec +% Convert MEALPix pixel numbers to cartesian location vectors + +%% Syntax +% [x,y,z] = pix2vec(nSide,pix,'Param1',Value1,...) +% xyz = pix2vec(nSide,pix,'Param1',Value1,...) + +%% Input Arguments +% nSide HEALPix resolution parameter +% pix (optional) numeric array of pixel numbers +% +% Param Value +% 'nest' indexing scheme is nested (true | {false}) + +%% Return Arguments +% x,y,z size(pix) size(pix) numeric array of unit vector coordinate +% components corresponding to pixels pix +% xyz size(pix) size(pix) cell array of cartesian unit vectors +% corresponding to pixels pix + +%% Example +nSide = 2^4; +nPix = nSide2nPix(nSide); +pix0 = reshape(1:6,3,2); +pix1 = reshape(nPix+(-5:0),3,2); +pix = [pix0,pix1]; +xyz = pix2vec(nSide,pix); +xyzn = pix2vec(nSide,pix,'nest',true); +size(xyz) +[xyz{1},xyz{end}] +[xyzn{1},xyzn{end}] + +%% See also +% ang2pix, pix2ang, vec2pix + +%% Requires +% nest2ring + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/pix2xy_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/pix2xy_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/pix2xy_help.m (revision 25836) @@ -0,0 +1,19 @@ +%% pix2xy +% Find pixel cartesian face coordinates + +%% Syntax +% xy = pix2xy(nSide,nPix) + +%% Input Arguments +% nSide HEALPix resolution parameter +% nPix nested indexing pixel numbers to find coordinates of + +%% Return Arguments +% xy size(nPix) cell array of pixel coordinates on face + +%% Example +nPix = reshape(1:24,[4,3,2]); +xy = pix2xy(2,nPix) + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/queryDisc_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/queryDisc_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/queryDisc_help.m (revision 25836) @@ -0,0 +1,40 @@ +%% queryDisc +% Find all pixels whose centers are within a specified disc + +%% Syntax +% pix = queryDisc(nSide,c0,r,'Param1',Value1,...) + +%% Input Arguments +% nSide HEALPix resolution parameter +% c0 disc center. May be specified as a pixel number, spherical +% coordinate location [theta, phi] in rads, or as a cartesian +% unit vector [x;y;z]. +% r disc radius (radians) +% +% Param Value +% 'nest' pixels are returned using nested indexing (true | {false}) + +%% Return Arguments +% pix list of pixels in disc + +%% Example +nSide=32; +% Pixels within pi/10 radians of north pole +pix = queryDisc(nSide,[0;0;1],pi/10); +numel(pix) +nSide2nPix(nSide)*((pi/10)/(4*pi)) +% Pixels within pi/10 radians of south pole +pix = queryDisc(nSide,[0;0;-1],pi/10); +numel(pix) +% Pixels within pi/10 radians of 0 long, lat +pix = queryDisc(nSide,[1;0;0],pi/10); +numel(pix) + +%% See also +% queryPolygon, queryStrip, queryTriangle + +%% Requires +% pix2vec, ang2vec, angDist + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/res2nSide_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/res2nSide_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/res2nSide_help.m (revision 25836) @@ -0,0 +1,21 @@ +%% res2nSide +% Find minimum HEALPix resolution parameter yielding required resolution + +%% Syntax +% nSide = res2nSide(r) + +%% Input Arguments +% r angular resolution (arc seconds) + +%% Return Arguments +% nSide minimum base pixel sub-divisions corresponding to resolution r + +%% Example +r = 100*rand(3,4); +nSide = res2nSide(r) + +%% See also +% nSide2res + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/ring2nest_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/ring2nest_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/ring2nest_help.m (revision 25836) @@ -0,0 +1,22 @@ +%% ring2nest +% Convert MEALPix pixel numbers from ring to nest indexing + +%% Syntax +% nPix = ring2nest(nSide,rPix) + +%% Input Arguments +% nSide HEALPix resolution parameter +% rPix ring indexed MEALPix pixel numbers + +%% Return Arguments +% nPix next indexed MEALPix pixel numbers + +%% Example +nPix = ring2nest(4,reshape(1:6,2,3)) +rPix = nest2ring(4,nPix) + +%% See also +% nest2ring + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/ring2z_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/ring2z_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/ring2z_help.m (revision 25836) @@ -0,0 +1,22 @@ +%% ring2z +% Find HEALPix ring number corresponding to a given z coordinate + +%% Syntax +% z = ring2z(nSide,nRing) + +%% Input Arguments +% nSide HEALPix resolution parameter +% nRing numeric array of ring numbers (in range [1,4*nSide-1]) + +%% Return Arguments +% z size(nRing) numeric array of pixel center z coordinates + +%% Example +nRing = reshape(1:15,3,5) +z = ring2z(4,nRing) + +%% See also +% z2ring + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/template_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/template_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/template_help.m (revision 25836) @@ -0,0 +1,64 @@ +%% NAME +% short descr + +%% Syntax + +%% Input Arguments + +%% Return Arguments + +%% Description + +%% Algorithm Notes + +%% Example + +%% See also + +%% Requires + +%% References +% K. M. Gorski et al. 2005. . The Astrophysical Journal 622 759 +% +% K. M. Gorski et al. 1999. . arXiv:astro-ph/9905275 +% +% K. M. Gorski et al. 2002. +% . +% In Astronomical Data Analysis Software and Systems XI, Bohlender, D. A. +% et al. ed. ASP Conference Series Vol 281, pp. 107-111 +% +% Mark R. Calabrettal and Boudewijn F. Roukema. 2007. +% . Monthly Notices of the Royal Astronomical Society 381:2 +% pp. 865 - 872. +% +% W. O'Mullane et al. 2001. . In Mining The Sky. Anthony Banday +% et al., Ed. Anthony ESO Astrophysics Symposia 2001, 638 - 648. +% +% L. Nicastro and Calderone, G. 2008. +% . In Astronomical Data +% Analysis Software and Systems (ADASS) XVII. A. W. Argle et. al, ed. +% Astronomical Society of the Pacific Conference Series vol. 394 pp. +% 486-490. + +%% Notices +% Copyright 2010-2011 Lee Samuel Finn +% Licensed under the Apache License, Version 2.0 (the "License"); +% you may not use this file except in compliance with the License. +% You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, software +% distributed under the License is distributed on an "AS IS" BASIS, +% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +% See the License for the specific language governing permissions and +% limitations under the License. + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/vec2ang_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/vec2ang_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/vec2ang_help.m (revision 25836) @@ -0,0 +1,42 @@ +%% vec2ang +% Convert from cartesian direction vector to position angle on sphere + +%% Syntax +% tp = vec2ang(xyz) + +%% Input Arguments +% xyz cell array of [3,1] cartesian coordinate direction vectors +% +% The direction vectors need not be normalized. + +%% Return Arguments +% tp cell array of [2,1] position angles ([theta, phi]) on sphere + +%% Example +% Create a [3,4] cell array of position angles and manually convert to +% cartesian direction vectors. Use vec2ang to convert back to position +% angles and compare with originals + +% angular position vectors +z = 2*rand(3,4)-1; +th = acos(z); +ph = 2*pi*rand(3,4)-pi; + +% convert to cartesian coordinate vectors +x = sqrt(1-z.^2).*cos(ph); +y = sqrt(1-z.^2).*sin(ph); +xyz = arrayfun(@(x,y,z)([x,y,z]),x,y,z,'UniformOutput',false); + +% use vec2ang to convert cartesian coordinate vectors to angular position +% vectors +tp = vec2ang(xyz); + +% Compare original vectors with final vectors +tp0 = arrayfun(@(t,p)([t;p]),th,ph,'UniformOutput',false); +tf = cellfun(@(x,y)(any(abs(x-y)>4*eps)),tp,tp0) + +%% See also +% ang2vec + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/vec2pix_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/vec2pix_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/vec2pix_help.m (revision 25836) @@ -0,0 +1,37 @@ +%% vec2pix +% Convert cartesian direction vectors to MEALPix pixel numbers + +%% Syntax +% nPix = vec2pix(nSide,xyz,'Param1',Value1,...); + +%% Input Arguments +% nSide HEALPix resolution parameter +% xyz cell array of [3,1] cartesian direction vectors +% +% Param Value +% 'nest' use nested indexing (true | {false}) + +%% Return Arguments +% nPix size(xyz) pixel number array + +%% Example +% Find pixels corresponding to a [4,5] set of (unnormalized) cartesian +% vectors: +nSide = 4; +xyz0 = squeeze(num2cell(2*rand(3,4,5)-1,1)); +nPix = vec2pix(nSide,xyz0) + +% Find the normalized vectors corresponding to the pixels +xyz1 = pix2vec(nSide,nPix); + +% Find angular distance from vectors to pixels +d = angDist(xyz0,xyz1) + +%% See also +% ang2pix, pix2ang, pix2vec + +%% Requires +% ring2nest + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/xy2pix_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/xy2pix_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/xy2pix_help.m (revision 25836) @@ -0,0 +1,37 @@ +%% xy2pix +% Find (nest indexed) MEALPix pixel number corresponding to a pixel index +% on a HEALPix face + +%% Syntax +% ipix = xy2pix(nSide, ix, iy, nFace) + +%% Input Arguments +% nside HEALPix resolution parameter (power of 2) +% ix,iy integer pixel location on face (1 <= ix, iy <= nSide) +% nFace HEALPix face number (1 <= nFace <= 12) +% +% One or both ix and iy may be scalars. If neither is a scalar both must +% have the same size. + +%% Return Arguments +% ipix NESTED pixel index for given x,y on the face + +%% Description +% At lowest resolution HEALPix divides the sphere into 12 faces, each with +% its own coordinate system. Each face is further subdivided in a regular +% fashion as the resolution parameter is increased. Given a face number +% (from 1 to 12), a resolution parameter, and a location on the face XY2PIX +% identifies the pixel number (in the nested indexing scheme). + +%% Example +nSide = 4; +nFace = 3; +ix = [1 2; 1 2]; +iy = [1 1; 2 2]; +nPix = xy2pix(nSide,ix,iy,nFace) + +%% See also +% pix2xy + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/ylm_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/ylm_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/ylm_help.m (revision 25836) @@ -0,0 +1,28 @@ +%% ylm +% Evaluate spherical harmonic basis functions $Y_{LM}$ at pixel centers + +%% Syntax +% v = ylm(nSide,L,M,'Param1',Value1,'Param2',Value2,...); + +%% Input Arguments +% nSide HEALPix resolution parameter (power of 2) +% L spherical harmonic degree (0 <= L) +% M spherical harmonic order (-M <= L <= M) +% +% Param Value +% 'real' return real values (true | {false}) +% 'nest' nested indexing flag (true | {false}) + +%% Return Arguments +% v spherical harmonics evaluated at pixel centers + +%% Example +% Plot Ylm for (L,M) = (4,2) on nSide = 16 HEALPix sphere +pix = ylm(16,4,2); +hp3d(pix); + +%% Requires +% pix2ang + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/help/z2ring_help.m =================================================================== --- /issm/trunk/externalpackages/mealpix/help/z2ring_help.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/help/z2ring_help.m (revision 25836) @@ -0,0 +1,27 @@ +%% z2ring +% Return HEALPix ring number for a given z + +%% Syntax +% zNum = z2ring(nSide,z) + +%% Input Arguments +% nSide HEALPix resolution parameter +% z numeric array of z values + +%% Return Arguments +% nRing size(z) numeric array of ring numbers + +%% Description +% HEALPix pixels centers are arranged in rings of constant z. Each ring +% spans a given range of z. z2ring returns the ring numbers that cover the +% input z values. + +%% Example +nSide = 4; +zNum = z2ring(nSide,reshape((-7:7)*2/15,3,5)) + +%% See also +% ring2z + +%% +% Copyright 2010-2011 Lee Samuel Finn. . Index: /issm/trunk/externalpackages/mealpix/info.xml =================================================================== --- /issm/trunk/externalpackages/mealpix/info.xml (revision 25836) +++ /issm/trunk/externalpackages/mealpix/info.xml (revision 25836) @@ -0,0 +1,61 @@ + + + + + + + + + 2010b + + MEALPix + + + toolbox + + + + ./help + + $toolbox/matlab/icons/bookicon.gif + + + + + + + + + + + + web ./helpfiles/mytoolbox_product_page.html -helpbrowser + + $toolbox/matlab/icons/bookicon.gif + + + + + + + + + + + + + + + + + + + + + web http://gwastro.org -browser; + $docroot/techdoc/matlab_env/examples/webicon.gif + + + + Index: /issm/trunk/externalpackages/mealpix/src/Contents.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/Contents.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/Contents.m (revision 25836) @@ -0,0 +1,28 @@ +% MEALPix +% alm2pix - Evaluate spherical harmonic function expansion on HEALPix pixels +% alm2spec - valuate angular power spectral density +% ang2pix - Convert spherical coordinate location to HEALPix pixel number +% ang2vec - Convert from spherical to cartesian coordinates +% angDist - Computes angular distance on the unit sphere +% corners - Find pixel corners +% hp3d - Plots a HEALPix dataset on a 3D sphere +% hpInterp - Interpolate data on sphere to MEALPix pixels +% hpStat - Compute descriptive statistics of a pixel value list +% inRing - return pixels in ring or ring section +% nPix2nSide - Convert number of pixels to number of facet side subdivisions +% nSide2nPix - Convert resolution parameter to number of pixels +% nSide2res - Calculates angular resolution of a HEALPix map in arcsec +% nest2ring - Convert MEALPix pixel numbers from nest to ring indexing +% pix2alm - Find spherical harmonic decomposition of function on sphere +% pix2ang - Find spherical coordinate location of HEALPix pixels +% pix2vec - convert HEALPix pixel numbers to (x,y,z) unit vector +% pix2xy - Find pixel cartesian face coordinates +% queryDisc - Find all pixels whose centers are within a specified disc +% res2nSide - Finds minimum base pixel sub-division for required resolution +% ring2nest - Convert MEALPix pixel numbers from ring to nest indexing +% ring2z - Find HEALPix ring number corresponding to a given z coordinate +% vec2ang - Convert cartesian direction vector to position angle on sphere +% vec2pix - Convert cartesian direction vectors to MEALPix pixel numbers +% xy2pix - gives the pixel number ipix (NESTED) of ix, iy and face_num +% ylm - returns spherical harmonic basis Y_L^M on the HEALPix sphere +% z2ring - Find HEALPix ring numbers from direction vector z coordinate Index: /issm/trunk/externalpackages/mealpix/src/alm2pix.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/alm2pix.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/alm2pix.m (revision 25836) @@ -0,0 +1,76 @@ +function v = alm2pix(nSide, alm, varargin) +% ALM2PIX Evaluate spherical harmonic function expansion on HEALPix pixels +% +% v = alm2pix( nSide, alm, 'Param1', Value1, 'Param2', Value2, ...) +% +% nSide HEALPix resolution parameter (power of 2) +% alm Spherical harmonic expansion coefficients +% +% Param Value +% 'lmax' max order of harmonic to calculate (default floor2*nSide/3) +% 'nest' (true | {false}) +% +% v array of function values at pixels (numel(v) = 12*nSide^2) +% +% Coefficient of Y_{lm} is alm((l+1)*(l+1)+m-1) +% +% Example +% % Shows the gibbs-like error at the poles +% hp3d(alm2pix(16,pix2alm(16,ones(1,12*16^2)))-1) +% +% Requires ylm +% See also pix2alm +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: alm2pix.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% Parse and validate input +p = inputParser; +p.addRequired('nSide',@qNSide); +p.addRequired('alm',@qALM); +p.addParamValue('lMax', 2*floor(nSide/3),@qLMax); %% SA corrected it on 11/03/2014 +%p.addParamValue('lMax', floor(2*nSide/3),@qLMax); +p.addParamValue('nest', false, @islogical) + +p.parse(nSide, alm, varargin{:}); + +nSide = p.Results.nSide; +alm = p.Results.alm; +lMax = p.Results.lMax; +nest = p.Results.nest; + +%% +nPix = nSide2nPix(nSide); +v = zeros(1,nPix); +p = 0; % alm index +lMax = max(lMax,sqrt(numel(alm))-1); +for L = 0:lMax + for M = -L:L + v = v + alm(1+p).*ylm(nSide,L,M,'nest',nest); + p = p + 1; + end +end + +return + +function tf = qLMax(lMax) +% QLMAX validate lMax +% +% lMax is a non-negative integer-valued scalar + +tf = isnumeric(lMax) && isscalar(lMax) && floor(lMax) == lMax && lMax >= 0; + +return Index: /issm/trunk/externalpackages/mealpix/src/alm2spec.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/alm2spec.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/alm2spec.m (revision 25836) @@ -0,0 +1,62 @@ +function cL = alm2spec(varargin) +% ALM2SPEC valuate angular power spectral density +% +% cL = alm2spec(alm) +% cL = alm2spec(alm, lMax) +% +% alm real valued coefficients +% lMax max order of harmonic to calculate (default 20) +% +% cL angular power spectrum +% +% Coefficients alm are arranged such that alm(k) is the coefficient +% corresponding to k = (L+1)^2 + M - L +% +% Example +% % Power spectrum estimate of dummy data +% pix = ylm(16,4,2) + ylm(16,7,2) + ylm(16,16,-4) + .1.*rand(1,12*16*16); +% alm = pix2alm(16,pix,100); +% cl = alm2spec(alm,100); +% plot(cl); +% +% See also pix2alm, alm2pix +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: alm2spec.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% Parse and validate input +p = inputParser; +p.addRequired('alm',@qAlm); +p.addOptional('lMax',20,@qLMax); +p.parse(varargin{:}); + +alm = p.Results.alm; +lMax = p.Results.lMax; + +%% Compute power spectrum +% Angular power spectrum for given L is sum over m of (|alm|^2/(2L+1)) + +% Preallocate +cL=zeros(1,lMax+1); + +cL(1) = abs(alm(1))^2; +for L = 1:lMax + % Coefficients for L run from L^2+1 to (L+1)^2 + cL(L+1) = sum(abs(alm(L^2+(1:(2*L+1)))).^2); +end +cL = cL./(2*(0:L)+1); + +return Index: /issm/trunk/externalpackages/mealpix/src/ang2pix.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/ang2pix.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/ang2pix.m (revision 25836) @@ -0,0 +1,175 @@ +function pix = ang2pix(varargin) +% ANG2PIX Convert spherical coordinate location to HEALPix pixel number +% +% pix = ang2pix(nSide, v); +% pix = ang2pix(nSide, v, nest); +% +% nSide HEALPix resolution parameter +% v (theta, phi) pairs in radians as either size(v,1) == 2 or as +% cellarray of [2,1] +% nest (optional) nested pixel number scheme (true | {false}) +% +% pix array of pix numbers: +% v on input output +% iscell(v) size(v) cell array of pixel numbers +% isnumeric(v) numeric array of pixel numbers +% +% Example +% vTheta = acos(2*rand(3,5)-1); +% vPhi = 2*pi*rand(3,5); +% v = arrayfun(@(x,y)([x,y]),vTheta,vPhi,'UniformOutput',false); +% nSide = 8; +% pix = ang2pix(nSide,v); +% +% NB: Matlab indexes pixels from 1 +% +% See also vec2pix, pix2ang, pix2vec +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: ang2pix.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% Parse and validate arguments +p = inputParser; +p.addRequired('nSide',@qNSide); +p.addRequired('v',@qV); +p.addOptional('nest',false,@islogical) +p.parse(varargin{:}); +nSide = p.Results.nSide; +v = p.Results.v; +nest = p.Results.nest; + +%% unpack v +if isnumeric(v) + ns = size(v); + ns = ns(2:end); + vt = reshape(v(1,:),ns); + vp = reshape(v(2,:),ns); +else + vt = cellfun(@(x)(x(1)),v); + vp = cellfun(@(x)(x(2)),v); +end + +%% Compute pix numbers +pix = f_ang2pix_ring(nSide,vt,vp); + +%% If required convert to nest indexing +if nest + pix = ring2nest(nSide,pix); +end + +return + +%% qV +function tf = qV(v) +% QV test v for inputParser + +if isnumeric(v) + tf = 2 == size(v,1); +elseif iscell(v) + nSize = cellfun('prodofsize',v); + tf = all(2 == nSize(:)); +else + tf = false; +end + +return + +%% f_ang2pix_ring +function ipix = f_ang2pix_ring(nside, theta, phi) + +%======================================================================= +% renders the pixel number ipix (RING scheme) for a pixel which contains +% a point on a sphere at coordinates theta and phi, given the map +% resolution parameter nside +%======================================================================= + +%% f90 I/O Check/Init +if(nside<1 || nside>8192) + msgid = [mfilename ':nSide']; + error(msgid,'%s nSide (%d) out of range',msgid,nside); +end; +if(theta<0 | theta>pi) %#ok + msgid = [mfilename ':theta']; + error(msgid,'%s %e is out of range [0,pi)',msgid,theta); +end; + +z = cos(theta); +za = abs(z); +% in [0,4) +tt = mod(phi,2*pi)/(pi/2); + +ip = zeros(size(z)); +ipix = zeros(size(z)); + +% Logical arrays of pix regions (to remove if statement and vectorize calc) +emask = za <= 2/3; +pmask = ~emask; + +%% Equatorial Region Calculation +temp1(emask) = nside*(0.5+tt(emask)); +temp2(emask) = nside*0.75*z(emask); + +% index of ascending edge line +jp(emask) = fix(temp1(emask)-temp2(emask)); + +% index of descending edge line +jm(emask) = fix(temp1(emask)+temp2(emask)); + +% in {1,2n+1} (ring number counted from z=2/3) +ir = zeros(size(emask)); +ir(emask) = fix(nside + 1 + jp(emask) - jm(emask)); + +% kshift=1 if ir even, 0 otherwise +kshift(emask) = fix(1 - mod(ir(emask),2)); + +%% What is this all about? +nl4 = 4*nside; +% in {0,4n-1} +ip(emask) = fix(fix((jp(emask)+jm(emask)-nside+kshift(emask)+1)/2)); +% if(ip(q) >= nl4) +ip(emask & (ip >= nl4)) = fix(ip(emask & (ip >= nl4)) - nl4); +% end; +ipix(emask) = fix(2*nside*(nside-1) + nl4*(ir(emask)-1) + ip(emask)); + +%% NorthSouth Polar Cap Calculation +%else; +%tt=mod(tt,1); +tp(pmask) = tt(pmask) - fix(tt(pmask)); +tmp(pmask) = nside*sqrt(3*(1-za(pmask))); +% increasing edge line index +jp(pmask) = fix(tp(pmask).*tmp(pmask)); +% decreasing edge line index +jm(pmask) = fix((1-tp(pmask)).*tmp(pmask)); +% ring number counted from the closest pole +ir = zeros(size(pmask)); +ir(pmask) = fix(jp(pmask) + jm(pmask) + 1); +% in {0,4*ir-1} +ip(pmask) = fix(fix(tt(pmask).*ir(pmask))); +newmask1 = (pmask&(ip >= 4*ir)); +%if(ip(pmask) >= 4.*ir(pmask)) +ip(newmask1) = fix(ip(newmask1) - 4*ir(newmask1)); +%end; +newmask2 = (pmask&(z>0)); +%if(z(pmask)>0.) +ipix(newmask2) = fix(2*ir(newmask2).*(ir(newmask2)-1) + ip(newmask2)); +newmask3 = (pmask&~(z>0)); +%else; +nPix = 12*nside^2; +ipix(newmask3) = fix(nPix-2*ir(newmask3).*(ir(newmask3)+1)+ip(newmask3)); +%end; + +ipix = ipix+1; %MEALPix numbering +return Index: /issm/trunk/externalpackages/mealpix/src/ang2vec.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/ang2vec.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/ang2vec.m (revision 25836) @@ -0,0 +1,61 @@ +function xyz = ang2vec(tp) +% ANG2VEC Convert from spherical to cartesian coordinates +% +% xyz = ang2vec(tp) +% +% tp cell of [2,1] angular locations [theta; phi] in radians +% +% xyz size(tp) celll array of [3,1] vectors +% +% Example +% tp = [acos(2*rand(1,12)-1); 2*pi*rand(1,12)]; +% tp = mat2cell(tp,2,ones(12,1)); +% tp = reshape(tp,3,4); +% xyz = ang2vec(tp); +% xyz{2,3} +% tp{2,3} +% +% See also vec2ang +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: ang2vec.m 5831 2011-02-25 23:55:19Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% IO check +error(nargchk(1,1,nargin,'struct')); +error(nargoutchk(1,1,nargout,'struct')); + +xyz = cellfun(@dAng2Vec,tp,'UniformOutput',false); + +return + +function xyz = dAng2Vec(tp) +% dAng2Vec location on sphere to unit cartesian direction vector +% +% xyz = dAng2Vec(tp) +% +% tp [theta, phi] in radians +% +% xyz [3,1] + +t = tp(1); +z = cos(t); +s = sin(t); +p = tp(2); +xyz = [cos(p)*s;sin(p)*s;z]; + +return Index: /issm/trunk/externalpackages/mealpix/src/angDist.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/angDist.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/angDist.m (revision 25836) @@ -0,0 +1,179 @@ +function rad = angDist(varargin) +%ANGDIST Computes angular distance on the unit sphere +% +% rad = angDist(v0,v1,'Param1',Value1,'Param2',Value2,...) +% +% v0, v1 (numerical or cell) array of points on sphere +% +% Param Value +% 'nSide' HEALPix resolution parameter (integer power 2) +% 'nest' nested indexing (true | {false}) +% +% rad array of angular distances (radians) +% +% Description +% angDist computes the angular distances between points on the sphere. +% Points may be specified as MEALPix pixel numbers, spherical coordinate +% location vectors, or cartesian coordinate vectors. Cartesian coordinate +% input vectors need not be normalized. +% +% Either or both of v0, v1 may be a scalar; otherwise they must both be +% the same size. When one is a scalar than the distance is computed between +% that point and all the points specified in the complementary argument. +% When pix0 and pix1 are arrays then the distances are returned between the +% corresponding points in the two arrays. +% +% If any location is specified as a pixel number then nSide must be +% specified. The indexing scheme for pixels center locations defaults to +% ring; to specify nested indexing set the 'nest' parameter to true. +% +% v0 or v1 specified as numeric arrays: +% If all points in v0 are pixel numbers then v0 may be specified as a +% numeric array (similarly v1, mutatis mundis). nSide must be specified. +% Pixels numbers may be specified in ring indexing or nested indexing. For +% nested indexing the nest parameter must be set to true. +% +% pix0 or pix1 specified as cell arrays: +% Either or both pix0 or pix1 may be specified as a cell array, in which +% case each cell specifies a location on the sphere as either a pixel +% number, a two-component ([theta; phi]) spherical coordinate vector, or a +% three component ([x;y;z]) cartesian vector. nSide must be specified if +% any location is identified as a pixel center. +% +% Example +% % angular distance from pole to equator: +% v0 = {[0;0;1]}; % north pole +% v1 = {[1;0;0]}; % point on equator +% rad = angDist(v0, v1); +% +% % angular distance from pole to pixels 1, 17, 33 for nSide = 4: +% v0 = {[0;0;1]}; +% rad = angDist([1, 17, 33], v0, 'nSide', 4); +% +% % angular distance from pixels 1 to 4, 2 to 5, and 3 to 6 for nSide = 8: +% rad = angDist(8, [1, 2, 3], [4, 5, 6]); +% +% Requires pix2vec, ang2vec +% +% See also queryDisc +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: angDist.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% Verify and parse arguments +error(nargoutchk(1,1,nargout,'struct')); + +p = inputParser; +p.addRequired('v0',@(x)(iscell(x) || isnumeric(x))); +p.addRequired('v1',@(x)(iscell(x) || isnumeric(x))); +p.addParamValue('nest',false,@islogical); +% nSide scalar non-negative integer +p.addParamValue('nSide',0,... + @(x)(isscalar(x) && isnumeric(x) && floor(abs(x)) == x)); +p.parse(varargin{:}); + +v0 = p.Results.v0; +v1 = p.Results.v1; +nest = p.Results.nest; +nSide = p.Results.nSide; + +if ~(1 == numel(v0) || 1 == numel(v1)) + nV0 = size(v0); + nV1 = size(v1); + assert(all(nV0 == nV1),[mfilename ':vDim']); +end + +%% +if isnumeric(v0) + v0 = pix2vec(nSide,v0); +else + v0 = cellfun(@(x)(v2vec(x,nSide,nest)),v0,'UniformOutput',false); +end +if isnumeric(v1) + v1 = pix2vec(nSide,v1); +else + v1 = cellfun(@(x)(v2vec(x,nSide,nest)),v1,'UniformOutput',false); +end + +if 1 == numel(v0) + rad = cellfun(@(x)(f_angdist(v0{1},x)),v1); +elseif 1 == numel(v1) + rad = cellfun(@(x)(f_angdist(x,v1{1})),v0); +else + rad = cellfun(@(x,y)(f_angdist(x,y)),v0,v1); +end + +return + +function dist = f_angdist(v1, v2) +% use pix_tools +%======================================================================= +% call angdist(v1, v2, dist) +% computes the angular distance dist (in rad) between 2 vectors v1 and v2 +% in general dist = acos ( v1 . v2 ) +% except if the 2 vectors are almost aligned. +%======================================================================= +% persistent diff r1 r2 sprod vdiff ; + +% if isempty(r1), r1=zeros(1,3); end; +% if isempty(r2), r2=zeros(1,3); end; +% if isempty(vdiff), vdiff=zeros(1,3); end; +% if isempty(diff), diff=0; end; +% if isempty(sprod), sprod=0; end; +%======================================================================= +% normalize both vectors +r1 = v1/norm(v1); +r2 = v2/norm(v2); +sprod = dot(r1, r2); +if(sprod > 0.999) + % almost colinear vectors + vdiff = r1 - r2; + % norm of difference + diff = sqrt(dot(vdiff,vdiff)); + dist = 2*asin(diff/2); +elseif(sprod < -0.999) ; + % almost anti-colinear vectors + vdiff = r1 + r2; + % norm of sum + diff = sqrt(dot(vdiff,vdiff)); + dist = pi - 2*asin(diff/2); +else + % other cases + dist = acos( sprod ); +end; +return + +function v = v2vec(v,nSide,nest) +% V2VEC pixel, angular locations or vectors to vectors + +switch numel(v) + case 1, % pixel + v = pix2vec(nSide,v,'nest',nest); + case 2, % angular coordinate location + z = cos(v(1)); + s = sin(v(1)); + v = [s*cos(v(2));s*sin(v(2));z]; + case 3, + % nop + otherwise, + msgid = [mfilename ':v2vec']; + error(msgid,msgid); +end +v = reshape(v,[],1); + +return Index: /issm/trunk/externalpackages/mealpix/src/corners.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/corners.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/corners.m (revision 25836) @@ -0,0 +1,75 @@ +function xyz = corners(nSide,varargin) +% CORNERS Find pixel corners +% +% xyz = corners(nSide,nPix,'Param1',Value1,...); +% +% nSide HEALPix resolution parameter +% nPix (optional) pixel list. Default all pixels. +% +% Param Value +% 'nest' nested indexing (true | {false}) +% +% xyz size(nPix) cell array of [3,1] cartesian vector pixel corner +% locations +% +% Example: +% nSide = 2^2; +% % Corners for all 48 nSide=4 pixels in ring-indexed order +% xyzR = corners(nSide); +% size(xyzR) +% xyzR{1} +% xyzR{end-1} +% +% nPix = randi(nSide2nPix(nSide), 3, 4); +% % Corners for an assortment of pixels in nested index order +% xyzN = corners(nSide,nPix,'nest',true); +% % Convert to pixel list to ring indexing +% r = xyzR{nest2ring(nSide,nPix(2,3))} +% % Corners for same pixels requested via ring indexing +% n = xyzN{2,3} +% % Compare +% all(r == n) +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: corners.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% Validate and parse input +p = inputParser; +p.addRequired('nSide',@qNSide); +p.addOptional('nPix',[],@isnumeric); +p.addParamValue('nest',false,@islogical); + +p.parse(nSide,varargin{:}); +nPix = p.Results.nPix; +nest = p.Results.nest; + +%% Get corners +if isempty(nPix) + nPix = 1:nSide2nPix(nSide); +end +if nest + % convert to ring indexing + nPix = nest2ring(nSide,nPix); +end +nPix = nPix - 1; % convert from MEALPix to HEALPix indexing +[~,xyzc]=f_pix2vec_ring(nSide,nPix(:)); + +xyz = reshape(xyzc,12,[]); +xyz = reshape(num2cell(xyz,1),size(nPix)); +xyz = cellfun(@(x)(reshape(x,3,4)),xyz,'UniformOutput',false); + +return Index: /issm/trunk/externalpackages/mealpix/src/hp3d.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/hp3d.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/hp3d.m (revision 25836) @@ -0,0 +1,88 @@ +function varargout = hp3d(vPix, varargin) +% HP3D Plots a HEALPix dataset on a 3D sphere +% +% h = hp3d(vPix,'Param1',Value1,'Param2',Value2,...); +% +% vPix vector of values at HEALPix pixels +% +% Param Value +% 'nest' nest indexing (true | {false}) +% +% h (optional) array of patch handles for the sphere +% +% Example +% % plot nested pixel numbers on a sphere +% hp3d(1:768,'nest',true); +% +% Requires corners, nPix2nSide +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: hp3d.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% Parse and validate input +p = inputParser; +p.addRequired('vPix',@qVPix); +p.addParamValue('nest',false,@(x)(isscalar(x) && islogical(x))); + +p.parse(vPix,varargin{:}); +nest = p.Results.nest; + +nSide = nPix2nSide(numel(vPix)); +vPix = reshape(vPix,[],1); + +%% Get pixel corners +c = corners(nSide,'nest',nest); + +%% Plot patches +patchPlot = @(c,v)(... + patch(c(1,:),c(2,:),c(3,:),v,'EdgeColor','none','FaceColor','flat')); + % SA :: patch(c(1,:),c(2,:),c(3,:),v,'EdgeColor','black','FaceColor','white')); +h = cellfun(patchPlot,c,num2cell(reshape(vPix,1,[]))); + +% Cleanup the plot +%view(3); +view([90 90]); +axis equal off +colormap(jet(1024)); +colorbar('southoutside'); + +% slower than opengl, but it doesnt crash X... +set(gcf, 'renderer', 'painters') + +if 1 == nargout + varargout{1} = h; +end + +return + +function tf = qVPix(vPix) +% QVPIX validate vPix +% +% vPix is a numeric vector of length 12*k^2 for k a non-negative integer +% power of 2 + +tf = isnumeric(vPix) && max(size(vPix)) == numel(vPix); + +if tf + nSide = floor(sqrt(numel(vPix)/12)); + ln2 = log2(nSide); + tf = tf && ... + numel(vPix) == 12*nSide^2 && ... + floor(ln2) == ln2; +end + +return Index: /issm/trunk/externalpackages/mealpix/src/hpStat.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/hpStat.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/hpStat.m (revision 25836) @@ -0,0 +1,56 @@ +function stats = hpStat(v) +% HPSTAT Compute descriptive statistics of a pixel value list +% +% stats = hpStat(v) +% +% v array of HEALPix pixel values +% +% stats struct +% field contents +% ntot total number of data points +% nvalid number n of valid data points +% mind minimum of valid data +% maxd maximum of valid data +% average average of valid points +% absdev absolute deviation +% var variance +% stddev standard deviation +% skew skewness factor +% kurt kurtosis factor +% +% Example +% % display stats of Y_3^1 +% v = ylm(32,3,1,'real',true); +% stats = hpStat(abs(v)) +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: hpStat.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +stats.ntot = numel(v); +nValid = sum(~isnan(v)); +stats.nValid = nValid; +v = v(~isnan(v)); +stats.mind = min(v); +stats.maxd = max(v); +stats.mean = mean(v); +stats.absdev = mean(abs(v-mean(v))); +stats.var = var(v); +stats.stddev = std(v); +stats.skew = skewness(v); +stats.kurt = kurtosis(v); + +return Index: /issm/trunk/externalpackages/mealpix/src/inRing.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/inRing.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/inRing.m (revision 25836) @@ -0,0 +1,229 @@ +function pixList = inRing(nSide, nRing, varargin) +% INRING return pixels in ring or ring section +% +% pixList = inRing(nSide, nRing, phi0, dPhi, 'Param1', Value1, ...); +% +% nSide HEALPix resolution parameter +% nRing Ring number (1 <= nRing <= 4*nSide-1) +% phi0, dPhi (optional) Ring section longitudes [phi-dPhi,phi+dPhi] +% +% Param Value +% 'nest' return pixels with nested indexing (true | {false}) +% 'strict' return only pixels whose center is in longitude range +% (true | {false}) +% +% pixList size(nRing) cell array of MEALPix pixels in ring defined by +% nRing, phi0, dPhi +% +% nRing may be a numeric array, in which case phi0, dPhi and nest may each +% be either scalar or a size(nRing) array. If strict is false (default) +% then all pixels intersected by longitude range are included in pixList. +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: inRing.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% Parse and validate arguments +p = inputParser; +p.addRequired('nSide',@qnSide); +p.addRequired('nRing',@(n)(qNRing(nSide,n))); +p.addOptional('phi0',0,@isnumeric); +p.addOptional('dPhi',2*pi,@isnumeric); +p.addParamValue('nest',false,@islogical); +p.addParamValue('strict',false,@islogical); + +p.parse(nSide,nRing,varargin{:}); + +phi0 = p.Results.phi0; +dPhi = p.Results.dPhi; +nest = p.Results.nest; +strict = p.Results.strict; + +% Validate dimensions +szRing = size(nRing); + +if 1 == prod(szRing) + if all(1 ~= [numel(phi0), numel(dPhi), numel(nest), numel(strict)]) + msgid = [mfilename ':dims']; + error(msgid,msgid); + end +else + if 1 < numel(phi0) + assert(all(size(phi0) == szRing),[mfilename ':phi0Dims']); + else + phi0 = repmat(phi0,szRing); + end + if 1 < numel(dPhi) + assert(all(size(dPhi) == szRing),[mfilename ':dPhiDims']); + else + dPhi = repmat(dPhi,szRing); + end + if 1 < numel(nest) + assert(all(size(nest) == szRing),[mfilename ':nestDims']); + else + nest = repmat(nest,szRing); + end + if 1 < numel(strict) + assert(all(size(strict) == szRing),[mfilename ':strictDims']); + else + strict = repmat(strict,szRing); + end +end + +%% Initializations +npix = nSide2nPix(nSide); +ncap = 2*nSide*(nSide-1); +pixList = cell(size(nRing)); + +%% Put phi0, dPhi in canonical form +dPhi = abs(dPhi); +phi_low = mod(phi0 - dPhi,2*pi); +phi_hi = mod(phi0 + dPhi,2*pi); +mLong = dPhi >= pi; +if 1 == numel(mLong) + mLong = repmat(mLong,size(nRing)); +end + +%% Identify ring number +nr = zeros(size(nRing)); % ring number +iPix1 = zeros(size(nRing)); % lowest pixel number in the ring +iPix2 = zeros(size(nRing)); % highest pixel number in the ring +kShift = zeros(size(nRing)); + +%%% equatorial region rings +mask = nSide <= nRing & nRing <= 3*nSide; +mir = nRing(mask) - nSide + 1; +iPix1(mask) = ncap + 4*nSide*(mir-1); +iPix2(mask) = iPix1(mask) + 4*nSide - 1; +kShift(mask) = mod(mir,2); +nr(mask) = 4*nSide; + +%%% north pole rings +mask = nRing < nSide; +mir = nRing(mask); +iPix1(mask) = 2*mir.*(mir-1); +iPix2(mask) = iPix1(mask) + 4*mir - 1; +kShift(mask) = 1; +nr(mask) = 4*mir; + +%%% south pole rings +mask = nRing > 3*nSide; +mir = 4*nSide - nRing(mask); +iPix1(mask) = npix - 2*mir.*(mir+1); +iPix2(mask) = iPix1(mask) + 4*mir - 1; +kShift(mask) = 1; +nr(mask) = 4*mir; + +%% Construct pixel list: Full ring case +if any(mLong(:)) + %%% Save all ring pixels: ring indexing + temp = arrayfun(... + @(i1,i2)(i1:i2),... + iPix1(mLong),... + iPix2(mLong),... + 'UniformOutput',false); + [pixList{mLong}] = deal(temp{:}); +end + +%% Construct pixel list: Partial ring case +if any(~mLong(:)) + shift = kShift/2; + + nip = sum(~mLong(:)); + ip_low = zeros(nip,1); + ip_hi = zeros(nip,1); + nList = false(nip,1); + + if any(~strict(:)) + % ~strict = conservative : include every intersected pixel, + % even if pixel CENTER is not in the range [phi_low, phi_hi] + mask = ~strict & ~mLong; + mnr = nr(mask); + mip_low = round(mnr.*phi_low(mask)/(2*pi) - shift(mask)); + mip_hi = round(mnr.*phi_hi(mask)/(2*pi) - shift(mask)); + ip_low(~strict(~mLong)) = mod(mip_low, mnr);% in {0,nr-1} + ip_hi(~strict(~mLong)) = mod(mip_hi, mnr); % in {0,nr-1} + end + + if any(strict) + mask = strict & ~mLong; + mnr = nr(mask); + % strict : include only pixels whose CENTER is in [phi_low, phi_hi] + mip_low = ceil(mnr.*phi_low(mask)/(2*pi) - shift(mask)); + mip_hi = floor(mnr.*phi_hi(mask)/(2*pi) - shift(mask)); + df = mod(mip_low - mip_hi, mnr); + df(df<0) = df(df<0) + mnr(df<0); + + % Mark intervals so small (and away from pixel center) that no pixel + % is included in it + n0 = (df == 1) & (dPhi(mask).*mnr < pi); + nList(n0) = true; + + m0 = mip_low >= mnr; + mip_low(m0) = mip_low(m0) - mnr(m0); + m0 = mip_hi < 0; + mip_hi(m0) = mip_hi(m0) + mnr(m0); + + ip_low(strict(~mLong)) = mip_low; + ip_hi(strict(~mLong)) = mip_hi; + end; + + ip_low = ip_low + iPix1(~mLong(:)); + ip_hi = ip_hi + iPix1(~mLong(:)); + + % identify rings with "wrap-around" longitudinal slices + mTop = ip_low > ip_hi; + ip2 = iPix2(~mLong(:)); + ip1 = iPix1(~mLong(:)); + + topList = arrayfun(... + @(pLow,p1,p2,pHi)([pLow:p2, p1:pHi]),... + ip_low(mTop),ip1(mTop),ip2(mTop),ip_hi(mTop), ... + 'UniformOutput',false); + + % rings with simply-connected longitudinal slices + nTopList = arrayfun(... + @(l,h)(l:h),... + ip_low(~mTop),ip_hi(~mTop),... + 'UniformOutput',false); + + mList = cell(sum(~mLong(:)),1); + [mList{mTop}] = deal(topList{:}); + [mList{~mTop}] = deal(nTopList{:}); + [mList{nList}] = deal([]); + + [pixList{~mLong}] = deal(mList{:}); + +end + +%% Convert ring indexed to nest index as required +if any(nest) + [nestList{1:sum(nest(:))}] = deal(pixList{nest}); + nestList = cellfun(... + @(n)(ring2nest(nSide,n)),... + nestList, 'UniformOutput',false); + [pixList{nest}] = deal(nestList{:}); +end + +%% Convert to MEALPix indexing +pixList = cellfun(@(x)(x+1),pixList,'UniformOutput',false); + +return + +function tf = qNRing(nSide,nRing) +tf = all(1 <= nRing(:)) && all(nRing(:) < 4*nSide); +return Index: /issm/trunk/externalpackages/mealpix/src/nPix2nSide.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/nPix2nSide.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/nPix2nSide.m (revision 25836) @@ -0,0 +1,36 @@ +function nSide = nPix2nSide(nPix) +% NPIX2NSIDE Convert number of pixels to number of facet side subdivisions +% +% nSide = nPix2nSide(nPix); +% +% nPix number of pixels on sphere +% nSide sub-divisions of HEALPix facet side +% +% Example +% nPix = 12*[1:4].^2; +% nSide = nPix2nSide(nPix) +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: nPix2nSide.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +nSide = sqrt(nPix/12); +if any(nSide(:) ~= fix(nSide(:))) + msgid = [mfilename ':nPix']; + error(msgid,msgid); +end + +return Index: /issm/trunk/externalpackages/mealpix/src/nSide2nPix.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/nSide2nPix.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/nSide2nPix.m (revision 25836) @@ -0,0 +1,39 @@ +function nPix = nSide2nPix(nSide) +% NSIDE2NPIX Convert resolution parameter to number of pixels +% +% nPix = nSide2nPix(nSide) +% +% nSide integer power-2 sub-divisions of facet sides. May be an array. +% nPix size(nSide) number of pixels on sphere corresponding to nSide. +% +% HEALPix divides the sphere into 12 basic facets. Each facet is further +% divided into nSide sub-divisions for a total of 12*nSide^2 pixels. +% +% Example +% nPix = nSide2nPix([1:4]) +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: nSide2nPix.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +lg = log2(nSide(:)); +if ~all(abs(lg) == fix(lg)) + msgid = [mfilename ':nSide']; + error(msgid,msgid); +end +nPix = 12*nSide.^2; + +return Index: /issm/trunk/externalpackages/mealpix/src/nSide2res.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/nSide2res.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/nSide2res.m (revision 25836) @@ -0,0 +1,37 @@ +function res = nSide2res(nSide) +% NSIDE2RES Calculates angular resolution of a HEALPix map in arcsec +% +% angres = nSide2res(nSide) +% +% nSide HEALPix Resolution (or array of nSides) +% +% angres Angular resolution of the given nSide in arcsec +% +% See also res2nSide +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: nSide2res.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +if ~(all(nSide > 0) && all(2.^fix(log2(nSide)) == nSide)) + msgid = [mfilename ':nSide']; + error(msgid,msgid); +end +area = 4*pi*(180*3600/pi)^2; +nPix = nSide2nPix(nSide); +res = sqrt(area./nPix); + +return Index: /issm/trunk/externalpackages/mealpix/src/nest2ring.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/nest2ring.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/nest2ring.m (revision 25836) @@ -0,0 +1,57 @@ +function rPix = nest2ring(nSide,nPix) +% NEST2RING Convert MEALPix pixel numbers from nest to ring indexing +% +% rPix = nest2ring(nSide,nPix) +% +% nSide HEALPix resolution parameters +% nPix numeric array of MEALPix nest indexed pixel numbers +% +% rPix size(nPix) numeric array of ring indexed pixel numbers +% +% See also ring2nest +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: nest2ring.