Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 28012) +++ /issm/trunk/configure.ac (revision 28013) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[4.22],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[4.23],[https://issm.ess.uci.edu/forum/],[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.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 28012) +++ /issm/trunk/etc/environment.sh (revision 28013) @@ -275,12 +275,12 @@ # Libraries / binaries ############################# -MPI_ROOT="${ISSM_EXT_DIR}/mpich/install" -if [ -d "${MPI_ROOT}" ]; then - export MPI_DIR=${MPI_ROOT} - export MPI_HOME=${MPI_ROOT} # Used in installation of Dakota - export MPI_INC_DIR="${MPI_ROOT}/include" - path_prepend "${MPI_ROOT}/bin" - cpath_prepend "${MPI_ROOT}/include" - ld_library_path_append "${MPI_ROOT}/lib" +MPI_ROOT_TEMP="${ISSM_EXT_DIR}/mpich/install" +if [ -d "${MPI_ROOT_TEMP}" ]; then + export MPI_DIR=${MPI_ROOT_TEMP} + export MPI_HOME=${MPI_ROOT_TEMP} # Used in installation of Dakota + export MPI_INC_DIR="${MPI_ROOT_TEMP}/include" + path_prepend "${MPI_ROOT_TEMP}/bin" + cpath_prepend "${MPI_ROOT_TEMP}/include" + ld_library_path_append "${MPI_ROOT_TEMP}/lib" fi @@ -484,4 +484,5 @@ if [ -d "${GSL_ROOT}" ]; then export GSL_HOME="${GSL_ROOT}" # Used in installation of Dakota + cpath_prepend "${GSL_ROOT}/include" ld_library_path_append "${GSL_ROOT}/lib" fi @@ -675,6 +676,9 @@ fi -VALGRIND_ROOT="${ISSM_EXT_DIR}/valgrind/install" -path_prepend "${VALGRIND_ROOT}/bin" +VALGRIND_ROOT="${ISSM_DIR}/externalpackages/valgrind/install" +if [ -d "${VALGRIND_ROOT="${ISSM_DIR}/valgrind/install" +}" ]; then + path_prepend "${VALGRIND_ROOT}/bin" +fi DOXYGEN_ROOT="${ISSM_EXT_DIR}/doxygen/install" Index: /issm/trunk/examples/EsaGRACE/runme.m =================================================================== --- /issm/trunk/examples/EsaGRACE/runme.m (revision 28012) +++ /issm/trunk/examples/EsaGRACE/runme.m (revision 28013) @@ -125,10 +125,10 @@ set(0,'DefaultAxesFontSize',18,'DefaultAxesLineWidth',1,'DefaultTextFontSize',18,'DefaultLineMarkerSize',8) figure1=figure('Position', [100, 100, 1000, 500]); - gcf; load coast; cla; + gcf; load coastlines; cla; pcolor(lon_grid,lat_grid,sol_grid); shading flat; hold on; if (kk==1) - geoshow(flipud(lat),flipud(long),'DisplayType','polygon','FaceColor','white'); + geoshow(flipud(coastlat),flipud(coastlon),'DisplayType','polygon','FaceColor','white'); end - plot(long,lat,'k'); hold off; + plot(coastlon,coastlat,'k'); hold off; c1=colorbar; colormap('haxby'); Index: /issm/trunk/examples/StISSM/DomainOutline.exp =================================================================== --- /issm/trunk/examples/StISSM/DomainOutline.exp (revision 28013) +++ /issm/trunk/examples/StISSM/DomainOutline.exp (revision 28013) @@ -0,0 +1,101 @@ +## Name: +## Icon:0 +# Points Count Value +95 25000.000000 +# X pos Y pos +-1712113.0179281300 -349656.0205056490 +-1711509.1917759699 -349354.1074295690 +-1709240.6586108401 -349354.1074295690 +-1707080.1508345299 -348922.0058743060 +-1705459.7700022999 -347193.5996532570 +-1703083.2114483600 -345249.1426545770 +-1701138.7544496800 -344168.8887664210 +-1698438.1197292900 -343952.8379887900 +-1698006.0181740201 -341900.3556012940 +-1693793.0280102200 -340279.9747690600 +-1691092.3932898301 -339631.8224361670 +-1688391.7585694401 -339415.7716585360 +-1686447.3015707601 -340063.9239914290 +-1683530.6160727399 -341036.1524907690 +-1682558.3875734000 -343304.6856558960 +-1682134.7209454600 -344182.1487658350 +-1682126.2860181299 -345681.2442098390 +-1681072.0444963200 -345932.4393879640 +-1680634.4718407800 -346682.5639403050 +-1680571.9614614199 -348557.8753211580 +-1677446.4424933300 -348370.3441830730 +-1675508.6207331200 -349495.5310115840 +-1676616.9911885399 -353567.0975933760 +-1672991.8601872099 -353799.6175753630 +-1668839.1631938200 -353999.1991486380 +-1667132.2298986400 -355121.4651541420 +-1666069.5534494901 -357496.8595698890 +-1662944.0344814099 -358309.4945015920 +-1660756.1712037399 -358747.0671571240 +-1657922.9836098100 -361682.8074238540 +-1656579.2228470000 -364003.8487410000 +-1653004.8841628900 -364748.0635758530 +-1653442.4568184200 -361622.5446077650 +-1651129.5727820301 -355684.0585683980 +-1648929.2928810001 -350845.9692010000 +-1646260.7698359799 -347802.2804785470 +-1644571.8968503401 -341785.6704672340 +-1643503.3064999001 -340869.0986596620 +-1643190.7546030900 -336680.9032424240 +-1642690.6715682000 -335243.1645171040 +-1641913.0916588283 -332341.0814454452 +-1640683.9739821283 -330436.6112348017 +-1637816.0327364956 -328532.1410241582 +-1635241.2508976001 -328652.8685499910 +-1631765.4107996500 -327017.1790921330 +-1625934.5618617306 -322342.6128395668 +-1620608.3852626982 -320438.1426289233 +-1616101.6204481323 -320438.1426289233 +-1611594.8556335662 -320914.2601815842 +-1607907.5026034669 -321866.4952869060 +-1602991.0318966676 -324723.2006028712 +-1599713.3847588014 -327579.9059188365 +-1593977.5022675355 -328532.1410241582 +-1590699.8551296694 -334721.6692087495 +-1589259.8391499999 -338300.0840570000 +-1588627.0898328500 -343572.9950327750 +-1588056.6000060199 -345432.3563530700 +-1586993.9235568701 -347432.6884926460 +-1589259.8391499999 -349315.9832070000 +-1585493.6744521901 -352996.1122558430 +-1585118.6121760199 -354496.3613605250 +-1585861.9157163899 -356240.3342513760 +-1586368.8197632500 -358747.0671571240 +-1587889.0972700799 -360996.6006787950 +-1586681.3716600600 -363935.4286441500 +-1585806.2263489999 -365748.2296456410 +-1586743.8820394201 -368373.6655788350 +-1586056.2678664399 -370123.9562009640 +-1585493.6744521901 -371124.1222707520 +-1586243.7990045301 -373562.0270658610 +-1414257.6683934701 -327460.5482541260 +-1412220.4351378100 -325972.8942023180 +-1404515.9240538401 -296165.1737279960 +-1387984.9332285200 -267002.0106682320 +-1360067.9373810000 -107884.1934940000 +-1423274.3497420000 -81217.9259650000 +-1402446.7987670000 -45916.9921070000 +-1478343.8065599999 60338.8188030000 +-1503760.4789370000 36334.1837800000 +-1528509.5619775900 63667.6809196406 +-1623055.4918765700 62841.1506965373 +-1725734.5897359999 -61372.6193030000 +-1719614.6457630000 -69022.5492690000 +-1759088.2843859999 -114004.1374660000 +-1755416.3180020000 -117064.1094530000 +-1761230.2647760001 -126856.0198080000 +-1758170.2927900001 -130527.9861920000 +-1762148.2563720001 -135423.9413700000 +-1764902.2311590000 -131445.9777880000 +-1769798.1863370000 -134199.9525750000 +-1775000.1387139999 -131445.9777880000 +-1794277.9622269999 -153477.7760890000 +-1712576.7101950001 -225081.1205660000 +-1729939.5891459100 -335652.4567604720 +-1712113.0179281300 -349656.0205056490 + Index: /issm/trunk/examples/StISSM/PigStISSM.par =================================================================== --- /issm/trunk/examples/StISSM/PigStISSM.par (revision 28013) +++ /issm/trunk/examples/StISSM/PigStISSM.par (revision 28013) @@ -0,0 +1,117 @@ + +% Name and Coordinate system +md.miscellaneous.name = 'PigStISSM'; +md.mesh.epsg = 3031; + +% NetCdf Loading +disp(' Loading SeaRISE data from NetCDF'); +ncdata ='../Data/Antarctica_5km_withshelves_v0.75.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +temp = ncread(ncdata,'presartm')'; +smb = ncread(ncdata,'presprcp')'; +gflux = ncread(ncdata,'bheatflx_fox')'; + +% Geometry +disp(' Interpolating surface and ice base'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); +clear usrf, topg; + +disp(' Constructing thickness'); +md.geometry.thickness = md.geometry.surface-md.geometry.base; + +% Ensure hydrostatic equilibrium on ice shelf: +di = md.materials.rho_ice/md.materials.rho_water; + +% Get the node numbers of floating nodes +pos = find(md.mask.ocean_levelset<0); + +% Apply a flotation criterion on the precedingly defined nodes and +% redefine base and thickness accordingly +md.geometry.thickness(pos) = 1/(1-di)*md.geometry.surface(pos); +md.geometry.base(pos) = md.geometry.surface(pos)-md.geometry.thickness(pos); +md.geometry.hydrostatic_ratio = ones(md.mesh.numberofvertices,1); %For Dakota + +% Set min thickness to 1 meter +pos0 = find(md.geometry.thickness<=1); +md.geometry.thickness(pos0) = 1; +md.geometry.surface = md.geometry.thickness+md.geometry.base; +md.geometry.bed = md.geometry.base; +md.geometry.bed(pos) = md.geometry.base(pos)-1000; + +% Initialization parameters +disp(' Interpolating temperatures'); +Temp_change = 0; +md.initialization.temperature = InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15+Temp_change; +clear temp; + +disp(' Loading velocities data from NetCDF'); +nsidc_vel = '../Data/Antarctica_ice_velocity.nc'; +xmin = ncreadatt(nsidc_vel,'/','xmin'); +ymax = ncreadatt(nsidc_vel,'/','ymax'); +spacing = ncreadatt(nsidc_vel,'/','spacing'); +nx = double(ncreadatt(nsidc_vel,'/','nx')); +ny = double(ncreadatt(nsidc_vel,'/','ny')); +velx = double(ncread(nsidc_vel,'vx')); +vely = double(ncread(nsidc_vel,'vy')); +% Read coordinates +xmin = strtrim(xmin); +xmin = str2num(xmin(1:end-2)); +ymax = strtrim(ymax); +ymax = str2num(ymax(1:end-2)); +spacing = strtrim(spacing); +spacing = str2num(spacing(1:end-2)); +% Build the coordinates +x2 = xmin+(0:1:nx)'*spacing; +y2 = (ymax-ny*spacing)+(0:1:ny)'*spacing; + +disp(' Set observed velocities') +md.initialization.vx = InterpFromGridToMesh(x2,y2,flipud(velx'),md.mesh.x,md.mesh.y,0); +md.initialization.vy = InterpFromGridToMesh(x2,y2,flipud(vely'),md.mesh.x,md.mesh.y,0); +md.initialization.vz = zeros(md.mesh.numberofvertices,1); +md.initialization.vel = sqrt(md.initialization.vx.^2+md.initialization.vy.^2); +clear velx vely; + +disp(' Set Pressure'); +md.initialization.pressure = md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +disp(' Construct ice rheological properties'); +md.materials.rheology_n = 3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B = paterson(md.initialization.temperature); + +%Forcings +disp(' Interpolating surface mass balance'); +mass_balance = InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance = mass_balance*md.materials.rho_water/md.materials.rho_ice; +clear smb; + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux = InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); +clear gflux; + +% Friction and inversion set up +disp(' Construct basal friction parameters'); +friction_coefficient = 10.0; +md.friction.coefficient = friction_coefficient*ones(md.mesh.numberofvertices,1); +md.friction.p = ones(md.mesh.numberofelements,1); +md.friction.q = ones(md.mesh.numberofelements,1); + +% No friction applied on floating ice +pos = find(md.mask.ocean_levelset<0); +md.friction.coefficient(pos) = 0; +md.groundingline.migration = 'SubelementMigration'; + +md.inversion = m1qn3inversion(); +md.inversion.vx_obs = md.initialization.vx; +md.inversion.vy_obs = md.initialization.vy; +md.inversion.vel_obs = md.initialization.vel; + +disp(' Set boundary conditions'); +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md = SetMarineIceSheetBC(md); +md.thermal.spctemperature = md.initialization.temperature; +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); Index: /issm/trunk/examples/StISSM/runme.m =================================================================== --- /issm/trunk/examples/StISSM/runme.m (revision 28013) +++ /issm/trunk/examples/StISSM/runme.m (revision 28013) @@ -0,0 +1,288 @@ + +%%% +% Tutorial for StISSM +%%% + +steps = [1]; + +if any(steps==1) + % Mesh parameters + domain = ['./DomainOutline.exp']; + hinit = 5000; % element size for the initial mesh + hmax = 40000; % maximum element size of the final mesh + hmin = 4000; % minimum element size of the final mesh + gradation = 1.7; % maximum size ratio between two neighboring elements + err = 8; % maximum error between interpolated and control field + + % Generate an initial uniform mesh (resolution = hinit m) + md = bamg(model,'domain',domain,'hmax',hinit); + + % Get necessary data to build up the velocity grid + nsidc_vel = '../Data/Antarctica_ice_velocity.nc'; + xmin = strsplit(ncreadatt(nsidc_vel,'/','xmin')); + xmin = str2num(xmin{2}); + ymax = strsplit(ncreadatt(nsidc_vel,'/','ymax')); + ymax = str2num(ymax{2}); + spacing = strsplit(ncreadatt(nsidc_vel,'/','spacing')); + spacing = str2num(spacing{2}); + nx = double(ncreadatt(nsidc_vel,'/','nx')); + ny = double(ncreadatt(nsidc_vel,'/','ny')); + vx = double(ncread(nsidc_vel,'vx')); + vy = double(ncread(nsidc_vel,'vy')); + + % Build the coordinates + x = xmin+(0:1:nx)'*spacing; + y = (ymax-ny*spacing)+(0:1:ny)'*spacing; + + % Interpolate velocities onto coarse mesh + vx_obs = InterpFromGridToMesh(x,y,flipud(vx'),md.mesh.x,md.mesh.y,0); + vy_obs = InterpFromGridToMesh(x,y,flipud(vy'),md.mesh.x,md.mesh.y,0); + vel_obs = sqrt(vx_obs.^2+vy_obs.^2); + clear vx vy x y; + + % Adapt the mesh to minimize error in velocity interpolation + md = bamg(md,'hmax',hmax,'hmin',hmin,'gradation',gradation,'field',vel_obs,'err',err); + + % Plot and save model + plotmodel(md,'data','mesh') + save ./Models/PIG_StISSM_Mesh_generation md; + +end + +if any(steps==2) %Masks #2 + md = loadmodel('./Models/PIG_StISSM_Mesh_generation'); + + % Load SeaRISe dataset for Antarctica http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica + searise = '../Data/Antarctica_5km_withshelves_v0.75.nc'; + + % Read thickness mask from SeaRISE + x1 = double(ncread(searise,'x1')); + y1 = double(ncread(searise,'y1')); + thkmask = double(ncread(searise,'thkmask')); + + % Interpolate onto our mesh vertices + groundedice = double(InterpFromGridToMesh(x1,y1,thkmask',md.mesh.x,md.mesh.y,0)); + groundedice(groundedice<=0) = -1; + clear thkmask; + + % Fill in the md.mask structure + 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.ocean_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') + + save ./Models/PIG_StISSM_SetMask md; +end + +if any(steps==3) %Parameterization #3 + + md = loadmodel('./Models/PIG_StISSM_SetMask'); + md = setflowequation(md,'SSA','all'); + md = parameterize(md,'./PigStISSM.par'); + + save ./Models/PIG_StISSM_Parameterization md; +end + +if any(steps==4) %Stochastic SMB + md = loadmodel('./Models/PIG_StISSM_Parameterization'); + + % Create the different subdomains for SMB % + ymax = max(md.mesh.y); + ymin = min(md.mesh.y); + xmax = max(md.mesh.x); + xmin = min(md.mesh.x); + idsmb = zeros(md.mesh.numberofelements,1); %subdomain ID is defined for each element + iid1 = find(md.mesh.x>=(xmax-2/3*(xmax-xmin))); %vertices in subdomain 1 + iid2 = find(md.mesh.x<(xmax-2/3*(xmax-xmin))); %vertices in subdomain 2 + for ii=1:md.mesh.numberofelements + for vertex=1:3 + if any(iid1==md.mesh.elements(ii,vertex)) %one vertex in subdomain 1 + idsmb(ii) = 1; + end + end + if idsmb(ii)==0 %no vertex was found in subdomain 1 + idsmb(ii) = 2; + end + end + + % SMBarma implementation + md.smb = SMBarma(); + md.smb.num_basins = 2; %we use two different subdomains + md.smb.basin_id = idsmb; %element subdomain IDs + md.smb.num_breaks = 1; %1 breakpoint in the piecewise polynomial + md.smb.datebreaks = [5;5]; %breakpoint occurs at year 5 in both subdomains + md.smb.num_params = 2; %use a constant and a linear trend for the piecwise polynomial + constsmb = [0.5,0.2;0.3,0.5]; %constant SMB term for subdomains pre- and post-breakpoint [m yr^-1] + trendsmb = [0,0;0.01,0.001]; %trend is SMB for subdomains pre- and post-breakpoint [m yr^-2] + md.smb.polynomialparams = cat(3,constsmb,trendsmb); %concatenating const and trend along a 3rd dimension + md.smb.ar_order = 1; %first-order AR + md.smb.ma_order = 1; %first-order MA + md.smb.arlag_coefs = [0.3;0]; %AR coefficients in each subdomain + md.smb.malag_coefs = zeros(md.smb.num_basins,md.smb.ma_order); %all zeros is equivalent to MA order 0 + md.smb.arma_timestep = 1.0; %yearly ARMA + md.smb.elevationbins = [300,1000;300,1000]; %elevations separating different lapse rate values [m] + md.smb.lapserates = 1e-2*[0.03,0.01,-1e-4;0.02,0.02,-1e-5]; %lapse rate values [m ice eq. m^-1 yr^-1] + md.smb.refelevation = [500,500]; %elevations at which the SMBarma calculated values apply (i.e., before using lapse rates) + + % Set-up the covariance matrix + sdevSMB1 = 0.01; %low standard deviation in subdomain 1 [m ice eq. yr^-1] + sdevSMB2 = 0.2; %higher variability in subdomain 2 [m ice eq. yr^-1] + correlationSMB = [1.0,0.5;0.5,1.0]; %moderate correlation between the subdomains + covarianceSMB = diag([sdevSMB1,sdevSMB2])*correlationSMB*diag([sdevSMB1,sdevSMB2]); %covariance matrix [(m ice eq. yr^-1)^2] + + % Stochasticforcing implementation + md.stochasticforcing.isstochasticforcing = 1; %activate stochasticity + md.stochasticforcing.fields = [{'SMBarma'}]; + md.stochasticforcing.covariance = covarianceSMB; %prescribe the SMB covariance + md.stochasticforcing.stochastictimestep = 1.0; %yearly stochasticity + + save ./Models/PIG_StISSM_StochSMB md; + +end + +if any(steps==5) % Transient Run #1 + + md = loadmodel('./Models/PIG_StISSM_StochSMB'); + + md.inversion.iscontrol = 0; + md.transient.ismasstransport = 1; + md.transient.isstressbalance = 1; + md.transient.isgroundingline = 1; + md.transient.ismovingfront = 0; + md.transient.isthermal = 0; + md.verbose.solution = 1; + md.timestepping.time_step = 0.1; + md.timestepping.final_time = 10; + md.transient.requested_outputs = {'default','SmbMassBalance','MaskIceLevelset'}; + + md = solve(md,'Transient'); + timing = cell2mat({md.results.TransientSolution(:).time}); + fullsmb = cell2mat({md.results.TransientSolution(:).SmbMassBalance}); + timemeansmb = mean(fullsmb,2); + timesdevsmb = std(fullsmb,0,2); + maxsmb = max(fullsmb,[],'all'); + minsmb = min(fullsmb,[],'all'); + + + plotmodel(md,'figure',1,... + 'data',md.results.TransientSolution(1).SmbMassBalance,'title','SMB at timestep 1','caxis#1',[minsmb,maxsmb],... + 'data',md.results.TransientSolution(end).SmbMassBalance,'title','SMB at last timestep','caxis#2',[minsmb,maxsmb]) + plotmodel(md,'figure',2,... + 'data',timemeansmb,'title','SMB mean over simulation',... + 'data',timesdevsmb,'title','SMB standard deviation over simulation') + + seriesSMB1 = fullsmb(1,:); + seriesSMB71 = fullsmb(71,:); + figure(3); + plot(timing,seriesSMB1,'b'); + hold on + plot(timing,seriesSMB71,'r'); + title('SMB at two different vertices'); + hold off + + save ./Models/PIG_StISSM_Transient1 md; + +end + +if any(steps==6) % Set up stochastic calving also + + md = loadmodel('./Models/PIG_StISSM_Transient1'); + + md.calving.calvingrate = 20*ones(md.mesh.numberofvertices,1); + md.frontalforcings.meltingrate = zeros(md.mesh.numberofvertices,1); + md.levelset.spclevelset = NaN(md.mesh.numberofvertices,1); + md.levelset.migration_max = 100.0; %avoid too fast advance/retreat of the front + md.transient.ismovingfront = 1; + + % Parameterize stochastic calving + idbasinsCalving = md.smb.basin_id; %same subdomains as for SMB + sdevClv1 = 0.5; %low standard deviation in subdomain 1 [m yr^-1] + sdevClv2 = 5; %higher variability in subdomain 2 [m yr^-1] + correlationClv = [1.0,0.0;0.0,1.0]; %no correlation between the subdomains + covarianceClv = diag([sdevClv1,sdevClv2])*correlationClv*diag([sdevClv1,sdevClv2]); %covariance matrix [(m yr^-1)^2] + + % Adjust stochastic forcing class + md.stochasticforcing.fields = [{'SMBarma'},{'DefaultCalving'}]; + oldcovarianceSMB = md.stochasticforcing.covariance; + covarianceGlobal = blkdiag(oldcovarianceSMB,covarianceClv); %independence between SMB and calving + md.stochasticforcing.covariance = covarianceGlobal; + md.stochasticforcing.defaultdimension = md.smb.num_basins; %2 basins for stochastic default (used for calving, same as SMB) + md.stochasticforcing.default_id = idbasinsCalving; + + save ./Models/PIG_StISSM_StochCalving md; + +end + +if any(steps==7) % Transient Run #2 + + md = loadmodel('./Models/PIG_StISSM_StochCalving'); + + md.verbose.solution = 1; + md.timestepping.start_time = md.timestepping.final_time; + md.timestepping.time_step = 0.1; + md.timestepping.final_time = md.timestepping.start_time+5; + md.transient.requested_outputs = {'default','SmbMassBalance','CalvingCalvingrate'}; + + % Set up initial conditions from previous transient results + md.geometry.thickness = md.results.TransientSolution(end).Thickness; + md.initialization.vx = md.results.TransientSolution(end).Vx; + md.initialization.vy = md.results.TransientSolution(end).Vy; + md.initialization.vel = md.results.TransientSolution(end).Vel; + md.mask.ocean_levelset = md.results.TransientSolution(end).MaskOceanLevelset; + md.initialization.pressure = md.results.TransientSolution(end).Pressure; + md.geometry.base = md.results.TransientSolution(end).Base; + md.geometry.surface = md.results.TransientSolution(end).Surface; + md.mask.ice_levelset = md.results.TransientSolution(end).MaskIceLevelset; + + md = solve(md,'Transient'); + md = loadresultsfromcluster(md); + timing = cell2mat({md.results.TransientSolution(:).time}); + fullsmb = cell2mat({md.results.TransientSolution(:).SmbMassBalance}); + fullclv = cell2mat({md.results.TransientSolution(:).CalvingCalvingrate}); + + timemeansmb = mean(fullsmb,2); + timesdevsmb = std(fullsmb,0,2); + maxsmb = max(fullsmb,[],'all'); + minsmb = min(fullsmb,[],'all'); + timemeanclv = mean(fullclv,2); + timesdevclv = std(fullclv,0,2); + maxclv = max(fullclv,[],'all'); + minclv = min(fullclv,[],'all'); + + plotmodel(md,'figure',1,... + 'data',md.results.TransientSolution(1).SmbMassBalance,'title','SMB at timestep 1','caxis#1',[minsmb,maxsmb],... + 'data',md.results.TransientSolution(end).SmbMassBalance,'title','SMB at last timestep','caxis#2',[minsmb,maxsmb]) + plotmodel(md,'figure',2,... + 'data',timemeansmb,'title','SMB mean over simulation',... + 'data',timesdevsmb,'title','SMB standard deviation over simulation') + plotmodel(md,'figure',3,... + 'data',timemeanclv,'title','Calving mean over simulation',... + 'data',timesdevclv,'title','Calving standard deviation over simulation') + + seriesSMB1 = fullsmb(1,:); + seriesSMB71 = fullsmb(71,:); + figure(4); + plot(timing,seriesSMB1,'b'); + hold on + plot(timing,seriesSMB71,'r'); + title('SMB at two different vertices'); + hold off + + seriesclv1 = fullclv(1,:); + seriesclv71 = fullclv(71,:); + figure(5); + plot(timing,seriesclv1,'b'); + hold on + plot(timing,seriesclv71,'r'); + title('Calving at two different vertices'); + hold off + +end + + + + + + + + Index: /issm/trunk/externalpackages/adjoinablempi/install-pleaides-gcc.sh =================================================================== --- /issm/trunk/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 28012) +++ /issm/trunk/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 28013) @@ -10,5 +10,5 @@ #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz' #Untar ADOL-C Index: /issm/trunk/externalpackages/adjoinablempi/install-pleaides.sh =================================================================== --- /issm/trunk/externalpackages/adjoinablempi/install-pleaides.sh (revision 28012) +++ /issm/trunk/externalpackages/adjoinablempi/install-pleaides.sh (revision 28013) @@ -10,5 +10,5 @@ #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz' #Untar ADOL-C Index: /issm/trunk/externalpackages/adolc/install-withampi-pleiades-gcc.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 28012) +++ /issm/trunk/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 28013) @@ -9,5 +9,5 @@ #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C' 'ADOL-C.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz' 'ADOL-C.tar.gz' #Untar ADOL-C Index: /issm/trunk/externalpackages/adolc/install-withampi-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi-pleiades.sh (revision 28012) +++ /issm/trunk/externalpackages/adolc/install-withampi-pleiades.sh (revision 28013) @@ -9,5 +9,5 @@ #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C' 'ADOL-C.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz' 'ADOL-C.tar.gz' #Untar ADOL-C Index: /issm/trunk/externalpackages/adolc/install.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install.sh (revision 28012) +++ /issm/trunk/externalpackages/adolc/install.sh (revision 28013) @@ -9,5 +9,5 @@ #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C' 'ADOL-C.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz' 'ADOL-C.tar.gz' #Untar ADOL-C Index: /issm/trunk/externalpackages/boost/install-1.55-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-pleiades.sh (revision 28012) +++ /issm/trunk/externalpackages/boost/install-1.55-pleiades.sh (revision 28013) @@ -7,4 +7,8 @@ #symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY #to get the boost library to include python support without doing that. + +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +export CXXFLAGS="-D_INTEL_LINUX_ -std=c++11" +export CFLAGS="-D_INTEL_LINUX_" #Some cleanup @@ -23,11 +27,12 @@ patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch +# Copy customized source and configuration files to 'src' directory +cp configs/1.55/boost/multi_index/ordered_index.hpp src/boost/multi_index #Configure and compile -cd src +cd src ./bootstrap.sh \ - --prefix="$ISSM_DIR/externalpackages/boost/install" \ - --with-python=python3.2 \ - --with-python-root="$ISSM_DIR/externalpackages/python/install" + --prefix=${BOOST_ROOT}/install \ + --with-python=python2.7 #Compile boost Index: /issm/trunk/externalpackages/boost/install-1.7-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.7-linux-static.sh (revision 28012) +++ /issm/trunk/externalpackages/boost/install-1.7-linux-static.sh (revision 28013) @@ -39,3 +39,3 @@ # TODO: Reconfigure so that dynamic libraries are not compiled at all # -rm -f $(find ${BOOST_ROOT}/install/lib -name *.so*) +rm -f $(find ${PREFIX}/lib -name *.so*) Index: /issm/trunk/externalpackages/boost/install-1.7-linux-valgrind.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 28012) +++ /issm/trunk/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 28013) @@ -10,5 +10,5 @@ # Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" # Unpack source @@ -23,6 +23,6 @@ rm -rf boost_${VER} -# Copy customized source and config files to 'src' directory -cp ./configs/1.73/boost/math/tools/user.hpp ./src/boost/math/tools/ +# Copy customized source and configuration files to 'src' directory +cp ./configs/1.73/boost/math/tools/user.hpp ./src/boost/math/tools # Configure Index: /issm/trunk/externalpackages/boost/install-1.7-mac-valgrind.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.7-mac-valgrind.sh (revision 28013) +++ /issm/trunk/externalpackages/boost/install-1.7-mac-valgrind.sh (revision 28013) @@ -0,0 +1,66 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + +## Environment +# +export LDFLAGS="-Wl,-headerpad_max_install_names" + +# Download source +${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 ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source into 'src' directory +mv boost_${VER}/* src +rm -rf boost_${VER} + +# Copy customized source and configuration files to 'src' directory +cp ./configs/1.73/boost/math/tools/user.hpp ./src/boost/math/tools + +# Configure +cd src +./bootstrap.sh \ + --prefix=${PREFIX} \ + --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 ${PREFIX}/lib +for name in *.dylib; do + install_name_tool -id ${PREFIX}/lib/${name} ${name} 2>/dev/null +done + +if [ "${VER}" == "1_79_0" ]; then + ## Patch install names for certain libraries + # + # TODO: Figure out how to reconfigure source to apply these install names at compile time + # + install_name_tool -change @rpath/libboost_atomic.dylib ${PREFIX}/lib/libboost_atomic.dylib libboost_filesystem.dylib +fi Index: /issm/trunk/externalpackages/chaco/configs/mac/code/util/smalloc.c.patch =================================================================== --- /issm/trunk/externalpackages/chaco/configs/mac/code/util/smalloc.c.patch (revision 28013) +++ /issm/trunk/externalpackages/chaco/configs/mac/code/util/smalloc.c.patch (revision 28013) @@ -0,0 +1,4 @@ +6c6 +< #include +--- +> #include Index: /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/Makefile =================================================================== --- /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/Makefile (revision 28013) +++ /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/Makefile (revision 28013) @@ -0,0 +1,202 @@ +DEST_DIR = ../exec +DEST= ${DEST_DIR}/chaco +CC = gcc +IFLAG = -Imain -I/mingw64/x86_64-w64-mingw32/include +CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -Wno-implicit-function-declaration -D_MSYS2_ +OFLAGS = -O2 +#AR = /usr/ccs/bin/ar rcv # for solaris 2 +#AR = /usr/bin/ar rcv +AR = ar cr +#RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +#RANLIB = /usr/bin/ranlib +RANLIB = ranlib + +FILES.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ + input/input_assign.c \ + input/check_input.c input/input.c input/input_geom.c \ + input/input_graph.c input/read_params.c input/reflect_input.c \ + input/read_val.c \ + graph/check_graph.c graph/free_graph.c \ + graph/reformat.c graph/subgraph.c graph/graph_out.c \ + inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \ + inertial/inertial1d.c inertial/inertial2d.c \ + inertial/inertial3d.c inertial/make_subgeom.c \ + klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \ + klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \ + klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \ + klspiff/klspiff.c klspiff/make_bndy_list.c \ + klspiff/make_kl_list.c klspiff/nway_kl.c \ + klvspiff/bpm_improve.c klvspiff/bucketsv.c \ + klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \ + klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \ + klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \ + klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \ + klvspiff/flatten.c \ + coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \ + coarsen/makeccoords.c \ + coarsen/coarsen1.c coarsen/makev2cv.c \ + coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \ + coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \ + connect/add_edges.c connect/connected.c connect/find_edges.c \ + eigen/bidir.c eigen/bisect.c eigen/checkeig.c \ + eigen/checkeig_ext.c \ + eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\ + eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \ + eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \ + eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\ + eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \ + eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \ + eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \ + eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \ + eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \ + eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \ + symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \ + symmlq/symmlq.c symmlq/symmlqblas.c \ + tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \ + optimize/determinant.c optimize/func2d.c \ + optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \ + assign/assign.c assign/assign_out.c assign/mapper.c \ + assign/median.c assign/merge_assign.c \ + assign/rec_median.c assign/rotate.c assign/y2x.c \ + bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \ + bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \ + bpmatch/map3d.c bpmatch/movevtxs.c \ + bpmatch/sorts2d.c bpmatch/sorts3d.c \ + refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \ + refine_map/refine_cube.c refine_map/update_cube_edata.c \ + refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \ + refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \ + refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \ + refine_map/init_mesh_edata.c refine_map/refine_mesh.c \ + refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \ + refine_map/refine_map.c refine_map/make_comm_graph.c \ + refine_part/refine_part.c refine_part/kl_refine.c \ + refine_part/make_maps_ref.c refine_part/make_terms_ref.c \ + internal/force_internal.c internal/improve_internal.c \ + internal/check_internal.c \ + misc/define_subcubes.c misc/define_submeshes.c \ + misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \ + misc/count.c misc/countup.c misc/countup_cube.c \ + misc/countup_mesh.c misc/make_subgoal.c \ + misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \ + misc/sequence.c misc/perturb.c misc/simple_part.c \ + misc/time_kernels.c misc/timing.c \ + util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \ + util/checkpnt.c util/cpvec.c util/dot.c \ + util/doubleout.c util/input_int.c util/gray.c \ + util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \ + util/normalize.c util/mergesort.c \ + util/randomize.c util/smalloc.c util/bail.c \ + util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \ + util/strout.c util/tri_prod.c util/true_or_false.c \ + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + + +FILESMINUSBLAS.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ + input/input_assign.c \ + input/check_input.c input/input.c input/input_geom.c \ + input/input_graph.c input/read_params.c input/reflect_input.c \ + input/read_val.c \ + graph/check_graph.c graph/free_graph.c \ + graph/reformat.c graph/subgraph.c graph/graph_out.c \ + inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \ + inertial/inertial1d.c inertial/inertial2d.c \ + inertial/inertial3d.c inertial/make_subgeom.c \ + klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \ + klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \ + klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \ + klspiff/klspiff.c klspiff/make_bndy_list.c \ + klspiff/make_kl_list.c klspiff/nway_kl.c \ + klvspiff/bpm_improve.c klvspiff/bucketsv.c \ + klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \ + klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \ + klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \ + klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \ + klvspiff/flatten.c \ + coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \ + coarsen/makeccoords.c \ + coarsen/coarsen1.c coarsen/makev2cv.c \ + coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \ + coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \ + connect/add_edges.c connect/connected.c connect/find_edges.c \ + eigen/bidir.c eigen/bisect.c eigen/checkeig.c \ + eigen/checkeig_ext.c \ + eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\ + eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \ + eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \ + eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\ + eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \ + eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \ + eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \ + eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \ + eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \ + eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \ + symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \ + symmlq/symmlq.c \ + tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \ + optimize/determinant.c optimize/func2d.c \ + optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \ + assign/assign.c assign/assign_out.c assign/mapper.c \ + assign/median.c assign/merge_assign.c \ + assign/rec_median.c assign/rotate.c assign/y2x.c \ + bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \ + bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \ + bpmatch/map3d.c bpmatch/movevtxs.c \ + bpmatch/sorts2d.c bpmatch/sorts3d.c \ + refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \ + refine_map/refine_cube.c refine_map/update_cube_edata.c \ + refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \ + refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \ + refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \ + refine_map/init_mesh_edata.c refine_map/refine_mesh.c \ + refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \ + refine_map/refine_map.c refine_map/make_comm_graph.c \ + refine_part/refine_part.c refine_part/kl_refine.c \ + refine_part/make_maps_ref.c refine_part/make_terms_ref.c \ + internal/force_internal.c internal/improve_internal.c \ + internal/check_internal.c \ + misc/define_subcubes.c misc/define_submeshes.c \ + misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \ + misc/count.c misc/countup.c misc/countup_cube.c \ + misc/countup_mesh.c misc/make_subgoal.c \ + misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \ + misc/sequence.c misc/perturb.c misc/simple_part.c \ + misc/time_kernels.c misc/timing.c \ + util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \ + util/checkpnt.c util/cpvec.c util/dot.c \ + util/doubleout.c util/input_int.c util/gray.c \ + util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \ + util/normalize.c util/mergesort.c \ + util/randomize.c util/smalloc.c util/bail.c \ + util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \ + util/strout.c util/tri_prod.c util/true_or_false.c \ + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + +FILES.o= $(FILES.c:.c=.o) +FILESMINUSBLAS.o= $(FILESMINUSBLAS.c:.c=.o) + + +${DEST}: ${FILES.c} chaco.a Makefile + ${CC} ${OFLAGS} chaco.a -lm -o ${DEST} + +chaco.a: ${FILES.o} + ${AR} $@ ${FILES.o} ; ${RANLIB} $@ + +chacominusblas.a: ${FILESMINUSBLAS.o} + ${AR} $@ ${FILESMINUSBLAS.o} ; ${RANLIB} $@ + +lint: + lint ${IFLAG} ${FILES.c} -lm + +alint: + alint ${IFLAG} ${FILES.c} -lm + +clean: + rm -f */*.o ${DEST_DIR}/core + +.c.o: + ${CC} -c ${IFLAG} ${CFLAGS} -o $*.o $*.c Index: /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/main/interface.c =================================================================== --- /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/main/interface.c (revision 28013) +++ /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/main/interface.c (revision 28013) @@ -0,0 +1,234 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#include +#include "defs.h" +#include "structs.h" + +int Using_Main = FALSE; /* Is main routine being called? */ + +int interface(nvtxs, start, adjacency, vwgts, ewgts, x, y, z, + outassignname, outfilename, + assignment, + architecture, ndims_tot, mesh_dims, goal, + global_method, local_method, rqi_flag, vmax, ndims, + eigtol, seed) +int nvtxs; /* number of vertices in full graph */ +int *start; /* start of edge list for each vertex */ +int *adjacency; /* edge list data */ +int *vwgts; /* weights for all vertices */ +float *ewgts; /* weights for all edges */ +float *x, *y, *z; /* coordinates for inertial method */ +char *outassignname; /* name of assignment output file */ +char *outfilename; /* output file name */ +short *assignment; /* set number of each vtx (length n) */ +int architecture; /* 0 => hypercube, d => d-dimensional mesh */ +int ndims_tot; /* total number of cube dimensions to divide */ +int mesh_dims[3]; /* dimensions of mesh of processors */ +double *goal; /* desired set sizes for each set */ +int global_method; /* global partitioning algorithm */ +int local_method; /* local partitioning algorithm */ +int rqi_flag; /* should I use RQI/Symmlq eigensolver? */ +int vmax; /* how many vertices to coarsen down to? */ +int ndims; /* number of eigenvectors (2^d sets) */ +double eigtol; /* tolerance on eigenvectors */ +long seed; /* for random graph mutations */ +{ + extern char *PARAMS_FILENAME; /* name of file with parameter updates */ + extern int MAKE_VWGTS; /* make vertex weights equal to degrees? */ + extern int MATCH_TYPE; /* matching routine to use */ + extern int FREE_GRAPH; /* free graph data structure after reformat? */ + extern int DEBUG_PARAMS; /* debug flag for reading parameters */ + extern int DEBUG_TRACE; /* trace main execution path */ + extern double start_time; /* time routine is entered */ + extern double reformat_time;/* time spent reformatting graph */ + FILE *params_file; /* file for reading new parameters */ + struct vtx_data **graph; /* graph data structure */ + double vwgt_sum; /* sum of vertex weights */ + double time; /* timing variable */ + float **coords; /* coordinates for vertices if used */ + int *vptr; /* loops through vertex weights */ + int flag; /* return code from balance */ + int nedges; /* number of edges in graph */ + int using_vwgts; /* are vertex weights being used? */ + int using_ewgts; /* are edge weights being used? */ + int nsets_tot; /* total number of sets being created */ + int igeom; /* geometric dimension for inertial method */ + int default_goal; /* using default goals? */ + int i; /* loop counter */ + double seconds(); + double *smalloc_ret(); + int sfree(), submain(), reformat(); + void free_graph(), read_params(), strout(); + + if (DEBUG_TRACE > 0) { + printf("\n"); + } + + flag = 0; + graph = NULL; + coords = NULL; + + if (!Using_Main) { /* If not using main, need to read parameters file. */ + start_time = seconds(); + params_file = fopen(PARAMS_FILENAME, "r"); + if (params_file == NULL && DEBUG_PARAMS > 1) { + printf("Parameter file `%s' not found; using default parameters.\n", + PARAMS_FILENAME); + } + read_params(params_file); + } + + if (goal == NULL) { /* If not passed in, default goals have equal set sizes. */ + default_goal = TRUE; + if (architecture == 0) + nsets_tot = 1 << ndims_tot; + else if (architecture == 1) + nsets_tot = mesh_dims[0]; + else if (architecture == 2) + nsets_tot = mesh_dims[0] * mesh_dims[1]; + else if (architecture > 2) + nsets_tot = mesh_dims[0] * mesh_dims[1] * mesh_dims[2]; + + if (MAKE_VWGTS && start != NULL) { + vwgt_sum = start[nvtxs] - start[0] + nvtxs; + } + else if (vwgts == NULL) { + vwgt_sum = nvtxs; + } + else { + vwgt_sum = 0; + vptr = vwgts; + for (i = nvtxs; i; i--) + vwgt_sum += *(vptr++); + } + + vwgt_sum /= nsets_tot; + goal = (double *) smalloc_ret((unsigned) nsets_tot * sizeof(double)); + if (goal == NULL) { + strout("\nERROR: No room to make goals.\n"); + flag = 1; + goto skip; + } + for (i = 0; i < nsets_tot; i++) + goal[i] = vwgt_sum; + } + else { + default_goal = FALSE; + } + + if (MAKE_VWGTS) { + /* Generate vertex weights equal to degree of node. */ + if (vwgts != NULL) { + strout("WARNING: Vertex weights being overwritten by vertex degrees."); + } + vwgts = (int *) smalloc_ret((unsigned) nvtxs * sizeof(int)); + if (vwgts == NULL) { + strout("\nERROR: No room to make vertex weights.\n"); + flag = 1; + goto skip; + } + if (start != NULL) { + for (i = 0; i < nvtxs; i++) + vwgts[i] = 1 + start[i + 1] - start[i]; + } + else { + for (i = 0; i < nvtxs; i++) + vwgts[i] = 1; + } + } + + using_vwgts = (vwgts != NULL); + using_ewgts = (ewgts != NULL); + + if (start != NULL || vwgts != NULL) { /* Reformat into our data structure. */ + time = seconds(); + flag = reformat(start, adjacency, nvtxs, &nedges, vwgts, ewgts, &graph); + + if (flag) { + strout("\nERROR: No room to reformat graph.\n"); + goto skip; + } + + reformat_time += seconds() - time; + } + else { + nedges = 0; + } + + if (FREE_GRAPH) { /* Free old graph data structures. */ + sfree((char *) start); + sfree((char *) adjacency); + if (vwgts != NULL) + sfree((char *) vwgts); + if (ewgts != NULL) + sfree((char *) ewgts); + start = NULL; + adjacency = NULL; + vwgts = NULL; + ewgts = NULL; + } + + + if (global_method == 3 || + (MATCH_TYPE == 5 && (global_method == 1 || + (global_method == 2 && rqi_flag)))) { + if (x == NULL) { + igeom = 0; + } + else { /* Set up coordinate data structure. */ + coords = (float **) smalloc_ret((unsigned) 3 * sizeof(float *)); + if (coords == NULL) { + strout("\nERROR: No room to make coordinate array.\n"); + flag = 1; + goto skip; + } + /* Minus 1's are to allow remainder of program to index with 1. */ + coords[0] = x - 1; + igeom = 1; + if (y != NULL) { + coords[1] = y - 1; + igeom = 2; + if (z != NULL) { + coords[2] = z - 1; + igeom = 3; + } + } + } + } + else { + igeom = 0; + } + + /* Subtract from assignment to allow code to index from 1. */ + assignment = assignment - 1; + flag = submain(graph, nvtxs, nedges, using_vwgts, using_ewgts, igeom, coords, + outassignname, outfilename, + assignment, goal, + architecture, ndims_tot, mesh_dims, + global_method, local_method, rqi_flag, vmax, ndims, + eigtol, seed); + +skip: + if (coords != NULL) + sfree((char *) coords); + + if (default_goal) + sfree((char *) goal); + + if (graph != NULL) + free_graph(graph); + + if (flag && FREE_GRAPH) { + sfree((char *) start); + sfree((char *) adjacency); + sfree((char *) vwgts); + sfree((char *) ewgts); + } + + if (!Using_Main && params_file != NULL) + fclose(params_file); + + return (flag); +} Index: /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/util/bail.c =================================================================== --- /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/util/bail.c (revision 28013) +++ /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/util/bail.c (revision 28013) @@ -0,0 +1,27 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#include +#include +#include +#include "defs.h" + +/* Wrapper for exit() - print message and exit with status code. Exit code + of 0 indicates normal termination. Exit code of 1 indicates early + termination following detection of some problem. Call with bail(NULL,status) + to suppress message. */ +void bail(msg, status) +char *msg; +int status; +{ + extern FILE *Output_File; /* Output file or NULL */ + + if (msg != NULL && (int) strlen(msg) > 0) { + printf("%s\n", msg); + if (Output_File != NULL) { + fprintf(Output_File, "%s\n", msg); + } + } + exit(status); +} Index: /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/util/seconds.c =================================================================== --- /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/util/seconds.c (revision 28013) +++ /issm/trunk/externalpackages/chaco/configs/win/msys2/mingw64/code/util/seconds.c (revision 28013) @@ -0,0 +1,35 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#if defined(_INTEL_WIN_) || defined(_MSYS2_) +#include +#else +#include +#include +#endif + +double seconds() +{ + double curtime; + +#ifdef RUSAGE_SELF + +/* This timer is faster and more robust (if it exists). */ + struct rusage rusage; + int getrusage(); + + getrusage(RUSAGE_SELF, &rusage); + curtime = ((rusage.ru_utime.tv_sec + rusage.ru_stime.tv_sec) + + 1.0e-6 * (rusage.ru_utime.tv_usec + rusage.ru_stime.tv_usec)); + +#else + +/* ANSI timer, but lower resolution & wraps around after ~36 minutes. */ + + curtime = clock()/((double) CLOCKS_PER_SEC); + +#endif + + return (curtime); +} Index: /issm/trunk/externalpackages/chaco/install-linux.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install-linux.sh (revision 28013) +++ /issm/trunk/externalpackages/chaco/install-linux.sh (revision 28013) @@ -0,0 +1,60 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER=2.2 + +PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed + +## Environment +# +export CFLAGS="-Wno-error=implicit-function-declaration" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf" + +# Unpack source +tar -xvzf Chaco-${VER}.tar.gz + +# Move source to 'src' directory +mv Chaco-${VER}/* src +rm -rf Chaco-${VER} + +# Apply patches +patch -R -p0 < chaco.patch # Written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch +patch src/code/Makefile < patches/Makefile.patch + +# Compile +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Install +cp -p src/exec/README ${PREFIX} +cp -p src/exec/User_Params ${PREFIX} +cp -p src/exec/*.coords ${PREFIX} +cp -p src/exec/*.graph ${PREFIX} +mkdir ${PREFIX}/include +cp -p src/code/main/defs.h ${PREFIX}/include/defs.h +cp -p src/code/main/params.h ${PREFIX}/include/params.h +cp -p chaco.h ${PREFIX}/include/chaco.h +mkdir ${PREFIX}/lib +mv src/code/chaco.a ${PREFIX}/lib/libchaco.a +mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a +mkdir ${PREFIX}/exec +mv src/exec/chaco ${PREFIX}/exec Index: sm/trunk/externalpackages/chaco/install-mac-sierra.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install-mac-sierra.sh (revision 28012) +++ (revision ) @@ -1,55 +1,0 @@ -#!/bin/bash -set -eu - -# Some cleanup -rm -rf Chaco-2.2 -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz' -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf' - -# Untar -tar -xvzf Chaco-2.2.tar.gz - -# Move chaco to src directory -mv Chaco-2.2/* src -rm -rf Chaco-2.2 - -# Apply patches (all at once) -# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch) -patch -R -p0 < chaco.patch - -# Patch src/code/Makefile -patch ./src/code/Makefile ./patches/Makefile.mac-sierra.patch - - -# Build chaco -cd src/code -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make chacominusblas.a - -# Clean up objects (but not library or executable) -make clean -cd ../.. - -# Populate install directory -cp -p src/exec/README install -cp -p src/exec/User_Params install -cp -p src/exec/*.coords install -cp -p src/exec/*.graph install -mkdir install/include -cp -p src/code/main/defs.h install/include/defs.h -cp -p src/code/main/params.h install/include/params.h -cp -p chaco.h install/include/chaco.h -mkdir install/lib -mv src/code/chaco.a install/lib/libchaco.a -mv src/code/chacominusblas.a install/lib/libchacominusblas.a -mkdir install/exec -mv src/exec/chaco install/exec Index: /issm/trunk/externalpackages/chaco/install-mac.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install-mac.sh (revision 28013) +++ /issm/trunk/externalpackages/chaco/install-mac.sh (revision 28013) @@ -0,0 +1,61 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER=2.2 + +PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed + +## Environment +# +export CFLAGS="-Wno-error=implicit-function-declaration" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf" + +# Unpack source +tar -xvzf Chaco-${VER}.tar.gz + +# Move source to 'src' directory +mv Chaco-${VER}/* src +rm -rf Chaco-${VER} + +# Apply patches +patch -R -p0 < chaco.patch # Written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch +patch src/code/Makefile < patches/Makefile.patch +patch src/code/util/smalloc.c < configs/mac/code/util/smalloc.c.patch + +# Compile +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Install +cp -p src/exec/README ${PREFIX} +cp -p src/exec/User_Params ${PREFIX} +cp -p src/exec/*.coords ${PREFIX} +cp -p src/exec/*.graph ${PREFIX} +mkdir ${PREFIX}/include +cp -p src/code/main/defs.h ${PREFIX}/include/defs.h +cp -p src/code/main/params.h ${PREFIX}/include/params.h +cp -p chaco.h ${PREFIX}/include/chaco.h +mkdir ${PREFIX}/lib +mv src/code/chaco.a ${PREFIX}/lib/libchaco.a +mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a +mkdir ${PREFIX}/exec +mv src/exec/chaco ${PREFIX}/exec Index: /issm/trunk/externalpackages/chaco/install-win-msys2-mingw.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install-win-msys2-mingw.sh (revision 28012) +++ /issm/trunk/externalpackages/chaco/install-win-msys2-mingw.sh (revision 28013) @@ -24,13 +24,12 @@ rm -rf Chaco-${VER} -# Apply patches (all at once) -# (written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch) -patch -R -p0 < chaco.patch +# Apply patches +patch -R -p0 < chaco.patch # Written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch # Copy customized source and configuration files to 'src' directory -cp configs/win/msys2/mingw64/src/code/Makefile src/code -cp configs/win/msys2/mingw64/src/code/main/interface.c src/code/main -cp configs/win/msys2/mingw64/src/code/util/bail.c src/code/util -cp configs/win/msys2/mingw64/src/code/util/seconds.c src/code/util +cp configs/win/msys2/mingw64/code/Makefile src/code +cp configs/win/msys2/mingw64/code/main/interface.c src/code/main +cp configs/win/msys2/mingw64/code/util/bail.c src/code/util +cp configs/win/msys2/mingw64/code/util/seconds.c src/code/util # Compile Index: sm/trunk/externalpackages/chaco/install.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install.sh (revision 28012) +++ (revision ) @@ -1,61 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER=2.2 - -PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed - -## Environment -# -export CFLAGS="-Wno-error=implicit-function-declaration" - -# Cleanup -rm -rf ${PREFIX} src -mkdir -p ${PREFIX} src - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz" -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf" - -# Unpack source -tar -xvzf Chaco-${VER}.tar.gz - -# Move source to 'src' directory -mv Chaco-${VER}/* src -rm -rf Chaco-${VER} - -# Apply patches (all at once) -# (written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch) -patch -R -p0 < chaco.patch -patch src/code/Makefile patches/Makefile.patch - -# Compile -cd src/code -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make chacominusblas.a - -# Clean up objects (but not library or executable) -make clean -cd ../.. - -# Install -cp -p src/exec/README ${PREFIX} -cp -p src/exec/User_Params ${PREFIX} -cp -p src/exec/*.coords ${PREFIX} -cp -p src/exec/*.graph ${PREFIX} -mkdir ${PREFIX}/include -cp -p src/code/main/defs.h ${PREFIX}/include/defs.h -cp -p src/code/main/params.h ${PREFIX}/include/params.h -cp -p chaco.h ${PREFIX}/include/chaco.h -mkdir ${PREFIX}/lib -mv src/code/chaco.a ${PREFIX}/lib/libchaco.a -mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a -mkdir ${PREFIX}/exec -mv src/exec/chaco ${PREFIX}/exec Index: /issm/trunk/externalpackages/codipack/install.sh =================================================================== --- /issm/trunk/externalpackages/codipack/install.sh (revision 28012) +++ /issm/trunk/externalpackages/codipack/install.sh (revision 28013) @@ -8,5 +8,5 @@ #Download development version -svn co https://github.com/SciCompKL/CoDiPack.git/trunk install +git clone https://github.com/SciCompKL/CoDiPack.git install ## Download source Index: /issm/trunk/externalpackages/dakota/install-6.2-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-linux-static.sh (revision 28012) +++ /issm/trunk/externalpackages/dakota/install-6.2-linux-static.sh (revision 28013) @@ -13,8 +13,11 @@ # TODO: # - Move this to etc/environment.sh +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. # -LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} -LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1 +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1) ## Environment Index: /issm/trunk/externalpackages/dakota/install-6.2-linux.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-linux.sh (revision 28012) +++ /issm/trunk/externalpackages/dakota/install-6.2-linux.sh (revision 28013) @@ -9,11 +9,20 @@ PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed +# Find libgfortran so that we do not have to hardcode it. +# +# TODO: +# - Move this to etc/environment.sh +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} + ## Environment # -export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS -export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it # Cleanup Index: /issm/trunk/externalpackages/dakota/install-6.2-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-mac-static.sh (revision 28012) +++ /issm/trunk/externalpackages/dakota/install-6.2-mac-static.sh (revision 28013) @@ -9,17 +9,15 @@ PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed -# 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. +# Find libgfortran and libgcc so we do not have to hardcode them # # TODO: # - Move this to etc/environment.sh -# - Test if -static-libgfortran flag will avoid all of this -# - Otherwise, refactor this to work with other gfortran installations +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. # -LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} -LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) ## Environment @@ -30,4 +28,5 @@ export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS export LAPACK_LIBS="-L${LAPACK_ROOT}/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 +export LDFLAGS="-framework CoreFoundation" # Cleanup @@ -75,4 +74,10 @@ # Configure +# +# NOTE: +# - The -w option has been added to CMAKE_C_FLAGS, CMAKE_CXX_FLAGS, and +# CMAKE_Fortran_FLAGS. This should be removed for more recent versions of +# Dakota. +# cd ${DAK_BUILD} cmake \ @@ -80,10 +85,10 @@ -DBUILD_STATIC_LIBS=ON \ -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \ - -DCMAKE_C_FLAGS="-fPIC -Wno-error=implicit-function-declaration" \ + -DCMAKE_C_FLAGS="-fPIC -Wno-error=implicit-function-declaration -w" \ -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \ - -DCMAKE_CXX_FLAGS="-fPIC -fdelayed-template-parsing" \ + -DCMAKE_CXX_FLAGS="-fPIC -fdelayed-template-parsing -w" \ -DCMAKE_CXX_STANDARD="11" \ -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \ - -DCMAKE_Fortran_FLAGS="-fPIC -fallow-argument-mismatch" \ + -DCMAKE_Fortran_FLAGS="-fPIC -fallow-argument-mismatch -w" \ -DBoost_NO_BOOST_CMAKE=TRUE \ -DHAVE_ACRO=OFF \ Index: /issm/trunk/externalpackages/dakota/install-6.2-mac.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-mac.sh (revision 28012) +++ /issm/trunk/externalpackages/dakota/install-6.2-mac.sh (revision 28013) @@ -11,11 +11,9 @@ # 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. -# # TODO: # - Move this to etc/environment.sh # -LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} @@ -27,4 +25,5 @@ export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export LDFLAGS="-framework CoreFoundation" # Cleanup @@ -59,5 +58,15 @@ sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake +echo "Debug:" +echo "GSL_HOME : ${GSL_HOME}" +echo "CPATH : ${CPATH}" + # Configure +# +# NOTE: +# - The -w option has been added to CMAKE_C_FLAGS, CMAKE_CXX_FLAGS, and +# CMAKE_Fortran_FLAGS. This should be removed for more recent versions of +# Dakota. +# cd ${DAK_BUILD} cmake \ @@ -65,6 +74,7 @@ -DBUILD_STATIC_LIBS=OFF \ -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \ + -DCMAKE_C_FLAGS="-w" \ -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \ - -DCMAKE_CXX_FLAGS="-fdelayed-template-parsing" \ + -DCMAKE_CXX_FLAGS="-fdelayed-template-parsing -w" \ -DCMAKE_CXX_STANDARD="11" \ -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \ @@ -101,5 +111,6 @@ ## Patch install names for certain libraries # -# TODO: Figure out how to reconfigure source to apply these install names at compile time +# TODO: Figure out how to reconfigure source to apply these install names at +# compile time # install_name_tool -change libdakota_src_fortran.dylib ${DAK_INSTALL}/lib/libdakota_src_fortran.dylib libdakota_src.dylib @@ -120,2 +131,11 @@ install_name_tool -change libteuchos.dylib ${DAK_INSTALL}/lib/libteuchos.dylib libpecos_src.dylib install_name_tool -change libsurfpack_fortran.dylib ${DAK_INSTALL}/lib/libsurfpack_fortran.dylib libsurfpack.dylib + +## Add LIBGFORTRAN_ROOT to rpath for libraries that need it +# +# TODO: Figure out how to reconfigure source to add to rpath at compile time +# +install_name_tool -add_rpath ${LIBGFORTRAN_ROOT} libpecos.dylib +install_name_tool -add_rpath ${LIBGFORTRAN_ROOT} libteuchos.dylib +install_name_tool -add_rpath ${LIBGFORTRAN_ROOT} liboptpp.dylib + Index: sm/trunk/externalpackages/dakota/install-6.2-macosx64-catalina.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-catalina.sh (revision 28012) +++ (revision ) @@ -1,76 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf build -rm -rf install -mkdir src build install - -#Download from ISSM server -#$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 - -#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 $1 install -fi -cd .. Index: sm/trunk/externalpackages/dakota/install-6.2-macosx64-highsierra.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-highsierra.sh (revision 28012) +++ (revision ) @@ -1,70 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf build -rm -rf install -mkdir src build install - -#Download from ISSM server -$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.mac.patch -patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch -patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.patch - -#Apply patches -patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch -patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch -patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch -patch src/packages/VPISparseGrid/src/sandia_rules.cpp configs/6.2/sandia_rules.cpp.patch - -export BOOST_ROOT=$ISSM_DIR/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=${BOOST_ROOT}/lib \ - -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ - -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ - -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ - -D CMAKE_CXX_FLAGS=-fdelayed-template-parsing \ - -DHAVE_ACRO=off \ - -DHAVE_JEGA=off \ - -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 $1 install -fi -cd .. Index: sm/trunk/externalpackages/dakota/install-6.2-macosx64-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-snowleopard.sh (revision 28012) +++ (revision ) @@ -1,69 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf build -rm -rf install -mkdir src build install - -#Download from ISSM server -$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.mac.patch -patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch -patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.patch - -#Apply patches -patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch -patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch -patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch - -export BOOST_ROOT=$ISSM_DIR/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=${BOOST_ROOT}/lib \ - -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ - -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ - -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ - -DHAVE_ACRO=off \ - -DHAVE_JEGA=off \ - -D LDFLAGS="-L/usr/lib/ -lstdc++ -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/ -lgfortran" \ - -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 $1 install -fi -cd .. Index: sm/trunk/externalpackages/dakota/install-6.2-macosx64-yosemite.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-yosemite.sh (revision 28012) +++ (revision ) @@ -1,63 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf build -rm -rf install -mkdir src build install - -#Download from ISSM server -$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.yosemite.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 - -#Configure dakota -cd $DAK_BUILD - -cmake -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ - -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ - -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ - -DHAVE_ACRO=off \ - -DHAVE_JEGA=off \ - -DBLAS_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a \ - -DLAPACK_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a \ - -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ - -C $DAK_SRC/cmake/DakotaDev.cmake \ - $DAK_SRC -cd .. - -#Make sure to include --download-fblaslapack=1 \ in petsc configure script to use the petsc blas and dlapack libs -#-DBLAS_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a -DLAPACK_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a - -#Compile and install dakota -cd $DAK_BUILD -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-pleiades_toss4.