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% Parse and validate input +p = inputParser; +p.addRequired('nSide',@qNSide); +p.addRequired('nPix',@(n)(qPix(nSide,n))); +p.parse(nSide,nPix); + +%% Convert +% Save shape +% convert HEALPix indexing as vector +% convert to MEALPix indexing and restore shape + +sz = size(nPix); +rPix = f_nest2ring(nSide,nPix(:)-1); +rPix = reshape(rPix+1,sz); + +return + +function tf = qPix(nSide,nPix) +tf = isnumeric(nPix); +if tf + nPix = nPix(:); + tf = ... + all(fix(abs(nPix)) == nPix) && ... + all(0 < nPix) && ... + all(nSide2nPix(nSide) >= nPix); +end +return Index: /issm/trunk/externalpackages/mealpix/src/pix2alm.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/pix2alm.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/pix2alm.m (revision 25836) @@ -0,0 +1,67 @@ +function alm = pix2alm(varargin) +% PIX2ALM Find spherical harmonic decomposition of function on sphere +% +% alm = pix2alm(v) +% alm = pix2alm(v, lmax) +% +% v array of pixel values +% lMax (optional) max order of harmonic to calculate +% +% nPix = numel(v), with nPix = 12*nSide^2 for nSide a power of 2. +% lMax defaults to 2*floor(nSide/3) +% +% alm Spherical harmonic expansion coefficients +% +% alm(j) is coefficient corresponding to order L, M with j = (L+1)^2+M-L +% +% Example +% % estimates |a_l^m| of dummy data +% pix = ylm(16,4,2) + ylm(16,7,2) + ylm(16,16,-4) + .1.*rand(1,12*16*16); +% alm = pix2alm(16,pix,100); +% plot(abs(alm)); +% +% Requires ylm +% See also alm2pix +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: pix2alm.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% Parse and validate input +p = inputParser; +p.addRequired('v',@qPix); +hLMax = @(v)(2*floor(nPix2nSide(numel(v))/3)); +p.addOptional('lMax', hLMax(varargin{1}), @qLMax); + +p.parse(varargin{:}); + +v = p.Results.v; +lMax = p.Results.lMax; + +%% +% Preallocate alm +alm = zeros(1,(lMax+1)^2); + +nSide = sqrt(numel(v)/12); +for L = 0:lMax + ndx = L^2+1; + for M = -L:L + alm(ndx+L+M) = sum(conj(ylm(nSide,L,M)).*v); + end +end +alm = alm*4*pi/numel(v); + +return Index: /issm/trunk/externalpackages/mealpix/src/pix2ang.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/pix2ang.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/pix2ang.m (revision 25836) @@ -0,0 +1,75 @@ +function tp = pix2ang(nSide, varargin) +% PIX2ANG Find spherical coordinate location of HEALPix pixels +% +% tp = pix2ang(nSide,pix,'Param1',Value1,...) +% +% nSide HEALPix resolution parameter (positive integer power of 2) +% pix (optional) array of pixel values to find coordinates of +% +% Param Values +% 'nest' pixels are given in nested indexing (true | {false}) +% +% tp cell array of [theta; phi] pixel locations (radians) +% +% Example +% % Return theta/phi for all pix of nSide=4, nest scheme +% tp = pix2ang(4,'nest') +% +% See also ang2pix, pix2vec, vec2pix +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: pix2ang.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% I/O Check +p = inputParser; +p.addRequired('nSide', @qNSide); +p.addOptional('pix',-1,@(n)(qPix(nSide,n))); +p.addParamValue('nest',false,@(n)(isscalar(n) && islogical(n))); + +p.parse(nSide,varargin{:}); + +pix = p.Results.pix; +nest = p.Results.nest; + +% Matlab indexes pixels from 1 +if pix < 0 + pix = 1:nSide2nPix(nSide); +end + +%% Work +% Save size +% Convert to HEALPix convention +% Get pixel location angles +% Restore size + +sz = size(pix); +pix = reshape(pix - 1,1,[]); +if nest + [tparray(1,:), tparray(2,:)]=f_pix2ang_nest(nSide,pix); +else + [tparray(1,:), tparray(2,:)]=f_pix2ang_ring(nSide,pix); +end +tp=reshape(num2cell(tparray,1),sz); + +return + +function tf = qPix(nSide,n) +tf = ... + isnumeric(n(:)) && ... + all(n(:) == fix(abs(n(:)))) && ... + all(n(:)<=nSide2nPix(nSide)); +return Index: /issm/trunk/externalpackages/mealpix/src/pix2vec.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/pix2vec.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/pix2vec.m (revision 25836) @@ -0,0 +1,104 @@ +function varargout = pix2vec(nSide, varargin) +% PIX2VEC convert HEALPix pixel numbers to (x,y,z) unit vector +% +% [x,y,z] = pix2vec(nSide,pix,'Param1',Value1,...) +% xyz = pix2vec(nSide,pix,'Param1',Value1,...) +% +% nSide HEALPix resolution parameter +% pix (optional) numeric array of pixel numbers to find cartesian +% coordinate vectors for +% +% Param Value +% 'nest' indexing scheme is nested (true | {false}) +% +% x,y,z size(pix) numeric array of unit vector coordinate +% components corresponding to pixels pix +% xyz size(pix) cell array of cartesian unit vectors +% corresponding to pixels pix +% +% Example +% % +% nSide = 2^4; +% nPix = nSide2nPix(nSide); +% pix = randi(nPix,2,3); +% xyz = pix2vec(nSide,pix); +% xyzn = pix2vec(nSide,pix,'nest',true); +% +% Requires nest2ring +% Required by angDist, hpInterp, inRing, queryDisc, ringNum +% See also ang2pix, pix2ang, vec2pix +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: pix2vec.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% IO Check +assert(1 == nargout || 3 == nargout,[mfilename ':nargout']); + +%%% Setup parser +p = inputParser; +p.FunctionName = mfilename; +p.StructExpand = true; + +% Argument declarations +p.addRequired('nSide',@qNSide); +p.addOptional('pix',-1,@(n)(isnumeric(n) && all(floor(n(:))==n(:)))); +p.addParamValue('nest',false,@islogical); + +%%% parse and validate input +p.parse(nSide,varargin{:}); +nSide = p.Results.nSide; +pix = p.Results.pix; +nest = p.Results.nest; + +%% Get pixel vector + +if 1 == numel(pix) && pix < 0 + pix = 1:nSide2nPix(nSide); +end +assert(... + all(0 < pix(:)) || all(pix(:) <= nSide2nPix(nSide)),... + [mfilename ':pix']); + +if nest + pix = nest2ring(nSide,pix); +end +xyz = f_pix2vec_ring(nSide,pix-1); + +%% Format return +switch nargout + case 1, + nSize = size(xyz); + if 2 == numel(nSize) + nSize = [nSize 1]; + end + xyz = reshape(xyz,3,[]); + xyz = num2cell(xyz,1); + varargout{1} = reshape(xyz,nSize(2:end)); + case 3, + nSize = size(xyz); + if 2 == numel(nSize); + nSize = [nSize 1]; + end + sz = nSize(2:end); + xyz = reshape(xyz,3,[]); + varargout{1} = reshape(xyz(1,:),sz); + varargout{2} = reshape(xyz(2,:),sz); + varargout{3} = reshape(xyz(3,:),sz); +end + +return Index: /issm/trunk/externalpackages/mealpix/src/pix2xy.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/pix2xy.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/pix2xy.m (revision 25836) @@ -0,0 +1,64 @@ +function xy = pix2xy(nSide, nPix) +%% PIX2XY Find pixel cartesian face coordinates +% +% xy = pix2xy(nSide,nPix) +% +% nSide HEALPix resolution parameter +% nPix nested indexing pixel numbers to find coordinates of +% +% xy size(nPix) cell array of pixel coordinates on face +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: pix2xy.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +if ~qNSide(nSide) + msgid = [mfilename ':nSide']; + error(msgid,msgid); +end + +if ~(all(nPix(:) > 0) && all(nPix(:) <= nSide2nPix(nSide))) + msgid = [mfilename ':nPix']; + error(msgid,msgid); +end +sPix = size(nPix); +if 2 == numel(sPix) + sPix = [sPix, 1]; +end +ixy = zeros([2,sPix(:)']); + +[pix2x,pix2y]=mk_pix2xy; + +ipf = nPix(:)-1; + +% content of the last 10 bits +ip_low = fix(mod(ipf,1024)); + +% truncation of the last 10 bits +ip_trunc = fix(ipf/1024); + +% content of the next 10 bits +ip_med = fix(mod(ip_trunc,1024)); + +% content of the high weight 10 bits +ip_hi = fix(ip_trunc/1024); +ixy(1,:) = fix(1024*pix2x(ip_hi+1) + 32*pix2x(ip_med+1) + pix2x(ip_low+1)); +ixy(2,:) = fix(1024*pix2y(ip_hi+1) + 32*pix2y(ip_med+1) + pix2y(ip_low+1)); + +xy = reshape(num2cell(ixy,1),sPix); + +return Index: /issm/trunk/externalpackages/mealpix/src/private/correct_ring_phi.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/correct_ring_phi.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/correct_ring_phi.m (revision 25836) @@ -0,0 +1,27 @@ +function [iring, iphi] = correct_ring_phi(location, iring, iphi) + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +delta = zeros(size(iphi)); +delta(iphi<0) = 1; +delta(iphi>4*iring) = -1; +nzMask = delta ~= 0; +if any(nzMask) + if any(abs(location(nzMask)) ~= 1) + msgid = [mfilename,':location']; + error(msgid,msgid); + end + iring(nzMask) = iring(nzMask) - location(nzMask).*delta(nzMask); + iphi(nzMask) = iphi(nzMask) + delta(nzMask).*(4*iring(nzMask)); +end +return Index: /issm/trunk/externalpackages/mealpix/src/private/f_nest2ring.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/f_nest2ring.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/f_nest2ring.m (revision 25836) @@ -0,0 +1,104 @@ +function ipring = f_nest2ring(nSide, ipnest) + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +% $Id: f_nest2ring.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +nPix = nSide2nPix(nSide); +if ~(all(ipnest>=0) && all(ipnest= nSide & (jr <= 3*nSide); +jrE = jr(mask); +nrE = fix(nSide); +n_before(mask) = fix(2*nrE*(2*jrE - nrE - 1)); +kshift(mask) = mod(jrE - nSide, 2); +nr(mask) = nrE; + +% south pole region +mask = jr > 3*nSide; +jrS = jr(mask); +nrS = fix(nl4 - jrS); +n_before(mask) = fix(nPix - 2*nrS.*(nrS + 1)); +kshift(mask) = 0; +nr(mask) = nrS; + +% computes the phi coordinate on the sphere, in [0,2Pi] +% 'phi' number in the ring in {1,4*nr} +jp = fix((jpll(face_num+1).*nr + jpt + 1 + kshift)/2); +maskH = jp>nl4; +maskL = jp<1; +jp(maskH) = fix(jp(maskH) - nl4); +jp(maskL) = fix(jp(maskL) + nl4); + +% in {0, nPix-1} +ipring = fix(n_before + jp - 1); + +return + Index: /issm/trunk/externalpackages/mealpix/src/private/f_pix2ang_nest.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/f_pix2ang_nest.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/f_pix2ang_nest.m (revision 25836) @@ -0,0 +1,108 @@ +function [theta, phi] = f_pix2ang_nest(nSide, ipix) + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +% $Id: f_pix2ang_nest.m 6016 2011-04-27 02:52:56Z lsf@GRAVITY.PSU.EDU $ + +% coordinate of the lowest corner of each face +% in unit of nSide +jrll =[ 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4 ]'; +% in unit of nSide/2 +jpll =[ 1, 3, 5, 7, 0, 2, 4, 6, 1, 3, 5, 7 ]'; +%----------------------------------------------------------------------- +% total number of points +npix = nSide2nPix(nSide); +if ~(all(ipix>=0) && all(ipix (x,y) mapping +[pix2x,pix2y] = mk_pix2xy; + +npface = nSide^2; +nl4 = 4*nSide; + +% find face and pixel number in the face +% face number in {0,11} +face_num = fix(ipix/npface); +% pixel number in the face {0,npface-1} +ipf = mod(ipix,npface); + +fact1 = 1/(3*nSide^2); +fact2 = 2/(3*nSide); +% finds the x,y on the face (starting from the lowest corner) +% from the pixel number +ix = 0; +iy = 0; +scalemlv = 1; +ismax = 4; +for i=0: ismax; + ip_low = mod(ipf,1024); + ix = fix(ix + scalemlv*pix2x(ip_low+1)); + iy = fix(iy + scalemlv*pix2y(ip_low+1)); + scalemlv = scalemlv*32; + ipf = fix(ipf/1024); +end +ix = fix(ix + scalemlv*pix2x(ipf+1)); +iy = fix(iy + scalemlv*pix2y(ipf+1)); + +%% transforms to (horizontal, vertical) coordinates +% 'vertical' in {0,2*(nSide-1)} +jrt = fix(ix + iy); +% 'horizontal' in {-nSide+1,nSide-1} +jpt = fix(ix - iy); + +%% compute z coordinate on the sphere +% ring number in {1,4*nSide-1} +jr = fix(jrll(face_num+1)*nSide - jrt - 1); + +z = zeros(size(jr)); +nr = zeros(size(jr)); +kshift = zeros(size(jr)); + +% north pole region +mask = jr 3*nSide; +nrM = fix(nl4 - jr(mask)); +z(mask) = - 1 + nrM.^2*fact1; +kshift(mask) = 0; +nr(mask) = nrM; + +%% Convert z to theta +theta = acos(z); + +%% Compute phi in [0,2*pi) +% 'phi' number in the ring in {1,4*nr} +jp =fix(((jpll(face_num+1).*nr) + jpt + 1 + kshift)/2); +if(jp > nl4) + jp = fix(jp - nl4); +end; +if(jp < 1) + jp = fix(jp + nl4); +end; +phi = (pi/2)*(jp -(kshift+1)/2)./nr; + +return Index: /issm/trunk/externalpackages/mealpix/src/private/f_pix2ang_ring.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/f_pix2ang_ring.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/f_pix2ang_ring.m (revision 25836) @@ -0,0 +1,78 @@ +function [theta, phi] = f_pix2ang_ring(nSide, iPix) +% F_PIX2ANG_RING convert ring-indexed pixel to angular position vector +% +% [theta, phi] = f_pix2ang_ring(nSide,iPix) +% +% nSide HEALPix resolution parameter +% iPix HEALPix ring-indexed pixel number +% +% Hand conversion of HEALPix distribution f90 code pix2ang_ring +% +% Author: Lee Samuel Finn +% Copyring 2011 + +% $Id: f_pix2ang_ring.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +npix = nSide2nPix(nSide); +if any(iPix<0) || any(iPix>npix-1) + msgid = [mfilename ':ndx']; + error(msgid,msgid); +end + +nl2 = 2*nSide; + +% points in each polar cap, =0 for nSide =1 +nCap = nl2*(nSide-1); + +% preallocate results +theta = zeros(size(iPix)); +phi = zeros(size(iPix)); + +%% North Polar cap ------------- +mask = iPix < nCap; +% counted from North pole +iPixM = iPix(mask); +iRingM = round(sqrt((iPixM+1)/2)); +iPhiM = fix(iPixM - 2*iRingM.*(iRingM - 1)); +% fix round-off error appearing at large nSide +[iRingM, iPhiM]=correct_ring_phi(1, iRingM, iPhiM); +theta(mask) = acos(1-(iRingM/nSide).^2/3); +phi(mask) = (pi/2)*(iPhiM + 0.5)./iRingM; + +%% Equatorial region ------ +mask = ~mask & (iPix < npix-nCap); +ipM = fix(iPix(mask) - nCap); +nl4 = 4*nSide; +% counted from North pole +iRingM = fix(ipM/nl4) + nSide; +iPhiM = mod(ipM,nl4); +% 0 if iring+nSide is odd, 1/2 otherwise +fodd = 0.5*mod(iRingM+nSide+1,2); +theta(mask) = acos((nl2 - iRingM)/(1.5*nSide)); +phi(mask) = (pi/2)*(iPhiM + fodd)/nSide; + +%% South Polar cap ----------------------------------- +mask = npix-nCap <= iPix; +ipM = fix(npix - iPix(mask)); +% counted from South pole +iRingM = round(sqrt(ipM/2)); +iPhiM = fix(2*iRingM.*(iRingM + 1) - ipM); +% fix round-off error appearing at large nSide +[iRingM, iPhiM]=correct_ring_phi(-1, iRingM, iPhiM); +theta(mask) = acos((iRingM/nSide).^2/3 - 1); +phi(mask) = (pi/2)*(iPhiM + 0.5)./iRingM; + +return Index: /issm/trunk/externalpackages/mealpix/src/private/f_pix2vec_ring.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/f_pix2vec_ring.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/f_pix2vec_ring.m (revision 25836) @@ -0,0 +1,202 @@ +function varargout = f_pix2vec_ring(nSide, hPix) +% F_PIX2VEC_RING conversion of f90 PIX2VEC_RING HEALPix code +% +% [vector, vertex] = f_pix2vec_ring(nSide,hPix) +% +% nSide (integer) sub-divisions of HEALPix facets +% hPix (vector integers) HEALPix pixel numbers +% (0 <= hPix < 12*nSide^2) +% +% vector cell(size(hPix)) of [3,1] unit vectors to pixel centers +% vertex (optional) cell(size(hPix)) of [3,4] unit vectors to pixel +% vertices (corners) +% +% renders vector (x,y,z) coordinates of the nominal pixel center +% for the pixel number hPix (RING scheme) +% given the map resolution parameter nSide +% also returns the (x,y,z) position of the 4 pixel vertices (=corners) +% in the order N,W,S,E +% +% Hand rewrite of f90 code +% +% Author: Lee Samuel Finn +% Copyright 2010 + +% $Id: f_pix2vec_ring.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% I/O Check/Init +error(nargoutchk(1,2,nargout,'struct')); +error(nargchk(2,2,nargin,'struct')); + +nPix = nSide2nPix(nSide); +if ~(... + all(floor(hPix(:)) == abs(hPix(:))) && all(hPix(:) < nPix)) + msgid = [mfilename ':hPix']; + error(msgid,msgid); +end + +% in {1, nPix} +hPix1 = fix(hPix + 1); +nl2 = fix(2*nSide); +nl4 = fix(4*nSide); +% points in each polar cap, = 0 for nSide = 1 +nCap = fix(2*nSide*(nSide-1)); +fact1 = 1.5*nSide; +fact2 = 3.0*nSide^2; + +% Calculate corners (vertices)? +do_vertex = (nargout == 2); + +% Associate pixels with regions (north cap, equatorial, south cap) +ncMask = hPix1 <= nCap; +eqMask = hPix1 <= nl2*(5*nSide+1) & ~ncMask; +scMask = ~(eqMask | ncMask); + +% Pre-allocate +z = zeros(size(hPix)); +phi = zeros(size(hPix)); +hDelta_Phi = zeros(size(hPix)); +z_nv = zeros(size(hPix)); +z_sv = zeros(size(hPix)); +phi_nv = zeros(size(hPix)); +phi_sv = zeros(size(hPix)); + +% North polar cap +if any(ncMask(:)) + hip = hPix1(ncMask)/2; + fihip = fix(hip); + iRing = fix(sqrt(hip-sqrt(fihip)))+1; + iPhi = hPix1(ncMask) - 2*iRing.*(iRing-1); + + z(ncMask) = 1-iRing.^2/fact2; + phi(ncMask) = (iPhi-0.5).*pi./(2*iRing); + + if (do_vertex) + hDelta_Phi(ncMask) = pi./(4*iRing); % half pixel width + z_nv(ncMask) = 1-(iRing-1).^2/fact2; + z_sv(ncMask) = 1-(iRing+1).^2/fact2; + iPhi_Mod = mod(iPhi-1,iRing); % in {0..iRing-1} + iPhi_Rat = fix((iPhi-1)./iRing); % in {0,1,2,3} + phi_nv_m = phi_nv(ncMask); + ndx = (1 < iRing); + phi_nv_m(ndx) = (iPhi_Rat(ndx)+iPhi_Mod(ndx)./(iRing(ndx)-1))*pi/2; + phi_nv(ncMask) = phi_nv_m; + phi_sv(ncMask) = (iPhi_Rat+(iPhi_Mod+1)./(iRing+1))*pi/2; + end +end + +% Equatorial region +if any(eqMask(:)) + ip = hPix1(eqMask) - nCap -1; + iRing = fix(ip/nl4) + nSide; % counted from north pole + iPhi = mod(ip,nl4)+1; + + fOdd = 0.5*(1+mod(iRing+nSide,2)); % 1 (1/2) if iRing+nSide is odd (even) + z(eqMask) = (nl2-iRing)/fact1; + phi(eqMask) = (iPhi-fOdd)*pi/(2*nSide); + + if (do_vertex) + hDelta_Phi(eqMask) = pi./(4*nSide); % half pixel width + phi_nv_m = phi(eqMask); + phi_sv_m = phi(eqMask); + z_nv_m = (nl2-iRing+1)/fact1; + z_sv_m = (nl2-iRing-1)/fact1; + nNdx = (iRing == nSide); % northern transition + sNdx = (iRing == 3*nSide); % southern transition + ndx = sNdx|nNdx; % transition + z_nv_m(nNdx) = 1-(nSide-1)^2/fact2; + z_sv_m(sNdx) = -1+(nSide-1)^2/fact2; + iPhi_Mod(ndx) = mod(iPhi(ndx)-1,nSide); % in {0..nSide-1} + iPhi_Rat(ndx) = fix((iPhi(ndx)-1)/nSide); % in {0..3} + if nSide > 1 + phi_nv_m(nNdx) = (iPhi_Rat(nNdx)+iPhi_Mod(nNdx)/(nSide-1))*pi/2; + phi_sv_m(sNdx) = (iPhi_Rat(sNdx)+iPhi_Mod(sNdx)/(nSide-1))*pi/2; + end + phi_nv(eqMask) = phi_nv_m; + phi_sv(eqMask) = phi_sv_m; + z_nv(eqMask) = z_nv_m; + z_sv(eqMask) = z_sv_m; + end +end + +% South polar cap +if any(scMask(:)) + ip = nPix - hPix1(scMask) + 1; + hip = ip/2; + fihip = fix(hip); + iRing = fix(sqrt(hip-sqrt(fihip)))+1; % counted from south pole + iPhi = 4*iRing+1-(ip-2*iRing.*(iRing-1)); + + z(scMask) = -1+iRing.^2/fact2; + phi(scMask) = (iPhi-0.5).*pi./(2*iRing); + + if (do_vertex) + hDelta_Phi(scMask) = pi./(4*iRing); + z_nv(scMask) = -1+(iRing+1).^2/fact2; + z_sv(scMask) = -1+(iRing-1).^2/fact2; + iPhi_Mod = mod(iPhi-1,iRing); % in {0..iRing-1} + iPhi_Rat = fix((iPhi-1)./iRing); % in {0..3} + phi_nv(scMask) = (iPhi_Rat+(iPhi_Mod+1)./(iRing+1))*pi/2; + ndx = iRing > 1; + phi_sv_m = phi_sv(scMask); + phi_sv_m(ndx) = (iPhi_Rat(ndx)+iPhi_Mod(ndx)./(iRing(ndx)-1))*pi/2; + phi_sv(scMask) = phi_sv_m; + end +end + +sth = sqrt(1-z).*sqrt(1+z); + +%% Vertices +if (do_vertex) + v = zeros(horzcat([3,4],size(hPix))); + + % West vertex + phi_wv = phi - hDelta_Phi; + v(1,2,:) = sth(:).*cos(phi_wv(:)); + v(2,2,:) = sth(:).*sin(phi_wv(:)); + v(3,2,:) = z(:); + + % East vertex + phi_ev = phi + hDelta_Phi; + v(1,4,:) = sth(:).*cos(phi_ev(:)); + v(2,4,:) = sth(:).*sin(phi_ev(:)); + v(3,4,:) = z(:); + + % North vertex + sth_nv = sqrt(1-z_nv).*sqrt(1+z_nv); + v(1,1,:) = sth_nv(:).*cos(phi_nv(:)); + v(2,1,:) = sth_nv(:).*sin(phi_nv(:)); + v(3,1,:) = z_nv(:); + + % South vertex + sth_sv = sqrt(1-z_sv).*sqrt(1+z_sv); + v(1,3,:) = sth_sv(:).*cos(phi_sv(:)); + v(2,3,:) = sth_sv(:).*sin(phi_sv(:)); + v(3,3,:) = z_sv(:); + + varargout{2} = v; +end + +%% Pixel centers +sth = reshape(sth,[],1); +phi = reshape(phi,[],1); +vector = zeros(horzcat(3,size(hPix))); +vector(1,:) = sth.*cos(phi); +vector(2,:) = sth.*sin(phi); +vector(3,:) = z(:); + +varargout{1} = vector; + +return Index: /issm/trunk/externalpackages/mealpix/src/private/f_ring2nest.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/f_ring2nest.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/f_ring2nest.m (revision 25836) @@ -0,0 +1,135 @@ +function ipnest = f_ring2nest(nside, ipring) + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +% $Id: f_ring2nest.m 6224 2011-08-22 18:49:47Z lsf@GRAVITY.PSU.EDU $ + +npix = nSide2nPix(nside); +assert(all(ipring>=0) && all(ipring mifm); +mface(smask) = fix(mifp(smask)+7); % (half-)faces 8 to 11 + +face_num(mask) = mface; +irn(mask) = mirn; +iphi(mask) = miphi; + +%% south polar cap +mask = ipring >= (npix - ncap); +mRing = ipring(mask); + +mip = fix(npix - mRing); +% counted from South pole +mirs = round(sqrt(mip/2)); +miphi = 2*mirs.*(mirs + 1) - mip; +[mirs, miphi] = correct_ring_phi(1, mirs, miphi); +kshift(mask) = 0; +nr(mask) = fix(mirs); +irn(mask) = fix(nl4 - mirs); +face_num(mask) = fix(miphi./mirs) + 8; +iphi(mask) = miphi; + +%% finds the (x,y) on the face +irt = irn - jrll(face_num+1)*nside + 1; % in {-nside+1,0} +ipt = 2*iphi - jpll(face_num+1).*nr - kshift + 1; % in {-nside+1,nside-1} + +mask = ipt >= nl2; % for the face #4 +ipt(mask) = ipt(mask) - 8*nside; + +ix = fix((ipt - irt )/2); +iy = -fix((ipt + irt )/2); + +scalemlv = 1; +scale_factor = 16384; +ipf = 0; +% for nside in [2^14, 2^20] +ismax = 1; +if (nside > 1048576) + ismax = 3; +end; +for i = 0:ismax + % last 7 bits + ix_low = mod(ix, 128); + iy_low = mod(iy, 128); + + ipf = fix(ipf +(x2pix(ix_low+1)+y2pix(iy_low+1))*scalemlv); + scalemlv = scalemlv*scale_factor; + % truncate out last 7 bits + ix = fix(ix/128); + iy = fix(iy/128); +end +ipf = fix(ipf +(x2pix(ix+1)+y2pix(iy+1))*scalemlv); + +% in {0, 12*nside**2 - 1} +ipnest = fix(ipf + (face_num.*(fix(npix/12)))); +return Index: /issm/trunk/externalpackages/mealpix/src/private/f_surface_triangle.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/f_surface_triangle.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/f_surface_triangle.m (revision 25836) @@ -0,0 +1,56 @@ +function surface = f_surface_triangle(vec1, vec2, vec3) + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +% $Id: f_surface_triangle.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% use pix_tools +%======================================================================= +% returns the surface in steradians +% of the spherical triangle with vertices vec1, vec2, vec3 +% +% algorithm : finds triangle sides and uses l'Huilier formula to compute +% 'spherical excess' = surface area of triangle on a sphere of radius one +% see, eg Bronshtein, Semendyayev Eq 2.86 +%======================================================================= +% real(kind=dp), dimension(1:3) :: v1, v2, v3 +% persistent side x0 x1 x2 x3 ; +% +% if isempty(side), side=zeros(1,3); end; +% % real(kind=dp) :: hp +% if isempty(x0), x0=0; end; +% if isempty(x1), x1=0; end; +% if isempty(x2), x2=0; end; +% if isempty(x3), x3=0; end; +%======================================================================= +% half perimeter +% hp = 0.5 * (side1 + side2 + side3) +% ! l'Huilier formula +% x0 = tan( hp * 0.5) +% x1 = tan((hp - side1) * 0.5) +% x2 = tan((hp - side2) * 0.5) +% x3 = tan((hp - side3) * 0.5) +% find triangle sides +side(1)=f_angdist(vec2, vec3); +side(2)=f_angdist(vec3, vec1); +side(3)=f_angdist(vec1, vec2); +% divide by 4 +side([1:3]) = side([1:3]) .* 0.25; +% l'Huilier formula +x0 = tan( side(1) + side(2) + side(3) ); +x1 = tan(-side(1) + side(2) + side(3) ); +x2 = tan( side(1) - side(2) + side(3) ); +x3 = tan( side(1) + side(2) - side(3) ); +surface = 4.0 .* atan( sqrt(x0 .* x1 .* x2 .* x3) ); + +return Index: /issm/trunk/externalpackages/mealpix/src/private/mk_pix2xy.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/mk_pix2xy.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/mk_pix2xy.m (revision 25836) @@ -0,0 +1,55 @@ +function [pix2x,pix2y] = mk_pix2xy + +%======================================================================= +% constructs the array giving x and y in the face from pixel number for the +% nested (quad-cube like) ordering of pixels +% +% the bits corresponding to x and y are interleaved in the pixel number one +% breaks up the pixel number by even and odd bits +%======================================================================= + +% $Id: mk_pix2xy.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +pix2x=zeros(1024,1); +pix2y=zeros(1024,1); +for kpix=0:1023 + jpix = kpix; + ix = 0; + iy = 0; + % bit position (in x and y) + ip = 1; + while (1); + % go through all the bits + if(jpix == 0) + break + end + % bit value (in kpix), goes in ix + id = mod(jpix,2); + jpix = fix(jpix/2); + ix = id.*ip+ix; + % bit value (in kpix), goes in iy + id = mod(jpix,2); + jpix = fix(jpix/2); + iy = id.*ip+iy; + % next bit (in x and y) + ip = 2*ip; + end + % in 0,31 + pix2x(kpix+1) = ix; + % in 0,31 + pix2y(kpix+1) = iy; +end + +return Index: /issm/trunk/externalpackages/mealpix/src/private/mk_xy2pix.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/mk_xy2pix.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/mk_xy2pix.m (revision 25836) @@ -0,0 +1,48 @@ +function [x2pix y2pix]=mk_xy2pix +%======================================================================= +% sets the array giving the number of the pixel lying in (x,y) +% x and y are in {1,128} +% the pixel number is in {0,128**2-1} +% +% if i-1 = sum_p=0 b_p * 2^p +% then ix = sum_p=0 b_p * 4^p +% iy = 2*ix +% ix + iy in {0, 128**2 -1} +%======================================================================= + +% $Id: mk_xy2pix.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%for converting x,y into pixel numbers +x2pix=zeros(128,1); +y2pix=zeros(128,1); +for i = 1:128; + j = (i-1); + k = 0; + ip = 1; + while (1); + if(j==0) + x2pix(i) = k; + y2pix(i) = 2*k; + break; + else + id = mod(j,2); + j = fix(j/2); + k = ip*id+k; + ip = 4*ip; + end + end +end +return Index: /issm/trunk/externalpackages/mealpix/src/private/qALM.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/qALM.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/qALM.m (revision 25836) @@ -0,0 +1,27 @@ +function tf = qALM(alm) +% QALM validate alm +% +% alm is a numeric vector and numel(alm) = k^2 for some +% postive integer k +% +% Required by alm2spec, alm2pix +% Author: Lee Samuel Finn +% Copyright 2010-2011 + +% $Id: qALM.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +tf = isnumeric(alm) && sqrt(numel(alm))^2 == numel(alm); + +return Index: /issm/trunk/externalpackages/mealpix/src/private/qLMax.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/qLMax.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/qLMax.m (revision 25836) @@ -0,0 +1,14 @@ +function tf = qLMax(lMax) +% QLMAX validate lMax +% +% lMax is a non-negative integer-valued scalar +% +% Required by alm2spec, alm2pix +% Author: Lee Samuel Finn +% Copyright 2010 + +% $Id: qLMax.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +tf = isnumeric(lMax) && isscalar(lMax) && floor(lMax) == abs(lMax); + +return Index: /issm/trunk/externalpackages/mealpix/src/private/qNSide.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/qNSide.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/qNSide.m (revision 25836) @@ -0,0 +1,27 @@ +function tf = qNSide(nSide) +% QNSIDE validate nSide +% +% tf = qNSide(nSide) +% +% returns true if nSide is a numeric scalar non-negative integer-valued +% power of 2 + +% $Id: qNSide.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +tf = isnumeric(nSide) && isscalar(nSide) && 2^floor(log2(nSide)) == nSide; + +return + Index: /issm/trunk/externalpackages/mealpix/src/private/qPix.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/qPix.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/qPix.m (revision 25836) @@ -0,0 +1,23 @@ +function tf = qPix(pix) +% QPIX validate list of pixel values +% +% pix is a numeric vector with length 12*k^2 for integer k + +% $Id: qPix.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +tf = isnumeric(pix) && numel(pix) == max(size(pix)); +tf = tf && floor(sqrt(numel(pix)/12))^2*12 == numel(pix); + +return Index: /issm/trunk/externalpackages/mealpix/src/private/ringNum.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/private/ringNum.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/private/ringNum.m (revision 25836) @@ -0,0 +1,60 @@ +function nRing = ringNum(nSide, z, varargin) +%% RINGNUM Find ring number for given z coordinate +% +% ring = ringNum(nSide, z, shift) +% +% nSide HEALPix resolution parameter (integer power 2) +% z numeric array of z coordinates on unit sphere +% shift (optional) ring number "rounding" mode +% shift = 0: return ring number whose center is closest to z +% shift < 0: return ring number immediately north of closest ring +% shift > 0: return ring number immediately south of closest ring +% +% nRing size(z) numeric array of ring numbers +% +% Author: Lee Samuel Finn +% Copyright: 2011 + +% $Id: ringNum.m 5792 2011-02-20 03:21:25Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% Parse and validate input +p = inputParser; +p.addRequired('nSide',@qNSide); +p.addRequired('z',@(x)(all(abs(x(:))<=1))); +p.addOptional('shift',0,@isnumeric); +p.parse(nSide,z,varargin{:}); +shift = p.Results.shift/2; + +%% preallocate +nRing = zeros(size(z)); + +%% equatorial regime +mask = abs(z) <= 2/3; +nRing(mask) = round(nSide*(2-1.5*z(mask)) + shift); + +%% north polar cap +mask = z > 2/3; +nTmp = round(nSide*sqrt(3*(1-z(mask))) + shift); +nTmp(0 == nTmp) = 1; +nRing(mask) = nTmp; + +%% south polar cap +mask = z < -2/3; +nTmp = round(nSide*sqrt(3*(1+z(mask))) - shift); % Yes: this is a -shift +nTmp(0 == nTmp) = 1; +nRing(mask) = 4*nSide - nTmp; + +return Index: /issm/trunk/externalpackages/mealpix/src/queryDisc.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/queryDisc.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/queryDisc.m (revision 25836) @@ -0,0 +1,86 @@ +function pix = queryDisc( nSide, c0, r0, varargin ) +% QUERYDISC Find all pixels whose centers are within a specified disc +% +% +% pix = queryDisc(nSide,c0,r,'Param1',Value1,...) +% +% nSide +% c0 disc center. May be specified as a pixel number, anuglar +% position vector [theta, phi] in rads, or as a cartesian unit +% vector [x;y;z]. +% r disc radius (rads) +% +% Param Value +% 'nest' pixel indexing is nested (true | {false}) +% +% pix list of pixels in disc +% +% Example +% nSide=8; +% pix = queryDisc(nSide,1,pi/10,'nest'); +% numel(pix) +% nSide2nPix(nSide)*((pi/10)/(4 Pi)) +% +% See also queryPolygon, queryStrip, queryTriangle +% +% Requires pix2vec, ang2vec, angDist +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: queryDisc.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% validate and parse arguments +p = inputParser; +p.addRequired('nSide',@qNSide); +p.addRequired('c0',@(x)(isnumeric(x) && any(numel(x) == 1:3))); +p.addRequired('r0',@(x)(isnumeric(x) && isscalar(x) && x > 0 && x <= pi)); +p.addParamValue('nest',false,@(n)(isscalar(n) && islogical(n))); +p.parse(nSide,c0,r0,varargin{:}); +nest = p.Results.nest; + +%% Setup vIn +switch numel(c0) + case 1 %pix + vc = cell2mat(pix2vec(nSide,c0,'nest',nest)); + case 2 %ang + vc = cell2mat(ang2vec(c0)); + case 3 %vec + vc = c0/norm(c0); +end + +%% Computation +% Find max, min z of disk +% Find corresponding ring numbers +% Find pixels in rings +% Select pixels within ring + +th = acos(vc(3)); +zMax = cos(max(th-r0,0)); +zMin = cos(min(th+r0,pi)); + +ringMin = z2ring(nSide,zMax); +ringMax = z2ring(nSide,zMin); + +rings = min(ringMin,ringMax):max(ringMin,ringMax); +pix = arrayfun(@(r)(cell2mat(inRing(nSide,r))),rings,'UniformOutput',false); +pix = cell2mat(pix); + +d = angDist(pix,{vc},'nSide',nSide); +pix = pix(d < r0); % closer than r0 +if nest + pix = ring2nest(nSide,pix); +end +return Index: /issm/trunk/externalpackages/mealpix/src/res2nSide.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/res2nSide.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/res2nSide.m (revision 25836) @@ -0,0 +1,35 @@ +function nSide = res2nSide(r) +% RES2NSIDE Finds minimum base pixel sub-division for required resolution +% +% nSide = res2nSide(r) +% +% r angular resolution (arc seconds) +% +% nSide minimum base pixel sub-divisions corresponding to resolution r +% +% See also nSide2res +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: res2nSide.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +nPix0 = 4*pi./(r*pi/(180*3600)).^2; +nSide0 = realsqrt(nPix0/12); +nSide = pow2(ceil(log2(nSide0)-2*eps)); +nSide(nSide<1) = 1; + +return Index: /issm/trunk/externalpackages/mealpix/src/ring2nest.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/ring2nest.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/ring2nest.m (revision 25836) @@ -0,0 +1,51 @@ +function nPix = ring2nest(nSide,rPix) +% RING2NEST Convert MEALPix pixel numbers from ring to nest indexing +% +% nPix = ring2nest(nSide,rPix) +% +% +% nSide HEALPix resolution parameter +% rPix ring indexed MEALPix pixel numbers +% +% nPix next indexed MEALPix pixel numbers +% +% See also nest2ring +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: ring2nest.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% Parse and validate input +error(nargchk(1,2,nargin,'struct')); +if ~qNSide(nSide) + msgid = [mfilename ':nSide']; + error(msgid,msgid); +end +if isempty(rPix) + rPix = 1:(12*nSide^2); +elseif any(fix(abs(rPix(:))) ~= rPix(:)) || any(rPix(:)<1) + msgid = [mfilename ':rPix']; + error(msgid,msgid); +end + +% Convert +sz = size(rPix); +rPix = rPix - 1; +nPix = f_ring2nest(nSide,reshape(rPix,[],1)); +nPix = reshape(nPix+1,sz); + +return Index: /issm/trunk/externalpackages/mealpix/src/ring2z.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/ring2z.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/ring2z.m (revision 25836) @@ -0,0 +1,69 @@ +function z = ring2z(nSide,nRing) +% RING2Z Find HEALPix ring number corresponding to a given z coordinate +% +% z = ring2z(nSide,nRing) +% +% nSide HEALPix base-pixel sub-divisions +% nRing numeric array of ring numbers +% +% z size(nRing) numeric array of pixel center z coordinates +% +% Example +% z = ring2z(4,reshape(1:15,3,5)); +% +% See also z2ring +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: ring2z.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% Parse and validate input +p = inputParser; +p.addRequired('nSide',@qNSide); +p.addRequired('nRing',@(n)(qNRing(nSide,nRing))); +p.parse(nSide,nRing); + +%% pre-allocate result +z = zeros(size(nRing)); + +%% north polar cap +mask = nRing < nSide; +z(mask) = 1 - nRing(mask).^2/(3*nSide^2); + +%% tropical band +mask = ~mask & nRing < 3*nSide; +z(mask) = (2*nSide-nRing(mask))*2/(3*nSide); + +%% south polar cap +mask = nRing >= 3*nSide; +z(mask) = -1 + (4*nSide-nRing(mask)).^2/(3*nSide^2); + +return + +function tf = qNRing(nSide,nRing) +% QNRING true if valid ring number + +tf = isnumeric(nRing); +if tf + nRing = nRing(:); + tf = ... + all(nRing == fix(abs(nRing))) && ... + all(nRing > 0) && ... + all(nRing < 4*nSide); +end + +return Index: /issm/trunk/externalpackages/mealpix/src/vec2ang.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/vec2ang.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/vec2ang.m (revision 25836) @@ -0,0 +1,54 @@ +function tp = vec2ang(xyz) +% VEC2ANG Convert cartesian direction vector to position angle on sphere +% +% tp = vec2ang(xyz) +% +% xyz cell array of [3,1] cartesian coordinate direction vectors +% +% The direction vectors need not be normalized. +% +% tp cell array of [2,1] position angles ([theta; phi], radians) on +% sphere +% +% See also ang2vec +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: vec2ang.m 5831 2011-02-25 23:55:19Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +if ~iscell(xyz) + msgid = [mfilename ':xyz']; + error(msgid,msgid); +end +tp = cellfun(@v2a,xyz,'UniformOutput',false); + +return + +function tp = v2a(xyz) +% dVec2Ang un-nomralized cartesian vector to position angle on sphere +% +% tp = v2a(xyz) +% +% xyz [3,1] +% +% tp [2,1] of [theta, phi] + +assert(numel(xyz)==3,[mfilename ':v2a'],[mfilename 'v2a']); +xyz = xyz/norm(xyz); +tp = [acos(xyz(3)); atan2(xyz(2),xyz(1))]; + +return Index: /issm/trunk/externalpackages/mealpix/src/vec2pix.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/vec2pix.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/vec2pix.m (revision 25836) @@ -0,0 +1,147 @@ +function nPix = vec2pix(nSide,xyz,varargin) +% VEC2PIX Convert cartesian direction vectors to MEALPix pixel numbers +% +% nPix = vec2pix(nSide,xyz,'Param1',Value1,...); +% +% nSide HEALPix resolution parameter +% xyz cell array of [3,1] cartesian direction vectors +% +% Param Value +% 'nest' use nested indexing (true | {false}) +% +% nPix size(xyz) pixel number array +% +% Example +% xyz = {[1;0;0],[0;1;0],[0;0;1]}; +% nPix = vec2pix(4,xyz); +% +% See also ang2pix, pix2ang, pix2vec +% +% Requires ring2nest +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: vec2pix.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + + +%% Validate and parse input +p = inputParser; + +p.addRequired('nSide', ... + @(x)(isscalar(x) && isnumeric(x) && x>0 && nextpow2(x) == log2(x))); +p.addRequired('xyz',@iscell); +p.addParamValue('nest',false,@(n)(isscalar(n) && islogical(n))); + +p.parse(nSide,xyz,varargin{:}); +nest = p.Results.nest; + +%% Convert vector(s) to pixel numbers +% Process xyz as a vector then restore shape + +% Save xyz shape +sXyz = size(xyz); + +% Insure cell vectors are [3,1] +xyz = cellfun(@(v)(reshape(v,[],1)),xyz,'UniformOutput',false); + +% Re-express xyz as a column vector +xyz = cell2mat(reshape(xyz,1,[])); + +% Find pixels +nPix = f_vec2pix_ring(nSide,xyz(1,:),xyz(2,:),xyz(3,:)); +nPix = nPix + 1; +if nest + nPix = ring2nest(nSide,nPix); +end + +% Restore shape +nPix = reshape(nPix,sXyz); + +return + +function iPix = f_vec2pix_ring(nSide, x, y, zin) + +%======================================================================= +% renders the pixel number iPix (RING scheme) for a pixel containing +% a point on a sphere at coordinate vector (=x,y,z), given the map +% resolution parameter nside +%======================================================================= + +dnorm = arrayfun(@(x,y,z)(norm([x,y,z])),x,y,zin); +z = zin./dnorm; + +phi = atan2(y,x); +za = abs(z); +% phi(phi < 0.0) = phi(phi < 0.0) + 2*pi; +phi = mod(phi,2*pi); +tt = phi/(pi/2); +nl4 = fix(4*nSide); + +%% preallocate result +iPix = zeros(size(x)); + +%% Equatorial region +% Identify pixels +pixMask = 3*za <= 2; +if ~isempty(pixMask) + ttPix = tt(pixMask); + zPix = z(pixMask); + + temp1 = nSide*(ttPix + 0.5); + temp2 = nSide*zPix*0.75; + + % find ascending, descending line indices + jp = fix(temp1-temp2); + jm = fix(temp1+temp2); + + ir = fix(nSide+jp-jm); + kShift = fix(bitand(ir,1)); + ip = fix((jp+jm-nSide+kShift+1)/2); + ip(ip>=nl4) = fix(ip(ip>=nl4)-nl4); % can this be replaced by a mod? + iPix(pixMask) = fix(2*nSide*(nSide-1) + nl4*fix(ir) + ip); +end +%% North, south polar cap +% Identify pixels +pixMask = ~pixMask; +if ~isempty(pixMask) + ttPix = tt(pixMask); + tp = ttPix - fix(ttPix); + tmp = nSide*sqrt(3*(1-za(pixMask))); + + % find increasing, decreasing edge line indices + jp = fix(tp.*tmp); + jm = fix((1-tp).*tmp); + + % ring number counted from the closest pole + ir = fix(jp+jm+1); + ip = fix(ttPix.*ir); + tMask = ip>=4*ir; + ip(tMask) = fix(ip(tMask)-4*ir(tMask)); + + % north pole pixels + nPixMask = pixMask & z > 0; + tMask = z(pixMask) > 0; + iPix(nPixMask) = fix(2*ir(tMask).*(ir(tMask)-1) + ip(tMask)); + + % south pole pixels + sPixMask = pixMask & z <= 0; + tMask = ~tMask; + iPix(sPixMask) = fix(... + 3*nSide*fix(nl4) - 2*ir(tMask).*(ir(tMask)+1)+ip(tMask)... + ); +end + +return Index: /issm/trunk/externalpackages/mealpix/src/xy2pix.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/xy2pix.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/xy2pix.m (revision 25836) @@ -0,0 +1,72 @@ +function ipix = xy2pix(nSide,ix,iy,nFace) +% XY2PIX gives the pixel number ipix (NESTED) of ix, iy and face_num +% +% ipix = xy2pix(nSide, ix, iy, nFace) +% +% nside HEALPix resolution parameter (power of 2) +% ix,iy x,y location on the Healpix face (1 <= ix, iy <= nSide) +% nFace HEALPix face number (1 <= nFace <= 12) +% +% ipix MEALPix NESTED pixel index for given x,y on the face +% +% See also pix2xy +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: xy2pix.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% Parse and validate arguments +p = inputParser; +p.KeepUnmatched = false; + +p.addRequired('nSide',@qNSide); +qNXY = @(n)(all(n(:)>0) && all(n(:)<=nSide)); +p.addRequired('ix',qNXY); +p.addRequired('iy',qNXY); +p.addRequired('nFace',... + @(n)(isscalar(n) && isnumeric(n) && ... + n == fix(n) && 0 < n && n <= 12)); +p.parse(nSide,ix,iy,nFace); + +%% Initialization +[x2pix y2pix]=mk_xy2pix; + +%% Convert to HEALPix indexing +ix = ix - 1; +iy = iy - 1; + +scale = 1; +scaleFactor = 16384; +ipf = 0; +ismax = 1; +if nSide > 1048576 + ismax = 3; +end +for k = 1:ismax + ix_low = mod(ix,128); + iy_low = mod(iy,128); + ipf = ipf + (x2pix(ix_low+1) + y2pix(iy_low+1))*scale; + scale = scale*scaleFactor; + ix = fix(ix/128); + iy = fix(iy/128); +end +ipf = ipf + (x2pix(ix+1) + y2pix(iy+1))*scale; + +ipix = ipf + nFace*nSide^2; + +ipix = ipix+1; % MEALPix numbering + +return Index: /issm/trunk/externalpackages/mealpix/src/ylm.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/ylm.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/ylm.m (revision 25836) @@ -0,0 +1,109 @@ +function v = ylm(nSide,L,M,varargin) +% YLM returns spherical harmonic basis Y_L^M on the HEALPix sphere +% +% v = ylm(nSide,L,M,'Param1',Value1,'Param2',Value2,...); +% +% nSide HEALPix resolution parameter (power of 2) +% L spherical harmonic degree (0 <= L) +% M spherical harmonic order (-M <= L <= M) +% +% Param Value +% 'real' return real values (true | {false}) +% 'nest' nested indexing flag (true | {false}) +% +% v spherical harmonics evaluated at pixel centers +% +% Example: +% +% % Plot Ylm for (L,M) = (4,2) on nSide = 16 HEALPix sphere +% pix = ylm(16,4,2); +% hp3d(pix); +% +% Requires pix2ang +% Required by alm2pix, pix2alm +% See also hp3d +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: ylm.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% Parse and validate input +p = inputParser; +p.KeepUnmatched = false; +p.FunctionName = mfilename; + +p.addRequired('nSide',@qNSide); +p.addRequired('L',@(x)(isnumeric(x) && round(x) == x && 0 <= x)); +p.addRequired('M',@(x)(isnumeric(x) && round(x) == x)); +p.addParamValue('real',false,@(x)(isscalar(x) && islogical(x))); +p.addParamValue('nest',false,@(x)(isscalar(x) && islogical(x))); + +p.parse(nSide,L,M,varargin{:}); +nSide = p.Results.nSide; +L = p.Results.L; +M = p.Results.M; +real = p.Results.real; +nest = p.Results.nest; + +% Check m is in range +assert(abs(M)<=L,[mfilename ':M'],[mfilename ':M']); + +% Setup HEALPix pixels to solve on +tp = pix2ang(nSide,'nest',nest); + +% Evaluate for positive M, using symmetry to find value for negative M +signM = sign(M); +M = abs(M); + +% Exploit HEALPix rings for legendre function calc +th = cellfun(@(tp)(tp(1)),tp); +[b, ~, n] = unique(th); +ringLmn = legendre(L,cos(b)); +if L~=0 + ringLmn = squeeze(ringLmn(M+1,:,:)); +end +Lmn = ringLmn(n); + +% Calculate normalization constant +%a1 = (2*L+1); % 4pi normalization +a1 = (2*L+1)/(4*pi); % orthonormalization (default) + +% a2 = factorial(L-M)/factorial(L+M); +a2 = 1/prod((L-M+1):(L+M)); + +C = sqrt(a1*a2); + +% Calculate complex Ymn +phi = cellfun(@(x)(x(2)),tp); +Ymn = C*Lmn.*exp(1i*M*phi); + +% Use symmetry to find value for negative M +if 0 > signM + Ymn = (-1)^M*conj(Ymn); +end + +% Set v +v = Ymn; + +% Convert to real form if true == real +if real && 0 ~= M + if 0 < signM + v = (Ymn+conj(Ymn))/sqrt(2); + else % 0 > signM + v = (-1)^M*(conj(Ymn)-Ymn)/sqrt(-2); + end +end + +return Index: /issm/trunk/externalpackages/mealpix/src/z2ring.m =================================================================== --- /issm/trunk/externalpackages/mealpix/src/z2ring.m (revision 25836) +++ /issm/trunk/externalpackages/mealpix/src/z2ring.m (revision 25836) @@ -0,0 +1,55 @@ +function nRing = z2ring(nSide,z) +%% Z2RING Find HEALPix ring numbers from direction vector z coordinate +% +% nRing = z2ring(nSide,z) +% +% nSide HEALPix resolution parameter +% z numeric array of z values +% +% nRing size(z) numeric array of ring numbers +% +% Description +% HEALPix pixels centers are arranged in 4*nSide-1 rings of constant z. +% Each ring spans a given range of z. z2ring returns the ring numbers that +% cover the input z values. +% +% Example: +% nRing = reshape(1:15,3,5); +% z = ring2z(4,nRing); +% +% See also ring2z +% +% Authors: Lee Samuel Finn, Matthew Kinsey +% Copyright 2010-2011 Lee Samuel Finn + +% $Id: z2ring.m 5795 2011-02-20 04:01:32Z lsf@GRAVITY.PSU.EDU $ + +% Copyright 2010-2011 by Lee Samuel Finn. +% This program file is part of MEALPix. It is licensed under the Apache +% License, Version 2.0 (the "License"); you may not use MEALPix except in +% compliance with the License. You may obtain a copy of the License at +% +% +% Unless required by applicable law or agreed to in writing, MEALPix +% software distributed under the License is distributed on an "AS IS" +% BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +% implied. See the License for the specific language governing permissions +% and limitations under the License. + +%% Parse and validate input +p = inputParser; +p.FunctionName = mfilename; +p.addRequired('nSide',@qNSide); +p.addRequired('z',@(x)(all(abs(x(:))<=1))); +p.parse(nSide,z); + +%% Work +% Save input size +% Flatten input +% Find ring numbers +% Reshape ring numbers to reflect input + +zSz = size(z); +nRing = reshape(ringNum(nSide, z(:)),zSz); + +return Index: /issm/trunk/externalpackages/netcdf-python/install.sh =================================================================== --- /issm/trunk/externalpackages/netcdf-python/install.sh (revision 25835) +++ /issm/trunk/externalpackages/netcdf-python/install.sh (revision 25836) @@ -2,29 +2,42 @@ set -eu -#Some cleanup -rm -rf install netCDF4-1.0 -mkdir install -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/netCDF4-1.0.tar.gz" "netCDF4-1.0.tar.gz" +# Constants +# +VER="1.5.3" -#Untar -tar -zxvf netCDF4-1.0.tar.gz +# Environment +# +export HDF5_DIR="${ISSM_DIR}/externalpackages/petsc/install" +export MPIINC_DIR="${ISSM_DIR}/externalpackages/petsc/install/include" +export NETCDF_DIR="${ISSM_DIR}/externalpackages/netcdf/install" +export PYTHONUSERBASE="${ISSM_DIR}/externalpackages/netcdf-python/install" # This variable and '--user' option supplied to 'setup.py install' are required to install to custom location (source: https://setuptools.readthedocs.io/en/latest/easy_install.html#custom-installation-locations) -#for later: -rm -rf ISSMDIR -echo $ISSM_DIR | sed 's/\//\\\//g' > ISSMDIR -ISSMDIR=`cat ISSMDIR` && rm -rf ISSMDIR +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/netcdf4-python-${VER}rel.tar.gz" "netcdf4-python-${VER}rel.tar.gz" -#Move netCDF4 to install directory -rm -rf install/* -mv netCDF4-1.0/* install/ -rm -rf netCDF4-1.0 +# Unpack source +tar -zxvf netcdf4-python-${VER}rel.tar.gz -#Configur and compile -cd install -#edit setup.cfg to point to hdf5 and netcdf -cat setup.cfg.template | sed "s/\#netCDF4_dir = \/usr\/local/netCDF4_dir = $ISSMDIR\/externalpackages\/netcdf\/install/g" | sed "s/\#HDF5_dir = \/usr\/local/HDF5_DIR = $ISSMDIR\/externalpackages\/hdf5\/install/g" > setup.cfg +# Cleanup +rm -rf install src +mkdir install src -python setup.py build -python setup.py install +# Move source to 'src' directory +mv netcdf4-python-${VER}rel/* src/ +rm -rf netcdf4-python-${VER}rel + +# Compile and install +cd src +python setup.py build +python setup.py install --user + +# Unzip eggs +for egg in $(find "${PYTHONUSERBASE}/lib" -name *.egg); do + parent_dir=$(dirname ${egg}) + filename=$(basename -- ${egg}) + extension="${filename##*.}" + filename="${filename%.*}" + src_dir="${parent_dir}/${filename}" + unzip ${egg} -d ${src_dir} +done Index: /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh (revision 25836) +++ /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh (revision 25836) @@ -0,0 +1,76 @@ +#!/bin/bash +set -eu + + +# Dependencies +# - MPI implementation (for parallel I/O support) +# - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support) +# - zlib (1.2.5 or later, for netCDF-4 compression) +# - curl (7.18.0 or later, for DAP remote access client support) +# +# For most ISSM installations, only hdf5 will be necessary +# +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# + +# NOTE: +# - Certain configuration tests fail if libraries are not supplied explicitly + +# Constants +# +VER="4.7.2" + +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +# Environment +# +export CC=mpicc +export CPPFLAGS="-I${ZLIB_ROOT}/include" + +export HDF5LIB="${HDF5_ROOT}/lib/libhdf5_hl.a ${HDF5_ROOT}/lib/libhdf5.a" +export ZLIB="${ZLIB_ROOT}/lib/libz.a" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/netcdf-c-${VER}.tar.gz" "netcdf-c-${VER}.tar.gz" + +# Unpack source +tar -zxvf netcdf-c-$VER.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv netcdf-c-$VER/* src/ +rm -rf netcdf-c-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-shared \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-doxygen \ + --enable-netcdf4 \ + --disable-dap \ + --disable-examples \ + --disable-filter-testing \ + --disable-dap-remote-tests \ + --enable-parallel-tests + +# Compile and install +if [ $# -eq 0 ]; then + make + make check + make install +else + make -j $1 + make -j $1 check + make -j $1 install +fi + +# Return to initial directory +cd .. Index: /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 25836) +++ /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 25836) @@ -0,0 +1,73 @@ +#!/bin/bash +set -eu + + +# Dependencies +# - MPI implementation (for parallel I/O support) +# - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support) +# - zlib (1.2.5 or later, for netCDF-4 compression) +# - curl (7.18.0 or later, for DAP remote access client support) +# +# For most ISSM installations, only hdf5 will be necessary +# +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# + +# NOTE: +# - Certain configuration tests fail if libraries are not supplied explicitly + +# Constants +# +VER="4.7.2" + +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +# Environment +# +export CC=mpicc +export CPPFLAGS="-I${ZLIB_ROOT}/include" + +export HDF5LIB="${HDF5_ROOT}/lib/libhdf5_hl.a ${HDF5_ROOT}/lib/libhdf5.a" +export ZLIB="${ZLIB_ROOT}/lib/libz.a" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/netcdf-c-${VER}.tar.gz" "netcdf-c-${VER}.tar.gz" + +# Unpack source +tar -zxvf netcdf-c-$VER.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv netcdf-c-$VER/* src/ +rm -rf netcdf-c-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-shared \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-doxygen \ + --enable-netcdf4 \ + --disable-dap \ + --disable-testsets \ + --disable-examples \ + --disable-filter-testing + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Return to initial directory +cd .. Index: /issm/trunk/externalpackages/netcdf/install-4.7-parallel-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-parallel-with_tests.sh (revision 25835) +++ /issm/trunk/externalpackages/netcdf/install-4.7-parallel-with_tests.sh (revision 25836) @@ -11,17 +11,21 @@ # For most ISSM installations, only hdf5 will be necessary # +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# # Constants # VER="4.7.2" -HDF5_ROOT="${ISSM_DIR}/externalpackages/hdf5/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" + +CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" # Environment # export CC=mpicc -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/hdf5/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" +export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${CURL_ROOT}/lib -L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source @@ -42,7 +46,14 @@ cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ - --enable-parallel-tests \ - --disable-doxygen + --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-static \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-doxygen \ + --enable-netcdf4 \ + --disable-examples \ + --disable-filter-testing \ + --disable-dap-remote-tests \ + --enable-parallel-tests # Compile, test, and install Index: /issm/trunk/externalpackages/netcdf/install-4.7-parallel.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-parallel.sh (revision 25835) +++ /issm/trunk/externalpackages/netcdf/install-4.7-parallel.sh (revision 25836) @@ -11,17 +11,21 @@ # For most ISSM installations, only hdf5 will be necessary # +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# # Constants # VER="4.7.2" + CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/hdf5/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" # Environment # export CC=mpicc -export CPPFLAGS="-I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include -I${CURL_ROOT}/include" -export LDFLAGS="-L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib -L${CURL_ROOT}/lib" +export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${CURL_ROOT}/lib -L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source @@ -42,6 +46,13 @@ cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ - --disable-doxygen + --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-static \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-doxygen \ + --enable-netcdf4 \ + --disable-testsets \ + --disable-examples \ + --disable-filter-testing # Compile and install Index: /issm/trunk/externalpackages/netcdf/install-4.7-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-with_tests.sh (revision 25835) +++ /issm/trunk/externalpackages/netcdf/install-4.7-with_tests.sh (revision 25836) @@ -4,4 +4,5 @@ # Dependencies +# - MPI implementation (for parallel I/O support) # - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support) # - zlib (1.2.5 or later, for netCDF-4 compression) @@ -10,16 +11,20 @@ # For most ISSM installations, only hdf5 will be necessary # +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# # Constants # VER="4.7.2" + CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/hdf5/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" # Environment # -export CPPFLAGS="-I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include -I${CURL_ROOT}/include" -export LDFLAGS="-L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib -L${CURL_ROOT}/lib" +export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${CURL_ROOT}/lib -L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source @@ -40,6 +45,13 @@ cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ - --disable-doxygen + --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-static \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-doxygen \ + --enable-netcdf4 \ + --disable-filter-testing \ + --disable-examples \ + --disable-dap-remote-tests # Compile, test, and install Index: /issm/trunk/externalpackages/netcdf/install-4.7.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7.sh (revision 25835) +++ /issm/trunk/externalpackages/netcdf/install-4.7.sh (revision 25836) @@ -4,4 +4,5 @@ # Dependencies +# - MPI implementation (for parallel I/O support) # - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support) # - zlib (1.2.5 or later, for netCDF-4 compression) @@ -9,4 +10,7 @@ # # For most ISSM installations, only hdf5 will be necessary +# +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building # @@ -20,6 +24,6 @@ # Environment # -export CPPFLAGS="-I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include -I${CURL_ROOT}/include" -export LDFLAGS="-L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib -L${CURL_ROOT}/lib" +export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${CURL_ROOT}/lib -L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source @@ -40,6 +44,12 @@ cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ - --disable-doxygen + --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-static \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-doxygen \ + --disable-testsets \ + --disable-examples \ + --enable-netcdf4 # Compile and install Index: sm/trunk/externalpackages/netcdf/install.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install.sh (revision 25835) +++ (revision ) @@ -1,30 +1,0 @@ -#!/bin/bash -set -eu -#you need hdf5 compiled - -#Some cleanup -rm -rf src install netcdf-4.3.2 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/netcdf-4.3.2.tar.gz" "netcdf-4.3.2.tar.gz" - -#Untar -tar -zxvf netcdf-4.3.2.tar.gz - -#Move netcdf to install directory -rm -rf src/* -mv netcdf-4.3.2/* src/ -rm -rf netcdf-4.3.2 - -#Configure and compile -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/netcdf/install" \ - --disable-doxygen -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk/externalpackages/petsc/install-3.11-linux-solid_earth.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.11-linux-solid_earth.sh (revision 25835) +++ (revision ) @@ -1,44 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.11.3" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-${VER}/* src/ -rm -rf petsc-${VER} - -# Configure -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.11-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.11-linux-static.sh (revision 25835) +++ (revision ) @@ -1,52 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.11.3" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-${VER}/* src/ -rm -rf petsc-${VER} - -# Configure -# -# NOTE: Cannot use --with-fpic option when compiling static libs, -# -# Cannot determine compiler PIC flags if shared libraries is turned off -# Either run using --with-shared-libraries or --with-pic=0 and supply the -# compiler PIC flag via CFLAGS, CXXXFLAGS, and FCFLAGS -# -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-shared-libraries=0 \ - --CFLAGS="-fPIC" \ - --CXXFLAGS="-fPIC" \ - --FFLAGS="-fPIC" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.11-linux.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.11-linux.sh (revision 25835) +++ (revision ) @@ -1,42 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.11.3" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-${VER}/* src/ -rm -rf petsc-${VER} - -# Configure -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.11-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.11-mac-static.sh (revision 25835) +++ (revision ) @@ -1,52 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.11.3" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-${VER}/* src/ -rm -rf petsc-${VER} - -# Configure -# -# NOTE: Cannot use --with-fpic option when compiling static libs, -# -# Cannot determine compiler PIC flags if shared libraries is turned off -# Either run using --with-shared-libraries or --with-pic=0 and supply the -# compiler PIC flag via CFLAGS, CXXXFLAGS, and FCFLAGS -# -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-shared-libraries=0 \ - --CFLAGS="-fPIC" \ - --CXXFLAGS="-fPIC" \ - --FFLAGS="-fPIC" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.11-mac.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.11-mac.sh (revision 25835) +++ (revision ) @@ -1,42 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.11.3" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-${VER}/* src/ -rm -rf petsc-${VER} - -# Configure -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 - -# Compile and install -make -make install Index: /issm/trunk/externalpackages/petsc/install-3.12-linux-solid_earth-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-linux-solid_earth-static.sh (revision 25836) +++ /issm/trunk/externalpackages/petsc/install-3.12-linux-solid_earth-static.sh (revision 25836) @@ -0,0 +1,60 @@ +#!/bin/bash +set -eu + + +# NOTE: There is a single difference between the Linux and macOS +# configurations, which is the addition of the -static-libgfortran +# option to FFLAGS on the macOS static configurations. For the sake of +# consistency, we maintain separate files for each, respective Linux and +# macOS configuration. + +## Constants +# +VER="3.12.3" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv petsc-${VER}/* src/ +rm -rf petsc-${VER} + +# Configure +# +# NOTE: Cannot use --with-fpic option when compiling static libs, +# +# Cannot determine compiler PIC flags if shared libraries is turned off +# Either run using --with-shared-libraries or --with-pic=0 and supply the +# compiler PIC flag via CFLAGS, CXXXFLAGS, and FCFLAGS +# +cd src +./config/configure.py \ + --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ + --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --with-shared-libraries=0 \ + --CFLAGS="-fPIC" \ + --CXXFLAGS="-fPIC" \ + --FFLAGS="-fPIC" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 + +# Compile and install +make +make install Index: sm/trunk/externalpackages/petsc/install-3.12-linux-solid_earth.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-linux-solid_earth.sh (revision 25835) +++ (revision ) @@ -1,44 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.12.3" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-${VER}/* src/ -rm -rf petsc-${VER} - -# Configure -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 - -# Compile and install -make -make install Index: /issm/trunk/externalpackages/petsc/install-3.12-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-linux-static.sh (revision 25835) +++ /issm/trunk/externalpackages/petsc/install-3.12-linux-static.sh (revision 25836) @@ -2,4 +2,10 @@ set -eu + +# NOTE: There is a single difference between the Linux and macOS +# configurations, which is the addition of the -static-libgfortran +# option to FFLAGS on the macOS static configurations. For the sake of +# consistency, we maintain separate files for each, respective Linux and +# macOS configuration. ## Constants @@ -23,5 +29,6 @@ # Configure # -# NOTE: Cannot use --with-fpic option when compiling static libs, +# NOTE: +# - Cannot use --with-fpic option when compiling static libs, # # Cannot determine compiler PIC flags if shared libraries is turned off @@ -46,5 +53,7 @@ --download-parmetis=1 \ --download-scalapack=1 \ - --download-mumps=1 + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 # Compile and install Index: /issm/trunk/externalpackages/petsc/install-3.12-linux.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-linux.sh (revision 25835) +++ /issm/trunk/externalpackages/petsc/install-3.12-linux.sh (revision 25836) @@ -36,5 +36,8 @@ --download-parmetis=1 \ --download-scalapack=1 \ - --download-mumps=1 + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 + # Compile and install Index: /issm/trunk/externalpackages/petsc/install-3.12-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-mac-static.sh (revision 25835) +++ /issm/trunk/externalpackages/petsc/install-3.12-mac-static.sh (revision 25836) @@ -23,9 +23,21 @@ # Configure # -# NOTE: Cannot use --with-fpic option when compiling static libs, +# NOTE: +# - Cannot use --with-fpic option when compiling static libs, # # Cannot determine compiler PIC flags if shared libraries is turned off # Either run using --with-shared-libraries or --with-pic=0 and supply the # compiler PIC flag via CFLAGS, CXXXFLAGS, and FCFLAGS +# +# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. +# (may need to remove it for earlier versions not using the C99 standard). +# - Added -fallow-argument-mismatch to FFLAGS in order to clear, +# +# error: The Fortran compiler gfortran will not compile files that call +# the same routine with arguments of different types. +# +# for gfortran 10 or later (may need to remove it for earlier versions). +# - Added -static-libgfortran to all macOS static builds, but this will not +# work out of the box on Linux. # cd src @@ -34,7 +46,7 @@ --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ --with-shared-libraries=0 \ - --CFLAGS="-fPIC" \ + --CFLAGS="-fPIC -Wno-error=implicit-function-declaration" \ --CXXFLAGS="-fPIC" \ - --FFLAGS="-fPIC -static-libgfortran" \ + --FFLAGS="-fPIC -fallow-argument-mismatch -static-libgfortran" \ --with-debugging=0 \ --with-valgrind=0 \ @@ -46,5 +58,7 @@ --download-parmetis=1 \ --download-scalapack=1 \ - --download-mumps=1 + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 # Compile and install Index: /issm/trunk/externalpackages/petsc/install-3.12-mac.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-mac.sh (revision 25835) +++ /issm/trunk/externalpackages/petsc/install-3.12-mac.sh (revision 25836) @@ -22,8 +22,21 @@ # Configure +# +# NOTE: +# - Added -fallow-argument-mismatch to FFLAGS in order to clear, +# +# error: The Fortran compiler gfortran will not compile files that call +# the same routine with arguments of different types. +# +# for gfortran 10 or later (may need to remove it for earlier versions). +# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. +# (may need to remove it for earlier versions not using the C99 standard). +# cd src ./config/configure.py \ --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --CFLAGS="-Wno-error=implicit-function-declaration" \ + --FFLAGS="-fallow-argument-mismatch" \ --with-debugging=0 \ --with-valgrind=0 \ @@ -36,5 +49,7 @@ --download-parmetis=1 \ --download-scalapack=1 \ - --download-mumps=1 + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 # Compile and install Index: sm/trunk/externalpackages/petsc/install-3.12-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-pleiades.sh (revision 25835) +++ (revision ) @@ -1,63 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.12.3 src -mkdir install src - -#Download from ISSM server -#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.12.3.tar.gz' 'petsc-3.12.3.tar.gz' -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.12.3.tar.gz' 'petsc-3.12.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.12.3.tar.gz -mv petsc-3.12.3/* src/ -rm -rf petsc-3.12.3 - -#configure (based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables look for CONFIGURE_OPTIONS) -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort --with-gnu-compilers=0 --with-cpp=/usr/bin/cpp \ - --with-vendor-compilers=intel \ - -COPTFLAGS=-g -O3 -axCORE-AVX2,AVX -xSSE4.2 -CXXOPTFLAGS=-g -O3 -axCORE-AVX2,AVX -xSSE4.2 -FOPTFLAGS=-g -O3 -axCORE-AVX2,AVX -xSSE4.2 \ - --with-blas-lapack-dir=/nasa/intel/Compiler/2016.2.181/mkl/lib/intel64 \ - --with-scalapack-include=/nasa/intel/Compiler/2016.2.181/mkl/include \ - --with-scalapack-lib="/nasa/intel/Compiler/2016.2.181/mkl/lib/intel64/libmkl_scalapack_lp64.so /nasa/intel/Compiler/2016.2.181/mkl/lib/intel64/libmkl_blacs_sgimpt_lp64.so" \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 - -# --download-superlu_dist=yes \ -# --download-hypre=yes - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=bro -#PBS -l walltime=200 -#PBS -W group_list=s1690 -#PBS -m e - -. /usr/share/modules/init/bash -module load pkgsrc -module load comp-intel/2016.2.181 -module load mpi-sgi/mpt - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/trunk/externalpackages/petsc/install-3.13-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.13-pleiades.sh (revision 25836) +++ /issm/trunk/externalpackages/petsc/install-3.13-pleiades.sh (revision 25836) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.13.3 src +mkdir install src + +#Download from ISSM server +#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.13.3.tar.gz' 'petsc-3.13.3.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.13.3.tar.gz' 'petsc-3.13.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.13.3.tar.gz +mv petsc-3.13.3/* src/ +rm -rf petsc-3.13.3 + +#configure (based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables look for CONFIGURE_OPTIONS) +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort\ + -COPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" -CXXOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" -FOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/" \ + --known-mpi-shared-libraries=1 \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-batch=1 \ + --with-shared-libraries=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-mumps=1 \ + --download-scalapack=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.14-greenplanet.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-greenplanet.sh (revision 25836) +++ /issm/trunk/externalpackages/petsc/install-3.14-greenplanet.sh (revision 25836) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + +#WARNING: make sure you have the right mpi + +#Some cleanup +rm -rf install petsc-3.14.0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.14.0.tar.gz' 'petsc-3.14.0.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.14.0.tar.gz +mv petsc-3.14.0/* src/ +rm -rf petsc-3.14.0 + +#configure +cd src +./config/configure.py \ + COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-blas-lapack-dir="/sopt/INTEL/compilers_and_libraries_2018.3.222/linux/mkl/" \ + --with-mpi-dir="/sopt/OpenMPI/3.1.2/intel-2018.3-slim/" \ + --known-mpi-shared-libraries=1 \ + --known-64-bit-blas-indices \ + --known-mpi-long-double=1 \ + --known-mpi-int64_t=1 \ + --known-mpi-c-double-complex=1 \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-batch=1 \ + --with-shared-libraries=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.14-linux.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-linux.sh (revision 25836) +++ /issm/trunk/externalpackages/petsc/install-3.14-linux.sh (revision 25836) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + + +## Constants +VER="3.14.0" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv petsc-${VER}/* src/ +rm -rf petsc-${VER} + +# Configure +cd src +./config/configure.py \ + --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ + --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 + + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.14-mac.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-mac.sh (revision 25836) +++ /issm/trunk/externalpackages/petsc/install-3.14-mac.sh (revision 25836) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + + +## Constants +VER="3.14.0" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv petsc-${VER}/* src/ +rm -rf petsc-${VER} + +# Configure +# +# NOTE: +# - Added -fallow-argument-mismatch to FFLAGS in order to clear, +# +# error: The Fortran compiler gfortran will not compile files that call +# the same routine with arguments of different types. +# +# for gfortran 10 or later (may need to remove it for earlier versions). +# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. +# (may need to remove it for earlier versions not using the C99 standard). +# +cd src +./config/configure.py \ + --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ + --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --CFLAGS="-Wno-error=implicit-function-declaration" \ + --FFLAGS="-fallow-argument-mismatch" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.14-tetralith.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-tetralith.sh (revision 25836) +++ /issm/trunk/externalpackages/petsc/install-3.14-tetralith.sh (revision 25836) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + + +# NOTE: There is a single difference between the Linux and macOS +# configurations, which is the addition of the -static-libgfortran +# option to FFLAGS on the macOS static configurations. For the sake of +# consistency, we maintain separate files for each, respective Linux and +# macOS configuration. + +# Constants +VER="3.14.0" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv petsc-${VER}/* src/ +rm -rf petsc-${VER} + +# Configure +cd src +./config/configure.py \ + COPTFLAGS="-g -O2" CXXOPTFLAGS="-g -O2" FOPTFLAGS="-g -O2" \ + --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ + --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --with-blas-lapack-dir="/software/sse/easybuild/prefix/software/imkl/2018.1.163-iimpi-2018a/mkl" \ + --with-cc="/software/sse/easybuild/prefix/software/impi/2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28/bin64/mpicc" \ + --with-cxx="/software/sse/easybuild/prefix/software/impi/2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28/bin64/mpicxx" \ + --with-fc="/software/sse/easybuild/prefix/software/impi/2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28/bin64/mpiifort" \ + --known-mpi-shared-libraries=1 \ + --known-64-bit-blas-indices \ + --known-mpi-long-double=1 \ + --known-mpi-int64_t=1 \ + --known-mpi-c-double-complex=1 \ + --with-shared-libraries=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 + +# Compile and install +make +make install Index: sm/trunk/externalpackages/petsc/install-3.4-acenet.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-acenet.sh (revision 25835) +++ (revision ) @@ -1,33 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.4.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.3.tar.gz -mv petsc-3.4.3/* src/ -rm -rf petsc-3.4.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_ARCH="linux-gnu-amd64" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-mpi-dir=$OPENMPI \ - --with-blas-lapack-dir=/usr/local/intel/composer_xe_2011_sp1.13.367/mkl/ \ - --download-scalapack=yes \ - --download-mumps=yes \ - --download-metis=yes \ - --download-parmetis=yes - -make -make install Index: sm/trunk/externalpackages/petsc/install-3.4-greenplanet.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-greenplanet.sh (revision 25835) +++ (revision ) @@ -1,55 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.4.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.3.tar.gz -mv petsc-3.4.3/* src/ -rm -rf petsc-3.4.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-batch=1 \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-mpi=1 \ - --with-mpi-dir=/sopt/mpi/openmpi-1.5.4_psm/intel/ \ - --with-blas-lapack-dir=/opt/intel/mkl/10.2.4.032/ \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-mumps=yes \ - --download-metis=yes \ - --download-parmetis=yes \ - --download-trilinos=yes \ - --download-euclid=yes \ - --download-hypre=yes \ - --COPTFLAGS="-lmpi -O3" \ - --FOPTFLAGS="-lmpi -O3" \ - --CXXOPTFLAGS="-lmpi -O3" - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l nodes=1:ppn=1 -#PBS -q c6145 -#PBS -l walltime=10 - -cd $(echo $ISSM_DIR)/externalpackages/petsc/src/ -mpiexec -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.4-hpc.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-hpc.sh (revision 25835) +++ (revision ) @@ -1,39 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.4.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.3.tar.gz -mv petsc-3.4.3/* src/ -rm -rf petsc-3.4.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-mpi=1 \ - --with-mpi-dir=/data/apps/mpi/openmpi-1.6.0/gcc-4.7.2// \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-blas=yes \ - --download-f-blas-lapack=yes \ - --download-mumps=yes \ - --download-metis=yes \ - --download-parmetis=yes \ - --COPTFLAGS="-O3" \ - --FOPTFLAGS="-O3" \ - --CXXOPTFLAGS="-O3" - -#Compile petsc and install it -make -make install Index: sm/trunk/externalpackages/petsc/install-3.4-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-linux64.sh (revision 25835) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.4.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.3.tar.gz -mv petsc-3.4.3/* src/ -rm -rf petsc-3.4.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_ARCH=linux-gnu-amd64 \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --download-parmetis=yes \ - --download-metis=yes \ - --download-mumps=yes \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-blas=yes \ - --download-f-blas-lapack=yes \ - --with-pic=1 - -#Compile petsc and install it -make -make install Index: sm/trunk/externalpackages/petsc/install-3.4-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-macosx64.sh (revision 25835) +++ (revision ) @@ -1,37 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.4.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.3.tar.gz -mv petsc-3.4.3/* src/ -rm -rf petsc-3.4.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_ARCH="macosx-gnu" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --download-metis=yes \ - --download-parmetis=yes \ - --download-mumps=yes \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-blas=yes \ - --download-f-blas-lapack=yes \ - --with-debugging=yes - - -#Compile petsc and install it -make -make install Index: sm/trunk/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 25835) +++ (revision ) @@ -1,61 +1,0 @@ -#!/bin/bash - -#Some cleanup -rm -rf install petsc-3.4.2 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.2.tar.gz -mv petsc-3.4.2/* src/ -rm -rf petsc-3.4.2 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-batch=1 \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-mpi=1 \ - --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \ - --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-mumps=yes \ - --download-metis=yes \ - --download-parmetis=yes \ - --download-trilinos=yes \ - --download-euclid=yes \ - --download-hypre=yes \ - --COPTFLAGS="-lmpi -O3" \ - --FOPTFLAGS="-lmpi -O3" \ - --CXXOPTFLAGS="-lmpi -O3" - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=wes -#PBS -l walltime=200 -#PBS -W group_list=s1010 -#PBS -m e - -. /usr/share/modules/init/bash -module load comp-intel/2012.0.032 -module load mpi-sgi/mpt.2.06rp16 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc444.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc444.sh (revision 25835) +++ (revision ) @@ -1,61 +1,0 @@ -#!/bin/bash - -#Some cleanup -rm -rf install petsc-3.4.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.3.tar.gz -mv petsc-3.4.3/* src/ -rm -rf petsc-3.4.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-batch=1 \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-mpi=1 \ - --with-mpi-lib="/nasa/mvapich2/1.4.1/gcc.sles11/lib/libmpich.a"\ - --with-mpi-include="/nasa/mvapich2/1.4.1/gcc.sles11/include"\ - --download-f-blas-lapack=yes \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-mumps=yes \ - --download-metis=yes \ - --download-parmetis=yes \ - --download-trilinos=yes \ - --download-euclid=yes \ - --download-hypre=yes \ - --COPTFLAGS="-lmpich" \ - --FOPTFLAGS="-lmpich" \ - --CXXOPTFLAGS="-lmpich" - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=wes -#PBS -l walltime=200 -#PBS -W group_list=s1010 -#PBS -m e - -. /usr/share/modules/init/bash -module load mpi-mvapich2/1.4.1/gcc -module load gcc/4.4.4 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc470.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc470.sh (revision 25835) +++ (revision ) @@ -1,61 +1,0 @@ -#!/bin/bash - -#Some cleanup -rm -rf install petsc-3.4.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.3.tar.gz -mv petsc-3.4.3/* src/ -rm -rf petsc-3.4.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-batch=1 \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-mpi=1 \ - --with-mpi-lib="/nasa/mvapich2/1.6.sles11/gcc/lib/libmpich.a"\ - --with-mpi-include="/nasa/mvapich2/1.6.sles11/gcc/include" \ - --download-f-blas-lapack=yes \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-mumps=yes \ - --download-metis=yes \ - --download-parmetis=yes \ - --download-trilinos=yes \ - --download-euclid=yes \ - --download-hypre=yes \ - --COPTFLAGS="-lmpich" \ - --FOPTFLAGS="-lmpich" \ - --CXXOPTFLAGS="-lmpich" - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=wes -#PBS -l walltime=200 -#PBS -W group_list=s1010 -#PBS -m e - -. /usr/share/modules/init/bash -module load mpi-mvapich2/1.6/gcc -module load gcc/4.7.0 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.4-pleiades-mpich2.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-pleiades-mpich2.sh (revision 25835) +++ (revision ) @@ -1,68 +1,0 @@ -#!/bin/bash - -#Some cleanup -rm -rf install petsc-3.4.2 src -mkdir install src - -export cc=gcc -alias cc='gcc' - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.2.tar.gz -mv petsc-3.4.2/* src/ -rm -rf petsc-3.4.2 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-batch=1 \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --with-mpi=1 \ - --with-mpi-lib="$ISSM_DIR/externalpackages/mpich/install/lib/libmpich.so"\ - --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \ - --known-mpi-shared-libraries=1 \ - --download-f-blas-lapack=yes \ - --download-scalapack=yes \ - --download-metis=yes \ - --download-parmetis=yes \ - --download-blacs=yes \ - --download-mumps=yes \ - --download-trilinos=yes \ - --download-euclid=yes \ - --download-hypre=yes \ - --COPTFLAGS=" -O3 -march=corei7-avx" \ - --FOPTFLAGS=" -O3 -march=corei7-avx" \ - --CXXOPTFLAGS=" -O3 -march=corei7-avx" - -#--with-mpi-lib="/nasa/mvapich2/1.4.1/gcc.sles11/lib/libmpich.a" \ -# --with-mpi-include="/nasa/mvapich2/1.4.1/gcc.sles11/include" \ - - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=wes -#PBS -l walltime=200 -#PBS -W group_list=s1010 -#PBS -m e - -. /usr/share/modules/init/bash -module load mpi-mvapich2/1.6/gcc -module load gcc/4.7.0 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.4-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-pleiades.sh (revision 25835) +++ (revision ) @@ -1,61 +1,0 @@ -#!/bin/bash - -#Some cleanup -rm -rf install petsc-3.4.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.3.tar.gz -mv petsc-3.4.3/* src/ -rm -rf petsc-3.4.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-batch=1 \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-mpi=1 \ - --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \ - --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2013.1.117/composer_xe_2013.1.117/mkl/lib/intel64" \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-mumps=yes \ - --download-metis=yes \ - --download-parmetis=yes \ - --download-trilinos=yes \ - --download-euclid=yes \ - --download-hypre=yes \ - --COPTFLAGS="-lmpi -O3" \ - --FOPTFLAGS="-lmpi -O3" \ - --CXXOPTFLAGS="-lmpi -O3" - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=wes -#PBS -l walltime=200 -#PBS -W group_list=s1010 -#PBS -m e - -. /usr/share/modules/init/bash -module load comp-intel/2013.1.117 -module load mpi-sgi/mpt.2.06rp16 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.4-pleiades2.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.4-pleiades2.sh (revision 25835) +++ (revision ) @@ -1,61 +1,0 @@ -#!/bin/bash - -#Some cleanup -rm -rf install petsc-3.4.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.4.3.tar.gz -mv petsc-3.4.3/* src/ -rm -rf petsc-3.4.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-batch=1 \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-mpi=1 \ - --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \ - --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2013.1.117/composer_xe_2013.1.117/mkl/lib/intel64" \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-mumps=yes \ - --download-metis=yes \ - --download-parmetis=yes \ - --download-trilinos=yes \ - --download-euclid=yes \ - --download-hypre=yes \ - --COPTFLAGS="-lmpi -O3" \ - --FOPTFLAGS="-lmpi -O3" \ - --CXXOPTFLAGS="-lmpi -O3" - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=wes -#PBS -l walltime=200 -#PBS -W group_list=s1010 -#PBS -m e - -. /usr/share/modules/init/bash -module load comp-intel/2013.1.117 -module load mpi-sgi/mpt.2.06rp16 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.5-greenplanet.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-greenplanet.sh (revision 25835) +++ (revision ) @@ -1,56 +1,0 @@ -#!/bin/bash -set -eu - -#WARNING: make sure you have the right mpi - -#Some cleanup -rm -rf install petsc-3.5.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.3.tar.gz' 'petsc-3.5.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.3.tar.gz -mv petsc-3.5.3/* src/ -rm -rf petsc-3.5.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-blas-lapack-dir="/sopt/Intel/composer_xe_2015.0.090/mkl/" \ - --with-mpi-dir="/sopt/mpi/openmpi-1.8.3/intel_15.0.0/bin/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#!/bin/bash -#SBATCH -p c6145 -#SBATCH -N 1 -n 1 -#SBATCH --mem-per-cpu=1gb -#SBATCH --time=10 -#SBATCH --job-name=test - -module load compiler/intel/15.0.0 -module load mpi/openmpi/1.8.3/intel_15.0.0 - -cd $(echo $ISSM_DIR)/externalpackages/petsc/src/ -mpiexec -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== sbatch script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.5-hpc.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-hpc.sh (revision 25835) +++ (revision ) @@ -1,50 +1,0 @@ -#!/bin/bash -set -eu - -#WARNING: make sure you have the right mpi: - -#Some cleanup -rm -rf install petsc-3.5.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.3.tar.gz' 'petsc-3.5.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.3.tar.gz -mv petsc-3.5.3/* src/ -rm -rf petsc-3.5.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-mpi-dir="/data/apps/mpi/openmpi-1.8.3/gcc/4.8.3/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-fblaslapack=1 \ - --download-mumps=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#!/bin/bash -#$ -N PETSC -#$ -q free*,pub64 - -cd $(echo $ISSM_DIR)/externalpackages/petsc/src/ -mpiexec -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.5-linux64-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-linux64-static.sh (revision 25835) +++ (revision ) @@ -1,35 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.5.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.3.tar.gz' 'petsc-3.5.