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-pleiades_toss4.sh (revision 28013) +++ /issm/trunk/externalpackages/dakota/install-6.2-pleiades_toss4.sh (revision 28013) @@ -0,0 +1,78 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed + +## Environment +# +export BLAS_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64 +export CXXFLAGS='-std=c++98' +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64 + +# Cleanup +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" + +# Unpack source +tar -zxvf dakota-${VER}-public-src.tar.gz + +# Move source to 'src' directory +mv dakota-${VER}.0.src/* ${DAK_SRC} +rm -rf dakota-${VER}.0.src + +# Copy customized source and configuration files to 'src' directory +cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer +cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src +cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm +cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src +cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src + +# Copy customized source and configuration files specific to Linux to 'src' directory +cp configs/${VER}/linux/cmake/BuildDakotaCustom.pleiades.cmake ${DAK_SRC}/cmake/BuildDakotaCustom.cmake +cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake + +# Configure +cd ${DAK_BUILD} +cmake \ + -DBUILD_SHARED_LIBS=ON \ + -DBUILD_STATIC_LIBS=OFF \ + -DCMAKE_C_COMPILER=mpicc \ + -DCMAKE_C_FLAGS="-Wno-error=implicit-function-declaration" \ + -DCMAKE_CXX_COMPILER=mpicxx \ + -DCMAKE_Fortran_COMPILER=gfortran \ + -DBoost_NO_BOOST_CMAKE=TRUE \ + -DHAVE_ACRO=OFF \ + -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ + -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ + -C${DAK_SRC}/cmake/DakotaDev.cmake \ + ${DAK_SRC} + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +cd ${DAK_INSTALL} + +# Comment out definition of HAVE_MPI in Teuchos config header file in order to +# avoid conflict with our definition +sed -i -e "s/#define HAVE_MPI/\/* #define HAVE_MPI *\//g" include/Teuchos_config.h Index: sm/trunk/externalpackages/gdal/install-1.10-debian-netcdf.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.10-debian-netcdf.sh (revision 28012) +++ (revision ) @@ -1,49 +1,0 @@ -#!/bin/bash -set -eu - - -# Constants -# -VER="1.10.0" -HDF5_ROOT="${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 -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gdal-${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} - -# Copy customized source files to 'src' directory -cp configs/1.10/linux/debian/frmts/wms/dataset.cpp src/frmts/wms -cp configs/1.10/linux/debian/ogr/ogrsf_frmts/vfk/vfkfeature.cpp src/ogr/ogrsf_frmts/vfk -cp configs/1.10/linux/debian/port/cplkeywordparser.cpp src/port - -# 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 $1 install -fi - -# Return to initial directory -cd .. Index: sm/trunk/externalpackages/gdal/install-1.10-linux64-nopython.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.10-linux64-nopython.sh (revision 28012) +++ (revision ) @@ -1,45 +1,0 @@ -#!/bin/bash -set -eu - -#WARNING: you need to have python installed in externalpackages - -#Some cleanup -rm -rf src -rm -rf install -rm -rf gdal-1.10.0 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gdal-1.10.0.tar.gz' 'gdal-1.10.0.tar.gz' - -#Untar -tar -zxvf gdal-1.10.0.tar.gz - -#Move gdal into src directory -mv gdal-1.10.0/* src -rm -rf gdal-1.10.0 - -export CFLAGS=-D_HAVE_STRNDUP -export CXXFLAGS=-D_HAVE_STRNDUP - -#Configure gdal -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/gdal/install" \ - --with-python=no \ - --with-netcdf=no \ - --with-jasper=no \ - --without-hdf5 - -#Compile and install gdal -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install - -#For some reasons, on thwaites, one needs to do the following to get the python bindings: -#cd src/swig/python/ -# python setup.py build -# python setup.py install Index: sm/trunk/externalpackages/gdal/install-1.10-linux64.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.10-linux64.sh (revision 28012) +++ (revision ) @@ -1,45 +1,0 @@ -#!/bin/bash -set -eu - -#WARNING: you need to have python installed in externalpackages - -#Some cleanup -rm -rf src -rm -rf install -rm -rf gdal-1.10.0 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gdal-1.10.0.tar.gz' 'gdal-1.10.0.tar.gz' - -#Untar -tar -zxvf gdal-1.10.0.tar.gz - -#Move gdal into src directory -mv gdal-1.10.0/* src -rm -rf gdal-1.10.0 - -export CFLAGS=-D_HAVE_STRNDUP -export CXXFLAGS=-D_HAVE_STRNDUP - -#Configure gdal -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/gdal/install" \ - --with-python=yes \ - --with-netcdf=no \ - --with-jasper=no \ - --without-hdf5 - -#Compile and install gdal -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install - -#For some reasons, on thwaites, one needs to do the following to get the python bindings: -#cd src/swig/python/ -# python setup.py build -# python setup.py install Index: sm/trunk/externalpackages/gdal/install-1.10-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.10-macosx64.sh (revision 28012) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - -GDAL_VER="1.10.0" - -# Some cleanup -rm -rf src -rm -rf install -rm -rf gdal-${GDAL_VER} -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gdal-${GDAL_VER}.tar.gz" "gdal-${GDAL_VER}.tar.gz" - -# Untar -tar -zxvf gdal-${GDAL_VER}.tar.gz - -# Move gdal into src directory -mv gdal-${GDAL_VER}/* src -rm -rf gdal-${GDAL_VER} - -# Configure gdal -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/gdal/install" \ - --with-python \ - --with-netcdf=no \ - --with-libiconv-prefix="/usr/lib/" \ - --without-hdf5 \ - --with-expat=$ISSM_DIR/externalpackages/expat/install -#Note: -# look for libiconv in /usr/lib/ because there seemed to be a conflict with port's library - -#Compile and install gdal -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk/externalpackages/gdal/install-1.11.2-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.11.2-macosx64.sh (revision 28012) +++ (revision ) @@ -1,38 +1,0 @@ -#!/bin/bash -set -eu - -GDAL_VER="1.11.2" - -# Some cleanup -rm -rf src -rm -rf install -rm -rf gdal-${GDAL_VER} -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gdal-${GDAL_VER}.tar.gz" "gdal-${GDAL_VER}.tar.gz" - -# Untar -tar -zxvf gdal-${GDAL_VER}.tar.gz - -# Move gdal into src directory -mv gdal-${GDAL_VER}/* src -rm -rf gdal-${GDAL_VER} - -# Configure gdal -# NOTE: Look for libiconv in /usr/lib/ because there seemed to be a conflict with port's library -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/gdal/install" \ - --with-python \ - --with-netcdf=no \ - --with-libiconv-prefix="/usr/lib/" \ - --without-hdf5 - -#Compile and install gdal -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk/externalpackages/gdal/install-3-python-static.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3-python-static.sh (revision 28012) +++ /issm/trunk/externalpackages/gdal/install-3-python-static.sh (revision 28013) @@ -9,12 +9,12 @@ ## Constants # -VER="3.5.1" +VER="3.5.3" ## Environment # export CC=mpicc +export CXXFLAGS="-std=c++11" export CXX=mpicxx -export LDFLAGS="-L${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 LIBS="-lsqlite3 -lhdf5_hl -lhdf5" export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) @@ -42,5 +42,5 @@ --enable-static \ --with-pic \ - --with-python=python3 \ + --with-python="python3" \ --with-curl="${CURL_ROOT}/bin/curl-config" \ --with-hdf5="${HDF5_ROOT}" \ Index: /issm/trunk/externalpackages/gdal/install-3-python.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3-python.sh (revision 28012) +++ /issm/trunk/externalpackages/gdal/install-3-python.sh (revision 28013) @@ -9,5 +9,5 @@ ## Constants # -VER="3.5.1" +VER="3.5.3" ## Environment @@ -34,5 +34,6 @@ --prefix="${PREFIX}" \ --enable-fast-install \ - --with-python=python3 \ + --with-python="python3" \ + --with-curl="${CURL_ROOT}/bin/curl-config" \ --with-hdf5="${HDF5_ROOT}" \ --with-libz="${ZLIB_ROOT}" \ Index: /issm/trunk/externalpackages/gdal/install-3-static.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3-static.sh (revision 28012) +++ /issm/trunk/externalpackages/gdal/install-3-static.sh (revision 28013) @@ -9,12 +9,12 @@ ## Constants # -VER="3.5.1" +VER="3.5.3" ## Environment # export CC=mpicc +export CXXFLAGS="-std=c++11" export CXX=mpicxx -export LDFLAGS="-L${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 LIBS="-lsqlite3 -lhdf5_hl -lhdf5" export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # NOTE: Need to export this to properly set destination root for Python libraries on macOS (should not affect Linux build). Set to location where external package should be installed. Index: /issm/trunk/externalpackages/gdal/install-3.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-3.sh (revision 28012) +++ /issm/trunk/externalpackages/gdal/install-3.sh (revision 28013) @@ -5,5 +5,5 @@ ## Constants # -VER="3.5.1" +VER="3.5.3" ## Environment @@ -30,5 +30,4 @@ --prefix="${PREFIX}" \ --enable-fast-install \ - --with-hdf5="${HDF5_ROOT}" \ --with-libz="${ZLIB_ROOT}" \ --with-netcdf="${NETCDF_ROOT}" \ Index: /issm/trunk/externalpackages/gmsh/configs/4.10.5/mac/CMakeLists.txt.patch =================================================================== --- /issm/trunk/externalpackages/gmsh/configs/4.10.5/mac/CMakeLists.txt.patch (revision 28013) +++ /issm/trunk/externalpackages/gmsh/configs/4.10.5/mac/CMakeLists.txt.patch (revision 28013) @@ -0,0 +1,4 @@ +284c284 +< set(CMAKE_INSTALL_RPATH "@executable_path/../lib") +--- +> set(CMAKE_INSTALL_RPATH "@executable_path/../lib;${LIBGFORTRAN_ROOT}") Index: /issm/trunk/externalpackages/gmsh/configs/4.10.5/static/CMakeLists.txt.patch =================================================================== --- /issm/trunk/externalpackages/gmsh/configs/4.10.5/static/CMakeLists.txt.patch (revision 28013) +++ /issm/trunk/externalpackages/gmsh/configs/4.10.5/static/CMakeLists.txt.patch (revision 28013) @@ -0,0 +1,9 @@ +858,861c860,862 +< 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") +--- +> if(METIS_ROOT) +> find_library(METIS_LIB metis PATHS ${METIS_ROOT} PATH_SUFFIXES lib) +> find_path(METIS_INC "metis.h" PATHS ${METIS_ROOT} PATH_SUFFIXES include) Index: /issm/trunk/externalpackages/gmsh/configs/4.10.5/static/mac/CMakeLists.txt.patch =================================================================== --- /issm/trunk/externalpackages/gmsh/configs/4.10.5/static/mac/CMakeLists.txt.patch (revision 28013) +++ /issm/trunk/externalpackages/gmsh/configs/4.10.5/static/mac/CMakeLists.txt.patch (revision 28013) @@ -0,0 +1,4 @@ +207a208 +> set(CMAKE_FIND_LIBRARY_SUFFIXES ".a" ".so") +226a228 +> set(CMAKE_FIND_LIBRARY_SUFFIXES ".a" ".so") Index: /issm/trunk/externalpackages/gmsh/install-4-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-4-linux-static.sh (revision 28012) +++ /issm/trunk/externalpackages/gmsh/install-4-linux-static.sh (revision 28013) @@ -24,7 +24,8 @@ # - Move this to etc/environment.sh # -LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} -LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1) +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1) # Cleanup @@ -41,4 +42,7 @@ mv gmsh-${VER}-source/* src rm -rf gmsh-${VER}-source + +# Apply patches +patch src/CMakeLists.txt < configs/${VER}/static/CMakeLists.txt.patch # Configure @@ -57,4 +61,5 @@ cmake \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release \ -DENABLE_BUILD_LIB=1 \ -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \ Index: /issm/trunk/externalpackages/gmsh/install-4-linux.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-4-linux.sh (revision 28012) +++ /issm/trunk/externalpackages/gmsh/install-4-linux.sh (revision 28013) @@ -24,5 +24,6 @@ # - Move this to etc/environment.sh # -LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} @@ -56,4 +57,6 @@ cmake \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_INSTALL_RPATH="${PREFIX}/lib" \ + -DCMAKE_BUILD_TYPE=Release \ -DENABLE_BUILD_DYNAMIC=1 \ -DENABLE_BUILD_SHARED=1 \ Index: /issm/trunk/externalpackages/gmsh/install-4-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-4-mac-static.sh (revision 28012) +++ /issm/trunk/externalpackages/gmsh/install-4-mac-static.sh (revision 28013) @@ -19,8 +19,5 @@ PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed - # Find libgfortran and libgcc so we do not have to hardcode them -# -# Should retrieve a copy of gfortran that is compiled from source before returning one that is installed via package manager # # TODO: @@ -29,7 +26,8 @@ # - Otherwise, refactor this to work with other gfortran installations. # -LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} -LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) # Cleanup @@ -47,6 +45,7 @@ rm -rf gmsh-${VER}-source -# Copy customized source and config files to 'src' directory -cp configs/${VER}/static/CMakeLists.txt src +# Apply patches +patch src/CMakeLists.txt < configs/${VER}/static/CMakeLists.txt.patch +patch src/CMakeLists.txt < configs/${VER}/static/mac/CMakeLists.txt.patch # Configure @@ -65,4 +64,5 @@ cmake \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release \ -DENABLE_BUILD_LIB=1 \ -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \ @@ -84,8 +84,2 @@ make -j $1 install fi - -# Make necessary link on RHEL -if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then - cd ${PREFIX} - ln -s ./lib64 ./lib -fi Index: /issm/trunk/externalpackages/gmsh/install-4-mac.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install-4-mac.sh (revision 28012) +++ /issm/trunk/externalpackages/gmsh/install-4-mac.sh (revision 28013) @@ -21,11 +21,9 @@ # Find libgfortran so that we do not have to hardcode it. # -# Should retrieve a copy of gfortran that is compiled from source before -# returning one that is installed via package manager. -# # TODO: # - Move this to etc/environment.sh # -LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} @@ -44,4 +42,7 @@ rm -rf gmsh-${VER}-source +# Apply patches +patch src/CMakeLists.txt < configs/${VER}/mac/CMakeLists.txt.patch + # Configure # @@ -59,7 +60,11 @@ cmake \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_MACOSX_RPATH=ON \ + -DCMAKE_INSTALL_RPATH="${PREFIX}/lib" \ + -DCMAKE_BUILD_TYPE=Release \ -DENABLE_BUILD_DYNAMIC=1 \ -DENABLE_BUILD_SHARED=1 \ -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" \ + -DLIBGFORTRAN_ROOT="${LIBGFORTRAN_ROOT}" \ -DENABLE_BLAS_LAPACK=1 \ -DENABLE_EIGEN=0 \ @@ -79,8 +84,2 @@ make -j $1 install fi - -# Make necessary link on RHEL -if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then - cd ${PREFIX} - ln -s ./lib64 ./lib -fi Index: /issm/trunk/externalpackages/gmt/configs/6/mac/cmake/modules/ConfigCMake.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/mac/cmake/modules/ConfigCMake.cmake (revision 28013) +++ /issm/trunk/externalpackages/gmt/configs/6/mac/cmake/modules/ConfigCMake.cmake (revision 28013) @@ -0,0 +1,250 @@ +# +# +# Useful CMake variables. +# +# There are five configuration files: +# +# 1) "ConfigDefault.cmake" - is version controlled and used to add new default +# variables and set defaults for everyone. +# 2) "ConfigUser.cmake" in the source tree - is not version controlled +# (currently listed in .gitignore) and used to override basic default settings on +# a per-user basis. +# 3) "ConfigUser.cmake" in the build tree - is used to override +# "ConfigUser.cmake" in the source tree. +# 4) "ConfigUserAdvanced.cmake" in the source tree - is not version controlled +# (currently listed in .gitignore) and used to override advanced default settings on +# a per-user basis. +# 5) "ConfigUserAdvanced.cmake" in the build tree - is used to override +# "ConfigUserAdvanced.cmake" in the source tree. +# +# NOTE: If you want to change CMake behaviour just for yourself, +# copy "ConfigUserTemplate.cmake" to "ConfigUser.cmake" and then edit +# "ConfigUser.cmake" for basic settings. For advanced settings, +# copy "ConfigUserAdvancedTemplate.cmake" to "ConfigUserAdvanced.cmake" and edit it. +# DO NOT EDIT "ConfigDefault.cmake" or the CMake template files. +# +include ("${CMAKE_SOURCE_DIR}/cmake/ConfigDefault.cmake") + +# A "ConfigUser.cmake" in the source tree overrides the advanced defaults. +if (EXISTS "${CMAKE_SOURCE_DIR}/cmake/ConfigUser.cmake") + include ("${CMAKE_SOURCE_DIR}/cmake/ConfigUser.cmake") +endif (EXISTS "${CMAKE_SOURCE_DIR}/cmake/ConfigUser.cmake") + +# If you've got a 'ConfigUser.cmake' in the build tree then that overrides the +# one in the source tree. +if (EXISTS "${CMAKE_BINARY_DIR}/cmake/ConfigUser.cmake") + include ("${CMAKE_BINARY_DIR}/cmake/ConfigUser.cmake") +endif (EXISTS "${CMAKE_BINARY_DIR}/cmake/ConfigUser.cmake") + +# A "ConfigUserAdvanced.cmake" in the source tree overrides the advanced defaults. +if (EXISTS "${CMAKE_SOURCE_DIR}/cmake/ConfigUserAdvanced.cmake") + include ("${CMAKE_SOURCE_DIR}/cmake/ConfigUserAdvanced.cmake") +endif (EXISTS "${CMAKE_SOURCE_DIR}/cmake/ConfigUserAdvanced.cmake") + +# If you've got a 'ConfigUserAdvanced.cmake' in the build tree then that overrides the +# one in the source tree. +if (EXISTS "${CMAKE_BINARY_DIR}/cmake/ConfigUserAdvanced.cmake") + include ("${CMAKE_BINARY_DIR}/cmake/ConfigUserAdvanced.cmake") +endif (EXISTS "${CMAKE_BINARY_DIR}/cmake/ConfigUserAdvanced.cmake") + +########################################################### +# Do any needed processing of the configuration variables # +########################################################### + +# Set default build type to 'Release' +if (NOT CMAKE_BUILD_TYPE) + set (CMAKE_BUILD_TYPE Release) +endif (NOT CMAKE_BUILD_TYPE) + +# Here we change it to add the git commit hash for non-public releases +set (GMT_PACKAGE_VERSION_WITH_GIT_REVISION ${GMT_PACKAGE_VERSION}) + +# Check if it's a git repository or not +if (EXISTS ${GMT_SOURCE_DIR}/.git) + set (HAVE_GIT_VERSION TRUE) +endif (EXISTS ${GMT_SOURCE_DIR}/.git) + +# Add the last git commit hash and date to the package version if this is a non-public release. +# A non-public release has a FALSE 'GMT_PUBLIC_RELEASE' variable in 'ConfigDefault.cmake'. +if (GIT_FOUND AND HAVE_GIT_VERSION AND NOT GMT_PUBLIC_RELEASE) + # Get the last git commit hash + execute_process ( + COMMAND ${GIT_EXECUTABLE} describe --abbrev=7 --always --dirty + WORKING_DIRECTORY ${GMT_SOURCE_DIR} + RESULT_VARIABLE GIT_RETURN_CODE + OUTPUT_VARIABLE GIT_COMMIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE) + + if (GIT_RETURN_CODE) + message (STATUS "Unable to determine git commit hash for non-public release - ignoring.") + else (GIT_RETURN_CODE) + if (GIT_COMMIT_HASH) + # For non-public release, add the last git commit hash and date + execute_process ( + COMMAND ${GIT_EXECUTABLE} log -1 --date=short --pretty=format:%cd + WORKING_DIRECTORY ${GMT_SOURCE_DIR} + RESULT_VARIABLE GIT_DATE_RETURN_CODE + OUTPUT_VARIABLE GIT_COMMIT_DATE + OUTPUT_STRIP_TRAILING_WHITESPACE) + string(REPLACE "-" "." GIT_COMMIT_DATE "${GIT_COMMIT_DATE}") + set (GMT_PACKAGE_VERSION_WITH_GIT_REVISION "${GMT_PACKAGE_VERSION}_${GIT_COMMIT_HASH}_${GIT_COMMIT_DATE}") + endif (GIT_COMMIT_HASH) + endif (GIT_RETURN_CODE) +endif (GIT_FOUND AND HAVE_GIT_VERSION AND NOT GMT_PUBLIC_RELEASE) + +# apply license restrictions +if (LICENSE_RESTRICTED) # on + if (LICENSE_RESTRICTED STREQUAL GPL) + # restrict to GPL + elseif (LICENSE_RESTRICTED STREQUAL LGPL) + # restrict to LGPL + else (LICENSE_RESTRICTED STREQUAL GPL) + # unknown license + message (WARNING "unknown license: ${LICENSE_RESTRICTED}") + endif (LICENSE_RESTRICTED STREQUAL GPL) + # restrictions that apply to any of the above licenses +else (LICENSE_RESTRICTED) # off + # no restrictions at all +endif (LICENSE_RESTRICTED) + +# reset list of extra license files +set (GMT_EXTRA_LICENSE_FILES) + +# location of GNU license files +set (COPYING_GPL ${GMT_SOURCE_DIR}/COPYINGv3) +set (COPYING_LGPL ${GMT_SOURCE_DIR}/COPYING.LESSERv3) + +# GMT paths used in the code +if (NOT GMT_DATADIR) + # do not reset user setting + if (GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_DATADIR "share") + else(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_DATADIR "share/gmt${GMT_INSTALL_NAME_SUFFIX}") + endif(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) +endif (NOT GMT_DATADIR) + +# Install path GMT_DOCDIR +if (NOT GMT_DOCDIR) + # do not reset user setting + if (GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_DOCDIR "${GMT_DATADIR}/doc") + else(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_DOCDIR "share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}") + endif(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) +endif (NOT GMT_DOCDIR) + +# Install path GMT_MANDIR +if (NOT GMT_MANDIR) + # do not reset user setting + if (GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_MANDIR "${GMT_DATADIR}/man") + else(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_MANDIR "${GMT_DOCDIR}/man") + endif(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) +endif (NOT GMT_MANDIR) + +# Install path for GMT binaries, headers and libraries +include (GNUInstallDirs) # defines CMAKE_INSTALL_LIBDIR (lib/lib64) +if (NOT GMT_LIBDIR) + set (GMT_LIBDIR ${CMAKE_INSTALL_LIBDIR}) +endif(NOT GMT_LIBDIR) + +if (NOT GMT_BINDIR) + set (GMT_BINDIR bin) +endif(NOT GMT_BINDIR) + +if (NOT GMT_INCLUDEDIR) + set (GMT_INCLUDEDIR include/gmt${GMT_INSTALL_NAME_SUFFIX}) +endif(NOT GMT_INCLUDEDIR) + +if (GMT_DATA_URL) # Backwards compatibility with old ConfigUser.cmake files + message (WARNING "CMake variable GMT_DATA_URL is deprecated and will be removed in the future releases. Use GMT_DATA_SERVER instead.") + set (GMT_DATA_SERVER ${GMT_DATA_URL}) +endif (GMT_DATA_URL) + +# use, i.e. don't skip the full RPATH for the build tree +set (CMAKE_SKIP_BUILD_RPATH FALSE) + +# when building, don't use the install RPATH already +# (but later on when installing) +set (CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + +# set the RPATH to be used when installing +if (NOT DEFINED GMT_INSTALL_RELOCATABLE) + set (GMT_INSTALL_RELOCATABLE FALSE) +endif (NOT DEFINED GMT_INSTALL_RELOCATABLE) +if (GMT_INSTALL_RELOCATABLE) + # make executables relocatable on supported platforms (relative RPATH) + if (UNIX AND NOT CYGWIN) + # find relative libdir from executable dir + file (RELATIVE_PATH _rpath /${GMT_BINDIR} /${GMT_LIBDIR}) + # remove trailing / + string (REGEX REPLACE "/$" "" _rpath "${_rpath}") + if (APPLE) + # relative RPATH on osx + # CMP0042: CMake 3.0: MACOSX_RPATH is enabled by default + set (CMAKE_MACOSX_RPATH ON) + set (CMAKE_INSTALL_NAME_DIR @rpath) + set (CMAKE_INSTALL_RPATH "@rpath;@executable_path/${_rpath};${LIBGFORTRAN_ROOT}") + else (APPLE) + # relative RPATH on Linux, Solaris, etc. + set (CMAKE_INSTALL_RPATH "\$ORIGIN/${_rpath}") + endif (APPLE) + endif (UNIX AND NOT CYGWIN) +else (GMT_INSTALL_RELOCATABLE) + # set absolute RPATH + if (APPLE) + # CMP0042: CMake 3.0: MACOSX_RPATH is enabled by default + set (CMAKE_MACOSX_RPATH OFF) + set (CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${GMT_LIBDIR}") + else (APPLE) + # the RPATH to be used when installing, but only if it's not a + # system directory + list (FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES + "${CMAKE_INSTALL_PREFIX}/${GMT_LIBDIR}" isSystemDir) + if ("${isSystemDir}" STREQUAL "-1") + set (CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${GMT_LIBDIR}") + endif ("${isSystemDir}" STREQUAL "-1") + endif (APPLE) +endif (GMT_INSTALL_RELOCATABLE) + +# 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) + +# When running examples/tests with CTest (out-of-source) we need support for +# running GMT programs from within ${GMT_BINARY_DIR}: +if (DO_EXAMPLES OR DO_TESTS AND NOT SUPPORT_EXEC_IN_BINARY_DIR) + message (WARNING "Enabling SUPPORT_EXEC_IN_BINARY_DIR (required for " + "testing). Please disable testing on release builds.") + set (SUPPORT_EXEC_IN_BINARY_DIR ON) +endif (DO_EXAMPLES OR DO_TESTS AND NOT SUPPORT_EXEC_IN_BINARY_DIR) + +# Some tests are known to fail, and can be excluded from the test by adding +# the comment "# GMT_KNOWN_FAILURE". +if (NOT DEFINED GMT_ENABLE_KNOWN2FAIL) + set (GMT_ENABLE_KNOWN2FAIL ON) +endif (NOT DEFINED GMT_ENABLE_KNOWN2FAIL) + +# Make GNU, Intel, Clang and AppleClang compilers default to C99 +if (CMAKE_C_COMPILER_ID MATCHES "(GNU|Intel|Clang)" AND NOT CMAKE_C_FLAGS MATCHES "-std=") + set (CMAKE_C_FLAGS "-std=gnu99 ${CMAKE_C_FLAGS}") +endif () + +# Suppress MSVC deprecation and security warnings +if (MSVC) + set (CMAKE_C_FLAGS "/D_CRT_SECURE_NO_WARNINGS /D_CRT_SECURE_NO_DEPRECATE ${CMAKE_C_FLAGS}") + set (CMAKE_C_FLAGS "/D_CRT_NONSTDC_NO_DEPRECATE /D_SCL_SECURE_NO_DEPRECATE ${CMAKE_C_FLAGS}") +endif (MSVC) + +# Handle the special developer option GMT_DOCS_DEPEND_ON_GMT +# Normally this is ON. +if (NOT DEFINED GMT_DOCS_DEPEND_ON_GMT) + set (GMT_DOCS_DEPEND_ON_GMT TRUE) +endif (NOT DEFINED GMT_DOCS_DEPEND_ON_GMT) +if (GMT_DOCS_DEPEND_ON_GMT) + add_custom_target (gmt_for_img_convert DEPENDS gmt) +else (GMT_DOCS_DEPEND_ON_GMT) + add_custom_target (gmt_for_img_convert) +endif (GMT_DOCS_DEPEND_ON_GMT) Index: /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake (revision 28012) +++ /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake (revision 28013) @@ -148,8 +148,8 @@ NAMES ${_extralib} HINTS + ${HDF5_ROOT} + $ENV{HDF5_ROOT} ${NETCDF_ROOT} $ENV{NETCDF_ROOT} - ${HDF5_ROOT} - $ENV{HDF5_ROOT} ${ZLIB_ROOT} $ENV{ZLIB_ROOT} @@ -166,5 +166,5 @@ # find all manually-supplied libs if (GDAL_EXTRA_LIBS) - # Ensure -l is precedeced by whitespace to not match + # Ensure -l is preceded 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}) Index: /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake (revision 28012) +++ /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake (revision 28013) @@ -59,5 +59,5 @@ OUTPUT_VARIABLE NETCDF_CONFIG_LIBS) if (NETCDF_CONFIG_LIBS) - # Ensure -l is precedeced by whitespace to not match + # Ensure -l is preceded by whitespace to not match # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' string (REGEX MATCHALL "(^| )-l[^ ]+" _netcdf_dashl ${NETCDF_CONFIG_LIBS}) Index: /issm/trunk/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake (revision 28012) +++ /issm/trunk/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake (revision 28013) @@ -191,5 +191,5 @@ # Create position independent code on all targets [auto] (needed for static # build on non-x86): -set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) +#set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) # Build GMT shared lib with supplemental modules [TRUE]: Index: /issm/trunk/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake (revision 28012) +++ /issm/trunk/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake (revision 28013) @@ -191,5 +191,5 @@ # Create position independent code on all targets [auto] (needed for static # build on non-x86): -set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) +#set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) # Build GMT shared lib with supplemental modules [TRUE]: Index: /issm/trunk/externalpackages/gmt/install-6-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-6-linux-static.sh (revision 28012) +++ /issm/trunk/externalpackages/gmt/install-6-linux-static.sh (revision 28013) @@ -5,5 +5,5 @@ ## Constants # -VER="6.4.0" +VER="6.0.0" # Find libgfortran and libgcc so we do not have to hardcode them @@ -11,8 +11,11 @@ # TODO: # - Move this to etc/environment.sh +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. # -LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} -LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1) +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1) GDAL_EXTRA_LIBS="-lstdc++" # Determined by running `$GDAL_ROOT/bin/gdal-config --dep-libs` then removing duplicate libs @@ -64,5 +67,4 @@ -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a" \ -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \ - -DHDF5_ROOT="${HDF5_ROOT}" \ -DLAPACK_LIBRARIES="${LAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ -DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \ Index: /issm/trunk/externalpackages/gmt/install-6-linux.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-6-linux.sh (revision 28012) +++ /issm/trunk/externalpackages/gmt/install-6-linux.sh (revision 28013) @@ -12,5 +12,6 @@ # - Move this to etc/environment.sh # -LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} Index: /issm/trunk/externalpackages/gmt/install-6-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-6-mac-static.sh (revision 28012) +++ /issm/trunk/externalpackages/gmt/install-6-mac-static.sh (revision 28013) @@ -5,9 +5,7 @@ ## Constants # -VER="6.4.0" +VER="6.0.0" # Find libgfortran and libgcc so we do not have to hardcode them -# -# Should retrieve a copy of gfortran that is compiled from source before returning one that is installed via package manager # # TODO: @@ -16,10 +14,11 @@ # - Otherwise, refactor this to work with other gfortran installations. # -LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} -LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) GDAL_EXTRA_LIBS="-lc++" # `$GDAL_ROOT/bin/gdal-config --dep-libs` does not report need to link to libc++ (see also customized configuration file ./configs/6/static/cmake/modules/FindGDAL.cmake) -NETCDF_EXTRA_LIBS="-lsqlite3 -lpthread -ldl -liconv" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6/static/cmake/modules/FindNETCDF.cmake) +NETCDF_EXTRA_LIBS="-lpthread -ldl -liconv" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6/static/cmake/modules/FindNETCDF.cmake) # Environment @@ -28,5 +27,5 @@ export CURL_INCLUDE_DIRS="${CURL_ROOT}/include" export CURL_LIBRARIES="${CURL_ROOT}/lib/libcurl.a;${ZLIB_ROOT}/lib/libz.a" -export LDFLAGS="-framework CoreFoundation -framework Security" +export LDFLAGS="-lsqlite3 -framework CoreFoundation -framework Security" export PREFIX="${ISSM_DIR}/externalpackages/gmt/install" # NOTE: Need to export this to be picked up by customized ConfigUser.cmake (see below). Set to location where external package should be installed. @@ -68,5 +67,4 @@ -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a" \ -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \ - -DHDF5_ROOT="${HDF5_ROOT}" \ -DLAPACK_LIBRARIES="${LAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ -DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \ Index: /issm/trunk/externalpackages/gmt/install-6-mac.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-6-mac.sh (revision 28012) +++ /issm/trunk/externalpackages/gmt/install-6-mac.sh (revision 28013) @@ -9,11 +9,9 @@ # 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. -# # TODO: # - Move this to etc/environment.sh # -LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} @@ -39,4 +37,5 @@ # Copy custom configuration files cp ./configs/6/mac/cmake/ConfigUser.cmake ./src/cmake +cp ./configs/6/mac/cmake/modules/ConfigCMake.cmake ./src/cmake/modules # Configure @@ -57,4 +56,5 @@ -DCURL_LIBRARY="-L${CURL_ROOT}/lib;-lcurl" \ -DLAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib;-lflapack;-L${LIBGFORTRAN_ROOT};-lgfortran" \ + -DLIBGFORTRAN_ROOT="${LIBGFORTRAN_ROOT}" \ .. Index: /issm/trunk/externalpackages/hdf5/install-1-parallel-static.