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.3.tar.gz -mv petsc-3.5.3/* src/ -rm -rf petsc-3.5.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=0 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 \ - --download-fblaslapack=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.5-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-linux64.sh (revision 25835) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.5.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.3.tar.gz' 'petsc-3.5.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.3.tar.gz -mv petsc-3.5.3/* src/ -rm -rf petsc-3.5.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 \ - --download-fblaslapack=1 \ - --with-pic=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.5-macosx64-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-macosx64-static.sh (revision 25835) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.5.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.3.tar.gz' 'petsc-3.5.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.3.tar.gz -mv petsc-3.5.3/* src/ -rm -rf petsc-3.5.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-ssl=0 \ - --with-x=0 \ - --with-shared-libraries=0 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-fblaslapack=1 \ - --download-scalapack=1 - - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.5-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-macosx64.sh (revision 25835) +++ (revision ) @@ -1,34 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.5.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.3.tar.gz' 'petsc-3.5.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.3.tar.gz -mv petsc-3.5.3/* src/ -rm -rf petsc-3.5.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 25835) +++ (revision ) @@ -1,62 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.5.1 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.1.tar.gz' 'petsc-3.5.1.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.1.tar.gz -mv petsc-3.5.1/* src/ -rm -rf petsc-3.5.1 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-batch=1 \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-mpi=1 \ - --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \ - --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \ - --download-scalapack=yes \ - --download-mumps=yes \ - --download-metis=yes \ - --download-parmetis=yes \ - --download-trilinos=yes \ - --download-euclid=yes \ - --download-hypre=yes \ - --COPTFLAGS="-lmpi -O3" \ - --FOPTFLAGS="-lmpi -O3" \ - --CXXOPTFLAGS="-lmpi -O3" - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=wes -#PBS -l walltime=200 -#PBS -W group_list=s1010 -#PBS -m e - -. /usr/share/modules/init/bash -module load comp-intel/2012.0.032 -module load math/intel_mkl_64_10.0.011 -module load mpi-sgi/mpt.2.06rp16 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.5-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-pleiades.sh (revision 25835) +++ (revision ) @@ -1,57 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.5.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.3.tar.gz' 'petsc-3.5.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.3.tar.gz -mv petsc-3.5.3/* src/ -rm -rf petsc-3.5.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/" \ - --with-mpi-lib="/nasa/sgi/mpt/2.11r13/lib/libmpi.so" \ - --with-mpi-include="/nasa/sgi/mpt/2.11r13/include" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 \ - --download-fblaslapack=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=wes -#PBS -l walltime=200 -#PBS -W group_list=s1010 -#PBS -m e - -. /usr/share/modules/init/bash -module load comp-intel/2015.0.090 -module load mpi-sgi/mpt.2.11r13 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.5-win-par.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-win-par.sh (revision 25835) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.5.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.3.tar.gz' 'petsc-3.5.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.3.tar.gz -mv petsc-3.5.3/* src/ -rm -rf petsc-3.5.3 - -export PETSC_DIR=`cygpath -u "$ISSM_DIR/externalpackages/petsc/src"` -export PREFIX_DIR=`cygpath -u "$ISSM_DIR/externalpackages/petsc/install"` - -#configure -cd src -./config/configure.py \ - --prefix=$PREFIX_DIR \ - --PETSC_ARCH=cygwin-intel \ - --PETSC_DIR=$PETSC_DIR \ - --with-mpi-dir="/cygdrive/c/Program\ Files/MPICH2/"\ - --with-debugging=1 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --download-f2cblaslapack=yes \ - --with-cc='win32fe cl' \ - --with-fc=0 \ - --with-cxx='win32fe cl' \ - --with-clanguage=cxx - -#Compile petsc and install it -make -make install - -patch ../install/include/petscfix.h ../configs/3.1/win7/petscfix.h.patch Index: sm/trunk/externalpackages/petsc/install-3.5-win7.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.5-win7.sh (revision 25835) +++ (revision ) @@ -1,41 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.5.3 src -mkdir install src - -#Download from ISSM server -#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.5.3.tar.gz' 'petsc-3.5.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.5.3.tar.gz -mv petsc-3.5.3/* src/ -rm -rf petsc-3.5.3 - -export PETSC_DIR=`cygpath -u "$ISSM_DIR/externalpackages/petsc/src"` -export PREFIX_DIR=`cygpath -u "$ISSM_DIR/externalpackages/petsc/install"` - -#configure -cd src -./config/configure.py \ - --with-parallel-no \ - --prefix=$PREFIX_DIR \ - --PETSC_ARCH=cygwin-intel \ - --PETSC_DIR=$PETSC_DIR \ - --with-mpi=0 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --download-f2cblaslapack=yes \ - --with-cc='win32fe cl' \ - --with-fc=0 \ - --with-cxx='win32fe cl' \ - --with-clanguage=cxx - -#Compile petsc and install it -make -make install - -patch ../install/include/petscfix.h ../configs/3.1/win7/petscfix.h.patch Index: sm/trunk/externalpackages/petsc/install-3.6-aurora.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-aurora.sh (revision 25835) +++ (revision ) @@ -1,58 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.3.tar.gz -mv petsc-3.6.3/* src/ -rm -rf petsc-3.6.3 - -#--with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort \ - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-blas-lapack-dir="/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/" \ - --with-mpi-dir="/opt/intel/impi/4.1.3/intel64/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:mpiprocs=1 -#PBS -l walltime=1:00:00 -#PBS -m e - -export RUN_DIR=$ISSM_DIR/externalpackages/petsc/src/ - -source /usr/share/Modules/init/bash -module load intel/cluster-toolkit-2013.5.192 - -export PATH="$PATH:.:/opt/intel/impi/4.1.3/intel64/bin/" -export MPI_GROUP_MAX=64 -cd $RUN_DIR -mpirun -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q debugq script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.6-discover.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-discover.sh (revision 25835) +++ (revision ) @@ -1,63 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.3.tar.gz -mv petsc-3.6.3/* src/ -rm -rf petsc-3.6.3 - -#--with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort \ - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-blas-lapack-dir="/usr/local/intel/2016/compilers_and_libraries_2016.2.181/linux/mkl/" \ - --with-mpi-lib="/usr/local/intel/2016/impi/5.1.3.181/lib64/libmpi.so" \ - --with-mpi-include="/usr/local/intel/2016/impi/5.1.3.181/include64/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#!/bin/bash -#SBATCH -J petscinstall # Job Name -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH -A s1690 -#SBATCH -t 00:01:00 # Run time (hh:mm:ss) - 1.5 hours -#SBATCH --qos=debug -#SBATCH -o petscinstall.outlog -#SBATCH -e petscinstall.errlog - -. /usr/share/modules/init/bash -module load comp/intel-16.0.2.181 -module load mpi/impi-5.1.3.181 -module load other/cmake-3.8.2 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpirun -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== sbatch script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.6-linux64-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-linux64-static.sh (revision 25835) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.3.tar.gz -mv petsc-3.6.3/* src/ -rm -rf petsc-3.6.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=0 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-fblaslapack=1 \ - --download-scalapack=1 \ - --CFLAGS="-fPIC" \ - --CC_LINKER_FLAGS="-fPIC" \ - --CXXFLAGS="-fPIC" \ - --FFLAGS="-fPIC" \ - --FC_LINKER_FLAGS="-fPIC" - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.6-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-linux64.sh (revision 25835) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.3.tar.gz -mv petsc-3.6.3/* src/ -rm -rf petsc-3.6.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 \ - --download-fblaslapack=1 \ - --with-pic=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.6-lonestar.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-lonestar.sh (revision 25835) +++ (revision ) @@ -1,51 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.3.tar.gz -mv petsc-3.6.3/* src/ -rm -rf petsc-3.6.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-blas-lapack-dir="$TACC_MKL_LIB" \ - --with-mpi-lib="/opt/cray/pe/mpt/7.7.3/gni/mpich-intel/16.0/lib/libmpich.so" \ - --with-mpi-include="/opt/cray/pe/mpt/7.7.3/gni/mpich-intel/16.0/include" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#!/bin/bash -#SBATCH -J petscinstall # Job Name -#SBATCH -n 24 # Requests 12 tasks/node, 12 cores total -#SBATCH -N 1 # Requests 12 tasks/node, 12 cores total -#SBATCH -p normal # Queue name normal -#SBATCH -t 00:01:00 # Run time (hh:mm:ss) - 1.5 hours - -ibrun -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== sbatch script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.6-macosx64-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-macosx64-static.sh (revision 25835) +++ (revision ) @@ -1,35 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.3.tar.gz -mv petsc-3.6.3/* src/ -rm -rf petsc-3.6.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=0 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-fblaslapack=1 \ - --download-scalapack=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.6-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-macosx64.sh (revision 25835) +++ (revision ) @@ -1,38 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.3.tar.gz -mv petsc-3.6.3/* src/ -rm -rf petsc-3.6.3 - -#patch -cat src/config/BuildSystem/config/packages/metis.py | sed -e "s/metis-5.1.0-p1/metis-5.1.0-p3/g" > TEMP -mv TEMP src/config/BuildSystem/config/packages/metis.py - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.6-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-pleiades.sh (revision 25835) +++ (revision ) @@ -1,55 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.3.tar.gz -mv petsc-3.6.3/* src/ -rm -rf petsc-3.6.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=wes -#PBS -l walltime=200 -#PBS -W group_list=s1010 -#PBS -m e - -. /usr/share/modules/init/bash -module load comp-intel/2016.2.181 -module load mpi-sgi/mpt - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.6-simba-intel-mvapich2-2.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-simba-intel-mvapich2-2.sh (revision 25835) +++ (revision ) @@ -1,69 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.3.tar.gz -mv petsc-3.6.3/* src/ -rm -rf petsc-3.6.3 - -# configure -cd src -./configure --prefix="$ISSM_DIR/externalpackages/petsc/install-$VER-intel-mvapich2-2" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src-$VER-intel-mvapich2-2"\ - --with-mpi-dir="/usr/local/mpi/intel18/mvapich2-2.2/" \ - --known-mpi-shared-libraries \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --with-batch=1 \ - --download-mumps=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-fblaslapack=1 \ - --download-scalapack=1 - -#prepare script to reconfigure petsc -cd $ISSM_DIR/externalpackages/petsc/src - -PBS_O_WORKDIR=$PWD - -cat > script.pbs << EOF -#PBS -S /bin/bash -#PBS -q batch -#PBS -l nodes=1:ppn=1 - -# Set qsub location -PBS_O_WORKDIR=$PWD -cd $PBS_O_WORKDIR - -# set mpi module -module load intel18/compiler-18 -module load intel18/mvapich2-2.2 -module rm intel18/openmpi-2.0.2 -module rm intel18/impi-18 - -echo "check module" -module list - -mpirun -machinefile $PBS_O_WORKDIR/mpi.host -np 1 $PBS_O_WORKDIR/conftest-arch-linux2-c-opt -EOF - -# generate mpi.host file -cat > mpi.host < script.queue << EOF -#!/bin/bash -#SBATCH -J petscinstall # Job Name -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH -t 00:01:00 # Run time (hh:mm:ss) - 1.5 hours -#SBATCH --qos=devel -#SBATCH -o petscinstall.outlog -#SBATCH -e petscinstall.errlog - -module purge -module load CMake/3.3.2-GNU-4.9.3-2.25 -module load Automake/1.15-GNU-4.9.3-2.25 -module load libtool/2.4.6-GNU-4.9.3-2.25 -module load intel/2015b - -mpirun -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== sbatch script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.7-aci.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-aci.sh (revision 25835) +++ (revision ) @@ -1,53 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.7.6 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.7.6.tar.gz -mv petsc-3.7.6/* src/ -rm -rf petsc-3.7.6 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-blas-lapack-dir="/opt/intel/compilers_and_libraries_2016.3.210/linux/mkl/lib/" \ - --with-mpi-dir="/opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -A open -#PBS -l nodes=1:ppn=1:stmem -#PBS -l walltime=200 - -module load intel/16.0.3 -module load impi/5.1.3 -module load mkl/11.3.3 - -export PATH="$PATH:." -cd $ISSM_DIR/externalpackages/petsc/src -mpirun -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.7-greenplanet.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-greenplanet.sh (revision 25835) +++ (revision ) @@ -1,57 +1,0 @@ -#!/bin/bash -set -eu - -#WARNING: make sure you have the right mpi - -#Some cleanup -rm -rf install petsc-3.7.6 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.7.6.tar.gz -mv petsc-3.7.6/* src/ -rm -rf petsc-3.7.6 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-blas-lapack-dir="/sopt/MKL/2018.3/" \ - --with-mpi-dir="/sopt/OpenMPI/3.1.2/intel-2018.3-slim" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --with-pic=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#!/bin/bash -#SBATCH -p ilg2.3 -#SBATCH -N 1 -n 1 -#SBATCH --mem-per-cpu=1gb -#SBATCH --time=10 -#SBATCH --job-name=test - -module load intel/2018.3 -module load openmpi/3.1.2-slim - -cd $(echo $ISSM_DIR)/externalpackages/petsc/src/ -mpiexec -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== sbatch script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.7-hpc.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-hpc.sh (revision 25835) +++ (revision ) @@ -1,50 +1,0 @@ -#!/bin/bash -set -eu - -#WARNING: make sure you have the right mpi: - -#Some cleanup -rm -rf install petsc-3.7.6 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.7.6.tar.gz -mv petsc-3.7.6/* src/ -rm -rf petsc-3.7.6 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-mpi-dir="/data/apps/mpi/openmpi-1.8.3/gcc/4.8.3/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-fblaslapack=1 \ - --download-mumps=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#!/bin/bash -#$ -N PETSC -#$ -q free*,pub64 - -cd $(echo $ISSM_DIR)/externalpackages/petsc/src/ -mpiexec -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.7-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-linux-static.sh (revision 25835) +++ (revision ) @@ -1,58 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.7.6" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-${VER}/* src/ -rm -rf petsc-${VER} - -# Configure -# -# NOTE: -# - Despite the fact that the with-pic option is used, external packages -# require the fPIC compiler flag to be supplied directly to the compilers in -# order for position independent code to be generated. -# -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-shared-libraries=0 \ - --with-mpi-dir="${ISSM_DIR}/externalpackages/mpich/install" \ - --with-blas-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -lblas" \ - --with-lapack-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -llapack" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --COPTFLAGS="-fPIC" \ - --CXXOPTFLAGS="-fPIC" \ - --FOPTFLAGS="-fPIC" - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: sm/trunk/externalpackages/petsc/install-3.7-linux.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-linux.sh (revision 25835) +++ (revision ) @@ -1,54 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.7.6" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-$VER.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-$VER/* src/ -rm -rf petsc-$VER - -# Configure -# -# NOTE: -# - Despite the fact that the with-pic option is used, external packages -# require the fPIC compiler flag to be supplied directly to the compilers in -# order for position independent code to be generated. -# -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-mpi-dir="${ISSM_DIR}/externalpackages/mpich/install" \ - --with-blas-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -lblas" \ - --with-lapack-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -llapack" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: sm/trunk/externalpackages/petsc/install-3.7-linux64-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-linux64-static.sh (revision 25835) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.7.6 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.7.6.tar.gz -mv petsc-3.7.6/* src/ -rm -rf petsc-3.7.6 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-single-library=1 \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-shared-libraries=0 \ - --with-debugging=0 \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --download-fblaslapack=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --with-x=0 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --with-ssl=0 \ - --with-valgrind=0 \ - --with-pic=1 \ - --COPTFLAGS="-fPIC" \ - --CXXOPTFLAGS="-fPIC" \ - --FOPTFLAGS="-fPIC" - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.7-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-linux64.sh (revision 25835) +++ (revision ) @@ -1,51 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.7.6" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-$VER.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-$VER/* src/ -rm -rf petsc-$VER - -# Configure -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-mpi-dir="${ISSM_DIR}/externalpackages/mpich/install" \ - --with-blas-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -lblas" \ - --with-lapack-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -llapack" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Return to initial directory -cd .. Index: sm/trunk/externalpackages/petsc/install-3.7-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-mac-static.sh (revision 25835) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.7.6 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.7.6.tar.gz -mv petsc-3.7.6/* src/ -rm -rf petsc-3.7.6 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-single-library=1 \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-shared-libraries=0 \ - --with-debugging=0 \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --download-fblaslapack=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --with-x=0 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --with-ssl=0 \ - --with-valgrind=0 \ - --with-pic=1 \ - --COPTFLAGS="-fPIC" \ - --CXXOPTFLAGS="-fPIC" \ - --FOPTFLAGS="-fPIC" - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.7-mac.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-mac.sh (revision 25835) +++ (revision ) @@ -1,46 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.7.6" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-${VER}/* src/ -rm -rf petsc-${VER} - -# Configure -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-mpi-dir="${ISSM_DIR}/externalpackages/mpich/install" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: sm/trunk/externalpackages/petsc/install-3.7-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-pleiades.sh (revision 25835) +++ (revision ) @@ -1,56 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.7.6 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.7.6.tar.gz -mv petsc-3.7.6/* src/ -rm -rf petsc-3.7.6 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:model=bro -#PBS -l walltime=200 -#PBS -W group_list=s1690 -#PBS -m e - -. /usr/share/modules/init/bash -module load pkgsrc -module load comp-intel/2016.2.181 -module load mpi-sgi/mpt - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q devel script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.8-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.8-linux64.sh (revision 25835) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.8.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.8.3.tar.gz' 'petsc-3.8.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.8.3.tar.gz -mv petsc-3.8.3/* src/ -rm -rf petsc-3.8.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=1 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 \ - --download-fblaslapack=1 \ - --with-pic=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.8-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.8-macosx64.sh (revision 25835) +++ (revision ) @@ -1,34 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.8.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.8.3.tar.gz' 'petsc-3.8.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.8.3.tar.gz -mv petsc-3.8.3/* src/ -rm -rf petsc-3.8.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=1 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.9-aurora.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.9-aurora.sh (revision 25835) +++ (revision ) @@ -1,58 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -#rm -rf install petsc-3.9.3 src -#mkdir install src -# -##Download from ISSM server -#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.9.3.tar.gz' 'petsc-3.9.3.tar.gz' -# -##Untar and move petsc to install directory -#tar -zxvf petsc-3.9.3.tar.gz -#mv petsc-3.9.3/* src/ -#rm -rf petsc-3.9.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-blas-lapack-dir="/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/" \ - --with-mpi-dir="/opt/intel/impi/4.1.3/intel64/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 \ - --known-64-bit-blas-indices \ - --COPTFLAGS="-O3" \ - --FOPTFLAGS="-O3" \ - --CXXOPTFLAGS="-O3" - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#PBS -S /bin/bash -#PBS -l select=1:ncpus=1:mpiprocs=1 -#PBS -l walltime=0:00:59 -#PBS -m e - -source /usr/share/Modules/init/bash -module load intel/cluster-toolkit-2013.5.192 - -export PATH="$PATH:.:/opt/intel/impi/4.1.3/intel64/bin/" -export MPI_GROUP_MAX=64 -cd $ISSM_DIR/externalpackages/petsc/src/ -mpirun -np 1 ./conftest-arch-linux2-c-opt -EOF - -#print instructions -echo "== Now: cd src/ " -echo "== qsub -q debugq script.queue " -echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: sm/trunk/externalpackages/petsc/install-3.9-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.9-linux64.sh (revision 25835) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.9.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.9.3.tar.gz' 'petsc-3.9.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.9.3.tar.gz -mv petsc-3.9.3/* src/ -rm -rf petsc-3.9.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=1 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 \ - --download-fblaslapack=1 \ - --with-pic=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.9-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.9-macosx64.sh (revision 25835) +++ (revision ) @@ -1,34 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.9.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.9.3.tar.gz' 'petsc-3.9.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.9.3.tar.gz -mv petsc-3.9.3/* src/ -rm -rf petsc-3.9.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=1 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#Compile and intall -make -make install Index: sm/trunk/externalpackages/petsc/install-3.9-sherlock.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.9-sherlock.sh (revision 25835) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.9.3 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.9.3.tar.gz' 'petsc-3.9.3.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.9.3.tar.gz -mv petsc-3.9.3/* src/ -rm -rf petsc-3.9.3 - -#configure -cd src -./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-dir="/share/software/user/restricted/impi/2019/impi/2019.0.117/intel64/" \ - --with-blas-lapack-dir="/share/software/user/restricted/imkl/2019/mkl/lib/intel64/" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=1 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=1 \ - --download-scalapack=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --with-pic=1 - -#Compile and intall -make -make install Index: /issm/trunk/externalpackages/proj/install-6.2-static-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-6.2-static-with_tests.sh (revision 25836) +++ /issm/trunk/externalpackages/proj/install-6.2-static-with_tests.sh (revision 25836) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="6.2.1" + +## Environnment +# +export CC=mpicc +export CXX=mpicxx +# NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently +# requires, +# +# SQLITE3_LIBS="-lsqlite3". +# +# On Ubuntu Linux, install the SQLite3 binary, libraries and headers +# with, +# +# `apt-get install sqlite3 libsqlite3-dev` +# +export SQLITE3_LIBS="-lsqlite3" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/proj-${VER}.tar.gz" "proj-${VER}.tar.gz" + +# Unpack source +tar -zxvf proj-$VER.tar.gz + +# Move source into 'src' directory +mv proj-$VER/* src +rm -rf proj-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-shared + +# Compile and install +if [ $# -eq 0 ]; then + make + make check + make install +else + make -j $1 + make -j $1 check + make -j $1 install +fi Index: /issm/trunk/externalpackages/proj/install-6.2-static.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-6.2-static.sh (revision 25836) +++ /issm/trunk/externalpackages/proj/install-6.2-static.sh (revision 25836) @@ -0,0 +1,54 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="6.2.1" + +## Environment +# +export CC=mpicc +export CXX=mpicxx +# NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently +# requires, +# +# SQLITE3_LIBS="-lsqlite3". +# +# On Ubuntu Linux, install the SQLite3 binary, libraries and headers +# with, +# +# `apt-get install sqlite3 libsqlite3-dev` +# +export SQLITE3_LIBS="-lsqlite3" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/proj-${VER}.tar.gz" "proj-${VER}.tar.gz" + +# Unpack source +tar -zxvf proj-$VER.tar.gz + +# Move source into 'src' directory +mv proj-$VER/* src +rm -rf proj-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-shared + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/proj/install-6.2-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-6.2-with_tests.sh (revision 25835) +++ /issm/trunk/externalpackages/proj/install-6.2-with_tests.sh (revision 25836) @@ -9,5 +9,6 @@ ## Environnment # - +export CC=mpicc +export CXX=mpicxx # NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently # requires, @@ -39,5 +40,7 @@ cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/proj/install" + --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --disable-dependency-tracking \ + --enable-fast-install # Compile and install Index: /issm/trunk/externalpackages/proj/install-6.2.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-6.2.sh (revision 25835) +++ /issm/trunk/externalpackages/proj/install-6.2.sh (revision 25836) @@ -9,5 +9,6 @@ ## Environnment # - +export CC=mpicc +export CXX=mpicxx # NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently # requires, @@ -39,5 +40,7 @@ cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/proj/install" + --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --disable-dependency-tracking \ + --enable-fast-install # Compile and install Index: /issm/trunk/externalpackages/proj/install.sh =================================================================== --- /issm/trunk/externalpackages/proj/install.sh (revision 25836) +++ /issm/trunk/externalpackages/proj/install.sh (revision 25836) @@ -0,0 +1,15 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install + +#Download trunk +svn checkout http://svn.osgeo.org/metacrs/proj/trunk/proj install + +#compile +cd install +./configure --prefix="$ISSM_DIR/externalpackages/proj/install" +make +make install +cd .. Index: /issm/trunk/externalpackages/valgrind/install-linux.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-linux.sh (revision 25836) +++ /issm/trunk/externalpackages/valgrind/install-linux.sh (revision 25836) @@ -0,0 +1,25 @@ +#!/bin/bash +set -eu + + +# Clean up +rm -rf install + +# Download development version +git clone git://sourceware.org/git/valgrind.git install + +# Configure +cd install +./autogen.sh +./configure \ + --prefix="$ISSM_DIR/externalpackages/valgrind/install" \ + --enable-only64bit + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make install -j $1 +fi Index: sm/trunk/externalpackages/valgrind/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-linux64.sh (revision 25835) +++ (revision ) @@ -1,21 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install - -#Download development version -git clone git://sourceware.org/git/valgrind.git install - -#configure -cd install -./autogen.sh -./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only64bit - -#Compile valgrind -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk/externalpackages/valgrind/install-mac.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-mac.sh (revision 25836) +++ /issm/trunk/externalpackages/valgrind/install-mac.sh (revision 25836) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + + +# Clean up +rm -rf install + +# Download development version (the current release never supports the latest +# OS X releases) +git clone git://sourceware.org/git/valgrind.git install + +# Configure +cd install +./autogen.sh +./configure \ + --prefix="$ISSM_DIR/externalpackages/valgrind/install" \ + --enable-only64bit + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make install -j $1 +fi + Index: sm/trunk/externalpackages/valgrind/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-macosx64.sh (revision 25835) +++ (revision ) @@ -1,21 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install - -#Download development version, the current release never supports the latest OS X releases -git clone git://sourceware.org/git/valgrind.git install - -#configure -cd install -./autogen.sh -./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only64bit - -#Compile valgrind -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk/jenkins/aws-amazon_linux-solid_earth =================================================================== --- /issm/trunk/jenkins/aws-amazon_linux-solid_earth (revision 25836) +++ /issm/trunk/jenkins/aws-amazon_linux-solid_earth (revision 25836) @@ -0,0 +1,82 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/usr/local/MATLAB/R2020a" +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-dir=/usr \ + --with-python-numpy-dir=/usr/lib64/python2.7/site-packages/numpy/core/include/numpy \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/7 -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpifort -lmpi" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux.sh + triangle install-linux.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + boost install-1.7-linux.sh + curl install-7-linux.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6-linux.sh + gmsh install-4.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=1 +PYTHON_TEST=1 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of cpus used in the nightly runs +# +# NOTE: Possible problem of access to all_vertices.txt if more than 1. +# +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +# NOTE: +# - Test 2021 is excluded as Gmsh produces different-sized meshes on macOS and Linux for 3d objects (archives are generated on macOS). +# +MATLAB_NROPTIONS="'benchmark','slr','exclude',[2021]" +PYTHON_NROPTIONS="--benchmark slr --exclude 2021" Index: /issm/trunk/jenkins/jenkins.sh =================================================================== --- /issm/trunk/jenkins/jenkins.sh (revision 25835) +++ /issm/trunk/jenkins/jenkins.sh (revision 25836) @@ -58,5 +58,5 @@ #Install ISSM -#Determinig Installation type depending on svn changes{{{ +#Determining installation type depending on svn changes{{{ echo "======================================================"; echo " Determining Installation type " @@ -153,5 +153,5 @@ NUMPACKAGES=$(($(echo ${EXTERNALPACKAGES} | wc -w ) / 2)) -#Jenkins xml files for individual packages +#Jenkins XML files for individual packages EXTERNAL_TEST_FILE="$ISSM_DIR/nightlylog/results/external.xml" mkdir -p $ISSM_DIR/nightlylog/results @@ -183,5 +183,5 @@ echo "======================================================"; - ./$PACKAGEINST &> compil.log + ./$PACKAGEINST $NUMCPUS_INSTALL &> compil.log if [ $? -ne 0 ] && [ "$PACKAGENAME" != "boost" ]; then cat compil.log @@ -389,5 +389,7 @@ # }}} -#python tests +# Python tests +# +# TODO: Figure out why "Running Python test for Rank $i" is printed twice for each CPU # {{{ if [ $PYTHON_TEST -eq 1 ]; then @@ -547,5 +549,5 @@ # Check that MATLAB did not exit in error - matlabExitedInError=`grep -E "Activation cannot proceed|license" matlab_log.log | wc -l` + matlabExitedInError=`grep -E "Activation cannot proceed|Error in matlab_run|license" matlab_log.log | wc -l` if [ $matlabExitedInError -ne 0 ] @@ -575,5 +577,5 @@ # Check that Python did not exit in error - pythonExitedInError=`grep -E "Error|Traceback|bad interpreter" python_log.log | wc -l` + pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python_log.log | wc -l` if [ $pythonExitedInError -ne 0 ] Index: /issm/trunk/jenkins/linux64_caladan =================================================================== --- /issm/trunk/jenkins/linux64_caladan (revision 25835) +++ /issm/trunk/jenkins/linux64_caladan (revision 25836) @@ -44,5 +44,5 @@ petsc install-3.7-linux64.sh triangle install-linux64.sh - boost install-1.55-linux.sh + boost install-1.7-linux.sh dakota install-6.2-linux64.sh chaco install.sh Index: /issm/trunk/jenkins/linux64_caladan_ad =================================================================== --- /issm/trunk/jenkins/linux64_caladan_ad (revision 25835) +++ /issm/trunk/jenkins/linux64_caladan_ad (revision 25836) @@ -7,15 +7,17 @@ MATLAB_PATH="/usr/local/MATLAB/R2015a" -#ISSM CONFIGURATION -ISSM_CONFIG='--prefix=$ISSM_DIR\ - --disable-static \ - --prefix=$ISSM_DIR \ - --without-kriging \ - --without-kml \ - --without-Gia \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ - --with-matlab-dir=$MATLAB_PATH \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install ' +#ISSM CONFIGURATION +ISSM_CONFIG='\ + --prefix=$ISSM_DIR\ + --disable-static \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --without-kml \ + --without-Gia \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ + --with-matlab-dir=$MATLAB_PATH \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install +' #PYTHON and MATLAB testing @@ -28,12 +30,14 @@ #List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES="autotools install.sh - cmake install.sh - mpich install-3.2-linux64.sh - petsc install-3.7-linux64.sh - triangle install-linux64.sh - gsl install-linux64.sh - adolc install.sh - shell2junit install.sh" +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh + gsl install.sh + triangle install-linux.sh + adolc install.sh + shell2junit install.sh +" #-----------------# Index: /issm/trunk/jenkins/linux64_caladan_ampi =================================================================== --- /issm/trunk/jenkins/linux64_caladan_ampi (revision 25835) +++ /issm/trunk/jenkins/linux64_caladan_ampi (revision 25836) @@ -7,24 +7,26 @@ MATLAB_PATH="/usr/local/MATLAB/R2015a" -#ISSM CONFIGURATION -ISSM_CONFIG='--prefix=$ISSM_DIR\ - --disable-static \ - --without-kriging \ - --without-kml \ - --without-Gia \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ - --with-ampi-dir=$ISSM_DIR/externalpackages/adjoinablempi/install \ - --with-matlab-dir=$MATLAB_PATH \ - --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-numthreads=4 \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \ - --enable-development ' +#ISSM CONFIGURATION +ISSM_CONFIG='\ + --prefix=$ISSM_DIR \ + --disable-static \ + --without-kriging \ + --without-kml \ + --without-Gia \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ + --with-ampi-dir=$ISSM_DIR/externalpackages/adjoinablempi/install \ + --with-matlab-dir=$MATLAB_PATH \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-numthreads=4 \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \ + --enable-development +' #PYTHON and MATLAB testing @@ -37,13 +39,15 @@ #List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES="autotools install.sh - cmake install.sh - mpich install-3.2-linux64.sh - petsc install-3.7-linux64.sh - triangle install-linux64.sh - gsl install-linux64.sh - adjoinablempi install.sh - adolc install-withampi.sh - shell2junit install.sh" +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh + gsl install.sh + triangle install-linux.sh + adjoinablempi install.sh + adolc install-with_ampi.sh + shell2junit install.sh +" #-----------------# Index: sm/trunk/jenkins/macosx_pine-island_examples =================================================================== --- /issm/trunk/jenkins/macosx_pine-island_examples (revision 25835) +++ (revision ) @@ -1,77 +1,0 @@ -#-------------------------------# -# 1: ISSM general configuration # -#-------------------------------# - -# MATLAB path -MATLAB_PATH="/Applications/MATLAB_R2015b.app" - -# ISSM CONFIGURATION -ISSM_CONFIG='\ - --prefix=$ISSM_DIR \ - --with-matlab-dir=$MATLAB_PATH \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ - --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ - --with-semic-dir=$ISSM_DIR/externalpackages/semic/install \ - --with-numthreads=4 \ - --enable-debugging \ - --enable-development \ -' - -# Test suites -MATLAB_TEST=0 -PYTHON_TEST=0 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=1 - -#-----------------------------------# -# 3: External packages installation # -#-----------------------------------# - -# List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES=" - autotools install.sh - cmake install.sh - mpich install-3.3.sh - petsc install-3.7-mac.sh - triangle install-mac.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - hdf5 install-1.10.sh - netcdf install-4.7.sh - proj install-6.2.sh - gdal install-3.0-netcdf.sh - gshhg install.sh - gmt install.sh - gmsh install.sh - shell2junit install.sh -" - -#-----------------# -# 4: test options # -#-----------------# - -# Number of CPUs used in ISSM compilation -# -# NOTE: One is usually safer as some packages are very sensitive to parallel -# compilation -# -NUMCPUS_INSTALL=4 - -# Number of CPUs used in the nightly runs -NUMCPUS_RUN=2 - -# Nightly run options -# -# See documentation in test/NightlyRun/runme.* for more information. -# -PYTHON_NROPTIONS="" -MATLAB_NROPTIONS="" - Index: sm/trunk/jenkins/pine_island-mac =================================================================== --- /issm/trunk/jenkins/pine_island-mac (revision 25835) +++ (revision ) @@ -1,74 +1,0 @@ -#--------------------# -# ISSM Configuration # -#--------------------# - -# MATLAB path -MATLAB_PATH="/Applications/MATLAB_R2018a.app" - -# ISSM CONFIGURATION -ISSM_CONFIG='\ - --prefix=${ISSM_DIR} \ - --disable-static \ - --enable-development \ - --enable-debugging \ - --with-numthreads=4 \ - --with-matlab-dir=${MATLAB_PATH} \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/9.3.0/lib/gcc/9 -lgfortran" \ - --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ - --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ -' - -# Test suites -MATLAB_TEST=1 -PYTHON_TEST=0 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - -#-------------------# -# External Packages # -#-------------------# - -# List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES=" - autotools install.sh - cmake install.sh - petsc install-3.12-mac.sh - triangle install-mac.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh -" - -#---------# -# Testing # -#---------# - -# Number of CPUs used in ISSM compilation -# -# NOTE: One is usually safer as some packages are very sensitive to parallel -# compilation -# -NUMCPUS_INSTALL=4 - -# Number of CPUs used in the nightly runs -NUMCPUS_RUN=2 - -# Nightly run options -# -# See documentation in test/NightlyRun/runme.* for more information -# -# NOTE: -# - test701 is skipped because it uses full Stokes equations -# -MATLAB_NROPTIONS="'exclude',[435,701,702,703,IdFromString('Dakota')]" -PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/pine_island-mac-adolc-ampion =================================================================== --- /issm/trunk/jenkins/pine_island-mac-adolc-ampion (revision 25836) +++ /issm/trunk/jenkins/pine_island-mac-adolc-ampion (revision 25836) @@ -0,0 +1,81 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/Applications/MATLAB_R2019b.app" + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --without-kriging \ + --without-kml \ + --without-Gia \ + --without-Love \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-ampi-dir=${ISSM_DIR}/externalpackages/adjoinablempi/install \ + --with-adolc-dir=${ISSM_DIR}/externalpackages/adolc/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +# NOTE: The PETSc libraries are compiled but not used as they conflict with +# ADOL-C: PETSc is really just being used as an installer for other +# external packages. +# +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + petsc install-3.12-mac.sh + gsl install.sh + triangle install-mac.sh + adjoinablempi install-mac.sh + adolc install-mac-with_ampi.