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1-parallel-static.sh (revision 28013) +++ /issm/trunk/externalpackages/hdf5/install-1-parallel-static.sh (revision 28013) @@ -0,0 +1,47 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="1.10.9" + +PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed + +## Environnment +# +export CC=mpicc + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/hdf5-${VER}.tar.gz" "hdf5-${VER}.tar.gz" + +# Untar source +tar -zxvf hdf5-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv hdf5-${VER}/* src/ +rm -rf hdf5-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-shared \ + --enable-parallel \ + --with-zlib="${ZLIB_ROOT}" \ + --enable-hl + +# Compile and install +# +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/hdf5/install-1-parallel-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1-parallel-with_tests.sh (revision 28012) +++ /issm/trunk/externalpackages/hdf5/install-1-parallel-with_tests.sh (revision 28013) @@ -3,7 +3,7 @@ -# Constants +## Constants # -VER="1.14.0" +VER="1.10.9" PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed @@ -31,4 +31,6 @@ ./configure \ --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-static \ --enable-parallel \ --with-zlib="${ZLIB_ROOT}" \ Index: /issm/trunk/externalpackages/hdf5/install-1-parallel.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1-parallel.sh (revision 28012) +++ /issm/trunk/externalpackages/hdf5/install-1-parallel.sh (revision 28013) @@ -3,7 +3,7 @@ -# Constants +## Constants # -VER="1.14.0" +VER="1.10.9" PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed @@ -31,4 +31,6 @@ ./configure \ --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-static \ --enable-parallel \ --with-zlib="${ZLIB_ROOT}" \ Index: /issm/trunk/externalpackages/hdf5/install-1-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1-with_tests.sh (revision 28012) +++ /issm/trunk/externalpackages/hdf5/install-1-with_tests.sh (revision 28013) @@ -5,5 +5,5 @@ ## Constants # -VER="1.14.0" +VER="1.10.9" PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed @@ -27,4 +27,6 @@ ./configure \ --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-static \ --with-zlib="${ZLIB_ROOT}" \ --enable-hl Index: /issm/trunk/externalpackages/hdf5/install-1.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1.sh (revision 28012) +++ /issm/trunk/externalpackages/hdf5/install-1.sh (revision 28013) @@ -5,5 +5,5 @@ ## Constants # -VER="1.14.0" +VER="1.10.9" PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed @@ -27,4 +27,6 @@ ./configure \ --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-static \ --with-zlib="${ZLIB_ROOT}" \ --enable-hl Index: /issm/trunk/externalpackages/m1qn3/install.sh =================================================================== --- /issm/trunk/externalpackages/m1qn3/install.sh (revision 28012) +++ /issm/trunk/externalpackages/m1qn3/install.sh (revision 28013) @@ -28,8 +28,11 @@ if which ifort >/dev/null; then FC="ifort" + FFLAGS="-traceback -check all" # -O2 is default else FC="gfortran" if [ `uname` == "Darwin" ]; then - FC="gfortran -arch x86_64" + FFLAGS="-arch $(uname -m)" + else + FFLAGS="" fi fi @@ -41,4 +44,5 @@ LIB_EXT=a FC=$FC +FFLAGS=$FFLAGS install: libm1qn3.\$(LIB_EXT) cp libm1qn3.\$(LIB_EXT) ${PREFIX} @@ -60,4 +64,5 @@ LIB_EXT=a FC=$FC +FFLAGS=$FFLAGS install: libddot.\$(LIB_EXT) cp libddot.\$(LIB_EXT) ${PREFIX} Index: /issm/trunk/externalpackages/medipack/install.sh =================================================================== --- /issm/trunk/externalpackages/medipack/install.sh (revision 28012) +++ /issm/trunk/externalpackages/medipack/install.sh (revision 28013) @@ -6,3 +6,3 @@ #Download development version -svn co https://github.com/SciCompKL/MeDiPack/trunk install +git clone https://github.com/SciCompKL/MeDiPack.git install Index: /issm/trunk/externalpackages/msmpi/install-static.sh =================================================================== --- /issm/trunk/externalpackages/msmpi/install-static.sh (revision 28013) +++ /issm/trunk/externalpackages/msmpi/install-static.sh (revision 28013) @@ -0,0 +1,77 @@ +#!/bin/bash +# +# Creates a local MS-MPI directory to be used for supplying MPI headers files +# and libraries to ISSM configuration and certain external packages. +# +# Assumes that Microsoft MPI and MPI SDK have been installed. To do so, +# - Navigate to https://docs.microsoft.com/en-us/message-passing-interface/microsoft-mpi +# - Under the 'MS-MPI Downloads' heading, click the link for +# 'MS-MPI v', where is the latest version available (as of +# this writing, 10.1.2) +# - Click the 'Download' button +# - Make sure both boxes are checked +# - Click the 'Save File' button in each prompt +# - When the downloads are complete, run each installer +# +# TODO: +# - Commit Microsoft MPI and Microsoft SDK installers or source code to +# external packages source repository, then update this documentation to note +# that they are available +# - Attempt to download Microsoft MPI and Microsoft SDK installers or source +# code and (compile and) install with this script +# - Alternatively, instruct users to install MSYS2 MinGW 64-bit MS-MPI package +# with, +# +# pacman -S mingw-w64-x86_64-msmpi +# +# remove this script, its parent directory, and references to it from +# configuration files in $ISSM_DIR/jenkins directory and documentation +# + + +## Constants +# +PREFIX="${ISSM_DIR}/externalpackages/msmpi/install" + +MSMPI_BIN_DIR=$(cygpath -u $(cygpath -ms "/c/Program Files/Microsoft MPI/Bin")) +MSMPI_INC_DIR=$(cygpath -u $(cygpath -ms "/c/Program Files (x86)/Microsoft SDKs/MPI/Include")) +MSMPI_LIB="/c/Windows/System32/msmpi.dll" +MSMPI_LIC_DIR=$(cygpath -u $(cygpath -ms "/c/Program Files (x86)/Microsoft SDKs/MPI/License")) + +# Cleanup +rm -rf ${PREFIX} +mkdir -p ${PREFIX} ${PREFIX}/bin ${PREFIX}/include ${PREFIX}/lib ${PREFIX}/license + +# Copy MS-MPI binaries to 'bin' directory +cp -R ${MSMPI_BIN_DIR}/* ${PREFIX}/bin + +# Copy MS-MPI header files to 'include' directory +cp ${MSMPI_INC_DIR}/mpi.h ${PREFIX}/include +cp ${MSMPI_INC_DIR}/mpi.f90 ${PREFIX}/include +cp ${MSMPI_INC_DIR}/mpif.h ${PREFIX}/include +cp ${MSMPI_INC_DIR}/mpio.h ${PREFIX}/include +cp ${MSMPI_INC_DIR}/x64/mpifptr.h ${PREFIX}/include + +# Generate static copy of MS-MPI library +gendef ${MSMPI_LIB} +dlltool -d msmpi.def -l libmsmpi.a -D ${MSMPI_LIB} + +# Copy MS-MPI library to 'lib' directory +cp libmsmpi.a ${PREFIX}/lib +cp libmsmpi.a ${PREFIX}/lib/msmpi.a +cp libmsmpi.a ${PREFIX}/lib/msmpi.lib + +# Copy MS-MPI license files to 'license' directory +cp -R ${MSMPI_LIC_DIR}/* ${PREFIX}/license + +# TODO: Remove all of the following once compilation of a newer version of +# PETSc that does not pick up system DLL is sorted out +# + +# Copy MS-MPI library to 'lib' directory +cp ${MSMPI_LIB} ${PREFIX}/lib + +# Create link to shared library so that libtool can find it +cd ${PREFIX}/lib +ln -s msmpi.dll libmsmpi.dll + Index: /issm/trunk/externalpackages/msmpi/install.sh =================================================================== --- /issm/trunk/externalpackages/msmpi/install.sh (revision 28012) +++ /issm/trunk/externalpackages/msmpi/install.sh (revision 28013) @@ -34,17 +34,18 @@ PREFIX="${ISSM_DIR}/externalpackages/msmpi/install" +MSMPI_BIN_DIR=$(cygpath -u $(cygpath -ms "/c/Program Files/Microsoft MPI/Bin")) +MSMPI_INC_DIR=$(cygpath -u $(cygpath -ms "/c/Program Files (x86)/Microsoft SDKs/MPI/Include")) MSMPI_LIB="/c/Windows/System32/msmpi.dll" -MSMPI_INC=$(cygpath -u $(cygpath -ms "/c/Program Files (x86)/Microsoft SDKs/MPI/Include")) # Cleanup rm -rf ${PREFIX} -mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib +mkdir -p ${PREFIX} ${PREFIX}/bin ${PREFIX}/include ${PREFIX}/lib # Copy MS-MPI header files to 'include' directory -cp ${MSMPI_INC}/mpi.h ${PREFIX}/include -cp ${MSMPI_INC}/mpi.f90 ${PREFIX}/include -cp ${MSMPI_INC}/mpif.h ${PREFIX}/include -cp ${MSMPI_INC}/mpio.h ${PREFIX}/include -cp ${MSMPI_INC}/x64/mpifptr.h ${PREFIX}/include +cp ${MSMPI_INC_DIR}/mpi.h ${PREFIX}/include +cp ${MSMPI_INC_DIR}/mpi.f90 ${PREFIX}/include +cp ${MSMPI_INC_DIR}/mpif.h ${PREFIX}/include +cp ${MSMPI_INC_DIR}/mpio.h ${PREFIX}/include +cp ${MSMPI_INC_DIR}/x64/mpifptr.h ${PREFIX}/include # Copy MS-MPI library to 'lib' directory Index: /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh (revision 28012) +++ /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh (revision 28013) @@ -17,5 +17,5 @@ # TODO: # - Compile and link curl statically (issue with DAP and system libs on macOS -# with more restirctive Gatekeeper; see also --disable-dap option in +# with more restrictive Gatekeeper; see also --disable-dap option in # configuration) # @@ -32,5 +32,4 @@ export CPPFLAGS="-I${ZLIB_ROOT}/include" -export HDF5LIB="${HDF5_ROOT}/lib/libhdf5_hl.a ${HDF5_ROOT}/lib/libhdf5.a" export ZLIB="${ZLIB_ROOT}/lib/libz.a" Index: /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 28012) +++ /issm/trunk/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 28013) @@ -17,5 +17,5 @@ # TODO: # - Compile and link curl statically (issue with DAP and system libs on macOS -# with more restirctive Gatekeeper; see also --disable-dap option in +# with more restrictive Gatekeeper; see also --disable-dap option in # configuration) # @@ -32,5 +32,4 @@ 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" Index: /issm/trunk/externalpackages/netcdf/install-4.7-parallel-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-parallel-with_tests.sh (revision 28012) +++ /issm/trunk/externalpackages/netcdf/install-4.7-parallel-with_tests.sh (revision 28013) @@ -22,6 +22,6 @@ # export CC=mpicc -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" +export CPPFLAGS="-I${HDF5_ROOT}/include -I${CURL_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${HDF5_ROOT}/lib -L${CURL_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source Index: /issm/trunk/externalpackages/netcdf/install-4.7-parallel.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-parallel.sh (revision 28012) +++ /issm/trunk/externalpackages/netcdf/install-4.7-parallel.sh (revision 28013) @@ -22,6 +22,6 @@ # export CC=mpicc -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" +export CPPFLAGS="-I${HDF5_ROOT}/include -I${CURL_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${HDF5_ROOT}/lib -L${CURL_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source Index: /issm/trunk/externalpackages/netcdf/install-4.7-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7-with_tests.sh (revision 28012) +++ /issm/trunk/externalpackages/netcdf/install-4.7-with_tests.sh (revision 28013) @@ -21,6 +21,6 @@ # Environment # -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" +export CPPFLAGS="-I${HDF5_ROOT}/include -I${CURL_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${HDF5_ROOT}/lib -L${CURL_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source Index: /issm/trunk/externalpackages/netcdf/install-4.7.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.7.sh (revision 28012) +++ /issm/trunk/externalpackages/netcdf/install-4.7.sh (revision 28013) @@ -21,6 +21,6 @@ # Environment # -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" +export CPPFLAGS="-I${HDF5_ROOT}/include -I${CURL_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${HDF5_ROOT}/lib -L${CURL_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source Index: sm/trunk/externalpackages/petsc/install-3.12-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-linux-static.sh (revision 28012) +++ (revision ) @@ -1,65 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.12.3" - -PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# 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 ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${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 -# -# - 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). -# -cd ${PETSC_DIR} -./config/configure.py \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --with-shared-libraries=0 \ - --CFLAGS="-fPIC" \ - --CXXFLAGS="-fPIC" \ - --FFLAGS="-fPIC" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.12-linux.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-linux.sh (revision 28012) +++ (revision ) @@ -1,47 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.12.3" - -PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# Download source -$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 ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${VER} - -# Configure -cd ${PETSC_DIR} -./config/configure.py \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.12-lonestar.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-lonestar.sh (revision 28012) +++ (revision ) @@ -1,49 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.12.3" - -PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# Download source -$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 ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${VER} - -# Configure -cd ${PETSC_DIR} -./config/configure.py \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --with-mpi-dir="/opt/cray/pe/mpt/7.7.3/gni/mpich-intel/16.0/" \ - --with-blas-lapack-dir="$TACC_MKL_LIB" \ - --with-scalapack-include="$TACC_MKL_INC" \ - --with-scalapack-lib="$TACC_MKL_LIB/libmkl_scalapack_lp64.so $TACC_MKL_LIB/libmkl_blacs_intelmpi_lp64.so" \ - --with-shared-libraries=1 \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.12-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-mac-static.sh (revision 28012) +++ (revision ) @@ -1,69 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.12.3" - -PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# Download source -$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 ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${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 -# -# - 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 ${PETSC_DIR} -./config/configure.py \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --with-shared-libraries=0 \ - --CFLAGS="-fPIC -Wno-error=implicit-function-declaration" \ - --CXXFLAGS="-fPIC" \ - --FFLAGS="-fPIC -fallow-argument-mismatch -static-libgfortran" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.12-mac.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-mac.sh (revision 28012) +++ (revision ) @@ -1,60 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.12.3" - -PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# Download source -$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 ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${VER} - -# Configure -# -# NOTE: -# - 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). -# -cd ${PETSC_DIR} -./config/configure.py \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --CFLAGS="-Wno-error=implicit-function-declaration" \ - --FFLAGS="-fallow-argument-mismatch" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.12-win-msys2-gcc-msmpi.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.12-win-msys2-gcc-msmpi.sh (revision 28012) +++ (revision ) @@ -1,65 +1,0 @@ -#!/bin/bash -set -u # NOTE: Do not set -e as it will cause this script to fail when there are errors in underlying Python scripts - - -## Constants -# -VER="3.12.3" - -PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# Download source -$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 ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${VER} - -# Configure -# -# - Added -fallow-argument-mismatch option to FFLAGS in order to clear "Error: -# Rank mismatch between actual argument at [...]" -# - Added -fallow-invalid-boz option to FFLAGS in order to clear "Error: BOZ -# literal constant at [...]" -# -cd ${PETSC_DIR} -./config/configure.py \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --FFLAGS="-fallow-argument-mismatch -fallow-invalid-boz" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --with-mpiexec="/c/PROGRA~1/MICROS~1/Bin/mpiexec.exe" \ - --with-mpi-lib="-L${MSMPI_ROOT}/lib -lmsmpi" \ - --with-mpi-include="${MSMPI_ROOT}/include" \ - --with-metis-dir=${METIS_ROOT} \ - --with-parmetis-dir=${PARMETIS_ROOT} \ - --with-blas-lib="-L${BLAS_ROOT}/lib -lblas" \ - --known-64-bit-blas-indices=0 \ - --with-lapack-lib="-L${LAPACK_ROOT}/lib -llapack" \ - --with-scalapack-dir=${SCALAPACK_ROOT} \ - --with-mumps-dir=${MUMPS_ROOT} - -# Compile and install -make -make install - -# NOTE: -# - Hack to recover from failed installation (appears to happen only on Windows -# when reproducing symbolic links in destination directory) rather than -# trying to patch src/config/install.py -# -if [ $? -ne 0 ]; then - make install -fi Index: sm/trunk/externalpackages/petsc/install-3.13-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.13-pleiades.sh (revision 28012) +++ (revision ) @@ -1,63 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.13.6" - -PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# Download source -echo "OK1 ($ISSM_DIR)" -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" -echo OK2 - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${VER} - - -# Configure -# -# NOTE: Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables; look for CONFIGURE_OPTIONS -# -cd ${PETSC_DIR} -./config/configure.py \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --with-cc=icc \ - --with-cpp=/usr/bin/cpp \ - --with-cxx=icpc \ - --with-fc=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/" \ - --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" \ - --known-mpi-shared-libraries=1 \ - --with-gnu-compilers=0 \ - --with-vendor-compilers=intel \ - --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-zlib=1 - -# Compile and install -make -make install Index: /issm/trunk/externalpackages/petsc/install-3.14-discover.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-discover.sh (revision 28012) +++ /issm/trunk/externalpackages/petsc/install-3.14-discover.sh (revision 28013) @@ -35,8 +35,8 @@ --with-ssl=0 \ --with-pic=1 \ - --with-blas-lapack-dir="/usr/local/intel/2020/compilers_and_libraries_2020.0.166/linux/mkl/" \ - --with-cc="/usr/local/sgi/mpi/mpt-2.17/bin/mpicc" \ - --with-cxx="/usr/local/sgi/mpi/mpt-2.17/bin/mpicxx" \ - --with-fc="/usr/local/sgi/mpi/mpt-2.17/bin/mpif90" \ + --with-blas-lapack-dir="/usr/local/intel/oneapi/2021/mkl/2021.4.0/" \ + --with-cc="/usr/local/intel/oneapi/2021/mpi/2021.4.0/bin/mpicc" \ + --with-cxx="/usr/local/intel/oneapi/2021/mpi/2021.4.0/bin/mpicxx" \ + --with-fc="/usr/local/intel/oneapi/2021/mpi/2021.4.0/bin/mpif90" \ --known-mpi-shared-libraries=1 \ --known-64-bit-blas-indices \ Index: /issm/trunk/externalpackages/petsc/install-3.14-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-linux-static.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.14-linux-static.sh (revision 28013) @@ -0,0 +1,58 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.14.6" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${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 ${PETSC_DIR} +./configure.py \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-shared-libraries=0 \ + --CFLAGS="-fPIC" \ + --CXXFLAGS="-fPIC" \ + --FFLAGS="-fPIC" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 + +# Compile and install +make +make install Index: sm/trunk/externalpackages/petsc/install-3.14-mac-nohdf5.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-mac-nohdf5.sh (revision 28012) +++ (revision ) @@ -1,59 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.14.6" - -PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# Download source -$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 ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${VER} - -# Configure -# -# NOTE: -# - 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). -# -cd ${PETSC_DIR} -./config/configure.py \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --CFLAGS="-Wno-error=implicit-function-declaration" \ - --FFLAGS="-fallow-argument-mismatch" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 - -# Compile and install -make -make install Index: /issm/trunk/externalpackages/petsc/install-3.14-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-mac-static.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.14-mac-static.sh (revision 28013) @@ -0,0 +1,68 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.14.6" + +PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Modify source so that Python 3 can be used to compile PETSc +sed -i'' 's|#!/usr/bin/env python|#!/usr/bin/env python3|g' ${PETSC_DIR}/config/configure.py + +# Modify source so that Python >= 3.9 can be used to compile PETSc +sed -i'' 's|thread.isAlive|thread.is_alive|g' ${PETSC_DIR}/config/BuildSystem/script.py + +# 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 +# +# - 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 -static-libgfortran to all macOS static builds, but this will not +# work out of the box on Linux. +# +cd ${PETSC_DIR} +./config/configure.py \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-shared-libraries=0 \ + --CFLAGS="-fPIC -Wno-error=implicit-function-declaration" \ + --CXXFLAGS="-fPIC" \ + --FFLAGS="-fPIC -static-libgfortran" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.14-mac-with-hdf5-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-mac-with-hdf5-static.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.14-mac-with-hdf5-static.sh (revision 28013) @@ -0,0 +1,69 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.14.6" + +PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Modify source so that Python 3 can be used to compile PETSc +sed -i'' 's|#!/usr/bin/env python|#!/usr/bin/env python3|g' ${PETSC_DIR}/config/configure.py + +# Modify source so that Python >= 3.9 can be used to compile PETSc +sed -i'' 's|thread.isAlive|thread.is_alive|g' ${PETSC_DIR}/config/BuildSystem/script.py + +# 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 +# +# - 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 -static-libgfortran to all macOS static builds, but this will not +# work out of the box on Linux. +# +cd ${PETSC_DIR} +./config/configure.py \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-shared-libraries=0 \ + --CFLAGS="-fPIC -Wno-error=implicit-function-declaration" \ + --CXXFLAGS="-fPIC" \ + --FFLAGS="-fPIC -static-libgfortran" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.14-mac-with-hdf5.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-mac-with-hdf5.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.14-mac-with-hdf5.sh (revision 28013) @@ -0,0 +1,59 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.14.6" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Modify source so that Python 3 can be used to compile PETSc +sed -i'' 's|#!/usr/bin/env python|#!/usr/bin/env python3|g' ${PETSC_DIR}/config/configure.py + +# Modify source so that Python >= 3.9 can be used to compile PETSc +sed -i'' 's|thread.isAlive|thread.is_alive|g' ${PETSC_DIR}/config/BuildSystem/script.py + +# Configure +# +# NOTE: +# - 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 ${PETSC_DIR} +./configure \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --CFLAGS="-Wno-error=implicit-function-declaration" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.14-mac.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-mac.sh (revision 28012) +++ /issm/trunk/externalpackages/petsc/install-3.14-mac.sh (revision 28013) @@ -24,4 +24,10 @@ rm -rf petsc-${VER} +# Modify source so that Python 3 can be used to compile PETSc +sed -i'' 's|#!/usr/bin/env python|#!/usr/bin/env python3|g' ${PETSC_DIR}/config/configure.py + +# Modify source so that Python >= 3.9 can be used to compile PETSc +sed -i'' 's|thread.isAlive|thread.is_alive|g' ${PETSC_DIR}/config/BuildSystem/script.py + # Configure # @@ -29,17 +35,10 @@ # - 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). # cd ${PETSC_DIR} -./config/configure.py \ +./configure \ --prefix="${PREFIX}" \ --PETSC_DIR="${PETSC_DIR}" \ --CFLAGS="-Wno-error=implicit-function-declaration" \ - --FFLAGS="-fallow-argument-mismatch" \ --with-debugging=0 \ --with-valgrind=0 \ @@ -53,6 +52,5 @@ --download-scalapack=1 \ --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 + --download-zlib=1 # Compile and install Index: /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi-static.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi-static.sh (revision 28013) @@ -0,0 +1,88 @@ +#!/bin/bash +set -u # NOTE: Do not set -e as it will cause this script to fail when there are errors in underlying Python scripts + +# NOTE: +# - You must install various needed packages with, +# +# pacman -S mingw-w64-x86_64-toolchain python +# +# - You must use MSYS2 MinGW 64-bit version of cmake to be able to install +# external packages correctly, +# +# pacman -R mingw-w64-x86_64-cmake +# +# Sources: +# - https://gitlab.com/petsc/petsc/-/issues/820#note_487483240 +# + +## Constants +# +VER="3.14.6" + +MAKEFILE_GENERATOR='-G "MSYS Makefiles"' +PETSC_ARCH="arch-mswin-c-opt" +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Patch source +sed -i -e 's|#!/usr/bin/env python|#!/usr/bin/python3|' ${PETSC_DIR}/config/configure.py +sed -i 's| chkusingwindowspython()|# chkusingwindowspython()|' ${PETSC_DIR}/config/configure.py +sed -i 's|(MAKEFLAGS)|(MAKEFLAGS:w=)|' ${PETSC_DIR}/makefile ${PETSC_DIR}/lib/petsc/conf/rules # Fix for issue with GNUMake 4.4.1 (https://gitlab.com/petsc/petsc/-/merge_requests/6140) + +# Configure +# - 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 -fallow-argument-mismatch option to FFLAGS in order to clear "Error: +# Rank mismatch between actual argument at [...]" +# - Added -fallow-invalid-boz option to FFLAGS in order to clear "Error: BOZ +# literal constant at [...]" +# - Argument to --with-mpi-include must be a list or it gets expanded +# incorrectly +# +cd ${PETSC_DIR} +./config/configure.py \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --PETSC_ARCH="${PETSC_ARCH}" \ + --CFLAGS="-fPIC -Wl,-static -Wno-error=implicit-function-declaration" \ + --CXXFLAGS="-fPIC -Wl,-static" \ + --FFLAGS="-fPIC -Wl,-static -fallow-argument-mismatch -fallow-invalid-boz" \ + --with-shared-libraries=0 \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-proc-filesystem=0 \ + --with-mpiexec="${MPIEXEC_DIR}/mpiexec.exe" \ + --with-mpi-lib="-L${MSMPI_ROOT}/lib -lmsmpi" \ + --with-mpi-include="${MSMPI_ROOT}/include" \ + --download-fblaslapack=1 \ + --download-metis=1 \ + --download-metis-cmake-arguments="${MAKEFILE_GENERATOR}" \ + --download-parmetis=1 \ + --download-parmetis-cmake-arguments="${MAKEFILE_GENERATOR}" \ + --download-scalapack=1 \ + --download-scalapack-cmake-arguments="${MAKEFILE_GENERATOR}" \ + --download-mumps=1 + +# Compile and install +make PETSC_DIR="${PETSC_DIR}" PETSC_ARCH="${PETSC_ARCH}" all +make PETSC_DIR="${PETSC_DIR}" PETSC_ARCH="${PETSC_ARCH}" install Index: /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh (revision 28012) +++ /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh (revision 28013) @@ -21,4 +21,5 @@ MAKEFILE_GENERATOR='-G "MSYS Makefiles"' +PETSC_ARCH="arch-mswin-c-opt" PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed @@ -38,6 +39,8 @@ rm -rf petsc-${VER} -# Copy customized source files to $PETSC_DIR -cp configs/3.14/win/msys2/mingw64/config/configure.py ${PETSC_DIR}/config +# Patch source +sed -i -e 's|#!/usr/bin/env python|#!/usr/bin/python3|' ${PETSC_DIR}/config/configure.py +sed -i 's| chkusingwindowspython()|# chkusingwindowspython()|' ${PETSC_DIR}/config/configure.py +sed -i 's|(MAKEFLAGS)|(MAKEFLAGS:w=)|' ${PETSC_DIR}/makefile ${PETSC_DIR}/lib/petsc/conf/rules # Fix for issue with GNUMake 4.4.1 (https://gitlab.com/petsc/petsc/-/merge_requests/6140) # Configure @@ -59,4 +62,5 @@ --prefix="${PREFIX}" \ --PETSC_DIR="${PETSC_DIR}" \ + --PETSC_ARCH="${PETSC_ARCH}" \ --CFLAGS="-fPIC -Wno-error=implicit-function-declaration" \ --CXXFLAGS="-fPIC" \ @@ -81,4 +85,4 @@ # Compile and install -make -make install +make PETSC_DIR="${PETSC_DIR}" PETSC_ARCH="${PETSC_ARCH}" all +make PETSC_DIR="${PETSC_DIR}" PETSC_ARCH="${PETSC_ARCH}" install Index: /issm/trunk/externalpackages/petsc/install-3.15-babylon.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.15-babylon.sh (revision 28012) +++ /issm/trunk/externalpackages/petsc/install-3.15-babylon.sh (revision 28013) @@ -41,6 +41,5 @@ --download-scalapack=1 \ --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 + --download-zlib=1 # Compile and install Index: /issm/trunk/externalpackages/petsc/install-3.16-linux.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.16-linux.sh (revision 28012) +++ /issm/trunk/externalpackages/petsc/install-3.16-linux.sh (revision 28013) @@ -29,10 +29,4 @@ # - 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). # cd ${PETSC_DIR} @@ -41,5 +35,4 @@ --PETSC_DIR="${PETSC_DIR}" \ --CFLAGS="-Wno-error=implicit-function-declaration" \ - --FFLAGS="-fallow-argument-mismatch" \ --with-debugging=0 \ --with-valgrind=0 \ @@ -53,6 +46,5 @@ --download-scalapack=1 \ --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 + --download-zlib=1 # Compile and install Index: /issm/trunk/externalpackages/petsc/install-3.16-mac.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.16-mac.sh (revision 28012) +++ /issm/trunk/externalpackages/petsc/install-3.16-mac.sh (revision 28013) @@ -29,10 +29,4 @@ # - 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). # cd ${PETSC_DIR} @@ -41,5 +35,4 @@ --PETSC_DIR="${PETSC_DIR}" \ --CFLAGS="-Wno-error=implicit-function-declaration" \ - --FFLAGS="-fallow-argument-mismatch" \ --with-debugging=0 \ --with-valgrind=0 \ @@ -53,6 +46,5 @@ --download-scalapack=1 \ --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 + --download-zlib=1 # Compile and install Index: /issm/trunk/externalpackages/petsc/install-3.17-discovery.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.17-discovery.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.17-discovery.sh (revision 28013) @@ -0,0 +1,50 @@ +#!/bin/bash +set -eu + +## Constants +# +VER="3.17.4" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# 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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Configure +cd ${PETSC_DIR} +./config/configure.py \ + COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-make-np=20 \ + --with-blas-lapack-dir=$MKL_ROOT \ + --with-mpi-dir="/optnfs/el7/mpich/3.3-intel19.3/" \ + --known-mpi-shared-libraries=1 \ + --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-pic=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-3.17-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.17-linux-static.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.17-linux-static.sh (revision 28013) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.17.4" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# 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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${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 ${PETSC_DIR} +./configure \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-shared-libraries=0 \ + --CFLAGS="-fPIC" \ + --CXXFLAGS="-fPIC" \ + --FFLAGS="-fPIC" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.17-linux.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.17-linux.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.17-linux.sh (revision 28013) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + +## Constants +VER="3.17.4" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Configure +cd ${PETSC_DIR} +./configure \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --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 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.17-mac-intel.