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# PYTHON and MATLAB testing +MATLAB_TEST=1 +PYTHON_TEST=1 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=2 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +# NOTE: +# - test3010 is skipped because it triggers GEMB module and a subsequent +# failure on ampioff configuration (really, likely a segmentation fault) +# +MATLAB_NROPTIONS="'benchmark','adolc','id',[3001, 3002, 3003, 3004, 3005, 3006, 3007, 3008, 3009, 3010, 3101, 3102, 3103, 3104, 3105, 3106, 3107, 3108, 3109, 3119],'exclude',3010" +PYTHON_NROPTIONS="--benchmark=adolc -i 3001 3002 3003 3004 3005 3006 3007 3008 3009 3010 3101 3102 3103 3104 3105 3106 3107 3108 3109 3119 --exclude=3010" Index: /issm/trunk/jenkins/pine_island-mac-basic =================================================================== --- /issm/trunk/jenkins/pine_island-mac-basic (revision 25836) +++ /issm/trunk/jenkins/pine_island-mac-basic (revision 25836) @@ -0,0 +1,72 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/Applications/MATLAB_R2018a.app" + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +# List of external pakages to be installed and their installation scripts +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + petsc install-3.12-mac.sh + triangle install-mac.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=1 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=4 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=2 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information +# +# NOTE: +# - test701 is skipped because it uses full Stokes equations +# +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),435,701,702,703]" +PYTHON_NROPTIONS="" Index: sm/trunk/jenkins/pine_island-mac-binaries =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries (revision 25835) +++ (revision ) @@ -1,75 +1,0 @@ -#--------------------# -# ISSM Configuration # -#--------------------# - -# MATLAB path -MATLAB_PATH="/Applications/MATLAB_R2018a.app" - -# NOTE: -# - We can disable dependency tracking in the Autotools because the binaries -# should always be a one-time build. -# - -# ISSM CONFIGURATION -ISSM_CONFIG='\ - --prefix=${ISSM_DIR} \ - --enable-standalone-executables \ - --enable-standalone-modules \ - --enable-standalone-libraries \ - --disable-dependency-tracking \ - --with-matlab-dir=${MATLAB_PATH} \ - --with-fortran-lib="/usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libgfortran.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libquadmath.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin15/9.3.0/libgcc.a" \ - --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ - --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ -' - -# Test suites -MATLAB_TEST=0 -PYTHON_TEST=0 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - -#-------------------# -# External Packages # -#-------------------# - -EXTERNALPACKAGES=" - autotools install.sh - cmake install.sh - petsc install-3.12-mac-static.sh - triangle install-mac-static.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh -" - -#---------# -# Testing # -#---------# - -# Number of CPUs used in ISSM compilation -# -# NOTE: One is usually safer as some packages are very sensitive to parallel -# compilation -# -NUMCPUS_INSTALL=1 - -# Number of CPUs used in the nightly runs -NUMCPUS_RUN=1 - -# Nightly run options -# -# See documentation in test/NightlyRun/runme.* for more information. -# -PYTHON_NROPTIONS="" -MATLAB_NROPTIONS="" Index: /issm/trunk/jenkins/pine_island-mac-binaries-matlab =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-matlab (revision 25836) +++ /issm/trunk/jenkins/pine_island-mac-binaries-matlab (revision 25836) @@ -0,0 +1,89 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +# MATLAB path +MATLAB_PATH="/Applications/MATLAB_R2018a.app" + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# + +# ISSM CONFIGURATION +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-fortran-lib="/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgfortran.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libquadmath.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin15/10.2.0/libgcc.a" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + petsc install-3.12-mac-static.sh + gsl install-static.sh + boost install-1.7-mac-static.sh + dakota install-6.2-mac-static.sh + curl install-7-mac-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6.2-static.sh + gdal install-3-netcdf-static.sh + gshhg install.sh + gmt install-6-mac-static.sh + gmsh install-4-mac-static.sh + triangle install-mac-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=4 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +PYTHON_NROPTIONS="" +MATLAB_NROPTIONS="" Index: /issm/trunk/jenkins/pine_island-mac-binaries-python =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-python (revision 25836) +++ /issm/trunk/jenkins/pine_island-mac-binaries-python (revision 25836) @@ -0,0 +1,87 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# + +# ISSM CONFIGURATION +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ + --with-fortran-lib="/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgfortran.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libquadmath.a /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin15/10.2.0/libgcc.a" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + petsc install-3.12-mac-static.sh + gsl install-static.sh + boost install-1.7-mac-static.sh + dakota install-6.2-mac-static.sh + curl install-7-mac-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6.2-static.sh + gdal install-3-python-netcdf-static.sh + gshhg install.sh + gmt install-6-mac-static.sh + gmsh install-4-mac-python-static.sh + triangle install-mac-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +PYTHON_NROPTIONS="" +MATLAB_NROPTIONS="" Index: sm/trunk/jenkins/pine_island-mac-binaries-with_dakota =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-with_dakota (revision 25835) +++ (revision ) @@ -1,81 +1,0 @@ -#--------------------# -# ISSM Configuration # -#--------------------# - -# MATLAB path -MATLAB_PATH="/Applications/MATLAB_R2018a.app" - -# NOTE: -# - We can disable dependency tracking in the Autotools because the binaries -# should always be a one-time build. -# - -# ISSM CONFIGURATION -ISSM_CONFIG='\ - --prefix=${ISSM_DIR} \ - --enable-standalone-executables \ - --enable-standalone-modules \ - --enable-standalone-libraries \ - --disable-dependency-tracking \ - --with-matlab-dir=${MATLAB_PATH} \ - --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ - --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="/usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libgfortran.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libquadmath.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin15/9.3.0/libgcc.a" \ - --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ - --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ - --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ - --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ -' - -# Test suites -MATLAB_TEST=0 -PYTHON_TEST=0 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - -#-------------------# -# External Packages # -#-------------------# - -EXTERNALPACKAGES=" - autotools install.sh - cmake install.sh - petsc install-3.12-mac-static.sh - boost install-1.72-mac-static.sh - dakota install-6.2-mac-static.sh - triangle install-mac-static.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh -" - -#---------# -# Testing # -#---------# - -# Number of CPUs used in ISSM compilation -# -# NOTE: One is usually safer as some packages are very sensitive to parallel -# compilation -# -NUMCPUS_INSTALL=1 - -# Number of CPUs used in the nightly runs -NUMCPUS_RUN=1 - -# Nightly run options -# -# See documentation in test/NightlyRun/runme.* for more information. -# -PYTHON_NROPTIONS="" -MATLAB_NROPTIONS="" Index: /issm/trunk/jenkins/pine_island-mac-dakota =================================================================== --- /issm/trunk/jenkins/pine_island-mac-dakota (revision 25835) +++ /issm/trunk/jenkins/pine_island-mac-dakota (revision 25836) @@ -3,8 +3,6 @@ #--------------------# -# MATLAB path MATLAB_PATH="/Applications/MATLAB_R2018a.app" -# ISSM CONFIGURATION ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -16,5 +14,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/9.3.0/lib/gcc/9 -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ @@ -23,7 +21,9 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ - --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ @@ -31,10 +31,4 @@ --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ ' - -# Test suites -MATLAB_TEST=1 -PYTHON_TEST=1 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 #-------------------# @@ -44,14 +38,22 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES=" - autotools install.sh - cmake install.sh - petsc install-3.12-mac.sh - boost install-1.72-mac.sh - dakota install-6.2-mac.sh - triangle install-mac.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh + autotools install.sh + cmake install.sh + petsc install-3.12-mac.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4.sh + triangle install-mac.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh " @@ -59,4 +61,10 @@ # Testing # #---------# + +# Test suites +MATLAB_TEST=1 +PYTHON_TEST=1 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 # Number of CPUs used in ISSM compilation @@ -75,8 +83,11 @@ # # NOTE: -# - See test418.py for reason why it is excluded for now -# - Error is large for test420 -# - test701 is skipped because it uses full Stokes equations +# - Errors are large for tests 234, 235, 418, and 420 under MATLAB +# - Tests 444 and 445 fail intermittently under MATLAB with "Index exceeds array bounds." +# - Errors are large for tests 234 418 and 420 under Python +# - See test417.py for why it is excluded +# - Test 444 fails intermittently under Python with "IndexError: list index out of range" +# - Excluding 2006 until it can be debugged (file I/O) # -MATLAB_NROPTIONS="'exclude',[234,243,420,435,701,702,703,'id',[IdFromString('Dakota')]" -PYTHON_NROPTIONS="--exclude 234 243 418 420 435 701 702 703 --include_name 'Dakota'" +MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234 235 418 420 444 445 2006]" +PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 417 418 420 444 445 2006" Index: /issm/trunk/jenkins/pine_island-mac-full =================================================================== --- /issm/trunk/jenkins/pine_island-mac-full (revision 25836) +++ /issm/trunk/jenkins/pine_island-mac-full (revision 25836) @@ -0,0 +1,84 @@ +# NOTE: This configuration adds solid earth and Dakota capabilities to the + basic build. + +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/Applications/MATLAB_R2018a.app" + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + petsc install-3.12-mac.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6.0-mac.sh + gmsh install-4.sh + triangle install-mac.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/pine_island-mac-full-valgrind =================================================================== --- /issm/trunk/jenkins/pine_island-mac-full-valgrind (revision 25836) +++ /issm/trunk/jenkins/pine_island-mac-full-valgrind (revision 25836) @@ -0,0 +1,85 @@ +# NOTE: This configuration adds solid earth and Dakota capabilities to the + basic build, as well as the ability to debug with Valgrind. + +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/Applications/MATLAB_R2018a.app" + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + petsc install-3.12-mac.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6.0-mac.sh + gmsh install-4.sh + triangle install-mac.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + valgrind install-mac.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/pine_island-mac-python =================================================================== --- /issm/trunk/jenkins/pine_island-mac-python (revision 25836) +++ /issm/trunk/jenkins/pine_island-mac-python (revision 25836) @@ -0,0 +1,88 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +# List of external pakages to be installed and their installation scripts +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + petsc install-3.12-mac.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4.sh + triangle install-mac.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=1 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=4 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=2 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +# NOTE: +# - Errors are large for tests 234 418 and 420 under Python +# - See test417.py for why it is excluded +# - Test 444 fails intermittently under Python with "IndexError: list index out of range" +# - Tests 701, 702, and 703 are skipped because they use full Stokes equations +# +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="--exclude 234 417 418 420 435 444 445 701 702 703" Index: /issm/trunk/jenkins/pine_island-mac-solid_earth =================================================================== --- /issm/trunk/jenkins/pine_island-mac-solid_earth (revision 25836) +++ /issm/trunk/jenkins/pine_island-mac-solid_earth (revision 25836) @@ -0,0 +1,88 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/Applications/MATLAB_R2018a.app" + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +#List of external pakages to be installed and their installation scripts +EXTERNALPACKAGES=" + autotools install.sh + cmake install.sh + petsc install-3.12-mac.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4.sh + triangle install-mac.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=1 +PYTHON_TEST=1 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=4 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=2 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +# NOTE: +# - Excluding 2006 until it can be debugged (file I/O) +# +MATLAB_NROPTIONS="'benchmark','slr','exclude',[2006]" +PYTHON_NROPTIONS="--benchmark slr --exclude 2005 2006" Index: sm/trunk/jenkins/ross-debian_linux =================================================================== --- /issm/trunk/jenkins/ross-debian_linux (revision 25835) +++ (revision ) @@ -1,67 +1,0 @@ -#--------------------# -# ISSM Configuration # -#--------------------# - -MATLAB_PATH="/usr/local/MATLAB/R2019b" -ISSM_CONFIG='\ - --prefix=${ISSM_DIR} \ - --disable-static \ - --enable-development \ - --enable-debugging \ - --with-numthreads=4 \ - --with-matlab-dir=${MATLAB_PATH} \ - --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ - --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ - --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ -' - -#-------------------# -# External Packages # -#-------------------# - -EXTERNALPACKAGES=" - autotools install-debian-linux.sh - cmake install.sh - petsc install-3.12-linux.sh - triangle install-linux.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh -" - -#---------# -# Testing # -#---------# - -# Test suites -MATLAB_TEST=1 -PYTHON_TEST=0 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - -# Number of CPUs used in ISSM compilation -# -# NOTE: One is usually safer as some packages are very sensitive to parallel -# compilation. -# -NUMCPUS_INSTALL=8 - -# Number of CPUs used in the nightly runs -NUMCPUS_RUN=2 - -# Nightly run options -# -# See documentation in test/NightlyRun/runme.* for more information. -# -MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" -PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-adolc-ampioff =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-adolc-ampioff (revision 25835) +++ /issm/trunk/jenkins/ross-debian_linux-adolc-ampioff (revision 25836) @@ -12,5 +12,5 @@ --without-kriging \ --without-kml \ - --without-GiaIvins \ + --without-Gia \ --without-Love \ --with-matlab-dir=${MATLAB_PATH} \ @@ -41,6 +41,6 @@ cmake install.sh petsc install-3.12-linux.sh + gsl install.sh triangle install-linux.sh - gsl install-linux64.sh adolc install.sh shell2junit install.sh @@ -76,3 +76,3 @@ # MATLAB_NROPTIONS="'benchmark','adolc','id',[3001:3019],'exclude',3010" -PYTHON_NROPTIONS="--benchmark=adolc -i 3001 3002 3003 3004 3005 3006 3007 3008 3009 3010 3011 3012 3013 3014 3015 3016 3017 3018 3019 --exclude=3010" +PYTHON_NROPTIONS="--benchmark=adolc -i 3001 3002 3003 3004 3005 3006 3007 3008 3009 3010 3011 3.14 3013 3014 3015 3016 3017 3018 3019 --exclude=3010" Index: /issm/trunk/jenkins/ross-debian_linux-adolc-ampion =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-adolc-ampion (revision 25835) +++ /issm/trunk/jenkins/ross-debian_linux-adolc-ampion (revision 25836) @@ -12,5 +12,5 @@ --without-kriging \ --without-kml \ - --without-GiaIvins \ + --without-Gia \ --without-Love \ --with-matlab-dir=${MATLAB_PATH} \ @@ -42,8 +42,8 @@ cmake install.sh petsc install-3.12-linux.sh + gsl install.sh triangle install-linux.sh - gsl install-linux64.sh - adjoinablempi install.sh - adolc install-withampi.sh + adjoinablempi install-linux.sh + adolc install-with_ampi.sh shell2junit install.sh " Index: /issm/trunk/jenkins/ross-debian_linux-basic =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-basic (revision 25836) +++ /issm/trunk/jenkins/ross-debian_linux-basic (revision 25836) @@ -0,0 +1,67 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/usr/local/MATLAB/R2019b" +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux.sh + triangle install-linux.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=1 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=2 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-binaries =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries (revision 25835) +++ /issm/trunk/jenkins/ross-debian_linux-binaries (revision 25836) @@ -63,5 +63,5 @@ # compilation. # -NUMCPUS_INSTALL=1 +NUMCPUS_INSTALL=8 # Number of CPUs used in the nightly runs Index: /issm/trunk/jenkins/ross-debian_linux-binaries-matlab =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-matlab (revision 25836) +++ /issm/trunk/jenkins/ross-debian_linux-binaries-matlab (revision 25836) @@ -0,0 +1,88 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/usr/local/MATLAB/R2019b" + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is +# copied by packaging script. +# +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-pic \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-fortran-lib="-L${ISSM_DIR}/lib -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux-static.sh + gsl install-static.sh + boost install-1.7-linux-static.sh + dakota install-6.2-linux-static.sh + curl install-7-linux-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6.2-static.sh + gdal install-3-netcdf-static.sh + gshhg install.sh + gmt install-6-linux-static.sh + gmsh install-4-linux-static.sh + triangle install-linux-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-binaries-python =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-python (revision 25836) +++ /issm/trunk/jenkins/ross-debian_linux-binaries-python (revision 25836) @@ -0,0 +1,87 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is +# copied by packaging script. +# +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-pic \ + --with-python-dir=/usr \ + --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-fortran-lib="-L${ISSM_DIR}/lib -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux-static.sh + gsl install-static.sh + boost install-1.7-linux-static.sh + dakota install-6.2-linux-static.sh + curl install-7-linux-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6.2-static.sh + gdal install-3-python-netcdf-static.sh + gshhg install.sh + gmt install-6-linux-static.sh + gmsh install-4-linux-static.sh + triangle install-linux-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: sm/trunk/jenkins/ross-debian_linux-binaries-with_dakota =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-with_dakota (revision 25835) +++ (revision ) @@ -1,83 +1,0 @@ -#--------------------# -# ISSM Configuration # -#--------------------# - -MATLAB_PATH="/usr/local/MATLAB/R2019b" - -# NOTE: -# - We can disable dependency tracking in the Autotools because the binaries -# should always be a one-time build. -# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is -# copied by packaging script. -# -ISSM_CONFIG='\ - --prefix="${ISSM_DIR}" \ - --enable-standalone-executables \ - --enable-standalone-modules \ - --enable-standalone-libraries \ - --disable-dependency-tracking \ - --with-cxxoptflags="-std=c++11" \ - --with-numthreads=4 \ - --with-pic \ - --with-matlab-dir=${MATLAB_PATH} \ - --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ - --with-fortran-lib="-L${ISSM_DIR}/lib -lgfortran" \ - --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ - --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ - --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ - --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ -' - -#-------------------# -# External Packages # -#-------------------# - -EXTERNALPACKAGES=" - autotools install-debian-linux.sh - cmake install.sh - petsc install-3.12-linux-static.sh - boost install-1.55-linux-static.sh - dakota install-6.2-linux-static.sh - triangle install-linux-static.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh -" - -#---------# -# Testing # -#---------# - -# Test suites -MATLAB_TEST=0 -PYTHON_TEST=0 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - -# Number of CPUs used in ISSM compilation -# -# NOTE: One is usually safer as some packages are very sensitive to parallel -# compilation. -# -NUMCPUS_INSTALL=1 - -# Number of CPUs used in the nightly runs -NUMCPUS_RUN=1 - -# Nightly run options -# -# See documentation in test/NightlyRun/runme.* for more information. -# -MATLAB_NROPTIONS="" -PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-codipack =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-codipack (revision 25835) +++ /issm/trunk/jenkins/ross-debian_linux-codipack (revision 25836) @@ -12,5 +12,5 @@ --without-kriging \ --without-kml \ - --without-GiaIvins \ + --without-Gia \ --without-Love \ --with-matlab-dir=${MATLAB_PATH} \ @@ -22,9 +22,9 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ - --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ --with-medipack-dir="${ISSM_DIR}/externalpackages/medipack/install" \ --with-codipack-dir="${ISSM_DIR}/externalpackages/codipack/install" \ @@ -39,9 +39,9 @@ cmake install.sh petsc install-3.12-linux.sh + gsl install.sh triangle install-linux.sh chaco install.sh m1qn3 install.sh semic install.sh - gsl install-linux64.sh medipack install.sh codipack install.sh @@ -73,4 +73,4 @@ # See documentation in test/NightlyRun/runme.* for more information. # -MATLAB_NROPTIONS="'benchmark','all','id',[3015,3119,3480]" +MATLAB_NROPTIONS="'benchmark','all','id',[3015,3119,3480,3201,3202]" PYTHON_NROPTIONS="--benchmark='all' -i 3015 3119 3480" Index: /issm/trunk/jenkins/ross-debian_linux-dakota =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-dakota (revision 25835) +++ /issm/trunk/jenkins/ross-debian_linux-dakota (revision 25836) @@ -4,4 +4,5 @@ MATLAB_PATH="/usr/local/MATLAB/R2019b" + ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -22,7 +23,9 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ - --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ @@ -36,14 +39,23 @@ EXTERNALPACKAGES=" - autotools install-debian-linux.sh - cmake install.sh - petsc install-3.12-linux.sh - boost install-1.55-linux.sh - dakota install-6.2-linux.sh - triangle install-linux.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux.sh + gsl install.sh + boost install-1.7-linux.sh + dakota install-6.2-linux.sh + boost install-1.7-linux.sh + curl install-7-linux.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6-linux.sh + gmsh install-4.sh + triangle install-linux.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh " @@ -73,6 +85,7 @@ # # NOTE: -# - See test418.py for reason why it is excluded for now. +# - Errors are large for tests 234, 418, and 420 under Python +# - Excluding 2006 until it can be debugged (PETSc crash) # -MATLAB_NROPTIONS="'exclude',[243,435,701,702],'id',[IdFromString('Dakota')]" -PYTHON_NROPTIONS="--exclude 243 418 435 701 702 --include_name 'Dakota'" +MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[2006]" +PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 418 420 2006" Index: /issm/trunk/jenkins/ross-debian_linux-full =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-full (revision 25836) +++ /issm/trunk/jenkins/ross-debian_linux-full (revision 25836) @@ -0,0 +1,84 @@ +# NOTE: This configuration adds solid earth and Dakota capabilities to the +# basic build. + +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/usr/local/MATLAB/R2019b" + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-dir=/usr \ + --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux.sh + gsl install.sh + boost install-1.7-linux-valgrind.sh + dakota install-6.2-linux.sh + curl install-7-linux.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6-linux.sh + gmsh install-4.sh + triangle install-linux.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-full-valgrind =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-full-valgrind (revision 25836) +++ /issm/trunk/jenkins/ross-debian_linux-full-valgrind (revision 25836) @@ -0,0 +1,85 @@ +# NOTE: This configuration adds solid earth and Dakota capabilities to the +# basic build, as well as the ability to debug with Valgrind. + +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/usr/local/MATLAB/R2019b" + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-dir=/usr \ + --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux.sh + gsl install.sh + boost install-1.7-linux-valgrind.sh + dakota install-6.2-linux.sh + curl install-7-linux.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6-linux.sh + gmsh install-4.sh + triangle install-linux.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + valgrind install-linux.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-gia =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-gia (revision 25835) +++ /issm/trunk/jenkins/ross-debian_linux-gia (revision 25836) @@ -36,5 +36,5 @@ triangle install-linux.sh math77 install.sh - gmsh install.sh + gmsh install-4.sh shell2junit install.sh " Index: /issm/trunk/jenkins/ross-debian_linux-javascript =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-javascript (revision 25835) +++ /issm/trunk/jenkins/ross-debian_linux-javascript (revision 25836) @@ -10,5 +10,5 @@ --with-javascript \ --without-fortran \ - --without-GiaIvins \ + --without-Gia \ --without-Love \ --without-kml \ Index: /issm/trunk/jenkins/ross-debian_linux-python =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-python (revision 25835) +++ /issm/trunk/jenkins/ross-debian_linux-python (revision 25836) @@ -18,5 +18,9 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ @@ -33,4 +37,14 @@ cmake install.sh petsc install-3.12-linux.sh + gsl install.sh + boost install-1.7-linux.sh + dakota install-6.2-linux.sh + curl install-7-linux.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6-linux.sh + gmsh install-4.sh triangle install-linux.sh chaco install.sh @@ -64,4 +78,10 @@ # See documentation in test/NightlyRun/runme.* for more information. # +# NOTE: +# - Errors are large for tests 234, 418, and 420 under Python +# - Tests 2002, 2003, 2010, 2101, and 2021 are excluded as Gmsh produces +# different-sized meshes on macOS and Linux for 3d objects (archives are +# generated on macOS). +# MATLAB_NROPTIONS="" -PYTHON_NROPTIONS="--exclude_name 'Dakota'" +PYTHON_NROPTIONS="--exclude 234 418 420 2002 2003 2010 2021 2101" Index: /issm/trunk/jenkins/ross-debian_linux-solid_earth =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-solid_earth (revision 25835) +++ /issm/trunk/jenkins/ross-debian_linux-solid_earth (revision 25836) @@ -4,4 +4,5 @@ MATLAB_PATH="/usr/local/MATLAB/R2019b" + ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -20,7 +21,13 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ ' @@ -30,20 +37,23 @@ EXTERNALPACKAGES=" - autotools install-debian-linux.sh - cmake install.sh - petsc install-3.12-linux-solid_earth.sh - triangle install-linux.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - boost install-1.55-linux.sh - curl install-7.67.sh - netcdf install-4.7.sh - proj install-6.2.sh - gdal install-3.0-python-netcdf.sh - gshhg install.sh - gmt install-6.0-linux.sh - gmsh install.sh - shell2junit install.sh + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux.sh + gsl install.sh + boost install-1.7-linux.sh + dakota install-6.2-linux.sh + boost install-1.7-linux.sh + curl install-7-linux.sh + netcdf install-4.7-parallel.sh + proj install-6.2.sh + gdal install-3-python-netcdf.sh + gshhg install.sh + gmt install-6-linux.sh + gmsh install-4.sh + triangle install-linux.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh " @@ -75,4 +85,10 @@ # See documentation in test/NightlyRun/runme.* for more information. # -MATLAB_NROPTIONS="'benchmark','slr'" -PYTHON_NROPTIONS="--benchmark=slr" +# NOTE: +# - Tests 2002, 2003, 2005, 2010, 2101, and 2021 are excluded as Gmsh produces +# different-sized meshes on macOS and Linux for 3d objects (archives are +# generated on macOS). +# - Excluding 2006 until it can be debugged (PETSc crash) +# +MATLAB_NROPTIONS="'benchmark','slr','exclude',[2002 2003 2005 2006 2010 2021 2101]" +PYTHON_NROPTIONS="--benchmark slr --exclude 2002 2003 2005 2006 2010 2021 2101" Index: /issm/trunk/jenkins/ross-debian_linux-trunk =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-trunk (revision 25836) +++ /issm/trunk/jenkins/ross-debian_linux-trunk (revision 25836) @@ -0,0 +1,67 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/usr/local/MATLAB/R2019b" +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux.sh + triangle install-linux.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=1 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=2 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/windows =================================================================== --- /issm/trunk/jenkins/windows (revision 25835) +++ /issm/trunk/jenkins/windows (revision 25836) @@ -5,5 +5,5 @@ #MATLAB path -MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a/" +MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2019a" #ISSM CONFIGURATION @@ -14,5 +14,5 @@ --enable-standalone-libraries \ --with-fortran=no \ - --without-GiaIvins \ + --without-Gia \ --without-Love \ --without-kriging \ @@ -38,9 +38,11 @@ #List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES="autotools install-win.sh - petsc install-3.6-win10.sh - metis install-4.0-win10.sh - triangle install-windows-static.sh - shell2junit install.sh" +EXTERNALPACKAGES=" + autotools install-win.sh + petsc install-3.6-win10.sh + metis install-4.0-win10.sh + triangle install-windows-static.sh + shell2junit install.sh +" #-----------------# @@ -61,4 +63,4 @@ #In Windows, we don't yet have MUMPS, can't do full stokes, so exclude all FS runs. Also exclude all runs with Dakota. And exclude higher order runs that have penalties. And 800+ tests because we don't want to have --with-development since we do the binaries with this version -MATLAB_NROPTIONS="'exclude',[104,119, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440,444, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280, 801, 802, 803, 804, 805, 291, 340, 341, 460, 243, 430, 441, 442, 463, 464, 465, 244, IdFromString('Dakota')]" +MATLAB_NROPTIONS="'exclude',[104,119,124,125,126,204,205,211,215,218,220,221,234,235,243,244,250,251,274,280,285,290,291,308,322,331,340,341,404,405,409,412,413,414,417,418,420,421,422,430,435,440,441,442,444,455,460,463,464,465,503,507,510,511,513,514,612,701,702,703,801,802,803,804,805,IdFromString('Dakota')]" PYTHON_NROPTIONS="--exclude_name 'Dakota'" Index: /issm/trunk/jenkins/windows_static =================================================================== --- /issm/trunk/jenkins/windows_static (revision 25835) +++ /issm/trunk/jenkins/windows_static (revision 25836) @@ -15,5 +15,5 @@ --with-vendor=MSVC-Win64 \ --with-fortran=no \ - --without-GiaIvins \ + --without-Gia \ --without-Love \ --without-kriging \ Index: /issm/trunk/m4/analyses.m4 =================================================================== --- /issm/trunk/m4/analyses.m4 (revision 25835) +++ /issm/trunk/m4/analyses.m4 (revision 25836) @@ -248,17 +248,17 @@ AC_MSG_RESULT($HAVE_GLHEIGHTADVECTION) dnl }}} -dnl with-GiaIvins{{{ -AC_ARG_WITH([GiaIvins], - AS_HELP_STRING([--with-GiaIvins = YES], [compile with GiaIvins capabilities (default is yes)]), - [GIAIVINS=$withval],[GIAIVINS=yes]) -AC_MSG_CHECKING(for GiaIvins capability compilation) - -HAVE_GIAIVINS=no -if test "x$GIAIVINS" = "xyes"; then - HAVE_GIAIVINS=yes - AC_DEFINE([_HAVE_GIAIVINS_],[1],[with GiaIvins capability]) -fi -AM_CONDITIONAL([GIAIVINS], [test x$HAVE_GIAIVINS = xyes]) -AC_MSG_RESULT($HAVE_GIAIVINS) +dnl with-Gia{{{ +AC_ARG_WITH([Gia], + AS_HELP_STRING([--with-Gia= YES], [compile with Gia capabilities (default is yes)]), + [GIA=$withval],[GIA=yes]) +AC_MSG_CHECKING(for Gia capability compilation) + +HAVE_GIA=no +if test "x$GIA" = "xyes"; then + HAVE_GIA=yes + AC_DEFINE([_HAVE_GIA_],[1],[with Giacapability]) +fi +AM_CONDITIONAL([GIA], [test x$HAVE_GIA = xyes]) +AC_MSG_RESULT($HAVE_GIA) dnl }}} dnl with-HydrologyDCEfficient{{{ Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 25835) +++ /issm/trunk/m4/issm_options.m4 (revision 25836) @@ -190,6 +190,36 @@ [VENDOR=""] dnl action if not given ) - dnl defaults for host OS related variables - IS_MAC=no + + AC_MSG_CHECKING([if this is a Mac build]) + case "${host_os}" in + *darwin*) + IS_MAC=yes + AC_DEFINE([_MAC_], [1], [is macOS]) + ;; + *) + IS_MAC=no + AC_DEFINE([_MAC_], [0], [is macOS]) + ;; + esac + AM_CONDITIONAL([MAC], [test "${IS_MAC}" == "yes"]) + AC_MSG_RESULT([${IS_MAC}]) + + dnl If macOS, check if system copy of libc has fmemopen (if it is not + dnl macOS, we do not check, but still must set SYSTEM_HAS_FMEMOPEN) + AC_MSG_CHECKING([if system copy of libc has fmemopen]) + SYSTEM_FMEMOPEN=1 + if test "${IS_MAC}" == "yes"; then + if [[ $(system_profiler SPSoftwareDataType | grep "System Version:" | sed -e "s/[[:space:]]*System Version: macOS //" | cut -d "." -f 2) -lt 13 ]]; then + SYSTEM_FMEMOPEN=0 + fi + fi + if test "${SYSTEM_FMEMOPEN}" == "1"; then + AC_MSG_RESULT([yes]) + else + AC_MSG_RESULT([no]) + fi + AC_DEFINE_UNQUOTED([_SYSTEM_HAS_FMEMOPEN_], $SYSTEM_FMEMOPEN, [does system copy of libc have fmemopen]) + AM_CONDITIONAL([SYSTEM_HAS_FMEMOPEN], [test "${SYSTEM_FMEMOPEN}" == "1"]) + IS_WINDOWS=no AC_MSG_CHECKING([for vendor compilers]) @@ -267,5 +297,5 @@ export CC=icc export CXX=icpc - export CXXFLAGS="-O3 -D_INTEL_LINUX_" + export CXXFLAGS="-O3 -D_INTEL_LINUX_ -std=c++11" export CFLAGS="-O3 -D_INTEL_LINUX_" elif test "${VENDOR}" == "intel-acenet"; then @@ -277,6 +307,10 @@ export CC=gcc export CXX=g++ - export CXXFLAGS="-O3 -march=corei7-avx" + export CXXFLAGS="-O3 -march=corei7-avx -std=c++11" export CFLAGS="-O3 -march=corei7-avx" + elif test "${VENDOR}" == "intel-pleiades-icpc"; then + export CXXFLAGS="-g -O3 -ipo -axAVX -ipo -no-inline-min-size -inline-max-size=345 -no-inline-max-total-size -no-inline-max-per-routine -no-inline-max-per-compile -restrict -std=c++11" + export CFLAGS="-g -O3 -ipo -axAVX -ipo -no-inline-min-size -inline-max-size=345 -no-inline-max-total-size -no-inline-max-per-routine -no-inline-max-per-compile -restrict" + AC_DEFINE([_HAVE_RESTRICT_], [1], [with restrict buffers]) else AC_MSG_ERROR([unknown compiler vendor!]) @@ -285,14 +319,4 @@ AC_SUBST([OSLIBS]) AC_MSG_RESULT([done]) - - AC_MSG_CHECKING([if this is a Mac build]) - dnl TODO: The following test is a POSIX-compliant way of testing for a - dnl substring, but is not very readable. Perhaps there is a more - dnl readable method of achieving the same? - if test "${host_os#*\"darwin\"}" == "$host_os"; then - IS_MAC=yes - fi - AM_CONDITIONAL([MAC], [test "${IS_MAC}" == "yes"]) - AC_MSG_RESULT([${IS_MAC}]) AC_MSG_CHECKING([if this is a Windows build]) @@ -366,4 +390,7 @@ MEXLIB=$(cat conftest.tmp | grep LINKLIBS | sed -e "s/LINKLIBS ://g") MEXEXT=$(cat conftest.tmp | grep LDEXT | sed -e "s/LDEXT ://g" | awk '{print $[1]}') + if test -z "${MEXEXT}"; then + cat conftest.tmp + fi rm -f conftest.tmp fi @@ -376,5 +403,5 @@ AC_MSG_RESULT([done]) if test -z "${MEXEXT}"; then - AC_MSG_ERROR([Couldn't find mex... check your installation of MATLAB]) + AC_MSG_ERROR([Couldn't use MATLAB's mex... check manual compilation with MATLAB or error message above]) fi @@ -514,8 +541,8 @@ AC_MSG_CHECKING(for Dakota version) - dnl TODO: Check if this method applies to all other versions of - dnl (it should as long as the Dakota binaries have been - dnl compiled). If so, we can remove the other methods of - dnl getting the version. + dnl TODO: Check if this method applies to all other versions of + dnl Dakota (it should as long as the Dakota binaries have been + dnl compiled). If so, we can remove the other methods of + dnl getting the version. dnl DAKOTA_VERSION_OUTPUT=`${DAKOTA_ROOT}/bin/dakota -v` @@ -537,6 +564,10 @@ dnl NOTE: - dnl - See $ISSM_DIR/dakota/build/src/Makefile.export.Dakota for the - dnl flags needed by your combination of Boost and Dakota versions + dnl - See, + dnl + dnl $ISSM_DIR/externalpackages/dakota/build/src/Makefile.export.Dakota + dnl + dnl for the flags needed by your combination of Boost and Dakota + dnl versions dnl - We know $DAKOTA_ROOT cannot be empty at this point, so no need to dnl check again in the following conditionals @@ -552,5 +583,5 @@ DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" DAKOTALIB="-L${DAKOTA_ROOT}/lib -L${BOOST_ROOT}/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -lscolib -ljega_fe -llhs -lpebbl -lcolin -linterfaces -llhs_mods -lmoga -loptpp -lsoga -lsurfpack -lutilib -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -l3po -lamplsolver -lcport -ldfftpack -leutils -lfsudace -lhopspack -ljega -lnidr -lpecos -lpsuade -ltinyxml -lutilities -lsparsegrid -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" - AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [disabling DAKOTA_CONFIG_H]) + AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H]) AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling parallel MPI]) else @@ -564,18 +595,14 @@ DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" DAKOTALIB="-L${DAKOTA_ROOT}/lib -L${BOOST_ROOT}/lib -ldakota_src -lpecos_src -lscolib -ljega_fe -llhs -lpebbl -lcolin -linterfaces -lmods -lmoga -loptpp -lsampling -lsoga -lsurfpack -lutilib -lconmin -ldakota_src_fortran -lmod -lncsuopt -lsurfpack_fortran -lteuchos -l3po -lamplsolver -lanalyzer -lbose -lcport -ldace -ldfftpack -leutils -lfsudace -lhopspack -ljega -lnidr -lpecos -lpsuade -lrandom -ltinyxml -lutilities -lsparsegrid -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" - AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [disabling DAKOTA_CONFIG_H]) + AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H]) AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI]) elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then if test "${BOOST_VERSION_MAJOR}" == "1"; then - if test "${BOOST_VERSION_MINOR}" == "55"; then - DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" - DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -L${BOOST_ROOT}/lib -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system ${BLASLAPACKLIB}" - elif test "${BOOST_VERSION_MINOR}" = "72"; then - DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" - dnl See $ISSM_DIR/dakota/build/src/Makefile.export.Dakota -> Dakota_LIBRARIES - DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system ${BLASLAPACKLIB}" - fi + DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" + DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lqueso -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver" + DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system" + DAKOTALIB+=" ${BLASLAPACKLIB}" fi - AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [disabling DAKOTA_CONFIG_H]) + AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H]) AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI]) elif test "${DAKOTA_VERSION}" == "6.11"; then @@ -589,5 +616,5 @@ fi fi - AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [disabling DAKOTA_CONFIG_H]) + AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H]) AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI]) else @@ -601,18 +628,14 @@ DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" DAKOTALIB="-L${DAKOTA_ROOT}/lib -L${BOOST_ROOT}/lib -ldakota_src -lpecos_src -lscolib -ljega_fe -llhs -lpebbl -lcolin -linterfaces -lmods -lmoga -loptpp -lsampling -lsoga -lsurfpack -lutilib -lconmin -ldakota_src_fortran -lmod -lncsuopt -lsurfpack_fortran -lteuchos -l3po -lamplsolver -lanalyzer -lbose -lcport -ldace -ldfftpack -leutils -lfsudace -lhopspack -ljega -lnidr -lpecos -lpsuade -lrandom -ltinyxml -lutilities -lsparsegrid -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" - AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [disabling DAKOTA_CONFIG_H]) + AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H]) AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI]) elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then if test "${BOOST_VERSION_MAJOR}" == "1"; then - if test "${BOOST_VERSION_MINOR}" == "55"; then - DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" - DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -L${BOOST_ROOT}/lib -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system ${BLASLAPACKLIB}" - elif test "${BOOST_VERSION_MINOR}" = "72"; then - DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" - dnl See $ISSM_DIR/dakota/build/src/Makefile.export.Dakota -> Dakota_LIBRARIES - DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system ${BLASLAPACKLIB}" - fi + DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" + DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lqueso -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver" + DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system" + DAKOTALIB+=" ${BLASLAPACKLIB}" fi - AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [disabling DAKOTA_CONFIG_H]) + AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H]) AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI]) elif test "${DAKOTA_VERSION}" == "6.11"; then @@ -626,5 +649,5 @@ fi fi - AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [disabling DAKOTA_CONFIG_H]) + AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H]) AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI]) else @@ -655,5 +678,5 @@ AC_MSG_RESULT(${DAKOTA_MINOR}) AC_DEFINE_UNQUOTED(_DAKOTA_MINOR_, $DAKOTA_MINOR, [Dakota minor version number]) - AC_MSG_CHECKING(for dakota build version) + AC_MSG_CHECKING(for Dakota build version) AC_MSG_RESULT(${DAKOTA_BUILD}) AC_DEFINE_UNQUOTED(_DAKOTA_BUILD_, $DAKOTA_BUILD, [Dakota build version number]) @@ -1125,4 +1148,43 @@ AM_CONDITIONAL([MEDIPACK], [test "x${HAVE_MEDIPACK}" == "xyes"]) dnl }}} + dnl HDF5 {{{ + AC_ARG_WITH( + [hdf5-dir], + AS_HELP_STRING([--with-hdf5-dir=DIR], [HDF5 root directory]), + [HDF5_ROOT=${withval}], + [HDF5_ROOT="no"] + ) + AC_MSG_CHECKING(for HDF5 libraries) + if test "x${HDF5_ROOT}" == "xno"; then + HAVE_HDF5=no + else + HAVE_HDF5=yes + if ! test -d "${HDF5_ROOT}"; then + AC_MSG_ERROR([HDF5 directory provided (${HDF5_ROOT}) does not exist!]); + fi + fi + AC_MSG_RESULT([${HAVE_HDF5}]) + + dnl HDF5 libraries and header files + dnl + dnl TODO: Add check for if we need to link to libhdf5_fortran and + dnl libhdf5hl_fortran, if and when necessary. + dnl + if test "x${HAVE_HDF5}" == "xyes"; then + case "${host_os}" in + *cygwin*) + HDF5LIB="-L`cygpath -m ${HDF5_ROOT}` -Wl,libhdf5.lib -Wl,libhdf5_hl.lib" + ;; + *linux*) + HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl" + ;; + *darwin*) + HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl" + ;; + esac + AC_DEFINE([_HAVE_HDF5_], [1], [with HDF5 in ISSM src]) + AC_SUBST([HDF5LIB]) + fi + dnl }}} dnl PETSc{{{ AC_ARG_WITH( @@ -1146,19 +1208,17 @@ dnl PETSc libraries and header files if test "x${HAVE_PETSC}" == "xyes"; then - AC_MSG_CHECKING(for PETSc version) if ! test -f "${PETSC_ROOT}/include/petscversion.h"; then AC_MSG_ERROR([PETSc not instaled correctly: file (${PETSC_ROOT}/include/petscversion.h) does not exist!]); fi + + AC_MSG_CHECKING(for PETSc version) PETSC_MAJOR=`cat ${PETSC_ROOT}/include/petscversion.h | grep "#define PETSC_VERSION_MAJOR" | sed 's/#define PETSC_VERSION_MAJOR//' | sed 's/ //g'` PETSC_MINOR=`cat ${PETSC_ROOT}/include/petscversion.h | grep "#define PETSC_VERSION_MINOR" | sed 's/#define PETSC_VERSION_MINOR//' | sed 's/ //g'` - AC_DEFINE_UNQUOTED(_PETSC_MAJOR_, $PETSC_MAJOR, [PETSc version major]) - AC_DEFINE_UNQUOTED(_PETSC_MINOR_, $PETSC_MINOR, [PETSc version minor]) + AC_DEFINE_UNQUOTED([_PETSC_MAJOR_], [$PETSC_MAJOR], [PETSc version major]) + AC_DEFINE_UNQUOTED([_PETSC_MINOR_], [$PETSC_MINOR], [PETSc version minor]) AC_MSG_RESULT([${PETSC_MAJOR}.