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.17-mac-intel.sh (revision 28012) +++ /issm/trunk/externalpackages/petsc/install-3.17-mac-intel.sh (revision 28013) @@ -25,8 +25,14 @@ # Configure +# +# NOTE: +# - 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 ${PETSC_DIR} ./configure \ --prefix="${PREFIX}" \ --PETSC_DIR="${PETSC_DIR}" \ + --CFLAGS="-Wno-error=implicit-function-declaration" \ --with-debugging=0 \ --with-valgrind=0 \ @@ -40,6 +46,5 @@ --download-scalapack=1 \ --download-mumps=1 \ - --download-zlib=1 \ - --download-hdf5=1 + --download-zlib=1 # Compile and install Index: sm/trunk/externalpackages/petsc/install-3.17-mac-m1-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.17-mac-m1-static.sh (revision 28012) +++ (revision ) @@ -1,64 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.17.4" - -PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# Download source -$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 ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${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 -# -# - 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). -cd ${PETSC_DIR} -./configure \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --LDFLAGS="-Wl,-no_compact_unwind" \ - --with-shared-libraries=0 \ - --CFLAGS="-fPIC" \ - --CXXFLAGS="-fPIC" \ - --FFLAGS="-fPIC" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 - -# Compile and install -make -make install Index: sm/trunk/externalpackages/petsc/install-3.17-mac-m1.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.17-mac-m1.sh (revision 28012) +++ (revision ) @@ -1,47 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.17.4" - -PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS -PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed - -# Download source -$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 ${PREFIX} ${PETSC_DIR} -mkdir -p ${PETSC_DIR} - -# Move source to $PETSC_DIR -mv petsc-${VER}/* ${PETSC_DIR} -rm -rf petsc-${VER} - -# Configure -cd ${PETSC_DIR} -./configure \ - --prefix="${PREFIX}" \ - --PETSC_DIR="${PETSC_DIR}" \ - --LDFLAGS="-Wl,-no_compact_unwind" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 - -# Compile and install -make -make install Index: /issm/trunk/externalpackages/petsc/install-3.17-mac-silicon-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.17-mac-silicon-static.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.17-mac-silicon-static.sh (revision 28013) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.17.4" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${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 ${PETSC_DIR} +./configure \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-shared-libraries=0 \ + --CFLAGS="-fPIC" \ + --CXXFLAGS="-fPIC" \ + --FFLAGS="-fPIC" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.17-mac-silicon.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.17-mac-silicon.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.17-mac-silicon.sh (revision 28013) @@ -0,0 +1,46 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.17.4" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$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 ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Configure +cd ${PETSC_DIR} +./configure \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.19-discovery.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.19-discovery.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.19-discovery.sh (revision 28013) @@ -0,0 +1,50 @@ +#!/bin/bash +set -eu + +## Constants +# +VER="3.19.1" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Configure +cd ${PETSC_DIR} +./config/configure.py \ + COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-make-np=20 \ + --with-blas-lapack-dir=$MKL_ROOT \ + --with-mpi-dir="/optnfs/el7/mpich/3.3-intel19.3/" \ + --known-mpi-shared-libraries=1 \ + --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-pic=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-3.19-mac-intel.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.19-mac-intel.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.19-mac-intel.sh (revision 28013) @@ -0,0 +1,54 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.19.5" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Configure +# +# NOTE: +# - 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 ${PETSC_DIR} +./configure \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --CFLAGS="-Wno-error=implicit-function-declaration" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-cmake=1 \ + --download-zlib=1 + +# Compile and install +make +make install + Index: /issm/trunk/externalpackages/petsc/install-3.20-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.20-pleiades.sh (revision 28013) +++ /issm/trunk/externalpackages/petsc/install-3.20-pleiades.sh (revision 28013) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.20.1" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir -p ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Configure +# +# NOTE: +# - Options from, +# +# cat /nasa/petsc/3.14.5_toss3/lib/petsc/conf/petscvariables | grep CONF +# +cd ${PETSC_DIR} +./configure \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --CFLAGS="-g -O3" \ + --CXXFLAGS="-g -O3" \ + --FFLAGS="-g -O3" \ + --with-make-np=10 \ + --with-batch=1 \ + --with-pic=1 \ + --with-shared-libraries=1 \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --download-fblaslapack=1 \ + --download-scalapack=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-mumps=1 + +# Compile and install +make +make install Index: sm/trunk/externalpackages/petsc/install-3.6-win10.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-win10.sh (revision 28012) +++ (revision ) @@ -1,41 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install petsc-3.6.2 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.2.tar.gz' 'petsc-3.6.2.tar.gz' - -#Untar and move petsc to install directory -tar -zxvf petsc-3.6.2.tar.gz -mv petsc-3.6.2/* src/ -rm -rf petsc-3.6.2 - -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-3.7-discover.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-discover.sh (revision 28012) +++ (revision ) @@ -1,62 +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="$ISSM_DIR/externalpackages/petsc/src" \ - --with-blas-lapack-dir="/usr/local/intel/2020/compilers_and_libraries_2020.0.166/linux/mkl/" \ - --with-mpi-lib="/usr/local/sgi/mpi/mpt-2.17/lib/libmpi.so" \ - --with-mpi-include="/usr/local/sgi/mpi/mpt-2.17/include/" \ - --known-mpi-shared-libraries=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-batch=1 \ - --with-shared-libraries=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-mumps=1 \ - --download-scalapack=1 - -#prepare script to reconfigure petsc -cat > script.queue << EOF -#!/bin/bash -#SBATCH -J petscinstall # Job Name -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH -A s1690 -#SBATCH -t 00:01:00 # Run time (hh:mm:ss) - 1.5 hours -#SBATCH --qos=debug -#SBATCH -o petscinstall.outlog -#SBATCH -e petscinstall.errlog - -. /usr/share/modules/init/bash -module purge -module load comp/intel/20.0.0.166 -module load mpi/sgi-mpt/2.17 -module load cmake/3.17.0 - -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -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-dev-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-dev-linux64.sh (revision 28012) +++ (revision ) @@ -1,49 +1,0 @@ -#!/bin/bash - -STEP=2 - -if [ $STEP -eq 1 ]; then - rm -rf src - git clone https://bitbucket.org/petsc/petsc src -fi - -# To update -# cd src -# git pull - -# configure script -# Note: -# SuperLU: -If download-..-=yes does not work try downloading from -# --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ - - -if [ $STEP -eq 2 ]; then - rm -rf install - cd src - ./configure \ - --prefix="$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 - -# --download-trilinos=yes \ -# --download-euclid=yes \ -# --download-spooles=yes \ -# --download-spai=yes \ -# --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ -# --download-hypre=yes \ - - #Compile petsc and install it - make - make install -fi Index: sm/trunk/externalpackages/petsc/install-dev-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh (revision 28012) +++ (revision ) @@ -1,78 +1,0 @@ -#!/bin/bash -#Step 0: download -#Step 1: install and write script -STEP=1 - -if [ $STEP -eq 0 ]; then - # Adapted from petsc 3.2. - # Used Mercurial to get code - rm -rf src - hg clone http://petsc.cs.iit.edu/petsc/petsc-dev src - cd src - hg clone http://petsc.cs.iit.edu/petsc/BuildSystem config/BuildSystem -fi - -# To update (via Mercurial): -# cd petsc-dev -# hg pull -u -# cd config/BuildSystem -# hg pull -u - -# configure script -# Note: using metis from externalpackages did not work... -# for now downloading new metis -# -then rename metis in externalpackages to metis2 -# -# --download-prometheus=yes \ -#--download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ -# --download-plapack=yes \ - -if [ $STEP -eq 1 ]; then - - #configure - cd src - ./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-batch=1 \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-shared-libraries=1 \ - --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ - --known-mpi-shared-libraries=1 \ - --with-mpi=1 \ - --download-mumps=yes \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-blas=yes \ - --download-f-blas-lapack=yes \ - --download-parmetis=yes \ - --download-metis=yes \ - --download-trilinos=yes \ - --download-euclid=yes \ - --download-spai=yes \ - --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ - --download-hypre=yes \ - --with-cxx=/nasa/sgi/mpt/2.06a67/bin/mpicxx \ - --with-fc=/nasa/sgi/mpt/2.06a67/bin/mpif90 \ - --COPTFLAGS="-lmpi -O3" \ - --FOPTFLAGS="-lmpi -O3" \ - --CXXOPTFLAGS="-lmpi -O3" - 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.2.06a67 -module load math/intel_mkl_64_10.0.011 -export PATH="$PATH:." -export MPI_GROUP_MAX=64 -mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py -EOF - echo "== Now: cd src/ " - echo "== qsub -q devel script.queue " - echo "== Then run reconfigure script generated by PETSc and follow instructions" -fi Index: sm/trunk/externalpackages/petsc/install-dev-win10-par.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-dev-win10-par.sh (revision 28012) +++ (revision ) @@ -1,35 +1,0 @@ -#!/bin/bash - -STEP=1 - -rm -rf src - -if [ $STEP -eq 1 ]; then - git clone -b maint https://bitbucket.org/petsc/petsc src -fi - -export PETSC_DIR=`cygpath -u "$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/Programs/MPICH2/"\ - --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-dev-win10.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-dev-win10.sh (revision 28012) +++ (revision ) @@ -1,34 +1,0 @@ -#!/bin/bash - -STEP=1 - -if [ $STEP -eq 1 ]; then - git clone -b maint https://bitbucket.org/petsc/petsc src -fi - -export PETSC_DIR=`cygpath -u "$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: /issm/trunk/externalpackages/semic/install.sh =================================================================== --- /issm/trunk/externalpackages/semic/install.sh (revision 28012) +++ /issm/trunk/externalpackages/semic/install.sh (revision 28013) @@ -16,10 +16,9 @@ if which ifort >/dev/null; then FC="ifort" - FFLAGS="-traceback -check all" #-O2 is default + FFLAGS="-traceback -check all" # -O2 is default else FC="gfortran" if [ `uname` == "Darwin" ]; then - FC="gfortran -arch x86_64" - FFLAGS="-fcheck=all" + FFLAGS="-fcheck=all -arch $(uname -m)" else FFLAGS="" Index: /issm/trunk/externalpackages/sqlite/install-static.sh =================================================================== --- /issm/trunk/externalpackages/sqlite/install-static.sh (revision 28013) +++ /issm/trunk/externalpackages/sqlite/install-static.sh (revision 28013) @@ -0,0 +1,43 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="3300100" + +PREFIX="${ISSM_DIR}/externalpackages/sqlite/install" # Set to location where external package should be installed + +# Environment +# +export CFLAGS="-DSQLITE_ENABLE_COLUMN_METADATA=1" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/sqlite-autoconf-${VER}.tar.gz" "sqlite-autoconf-${VER}.tar.gz" + +# Unpack source +tar -zxvf sqlite-autoconf-${VER}.tar.gz + +# Move source into 'src' directory +mv sqlite-autoconf-${VER}/* src +rm -rf sqlite-autoconf-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --enable-shared=no + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/sqlite/install.sh =================================================================== --- /issm/trunk/externalpackages/sqlite/install.sh (revision 28012) +++ /issm/trunk/externalpackages/sqlite/install.sh (revision 28013) @@ -30,5 +30,7 @@ cd src ./configure \ - --prefix="${PREFIX}" + --prefix="${PREFIX}" \ + --enable-fast-install \ + --enable-static=no # Compile and install Index: /issm/trunk/externalpackages/triangle/install-win-msys2-mingw-static.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-win-msys2-mingw-static.sh (revision 28013) +++ /issm/trunk/externalpackages/triangle/install-win-msys2-mingw-static.sh (revision 28013) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + + +# Constants +# +export PREFIX="${ISSM_DIR}/externalpackages/triangle/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/triangle.zip" "triangle.zip" + +# Unpack source +unzip triangle.zip -d src + +# Copy customized source files to 'src' directory +cp configs/makefile src +cp configs/triangle.h src +cp configs/win/msys2/mingw64/configure.make src + +# Compile +cd src +make static + +# Install +cd .. +cp src/libtriangle.* ${PREFIX}/lib +cp src/triangle.h ${PREFIX}/include + +# Cleanup +rm -rf src Index: /issm/trunk/externalpackages/valgrind/install-linux.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-linux.sh (revision 28012) +++ /issm/trunk/externalpackages/valgrind/install-linux.sh (revision 28013) @@ -3,15 +3,20 @@ +## Constants +# +PREFIX="${ISSM_DIR}/externalpackages/valgrind/install" # Set to location where external package should be installed + # Clean up -rm -rf install +rm -rf ${PREFIX} src -# Download development version -git clone git://sourceware.org/git/valgrind.git install +# Download development version (the current release never supports the latest +# OS X releases) +git clone git://sourceware.org/git/valgrind.git src # Configure -cd install +cd src ./autogen.sh ./configure \ - --prefix="$ISSM_DIR/externalpackages/valgrind/install" \ + --prefix="${PREFIX}" \ --enable-only64bit Index: /issm/trunk/externalpackages/valgrind/install-mac.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-mac.sh (revision 28012) +++ /issm/trunk/externalpackages/valgrind/install-mac.sh (revision 28013) @@ -8,12 +8,12 @@ # Clean up -rm -rf ${PREFIX} +rm -rf ${PREFIX} src # Download development version (the current release never supports the latest # OS X releases) -git clone git://sourceware.org/git/valgrind.git ${PREFIX} +git clone git://sourceware.org/git/valgrind.git src # Configure -cd install +cd src ./autogen.sh ./configure \ Index: /issm/trunk/externalpackages/vim/addons/vimrc =================================================================== --- /issm/trunk/externalpackages/vim/addons/vimrc (revision 28012) +++ /issm/trunk/externalpackages/vim/addons/vimrc (revision 28013) @@ -208,4 +208,5 @@ au BufRead,BufNewFile *.html iabbr CO =Eatchar('\s') au BufRead,BufNewFile *.html iabbr PP

=Eatchar('\s') +au BufRead,BufNewFile *.jl iabbr p1 println("")=Eatchar('\s') au BufRead,BufNewFile *.m iabbr p1 disp('');=Eatchar('\s') au BufRead,BufNewFile *.m iab p0 "disp('-------------- file: ".expand('%')." line: ".line(".")."');" @@ -217,4 +218,5 @@ au BufRead,BufNewFile *.c* ab VV VecView(ug,PETSC_VIEWER_STDOUT_WORLD); au BufRead,BufNewFile *.c*,*.h ab AS _assert_();=Eatchar('\s') +au BufRead,BufNewFile *jl iab p0 "print(\"-------------- file: ".expand('%')." line: $(@__LINE__)\\n\")" au BufRead,BufNewFile *.c*,*.h iab p0 "printf(\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);" au BufRead,BufNewFile *.c*,*.h iab pp0 "PetscSynchronizedPrintf(MPI_COMM_WORLD,\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);\nPetscSynchronizedFlush(MPI_COMM_WORLD);" Index: /issm/trunk/jenkins/aws-amazon_linux-solid_earth =================================================================== --- /issm/trunk/jenkins/aws-amazon_linux-solid_earth (revision 28012) +++ /issm/trunk/jenkins/aws-amazon_linux-solid_earth (revision 28013) @@ -1,7 +1,8 @@ +MATLAB_PATH="/usr/local/MATLAB/R2020a" + #--------------------# # ISSM Configuration # #--------------------# -MATLAB_PATH="/usr/local/MATLAB/R2020a" ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -34,7 +35,7 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.14-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/eis-daskhub-python-modules =================================================================== --- /issm/trunk/jenkins/eis-daskhub-python-modules (revision 28013) +++ /issm/trunk/jenkins/eis-daskhub-python-modules (revision 28013) @@ -0,0 +1,83 @@ +# NOTE: This configuration adds solid earth and Dakota capabilities to the +# basic build. + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix="${ISSM_DIR}" \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-python-dir="/srv/conda/envs/notebook" \ + --with-python-version="3.9" \ + --with-python-numpy-dir="/srv/conda/envs/notebook/lib/python3.9/site-packages/numpy/core/include/numpy" \ + --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ + --with-mpi-include="${ISSM_EXT_DIR}/petsc/install/include" \ + --with-mpi-libflags="-L${ISSM_EXT_DIR}/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir="${ISSM_EXT_DIR}/petsc/install" \ + --with-metis-dir="${ISSM_EXT_DIR}/petsc/install" \ + --with-parmetis-dir="${ISSM_EXT_DIR}/petsc/install" \ + --with-scalapack-dir="${ISSM_EXT_DIR}/petsc/install" \ + --with-mumps-dir="${ISSM_EXT_DIR}/petsc/install" \ + --with-hdf5-dir="${ISSM_EXT_DIR}/petsc/install" \ + --with-petsc-dir="${ISSM_EXT_DIR}/petsc/install" \ + --with-gsl-dir="${ISSM_EXT_DIR}/gsl/install" \ + --with-boost-dir="${ISSM_EXT_DIR}/boost/install" \ + --with-dakota-dir="${ISSM_EXT_DIR}/dakota/install" \ + --with-proj-dir="${ISSM_EXT_DIR}/proj/install" \ + --with-triangle-dir="${ISSM_EXT_DIR}/triangle/install" \ + --with-chaco-dir="${ISSM_EXT_DIR}/chaco/install" \ + --with-m1qn3-dir="${ISSM_EXT_DIR}/m1qn3/install" \ + --with-semic-dir="${ISSM_EXT_DIR}/semic/install" \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-linux.sh + cmake install.sh + petsc install-3.16-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.sh + gdal install-3-python.sh + gshhg install.sh + gmt install-6-linux.sh + gmsh install-4-linux.sh + triangle install-linux.sh + chaco install-linux.sh + m1qn3 install.sh + semic 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: sm/trunk/jenkins/eis-daskhub-python-nodules =================================================================== --- /issm/trunk/jenkins/eis-daskhub-python-nodules (revision 28012) +++ (revision ) @@ -1,83 +1,0 @@ -# NOTE: This configuration adds solid earth and Dakota capabilities to the -# basic build. - -#--------------------# -# ISSM Configuration # -#--------------------# - -ISSM_CONFIG='\ - --prefix="${ISSM_DIR}" \ - --disable-static \ - --enable-development \ - --enable-debugging \ - --with-numthreads=4 \ - --with-python-dir="/srv/conda/envs/notebook" \ - --with-python-version="3.9" \ - --with-python-numpy-dir="/srv/conda/envs/notebook/lib/python3.9/site-packages/numpy/core/include/numpy" \ - --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ - --with-mpi-include="${ISSM_EXT_DIR}/petsc/install/include" \ - --with-mpi-libflags="-L${ISSM_EXT_DIR}/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir="${ISSM_EXT_DIR}/petsc/install" \ - --with-metis-dir="${ISSM_EXT_DIR}/petsc/install" \ - --with-parmetis-dir="${ISSM_EXT_DIR}/petsc/install" \ - --with-scalapack-dir="${ISSM_EXT_DIR}/petsc/install" \ - --with-mumps-dir="${ISSM_EXT_DIR}/petsc/install" \ - --with-hdf5-dir="${ISSM_EXT_DIR}/petsc/install" \ - --with-petsc-dir="${ISSM_EXT_DIR}/petsc/install" \ - --with-gsl-dir="${ISSM_EXT_DIR}/gsl/install" \ - --with-boost-dir="${ISSM_EXT_DIR}/boost/install" \ - --with-dakota-dir="${ISSM_EXT_DIR}/dakota/install" \ - --with-proj-dir="${ISSM_EXT_DIR}/proj/install" \ - --with-triangle-dir="${ISSM_EXT_DIR}/triangle/install" \ - --with-chaco-dir="${ISSM_EXT_DIR}/chaco/install" \ - --with-m1qn3-dir="${ISSM_EXT_DIR}/m1qn3/install" \ - --with-semic-dir="${ISSM_EXT_DIR}/semic/install" \ -' - -#-------------------# -# External Packages # -#-------------------# - -EXTERNALPACKAGES=" - autotools install-linux.sh - cmake install.sh - petsc install-3.16-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.sh - gdal install-3-python.sh - gshhg install.sh - gmt install-6-linux.sh - gmsh install-4-linux.sh - triangle install-linux.sh - chaco install.sh - m1qn3 install.sh - semic 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/eis-smce-binaries =================================================================== --- /issm/trunk/jenkins/eis-smce-binaries (revision 28012) +++ /issm/trunk/jenkins/eis-smce-binaries (revision 28013) @@ -40,5 +40,5 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.14-linux.sh gsl install.sh boost install-1.7-linux.sh @@ -53,5 +53,5 @@ gmsh install-4.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/examples_tests.sh =================================================================== --- /issm/trunk/jenkins/examples_tests.sh (revision 28012) +++ /issm/trunk/jenkins/examples_tests.sh (revision 28013) @@ -6,5 +6,5 @@ # called from jenkins/jenkins.sh. # -# runme files are modifed as needed to fill in statements that would otherwise +# runme files are modified as needed to fill in statements that would otherwise # be added by user. # Index: /issm/trunk/jenkins/jenkins.sh =================================================================== --- /issm/trunk/jenkins/jenkins.sh (revision 28012) +++ /issm/trunk/jenkins/jenkins.sh (revision 28013) @@ -28,6 +28,6 @@ SERVER='https://ross.ics.uci.edu/jenkins' -#Get configuration -#Source config file{{{ +# Get configuration +# Source config file {{{ if [ $# -ne 1 ]; then #no config file specified: exit @@ -46,12 +46,11 @@ EXAMPLES_TEST=0 -# Initialize resource variables (to avoid "i<=: syntax error: operand expected" -# in for loops) +# Initialize resource variables (to avoid "i<=: syntax error: operand expected" in for loops) NUMCPUS_INSTALL=1 NUMCPUS_RUN=1 -#source configuration script +# Source configuration script source $1; -#}}} +# }}} if [[ $EXAMPLES_TEST -eq 1 && $MATLAB_TEST+$PYTHON_TEST+$JAVASCRIPT_TEST -ne 0 ]]; then @@ -60,6 +59,6 @@ fi -#Install ISSM -#Determining installation type depending on svn changes{{{ +# Install ISSM +# Determining installation type depending on svn changes {{{ echo "======================================================"; echo " Determining Installation type " @@ -92,7 +91,6 @@ echo " " - ################################### - ### Determine installation type ### - ################################### + ## Determine installation type + # echo "Determining installation type" @@ -107,5 +105,5 @@ fi - # If the Makefile or m4 diirectory were changed in any way or if certain + # If the Makefile or m4 directory were changed in any way or if certain # binary files from a previous compilation do not exist, reconfigure if [ ! -z "$(cat ${ISSM_DIR}/TEMP | grep -e "Makefile.am" -e "m4" )" ] || @@ -145,5 +143,5 @@ echo "Recording current svn version: $SVN_REVISION_1" echo $SVN_REVISION_1 > ${ISSM_DIR}/svn_revision_old -#}}} +# }}} ## External Packages @@ -153,16 +151,11 @@ NUMPACKAGES=$(($(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 echo "" > $EXTERNAL_TEST_FILE -# Need a source here for when builds start midway through installation of externalpackages. +# Need a source here for when builds start midway through installation of externalpackages source ${ISSM_DIR}/etc/environment.sh - -if [ "${OS}" == CYGWIN* ]; then - echo " == WINDOWS ENVIRONMENT DETECTED ==" - source ${ISSM_DIR}/externalpackages/windows/windows_environment.sh -fi EXTERNALPACKAGES_FAILED=0; @@ -174,5 +167,5 @@ PACKAGEINST=$(echo $EXTERNALPACKAGES | cut -d " " -f $NUM2-$NUM2) - #install if requested or if previous install has not been successful + # Install if requested or if previous install has not been successful if [ "${ISSM_EXTERNALPACKAGES}" == "yes" ]; then # NOTE: Removed check on if 'install' directory exist cd ${ISSM_DIR}/externalpackages/$PACKAGENAME @@ -199,5 +192,6 @@ echo '' >> $EXTERNAL_TEST_FILE echo '' >> $EXTERNAL_TEST_FILE - EXTERNALPACKAGES_FAILED=1; + echo '' >> $EXTERNAL_TEST_FILE + exit 1; else echo "" >> $EXTERNAL_TEST_FILE @@ -224,11 +218,4 @@ echo '' >> $EXTERNAL_TEST_FILE -if [ $EXTERNALPACKAGES_FAILED -eq 1 ]; then - echo "==================================================================================================="; - echo " ERROR: One or more of the externalpackages has failed. Skipping everything remaining steps. "; - echo "==================================================================================================="; - exit 1; -fi - # Source here to include any newly-installed external packages on the path source ${ISSM_DIR}/etc/environment.sh @@ -246,5 +233,5 @@ # independent from running JavaScript tests (one should be able to do the # former without having to do the latter). -# - Revisit enviroment variables (especially EMCC_CFLAGS) once support for +# - Revisit environment variables (especially EMCC_CFLAGS) once support for # Fortran has been accomplished. # @@ -261,6 +248,6 @@ fi -#}}} -#ISSM compilation yes/no (ISSM_COMPILATION) {{{ +# }}} +# ISSM compilation yes/no (ISSM_COMPILATION) {{{ if [ "${ISSM_COMPILATION}" == "yes" ]; then cd $ISSM_DIR @@ -285,10 +272,10 @@ fi - #4: compile and install ISSM + # Compile and install ISSM echo "======================================================" echo " Compiling ISSM " echo "======================================================" if [ $NUMCPUS_INSTALL -gt 1 ]; then - echo "Making with ${NUMCPUS_INSTALL} cpus" + echo "Making with ${NUMCPUS_INSTALL} CPUs" # To debug compilation/linking, add 'V=1' option to the call to make @@ -313,15 +300,14 @@ echo "Skipping ISSM compilation" else - echo "ISSM_COMPILATION supported values are: yes and no. Exiting..." >&2 # Error message to stderr. + echo "ISSM_COMPILATION supported values are: yes and no. Exiting..." >&2 # Redirect error messages to stderr exit 1 fi -#}}} - -#Restore CXX/CC to their previous values +# }}} + +# Restore CC/CXX to their previous values +export CC=$CC_PREVIOUS export CXX=$CXX_PREVIOUS -export CC=$CC_PREVIOUS - -#matlab tests -# {{{ + +# MATLAB tests {{{ if [ $MATLAB_TEST -eq 1 ]; then MINGW=0 @@ -333,7 +319,7 @@ fi - #Launch all tests on different cpus + # Launch all tests on different CPUs for (( i=1;i<=$NUMCPUS_RUN;i++ )); do - #Launch matlab and the nightly run script + # Launch MATLAB and the nightly run script cat > ${ISSM_DIR}/nightlylog/matlab_run$i.m << EOF warning off %necessary to avoid a log of several Go for parallel runs @@ -358,6 +344,6 @@ cd $ISSM_DIR/test/NightlyRun - # NOTE: We redirect all output to logfile in order to catch certain errors. For some reason, this does not work under Windows: the logifle option must be used and process must be run in background - if [[ "${OS}" == CYGWIN* || ${MINGW} -eq 1 ]]; then + # NOTE: We redirect all output to logfile in order to catch certain errors. For some reason, this does not work under Windows: the logfile option must be used and process must be run in background + if [[ ${MINGW} -eq 1 ]]; then $MATLAB_PATH/bin/matlab -nodesktop -nosplash -nojvm -r "addpath ${ISSM_DIR_WIN}/src/m/dev; devpath; addpath ${ISSM_DIR_WIN}/nightlylog; matlab_run$i" -logfile ${ISSM_DIR_WIN}/nightlylog/matlab_log$i.log & else @@ -371,18 +357,5 @@ # - Replace by adding -wait option to above calls to matlab? # - if [[ "${OS}" == CYGWIN* ]]; then - sleep 5; - echo "Waiting for MATLAB to exit" - pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}') - echo '-----------------------------' - echo "pid: ${pid}" - echo '-----------------------------' - while [ -n "${pid}" ]; do - pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}') - sleep 1; - done - echo "DONE!" - elif [[ ${MINGW} -eq 1 ]]; then - # NOTE: The PID query used here may work as well on Cygwin. If so, combine the two conditional blocks. + if [[ ${MINGW} -eq 1 ]]; then sleep 5; echo "Waiting for MATLAB to exit" @@ -429,18 +402,18 @@ done - #filter out windows characters: + # Filter out Windows characters cat matlab_log.log | tr -cd '\11\12\40-\176' > matlab_log.log2 && mv matlab_log.log2 matlab_log.log fi # }}} -# Python tests +# Python tests # {{{ # # TODO: Figure out why "Running Python test for Rank $i" is printed twice for each CPU -# {{{ +# if [ $PYTHON_TEST -eq 1 ]; then - #Launch all tests on different cpus + # Launch all tests on different CPUs export PYTHONPATH="${ISSM_DIR}/src/m/dev" export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" - export PYTHONUNBUFFERED=1 #we don't want python to buffer otherwise issm.exe output is not captured + export PYTHONUNBUFFERED=1 # We don't want Python to buffer otherwise issm.exe output is not captured for (( i=1;i<=$NUMCPUS_RUN;i++ )) do @@ -474,14 +447,18 @@ rm -f $ISSM_DIR/execution/*/ADOLC-* -# Examples Tests -# {{{ +# Examples Tests # {{{ if [ $EXAMPLES_TEST -eq 1 ]; then export MATLAB_PATH + + # Download examples datasets if they are not already present + if [[ -z $(ls -A1q $ISSM_DIR/examples/Data) ]]; then + $ISSM_DIR/scripts/DownloadExamplesDatasets.sh + fi + $ISSM_DIR/jenkins/examples_tests.sh fi # }}} -# Process logs to be JUnit compatible -#{{{ +# Process logs to be JUnit compatible # {{{ cd $ISSM_DIR/nightlylog source $ISSM_EXT_DIR/shell2junit/install/bin/sh2ju.sh @@ -489,5 +466,5 @@ if [ $MATLAB_TEST -eq 1 ]; then - #number tests: + # Number tests numtests=`cat matlab_log.log | grep "\-\-\-\-\-\-\-\-starting" | wc -l` testlist=`cat matlab_log.log | grep "\-\-\-\-\-\-\-\-starting" | sed 's/----------------starting://g' | sed 's/-//g'` @@ -500,5 +477,5 @@ # Check that MATLAB did not exit in error - matlabExitedInError=`grep -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword" matlab_log.log | wc -l` + matlabExitedInError=`grep -E "Activation cannot proceed|Error in|Illegal|Invalid MEX-file|license|Warning: Name is nonexistent or not a directory" matlab_log.log | wc -l` if [ $matlabExitedInError -ne 0 ]; then @@ -515,5 +492,5 @@ if [ $PYTHON_TEST -eq 1 ]; then - #number tests: + # Number tests numtests=`cat python_log.log | grep "\-\-\-\-\-\-\-\-starting" | wc -l` testlist=`cat python_log.log | grep "\-\-\-\-\-\-\-\-starting" | sed 's/----------------starting://g' | sed 's/-//g'` @@ -526,5 +503,5 @@ # Check that Python did not exit in error - pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python_log.log | wc -l` + pythonExitedInError=`grep -c -E "Error|No such file or directory|Permission denied|Standard exception|Traceback|bad interpreter|syntax error" python_log.log` if [ $pythonExitedInError -ne 0 ]; then @@ -553,5 +530,5 @@ # Check that MATLAB did not exit in error - matlabExitedInError=`grep -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword" matlab_log_examples.log | wc -l` + matlabExitedInError=`grep -E "Activation cannot proceed|Error in|Illegal|Invalid MEX-file|license|Warning: Name is nonexistent or not a directory" matlab_log_examples.log | wc -l` if [ $matlabExitedInError -ne 0 ]; then @@ -569,3 +546,3 @@ # Clean up execution directory rm -rf $ISSM_DIR/execution/* -#}}} +# }}} Index: /issm/trunk/jenkins/linux64_caladan =================================================================== --- /issm/trunk/jenkins/linux64_caladan (revision 28012) +++ /issm/trunk/jenkins/linux64_caladan (revision 28013) @@ -39,5 +39,5 @@ #-----------------------------------# -#List of external pakages to be installed and their installation scripts +#List of external packages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh cmake install.sh @@ -47,5 +47,5 @@ boost install-1.7-linux.sh dakota install-6.2-linux64.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh shell2junit install.sh" Index: /issm/trunk/jenkins/linux64_caladan_ad =================================================================== --- /issm/trunk/jenkins/linux64_caladan_ad (revision 28012) +++ /issm/trunk/jenkins/linux64_caladan_ad (revision 28013) @@ -29,5 +29,5 @@ #-----------------------------------# -#List of external pakages to be installed and their installation scripts +#List of external packages to be installed and their installation scripts EXTERNALPACKAGES=" autotools install-linux.sh Index: /issm/trunk/jenkins/linux64_caladan_ampi =================================================================== --- /issm/trunk/jenkins/linux64_caladan_ampi (revision 28012) +++ /issm/trunk/jenkins/linux64_caladan_ampi (revision 28013) @@ -39,5 +39,5 @@ #-----------------------------------# -#List of external pakages to be installed and their installation scripts +#List of external packages to be installed and their installation scripts EXTERNALPACKAGES=" autotools install-linux.sh Index: /issm/trunk/jenkins/mac-intel-basic =================================================================== --- /issm/trunk/jenkins/mac-intel-basic (revision 28013) +++ /issm/trunk/jenkins/mac-intel-basic (revision 28013) @@ -0,0 +1,70 @@ +MATLAB_PATH="/Applications/MATLAB_R2022b.app" + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/13.1.0/lib/gcc/13 -lgfortran" \ + --with-mpi-include=${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=${ISSM_DIR}/externalpackages/petsc/install \ + --with-parmetis-dir=${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=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +# List of external packages to be installed and their installation scripts +EXTERNALPACKAGES=" + autotools install-mac.sh + cmake install.sh + petsc install-3.14-mac.sh + triangle install-mac.sh + chaco install-mac.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=1 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=4 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=2 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information +# +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/mac-intel-binaries-matlab =================================================================== --- /issm/trunk/jenkins/mac-intel-binaries-matlab (revision 28013) +++ /issm/trunk/jenkins/mac-intel-binaries-matlab (revision 28013) @@ -0,0 +1,93 @@ +MATLAB_PATH="/Applications/MATLAB_R2022b.app" + +#--------------------# +# ISSM Configuration # +#--------------------# + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# +# TODO: +# - Add static copy of libsqlite and make sure it is found during GMT configuration +# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-fortran-lib="/usr/local/Cellar/gcc/13.1.0/lib/gcc/13/libgfortran.a /usr/local/Cellar/gcc/13.1.0/lib/gcc/13/libquadmath.a /usr/local/Cellar/gcc/13.1.0/lib/gcc/13/gcc/x86_64-apple-darwin21/13/libgcc.a" \ + --with-mpi-include=${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=${ISSM_DIR}/externalpackages/petsc/install \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-proj-dir=${ISSM_DIR}/externalpackages/proj/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-mac.sh + cmake install.sh + petsc install-3.14-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 + hdf5 install-1-parallel-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6-static.sh + gdal install-3-static.sh + gshhg install.sh + gmt install-6-mac-static.sh + gmsh install-4-mac-static.sh + triangle install-mac-static.sh + chaco install-mac.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/mac-intel-binaries-python-3 =================================================================== --- /issm/trunk/jenkins/mac-intel-binaries-python-3 (revision 28013) +++ /issm/trunk/jenkins/mac-intel-binaries-python-3 (revision 28013) @@ -0,0 +1,93 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# +# TODO: +# - Add static copy of libsqlite and make sure it is found during GMT configuration +# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-python-version=3.9 \ + --with-python-dir=/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \ + --with-python-numpy-dir=/Library/Python/3.9/site-packages/numpy/core/include/numpy \ + --with-fortran-lib="/usr/local/Cellar/gcc/13.1.0/lib/gcc/13/libgfortran.a /usr/local/Cellar/gcc/13.1.0/lib/gcc/13/libquadmath.a /usr/local/Cellar/gcc/13.1.0/lib/gcc/13/gcc/x86_64-apple-darwin21/13/libgcc.a" \ + --with-mpi-include=${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=${ISSM_DIR}/externalpackages/petsc/install \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-proj-dir=${ISSM_DIR}/externalpackages/proj/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-mac.sh + cmake install.sh + petsc install-3.14-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 + hdf5 install-1-parallel-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6-static.sh + gdal install-3-python-static.sh + gshhg install.sh + gmt install-6-mac-static.sh + gmsh install-4-mac-static.sh + triangle install-mac-static.sh + chaco install-mac.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: /issm/trunk/jenkins/mac-intel-dakota =================================================================== --- /issm/trunk/jenkins/mac-intel-dakota (revision 28013) +++ /issm/trunk/jenkins/mac-intel-dakota (revision 28013) @@ -0,0 +1,102 @@ +# TODO: +# - Change PROJ installation script to latest version once Jenkins macOS build +# node has been upgraded. +# + +MATLAB_PATH="/Applications/MATLAB_R2022b.app" + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.9 \ + --with-python-dir=/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \ + --with-python-numpy-dir=/Library/Python/3.9/site-packages/numpy/core/include/numpy \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/13.1.0/lib/gcc/13 -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-parmetis-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/hdf5/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-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${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 packages to be installed and their installation scripts +EXTERNALPACKAGES=" + autotools install-mac.sh + cmake install.sh + petsc install-3.14-mac.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + hdf5 install-1-parallel.sh + netcdf install-4.7-parallel.sh + proj install-6.sh + gdal install-3-python.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4-mac.sh + triangle install-mac.sh + chaco install-mac.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: +# - 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="'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/mac-intel-examples =================================================================== --- /issm/trunk/jenkins/mac-intel-examples (revision 28013) +++ /issm/trunk/jenkins/mac-intel-examples (revision 28013) @@ -0,0 +1,90 @@ +# NOTE: +# - Same configuration as mac-intel-full +# +# TODO: +# - Change PROJ installation script to latest version once Jenkins macOS build +# node has been upgraded. +# + +MATLAB_PATH="/Applications/MATLAB_R2022b.app" + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/13.1.0/lib/gcc/13 -lgfortran" \ + --with-mpi-include=${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=${ISSM_DIR}/externalpackages/petsc/install \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-proj-dir=${ISSM_DIR}/externalpackages/proj/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-mac.sh + cmake install.sh + petsc install-3.14-mac.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + hdf5 install-1-parallel.sh + netcdf install-4.7-parallel.sh + proj install-6.sh + gdal install-3.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4-mac.sh + triangle install-mac.sh + chaco install-mac.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=1 + +# 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 +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/mac-intel-full =================================================================== --- /issm/trunk/jenkins/mac-intel-full (revision 28013) +++ /issm/trunk/jenkins/mac-intel-full (revision 28013) @@ -0,0 +1,94 @@ +# NOTE: +# - This configuration adds solid earth and Dakota capabilities to the basic +# build. +# +# TODO: +# - Change PROJ installation script to latest version once Jenkins macOS build +# node has been upgraded. +# + +MATLAB_PATH="/Applications/MATLAB_R2022b.app" + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.9 \ + --with-python-dir=/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \ + --with-python-numpy-dir=/Library/Python/3.9/site-packages/numpy/core/include/numpy \ + --with-fortran-lib="-L/opt/homebrew/Cellar/gcc/13.1.0/lib/gcc/13 -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-parmetis-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/hdf5/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-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-mac.sh + cmake install.sh + petsc install-3.14-mac.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + hdf5 install-1-parallel.sh + netcdf install-4.7-parallel.sh + proj install-6.sh + gdal install-3-python.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4-mac.sh + triangle install-mac.sh + chaco install-mac.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=4 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/mac-intel-solid_earth =================================================================== --- /issm/trunk/jenkins/mac-intel-solid_earth (revision 28013) +++ /issm/trunk/jenkins/mac-intel-solid_earth (revision 28013) @@ -0,0 +1,102 @@ +# NOTE: +# - Same configuration as mac-intel-full +# +# TODO: +# - Change PROJ installation script to latest version once Jenkins macOS build +# node has been upgraded. +# + +MATLAB_PATH="/Applications/MATLAB_R2022b.app" + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.9 \ + --with-python-dir=/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \ + --with-python-numpy-dir=/Library/Python/3.9/site-packages/numpy/core/include/numpy \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/13.1.0/lib/gcc/13 -lgfortran" \ + --with-mpi-include=${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=${ISSM_DIR}/externalpackages/petsc/install \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-proj-dir=${ISSM_DIR}/externalpackages/proj/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 packages to be installed and their installation scripts +EXTERNALPACKAGES=" + autotools install-mac.sh + cmake install.sh + petsc install-3.14-mac.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + hdf5 install-1-parallel.sh + netcdf install-4.7-parallel.sh + proj install-6.sh + gdal install-3-python.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4-mac.sh + triangle install-mac.sh + chaco install-mac.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) +# - Excluding 2012 until it can be looked at by Eric ("FindParam error message: Parameter HydrologyModel not set") +# - Excluding 2091 until it can be debugged (resource starvation) +# +MATLAB_NROPTIONS="'benchmark','slc','exclude',[2004 2006 2012 2051 2052 2053 2085 2424 2425]" +PYTHON_NROPTIONS="--benchmark slc --exclude 2004 2006 2012 2051 2052 2053 2085 2424 2425" Index: /issm/trunk/jenkins/mac-silicon-basic =================================================================== --- /issm/trunk/jenkins/mac-silicon-basic (revision 28013) +++ /issm/trunk/jenkins/mac-silicon-basic (revision 28013) @@ -0,0 +1,88 @@ +# NOTE: +# - Currently, this configuration does not compile the MATLAB API. After +# compiling, you will need to download the ISSM pre-compiled binaries from +# https://issm.jpl.nasa.gov/download/binaries, copy the contents of lib/ to +# $ISSM_DIR/lib-precompiled, then add $ISSM_DIR/lib-precompiled to the path +# in MATLAB. +# +# TODO: +# - Change PROJ installation script to latest version once Jenkins macOS build +# node has been upgraded. +# + +MATLAB_PATH="/Applications/MATLAB_R2022b.app" # NOTE: Although we do not configure/compile MATLAB wrappers, we need to set this variable for testing + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --without-wrappers \ + --with-numthreads=8 \ + --with-fortran-lib="-L/opt/homebrew/lib/gcc/current -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-parmetis-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 packages to be installed and their installation scripts +EXTERNALPACKAGES=" + autotools install-mac.sh + cmake install.sh + petsc install-3.17-mac-silicon.sh + triangle install-mac.sh + chaco install-mac.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: +# - Tests 430, 441:442, 470:476 excluded because of large errors. +# - Tests 462-464, 517 excluded because of "Arrays have incompatible sizes for +# this operation." +# - Test 701:703 excluded because they use full Stokes equations +# +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),430,435,441:442,462:464,470:476,517,701:703]" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/mac-silicon-dakota =================================================================== --- /issm/trunk/jenkins/mac-silicon-dakota (revision 28013) +++ /issm/trunk/jenkins/mac-silicon-dakota (revision 28013) @@ -0,0 +1,107 @@ +# NOTE: +# - Currently, this configuration does not compile the MATLAB API. After +# compiling, you will need to download the ISSM pre-compiled binaries from +# https://issm.jpl.nasa.gov/download/binaries, copy the contents of lib/ to +# $ISSM_DIR/lib-precompiled, then add $ISSM_DIR/lib-precompiled to the path +# in MATLAB. +# +# TODO: +# - Change PROJ installation script to latest version once Jenkins macOS build +# node has been upgraded. +# + +MATLAB_PATH="/Applications/MATLAB_R2022b.app" # NOTE: Although we do not configure/compile MATLAB wrappers, we need to set this variable for testing + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=8 \ + --with-python-version=3.9 \ + --with-python-dir=/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \ + --with-python-numpy-dir=/Library/Python/3.9/site-packages/numpy/core/include/numpy \ + --with-fortran-lib="-L/opt/homebrew/lib/gcc/current -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-parmetis-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/hdf5/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-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${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-mac.sh + cmake install.sh + petsc install-3.17-mac-silicon.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + hdf5 install-1-parallel.sh + netcdf install-4.7-parallel.sh + proj install-6.sh + gdal install-3-python.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4-mac.sh + triangle install-mac.sh + chaco install-mac.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: +# - 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="'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/mac-silicon-examples =================================================================== --- /issm/trunk/jenkins/mac-silicon-examples (revision 28013) +++ /issm/trunk/jenkins/mac-silicon-examples (revision 28013) @@ -0,0 +1,94 @@ +# NOTE: +# - Same configuration as mac-silicon-full +# - Currently, this configuration does not compile the MATLAB API. After +# compiling, you will need to download the ISSM pre-compiled binaries from +# https://issm.jpl.nasa.gov/download/binaries, copy the contents of lib/ to +# $ISSM_DIR/lib-precompiled, then add $ISSM_DIR/lib-precompiled to the path +# in MATLAB. +# +# TODO: +# - Change PROJ installation script to latest version once Jenkins macOS build +# node has been upgraded. +# + +MATLAB_PATH="/Applications/MATLAB_R2022b.app" # NOTE: Although we do not configure/compile MATLAB wrappers, we need to set this variable for testing + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=8 \ + --with-fortran-lib="-L/opt/homebrew/lib/gcc/current -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-parmetis-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/hdf5/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-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${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-mac.sh + cmake install.sh + petsc install-3.17-mac-silicon.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + hdf5 install-1-parallel.sh + netcdf install-4.7-parallel.sh + proj install-6.sh + gdal install-3.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4-mac.sh + triangle install-mac.sh + chaco install-mac.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=1 + +# 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 +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/mac-silicon-full =================================================================== --- /issm/trunk/jenkins/mac-silicon-full (revision 28013) +++ /issm/trunk/jenkins/mac-silicon-full (revision 28013) @@ -0,0 +1,98 @@ +# NOTE: +# - This configuration adds solid earth and Dakota capabilities to the basic +# build. +# - Currently, this configuration does not compile the MATLAB API. After +# compiling, you will need to download the ISSM pre-compiled binaries from +# https://issm.jpl.nasa.gov/download/binaries, copy the contents of lib/ to +# $ISSM_DIR/lib-precompiled, then add $ISSM_DIR/lib-precompiled to the path +# in MATLAB. +# +# TODO: +# - Change PROJ installation script to latest version once Jenkins macOS build +# node has been upgraded. +# + +MATLAB_PATH="/Applications/MATLAB_R2022b.app" # NOTE: Although we do not configure/compile MATLAB wrappers, we need to set this variable for testing + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=8 \ + --with-python-version=3.9 \ + --with-python-dir=/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \ + --with-python-numpy-dir=/Library/Python/3.9/site-packages/numpy/core/include/numpy \ + --with-fortran-lib="-L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/12 -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-parmetis-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/hdf5/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-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${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-mac.sh + cmake install.sh + petsc install-3.17-mac-silicon.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + hdf5 install-1-parallel.sh + netcdf install-4.7-parallel.sh + proj install-6.sh + gdal install-3-python.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4-mac.sh + triangle install-mac.sh + chaco install-mac.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=2 + +# Nightly run options +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/mac-silicon-solid_earth =================================================================== --- /issm/trunk/jenkins/mac-silicon-solid_earth (revision 28013) +++ /issm/trunk/jenkins/mac-silicon-solid_earth (revision 28013) @@ -0,0 +1,105 @@ +# NOTE: +# - Currently, this configuration does not compile the MATLAB API. After +# compiling, you will need to download the ISSM pre-compiled binaries from +# https://issm.jpl.nasa.gov/download/binaries, copy the contents of lib/ to +# $ISSM_DIR/lib-precompiled, then add $ISSM_DIR/lib-precompiled to the path +# in MATLAB. +# +# TODO: +# - Change PROJ installation script to latest version once Jenkins macOS build +# node has been upgraded. +# + +MATLAB_PATH="/Applications/MATLAB_R2022b.app" # NOTE: Although we do not configure/compile MATLAB wrappers, we need to set this variable for testing + +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-numthreads=4 \ + --with-python-version=3.9 \ + --with-python-dir=/System/Volumes/Data/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \ + --with-python-numpy-dir=/Library/Python/3.9/site-packages/numpy/core/include/numpy \ + --with-fortran-lib="-L/opt/homebrew/lib/gcc/current -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-parmetis-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/hdf5/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-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${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-mac.sh + cmake install.sh + petsc install-3.17-mac-silicon.sh + gsl install.sh + boost install-1.7-mac.sh + dakota install-6.2-mac.sh + curl install-7-mac.sh + hdf5 install-1-parallel.sh + netcdf install-4.7-parallel.sh + proj install-6.sh + gdal install-3-python.sh + gshhg install.sh + gmt install-6-mac.sh + gmsh install-4-mac.sh + triangle install-mac.sh + chaco install-mac.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) +# - Excluding 2012 until it can be looked at by Eric ("FindParam error message: Parameter HydrologyModel not set") +# - Excluding 2091 until it can be debugged (resource starvation) +# - Excluding 2110:2113 until we can compile MEX modules natively for Silicon and then can debug differences in mesh generation between different platforms +# +MATLAB_NROPTIONS="'benchmark','slc','exclude',[2004 2006 2012 2051 2052 2053 2085 2424 2425]" +PYTHON_NROPTIONS="--benchmark slc --exclude 2004 2006 2012 2051 2052 2053 2085 2110:2113 2424 2425" Index: /issm/trunk/jenkins/pine_island-mac-basic =================================================================== --- /issm/trunk/jenkins/pine_island-mac-basic (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-basic (revision 28013) @@ -31,5 +31,5 @@ #-------------------# -# List of external pakages to be installed and their installation scripts +# List of external packages to be installed and their installation scripts EXTERNALPACKAGES=" autotools install-mac.sh @@ -37,5 +37,5 @@ petsc install-3.12-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pine_island-mac-binaries-matlab =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-matlab (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-binaries-matlab (revision 28013) @@ -9,4 +9,7 @@ # - We can disable dependency tracking in the Autotools because the binaries # should always be a one-time build. +# +# TODO: +# - Add static copy of libsqlite and make sure it is found during GMT configuration # @@ -58,5 +61,5 @@ gmsh install-4-mac-static.sh triangle install-mac-static.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pine_island-mac-binaries-python-2 =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-python-2 (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-binaries-python-2 (revision 28013) @@ -6,4 +6,7 @@ # - We can disable dependency tracking in the Autotools because the binaries # should always be a one-time build. +# +# TODO: +# - Add static copy of libsqlite and make sure it is found during GMT configuration # @@ -56,5 +59,5 @@ gmsh install-4-mac-static.sh triangle install-mac-static.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pine_island-mac-binaries-python-3 =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-python-3 (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-binaries-python-3 (revision 28013) @@ -6,4 +6,7 @@ # - We can disable dependency tracking in the Autotools because the binaries # should always be a one-time build. +# +# TODO: +# - Add static copy of libsqlite and make sure it is found during GMT configuration # @@ -57,5 +60,5 @@ gmsh install-4-mac-static.sh triangle install-mac-static.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pine_island-mac-dakota =================================================================== --- /issm/trunk/jenkins/pine_island-mac-dakota (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-dakota (revision 28013) @@ -42,5 +42,5 @@ #-------------------# -#List of external pakages to be installed and their installation scripts +#List of external packages to be installed and their installation scripts EXTERNALPACKAGES=" autotools install-mac.sh @@ -58,5 +58,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pine_island-mac-examples =================================================================== --- /issm/trunk/jenkins/pine_island-mac-examples (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-examples (revision 28013) @@ -59,5 +59,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pine_island-mac-full =================================================================== --- /issm/trunk/jenkins/pine_island-mac-full (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-full (revision 28013) @@ -56,5 +56,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pine_island-mac-full-valgrind =================================================================== --- /issm/trunk/jenkins/pine_island-mac-full-valgrind (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-full-valgrind (revision 28013) @@ -46,9 +46,10 @@ petsc install-3.16-mac.sh gsl install.sh - boost install-1.7-mac.sh + boost install-1.7-mac-valgrind.sh dakota install-6.2-mac.sh curl install-7-mac.sh netcdf install-4.7-parallel.sh proj install-6.sh + sqlite install.sh gdal install-3-python.sh gshhg install.sh @@ -56,5 +57,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pine_island-mac-solid_earth =================================================================== --- /issm/trunk/jenkins/pine_island-mac-solid_earth (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-solid_earth (revision 28013) @@ -42,5 +42,5 @@ #-------------------# -#List of external pakages to be installed and their installation scripts +#List of external packages to be installed and their installation scripts EXTERNALPACKAGES=" autotools install-mac.sh @@ -58,5 +58,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pine_island-mac-solid_earth-lambert =================================================================== --- /issm/trunk/jenkins/pine_island-mac-solid_earth-lambert (revision 28012) +++ /issm/trunk/jenkins/pine_island-mac-solid_earth-lambert (revision 28013) @@ -42,5 +42,5 @@ #-------------------# -#List of external pakages to be installed and their installation scripts +#List of external packages to be installed and their installation scripts EXTERNALPACKAGES=" autotools install-mac.sh @@ -58,5 +58,5 @@ gmsh install-4-mac.sh triangle install-mac.sh - chaco install.sh + chaco install-mac.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/pleiades-solid_earth =================================================================== --- /issm/trunk/jenkins/pleiades-solid_earth (revision 28012) +++ /issm/trunk/jenkins/pleiades-solid_earth (revision 28013) @@ -51,5 +51,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/ross-debian_linux-adolc-ampioff =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-adolc-ampioff (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-adolc-ampioff (revision 28013) @@ -1,7 +1,8 @@ +MATLAB_PATH="/usr/local/MATLAB/R2019b" + #--------------------# # ISSM Configuration # #--------------------# -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -15,6 +16,7 @@ --without-Love \ --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ @@ -41,5 +43,5 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh gsl install.sh triangle install-linux.sh @@ -76,4 +78,4 @@ # failure on ampioff configuration (really, likely a segmentation fault) # -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 3.14 3013 3014 3015 3016 3017 3018 3019 --exclude=3010" +MATLAB_NROPTIONS="'benchmark','adolc','exclude',[3010]" +PYTHON_NROPTIONS="--benchmark adolc --exclude 3010" Index: /issm/trunk/jenkins/ross-debian_linux-adolc-ampion =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-adolc-ampion (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-adolc-ampion (revision 28013) @@ -1,7 +1,8 @@ +MATLAB_PATH="/usr/local/MATLAB/R2019b" + #--------------------# # ISSM Configuration # #--------------------# -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -12,9 +13,9 @@ --without-kriging \ --without-kml \ - --without-Sealevelchange \ --without-Love \ --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ @@ -42,5 +43,5 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh gsl install.sh triangle install-linux.sh @@ -78,4 +79,4 @@ # failure on ampioff configuration (really, likely a segmentation fault) # -MATLAB_NROPTIONS="'benchmark','adolc','id',[3001, 3002, 3003, 3004, 3005, 3006, 3007, 3008, 3009, 3010, 3101, 3102, 3103, 3104, 3105, 3106, 3107, 3108, 3109, 3119],'exclude',3010" -PYTHON_NROPTIONS="--benchmark=adolc -i 3001 3002 3003 3004 3005 3006 3007 3008 3009 3010 3101 3102 3103 3104 3105 3106 3107 3108 3109 3119 --exclude=3010" +MATLAB_NROPTIONS="'benchmark','adolc','exclude',[3010 3019 3020 3021 3110]" +PYTHON_NROPTIONS="--benchmark adolc --exclude 3010 3019 3020 3021 3110" Index: /issm/trunk/jenkins/ross-debian_linux-basic =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-basic (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-basic (revision 28013) @@ -1,7 +1,8 @@ +MATLAB_PATH="/usr/local/MATLAB/R2019b" + #--------------------# # ISSM Configuration # #--------------------# -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -33,7 +34,7 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: sm/trunk/jenkins/ross-debian_linux-binaries =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries (revision 28012) +++ (revision ) @@ -1,76 +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-numthreads=4 \ - --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-parmetis-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-linux.sh - cmake install.sh - petsc install-3.12-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-matlab =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-matlab (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-binaries-matlab (revision 28013) @@ -1,7 +1,7 @@ +MATLAB_PATH="/usr/local/MATLAB/R2019b" + #--------------------# # ISSM Configuration # #--------------------# - -MATLAB_PATH="/usr/local/MATLAB/R2019b" # NOTE: @@ -11,4 +11,5 @@ # copied by packaging script. # + ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -26,5 +27,5 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ @@ -44,9 +45,10 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux-static.sh + petsc install-3.17-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 + hdf5 install-1-parallel-static.sh netcdf install-4.7-parallel-static.sh proj install-6-static.sh @@ -56,5 +58,5 @@ gmsh install-4-linux-static.sh triangle install-linux-static.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: sm/trunk/jenkins/ross-debian_linux-binaries-python-2 =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-python-2 (revision 28012) +++ (revision ) @@ -1,89 +1,0 @@ -#--------------------# -# 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=${ISSM_DIR}/externalpackages/petsc/install \ - --with-parmetis-dir=${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=${ISSM_DIR}/externalpackages/dakota/install \ - --with-proj-dir=${ISSM_DIR}/externalpackages/proj/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-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-static.sh - gdal install-3-python-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-3 =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-python-3 (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-binaries-python-3 (revision 28013) @@ -9,4 +9,5 @@ # copied by packaging script. # + ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -16,6 +17,6 @@ --disable-dependency-tracking \ --with-pic \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-version=3.7 \ --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L${ISSM_DIR}/lib -lgfortran" \ @@ -27,5 +28,5 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ @@ -45,9 +46,10 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux-static.sh + petsc install-3.17-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 + hdf5 install-1-parallel-static.sh netcdf install-4.7-parallel-static.sh proj install-6-static.sh @@ -57,5 +59,5 @@ gmsh install-4-linux-static.sh triangle install-linux-static.