${PETSC_MINOR}]) - dnl PETSC_VERSION_DATE_HG=`cat ${PETSC_ROOT}/include/petscversion.h | grep "#define PETSC_VERSION_DATE_HG" | sed 's/#define PETSC_VERSION_DATE_HG//' | sed 's/ //g' | sed -e 's/\"//g' ` + AC_MSG_CHECKING(whether PETSc is the development version) PETSC_RELEASE=`cat ${PETSC_ROOT}/include/petscversion.h | grep "#define PETSC_VERSION_RELEASE" | sed 's/#define PETSC_VERSION_RELEASE//' | sed 's/ //g'` - - AC_MSG_CHECKING(whether PETSc is the development version) - dnl if test "x${PETSC_VERSION_DATE_HG}" == "xunknown"; then if test "${PETSC_RELEASE}" == "0"; then AC_DEFINE([_HAVE_PETSCDEV_], [1], [with PETSc-dev]) @@ -1210,4 +1270,7 @@ if test "x$host_os_version" = "x3.0.101-0.31.1_1.0502.8394-cray_gem_s"; then PETSCLIB="-L${PETSC_ROOT}/lib -lcraypetsc_gnu_real -lmetis" + fi + if test x$HOST = "xmaui01"; then + PETSCLIB="-L${PETSC_ROOT}/lib -lcraypetsc_intel_real -lmetis" fi ;; @@ -1471,31 +1534,31 @@ fi dnl }}} - dnl PROJ.4{{{ - AC_ARG_WITH( - [proj4-dir], - AS_HELP_STRING([--with-proj4-dir=DIR], [PROJ.4 root directory]), - [PROJ4_ROOT=${withval}], - [PROJ4_ROOT="no"] - ) - AC_MSG_CHECKING([for PROJ.4]) - if test "x${PROJ4_ROOT}" == "xno"; then - HAVE_PROJ4=no - else - HAVE_PROJ4=yes - if ! test -d "${PROJ4_ROOT}"; then - AC_MSG_ERROR([PROJ.4 directory provided (${PROJ4_ROOT}) does not exist!]); - fi - fi - AC_MSG_RESULT([${HAVE_PROJ4}]) - - dnl PROJ.4 libraries and header files - if test "x${HAVE_PROJ4}" == "xyes"; then - PROJ4INCL="-I${PROJ4_ROOT}/include" - PROJ4LIB="-L${PROJ4_ROOT}/lib -lproj" - AC_DEFINE([_HAVE_PROJ4_], [1], [with PROJ4 in ISSM src]) - AC_SUBST([PROJ4INCL]) - AC_SUBST([PROJ4LIB]) - fi - AM_CONDITIONAL([PROJ4], [test "x${HAVE_PROJ4}" == "xyes"]) + dnl PROJ{{{ + AC_ARG_WITH( + [proj-dir], + AS_HELP_STRING([--with-proj-dir=DIR], [PROJ root directory]), + [PROJ_ROOT=${withval}], + [PROJ_ROOT="no"] + ) + AC_MSG_CHECKING([for PROJ]) + if test "x${PROJ_ROOT}" == "xno"; then + HAVE_PROJ=no + else + HAVE_PROJ=yes + if ! test -d "${PROJ_ROOT}"; then + AC_MSG_ERROR([PROJ directory provided (${PROJ_ROOT}) does not exist!]); + fi + fi + AC_MSG_RESULT([${HAVE_PROJ}]) + + dnl PROJ libraries and header files + if test "x${HAVE_PROJ}" == "xyes"; then + PROJINCL="-I${PROJ_ROOT}/include" + PROJLIB="-L${PROJ_ROOT}/lib -lproj" + AC_DEFINE([_HAVE_PROJ_], [1], [with PROJ in ISSM src]) + AC_SUBST([PROJINCL]) + AC_SUBST([PROJLIB]) + fi + AM_CONDITIONAL([PROJ], [test "x${HAVE_PROJ}" == "xyes"]) dnl }}} dnl SLEPc{{{ @@ -1696,5 +1759,5 @@ HAVE_PLAPACK=no fi - elses + else HAVE_PLAPACK=no fi @@ -2263,4 +2326,32 @@ AM_CONDITIONAL([NEOPZ], [test "x${HAVE_NEOPZ}" == "xyes"]) dnl }}} + dnl Gmsh{{{ + AC_MSG_CHECKING([for Gmsh]) + AC_ARG_WITH( + [gmsh-dir], + AS_HELP_STRING([--with-gmsh-dir=DIR], [Gmsh root directory]), + [GMSH_ROOT=${withval}], + [GMSH_ROOT="no"] + ) + if test "x${GMSH_ROOT}" == "xno"; then + HAVE_GMSH=no + else + HAVE_GMSH=yes + if ! test -d "${GMSH_ROOT}"; then + AC_MSG_ERROR([Gmsh directory provided (${GMSH_ROOT}) does not exist!]); + fi + fi + AC_MSG_RESULT([${HAVE_GMSH}]) + AM_CONDITIONAL([GMSH], [test "x${HAVE_GMSH}" == "xyes"]) + + if test "x${HAVE_GMSH}" == "xyes"; then + AC_DEFINE([_HAVE_GMSH_], [1], [with Gmsh in ISSM src]) + + AC_MSG_CHECKING(for Gmsh version) + GMSH_VERSION_MAJOR=`${GMSH_ROOT}/bin/gmsh -info | grep "Version" | sed -e "s/Version@<:@@<:@:blank:@:>@@:>@*:@<:@@<:@:blank:@:>@@:>@//" | cut -d "." -f 1` + AC_MSG_RESULT([${GMSH_VERSION_MAJOR}]) + AC_DEFINE_UNQUOTED(_GMSH_VERSION_MAJOR_, $GMSH_VERSION_MAJOR, [Gmsh major version]) + fi + dnl }}} dnl Capabilities dnl with-bamg{{{ @@ -2400,10 +2491,10 @@ dnl other options dnl optimization{{{ - dnl -- bypass standard optimization -g -O2 -fPIC ? + dnl -- bypass standard optimization -g -O2 -fPIC -std=c++11? AC_ARG_WITH( [cxxoptflags], - AS_HELP_STRING([--with-cxxoptflags=CXXOPTFLAGS], [C++ optimization flags (i.e. --with-cxxoptflags="-march=opteron -O3"]), + AS_HELP_STRING([--with-cxxoptflags=CXXOPTFLAGS], [C++ optimization flags (i.e. --with-cxxoptflags="-march=opteron -O3 -std=c++11"]), [CXXOPTFLAGS=${withval}], - [CXXOPTFLAGS="-g -O2 -fPIC"] + [CXXOPTFLAGS="-g -O2 -fPIC -std=c++11"] ) AC_MSG_CHECKING(for C++ optimization flags) @@ -2478,7 +2569,7 @@ fi - dnl Check that Fortran is provided if GiaIvins is on - if test "x${HAVE_GIAIVINS}" == "xyes" && test "${HAVE_FORTRAN}" == "xno"; then - AC_MSG_ERROR([need Fortran compiler to compile GiaIvins! (or use --without-GiaIvins )]); + dnl Check that Fortran is provided if Gia is on + if test "x${HAVE_GIA}" == "xyes" && test "${HAVE_FORTRAN}" == "xno"; then + AC_MSG_ERROR([need Fortran compiler to compile Gia! (or use --without-Gia)]); fi Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh (revision 25836) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh (revision 25836) @@ -0,0 +1,185 @@ +#!/bin/bash + +################################################################################ +# To be used after running, +# +# ${ISSM_DIR}/jenkins/jenkins.sh ${ISSM_DIR}/jenkins/ross-debian_linux-binaries-matlab +# +# in the context of a Jenkins project. +# +# When no runtime errors occur, performs the following: +# - Checks resulting executables and libraries against test suite. +# - Packages and compresses executables and libraries. +# - Transmits it to ISSM Web site for distribution. +# +# Options: +# -s/--skiptests Skip tests (use if this script fails for some reason +# after tests have successfully passed to save time) +# -t/--transferonly Transfer package to ISSM Web site only (use if +# transfer fails for some reason to skip testing and +# signing) +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +## Override certain aliases +# +alias grep=$(which grep) + +## Constants +# +LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself +LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it +MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2005,2006,2010,2020,2021,2051,2052,2053,2101,2102,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded +MATLAB_PATH="/usr/local/MATLAB/R2019b" +PKG="ISSM-Linux-MATLAB" # Name of directory to copy distributable files to + +COMPRESSED_PKG="${PKG}.tar.gz" + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +skip_tests=0 +transfer_only=0 +while [ $# -gt 0 ]; do + case $1 in + -s|--skiptests) skip_tests=1; shift ;; + -t|--transferonly) transfer_only=1; shift ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac + shift +done + +if [ ${transfer_only} -eq 0 ]; then + # Check if MATLAB exists + if ! [ -d ${MATLAB_PATH} ]; then + echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again." + exit 1 + fi + + # Clean up from previous packaging + echo "Cleaning up existing assets" + cd ${ISSM_DIR} + rm -rf ${PKG} ${COMPRESSED_PKG} + mkdir ${PKG} + + # Add/modify required binaries and libraries + cd ${ISSM_DIR}/bin + + echo "Modify generic" + cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m + + echo "Moving MPICH binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . + elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . + else + echo "MPICH not found" + exit 1 + fi + + echo "Moving GDAL binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . + else + echo "GDAL not found" + exit 1 + fi + + echo "Moving GMT binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . + else + echo "GMT not found" + exit 1 + fi + + echo "Moving Gmsh binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then + cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . + else + echo "Gmsh not found" + exit 1 + fi + + echo "Moving libgfortran to lib/" + cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null + + + # Run tests + if [ ${skip_tests} -eq 0 ]; then + echo "Running tests" + cd ${ISSM_DIR}/test/NightlyRun + rm matlab.log 2> /dev/null + + # Run tests, redirecting output to logfile and suppressing output to console + ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null + + # Check that MATLAB did not exit in error + matlabExitCode=`echo $?` + matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l` + + if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then + echo "----------MATLAB exited in error!----------" + cat matlab.log + echo "-----------End of matlab.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 + fi + + # Check that all tests passed + numTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"` + + if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 + else + echo "All tests PASSED" + fi + else + echo "Skipping tests" + fi + + # Create package + cd ${ISSM_DIR} + svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) + echo "Copying assets to package: ${PKG}" + cp -rf bin examples lib scripts test ${PKG}/ + mkdir ${PKG}/execution + echo "Cleaning up unneeded/unwanted files" + rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes + rm -f ${PKG}/lib/*.a # Remove static libraries from package + rm -f ${PKG}/lib/*.la # Remove libtool libraries from package + rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package + + # Compress package + echo "Compressing package" + tar -czf ${COMPRESSED_PKG} ${PKG} + ls -lah ${ISSM_DIR}/${COMPRESSED_PKG} +fi + +# Transfer package to ISSM Web site +echo "Transferring package to ISSM Web site" +scp -i ~/.ssh/debian_linux-vm_to_ross ${COMPRESSED_PKG} jenkins@ross.ics.uci.edu:/var/www/html/${COMPRESSED_PKG} + +if [ $? -ne 0 ]; then + echo "Transfer failed! Verify connection then build this project again." + exit 1 +fi Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-python.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-python.sh (revision 25836) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries-python.sh (revision 25836) @@ -0,0 +1,191 @@ +#!/bin/bash + +################################################################################ +# To be used after running, +# +# ${ISSM_DIR}/jenkins/jenkins.sh ${ISSM_DIR}/jenkins/ross-debian_linux-binaries-matlab +# +# in the context of a Jenkins project. +# +# When no runtime errors occur, performs the following: +# - Checks resulting executables and libraries against test suite. +# - Packages and compresses executables and libraries. +# - Transmits it to ISSM Web site for distribution. +# +# Options: +# -s/--skiptests Skip tests (use if this script fails for some reason +# after tests have successfully passed to save time) +# -t/--transferonly Transfer package to ISSM Web site only (use if +# transfer fails for some reason to skip testing and +# signing) +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +## Override certain aliases +# +alias grep=$(which grep) + +## Constants +# +LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself +LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2005 2006 2010 2020 2021 2051 2052 2053 2101 2102 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded +PKG="ISSM-Linux-Python" # Name of directory to copy distributable files to + +COMPRESSED_PKG="${PKG}.tar.gz" + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +skip_tests=0 +transfer_only=0 +while [ $# -gt 0 ]; do + case $1 in + -s|--skiptests) skip_tests=1; shift ;; + -t|--transferonly) transfer_only=1; shift ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac + shift +done + +if [ ${transfer_only} -eq 0 ]; then + # Check if MATLAB exists + if ! [ -d ${MATLAB_PATH} ]; then + echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again." + exit 1 + fi + + # Clean up from previous packaging + echo "Cleaning up existing assets" + cd ${ISSM_DIR} + rm -rf ${PKG} ${COMPRESSED_PKG} + mkdir ${PKG} + + # Add/modify required binaries and libraries + cd ${ISSM_DIR}/bin + + echo "Modify generic" + cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py + + echo "Moving MPICH binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . + elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . + else + echo "MPICH not found" + exit 1 + fi + + echo "Moving GDAL binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . + else + echo "GDAL not found" + exit 1 + fi + + echo "Moving GMT binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . + else + echo "GMT not found" + exit 1 + fi + + echo "Moving Gmsh binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then + cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . + else + echo "Gmsh not found" + exit 1 + fi + + echo "Moving libgfortran to lib/" + cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null + + + # Run tests + if [ ${skip_tests} -eq 0 ]; then + echo "Running tests" + cd ${ISSM_DIR}/test/NightlyRun + rm python.log 2> /dev/null + + # Set Python environment + export PYTHONPATH="${ISSM_DIR}/src/m/dev" + export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" + export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + + # Run tests, redirecting output to logfile and suppressing output to console + ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + + # Check that Python did not exit in error + pythonExitCode=`echo $?` + pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l` + + if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 + fi + + # Check that all tests passed + numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + + if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 + else + echo "All tests PASSED" + fi + else + echo "Skipping tests" + fi + + # Create package + cd ${ISSM_DIR} + svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) + echo "Copying assets to package: ${PKG}" + cp -rf bin examples lib scripts test ${PKG}/ + mkdir ${PKG}/execution + ${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files + echo "Cleaning up unneeded/unwanted files" + rm -f ${PKG}/bin/*.py # Remove all Python scripts + rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes + rm -f ${PKG}/lib/*.a # Remove static libraries from package + rm -f ${PKG}/lib/*.la # Remove libtool libraries from package + rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package + + # Compress package + echo "Compressing package" + tar -czf ${COMPRESSED_PKG} ${PKG} + ls -lah ${ISSM_DIR}/${COMPRESSED_PKG} +fi + +# Transfer package to ISSM Web site +echo "Transferring package to ISSM Web site" +scp -i ~/.ssh/debian_linux-vm_to_ross ${COMPRESSED_PKG} jenkins@ross.ics.uci.edu:/var/www/html/${COMPRESSED_PKG} + +if [ $? -ne 0 ]; then + echo "Transfer failed! Verify connection then build this project again." + exit 1 +fi Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-solid_earth.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-solid_earth.sh (revision 25836) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries-solid_earth.sh (revision 25836) @@ -0,0 +1,181 @@ +#!/bin/bash + + +# Script to test, package, and transfer distributable to ISSM Web site. +# Corresponds with build generated by configuration in +# $ISSM_DIR/jenkins/ross-debian_linux-binaries-solid_earth. +# + +## Constants +# +LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself +LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it +MATLAB_NROPTIONS="'benchmark','slr','exclude',[2002 2003 2010 2020 2021 2101]" +MATLAB_PATH="/usr/local/MATLAB/R2019b" +PACKAGE="ISSM-Solid_Earth" # Name of directory to copy distributable files to +PYTHON_NROPTIONS="--benchmark slr --exclude 2002 2003 2010 2020 2021 2101" +TARBALL_NAME="issm-linux-solid_earth" +TARBALL="${TARBALL_NAME}.tar.gz" + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +# Check if MATLAB exists +if ! [ -d ${MATLAB_PATH} ]; then + echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again." + exit 1 +fi + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd ${ISSM_DIR} +rm -rf ${PACKAGE} +mkdir ${PACKAGE} + +# Add/modify required binaries +cd ${ISSM_DIR}/bin + +echo "Modifying generic" +cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m +cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py + +echo "Moving MPICH binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . +elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "MPICH not found" + exit 1 +fi + +echo "Moving GDAL binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . +else + echo "GDAL not found" + exit 1 +fi + +echo "Moving GMT binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . +else + echo "GMT not found" + exit 1 +fi + +echo "Moving Gmsh binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then + cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . +else + echo "Gmsh not found" + exit 1 +fi + +# Add/modify required libraries +echo "Moving libgfortran to lib/" +cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null + +# Run tests +echo "Running tests" +cd ${ISSM_DIR}/test/NightlyRun + +# Check that MATLAB tests run +echo "Running MATLAB tests" + +rm matlab.log 2> /dev/null + +# Run MATLAB tests redirecting output to logfile and suppressing output to console +${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null + +# Check that MATLAB did not exit in error +matlabExitCode=`echo $?` +matlabExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" matlab.log | wc -l` + +if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then + echo "----------MATLAB exited in error!----------" + cat matlab.log + echo "-----------End of matlab.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 +fi + +# Check that all MATLAB tests passed +numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numMatlabTestsFailed} -ne 0 ]]; then + echo "One or more MATLAB tests FAILED" + exit 1; +else + echo "All MATLAB tests PASSED" +fi + +# Check that Python tests run +echo "Running Python tests" + +export PATH="${PATH}:${ISSM_DIR}/bin" +export PYTHONPATH="${ISSM_DIR}/src/m/dev" +export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" +export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + +rm python.log 2> /dev/null +./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + +# Check that Python did not exit in error +pythonExitCode=`echo $?` +pythonExitedInError=`grep -E "Error|Traceback|bad interpreter" python.log | wc -l` + +if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 +fi + +# Check that all Python tests passed +numPythonTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numPythonTestsFailed} -ne 0 ]]; then + echo "One or more Python tests FAILED" + exit 1 +else + echo "All Python tests PASSED" +fi + +# Create tarball +cd ${ISSM_DIR} +rm -f ${TARBALL} +svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) +echo "Copying assets to package: ${PACKAGE}" +cp -rf bin examples lib scripts test ${PACKAGE}/ +echo "Cleaning up unneeded/unwanted files" +python -m compileall ${PACKAGE}/bin # Precompile all Python scripts to bytecode +rm -f ${PACKAGE}/bin/*.py # Remove all Python scripts +rm -f ${PACKAGE}/bin/generic_static.* # Remove static versions of generic cluster classes +rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package +rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package +rm -rf ${PACKAGE}/test/SandBox # Remove testing sandbox from package +echo "Creating tarball: ${TARBALL_NAME}" +tar -czf ${TARBALL} ${PACKAGE} +ls -lah ${ISSM_DIR}/${TARBALL} + +echo "Transferring binaries to ISSM Web site" +scp -i ~/.ssh/debian_linux-vm_to_ross ${TARBALL} jenkins@ross.ics.uci.edu:/var/www/html/${TARBALL} + +if [ $? -ne 0 ]; then + echo "FAILED: Manually check connection" + exit 1 +fi Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-with_dakota.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-with_dakota.sh (revision 25835) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries-with_dakota.sh (revision 25836) @@ -1,4 +1,9 @@ #!/bin/bash + +# Script to test, package, and transfer distributable to ISSM Web site. +# Corresponds with build generated by configuration in +# $ISSM_DIR/jenkins/ross-debian_linux-binaries-with_dakota. +# ## Constants @@ -6,17 +11,20 @@ LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it -MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,243,244,250,417,444,445,701,702]" # Exclude any tests with transient solutions that require a restart +MATLAB_NROPTIONS="'id',[IdFromString('Dakota')]" MATLAB_PATH="/usr/local/MATLAB/R2019b" PACKAGE="ISSM" # Name of directory to copy distributable files to - -# Exclude any tests with transient solutions that require a restart -# -# NOTE: -# - All non-excluded tests were running until recent changes to QMU -# - 418 fails with "malloc(): invalid next size (unsorted)"" -# -PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 243 244 250 417 418 435 444 445 701 702" +PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 418 420" TARBALL_NAME="issm-linux-with_dakota" TARBALL="${TARBALL_NAME}.tar.gz" + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +# Check if MATLAB exists +if ! [ -d ${MATLAB_PATH} ]; then + echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again." + exit 1 +fi # Clean up from previous packaging @@ -63,5 +71,5 @@ # Check that MATLAB did not exit in error matlabExitCode=`echo $?` -matlabExitedInError=`grep -E "Activation cannot proceed|license" matlab.log | wc -l` +matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l` if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then @@ -99,5 +107,5 @@ # Check that Python did not exit in error pythonExitCode=`echo $?` -pythonExitedInError=`grep -E "Error|Traceback|bad interpreter" python.log | wc -l` +pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l` if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then @@ -117,5 +125,5 @@ if [[ ${numPythonTestsFailed} -ne 0 ]]; then echo "One or more Python tests FAILED" - exit 1; + exit 1 else echo "All Python tests PASSED" @@ -134,29 +142,14 @@ rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package +rm -rf ${PACKAGE}/test/SandBox # Remove testing sandbox from package echo "Creating tarball: ${TARBALL_NAME}" tar -czf ${TARBALL} ${PACKAGE} ls -lah ${ISSM_DIR}/${TARBALL} -echo "Shipping binaries to website" - -# We're using public key authentication method to upload the tarball The -# following lines check to see if the SSH Agent is running. If not, then it is -# started and relevant information is forwarded to a script. -pgrep "ssh-agent" > /dev/null -if [ $? -ne 0 ]; then - echo "SSH Agent is not running. Starting it..." - ssh-agent > ~/.ssh/agent.sh -else - echo "SSH Agent is running..." -fi - -source ~/.ssh/agent.sh -ssh-add ~/.ssh/debian_linux-vm-to-ross - -scp ${TARBALL} ross.ics.uci.edu:/var/www/html/${TARBALL} +echo "Transferring binaries to ISSM Web site" +scp -i ~/.ssh/debian_linux-vm_to_ross ${TARBALL} jenkins@ross.ics.uci.edu:/var/www/html/${TARBALL} if [ $? -ne 0 ]; then - echo "The upload failed." - echo "Perhaps the SSH Agent was started by some other means." - echo "Try killing the agent and running again." + echo "FAILED: Manually check connection" + exit 1 fi Index: /issm/trunk/packagers/linux/package-issm-linux-binaries.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries.sh (revision 25835) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries.sh (revision 25836) @@ -1,4 +1,9 @@ #!/bin/bash + +# Script to test, package, and transfer distributable to ISSM Web site. +# Corresponds with build generated by configuration in +# $ISSM_DIR/jenkins/ross-debian_linux-binaries. +# ## Constants @@ -6,9 +11,19 @@ LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it -MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),125,126]" # Exclude Dakota tests and any tests with transient solutions that require a restart +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" MATLAB_PATH="/usr/local/MATLAB/R2019b" PACKAGE="ISSM" # Name of directory to copy distributable files to TARBALL_NAME="issm-linux" TARBALL="${TARBALL_NAME}.tar.gz" + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +# Check if MATLAB exists +if ! [ -d ${MATLAB_PATH} ]; then + echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again." + exit 1 +fi # Clean up from previous packaging @@ -53,5 +68,5 @@ # Check that MATLAB did not exit in error matlabExitCode=`echo $?` -matlabExitedInError=`grep -E "Activation cannot proceed|license" matlab.log | wc -l` +matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l` if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then @@ -71,5 +86,5 @@ if [[ ${numMatlabTestsFailed} -ne 0 ]]; then echo "One or more MATLAB tests FAILED" - exit 1; + exit 1 else echo "All MATLAB tests PASSED" @@ -86,29 +101,14 @@ rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package +rm -rf ${PACKAGE}/test/SandBox # Remove testing sandbox from package echo "Creating tarball: ${TARBALL_NAME}" tar -czf ${TARBALL} ${PACKAGE} ls -lah ${ISSM_DIR}/${TARBALL} -echo "Shipping binaries to website" - -# We're using public key authentication method to upload the tarball The -# following lines check to see if the SSH Agent is running. If not, then it is -# started and relevant information is forwarded to a script. -pgrep "ssh-agent" > /dev/null -if [ $? -ne 0 ]; then - echo "SSH Agent is not running. Starting it..." - ssh-agent > ~/.ssh/agent.sh -else - echo "SSH Agent is running..." -fi - -source ~/.ssh/agent.sh -ssh-add ~/.ssh/debian_linux-vm-to-ross - -scp ${TARBALL} ross.ics.uci.edu:/var/www/html/${TARBALL} +echo "Transferring binaries to ISSM Web site" +scp -i ~/.ssh/debian_linux-vm_to_ross ${TARBALL} jenkins@ross.ics.uci.edu:/var/www/html/${TARBALL} if [ $? -ne 0 ]; then - echo "The upload failed." - echo "Perhaps the SSH Agent was started by some other means." - echo "Try killing the agent and running again." + echo "FAILED: Manually check connection" + exit 1 fi Index: /issm/trunk/packagers/mac/issm-executable_entitlements.plist =================================================================== --- /issm/trunk/packagers/mac/issm-executable_entitlements.plist (revision 25836) +++ /issm/trunk/packagers/mac/issm-executable_entitlements.plist (revision 25836) @@ -0,0 +1,8 @@ + + + + + com.apple.security.cs.disable-library-validation + + + Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh (revision 25836) +++ /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh (revision 25836) @@ -0,0 +1,355 @@ +#!/bin/bash + +################################################################################ +# To be used after running, +# +# ${ISSM_DIR}/jenkins/jenkins.sh ${ISSM_DIR}/jenkins/pine_island-mac-binaries-matlab +# +# in the context of a Jenkins project. +# +# When no runtime errors occur, performs the following: +# - Checks resulting executables and libraries against test suite. +# - Packages and compresses executables and libraries. +# - Commits compressed package to repository to be signed by JPL Cybersecurity. +# - Retrieves signed package and transmits it to ISSM Web site for +# distribution. +# +# Options: +# -c/--cleanup Remove lock file from signed package repository (use if +# build is aborted to allow for subsequent fresh build) +# -n/--notarizeonly Sign/notarize only (use if signing/notarization fails +# to skip tests/packaging) +# -s/--skiptests Skip tests (use if this script fails for some reason +# after tests have successfully passed to save time) +# -t/--transferonly Transfer package to ISSM Web site only (use if +# transfer fails for some reason to skip testing and +# signing) +# +# Debugging: +# - Relies on a very tight handshake with project on remote JPL Cybersecurity +# Jenkins server. Debugging may be perfomed locally by running, +# +# packagers/mac/sign-issm-mac-binaries-matlab.sh +# +# with Apple Developer credentials. +# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can +# help debug potential SVN issues. +# +# NOTE: +# - Assumes that 'issm-binaries-user' and 'issm-binaries-pass' are set up in +# the 'Bindings' section under a 'Username and password (separated)' binding +# (requires 'Credentials Binding Plugin'). +# - For local debugging, the aformentioned credentials can be hardcoded into +# the 'USERNAME' and 'PASSWORD' constants below. +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +# NOTE: May be able to remove this after updating macOS. +# +alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias grep=$(which grep) + +## Constants +# +MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2006,2020,2021,2051,2052,2053,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded +MATLAB_PATH="/Applications/MATLAB_R2019b.app" +NOTARIZATION_LOGFILE="notarization.log" +PASSWORD=$env:issm-binaries-pass +PKG="ISSM-macOS-MATLAB" # Name of directory to copy distributable files to +RETRIGGER_SIGNING_FILE="retrigger.txt" +SIGNED_REPO_COPY="./signed" +SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/signed" +SIGNING_CHECK_PERIOD=60 # in seconds +SIGNING_LOCK_FILE="signing.lock" +UNSIGNED_REPO_COPY="./unsigned" +UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned" +USERNAME=$env:issm-binaries-user + +COMPRESSED_PKG="${PKG}.zip" + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +cleanup=0 +notarize_only=0 +skip_tests=0 +transfer_only=0 +while [ $# -gt 0 ]; do + case $1 in + -c|--cleanup) cleanup=1; shift ;; + -n|--notarizeonly) notarize_only=1; shift ;; + -s|--skiptests) skip_tests=1; shift ;; + -t|--transferonly) transfer_only=1; shift ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac + shift +done + +if [ ${cleanup} -eq 1 ]; then + # Remove signing lock file from signed package repository so that a new + # build can run + echo "Removing lock file from repository for signed packages" + svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + --depth empty \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + svn up ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn commit --message "DEL: Removing lock file after failed build" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + svn cleanup ${SIGNED_REPO_COPY} > /dev/null 2>&1 + exit 1 +fi + +if [ ${transfer_only} -eq 0 ]; then + if [ ${notarize_only} -eq 0 ]; then + # Check if MATLAB exists + if ! [ -d ${MATLAB_PATH} ]; then + echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again." + exit 1 + fi + + # Clean up from previous packaging + echo "Cleaning up existing assets" + cd ${ISSM_DIR} + rm -rf ${PKG} ${COMPRESSED_PKG} ${SIGNED_REPO_COPY} ${UNSIGNED_REPO_COPY} + mkdir ${PKG} + + # Check out copy of SVN repository for signed packages + # + # NOTE: Get empty copy because we do not want to have to check out package from + # previous signing. + # + echo "Checking out copy of repository for signed packages" + svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + --depth empty \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + # If lock file exists, a signing build is still in process by JPL Cybersecurity + svn up ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + if [[ -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]]; then + echo "Previous signing job still in process by JPL Cybersecurity. Please try again later." + exit 1 + fi + + # Add required binaries and libraries to package and modify them where needed + cd ${ISSM_DIR}/bin + + echo "Modify generic" + cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m + + echo "Moving MPICH binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . + elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . + else + echo "MPICH not found" + exit 1 + fi + + echo "Moving GDAL binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . + else + echo "GDAL not found" + exit 1 + fi + + echo "Moving GMT binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . + else + echo "GMT not found" + exit 1 + fi + + echo "Moving Gmsh binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then + cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . + else + echo "Gmsh not found" + exit 1 + fi + + # Run tests + if [ ${skip_tests} -eq 0 ]; then + echo "Running tests" + cd ${ISSM_DIR}/test/NightlyRun + rm matlab.log 2> /dev/null + + # Run tests, redirecting output to logfile and suppressing output to console + ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null + + # Check that MATLAB did not exit in error + matlabExitCode=`echo $?` + matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l` + + if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then + echo "----------MATLAB exited in error!----------" + cat matlab.log + echo "-----------End of matlab.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 + fi + + # Check that all tests passed + numTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"` + + if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 + else + echo "All tests PASSED" + fi + else + echo "Skipping tests" + fi + + # Create package + cd ${ISSM_DIR} + svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) + echo "Copying assets to package: ${PKG}" + cp -rf bin examples lib scripts test ${PKG}/ + mkdir ${PKG}/execution + cp packagers/mac/issm-executable_entitlements.plist ${PKG}/bin/entitlements.plist + echo "Cleaning up unneeded/unwanted files" + rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes + rm -f ${PKG}/lib/*.a # Remove static libraries from package + rm -f ${PKG}/lib/*.la # Remove libtool libraries from package + rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package + + # Compress package + echo "Compressing package" + ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + fi + + # Commit lock file to repository for signed packages + echo "Committing lock file to repository for signed packages" + touch ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} + svn add ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn commit --message "ADD: New lock file" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + # Save current working copy revision number + svn up ${SIGNED_REPO_COPY} > /dev/null 2>&1 + CURRENT_REV=$(svn info --show-item last-changed-revision ${SIGNED_REPO_COPY}) + + # Check out copy of SVN repository for unsigned packages + echo "Checking out copy of repository for unsigned packages" + svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + ${UNSIGNED_REPO_URL} \ + ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + + if [ ${notarize_only} -eq 0 ]; then + # Commit new compressed package to repository for unsigned binaries + # + # NOTE: This will not work if, for any reason, the checksum on the compressed + # package is unchanged. + # + echo "Committing package to repository for unsigned packages" + cp ${COMPRESSED_PKG} ${UNSIGNED_REPO_COPY} + svn add ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + svn commit --message "CHG: New unsigned package" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + else + # NOTE: If notarize_only == 1, we commit a dummy file as the signing + # build on the remote JPL Cybersecurity Jenkins server is + # triggered by polling SCM. + # + echo "Attempting to sign existing package again" + touch ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} + svn add ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} > /dev/null 2>&1 + svn commit --message "ADD: Retriggering signing with same package (previous attempt failed)" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + fi + + # Check status of signing + echo "Checking progress of signing..." + IN_PROCESS=1 + SUCCESS=0 + + while [ ${IN_PROCESS} -eq 1 ]; do + echo "...in progress still; checking again in ${SIGNING_CHECK_PERIOD} seconds" + sleep ${SIGNING_CHECK_PERIOD} + svn up ${SIGNED_REPO_COPY} > /dev/null 2>&1 + NEW_REV=$(svn info --show-item last-changed-revision ${SIGNED_REPO_COPY}) + + if [ ${NEW_REV} -ne ${CURRENT_REV} ]; then + IN_PROCESS=0 + + svn up ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} > /dev/null 2>&1 + svn up ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + + # No error, so check status + STATUS=$(grep 'Status:' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') + if [[ "${STATUS}" == "success" ]]; then + echo "Notarization successful!" + + # Set flag indicating notarization was successful + SUCCESS=1 + else + echo "Notarization failed!" + fi + fi + done +else + # Assume that previous build resulted in successful signing of package but + # that transfer to ISSM Web site failed and user built this project again + # with -t/--transferonly option. + SUCCESS=1 +fi + +# Handle result of signing +if [ ${SUCCESS} -eq 1 ]; then + # Transfer signed package to ISSM Web site + echo "Transferring signed package to ISSM Web site" + scp -i ~/.ssh/pine_island_to_ross ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} jenkins@ross.ics.uci.edu:/var/www/html/${COMPRESSED_PKG} + + if [ $? -ne 0 ]; then + echo "Transfer failed! Verify connection then build this project again (with -t/--transferonly option to skip testing and signing)." + exit 1 + fi +else + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" + + exit 1 +fi Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-python.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-python.sh (revision 25836) +++ /issm/trunk/packagers/mac/package-issm-mac-binaries-python.sh (revision 25836) @@ -0,0 +1,356 @@ +#!/bin/bash + +################################################################################ +# To be used after running, +# +# ${ISSM_DIR}/jenkins/jenkins.sh ${ISSM_DIR}/jenkins/pine_island-mac-binaries-python +# +# in the context of a Jenkins project. +# +# When no runtime errors occur, performs the following: +# - Checks resulting executables and libraries against test suite. +# - Packages and compresses executables and libraries. +# - Commits compressed package to repository to be signed by JPL Cybersecurity. +# - Retrieves signed package and transmits it to ISSM Web site for +# distribution. +# +# Options: +# -c/--cleanup Remove lock file from signed package repository (use if +# build is aborted to allow for subsequent fresh build) +# -n/--notarizeonly Sign/notarize only (use if signing/notarization fails +# to skip tests/packaging) +# -s/--skiptests Skip tests (use if this script fails for some reason +# after tests have successfully passed to save time) +# -t/--transferonly Transfer package to ISSM Web site only (use if +# transfer fails for some reason to skip testing and +# signing) +# +# Debugging: +# - Relies on a very tight handshake with project on remote JPL Cybersecurity +# Jenkins server. Debugging may be perfomed locally by running, +# +# packagers/mac/sign-issm-mac-binaries-python.sh +# +# with Apple Developer credentials. +# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can +# help debug potential SVN issues. +# +# NOTE: +# - Assumes that 'issm-binaries-user' and 'issm-binaries-pass' are set up in +# the 'Bindings' section under a 'Username and password (separated)' binding +# (requires 'Credentials Binding Plugin'). +# - For local debugging, the aformentioned credentials can be hardcoded into +# the 'USERNAME' and 'PASSWORD' constants below. +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +# NOTE: May be able to remove this after updating macOS. +# +alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias grep=$(which grep) + +## Constants +# +NOTARIZATION_LOGFILE="notarization.log" +PASSWORD=$env:issm-binaries-pass +PKG="ISSM-macOS-Python" # Name of directory to copy distributable files to +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2006 2020 2021 2051 2052 2053 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded +RETRIGGER_SIGNING_FILE="retrigger.txt" +SIGNED_REPO_COPY="./signed" +SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/signed" +SIGNING_CHECK_PERIOD=60 # in seconds +SIGNING_LOCK_FILE="signing.lock" +UNSIGNED_REPO_COPY="./unsigned" +UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/unsigned" +USERNAME=$env:issm-binaries-user + +COMPRESSED_PKG="${PKG}.zip" + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +cleanup=0 +notarize_only=0 +skip_tests=0 +transfer_only=0 +while [ $# -gt 0 ]; do + case $1 in + -c|--cleanup) cleanup=1; shift ;; + -n|--notarizeonly) notarize_only=1; shift ;; + -s|--skiptests) skip_tests=1; shift ;; + -t|--transferonly) transfer_only=1; shift ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac + shift +done + +if [ ${cleanup} -eq 1 ]; then + # Remove signing lock file from signed package repository so that a new + # build can run + echo "Removing lock file from repository for signed packages" + svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + --depth empty \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + svn up ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn commit --message "DEL: Removing lock file after failed build" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + svn cleanup ${SIGNED_REPO_COPY} > /dev/null 2>&1 + exit 1 +fi + +if [ ${transfer_only} -eq 0 ]; then + if [ ${notarize_only} -eq 0 ]; then + # Clean up from previous packaging + echo "Cleaning up existing assets" + cd ${ISSM_DIR} + rm -rf ${PKG} ${COMPRESSED_PKG} ${SIGNED_REPO_COPY} ${UNSIGNED_REPO_COPY} + mkdir ${PKG} + + # Check out copy of SVN repository for signed packages + # + # NOTE: Get empty copy because we do not want to have to check out package + # from previous signing. + # + echo "Checking out copy of repository for signed packages" + svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + --depth empty \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + # If lock file exists, a signing build is still in process by JPL Cybersecurity + svn up ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + if [[ -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]]; then + echo "Previous signing job still in process by JPL Cybersecurity. Please try again later." + exit 1 + fi + + # Add required binaries and libraries to package and modify them where needed + cd ${ISSM_DIR}/bin + + echo "Modify generic" + cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py + + echo "Moving MPICH binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . + elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . + else + echo "MPICH not found" + exit 1 + fi + + echo "Moving GDAL binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . + else + echo "GDAL not found" + exit 1 + fi + + echo "Moving GMT binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . + else + echo "GMT not found" + exit 1 + fi + + echo "Moving Gmsh binaries to bin/" + if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then + cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . + else + echo "Gmsh not found" + exit 1 + fi + + # Run tests + if [ ${skip_tests} -eq 0 ]; then + echo "Running tests" + + cd ${ISSM_DIR}/test/NightlyRun + rm python.log 2> /dev/null + + # Set Python environment + export PYTHONPATH="${ISSM_DIR}/src/m/dev" + export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" + export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + + # Run tests, redirecting output to logfile and suppressing output to console + ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + + # Check that Python did not exit in error + pythonExitCode=`echo $?` + pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l` + + if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 + fi + + # Check that all tests passed + numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + + if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 + else + echo "All tests PASSED" + fi + else + echo "Skipping tests" + fi + + # Create package + cd ${ISSM_DIR} + svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) + echo "Copying assets to package: ${PKG}" + cp -rf bin examples lib scripts test ${PKG}/ + mkdir ${PKG}/execution + cp packagers/mac/issm-executable_entitlements.plist ${PKG}/bin/entitlements.plist + ${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files + echo "Cleaning up unneeded/unwanted files" + rm -f ${PKG}/bin/*.py # Remove all Python scripts + rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes + rm -f ${PKG}/lib/*.a # Remove static libraries from package + rm -f ${PKG}/lib/*.la # Remove libtool libraries from package + rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package + + # Compress package + echo "Compressing package" + ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + fi + + # Commit lock file to repository for signed packages + echo "Committing lock file to repository for signed packages" + touch ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} + svn add ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn commit --message "ADD: New lock file" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + # Save current working copy revision number + svn up ${SIGNED_REPO_COPY} > /dev/null 2>&1 + CURRENT_REV=$(svn info --show-item last-changed-revision ${SIGNED_REPO_COPY}) + + # Check out copy of SVN repository for unsigned packages + echo "Checking out copy of repository for unsigned packages" + svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + ${UNSIGNED_REPO_URL} \ + ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + + if [ ${notarize_only} -eq 0 ]; then + # Commit new compressed package to repository for unsigned binaries + # + # NOTE: This will not work if, for any reason, the checksum on the compressed + # package is unchanged. + # + echo "Committing package to repository for unsigned packages" + cp ${COMPRESSED_PKG} ${UNSIGNED_REPO_COPY} + svn add ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + svn commit --message "CHG: New unsigned package" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + else + # NOTE: If notarize_only == 1, we commit a dummy file as the signing + # build on the remote JPL Cybersecurity Jenkins server is + # triggered by polling SCM. + # + echo "Attempting to sign existing package again" + touch ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} + svn add ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} > /dev/null 2>&1 + svn commit --message "ADD: Retriggering signing with same package (previous attempt failed)" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + fi + + # Check status of signing + echo "Checking progress of signing..." + IN_PROCESS=1 + SUCCESS=0 + + while [ ${IN_PROCESS} -eq 1 ]; do + echo "...in progress still; checking again in ${SIGNING_CHECK_PERIOD} seconds" + sleep ${SIGNING_CHECK_PERIOD} + svn up ${SIGNED_REPO_COPY} > /dev/null 2>&1 + NEW_REV=$(svn info --show-item last-changed-revision ${SIGNED_REPO_COPY}) + + if [ ${NEW_REV} -ne ${CURRENT_REV} ]; then + IN_PROCESS=0 + + svn up ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} > /dev/null 2>&1 + svn up ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + + # No error, so check status + STATUS=$(grep 'Status:' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') + if [[ "${STATUS}" == "success" ]]; then + echo "Notarization successful!" + + # Set flag indicating notarization was successful + SUCCESS=1 + else + echo "Notarization failed!" + fi + fi + done +else + # Assume that previous build resulted in successful signing of package but + # that transfer to ISSM Web site failed and user built this project again + # with -t/--transferonly option. + SUCCESS=1 +fi + +# Handle result of signing +if [ ${SUCCESS} -eq 1 ]; then + # Transfer signed package to ISSM Web site + echo "Transferring signed package to ISSM Web site" + scp -i ~/.ssh/pine_island_to_ross ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} jenkins@ross.ics.uci.edu:/var/www/html/${COMPRESSED_PKG} + + if [ $? -ne 0 ]; then + echo "Transfer failed! Verify connection then build this project again (with -t/--transferonly option to skip testing and signing)." + exit 1 + fi +else + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" + + exit 1 +fi Index: sm/trunk/packagers/mac/package-issm-mac-binaries-with_dakota.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-with_dakota.sh (revision 25835) +++ (revision ) @@ -1,155 +1,0 @@ -#!/bin/bash - - -## Constants -# -MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234 243 420 435 701 702 703]" # Exclude any tests with transient solutions that require a restart, and any tests that are excluded in the standard build -MATLAB_PATH="/Applications/MATLAB_R2018a.app" -PACKAGE="ISSM" # Name of directory to copy distributable files to - -# Exclude any tests with transient solutions that require a restart -# -# NOTE: -# - 418 fails with "malloc(): invalid next size (unsorted)"" -# -PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 243 418 420 435 701 702 703" -TARBALL_NAME="issm-mac-with_dakota" -TARBALL="${TARBALL_NAME}.tar.gz" - -# Clean up from previous packaging -echo "Cleaning up existing assets" -cd ${ISSM_DIR} -rm -rf ${PACKAGE} -mkdir ${PACKAGE} - -# Add/modify required binaries -cd ${ISSM_DIR}/bin - -echo "Modifying generic" -cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m -cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py - -echo "Moving MPICH binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then - cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . - cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . -elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then - cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . - cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . -else - echo "MPICH not found" - exit 1 -fi - -# Run tests -echo "Running tests" -cd ${ISSM_DIR}/test/NightlyRun - -# Check that MATLAB tests run -echo "Running MATLAB tests" - -rm matlab.log 2> /dev/null - -# Run MATLAB tests redirecting output to logfile and suppressing output to console -${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null - -# Check that MATLAB did not exit in error -matlabExitCode=`echo $?` -matlabExitedInError=`grep -E "Activation cannot proceed|license" matlab.log | wc -l` - -if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then - echo "----------MATLAB exited in error!----------" - cat matlab.log - echo "-----------End of matlab.log-----------" - - # Clean up execution directory - rm -rf ${ISSM_DIR}/execution/* - - exit 1 -fi - -# Check that all MATLAB tests passed -numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"` - -if [[ ${numMatlabTestsFailed} -ne 0 ]]; then - echo "One or more MATLAB tests FAILED" - exit 1; -else - echo "All MATLAB tests PASSED" -fi - -# Check that Python tests run -echo "Running Python tests" - -export PATH="${PATH}:${ISSM_DIR}/bin" -export PYTHONPATH="${ISSM_DIR}/src/m/dev" -export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" -export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured - -rm python.log 2> /dev/null -./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 - -# Check that Python did not exit in error -pythonExitCode=`echo $?` -pythonExitedInError=`grep -E "Error|Traceback|bad interpreter" python.log | wc -l` - -if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then - echo "----------Python exited in error!----------" - cat python.log - echo "-----------End of python.log-----------" - - # Clean up execution directory - rm -rf ${ISSM_DIR}/execution/* - - exit 1 -fi - -# Check that all Python tests passed -numPythonTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` - -if [[ ${numPythonTestsFailed} -ne 0 ]]; then - echo "One or more Python tests FAILED" - exit 1; -else - echo "All Python tests PASSED" -fi - -# Create tarball -cd ${ISSM_DIR} -rm -f ${TARBALL} -svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) -echo "Copying assets to package: ${PACKAGE}" -cp -rf bin examples lib scripts test ${PACKAGE}/ -echo "Cleaning up unneeded/unwanted files" -python -m compileall ${PACKAGE}/bin # Precompile all Python scripts to bytecode -rm -f ${PACKAGE}/bin/*.py # Remove all Python scripts -rm -f ${PACKAGE}/bin/generic_static.* # Remove static versions of generic cluster classes -rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package -rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package -echo "Creating tarball: ${TARBALL_NAME}" -tar -czf ${TARBALL} ${PACKAGE} -ls -lah ${ISSM_DIR}/${TARBALL} - -echo "Shipping binaries to website" - -# We're using public key authentication method to upload the tarball The -# following lines check to see if the SSH Agent is running. If not, then it is -# started and relevant information is forwarded to a script. -pgrep "ssh-agent" > /dev/null -if [ $? -ne 0 ]; then - echo "SSH Agent is not running. Starting it..." - ssh-agent > ~/.ssh/agent.sh -else - echo "SSH Agent is running..." -fi - -source ~/.ssh/agent.sh -ssh-add ~/.ssh/debian_linux-vm-to-ross - -scp ${TARBALL} ross.ics.uci.edu:/var/www/html/${TARBALL} - -if [ $? -ne 0 ]; then - echo "The upload failed." - echo "Perhaps the SSH Agent was started by some other means." - echo "Try killing the agent and running again." -fi Index: sm/trunk/packagers/mac/package-issm-mac-binaries.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries.sh (revision 25835) +++ (revision ) @@ -1,109 +1,0 @@ -#!/bin/bash - - -## Constants -# -MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),125,126,435,701,702,703]" # Exclude Dakota tests, any tests with transient solutions that require a restart, and any tests that are excluded in the standard build -MATLAB_PATH="/Applications/MATLAB_R2018a.app" -PACKAGE="ISSM" # Name of directory to copy distributable files to -TARBALL_NAME="issm-mac" -TARBALL="${TARBALL_NAME}.tar.gz" - -# Clean up from previous packaging -echo "Cleaning up existing assets" -cd ${ISSM_DIR} -rm -rf ${PACKAGE} -mkdir ${PACKAGE} - -# Add/modify required binaries and libraries -cd ${ISSM_DIR}/bin - -echo "Modify generic" -cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m - -echo "Moving MPICH binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then - cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . - cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . -elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then - cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . - cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . -else - echo "MPICH not found" - exit 1 -fi - -# Run tests -echo "Running tests" -cd ${ISSM_DIR}/test/NightlyRun - -# Check that MATLAB tests run -echo "Running MATLAB tests" - -rm matlab.log 2> /dev/null - -# Run MATLAB tests redirecting output to logfile and suppressing output to console -${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log 2> /dev/null - -# Check that MATLAB did not exit in error -matlabExitCode=`echo $?` -matlabExitedInError=`grep -E "Activation cannot proceed|license" matlab.log | wc -l` - -if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then - echo "----------MATLAB exited in error!----------" - cat matlab.log - echo "-----------End of matlab.log-----------" - - # Clean up execution directory - rm -rf ${ISSM_DIR}/execution/* - - exit 1 -fi - -# Check that all MATLAB tests passed -numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"` - -if [[ ${numMatlabTestsFailed} -ne 0 ]]; then - echo "One or more MATLAB tests FAILED" - exit 1; -else - echo "All MATLAB tests PASSED" -fi - -# Create tarball -cd ${ISSM_DIR} -rm -f ${TARBALL} -svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) -echo "Copying assets to package: ${PACKAGE}" -cp -rf bin examples lib scripts test ${PACKAGE}/ -echo "Cleaning up unneeded/unwanted files" -rm -f ${PACKAGE}/bin/generic_static.* # Remove static versions of generic cluster classes -rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package (we only need MEX-files) -rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package -echo "Creating tarball: ${TARBALL_NAME}" -tar -czf ${TARBALL} ${PACKAGE} -ls -lah ${ISSM_DIR}/${TARBALL} - -echo "Shipping binaries to website" - -# We're using public key authentication method to upload the tarball The -# following lines check to see if the SSH Agent is running. If not, then it is -# started and relevant information is forwarded to a script. -pgrep "ssh-agent" > /dev/null -if [ $? -ne 0 ]; then - echo "SSH Agent is not running. Starting it..." - ssh-agent > ~/.ssh/agent.sh -else - echo "SSH Agent is running..." -fi - -source ~/.ssh/agent.sh -ssh-add ~/.ssh/debian_linux-vm-to-ross - -scp ${TARBALL} ross.ics.uci.edu:/var/www/html/${TARBALL} - -if [ $? -ne 0 ]; then - echo "The upload failed." - echo "Perhaps the SSH Agent was started by some other means." - echo "Try killing the agent and running again." -fi Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh (revision 25836) +++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh (revision 25836) @@ -0,0 +1,272 @@ +#!/bin/bash + +################################################################################ +# Intended to be run in the context of a Jenkins project on a JPL +# Cybersecurity server for signing macOS applications. Polls SCM of the +# Subversion repository hosted at +# https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned to trigger new +# builds. +# +# In order to replicate the requried Jenkins project configuration: +# - First, navigate to 'Manage Jenkins' -> 'Manage Plugins' and install the +# 'Credentials Bindings Plugin' if it is not already installed. +# - Contact one of the members of the ISSM development team for crendentials +# for the ISSM binaries repository (mention that the credentials are stored +# in ISSM-Infrastructure.pdf). +# - Navigate to 'Manage Jenkins' -> 'Manage Credentials' -> -> +# 'Add Credentials' and enter the crendentials from above. +# - From the 'Dashboard', select 'New Item' -> 'Freestyle project'. +# - Under 'Source Code Management', select 'Subversion'. +# - The 'Repository URL' text field should be set to +# "https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned" +# - The 'Credentials' select menu should be set to the new credentials +# created previously. +# - Under 'Build Trigggers', check the box for 'Poll SCM' and set the +# 'Schedule' text area to "H/5 * * * *". +# - Under 'Build Environment', check the box for 'Use secret text(s) or +# file(s)', then under 'Bindings' click the 'Add...' button and select +# 'Username and password (separated)'. +# - Set 'Username Variable' to "issm-binaries-user”. +# - Set 'Password Variable' to "issm-binaries-pass”. +# - Under 'Credentials', select the same, new credentials that created +# previously. +# - The contents of this script can be copied/pasted directly into the ‘Build' +# -> 'Execute Shell' -> ‘Command' textarea of the project configuration (or +# you can simply store the script on disk and call it from there). +# - Make sure to click the 'Save' button. +# +# Current point of contact at JPL Cybersecurity: +# Alex Coward, alexander.g.coward@jpl.nasa.gov +# +# NOTE: +# - Assumes that 'issm-binaries-user' and 'issm-binaries-pass' are set up in +# the 'Bindings' section under a 'Username and password (separated)' binding +# (requires 'Credentials Binding Plugin'). +# - For local debugging, the aformentioned credentials can be hardcoded into +# the 'USERNAME' and 'PASSWORD' constants below. +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +# NOTE: May be able to remove this after updating macOS. +# +alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias cp=$(which cp) +alias grep=$(which grep) + +## Constants +# +AD_IDENTITY="**********" # Apple Developer identity +AD_USERNAME="**********" # Apple Developer username +ALTOOL_PASSWORD="@keychain:**********" # altool password (assumed to be stored in keychain) +ASC_PROVIDER="**********" +NOTARIZATION_CHECK_ATTEMPTS=60 +NOTARIZATION_CHECK_PERIOD=60 +NOTARIZATION_LOGFILE="notarization.log" +NOTARIZATION_LOGFILE_PATH="." +PKG="ISSM-macOS-MATLAB" +PRIMARY_BUNDLE_ID="**********.issm.matlab" # Maybe "nasa.jpl.issm.matlab"? +RETRIGGER_SIGNING_FILE="retrigger.txt" +SIGNED_REPO_COPY="./signed" +SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/signed" +SIGNING_LOCK_FILE="signing.lock" +SUCCESS_LOGFILE="${SIGNED_REPO_COPY}/success.log" +UNSIGNED_REPO_COPY="./unsigned" +UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned" + +COMPRESSED_PKG="${PKG}.zip" +EXE_ENTITLEMENTS_PLIST="${PKG}/bin/entitlements.plist" + +# Clean up from previous packaging (not necessary for single builds on Jenkins, +# but useful when testing packaging locally) +echo "Cleaning up existing assets" +rm -rf ${PKG} ${COMPRESSED_PKG} ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${SIGNED_REPO_COPY} ${UNSIGNED_REPO_COPY} +mkdir ${PKG} + +# Check out copy of repository for unsigned packages +echo "Checking out copy of respository for unsigned packages" +svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + ${UNSIGNED_REPO_URL} \ + ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + +# Extract package contents +echo "Extracting package contents" +ditto -xk ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} . + +# Clear extended attributes on all files +xattr -cr ${PKG} + +# Build list of ISSM executables +ISSM_BINS=$(\ + find ${PKG}/bin -type f -name *.exe; \ + find ${PKG}/lib -type f -name *.mexmaci64; \ +) + +# Build list of third party executables +THIRD_PARTY_BINS=$(\ + echo ${PKG}/bin/mpiexec; \ + echo ${PKG}/bin/hydra_pmi_proxy; \ + echo ${PKG}/bin/gdalsrsinfo; \ + echo ${PKG}/bin/gdaltransform; \ + echo ${PKG}/bin/gmt; \ + echo ${PKG}/bin/gmtselect; \ + echo ${PKG}/bin/gmsh; \ +) + +# Sign all executables in package +echo "Signing all executables in package" +codesign -s ${AD_IDENTITY} --timestamp --options=runtime --entitlements ${EXE_ENTITLEMENTS_PLIST} ${ISSM_BINS} +codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${THIRD_PARTY_BINS} + +# NOTE: Skipping signature validation because this is not a true package nor app + +# Compress signed package +echo "Compressing signed package" +ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + +# Submit compressed package for notarization +echo "Submitting signed package to Apple for notarization" +xcrun altool --notarize-app --primary-bundle-id ${PRIMARY_BUNDLE_ID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} --asc-provider ${ASC_PROVIDER} --file ${COMPRESSED_PKG} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + +# Sleep until notarization request response is received +echo "Waiting for notarizaion request response" +while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do + sleep 30 +done + +echo "Notarizaion request response received" + +# Check if UUID exists in response +HAS_UUID=$(grep 'RequestUUID = ' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) # NOTE: Checking for "RequestUUID = " because "RequestUUID" shows up in some error messages +if [[ -z "${HAS_UUID}" ]]; then + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" + + # Clean up + rm -rf ${PKG} ${COMPRESSED_PKG} + + exit 1 +fi + +# Get UUID from notarization request response +UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*RequestUUID = //') +echo "UUID: ${UUID}" + +# Check notarization status +# +# NOTE: Currently, this checks if notarization was successful, but we are not +# able to staple notarization as this is not a true package nor app and, +# at the very least, MATLAB Mex files cannot be stapled. As such, clients +# will not be able to clear Gatekeeper if they are offline. +# +echo "Checking notarization status" +SUCCESS=0 +for ATTEMPT in $(seq 1 ${NOTARIZATION_CHECK_ATTEMPTS}); do + echo " Attempt #${ATTEMPT}..." + xcrun altool --notarization-info ${UUID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + if [[ -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} && -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; then + + # First, check if there is an error + ERROR_CHECK=$(grep 'Error' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) + if [[ ! -z "${ERROR_CHECK}" ]]; then + break + fi + + # No error, so check status + STATUS=$(grep 'Status:' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') + if [[ "${STATUS}" == "success" ]]; then + # Staple notarization to all elements of package that were previously signed + #xcrun stapler staple ${EXECUTABLES} # NOTE: Fails with "Stapler is incapable of working with MATLAB Mex files." + + # Validate stapling of notarization + #xcrun stapler validation ${EXECUTABLES} # NOTE: Skipping notarization stapling validation because this is not a true package nor app + + # Compress signed and notarized package + ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + + # Set flag indicating notarization was successful + SUCCESS=1 + + break + elif [[ "${STATUS}" == "in progress" ]]; then + echo " ...in progress still; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds." + sleep ${NOTARIZATION_CHECK_PERIOD} + elif [[ "${STATUS}" == "invalid" ]]; then + break + fi + else + if [ ${ATTEMPT} -lt ${NOTARIZATION_CHECK_ATTEMPTS} ]; then + echo " ...not ready yet; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds." + sleep ${NOTARIZATION_CHECK_PERIOD} + else + echo " ...maximum attempts reached, but no response, or something else went wrong." + echo " If contents of notarization status check logfile appear to be valid, increase NOTARIZATION_CHECK_ATTEMPTS and run again." + break + fi + fi +done + +if [ ${SUCCESS} -eq 1 ]; then + echo "Notarization successful!" +else + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" +fi + +# Remove dummy file for retriggering signing/notarization (if it exists) +svn delete ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} > /dev/null 2>&1 +svn commit --message "DEL: Removing dummy file for retriggering signing of same package" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + +# Check out copy of repository for signed packages +echo "Checking out copy of respository for signed packages" +svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + +# Copy notarization file to repository for signed packages +cp ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${SIGNED_REPO_COPY} +svn add ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} > /dev/null 2>&1 + +# Remove lock file from repository for signed packages +svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + +if [ ${SUCCESS} -eq 1 ]; then + # Copy signed package to repository for signed packages + cp ${COMPRESSED_PKG} ${SIGNED_REPO_COPY} + svn add ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + + # Commit changes + echo "Committing changes to repository for signed packages" + svn commit --message "CHG: New signed package (success)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 +else + # Commit changes + echo "Committing changes to repository for signed packages" + svn commit --message "CHG: New signed package (failure)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + exit 1 +fi Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-python.sh =================================================================== --- /issm/trunk/packagers/mac/sign-issm-mac-binaries-python.sh (revision 25836) +++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-python.sh (revision 25836) @@ -0,0 +1,277 @@ +#!/bin/bash + +################################################################################ +# Intended to be run in the context of a Jenkins project on a JPL +# Cybersecurity server for signing macOS applications. Polls SCM of the +# Subversion repository hosted at +# https://issm.ess.uci.edu/svn/issm-binaries/mac/python/unsigned to trigger new +# builds. +# +# In order to replicate the requried Jenkins project configuration: +# - First, navigate to 'Manage Jenkins' -> 'Manage Plugins' and install the +# 'Credentials Bindings Plugin' if it is not already installed. +# - Contact one of the members of the ISSM development team for crendentials +# for the ISSM binaries repository (mention that the credentials are stored +# in ISSM-Infrastructure.pdf). +# - Navigate to 'Manage Jenkins' -> 'Manage Credentials' -> -> +# 'Add Credentials' and enter the crendentials from above. +# - From the 'Dashboard', select 'New Item' -> 'Freestyle project'. +# - Under 'Source Code Management', select 'Subversion'. +# - The 'Repository URL' text field should be set to +# "https://issm.ess.uci.edu/svn/issm-binaries/mac/python/unsigned" +# - The 'Credentials' select menu should be set to the new credentials +# created previously. +# - Under 'Build Trigggers', check the box for 'Poll SCM' and set the +# 'Schedule' text area to "H/5 * * * *". +# - Under 'Build Environment', check the box for 'Use secret text(s) or +# file(s)', then under 'Bindings' click the 'Add...' button and select +# 'Username and password (separated)'. +# - Set 'Username Variable' to "issm-binaries-user”. +# - Set 'Password Variable' to "issm-binaries-pass”. +# - Under 'Credentials', select the same, new credentials that created +# previously. +# - The contents of this script can be copied/pasted directly into the ‘Build' +# -> 'Execute Shell' -> ‘Command' textarea of the project configuration (or +# you can simply store the script on disk and call it from there). +# - Make sure to click the 'Save' button. +# +# Current point of contact at JPL Cybersecurity: +# Alex Coward, alexander.g.coward@jpl.nasa.gov +# +# NOTE: +# - Assumes that 'issm-binaries-user' and 'issm-binaries-pass' are set up in +# the 'Bindings' section under a 'Username and password (separated)' binding +# (requires 'Credentials Binding Plugin'). +# - For local debugging, the aformentioned credentials can be hardcoded into +# the 'USERNAME' and 'PASSWORD' constants below. +################################################################################ + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +shopt -s expand_aliases +alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias cp=$(which cp) +alias grep=$(which grep) + +## Constants +# +AD_IDENTITY="**********" # Apple Developer identity +AD_USERNAME="**********" # Apple Developer username +ALTOOL_PASSWORD="@keychain:**********" # altool password (assumed to be stored in keychain) +ASC_PROVIDER="**********" +NOTARIZATION_CHECK_ATTEMPTS=60 +NOTARIZATION_CHECK_PERIOD=60 +NOTARIZATION_LOGFILE="notarization.log" +NOTARIZATION_LOGFILE_PATH="." +PKG="ISSM-macOS-Python" +PRIMARY_BUNDLE_ID="**********.issm.python" # Maybe "nasa.jpl.issm.matlab"? +RETRIGGER_SIGNING_FILE="retrigger.txt" +SIGNED_REPO_COPY="./signed" +SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/signed" +SIGNING_LOCK_FILE="signing.lock" +SUCCESS_LOGFILE="${SIGNED_REPO_COPY}/success.log" +UNSIGNED_REPO_COPY="./unsigned" +UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/unsigned" + +COMPRESSED_PKG="${PKG}.zip" +EXE_ENTITLEMENTS_PLIST="${PKG}/bin/entitlements.plist" + +# Clean up from previous packaging (not necessary for single builds on Jenkins, +# but useful when testing packaging locally) +echo "Cleaning up existing assets" +rm -rf ${PKG} ${COMPRESSED_PKG} ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${SIGNED_REPO_COPY} ${UNSIGNED_REPO_COPY} +mkdir ${PKG} + +# Check out copy of repository for unsigned packages +echo "Checking out copy of respository for unsigned packages" +svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + ${UNSIGNED_REPO_URL} \ + ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + +# Extract package contents +echo "Extracting package contents" +ditto -xk ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} . + +# Clear extended attributes on all files +xattr -cr ${PKG} + +# Build list of ISSM executables +ISSM_BINS=$(\ + find ${PKG}/bin -type f -name *.exe; \ + find ${PKG}/bin -type f -name *.pyc; \ +) + +# Build list of third party executables +THIRD_PARTY_BINS=$(\ + echo ${PKG}/bin/mpiexec; \ + echo ${PKG}/bin/hydra_pmi_proxy; \ + echo ${PKG}/bin/gdalsrsinfo; \ + echo ${PKG}/bin/gdaltransform; \ + echo ${PKG}/bin/gmt; \ + echo ${PKG}/bin/gmtselect; \ + echo ${PKG}/bin/gmsh; \ +) + +# Sign all executables in package +echo "Signing all executables in package" +codesign -s ${AD_IDENTITY} --timestamp --options=runtime --entitlements ${EXE_ENTITLEMENTS_PLIST} ${ISSM_BINS} +codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${THIRD_PARTY_BINS} + +# Build list of ISSM libraries +ISSM_LIBS=$(\ + find ${PKG}/lib -type f -name *.so; \ +) + +# Sign all libraries in package +echo "Signing all libraries in package" +codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${ISSM_LIBS} + +# NOTE: Skipping signature validation because this is not a true package nor app + +# Compress signed package +echo "Compressing signed package" +ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + +# Submit compressed package for notarization +echo "Submitting signed package to Apple for notarization" +xcrun altool --notarize-app --primary-bundle-id ${PRIMARY_BUNDLE_ID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} --asc-provider ${ASC_PROVIDER} --file ${COMPRESSED_PKG} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + +# Sleep until notarization request response is received +echo "Waiting for notarizaion request response" +while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do + sleep 30 +done + +echo "Notarizaion request response received" + +# Check if UUID exists in response +HAS_UUID=$(grep 'RequestUUID = ' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) # NOTE: Checking for "RequestUUID = " because "RequestUUID" shows up in some error messages +if [[ -z "${HAS_UUID}" ]]; then + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" + + # Clean up + rm -rf ${PKG} ${COMPRESSED_PKG} + + exit 1 +fi + +# Get UUID from notarization request response +UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*RequestUUID = //') +echo "UUID: ${UUID}" + +# Check notarization status +# +# NOTE: Currently, this checks if notarization was successful, but we are not +# able to staple notarization as this is not a true package nor app and, +# at the very least, MATLAB Mex files cannot be stapled. As such, clients +# will not be able to clear Gatekeeper if they are offline. +# +echo "Checking notarization status" +SUCCESS=0 +for ATTEMPT in $(seq 1 ${NOTARIZATION_CHECK_ATTEMPTS}); do + echo " Attempt #${ATTEMPT}..." + xcrun altool --notarization-info ${UUID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + if [[ -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} && -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; then + + # First, check if there is an error + ERROR_CHECK=$(grep 'Error' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) + if [[ ! -z "${ERROR_CHECK}" ]]; then + break + fi + + # No error, so check status + STATUS=$(grep 'Status:' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') + if [[ "${STATUS}" == "success" ]]; then + # Staple notarization to all elements of package that were previously signed + #xcrun stapler staple ${THIRD_PARTY_BINS} # NOTE: Fails with "Stapler is incapable of working with MATLAB Mex files." + + # Validate stapling of notarization + #xcrun stapler validation ${THIRD_PARTY_BINS} # NOTE: Skipping notarization stapling validation because this is not a true package nor app + + # Compress signed and notarized package + ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + + # Set flag indicating notarization was successful + SUCCESS=1 + + break + elif [[ "${STATUS}" == "in progress" ]]; then + echo " ...in progress still; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds." + sleep ${NOTARIZATION_CHECK_PERIOD} + elif [[ "${STATUS}" == "invalid" ]]; then + break + fi + else + if [ ${ATTEMPT} -lt ${NOTARIZATION_CHECK_ATTEMPTS} ]; then + echo " ...not ready yet; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds" + sleep ${NOTARIZATION_CHECK_PERIOD} + else + echo " ...maximum attempts reached, but no response, or something else went wrong" + echo " If contents of notarization status check logfile appear to be valid, increase NOTARIZATION_CHECK_ATTEMPTS and run again" + break + fi + fi +done + +if [ ${SUCCESS} -eq 1 ]; then + echo "Notarization successful!" +else + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" +fi + +# Remove dummy file for retriggering signing/notarization (if it exists) +svn delete ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} > /dev/null 2>&1 +svn commit --message "DEL: Removing dummy file for retriggering signing of same package" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 + +# Check out copy of repository for signed packages +echo "Checking out copy of respository for signed packages" +svn co \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + +# Copy notarization file to repository for signed packages +cp ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${SIGNED_REPO_COPY} +svn add ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} > /dev/null 2>&1 + +# Remove lock file from repository for signed packages +svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + +if [ ${SUCCESS} -eq 1 ]; then + # Copy signed package to repository for signed packages + cp ${COMPRESSED_PKG} ${SIGNED_REPO_COPY} + svn add ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + + # Commit changes + echo "Committing changes to repository for signed packages" + svn commit --message "CHG: New signed package (success)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 +else + # Commit changes + echo "Committing changes to repository for signed packages" + svn commit --message "CHG: New signed package (failure)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + exit 1 +fi Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh (revision 25836) +++ /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh (revision 25836) @@ -0,0 +1,54 @@ +#!/bin/bash + +################################################################################ +# This script is intended to test ISSM macOS MATLAB binaries on an end-user +# machine after successful packaging and signing. +# +# NOTE: Tarball must already exist in INSTALL_DIR +################################################################################ + +## Constants +# +INSTALL_DIR=. +MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2006,2020,2021,2051,2052,2053,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded +MATLAB_PATH="/Applications/MATLAB_R2018a.app" +PKG="ISSM-macOS-MATLAB" + +COMPRESSED_PKG="${PKG}.zip" + +## Environment +# +export ISSM_DIR="${INSTALL_DIR}/${PKG}" +export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" + +cd ${INSTALL_DIR} +rm -rf ${PKG} +ditto -xk ${COMPRESSED_PKG} . +cd ${PKG}/test/NightlyRun + +# Run tests, redirecting output to logfile and suppressing output to console +echo "Running tests" +rm matlab.log 2> /dev/null +${MATLAB_PATH}/bin/matlab -nosplash -nodesktop -nojvm -r "try, addpath ../../bin; addpath ../../lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null + +# Check that MATLAB did not exit in error +matlabExitCode=`echo $?` +matlabExitedInError=`grep -E "Activation cannot proceed|license|Error|Warning: Name is nonexistent or not a directory" matlab.log | wc -l` + +if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then + echo "----------MATLAB exited in error!----------" + cat matlab.log + echo + echo "-----------End of matlab.log-----------" + exit 1 +fi + +# Check that all tests passed +numTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 +else + echo "All tests PASSED" +fi Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-python.sh =================================================================== --- /issm/trunk/packagers/mac/test-issm-mac-binaries-python.sh (revision 25836) +++ /issm/trunk/packagers/mac/test-issm-mac-binaries-python.sh (revision 25836) @@ -0,0 +1,53 @@ +#!/bin/bash + +################################################################################ +# This script is intended to test ISSM macOS MATLAB binaries on an end-user +# machine after successful packaging and signing. +# +# NOTE: Tarball must already exist in INSTALL_DIR +################################################################################ + +## Constants +# +INSTALL_DIR=. +PKG="ISSM-macOS-Python" +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2006 2020 2021 2051 2052 2053 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded + +COMPRESSED_PKG="${PKG}.zip" + +export ISSM_DIR="${INSTALL_DIR}/${PKG}" +export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" +export PYTHONPATH="${ISSM_DIR}/scripts" +export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" +export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + +cd ${INSTALL_DIR} +rm -rf ${PKG} +ditto -xk ${COMPRESSED_PKG} . +cd ${PKG}/test/NightlyRun + +# Run tests, redirecting output to logfile and suppressing output to console +echo "Running tests" +rm python.log 2> /dev/null +./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + +# Check that Python did not exit in error +pythonExitCode=`echo $?` +pythonExitedInError=`grep -E "runme.py: error" python.log | wc -l` + +if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + exit 1 +fi + +# Check that all tests passed +numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 +else + echo "All tests PASSED" +fi Index: /issm/trunk/scripts/BinRead.py =================================================================== --- /issm/trunk/scripts/BinRead.py (revision 25835) +++ /issm/trunk/scripts/BinRead.py (revision 25836) @@ -5,5 +5,4 @@ import struct from argparse import ArgumentParser - def BinRead(filin, filout='', verbose=0): #{{{ @@ -123,5 +122,4 @@ #}}} - def FormatToCode(format): # {{{ """ @@ -154,5 +152,4 @@ return code # }}} - def CodeToFormat(code): # {{{ @@ -187,18 +184,5 @@ # }}} - if __name__ == '__main__': #{{{ - if 'PYTHONSTARTUP' in environ: - PYTHONSTARTUP = environ['PYTHONSTARTUP'] - print('PYTHONSTARTUP = {}'.format(PYTHONSTARTUP)) - if path.exists(PYTHONSTARTUP): - try: - exec(compile(open(PYTHONSTARTUP).read(), PYTHONSTARTUP, 'exec'), globals()) - - except Exception as e: - print("PYTHONSTARTUP error: ", e) - else: - print("PYTHONSTARTUP file '{}' does not exist.".format(PYTHONSTARTUP)) - parser = ArgumentParser(description='BinRead - function to read binary input file.') parser.add_argument('-f', '--filin', help='name of binary input file', default='') Index: /issm/trunk/scripts/OutbinRead.py =================================================================== --- /issm/trunk/scripts/OutbinRead.py (revision 25836) +++ /issm/trunk/scripts/OutbinRead.py (revision 25836) @@ -0,0 +1,142 @@ +#!/usr/bin/env python +import numpy as np +from os import environ, path +import sys +import struct +from argparse import ArgumentParser + +def OutbinRead(filin, filout='', verbose=0): #{{{ + + yts = 365*24*3600. + + print("reading binary file.") + f = open(filin, 'rb') + + if filout: + sys.stdout = open(filout, 'w') + + while True: + try: + #Step 1: read size of record name + recordnamesize = struct.unpack('i', f.read(struct.calcsize('i')))[0] + except struct.error as e: + print("probable EOF: {}".format(e)) + break + + print("============================================================================ ") + if verbose > 2: + print("\n recordnamesize = {}".format(recordnamesize)) + recordname = struct.unpack('{}s'.format(recordnamesize), f.read(recordnamesize))[0] + print("field: {}".format(recordname)) + + #read time and step + time = struct.unpack('d', f.read(struct.calcsize('d')))[0] + step = struct.unpack('i', f.read(struct.calcsize('i')))[0] + if time!