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/ross-debian_linux-codipack =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-codipack (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-codipack (revision 28013) @@ -1,7 +1,8 @@ +MATLAB_PATH="/usr/local/MATLAB/R2019b" + #--------------------# # ISSM Configuration # #--------------------# -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -39,8 +40,8 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh gsl install.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh @@ -74,4 +75,4 @@ # See documentation in test/NightlyRun/runme.* for more information. # -MATLAB_NROPTIONS="'benchmark','all','id',[3015,3119,3480,3201:3205]" +MATLAB_NROPTIONS="'benchmark','all','id',[3015,3119,3480,3201:3206]" PYTHON_NROPTIONS="--benchmark='all' -i 3015 3119 3480" Index: /issm/trunk/jenkins/ross-debian_linux-dakota =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-dakota (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-dakota (revision 28013) @@ -1,7 +1,7 @@ +MATLAB_PATH="/usr/local/MATLAB/R2019b" + #--------------------# # ISSM Configuration # #--------------------# - -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ @@ -14,6 +14,7 @@ --with-numthreads=4 \ --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ @@ -24,5 +25,5 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ @@ -43,9 +44,10 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh gsl install.sh boost install-1.7-linux.sh dakota install-6.2-linux.sh curl install-7-linux.sh + hdf5 install-1-parallel.sh netcdf install-4.7-parallel.sh proj install-6.sh @@ -55,5 +57,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/ross-debian_linux-full =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-full (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-full (revision 28013) @@ -1,10 +1,10 @@ # NOTE: This configuration adds solid earth and Dakota capabilities to the # basic build. + +MATLAB_PATH="/usr/local/MATLAB/R2019b" #--------------------# # ISSM Configuration # #--------------------# - -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ @@ -15,6 +15,7 @@ --with-numthreads=4 \ --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ --with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \ @@ -25,5 +26,5 @@ --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \ --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \ - --with-hdf5-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-hdf5-dir="${ISSM_DIR}/externalpackages/hdf5/install" \ --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \ --with-gsl-dir="${ISSM_DIR}/externalpackages/gsl/install" \ @@ -44,9 +45,10 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh gsl install.sh boost install-1.7-linux.sh dakota install-6.2-linux.sh curl install-7-linux.sh + hdf5 install-1-parallel.sh netcdf install-4.7-parallel.sh proj install-6.sh @@ -56,5 +58,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/ross-debian_linux-full-mplapack =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-full-mplapack (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-full-mplapack (revision 28013) @@ -1,10 +1,7 @@ -# NOTE: This configuration adds solid earth and Dakota capabilities to the -# basic build. +MATLAB_PATH="/usr/local/MATLAB/R2019b" #--------------------# # ISSM Configuration # #--------------------# - -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ @@ -16,6 +13,7 @@ --with-numthreads=4 \ --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ --with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \ @@ -26,5 +24,5 @@ --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \ --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \ - --with-hdf5-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-hdf5-dir="${ISSM_DIR}/externalpackages/hdf5/install" \ --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \ --with-mplapack-dir="${ISSM_DIR}/externalpackages/mplapack/install" \ @@ -46,5 +44,5 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh mplapack install-2-linux.sh gsl install.sh @@ -52,4 +50,5 @@ dakota install-6.2-linux.sh curl install-7-linux.sh + hdf5 install-1-parallel.sh netcdf install-4.7-parallel.sh proj install-6.sh @@ -59,5 +58,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/ross-debian_linux-full-valgrind =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-full-valgrind (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-full-valgrind (revision 28013) @@ -1,4 +1,6 @@ # NOTE: This configuration adds solid earth and Dakota capabilities to the # basic build, as well as the ability to debug with Valgrind. + +MATLAB_PATH="/usr/local/MATLAB/R2019b" #--------------------# @@ -6,15 +8,13 @@ #--------------------# -MATLAB_PATH="/usr/local/MATLAB/R2019b" - ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ --disable-static \ --enable-development \ - --enable-debugging \ - --with-numthreads=4 \ + --enable-debugging \ --with-numthreads=4 \ --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ @@ -25,5 +25,5 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ @@ -44,9 +44,10 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh gsl install.sh boost install-1.7-linux-valgrind.sh dakota install-6.2-linux.sh curl install-7-linux.sh + hdf5 install-1-parallel.sh netcdf install-4.7-parallel.sh proj install-6.sh @@ -56,5 +57,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh Index: /issm/trunk/jenkins/ross-debian_linux-gia =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-gia (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-gia (revision 28013) @@ -1,7 +1,8 @@ +MATLAB_PATH="/usr/local/MATLAB/R2019b" + #--------------------# # ISSM Configuration # #--------------------# -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -12,6 +13,7 @@ --with-numthreads=4 --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/lib/python2.7/dist-packages/numpy \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ @@ -34,5 +36,5 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh triangle install-linux.sh math77 install.sh Index: /issm/trunk/jenkins/ross-debian_linux-iceocean =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-iceocean (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-iceocean (revision 28013) @@ -1,7 +1,8 @@ +MATLAB_PATH="/usr/local/MATLAB/R2019b" + #--------------------# # ISSM Configuration # #--------------------# -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -34,7 +35,7 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh @@ -66,7 +67,7 @@ # See documentation in test/NightlyRun/runme.* for more information. # -# NOTE: Currently not including 4003 while Dimitri and Helenen work on the +# NOTE: Currently not including 4002:4003 while Dimitri and Helene work on the # coupling # -MATLAB_NROPTIONS="'benchmark','all','id',[4001,4002]" +MATLAB_NROPTIONS="'benchmark','all','id',[4001]" PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-python =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-python (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-python (revision 28013) @@ -9,6 +9,6 @@ --enable-debugging \ --with-numthreads=4 \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-version=3.7 \ --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ @@ -20,5 +20,5 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ @@ -39,9 +39,10 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh gsl install.sh boost install-1.7-linux.sh dakota install-6.2-linux.sh curl install-7-linux.sh + hdf5 install-1-parallel.sh netcdf install-4.7-parallel.sh proj install-6.sh @@ -51,5 +52,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh @@ -83,8 +84,5 @@ # 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 234 418 420 2002 2003 2010 2021 2101" +PYTHON_NROPTIONS="--exclude 234 418 420" Index: /issm/trunk/jenkins/ross-debian_linux-solid_earth =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-solid_earth (revision 28012) +++ /issm/trunk/jenkins/ross-debian_linux-solid_earth (revision 28013) @@ -1,7 +1,7 @@ +MATLAB_PATH="/usr/local/MATLAB/R2019b" + #--------------------# # ISSM Configuration # #--------------------# - -MATLAB_PATH="/usr/local/MATLAB/R2019b" ISSM_CONFIG='\ @@ -12,6 +12,7 @@ --with-numthreads=4 \ --with-matlab-dir=${MATLAB_PATH} \ + --with-python-version=3.7 \ --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ @@ -22,5 +23,5 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/hdf5/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ @@ -41,9 +42,10 @@ autotools install-linux.sh cmake install.sh - petsc install-3.12-linux.sh + petsc install-3.17-linux.sh gsl install.sh boost install-1.7-linux.sh dakota install-6.2-linux.sh curl install-7-linux.sh + hdf5 install-1-parallel.sh netcdf install-4.7-parallel.sh proj install-6.sh @@ -53,5 +55,5 @@ gmsh install-4-linux.sh triangle install-linux.sh - chaco install.sh + chaco install-linux.sh m1qn3 install.sh semic install.sh @@ -90,4 +92,4 @@ # - Excluding 2012 until it can be looked at by Eric ("FindParam error message: Parameter HydrologyModel not set") # -MATLAB_NROPTIONS="'benchmark','slc','exclude',[2004 2006 2012 2021 2051 2052 2053 2085 2090 2101 2424 2425]" -PYTHON_NROPTIONS="--benchmark slc --exclude 2004 2006 2012 2021 2051 2052 2053 2085 2090 2101 2424 2425" +MATLAB_NROPTIONS="'benchmark','slc','exclude',[2004 2006 2012 2051 2052 2053 2085 2424 2425]" +PYTHON_NROPTIONS="--benchmark slc --exclude 2004 2006 2012 2021 2051 2052 2053 2085 2424 2425" Index: /issm/trunk/jenkins/ross-win-msys2-gcc-msmpi-basic =================================================================== --- /issm/trunk/jenkins/ross-win-msys2-gcc-msmpi-basic (revision 28012) +++ /issm/trunk/jenkins/ross-win-msys2-gcc-msmpi-basic (revision 28013) @@ -1,2 +1,4 @@ +MATLAB_PATH=$(cygpath -u $(cygpath -ms "/c/Program Files/MATLAB/R2019b")) + ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ @@ -23,5 +25,5 @@ #-------------------# -#List of external pakages to be installed and their installation scripts +#List of external packages to be installed and their installation scripts EXTERNALPACKAGES=" metis install-5-win-msys2-gcc.sh @@ -31,5 +33,5 @@ scalapack install-2-win-msys2-gcc-msmpi.sh mumps install-5-win-msys2-gcc-msmpi.sh - petsc install-3.12-win-msys2-gcc-msmpi.sh + petsc install-3.14-win-msys2-gcc-msmpi.sh triangle install-win-msys2-gcc.sh shell2junit install.sh Index: /issm/trunk/jenkins/ross-win-msys2-mingw-msmpi-basic =================================================================== --- /issm/trunk/jenkins/ross-win-msys2-mingw-msmpi-basic (revision 28012) +++ /issm/trunk/jenkins/ross-win-msys2-mingw-msmpi-basic (revision 28013) @@ -9,7 +9,7 @@ --with-matlab-dir="${MATLAB_PATH}" \ --with-mpi-include="${MSMPI_ROOT}/include" \ - --with-mpi-libdir="${MSMPI_ROOT}/lib" \ - --with-mpi-libflags="-lmsmpi" \ - --with-fortran-lib="-L/c/msys64/mingw64/lib/gcc/x86_64-w64-mingw32/10.2.0/ -lgfortran" \ + --with-mpi-libdir="-Wl,-L${MSMPI_ROOT}/lib" \ + --with-mpi-libflags="-Wl,-lmsmpi" \ + --with-fortran-lib="-Wl,-L/c/msys64/mingw64/lib/gcc/x86_64-w64-mingw32/13.2.0 -Wl,-lgfortran" \ --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ @@ -28,5 +28,5 @@ #-------------------# -#List of external pakages to be installed and their installation scripts +#List of external packages to be installed and their installation scripts EXTERNALPACKAGES=" msmpi install.sh Index: /issm/trunk/jenkins/ross-win-msys2-mingw-msmpi-binaries-matlab =================================================================== --- /issm/trunk/jenkins/ross-win-msys2-mingw-msmpi-binaries-matlab (revision 28013) +++ /issm/trunk/jenkins/ross-win-msys2-mingw-msmpi-binaries-matlab (revision 28013) @@ -0,0 +1,65 @@ +MATLAB_PATH=$(cygpath -u $(cygpath -ms "/c/Program Files/MATLAB/R2019b")) + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-vendor="win-msys2" \ + --with-matlab-dir="${MATLAB_PATH}" \ + --with-fortran-lib="-Wl,-L/c/msys64/mingw64/lib/gcc/x86_64-w64-mingw32/13.2.0 -Wl,-lgfortran" \ + --with-mpi-include="${MSMPI_ROOT}/include" \ + --with-mpi-libdir="-Wl,-L${MSMPI_ROOT}/lib" \ + --with-mpi-libflags="-Wl,-lmsmpi" \ + --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-blas-lapack-dir="${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="${ISSM_DIR}/externalpackages/semic/install" \ +' + +#-------------------# +# External Packages # +#-------------------# + +#List of external packages to be installed and their installation scripts +EXTERNALPACKAGES=" + msmpi install-static.sh + petsc install-3.14-win-msys2-mingw-msmpi-static.sh + triangle install-win-msys2-mingw-static.sh + chaco install-win-msys2-mingw.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=4 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=2 + +# Nightly run options +# +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: sm/trunk/jenkins/windows =================================================================== --- /issm/trunk/jenkins/windows (revision 28012) +++ (revision ) @@ -1,66 +1,0 @@ - -#-------------------------------# -# 1: ISSM general configuration # -#-------------------------------# - -#MATLAB path -MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2019a" - -#ISSM CONFIGURATION -ISSM_CONFIG='--prefix=$ISSM_DIR \ - --with-vendor=MSVC-Win64 \ - --with-cxxoptflags='-fp:strict' \ - --disable-static \ - --enable-standalone-libraries \ - --with-fortran=no \ - --without-Sealevelchange \ - --without-Love \ - --without-kriging \ - --without-kml \ - --with-matlab-dir=$MATLAB_PATH \ - --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ - --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ - --with-mpi-libdir="$ISSM_DIR/externalpackages/petsc/install/lib" \ - --with-mpi-libflags="-Wl,libpetsc.lib" \ - --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include/petsc/mpiuni" \ - --enable-development \ - --enable-debugging ' - -#PYTHON and MATLAB testing -MATLAB_TEST=1 -PYTHON_TEST=0 - -#-----------------------------------# -# 3: External packages installation # -#-----------------------------------# - -#List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES=" - autotools install-win.sh - petsc install-3.6-win10.sh - metis install-4.0-win10.sh - triangle install-windows-static.sh - shell2junit install.sh -" - -#-----------------# -# 4: test options # -#-----------------# - -#number of cpus used in ISSM installation and compilation (one is usually -#safer as some packages are very sensitive to parallel compilation) -NUMCPUS_INSTALL=8 - -#number of cpus used in the nightly runs. -NUMCPUS_RUN=8 - -#Nightly run options. The matlab routine runme.m will be called -#as follows: runme($MATLAB_NROPTIONS). The options must be understandable -#by Matlab and runme.m -#ex: "'id',[101 102 103]" - -#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',[104,119,124,125,126,204,205,211,215,218,220,221,234,235,243,244,250,251,274,280,285,290,291,308,322,331,340,341,404,405,409,412,413,414,417,418,420,421,422,430,435,440,441,442,444,455,460,463,464,465,503,507,510,511,513,514,612,701,702,703,801,802,803,804,805,IdFromString('Dakota')]" -PYTHON_NROPTIONS="--exclude_name 'Dakota'" Index: sm/trunk/jenkins/windows-par =================================================================== --- /issm/trunk/jenkins/windows-par (revision 28012) +++ (revision ) @@ -1,62 +1,0 @@ - -#-------------------------------# -# 1: ISSM general configuration # -#-------------------------------# - -#MATLAB path -MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a/" - -#ISSM CONFIGURATION -ISSM_CONFIG='--prefix=$ISSM_DIR \ - --with-vendor=MSVC-Win64 \ - --disable-static \ - --enable-standalone-libraries \ - --with-fortran=no \ - --without-Sealevelchange \ - --without-kriging \ - --without-kml \ - --with-matlab-dir=$MATLAB_PATH \ - --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ - --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mpi-include="/cygdrive/c/Programs/MPICH2/include" \ - --with-mpi-libflags="-Wl,mpi.lib -Wl,/LIBPATH:C:/Programs/MPICH2/lib" \ - --enable-development \ - --enable-debugging ' - -#PYTHON and MATLAB testing -MATLAB_TEST=1 -PYTHON_TEST=0 - -#-----------------------------------# -# 3: External packages installation # -#-----------------------------------# - -#List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES="autotools install-win.sh - petsc install-dev-win10-par.sh - metis install-4.0-win7.sh - triangle install-win7.sh - shell2junit install.sh" - -#-----------------# -# 4: test options # -#-----------------# - -#number of cpus used in ISSM installation and compilation (one is usually -#safer as some packages are very sensitive to parallel compilation) -NUMCPUS_INSTALL=8 - -#number of cpus used in the nightly runs. -NUMCPUS_RUN=1 - -#Nightly run options. The matlab routine runme.m will be called -#as follows: runme($MATLAB_NROPTIONS). The options must be understandable -#by Matlab and runme.m -#ex: "'id',[101 102 103]" - -#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, 124, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 412, 413, 414, 417, 418, 420, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341]" -PYTHON_NROPTIONS="" Index: sm/trunk/jenkins/windows_static =================================================================== --- /issm/trunk/jenkins/windows_static (revision 28012) +++ (revision ) @@ -1,65 +1,0 @@ - -#-------------------------------# -# 1: ISSM general configuration # -#-------------------------------# - -#MATLAB path -MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a/" - -#ISSM CONFIGURATION -ISSM_CONFIG='--prefix=$ISSM_DIR \ - --disable-static \ - --enable-standalone-executables \ - --enable-standalone-libraries \ - --with-matlab-dir=$MATLAB_PATH \ - --with-vendor=MSVC-Win64 \ - --with-fortran=no \ - --without-Sealevelchange \ - --without-Love \ - --without-kriging \ - --without-kml \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib \ - --with-mpi-libdir=$ISSM_DIR/externalpackages/petsc/install/lib \ - --with-mpi-libflags="-Wl,libpetsc.lib" \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \ - --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include/petsc/mpiuni" \ - --with-cxxoptflags="-fp:strict"' - -#PYTHON and MATLAB testing -MATLAB_TEST=0 -PYTHON_TEST=0 - -#-----------------------------------# -# 3: External packages installation # -#-----------------------------------# - -#List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES="autotools install-win.sh - petsc install-3.6-win10.sh - metis install-4.0-win10.sh - triangle install-win10.sh - math77 install.sh - gmt install-win64-precompiled.sh - gmsh install-win64-precompiled.sh - shell2junit install.sh" - -#-----------------# -# 4: test options # -#-----------------# - -#number of cpus used in ISSM installation and compilation (one is usually -#safer as some packages are very sensitive to parallel compilation) -NUMCPUS_INSTALL=8 - -#number of cpus used in the nightly runs. -NUMCPUS_RUN=8 - -#Nightly run options. The matlab routine runme.m will be called -#as follows: runme($MATLAB_NROPTIONS). The options must be understandable -#by Matlab and runme.m -#ex: "'id',[101 102 103]" -MATLAB_NROPTIONS="" -PYTHON_NROPTIONS="" Index: sm/trunk/jenkins/windows_test =================================================================== --- /issm/trunk/jenkins/windows_test (revision 28012) +++ (revision ) @@ -1,34 +1,0 @@ -#-------------------------------# -# 1: ISSM general configuration # -#-------------------------------# - -#MATLAB path -MATLAB_PATH="/cygdrive/c/Program\ Files/MATLAB/R2014b/" - -#PYTHON and MATLAB testing -MATLAB_TEST=1 -PYTHON_TEST=0 - -#-----------------------------------# -# 3: External packages installation # -#-----------------------------------# - -#-----------------# -# 4: test options # -#-----------------# - -#number of cpus used in ISSM installation and compilation (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. The matlab routine runme.m will be called -#as follows: runme($MATLAB_NROPTIONS). The options must be understandable -#by Matlab and runme.m -#ex: "'id',[101 102 103]" - -#In Windows, we don't yet have MUMPS, can't do full stokes, so exclude all FS runs. Also exclude all runs with Dakota. And exclude higher order runs that have penalties. And 800+ tests because we don't want to have --with-development since we do the binaries with this version -MATLAB_NROPTIONS="'exclude',[104, 124, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 412, 413, 414, 417, 418, 420, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280, 801, 802, 803, 804, 805, 291, 340, 341]" -PYTHON_NROPTIONS="" Index: /issm/trunk/m4/analyses.m4 =================================================================== --- /issm/trunk/m4/analyses.m4 (revision 28012) +++ /issm/trunk/m4/analyses.m4 (revision 28013) @@ -374,4 +374,18 @@ AC_MSG_RESULT($HAVE_HYDROLOGYSHREVE) dnl }}} +dnl with-HydrologyArmapw{{{ +AC_ARG_WITH([HydrologyArmapw], + AS_HELP_STRING([--with-HydrologyArmapw = YES], [compile with HydrologyArmapw capabilities (default is yes)]), + [HYDROLOGYARMAPW=$withval],[HYDROLOGYARMAPW=yes]) +AC_MSG_CHECKING(for HydrologyArmapw capability compilation) + +HAVE_HYDROLOGYARMAPW=no +if test "x$HYDROLOGYARMAPW" = "xyes"; then + HAVE_HYDROLOGYARMAPW=yes + AC_DEFINE([_HAVE_HYDROLOGYARMAPW_],[1],[with HydrologyArmapw capability]) +fi +AM_CONDITIONAL([HYDROLOGYARMAPW], [test x$HAVE_HYDROLOGYARMAPW = xyes]) +AC_MSG_RESULT($HAVE_HYDROLOGYARMAPW) +dnl }}} dnl with-L2ProjectionBase{{{ AC_ARG_WITH([L2ProjectionBase], Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 28012) +++ /issm/trunk/m4/issm_options.m4 (revision 28013) @@ -200,4 +200,14 @@ export CFLAGS="-Wno-deprecated-register -Wno-return-type" export CXXFLAGS="-Wno-deprecated-register -Wno-return-type" + dnl NOTE: Commenting out the following, for now, as ISSM seems to + dnl compile and run fine, but certain errors (e.g. file not + dnl found) were not bubbling up, and instead causing MATLAB + dnl to crash. + dnl +# if test "${LDFLAGS}" == ""; then +# export LDFLAGS="-Wl,-no_compact_unwind" +# else +# export LDFLAGS="${LDFLAGS} -Wl,-no_compact_unwind" +# fi ;; *) @@ -327,5 +337,5 @@ export CXXFLAGS="-D_MSYS2_" export LDFLAGS="${LDFLAGS} -no-undefined" - export OSLIBS="-Wl,-L/mingw64/lib/gcc/x86_64-w64-mingw32/10.2.0 -Wl,-L/mingw64/x86_64-w64-mingw32/lib -Wl,-lstdc++ -Wl,-lgfortran -Wl,-lmingw32 -Wl,-lgcc_s -Wl,-lmoldname -Wl,-lmingwex -Wl,-lmsvcrt -Wl,-lm -Wl,-lpthread -Wl,-lshell32 -Wl,-luser32 -Wl,-lgdi32 -Wl,-luser32 -Wl,-ladvapi32 -Wl,-lkernel32 -Wl,-lquadmath -Wl,-lstdc++ -Wl,-lgcc" + export OSLIBS="-Wl,-L/c/msys64/mingw64/lib -Wl,-lstdc++ -Wl,-lmingw32 -Wl,-lgcc_s -Wl,-lmoldname -Wl,-lmingwex -Wl,-lmsvcrt -Wl,-lm -Wl,-lpthread -Wl,-lshell32 -Wl,-luser32 -Wl,-lgdi32 -Wl,-luser32 -Wl,-ladvapi32 -Wl,-lkernel32 -Wl,-lgcc" IS_MSYS2=yes else @@ -384,21 +394,4 @@ dnl case "${host_os}" in - *cygwin*) - if test "${VENDOR}" == "intel-win7-32"; then - MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" - MEXLINKFLAGS="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win32/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" - MEXEXT=`${MATLAB_ROOT}/bin/mexext.bat` - MEXEXT=".${MEXEXT}" - elif test "${VENDOR}" == "intel-win7-64"; then - MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" - MEXLINKFLAGS="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" - MEXEXT=".mexw64" - elif test "${VENDOR}" == "MSVC-Win64" || test "${VENDOR}" == "MSVC-Win64-par"; then - MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" - MEXLINKFLAGS="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" - MATLABINCL="-I`cygpath -m ${MATLAB_ROOT}/extern/include`" - MEXEXT=".mexw64" - fi - ;; *mingw*) if test "${IS_MSYS2}" == "yes"; then @@ -413,15 +406,4 @@ MEXLIB="-L${MEXLIB_DIR} -lmx -lmex -lmat -lm -lmwlapack -lmwblas" fi - ;; - *msys*) - dnl Value to set MEXEXT to can be found on Windows by running $MATLAB_ROOT/bin/mexext.bat - MEXEXT=".mexw64" - MATLABINCL="-I${MATLAB_ROOT}/extern/include" - MEXOPTFLAGS="-O2 -fwrapv -DNDEBUG -g" - MEXCFLAGS="-fexceptions -fno-omit-frame-pointer -m64 -DMATLAB_MEX_FILE" - MEXCXXFLAGS="-fexceptions -fno-omit-frame-pointer -std=c++11 -m64 -DMATLAB_MEX_FILE" - MEXLINKFLAGS="-m64 -Wl,--no-undefined -shared -static -Wl,${MATLAB_ROOT}/extern/lib/win64/mingw64/mexFunction.def" - MEXLIB_DIR="${MATLAB_ROOT}/extern/lib/win64/mingw64" - MEXLIB="-L${MEXLIB_DIR} -lmx -lmex -lmat -lm -lmwlapack -lmwblas" ;; *) @@ -508,8 +490,4 @@ TRIANGLEINCL=-I${TRIANGLE_ROOT}/include case "${host_os}" in - *cygwin*) - TRIANGLEINCL="/I`cygpath -m ${TRIANGLE_ROOT}/include`" - TRIANGLELIB="-Wl,`cygpath -m ${TRIANGLE_ROOT}/lib/libtriangle.lib`" - ;; *darwin*) if test "x${HAVE_JAVASCRIPT}" == "xyes"; then @@ -533,13 +511,5 @@ TRIANGLELIB=${TRIANGLE_ROOT}/share/triangle.o else - TRIANGLELIB="-L${TRIANGLE_ROOT}/lib -ltriangle" - fi - ;; - *msys*) - if test "x${HAVE_JAVASCRIPT}" == "xyes"; then - dnl Link to the object file, not the library - TRIANGLELIB=${TRIANGLE_ROOT}/share/triangle.o - else - TRIANGLELIB="-L${TRIANGLE_ROOT}/lib -ltriangle" + TRIANGLELIB="-Wl,-L${TRIANGLE_ROOT}/lib -Wl,-ltriangle" fi ;; @@ -651,16 +621,4 @@ dnl case "${host_os}" in - *cygwin*) - if test "${DAKOTA_VERSION}" == "5.1" || test "${DAKOTA_VERSION}" == "5.2"; then - DAKOTALIB="-L${DAKOTA_ROOT}/lib -L${BOOST_ROOT}/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem" - elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then - DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" - DAKOTALIB="-L${DAKOTA_ROOT}/lib -L${BOOST_ROOT}/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -lscolib -ljega_fe -llhs -lpebbl -lcolin -linterfaces -llhs_mods -lmoga -loptpp -lsoga -lsurfpack -lutilib -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -l3po -lamplsolver -lcport -ldfftpack -leutils -lfsudace -lhopspack -ljega -lnidr -lpecos -lpsuade -ltinyxml -lutilities -lsparsegrid -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" - AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H]) - AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling parallel MPI]) - else - AC_MSG_ERROR([Dakota version not found or version (${DAKOTA_VERSION}) not supported!]); - fi - ;; *darwin*) if test "${DAKOTA_VERSION}" == "5.1" || test "${DAKOTA_VERSION}" == "5.2"; then @@ -842,9 +800,6 @@ AC_MSG_RESULT([found]) - PYTHONEXT=.so + PYWRAPPEREXT=.so case "${host_os}" in - *cygwin*) - PYTHONLINK="-shared" - ;; *darwin*) PYTHONLINK="-dynamiclib" @@ -856,12 +811,9 @@ PYTHONLINK="-shared" ;; - *msys*) - PYTHONLINK="-shared" - ;; esac AC_DEFINE([_HAVE_PYTHON_], [1], [with Python in ISSM src]) AC_SUBST([PYTHONINCL]) AC_SUBST([PYTHONLIB]) - PYTHONWRAPPEREXT=${PYTHONEXT} + PYTHONWRAPPEREXT=${PYWRAPPEREXT} AC_SUBST([PYTHONWRAPPEREXT]) AC_SUBST([PYTHONLINK]) @@ -1110,7 +1062,4 @@ if test "x${HAVE_ATLAS}" == "xyes"; then case "${host_os}" in - *cygwin*) - ATLASLIB="-L`cygpath -m ${ATLAS_ROOT}` -Wl,libatlas.lib -Wl,libcblas.lib" - ;; *darwin*) ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm" @@ -1122,7 +1071,4 @@ ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm" ;; - *msys*) - ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm" - ;; esac AC_DEFINE([_HAVE_ATLAS_], [1], [with ATLAS in ISSM src]) @@ -1289,7 +1235,4 @@ if test "x${HAVE_HDF5}" == "xyes"; then case "${host_os}" in - *cygwin*) - HDF5LIB="-L`cygpath -m ${HDF5_ROOT}` -Wl,libhdf5.lib -Wl,libhdf5_hl.lib" - ;; *darwin*) HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl" @@ -1299,7 +1242,4 @@ ;; *mingw*) - HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl" - ;; - *msys*) HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl" ;; @@ -1373,12 +1313,4 @@ case "${host_os}" in - *cygwin*) - if test ${PETSC_MAJOR} -lt 3; then - PETSCLIB=-Wl,/LIBPATH:`cygpath -w ${PETSC_ROOT}/lib` -Wl,libpetscksp.lib -Wl,libpetscdm.lib -Wl,libpetscmat.lib -Wl,libpetscvec.lib -Wl,libpetscsnes.lib -Wl,libpetscts.lib -Wl,libmpiuni.lib -Wl,libpetsc.lib - else - PETSCLIB="/link -Wl,/LIBPATH:`cygpath -m ${PETSC_ROOT}/lib` -Wl,libpetsc.lib" - PETSCINCL="/I`cygpath -m ${PETSC_ROOT}/include`" - fi - ;; *darwin*) if test ${PETSC_MAJOR} -lt 3; then @@ -1408,8 +1340,5 @@ ;; *mingw*) - PETSCLIB="-Wl,${PETSC_ROOT}/lib/libpetsc.a" - ;; - *msys*) - PETSCLIB="${PETSC_ROOT}/lib -lpetsc" + PETSCLIB="-Wl,-L${PETSC_ROOT}/lib -Wl,-lpetsc" ;; esac @@ -1464,5 +1393,5 @@ MPILIB="${MPI_LIBFLAGS}" else - MPILIB="-L${MPI_LIBDIR} ${MPI_LIBFLAGS}" + MPILIB="${MPI_LIBDIR} ${MPI_LIBFLAGS}" fi @@ -1547,8 +1476,4 @@ METISINCL="-I${METIS_ROOT}/Lib" case "${host_os}" in - *cygwin*) - METISINCL="/I`cygpath -m ${METIS_ROOT}/Lib`" - METISLIB="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${METIS_ROOT}` -Wl,libmetis.lib" - ;; *darwin*) METISLIB="-L${METIS_ROOT} -lmetis" @@ -1558,8 +1483,5 @@ ;; *mingw*) - METISLIB="-Wl,${METIS_ROOT}/lib/libmetis.a" - ;; - *msys*) - METISLIB="-L${METIS_ROOT} -lmetis" + METISLIB="-Wl,-L${METIS_ROOT}/lib -Wl,-lmetis" ;; esac @@ -1567,7 +1489,4 @@ METISINCL="-I${METIS_ROOT}/include" case "${host_os}" in - *cygwin*) - METISLIB="-L${METIS_ROOT} libmetis.lib" - ;; *darwin*) METISLIB="-L${METIS_ROOT}/lib -lmetis" @@ -1577,8 +1496,5 @@ ;; *mingw*) - METISLIB="-Wl,${METIS_ROOT}/lib/libmetis.a" - ;; - *msys*) - METISLIB="-L${METIS_ROOT}/lib -lmetis" + METISLIB="-Wl,-L${METIS_ROOT}/lib -Wl,-lmetis" ;; esac @@ -1624,7 +1540,4 @@ PARMETISINCL="-I${PARMETIS_ROOT}/include" case "${host_os}" in - *cygwin*) - PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis" - ;; *darwin*) PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis" @@ -1634,8 +1547,5 @@ ;; *mingw*) - PARMETISLIB="-Wl,${PARMETIS_ROOT}/lib/libparmetis.a" - ;; - *msys*) - PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis" + PARMETISLIB="-Wl,-L${PARMETIS_ROOT}/lib -Wl,-lparmetis" ;; esac @@ -1706,5 +1616,5 @@ if test "x${HAVE_M1QN3}" == "xyes"; then if test "${IS_MSYS2}" == "yes"; then - M1QN3LIB="-Wl,${M1QN3_ROOT}/libm1qn3.a -Wl,${M1QN3_ROOT}/libddot.a" + M1QN3LIB="-Wl,-L${M1QN3_ROOT} -Wl,-lm1qn3 -Wl,-lddot" else M1QN3LIB="${M1QN3_ROOT}/libm1qn3.a ${M1QN3_ROOT}/libddot.a" @@ -1826,5 +1736,5 @@ HAVE_SCALAPACK=yes if test "${VENDOR}" == "win-msys2"; then - SCALAPACKLIB="-Wl,${SCALAPACK_ROOT}/lib/libscalapack.a" + SCALAPACKLIB="-Wl,-L${SCALAPACK_ROOT}/lib -Wl,-lscalapack" else SCALAPACKLIB="-L${SCALAPACK_ROOT}/lib -lscalapack" @@ -1879,7 +1789,4 @@ if test "x${HAVE_BLASLAPACK}" == "xyes"; then case "${host_os}" in - *cygwin*) - BLASLAPACKLIB="-L`cygpath -m ${BLASLAPACK_ROOT}` -Wl,libf2cblas.lib -Wl,libf2clapack.lib" - ;; *darwin*) BLASLAPACKLIB="-L${BLASLAPACK_ROOT}/lib" @@ -1908,5 +1815,5 @@ *mingw*) if test -d "${BLASLAPACK_ROOT}"; then - BLASLAPACKLIB="-L${BLASLAPACK_ROOT}/lib" + BLASLAPACKLIB="-Wl,-L${BLASLAPACK_ROOT}/lib" if ls ${BLASLAPACK_ROOT}/lib/libopenblas.