=-9999.: time = time/yts + print("time = {} step = {}".format(time,step)) + + #read data code: + code = struct.unpack('i', f.read(struct.calcsize('i')))[0] + print("Format = {} (code {})".format(CodeToFormat(code), code)) + + #read size: + M = struct.unpack('i', f.read(struct.calcsize('i')))[0] + N = 1 #default + + #Step 2: read the data itself. + if code == FormatToCode('Double'): + dval = struct.unpack('d', f.read(struct.calcsize('d')))[0] + print("value = {}".format(dval)) + + elif code == FormatToCode('String'): + strlen = M + if verbose > 1: + print("strlen = {}".format(strlen)) + sval = struct.unpack('{}s'.format(strlen), f.read(strlen))[0] + print("value = '{}'".format(sval)) + + elif code == FormatToCode('IntMat'): + s = [0, 0] + s[0] = M + s[1] = struct.unpack('i', f.read(struct.calcsize('i')))[0] + print("size = [{}x{}]".format(s[0], s[1])) + data = np.zeros((s[0], s[1])) + for i in range(s[0]): + for j in range(s[1]): + data[i][j] = struct.unpack('d', f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose + if verbose > 2: + print("data[{}, {}] = {}".format(i, j, data[i][j])) + + elif code == FormatToCode('DoubleMat'): + #now read matrix + s = [0, 0] + s[0] = M + s[1] = struct.unpack('i', f.read(struct.calcsize('i')))[0] + print("size = [{}x{}]".format(s[0], s[1])) + if True: + f.read(struct.calcsize('d')*s[0]*s[1]) + else: + data = np.zeros((s[0], s[1])) + for i in range(s[0]): + for j in range(s[1]): + data[i][j] = struct.unpack('d', f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose + if verbose > 2: + print("data[{}, {}] = {}".format(i, j, data[i][j])) + + else: + raise TypeError('OutbinRead error message: data type: {} not supported yet! ({})'.format(code, recordname)) + + f.close() +#}}} + +def FormatToCode(format): # {{{ + """ + This routine takes the format string, and hardcodes it into an integer, which + is passed along the record, in order to identify the nature of the dataset being + sent. + """ + + if format == 'Double': + code = 1 + elif format == 'String': + code = 2 + elif format == 'DoubleMat': + code = 3 + elif format == 'IntMat': + code = 4 + else: + raise IOError('FormatToCode error message: data type not supported yet!') + + return code +# }}} + +def CodeToFormat(code): # {{{ + """ + This routine takes the format string, and hardcodes it into an integer, which + is passed along the record, in order to identify the nature of the dataset being + sent. + """ + + if code == 1: + format = 'Double' + elif code == 2: + format = 'String' + elif code == 3: + format = 'DoubleMat' + elif code == 4: + format = 'IntMat' + else: + raise TypeError('FormatToCode error message: code {} not supported yet!'.format(code)) + + return format +# }}} + +if __name__ == '__main__': #{{{ + parser = ArgumentParser(description='OutbinRead - function to read binary input file.') + parser.add_argument('-f', '--filin', help='name of binary input file', default='') + parser.add_argument('-o', '--filout', help='optional name of text output file', default='') + parser.add_argument('-v', '--verbose', help='optional level of output', default=0) + args = parser.parse_args() + + OutbinRead(args.filin, args.filout, args.verbose) +#}}} Index: /issm/trunk/scripts/cloc =================================================================== --- /issm/trunk/scripts/cloc (revision 25836) +++ /issm/trunk/scripts/cloc (revision 25836) @@ -0,0 +1,11676 @@ +#!/usr/bin/env perl +# cloc -- Count Lines of Code {{{1 +# Copyright (C) 2006-2017 Al Danial +# First release August 2006 +# +# Includes code from: +# - SLOCCount v2.26 +# http://www.dwheeler.com/sloccount/ +# by David Wheeler. +# - Regexp::Common v2013031301 +# http://search.cpan.org/~abigail/Regexp-Common-2013031301/lib/Regexp/Common.pm +# by Damian Conway and Abigail. +# - Win32::Autoglob +# http://search.cpan.org/~sburke/Win32-Autoglob-1.01/Autoglob.pm +# by Sean M. Burke. +# - Algorithm::Diff +# http://search.cpan.org/~tyemq/Algorithm-Diff-1.1902/lib/Algorithm/Diff.pm +# by Tye McQueen. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details: +# . +# +# 1}}} +my $VERSION = "1.72"; # odd number == beta; even number == stable +my $URL = "github.com/AlDanial/cloc"; # 'https://' pushes header too wide +require 5.006; +# use modules {{{1 +use warnings; +use strict; +use Getopt::Long; +use File::Basename; +use File::Temp qw { tempfile tempdir }; +use File::Find; +use File::Path; +use File::Spec; +use IO::File; +use POSIX "strftime"; + +# Digest::MD5 isn't in the standard distribution. Use it only if installed. +my $HAVE_Digest_MD5 = 0; +eval "use Digest::MD5;"; +if (defined $Digest::MD5::VERSION) { + $HAVE_Digest_MD5 = 1; +} else { + warn "Digest::MD5 not installed; will skip file uniqueness checks.\n"; +} + +# Time::HiRes became standard with Perl 5.8 +my $HAVE_Time_HiRes = 0; +eval "use Time::HiRes;"; +$HAVE_Time_HiRes = 1 if defined $Time::HiRes::VERSION; + +my $HAVE_Rexexp_Common; +# Regexp::Common isn't in the standard distribution. It will +# be installed in a temp directory if necessary. +BEGIN { + if (eval "use Regexp::Common;") { + $HAVE_Rexexp_Common = 1; + } else { + $HAVE_Rexexp_Common = 0; + } +} + +my $HAVE_Algorith_Diff = 0; +# Algorithm::Diff isn't in the standard distribution. It will +# be installed in a temp directory if necessary. +eval "use Algorithm::Diff qw ( sdiff ) "; +if (defined $Algorithm::Diff::VERSION) { + $HAVE_Algorith_Diff = 1; +} else { + Install_Algorithm_Diff(); +} +# print "2 HAVE_Algorith_Diff = $HAVE_Algorith_Diff\n"; +# test_alg_diff($ARGV[$#ARGV - 1], $ARGV[$#ARGV]); die; +# die "Hre=$HAVE_Rexexp_Common Had=$HAVE_Algorith_Diff"; + +# Uncomment next two lines when building Windows executable with perl2exe +# or if running on a system that already has Regexp::Common. +#use Regexp::Common; +#$HAVE_Rexexp_Common = 1; + +#perl2exe_include "Regexp/Common/whitespace.pm" +#perl2exe_include "Regexp/Common/URI.pm" +#perl2exe_include "Regexp/Common/URI/fax.pm" +#perl2exe_include "Regexp/Common/URI/file.pm" +#perl2exe_include "Regexp/Common/URI/ftp.pm" +#perl2exe_include "Regexp/Common/URI/gopher.pm" +#perl2exe_include "Regexp/Common/URI/http.pm" +#perl2exe_include "Regexp/Common/URI/pop.pm" +#perl2exe_include "Regexp/Common/URI/prospero.pm" +#perl2exe_include "Regexp/Common/URI/news.pm" +#perl2exe_include "Regexp/Common/URI/tel.pm" +#perl2exe_include "Regexp/Common/URI/telnet.pm" +#perl2exe_include "Regexp/Common/URI/tv.pm" +#perl2exe_include "Regexp/Common/URI/wais.pm" +#perl2exe_include "Regexp/Common/CC.pm" +#perl2exe_include "Regexp/Common/SEN.pm" +#perl2exe_include "Regexp/Common/number.pm" +#perl2exe_include "Regexp/Common/delimited.pm" +#perl2exe_include "Regexp/Common/profanity.pm" +#perl2exe_include "Regexp/Common/net.pm" +#perl2exe_include "Regexp/Common/zip.pm" +#perl2exe_include "Regexp/Common/comment.pm" +#perl2exe_include "Regexp/Common/balanced.pm" +#perl2exe_include "Regexp/Common/lingua.pm" +#perl2exe_include "Regexp/Common/list.pm" +#perl2exe_include "File/Glob.pm" + +use Text::Tabs qw { expand }; +use Cwd qw { cwd }; +use File::Glob; +# 1}}} +# Usage information, options processing. {{{1 +my $ON_WINDOWS = 0; + $ON_WINDOWS = 1 if ($^O =~ /^MSWin/) or ($^O eq "Windows_NT"); +if ($ON_WINDOWS and $ENV{'SHELL'}) { + if ($ENV{'SHELL'} =~ m{^/}) { + $ON_WINDOWS = 0; # make Cygwin look like Unix + } else { + $ON_WINDOWS = 1; # MKS defines $SHELL but still acts like Windows + } +} + +my $NN = chr(27) . "[0m"; # normal + $NN = "" if $ON_WINDOWS or !(-t STDERR); # -t STDERR: is it a terminal? +my $BB = chr(27) . "[1m"; # bold + $BB = "" if $ON_WINDOWS or !(-t STDERR); +my $script = basename $0; +my $brief_usage = " + cloc -- Count Lines of Code + +Usage: + $script [options] + Count physical lines of source code and comments in the given files + (may be archives such as compressed tarballs or zip files) and/or + recursively below the given directories. + Example: cloc src/ include/ main.c + + $script [options] --diff + Compute differences of physical lines of source code and comments + between a pair of directories or archive files. + Example: cloc --diff Python-3.5.tar.xz python-3.6/ + +$script --help shows full documentation on the options. +http://$URL has numerous examples and more information. +"; +my $usage = " +Usage: $script [options] | | + + Count, or compute differences of, physical lines of source code in the + given files (may be archives such as compressed tarballs or zip files) + and/or recursively below the given directories. + + ${BB}Input Options${NN} + --extract-with= This option is only needed if cloc is unable + to figure out how to extract the contents of + the input file(s) by itself. + Use to extract binary archive files (e.g.: + .tar.gz, .zip, .Z). Use the literal '>FILE<' as + a stand-in for the actual file(s) to be + extracted. For example, to count lines of code + in the input files + gcc-4.2.tar.gz perl-5.8.8.tar.gz + on Unix use + --extract-with='gzip -dc >FILE< | tar xf -' + or, if you have GNU tar, + --extract-with='tar zxf >FILE<' + and on Windows use, for example: + --extract-with=\"\\\"c:\\Program Files\\WinZip\\WinZip32.exe\\\" -e -o >FILE< .\" + (if WinZip is installed there). + --list-file= Take the list of file and/or directory names to + process from , which has one file/directory + name per line. Only exact matches are counted; + relative path names will be resolved starting from + the directory where cloc is invoked. + See also --exclude-list-file. + --vcs= Invoke a system call to to obtain a list of + files to work on. If is 'git', then will + invoke 'git ls-files' to get a file list and + 'git submodule status' to get a list of submodules + whose contents will be ignored. If is 'svn' + then will invoke 'svn list -R'. The primary benefit + is that cloc will then skip files explicitly + excluded by the versioning tool in question, + ie, those in .gitignore or have the svn:ignore + property. + Alternatively may be any system command + that generates a list of files. + Note: cloc must be in a directory which can read + the files as they are returned by . cloc will + not download files from remote repositories. + 'svn list -R' may refer to a remote repository + to obtain file names (and therefore may require + authentication to the remote repository), but + the files themselves must be local. + --unicode Check binary files to see if they contain Unicode + expanded ASCII text. This causes performance to + drop noticeably. + + ${BB}Processing Options${NN} + --autoconf Count .in files (as processed by GNU autoconf) of + recognized languages. + --by-file Report results for every source file encountered. + --by-file-by-lang Report results for every source file encountered + in addition to reporting by language. + --count-and-diff + First perform direct code counts of source file(s) + of and separately, then perform a diff + of these. Inputs may be pairs of files, directories, + or archives. See also --diff, --diff-alignment, + --diff-timeout, --ignore-case, --ignore-whitespace. + --diff Compute differences in code and comments between + source file(s) of and . The inputs + may be pairs of files, directories, or archives. + Use --diff-alignment to generate a list showing + which file pairs where compared. See also + --count-and-diff, --diff-alignment, --diff-timeout, + --ignore-case, --ignore-whitespace. + --diff-timeout Ignore files which take more than seconds + to process. Default is 10 seconds. + (Large files with many repeated lines can cause + Algorithm::Diff::sdiff() to take hours.) + --follow-links [Unix only] Follow symbolic links to directories + (sym links to files are always followed). + --force-lang=[,] + Process all files that have a extension + with the counter for language . For + example, to count all .f files with the + Fortran 90 counter (which expects files to + end with .f90) instead of the default Fortran 77 + counter, use + --force-lang=\"Fortran 90\",f + If is omitted, every file will be counted + with the counter. This option can be + specified multiple times (but that is only + useful when is given each time). + See also --script-lang, --lang-no-ext. + --force-lang-def= Load language processing filters from , + then use these filters instead of the built-in + filters. Note: languages which map to the same + file extension (for example: + MATLAB/Mathematica/Objective C/MUMPS/Mercury; + Pascal/PHP; Lisp/OpenCL; Lisp/Julia; Perl/Prolog) + will be ignored as these require additional + processing that is not expressed in language + definition files. Use --read-lang-def to define + new language filters without replacing built-in + filters (see also --write-lang-def). + --ignore-whitespace Ignore horizontal white space when comparing files + with --diff. See also --ignore-case. + --ignore-case Ignore changes in case; consider upper- and lower- + case letters equivalent when comparing files with + --diff. See also --ignore-whitespace. + --lang-no-ext= Count files without extensions using the + counter. This option overrides internal logic + for files without extensions (where such files + are checked against known scripting languages + by examining the first line for #!). See also + --force-lang, --script-lang. + --max-file-size= Skip files larger than megabytes when + traversing directories. By default, =100. + cloc's memory requirement is roughly twenty times + larger than the largest file so running with + files larger than 100 MB on a computer with less + than 2 GB of memory will cause problems. + Note: this check does not apply to files + explicitly passed as command line arguments. + --original-dir [Only effective in combination with + --strip-comments] Write the stripped files + to the same directory as the original files. + --read-binary-files Process binary files in addition to text files. + This is usually a bad idea and should only be + attempted with text files that have embedded + binary data. + --read-lang-def= Load new language processing filters from + and merge them with those already known to cloc. + If defines a language cloc already knows + about, cloc's definition will take precedence. + Use --force-lang-def to over-ride cloc's + definitions (see also --write-lang-def ). + --script-lang=, Process all files that invoke as a #! + scripting language with the counter for language + . For example, files that begin with + #!/usr/local/bin/perl5.8.8 + will be counted with the Perl counter by using + --script-lang=Perl,perl5.8.8 + The language name is case insensitive but the + name of the script language executable, , + must have the right case. This option can be + specified multiple times. See also --force-lang, + --lang-no-ext. + --sdir= Use as the scratch directory instead of + letting File::Temp chose the location. Files + written to this location are not removed at + the end of the run (as they are with File::Temp). + --skip-uniqueness Skip the file uniqueness check. This will give + a performance boost at the expense of counting + files with identical contents multiple times + (if such duplicates exist). + --stdin-name= Give a file name to use to determine the language + for standard input. (Use - as the input name to + receive source code via STDIN.) + --strip-comments= For each file processed, write to the current + directory a version of the file which has blank + lines and comments removed. The name of each + stripped file is the original file name with + . appended to it. It is written to the + current directory unless --original-dir is on. + --sum-reports Input arguments are report files previously + created with the --report-file option. Makes + a cumulative set of results containing the + sum of data from the individual report files. + --unix Override the operating system autodetection + logic and run in UNIX mode. See also + --windows, --show-os. + --use-sloccount If SLOCCount is installed, use its compiled + executables c_count, java_count, pascal_count, + php_count, and xml_count instead of cloc's + counters. SLOCCount's compiled counters are + substantially faster than cloc's and may give + a performance improvement when counting projects + with large files. However, these cloc-specific + features will not be available: --diff, + --count-and-diff, --strip-comments, --unicode. + --windows Override the operating system autodetection + logic and run in Microsoft Windows mode. + See also --unix, --show-os. + + ${BB}Filter Options${NN} + --exclude-dir=[,D2,] Exclude the given comma separated directories + D1, D2, D3, et cetera, from being scanned. For + example --exclude-dir=.cache,test will skip + all files and subdirectories that have /.cache/ + or /test/ as their parent directory. + Directories named .bzr, .cvs, .hg, .git, and + .svn are always excluded. + This option only works with individual directory + names so including file path separators is not + allowed. Use --fullpath and --not-match-d= + to supply a regex matching multiple subdirectories. + --exclude-ext=[,[...]] + Do not count files having the given file name + extensions. + --exclude-lang=[,L2,] Exclude the given comma separated languages + L1, L2, L3, et cetera, from being counted. + --exclude-list-file= Ignore files and/or directories whose names + appear in . should have one file + name per line. Only exact matches are ignored; + relative path names will be resolved starting from + the directory where cloc is invoked. + See also --list-file. + --fullpath Modifies the behavior of --match-f, --not-match-f, + and --not-match-d to include the file's path + in the regex, not just the file's basename. + (This does not expand each file to include its + absolute path, instead it uses as much of + the path as is passed in to cloc.) + Note: --match-d always looks at the full + path and therefore is unaffected by --fullpath. + --include-lang=[,L2,] Count only the given comma separated languages + L1, L2, L3, et cetera. + --match-d= Only count files in directories matching the Perl + regex. For example + --match-d='/(src|include)/' + only counts files in directories containing + /src/ or /include/. Unlike --not-match-d, + --match-f, and --not-match-f, --match-d always + compares the fully qualified path against the regex. + --not-match-d= Count all files except those in directories + matching the Perl regex. Only the trailing + directory name is compared, for example, when + counting in /usr/local/lib, only 'lib' is + compared to the regex. + Add --fullpath to compare parent directories to + the regex. + Do not include file path separators at the beginning + or end of the regex. + --match-f= Only count files whose basenames match the Perl + regex. For example + --match-f='^[Ww]idget' + only counts files that start with Widget or widget. + Add --fullpath to include parent directories + in the regex instead of just the basename. + --not-match-f= Count all files except those whose basenames + match the Perl regex. Add --fullpath to include + parent directories in the regex instead of just + the basename. + --skip-archive= Ignore files that end with the given Perl regular + expression. For example, if given + --skip-archive='(zip|tar(\.(gz|Z|bz2|xz|7z))?)' + the code will skip files that end with .zip, + .tar, .tar.gz, .tar.Z, .tar.bz2, .tar.xz, and + .tar.7z. + --skip-win-hidden On Windows, ignore hidden files. + + ${BB}Debug Options${NN} + --categorized= Save names of categorized files to . + --counted= Save names of processed source files to . + --diff-alignment= Write to a list of files and file pairs + showing which files were added, removed, and/or + compared during a run with --diff. This switch + forces the --diff mode on. + --explain= Print the filters used to remove comments for + language and exit. In some cases the + filters refer to Perl subroutines rather than + regular expressions. An examination of the + source code may be needed for further explanation. + --help Print this usage information and exit. + --found= Save names of every file found to . + --ignored= Save names of ignored files and the reason they + were ignored to . + --print-filter-stages Print processed source code before and after + each filter is applied. + --show-ext[=] Print information about all known (or just the + given) file extensions and exit. + --show-lang[=] Print information about all known (or just the + given) languages and exit. + --show-os Print the value of the operating system mode + and exit. See also --unix, --windows. + -v[=] Verbose switch (optional numeric value). + -verbose[=] Long form of -v. + --version Print the version of this program and exit. + --write-lang-def= Writes to the language processing filters + then exits. Useful as a first step to creating + custom language definitions (see also + --force-lang-def, --read-lang-def). + + ${BB}Output Options${NN} + --3 Print third-generation language output. + (This option can cause report summation to fail + if some reports were produced with this option + while others were produced without it.) + --by-percent X Instead of comment and blank line counts, show + these values as percentages based on the value + of X in the denominator: + X = 'c' -> # lines of code + X = 'cm' -> # lines of code + comments + X = 'cb' -> # lines of code + blanks + X = 'cmb' -> # lines of code + comments + blanks + For example, if using method 'c' and your code + has twice as many lines of comments as lines + of code, the value in the comment column will + be 200%. The code column remains a line count. + --csv Write the results as comma separated values. + --csv-delimiter= Use the character as the delimiter for comma + separated files instead of ,. This switch forces + --json Write the results as JavaScript Object Notation + (JSON) formatted output. + --md Write the results as Markdown-formatted text. + --out= Synonym for --report-file=. + --progress-rate= Show progress update after every files are + processed (default =100). Set to 0 to + suppress progress output (useful when redirecting + output to STDOUT). + --quiet Suppress all information messages except for + the final report. + --report-file= Write the results to instead of STDOUT. + --sql= Write results as SQL create and insert statements + which can be read by a database program such as + SQLite. If is -, output is sent to STDOUT. + --sql-append Append SQL insert statements to the file specified + by --sql and do not generate table creation + statements. Only valid with the --sql option. + --sql-project= Use as the project identifier for the + current run. Only valid with the --sql option. + --sql-style= + + +

+';
+    print "<- html_header\n" if $opt_v > 2;
+} # 1}}}
+sub html_end {                               # {{{1
+return
+'
+ + +'; +} # 1}}} +sub die_unknown_lang { # {{{1 + my ($lang, $option_name) = @_; + die "Unknown language '$lang' used with $option_name option. " . + "The command\n $script --show-lang\n" . + "will print all recognized languages. Language names are " . + "case sensitive.\n" ; +} # 1}}} +sub unicode_file { # {{{1 + my $file = shift @_; + + print "-> unicode_file($file)\n" if $opt_v > 2; + return 0 if (-s $file > 2_000_000); + # don't bother trying to test binary files bigger than 2 MB + + my $IN = new IO::File $file, "r"; + if (!defined $IN) { + warn "Unable to read $file; ignoring.\n"; + return 0; + } + my @lines = <$IN>; + $IN->close; + + if (unicode_to_ascii( join('', @lines) )) { + print "<- unicode_file()\n" if $opt_v > 2; + return 1; + } else { + print "<- unicode_file()\n" if $opt_v > 2; + return 0; + } + +} # 1}}} +sub unicode_to_ascii { # {{{1 + my $string = shift @_; + + # A trivial attempt to convert UTF-16 little or big endian + # files into ASCII. These files exhibit the following byte + # sequence: + # byte 1: 255 + # byte 2: 254 + # byte 3: ord of ASCII character + # byte 4: 0 + # byte 3+i: ord of ASCII character + # byte 4+i: 0 + # or + # byte 1: 255 + # byte 2: 254 + # byte 3: 0 + # byte 4: ord of ASCII character + # byte 3+i: 0 + # byte 4+i: ord of ASCII character + + my $length = length $string; +#print "length=$length\n"; + return '' if $length <= 3; + my @unicode = split(//, $string); + + # check the first 100 characters for big or little endian UTF-16 encoding + my $max_peek = $length < 200 ? $length : 200; + my @view_1 = (); + for (my $i = 2; $i < $max_peek; $i += 2) { push @view_1, $unicode[$i] } + my @view_2 = (); + for (my $i = 3; $i < $max_peek; $i += 2) { push @view_2, $unicode[$i] } + + my $points_1 = 0; + foreach my $C (@view_1) { + ++$points_1 if (32 <= ord($C) and ord($C) <= 127) or ord($C) == 13 + or ord($C) == 10 + or ord($C) == 9; + } + + my $points_2 = 0; + foreach my $C (@view_2) { + ++$points_2 if (32 <= ord($C) and ord($C) <= 127) or ord($C) == 13 + or ord($C) == 10 + or ord($C) == 9; + } +#print "points 1: $points_1\n"; +#print "points 2: $points_2\n"; + + my $offset = undef; + if ($points_1 > 90) { $offset = 2; } + elsif ($points_2 > 90) { $offset = 3; } + else { return '' } # neither big or little endian UTF-16 + + my @ascii = (); + for (my $i = $offset; $i < $length; $i += 2) { push @ascii, $unicode[$i]; } + return join("", @ascii); +} # 1}}} +sub uncompress_archive_cmd { # {{{1 + my ($archive_file, ) = @_; + + # Wrap $archive_file in single or double quotes in the system + # commands below to avoid filename chicanery (including + # spaces in the names). + + print "-> uncompress_archive_cmd($archive_file)\n" if $opt_v > 2; + my $extract_cmd = ""; + my $missing = ""; + if ($opt_extract_with) { + ( $extract_cmd = $opt_extract_with ) =~ s/>FILE -"; + } elsif (($archive_file =~ /\.tar\.(gz|Z)$/ or + $archive_file =~ /\.tgz$/ ) and !$ON_WINDOWS) { + if (external_utility_exists("gzip --version")) { + if (external_utility_exists("tar --version")) { + $extract_cmd = "gzip -dc '$archive_file' | tar xf -"; + } else { + $missing = "tar"; + } + } else { + $missing = "gzip"; + } + } elsif ($archive_file =~ /\.tar\.bz2$/ and !$ON_WINDOWS) { + if (external_utility_exists("bzip2 --help")) { + if (external_utility_exists("tar --version")) { + $extract_cmd = "bzip2 -dc '$archive_file' | tar xf -"; + } else { + $missing = "tar"; + } + } else { + $missing = "bzip2"; + } + } elsif ($archive_file =~ /\.tar\.xz$/ and !$ON_WINDOWS) { + if (external_utility_exists("unxz --version")) { + if (external_utility_exists("tar --version")) { + $extract_cmd = "unxz -dc '$archive_file' | tar xf -"; + } else { + $missing = "tar"; + } + } else { + $missing = "bzip2"; + } + } elsif ($archive_file =~ /\.tar$/ and !$ON_WINDOWS) { + $extract_cmd = "tar xf '$archive_file'"; + } elsif ($archive_file =~ /\.src\.rpm$/i and !$ON_WINDOWS) { + if (external_utility_exists("cpio --version")) { + if (external_utility_exists("rpm2cpio")) { + $extract_cmd = "rpm2cpio '$archive_file' | cpio -i"; + } else { + $missing = "rpm2cpio"; + } + } else { + $missing = "bzip2"; + } + } elsif ($archive_file =~ /\.zip$/i and !$ON_WINDOWS) { + if (external_utility_exists("unzip")) { + $extract_cmd = "unzip -qq -d . '$archive_file'"; + } else { + $missing = "unzip"; + } + } elsif ($archive_file =~ /\.deb$/i and !$ON_WINDOWS) { + # only useful if the .deb contains source code--most + # .deb files just have compiled executables + if (external_utility_exists("dpkg-deb")) { + $extract_cmd = "dpkg-deb -x '$archive_file' ."; + } else { + $missing = "dpkg-deb"; + } + } elsif ($ON_WINDOWS and $archive_file =~ /\.zip$/i) { + # zip on Windows, guess default Winzip install location + $extract_cmd = ""; + my $WinZip = '"C:\\Program Files\\WinZip\\WinZip32.exe"'; + if (external_utility_exists($WinZip)) { + $extract_cmd = "$WinZip -e -o \"$archive_file\" ."; +#print "trace 5 extract_cmd=[$extract_cmd]\n"; + } else { +#print "trace 6\n"; + $missing = $WinZip; + } + } + print "<- uncompress_archive_cmd\n" if $opt_v > 2; + if ($missing) { + die "Unable to expand $archive_file because external\n", + "utility '$missing' is not available.\n", + "Another possibility is to use the --extract-with option.\n"; + } else { + return $extract_cmd; + } +} +# 1}}} +sub read_list_file { # {{{1 + my ($file, ) = @_; + + print "-> read_list_file($file)\n" if $opt_v > 2; + my $IN = new IO::File $file, "r"; + if (!defined $IN) { + warn "Unable to read $file; ignoring.\n"; + return (); + } + my @entry = (); + while (<$IN>) { + next if /^\s*$/ or /^\s*#/; # skip empty or commented lines + s/\cM$//; # DOS to Unix + chomp; + push @entry, $_; + } + $IN->close; + + print "<- read_list_file\n" if $opt_v > 2; + return @entry; +} +# 1}}} +sub external_utility_exists { # {{{1 + my $exe = shift @_; + + my $success = 0; + if ($ON_WINDOWS) { + $success = 1 unless system $exe . ' > nul'; + } else { + $success = 1 unless system $exe . ' >/dev/null 2>&1'; + if (!$success) { + $success = 1 unless system "which" . " $exe" . ' >/dev/null 2>&1'; + } + } + + return $success; +} # 1}}} +sub write_xsl_file { # {{{1 + my $OUT = new IO::File $CLOC_XSL, "w"; + if (!defined $OUT) { + warn "Unable to write $CLOC_XSL $!\n"; + return; + } + my $XSL = # {{{2 +' + + + + + + + CLOC Results + + + +

+'; +# 2}}} + + if ($opt_by_file) { + $XSL .= #
{{{2 +' + + + + + + + +'; + $XSL .= +' + +' if $opt_3; + $XSL .= +' + + + + + + + + + +'; + $XSL .= +' + +' if $opt_3; + $XSL .= +' + + + + + + + +'; + $XSL .= +' + +' if $opt_3; + $XSL .= +' + +
FileBlankCommentCodeLanguage3rd Generation EquivalentScale
Total
+
+'; +# 2}}} + } + + if (!$opt_by_file or $opt_by_file_by_lang) { + $XSL .= #
{{{2 +' + + + + + + + +'; + $XSL .= +' + +' if $opt_3; + $XSL .= +' + + + + + + + + + +'; + $XSL .= +' + +' if $opt_3; + $XSL .= +' + + + + + + + +'; + $XSL .= +' + +' if $opt_3; + $XSL .= +' + +
LanguageFilesBlankCommentCodeScale3rd Generation Equivalent
Total
+'; +# 2}}} + } + + $XSL.= <<'EO_XSL'; # {{{2 + + + + + +EO_XSL +# 2}}} + + my $XSL_DIFF = <<'EO_DIFF_XSL'; # {{{2 + + + + + + + + CLOC Results + + + +

+EO_DIFF_XSL +# 2}}} + + if ($opt_by_file) { + $XSL_DIFF.= <<'EO_DIFF_XSL'; # {{{2 + + + + + + + + + + + + + + + + + + + + + +
Same
FileBlankCommentCode
+ + + + + + + + + + + + + + + + + + + + + + +
Modified
FileBlankCommentCode
+ + + + + + + + + + + + + + + + + + + + + + +
Added
FileBlankCommentCode
+ + + + + + + + + + + + + + + + + + + + + + +
Removed
FileBlankCommentCode
+EO_DIFF_XSL +# 2}}} + } + + if (!$opt_by_file or $opt_by_file_by_lang) { + $XSL_DIFF.= <<'EO_DIFF_XSL'; # {{{2 + + + + + + + + + + + + + + + + + + + + + + + +
Same
LanguageFilesBlankCommentCode
+ + + + + + + + + + + + + + + + + + + + + + + + +
Modified
LanguageFilesBlankCommentCode
+ + + + + + + + + + + + + + + + + + + + + + + + +
Added
LanguageFilesBlankCommentCode
+ + + + + + + + + + + + + + + + + + + + + + + + +
Removed
LanguageFilesBlankCommentCode
+EO_DIFF_XSL +# 2}}} + + } + + $XSL_DIFF.= <<'EO_DIFF_XSL'; # {{{2 + + + + +EO_DIFF_XSL +# 2}}} + if ($opt_diff) { + print $OUT $XSL_DIFF; + } else { + print $OUT $XSL; + } + $OUT->close(); +} # 1}}} +sub normalize_file_names { # {{{1 + my (@files, ) = @_; + + # Returns a hash of file names reduced to a canonical form + # (fully qualified file names, all path separators changed to /, + # Windows file names lowercased). Hash values are the original + # file name. + + my %normalized = (); + foreach my $F (@files) { + my $F_norm = $F; + if ($ON_WINDOWS) { + $F_norm = lc $F_norm; # for case insensitive file name comparisons + $F_norm =~ s{\\}{/}g; # Windows directory separators to Unix + $F_norm =~ s{^\./}{}g; # remove leading ./ + if (($F_norm !~ m{^/}) and ($F_norm !~ m{^\w:/})) { + # looks like a relative path; prefix with cwd + $F_norm = lc "$cwd/$F_norm"; + } + } else { + $F_norm =~ s{^\./}{}g; # remove leading ./ + if ($F_norm !~ m{^/}) { + # looks like a relative path; prefix with cwd + $F_norm = lc "$cwd/$F_norm"; + } + } + # Remove trailing / so it does not interfere with further regex code + # that does not expect it + $F_norm =~ s{/+$}{}; + $normalized{ $F_norm } = $F; + } + return %normalized; +} # 1}}} +sub combine_diffs { # {{{1 + # subroutine by Andy (awalshe@sf.net) + # https://sourceforge.net/tracker/?func=detail&aid=3261017&group_id=174787&atid=870625 + my ($ra_files) = @_; + + my $res = "$URL v $VERSION\n"; + my $dl = '-'; + my $width = 79; + # columns are in this order + my @cols = ('files', 'blank', 'comment', 'code'); + my %HoH = (); + + foreach my $file (@{$ra_files}) { + my $IN = new IO::File $file, "r"; + if (!defined $IN) { + warn "Unable to read $file; ignoring.\n"; + next; + } + + my $sec; + while (<$IN>) { + chomp; + s/\cM$//; + next if /^(http|Language|-----)/; + if (/^[A-Za-z0-9]+/) { # section title + $sec = $_; + chomp($sec); + $HoH{$sec} = () if ! exists $HoH{$sec}; + next; + } + + if (/^\s(same|modified|added|removed)/) { # calculated totals row + my @ar = grep { $_ ne '' } split(/ /, $_); + chomp(@ar); + my $ttl = shift @ar; + my $i = 0; + foreach(@ar) { + my $t = "${ttl}${dl}${cols[$i]}"; + $HoH{$sec}{$t} = 0 if ! exists $HoH{$sec}{$t}; + $HoH{$sec}{$t} += $_; + $i++; + } + } + } + $IN->close; + } + + # rows are in this order + my @rows = ('same', 'modified', 'added', 'removed'); + + $res .= sprintf("%s\n", "-" x $width); + $res .= sprintf("%-19s %14s %14s %14s %14s\n", 'Language', + $cols[0], $cols[1], $cols[2], $cols[3]); + $res .= sprintf("%s\n", "-" x $width); + + for my $sec ( keys %HoH ) { + next if $sec =~ /SUM:/; + $res .= "$sec\n"; + foreach (@rows) { + $res .= sprintf(" %-18s %14s %14s %14s %14s\n", + $_, $HoH{$sec}{"${_}${dl}${cols[0]}"}, + $HoH{$sec}{"${_}${dl}${cols[1]}"}, + $HoH{$sec}{"${_}${dl}${cols[2]}"}, + $HoH{$sec}{"${_}${dl}${cols[3]}"}); + } + } + $res .= sprintf("%s\n", "-" x $width); + my $sec = 'SUM:'; + $res .= "$sec\n"; + foreach (@rows) { + $res .= sprintf(" %-18s %14s %14s %14s %14s\n", + $_, $HoH{$sec}{"${_}${dl}${cols[0]}"}, + $HoH{$sec}{"${_}${dl}${cols[1]}"}, + $HoH{$sec}{"${_}${dl}${cols[2]}"}, + $HoH{$sec}{"${_}${dl}${cols[3]}"}); + } + $res .= sprintf("%s\n", "-" x $width); + + return $res; +} # 1}}} +sub get_time { # {{{1 + if ($HAVE_Time_HiRes) { + return Time::HiRes::time(); + } else { + return time(); + } +} # 1}}} +sub really_is_D { # {{{1 + # Ref bug 131, files ending with .d could be init.d scripts + # instead of D language source files. + my ($file , # in + $rh_Err , # in hash of error codes + $raa_errors , # out + ) = @_; + print "-> really_is_D($file)\n" if $opt_v > 2; + my $possible_script = peek_at_first_line($file, $rh_Err, $raa_errors); + + print "<- really_is_D($file)\n" if $opt_v > 2; + return $possible_script; # null string if D, otherwise a language +} # 1}}} +# subroutines copied from SLOCCount +my %lex_files = (); # really_is_lex() +my %expect_files = (); # really_is_expect() +my %php_files = (); # really_is_php() +sub really_is_lex { # {{{1 +# Given filename, returns TRUE if its contents really is lex. +# lex file must have "%%", "%{", and "%}". +# In theory, a lex file doesn't need "%{" and "%}", but in practice +# they all have them, and requiring them avoid mislabeling a +# non-lexfile as a lex file. + + my $filename = shift; + chomp($filename); + + my $is_lex = 0; # Value to determine. + my $percent_percent = 0; + my $percent_opencurly = 0; + my $percent_closecurly = 0; + + # Return cached result, if available: + if ($lex_files{$filename}) { return $lex_files{$filename};} + + open(LEX_FILE, "<$filename") || + die "Can't open $filename to determine if it's lex.\n"; + while() { + $percent_percent++ if (m/^\s*\%\%/); + $percent_opencurly++ if (m/^\s*\%\{/); + $percent_closecurly++ if (m/^\s*\%\}/); + } + close(LEX_FILE); + + if ($percent_percent && $percent_opencurly && $percent_closecurly) + {$is_lex = 1;} + + $lex_files{$filename} = $is_lex; # Store result in cache. + + return $is_lex; +} # 1}}} +sub really_is_expect { # {{{1 +# Given filename, returns TRUE if its contents really are Expect. +# Many "exp" files (such as in Apache and Mesa) are just "export" data, +# summarizing something else # (e.g., its interface). +# Sometimes (like in RPM) it's just misc. data. +# Thus, we need to look at the file to determine +# if it's really an "expect" file. + + my $filename = shift; + chomp($filename); + +# The heuristic is as follows: it's Expect _IF_ it: +# 1. has "load_lib" command and either "#" comments or {}. +# 2. {, }, and one of: proc, if, [...], expect + + my $is_expect = 0; # Value to determine. + + my $begin_brace = 0; # Lines that begin with curly braces. + my $end_brace = 0; # Lines that begin with curly braces. + my $load_lib = 0; # Lines with the Load_lib command. + my $found_proc = 0; + my $found_if = 0; + my $found_brackets = 0; + my $found_expect = 0; + my $found_pound = 0; + + # Return cached result, if available: + if ($expect_files{$filename}) { return expect_files{$filename};} + + open(EXPECT_FILE, "<$filename") || + die "Can't open $filename to determine if it's expect.\n"; + while() { + + if (m/#/) {$found_pound++; s/#.*//;} + if (m/^\s*\{/) { $begin_brace++;} + if (m/\{\s*$/) { $begin_brace++;} + if (m/^\s*\}/) { $end_brace++;} + if (m/\};?\s*$/) { $end_brace++;} + if (m/^\s*load_lib\s+\S/) { $load_lib++;} + if (m/^\s*proc\s/) { $found_proc++;} + if (m/^\s*if\s/) { $found_if++;} + if (m/\[.*\]/) { $found_brackets++;} + if (m/^\s*expect\s/) { $found_expect++;} + } + close(EXPECT_FILE); + + if ($load_lib && ($found_pound || ($begin_brace && $end_brace))) + {$is_expect = 1;} + if ( $begin_brace && $end_brace && + ($found_proc || $found_if || $found_brackets || $found_expect)) + {$is_expect = 1;} + + $expect_files{$filename} = $is_expect; # Store result in cache. + + return $is_expect; +} # 1}}} +sub really_is_pascal { # {{{1 +# Given filename, returns TRUE if its contents really are Pascal. + +# This isn't as obvious as it seems. +# Many ".p" files are Perl files +# (such as /usr/src/redhat/BUILD/ispell-3.1/dicts/czech/glob.p), +# others are C extractions +# (such as /usr/src/redhat/BUILD/linux/include/linux/umsdos_fs.p +# and some files in linuxconf). +# However, test files in "p2c" really are Pascal, for example. + +# Note that /usr/src/redhat/BUILD/ucd-snmp-4.1.1/ov/bitmaps/UCD.20.p +# is actually C code. The heuristics determine that they're not Pascal, +# but because it ends in ".p" it's not counted as C code either. +# I believe this is actually correct behavior, because frankly it +# looks like it's automatically generated (it's a bitmap expressed as code). +# Rather than guess otherwise, we don't include it in a list of +# source files. Let's face it, someone who creates C files ending in ".p" +# and expects them to be counted by default as C files in SLOCCount needs +# their head examined. I suggest examining their head +# with a sucker rod (see syslogd(8) for more on sucker rods). + +# This heuristic counts as Pascal such files such as: +# /usr/src/redhat/BUILD/teTeX-1.0/texk/web2c/tangleboot.p +# Which is hand-generated. We don't count woven documents now anyway, +# so this is justifiable. + + my $filename = shift; + chomp($filename); + +# The heuristic is as follows: it's Pascal _IF_ it has all of the following +# (ignoring {...} and (*...*) comments): +# 1. "^..program NAME" or "^..unit NAME", +# 2. "procedure", "function", "^..interface", or "^..implementation", +# 3. a "begin", and +# 4. it ends with "end.", +# +# Or it has all of the following: +# 1. "^..module NAME" and +# 2. it ends with "end.". +# +# Or it has all of the following: +# 1. "^..program NAME", +# 2. a "begin", and +# 3. it ends with "end.". +# +# The "end." requirements in particular filter out non-Pascal. +# +# Note (jgb): this does not detect Pascal main files in fpc, like +# fpc-1.0.4/api/test/testterminfo.pas, which does not have "program" in +# it + + my $is_pascal = 0; # Value to determine. + + my $has_program = 0; + my $has_unit = 0; + my $has_module = 0; + my $has_procedure_or_function = 0; + my $found_begin = 0; + my $found_terminating_end = 0; + my $has_begin = 0; + + open(PASCAL_FILE, "<$filename") || + die "Can't open $filename to determine if it's pascal.\n"; + while() { + s/\{.*?\}//g; # Ignore {...} comments on this line; imperfect, but effective. + s/\(\*.*?\*\)//g; # Ignore (*...*) comments on this line; imperfect, but effective. + if (m/\bprogram\s+[A-Za-z]/i) {$has_program=1;} + if (m/\bunit\s+[A-Za-z]/i) {$has_unit=1;} + if (m/\bmodule\s+[A-Za-z]/i) {$has_module=1;} + if (m/\bprocedure\b/i) { $has_procedure_or_function = 1; } + if (m/\bfunction\b/i) { $has_procedure_or_function = 1; } + if (m/^\s*interface\s+/i) { $has_procedure_or_function = 1; } + if (m/^\s*implementation\s+/i) { $has_procedure_or_function = 1; } + if (m/\bbegin\b/i) { $has_begin = 1; } + # Originally I said: + # "This heuristic fails if there are multi-line comments after + # "end."; I haven't seen that in real Pascal programs:" + # But jgb found there are a good quantity of them in Debian, specially in + # fpc (at the end of a lot of files there is a multiline comment + # with the changelog for the file). + # Therefore, assume Pascal if "end." appears anywhere in the file. + if (m/end\.\s*$/i) {$found_terminating_end = 1;} +# elsif (m/\S/) {$found_terminating_end = 0;} + } + close(PASCAL_FILE); + + # Okay, we've examined the entire file looking for clues; + # let's use those clues to determine if it's really Pascal: + + if ( ( ($has_unit || $has_program) && $has_procedure_or_function && + $has_begin && $found_terminating_end ) || + ( $has_module && $found_terminating_end ) || + ( $has_program && $has_begin && $found_terminating_end ) ) + {$is_pascal = 1;} + + return $is_pascal; +} # 1}}} +sub really_is_incpascal { # {{{1 +# Given filename, returns TRUE if its contents really are Pascal. +# For .inc files (mainly seen in fpc) + + my $filename = shift; + chomp($filename); + +# The heuristic is as follows: it is Pascal if any of the following: +# 1. really_is_pascal returns true +# 2. Any usual reserved word is found (program, unit, const, begin...) + + # If the general routine for Pascal files works, we have it + if (really_is_pascal($filename)) { + return 1; + } + + my $is_pascal = 0; # Value to determine. + my $found_begin = 0; + + open(PASCAL_FILE, "<$filename") || + die "Can't open $filename to determine if it's pascal.\n"; + while() { + s/\{.*?\}//g; # Ignore {...} comments on this line; imperfect, but effective. + s/\(\*.*?\*\)//g; # Ignore (*...*) comments on this line; imperfect, but effective. + if (m/\bprogram\s+[A-Za-z]/i) {$is_pascal=1;} + if (m/\bunit\s+[A-Za-z]/i) {$is_pascal=1;} + if (m/\bmodule\s+[A-Za-z]/i) {$is_pascal=1;} + if (m/\bprocedure\b/i) {$is_pascal = 1; } + if (m/\bfunction\b/i) {$is_pascal = 1; } + if (m/^\s*interface\s+/i) {$is_pascal = 1; } + if (m/^\s*implementation\s+/i) {$is_pascal = 1; } + if (m/\bconstant\s+/i) {$is_pascal=1;} + if (m/\bbegin\b/i) { $found_begin = 1; } + if ((m/end\.\s*$/i) && ($found_begin = 1)) {$is_pascal = 1;} + if ($is_pascal) { + last; + } + } + + close(PASCAL_FILE); + return $is_pascal; +} # 1}}} +sub really_is_php { # {{{1 +# Given filename, returns TRUE if its contents really is php. + + my $filename = shift; + chomp($filename); + + my $is_php = 0; # Value to determine. + # Need to find a matching pair of surrounds, with ending after beginning: + my $normal_surround = 0; # + my $script_surround = 0; # ; bit 0 =