* 1> /dev/null 2>&1; then BLASLAPACKLIB+=" -lopenblas" @@ -1914,25 +1821,10 @@ BLASLAPACKLIB+=" -lf2clapack -lf2cblas" elif ls ${BLASLAPACK_ROOT}/lib/libflapack.* 1> /dev/null 2>&1; then - BLASLAPACKLIB="-Wl,${BLASLAPACK_ROOT}/lib/libflapack.a -Wl,${BLASLAPACK_ROOT}/lib/libfblas.a" + BLASLAPACKLIB="-Wl,-L${BLASLAPACK_ROOT}/lib -Wl,-lflapack -Wl,-lfblas" else - BLASLAPACKLIB+=" -llapack -lblas" + BLASLAPACKLIB+=" -Wl,-llapack -Wl,-lblas" fi else - BLASLAPACKLIB="-Wl,${LAPACK_ROOT}/lib/liblapack.a -Wl,${BLAS_ROOT}/lib/libblas.a" - fi - ;; - *msys*) - if test -d "${BLASLAPACK_ROOT}"; then - if ls ${BLASLAPACK_ROOT}/lib/libopenblas.* 1> /dev/null 2>&1; then - BLASLAPACKLIB=" -lopenblas" - elif ls ${BLASLAPACK_ROOT}/lib/libf2clapack.* 1> /dev/null 2>&1; then - BLASLAPACKLIB=" -lf2clapack -lf2cblas" - elif ls ${BLASLAPACK_ROOT}/lib/libflapack.* 1> /dev/null 2>&1; then - BLASLAPACKLIB+=" -lflapack -lfblas" - else - BLASLAPACKLIB=" -llapack -lblas" - fi - else - BLASLAPACKLIB="-L${LAPACK_ROOT}/lib -llapack -L${BLAS_ROOT}/lib -lblas" + BLASLAPACKLIB="${LAPACK_ROOT}/lib/liblapack.a ${BLAS_ROOT}/lib/libblas.a" fi ;; @@ -2046,5 +1938,5 @@ if test "x${MUMPS_ROOT}" == "x${PETSC_ROOT}"; then if test "${VENDOR}" == "win-msys2"; then - MUMPSLIB="-Wl,${MUMPS_ROOT}/lib/libcmumps.a -Wl,${MUMPS_ROOT}/lib/libdmumps.a -Wl,${MUMPS_ROOT}/lib/libsmumps.a -Wl,${MUMPS_ROOT}/lib/libzmumps.a -Wl,${MUMPS_ROOT}/lib/libmumps_common.a -Wl,${MUMPS_ROOT}/lib/libpord.a" + MUMPSLIB="-Wl,-L${MUMPS_ROOT}/lib -Wl,-lcmumps -Wl,-ldmumps -Wl,-lsmumps -Wl,-lzmumps -Wl,-lmumps_common -Wl,-lpord" else MUMPSLIB="-L${MUMPS_ROOT}/lib -ldmumps -lcmumps -lmumps_common -lpord -lparmetis -lzmumps -lmetis" @@ -2428,4 +2320,5 @@ AC_MSG_RESULT([${FORTRAN}]) + IS_FORTRANDIR_A_DIR=no if test "x${FORTRAN}" == "xyes"; then dnl Fortran library @@ -2438,8 +2331,13 @@ ) if test -n "${FORTRAN_LIB}"; then - FORTRAN_DIR=$(echo ${FORTRAN_LIB} | sed -e "s/-L//g" | awk '{print $[1]}') + FORTRAN_DIR=$(echo ${FORTRAN_LIB} | sed -e "s/-Wl,//g" | sed -e "s/-L//g" | awk '{print $[1]}') if test -d "${FORTRAN_DIR}" || test -f "${FORTRAN_DIR}"; then + FORTRANDIR="${FORTRAN_DIR}" + if test -n "${FORTRAN_DIR}"; then + IS_FORTRANDIR_A_DIR=yes + fi FORTRANLIB="${FORTRAN_LIB}" AC_DEFINE([_HAVE_FORTRAN_], [1], [with Fortran library in ISSM src]) + AC_SUBST([FORTRANDIR]) AC_SUBST([FORTRANLIB]) else @@ -2455,4 +2353,5 @@ AC_MSG_RESULT([done]) fi + AM_CONDITIONAL([HAVE_FORTRANDIR], [test "x${IS_FORTRANDIR_A_DIR}" == "xyes"]) dnl }}} dnl Xlib (graphics library){{{ @@ -2779,7 +2678,4 @@ MULTITHREADINGLIB="-lpthread -lrt" case "${host_os}" in - *cygwin*) - MULTITHREADINGLIB="-lpthread -lrt" - ;; *darwin*) MULTITHREADINGLIB="-lpthread" @@ -2791,7 +2687,4 @@ MULTITHREADINGLIB="" ;; - *msys*) - MULTITHREADINGLIB="" - ;; esac AC_DEFINE([_MULTITHREADING_], [1], [with multithreading enabled]) Index: sm/trunk/packagers/linux/complete-issm-linux-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-2.sh (revision 28012) +++ (revision ) @@ -1,94 +1,0 @@ -#!/bin/bash - -################################################################################ -# Wrapper script to build, package, and transfer to ISSM Web site ISSM -# distributable package for Linux with Python 2 API. -# -# Normally, we would put this directly into the project configuration under -# 'Build' -> 'Execute shell', but because it is a bit more involved, it is a -# good idea to version it. -# -# When no failures/errors occur, performs the following: -# - Builds ISSM according to configuration. -# - Packages executables and libraries. -# - Runs test suite against package. -# - Transmits package to ISSM Web site for distribution. -# -# Options: -# -b/--skipbuild Skip ISSM compilation. -# -s/--skiptests Skip ISSM compilation and testing during packaging -# step. Use if packaging fails for some reason but build -# is valid. -# -t/--transferonly Transfer package to ISSM Web site only. Use if transfer -# fails for some reason to skip building, packaging, and -# signing. -# -# NOTE: -# - Use only *one* of the above options at a time, and make sure it is removed -# again after a single run. -# - Builds will fail when any of the above options are used on a clean -# workspace. For example, if 'Source Code Management' -> 'Check-out Strategy' -# select menu is set to "Always check out a fresh copy". -################################################################################ - -## Constants -# -PKG="ISSM-Linux-Python-2" # Name of directory to copy distributable files to - -COMPRESSED_PKG="${PKG}.tar.gz" - -## Environment -# -export COMPRESSED_PKG -export PKG - -## Parse options -# -if [ $# -gt 1 ]; then - echo "Can use only one option at a time" - exit 1 -fi - -# NOTE: We could do this with binary switching (i.e. 0011 to sign and transfer, -# but the following is self-documenting). -# -build=1 -package=1 -transfer=1 - -if [ $# -eq 1 ]; then - case $1 in - -b|--skipbuild) build=0; shift ;; - -s|--skiptests) build=0; ;; - -t|--transferonly) build=0; package=0; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -# Build -if [ ${build} -eq 1 ]; then - ./jenkins/jenkins.sh ./jenkins/ross-debian_linux-binaries-python-2 - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - -# Package -if [ ${package} -eq 1 ]; then - ./packagers/linux/package-issm-linux-binaries-python-2.sh $1 - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - -# Transfer distributable package to ISSM Web site -if [ ${transfer} -eq 1 ]; then - ./packagers/linux/transfer-issm-linux-binaries.sh - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh (revision 28012) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh (revision 28013) @@ -30,5 +30,5 @@ LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself LIBGFORTRAN_DIST="${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',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # 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_NROPTIONS="'benchmark','all','exclude',[125,126,129,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2012,2013,2020,2021,2051,2052,2053,2084,2085,2090,2091,2092,2101,2424,2425,3001:3300,3480,3481,4001:4100]" # 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" @@ -140,5 +140,5 @@ # Check that MATLAB did not exit in error - matlabExitedInError=`grep -c -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword|Invalid MEX-file" matlab.log` + matlabExitedInError=`grep -c -E "Activation cannot proceed|Error in|Illegal|Invalid MEX-file|license|Warning: Name is nonexistent or not a directory" matlab.log` if [ ${matlabExitedInError} -ne 0 ]; then Index: sm/trunk/packagers/linux/package-issm-linux-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-python-2.sh (revision 28012) +++ (revision ) @@ -1,185 +1,0 @@ -#!/bin/bash - -################################################################################ -# Packages and tests ISSM distributable package for Linux with Python 2 API. -# -# Options: -# -s/--skiptests Skip testing during packaging Use if packaging fails -# for some reason but build is valid. -# -# NOTE: -# - Assumes that the following constants are defined, -# -# COMPRESSED_PKG -# ISSM_DIR -# PKG -# -# See also: -# - packagers/linux/complete-issm-linux-binaries-python-2.sh -################################################################################ - -# Expand aliases within the context of this script -shopt -s expand_aliases - -## Override certain aliases -# -alias grep=$(which grep) - -## Constants -# -LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself -LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it -PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded - -## Environment -# -export PATH="${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 - -if [ $# -eq 1 ]; then - case $1 in - -s|--skiptests) skip_tests=1; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -# Clean up from previous packaging -echo "Cleaning up existing assets" -cd ${ISSM_DIR} -rm -rf ${PKG} ${COMPRESSED_PKG} -mkdir ${PKG} - -# 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 - -echo "Moving libgfortran to lib/" -cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null - -echo "Moving GSHHG assets to share/" -if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then - mkdir ${ISSM_DIR}/share 2> /dev/null - cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share -else - echo "GSHHG not found" - exit 1 -fi - -echo "Moving PROJ assets to share/" -if [ -d ${ISSM_DIR}/externalpackages/proj/install/share/proj ]; then - mkdir ${ISSM_DIR}/share 2> /dev/null - cp -R ${ISSM_DIR}/externalpackages/proj/install/share/proj ${ISSM_DIR}/share -else - echo "PROJ 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 -c -E "Error|Standard exception|Traceback|bad interpreter" python.log` - - 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 - sed -i "/FAILED TO establish the default connection to the WindowServer/d" python.log # First, need to remove WindowServer error message - numTestsFailed=`grep -c -E "FAILED|ERROR" python.log` - - if [[ ${numTestsFailed} -ne 0 ]]; then - echo "One or more tests FAILED" - cat python.log - 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 share 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} ${PKG} Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-python-3.sh (revision 28012) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries-python-3.sh (revision 28013) @@ -30,5 +30,5 @@ LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself LIBGFORTRAN_DIST="${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 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 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 +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 129 234 235 418 420 435 444 445 701 702 703 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 2004 2005 2006 2007 2008 2010 2011 2012 2013 2020 2021 2051 2052 2053 2084 2085 2090 2091 2092 2101 2424 2425 3001:3300 3480 3481 4001:4100" # 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 ## Environment @@ -134,7 +134,4 @@ export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured - # Ensure that runme.py uses Python 3 interpreter - sed -i "s|/usr/bin/env python|/usr/bin/python3|g" ./runme.py - # Run tests, redirecting output to logfile and suppressing output to console ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 @@ -142,5 +139,5 @@ # Check that Python did not exit in error pythonExitCode=`echo $?` - pythonExitedInError=`grep -c -E "Error|Standard exception|Traceback|bad interpreter" python.log` + pythonExitedInError=`grep -c -E "Error|No such file or directory|Permission denied|Standard exception|Traceback|bad interpreter|syntax error" python.log` if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then @@ -176,7 +173,7 @@ cp -rf bin examples lib scripts share test ${PKG} mkdir ${PKG}/execution -${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files +# ${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/*.py # Remove all Python scripts rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes rm -f ${PKG}/lib/*.a # Remove static libraries from package Index: /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh (revision 28012) +++ /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh (revision 28013) @@ -35,20 +35,13 @@ shopt -s expand_aliases -# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, -# -# Command line tool support for Subversion — including svn, git-svn, and -# related commands — is no longer provided by Xcode. (50266910) -# -# which results in, -# -# svn: error: The subversion command line tools are no longer provided by -# Xcode. -# -# when calling svn, even when subversion is installed via Homebrew and its path -# is available in PATH. -# -# NOTE: May be able to remove this after updating macOS. -# -#alias svn='/usr/local/bin/svn' +# NOTE: For some reason, calling svn from within the context of this script +# gives, +# +# svn: command not found +# +# even though it is installed via Homebrew and available at the following +# path. +# +alias svn='/usr/local/bin/svn' ## Override certain other aliases @@ -234,6 +227,7 @@ # Check status - STATUS=$(grep 'Status:' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') - if [[ "${STATUS}" == "success" ]]; then + STATUS=$(grep '"status": "Accepted"' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | wc -l) + + if [[ ${STATUS} -gt 0 ]]; then echo "Notarization successful!" break Index: sm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh (revision 28012) +++ (revision ) @@ -1,256 +1,0 @@ -#!/bin/bash - -################################################################################ -# Commits ISSM distributable package for macOS with Python 2 API to repository -# for signing. This repository is polled by a project running on a JPL -# Cybersecurity Jenkins server and performs the actual signing and -# notarization. -# -# Options: -# -r/--resign Skip ISSM compilation and packaging. Use to retrigger -# signing/notarization if it fails but build and package -# are valid. -# -u/--unlock Remove lock file from signed package repository. Use if -# build is aborted to allow for subsequent fresh build. -# -# NOTE: -# - Assumes that the following constants are defined, -# -# COMPRESSED_PKG -# ISSM_BINARIES_REPO_PASS -# ISSM_BINARIES_REPO_USER -# SIGNED_REPO_COPY -# SIGNED_REPO_URL -# -# See also: -# - packagers/mac/complete-issm-mac-binaries-python-2.sh -# - packagers/mac/sign-issm-mac-binaries-python-2.sh -# -# TODO: -# - Generalize checkout_*_repo_copy and validate_*_repo_copy functions (e.g. -# pass 'signed' or 'unsigned' as argument) -################################################################################ - -# 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 -# -MAX_SIGNING_CHECK_ATTEMPTS=30 -NOTARIZATION_LOGFILE="notarization.log" -RETRIGGER_SIGNING_FILE="retrigger.txt" -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/2/unsigned" - -## Functions -# -checkout_signed_repo_copy(){ - echo "Checking out copy of repository for signed packages" - - # NOTE: Get empty copy because we do not want to have to check out package - # from previous signing. - # - svn checkout \ - --trust-server-cert \ - --non-interactive \ - --depth empty \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_URL} \ - ${SIGNED_REPO_COPY} > /dev/null 2>&1 -} -checkout_unsigned_repo_copy(){ - echo "Checking out copy of repository for unsigned packages" - svn checkout \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${UNSIGNED_REPO_URL} \ - ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 -} -validate_signed_repo_copy(){ - # Validate copy of repository for signed binaries (e.g. - # 'Check-out Strategy' was set to 'Use 'svn update' as much as possible'; - # initial checkout failed) - if [[ ! -d ${SIGNED_REPO_COPY} || ! -d ${SIGNED_REPO_COPY}/.svn ]]; then - rm -rf ${SIGNED_REPO_COPY} - checkout_signed_repo_copy - fi -} -validate_unsigned_repo_copy(){ - # Validate copy of repository for unsigned binaries (e.g. - # 'Check-out Strategy' was set to 'Use 'svn update' as much as possible'; - # initial checkout failed) - if [[ ! -d ${UNSIGNED_REPO_COPY} || ! -d ${UNSIGNED_REPO_COPY}/.svn ]]; then - rm -rf ${UNSIGNED_REPO_COPY} - checkout_unsigned_repo_copy - fi -} - -## Parse options -# -if [ $# -gt 1 ]; then - echo "Can use only one option at a time" - exit 1 -fi - -retrigger_signing=0 -unlock=0 - -if [ $# -eq 1 ]; then - case $1 in - -r|--resign) retrigger_signing=1; ;; - -u|--unlock) unlock=1; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -validate_signed_repo_copy - -if [ ${unlock} -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 update \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 - svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 - svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - --message "DEL: Removing lock file after failed build" ${SIGNED_REPO_COPY} > /dev/null 2>&1 - svn cleanup ${SIGNED_REPO_COPY} > /dev/null 2>&1 - - echo "Remove -u/--unlock option from configuration and run again" - exit 1 -fi - -# If lock file exists, a signing build is still in process by JPL Cybersecurity -svn update \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_COPY}/${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 - -# 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 \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - --message "ADD: New lock file" ${SIGNED_REPO_COPY} > /dev/null 2>&1 - -# Check out copy of repository for unsigned packages -validate_unsigned_repo_copy - -if [ ${retrigger_signing} -eq 0 ]; then - # Commit new compressed package to repository for unsigned binaries - 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 \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - --message "CHG: New unsigned package" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 -else - # NOTE: If notarize_only == 1, we commit a dummy file as we do not want to - # have to commit the entire compressed package again simply to - # retrigger the signing build on the remote JPL Cybersecurity Jenkins - # server. - # - echo "Attempting to sign existing package again" - echo $(date +'%Y-%m-%d-%H-%M-%S') > ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} # Write datetime stamp to file to ensure modification is made - svn add ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} > /dev/null 2>&1 - svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - --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..." -SIGNING_CHECK_ATTEMPT=0 -while [ ${SIGNING_CHECK_ATTEMPT} -lt ${MAX_SIGNING_CHECK_ATTEMPTS} ]; do - echo "...in progress still; checking again in ${SIGNING_CHECK_PERIOD} seconds" - sleep ${SIGNING_CHECK_PERIOD} - svn update \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_COPY} > /dev/null 2>&1 - - if [ ! -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]; then - # Retrieve notarization lock file - svn update \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} - - # Check status - STATUS=$(grep 'Status:' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') - if [[ "${STATUS}" == "success" ]]; then - echo "Notarization successful!" - break - else - echo "Notarization failed!" - echo "----------------------- Contents of notarization logfile -----------------------" - cat ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} - echo "--------------------------------------------------------------------------------" - - exit 1 - fi - else - ((++SIGNING_CHECK_ATTEMPT)) - fi -done - -if [ ! -f ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} ]; then - echo "Signing timed out!" - exit 1 -fi Index: /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh (revision 28012) +++ /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh (revision 28013) @@ -35,20 +35,13 @@ 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' +# NOTE: For some reason, calling svn from within the context of this script +# gives, +# +# svn: command not found +# +# even though it is installed via Homebrew and available at the following +# path. +# +alias svn='/usr/local/bin/svn' ## Override certain other aliases @@ -234,6 +227,7 @@ # Check status - STATUS=$(grep 'Status:' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') - if [[ "${STATUS}" == "success" ]]; then + STATUS=$(grep '"status": "Accepted"' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | wc -l) + + if [[ ${STATUS} -gt 0 ]]; then echo "Notarization successful!" break Index: /issm/trunk/packagers/mac/complete-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/complete-issm-mac-binaries-matlab.sh (revision 28012) +++ /issm/trunk/packagers/mac/complete-issm-mac-binaries-matlab.sh (revision 28013) @@ -98,5 +98,5 @@ # Build if [ ${build} -eq 1 ]; then - ./jenkins/jenkins.sh ./jenkins/pine_island-mac-binaries-matlab + ./jenkins/jenkins.sh ./jenkins/mac-intel-binaries-matlab if [ $? -ne 0 ]; then @@ -128,12 +128,21 @@ fi -# Transfer distributable package to ISSM Web site -if [ ${transfer} -eq 1 ]; then - ./packagers/mac/transfer-issm-mac-binaries.sh +# NOTE: Because Mac build nodes are no longer directly connected to UCI +# network and because remote access requires a VPN connection, we can +# no longer transfer signed distributables via SSH. For now, there is +# a cron job running every five minutes under user jenkins on +# ross.ics.uci.edu that runs +# /home/jenkins/bin/update-issm-mac-binaries.sh, which checks for +# updated, signed distributables in the ISSM Binaries SVN repository +# and if they are available, copies them to the public directory. +# - if [ $? -ne 0 ]; then - echo "Failure while transferring package to ISSM server" - exit 1 - fi -fi +# # Transfer distributable package to ISSM Web site +# if [ ${transfer} -eq 1 ]; then +# ./packagers/mac/transfer-issm-mac-binaries.sh +# if [ $? -ne 0 ]; then +# exit 1 +# fi +# fi + Index: sm/trunk/packagers/mac/complete-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-2.sh (revision 28012) +++ (revision ) @@ -1,135 +1,0 @@ -#!/bin/bash - -################################################################################ -# Wrapper script to build, package, send for signing, and transfer to ISSM Web -# site ISSM distributable package for macOS with Python 2 API. -# -# Normally, we would put this directly into the project configuration under -# 'Build' -> 'Execute shell', but because it is a bit more involved, it is a -# good idea to version it. -# -# When no failures/errors occur, performs the following: -# - Builds ISSM according to configuration. -# - Packages executables and libraries. -# - Runs test suite against package. -# - Commits compressed package to repository to be signed by JPL Cybersecurity. -# - Retrieves signed package and transmits it to ISSM Web site for -# distribution. -# -# Options: -# -b/--skipbuild Skip ISSM compilation. -# -r/--resign Skip ISSM compilation and packaging. Use to retrigger -# signing/notarization if it fails but build and package -# are valid. -# -s/--skiptests Skip ISSM compilation and testing during packaging -# step. Use if packaging fails for some reason but build -# is valid. -# -t/--transferonly Transfer package to ISSM Web site only. Use if transfer -# fails for some reason to skip building, packaging, and -# signing. -# -u/--unlock Remove lock file from signed package repository. Use if -# build is aborted to allow for subsequent fresh build. -# -# Debugging: -# - Relies on a very tight handshake with project on remote JPL Cybersecurity -# Jenkins server. Debugging may be performed locally by running, -# -# packagers/mac/sign-issm-mac-binaries-python-2.sh -# -# with "AD_IDENTITY", "AD_USERNAME", and "ASC_PROVIDER" hardcoded to Apple -# Developer credentials (make sure to also set keychain password in -# "ALTOOL_PASSWORD"). -# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can -# help debug potential SVN issues. -# -# NOTE: -# - Use only *one* of the above options at a time, and make sure it is removed -# again after a single run. -# - Builds will fail when any of the above options are used on a clean -# workspace. For example, if 'Source Code Management' -> 'Check-out Strategy' -# select menu is set to "Always check out a fresh copy". -# - 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') with 'Credentials' select menu set -# to "jenkins/****** (SVN repository for ISSM binaries)". -################################################################################ - -## Constants -# -PKG="ISSM-macOS-Python-2" # Name of directory to copy distributable files to -SIGNED_REPO_COPY="./signed" -SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/2/signed" - -COMPRESSED_PKG="${PKG}.zip" - -## Environment -# -export COMPRESSED_PKG -export PKG -export SIGNED_REPO_COPY -export SIGNED_REPO_URL - -## Parse options -# -if [ $# -gt 1 ]; then - echo "Can use only one option at a time" - exit 1 -fi - -# NOTE: We could do this with binary switching (i.e. 0011 to sign and transfer, -# but the following is self-documenting). -# -build=1 -package=1 -sign=1 -transfer=1 - -if [ $# -eq 1 ]; then - case $1 in - -b|--skipbuild) build=0; shift ;; - -r|--resign) build=0; package=0; ;; - -s|--skiptests) build=0; ;; - -t|--transferonly) build=0; package=0; sign=0; ;; - -u|--unlock) build=0; package=0; transfer=0; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -# Build -if [ ${build} -eq 1 ]; then - ./jenkins/jenkins.sh ./jenkins/pine_island-mac-binaries-python-2 - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - -# Package -if [ ${package} -eq 1 ]; then - ./packagers/mac/package-issm-mac-binaries-python-2.sh $1 - - if [ $? -ne 0 ]; then - exit 1 - fi - - shift # Clear $1 so that it is not passed to commit_for_signing script -fi - -# Commit for signing -if [ ${sign} -eq 1 ]; then - ./packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh $1 - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - -# Transfer distributable package to ISSM Web site -if [ ${transfer} -eq 1 ]; then - ./packagers/mac/transfer-issm-mac-binaries.sh - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - Index: /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-3.sh (revision 28012) +++ /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-3.sh (revision 28013) @@ -98,5 +98,5 @@ # Build if [ ${build} -eq 1 ]; then - ./jenkins/jenkins.sh ./jenkins/pine_island-mac-binaries-python-3 + ./jenkins/jenkins.sh ./jenkins/mac-intel-binaries-python-3 if [ $? -ne 0 ]; then @@ -125,11 +125,21 @@ fi -# Transfer distributable package to ISSM Web site -if [ ${transfer} -eq 1 ]; then - ./packagers/mac/transfer-issm-mac-binaries.sh +# NOTE: Because Mac build nodes are no longer directly connected to UCI +# network and because remote access requires a VPN connection, we can +# no longer transfer signed distributables via SSH. For now, there is +# a cron job running every five minutes under user jenkins on +# ross.ics.uci.edu that runs +# /home/jenkins/bin/update-issm-mac-binaries.sh, which checks for +# updated, signed distributables in the ISSM Binaries SVN repository +# and if they are available, copies them to the public directory. +# - if [ $? -ne 0 ]; then - exit 1 - fi -fi +# # Transfer distributable package to ISSM Web site +# if [ ${transfer} -eq 1 ]; then +# ./packagers/mac/transfer-issm-mac-binaries.sh +# if [ $? -ne 0 ]; then +# exit 1 +# fi +# fi + Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh (revision 28012) +++ /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh (revision 28013) @@ -23,20 +23,13 @@ shopt -s expand_aliases -# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# NOTE: For some reason, calling svn from within the context of this script +# gives, # -# Command line tool support for Subversion — including svn, git-svn, and -# related commands — is no longer provided by Xcode. (50266910) +# svn: command not found # -# which results in, +# even though it is installed via Homebrew and available at the following +# path. # -# 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' +alias svn='/usr/local/bin/svn' ## Override certain other aliases @@ -47,6 +40,6 @@ ## Constants # -MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # 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" +MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,129,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2012,2013,2020,2021,2051,2052,2053,2084,2085,2090,2091,2092,2101,2424,2425,3001:3300,3480,3481,4001:4100]" # 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_R2022b.app" ## Environment @@ -154,5 +147,5 @@ # Check that MATLAB did not exit in error - matlabExitedInError=`grep -c -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword" matlab.log` + matlabExitedInError=`grep -c -E "Activation cannot proceed|Error in|Illegal|Invalid MEX-file|license|Warning: Name is nonexistent or not a directory" matlab.log` if [ ${matlabExitedInError} -ne 0 ]; then Index: sm/trunk/packagers/mac/package-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-python-2.sh (revision 28012) +++ (revision ) @@ -1,199 +1,0 @@ -#!/bin/bash - -################################################################################ -# Packages and tests ISSM distributable package for macOS with Python 2 API. -# -# Options: -# -s/--skiptests Skip testing during packaging Use if packaging fails -# for some reason but build is valid. -# -# NOTE: -# - Assumes that the following constants are defined, -# -# COMPRESSED_PKG -# ISSM_DIR -# PKG -# -# See also: -# - packagers/mac/complete-issm-mac-binaries-python-2.sh -# - packagers/mac/sign-issm-mac-binaries-python-2.sh -################################################################################ - -# Expand aliases within the context of this script -shopt -s expand_aliases - -# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, -# -# Command line tool support for Subversion — including svn, git-svn, and -# related commands — is no longer provided by Xcode. (50266910) -# -# which results in, -# -# svn: error: The subversion command line tools are no longer provided by -# Xcode. -# -# when calling svn, even when subversion is installed via Homebrew and its path -# is available in PATH. -# -# NOTE: May be able to remove this after updating macOS. -# -#alias svn='/usr/local/bin/svn' - -## Override certain other aliases -# -alias grep=$(which grep) - -## Constants -# -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 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 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 - -## 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 - -if [ $# -eq 1 ]; then - case $1 in - -s|--skiptests) skip_tests=1; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -# Clean up from previous packaging -echo "Cleaning up existing assets" -cd ${ISSM_DIR} -rm -rf ${PKG} ${COMPRESSED_PKG} -mkdir ${PKG} - -# 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 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 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 GSHHG assets to share/" -if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then - mkdir ${ISSM_DIR}/share 2> /dev/null - cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share -else - echo "GSHHG not found" - exit 1 -fi - -echo "Moving PROJ assets to share/" -if [ -d ${ISSM_DIR}/externalpackages/proj/install/share/proj ]; then - mkdir ${ISSM_DIR}/share 2> /dev/null - cp -R ${ISSM_DIR}/externalpackages/proj/install/share/proj ${ISSM_DIR}/share -else - echo "PROJ 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 -c -E "Error|Standard exception|Traceback|bad interpreter" python.log` - - 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 - sed -i '' "/FAILED TO establish the default connection to the WindowServer/d" python.log # First, need to remove WindowServer error message - numTestsFailed=`grep -c -E "FAILED|ERROR" python.log` - - if [ ${numTestsFailed} -ne 0 ]; then - echo "One or more tests FAILED" - cat python.log - 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 share 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} Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-python-3.sh (revision 28012) +++ /issm/trunk/packagers/mac/package-issm-mac-binaries-python-3.sh (revision 28013) @@ -23,20 +23,13 @@ shopt -s expand_aliases -# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# NOTE: For some reason, calling svn from within the context of this script +# gives, # -# Command line tool support for Subversion — including svn, git-svn, and -# related commands — is no longer provided by Xcode. (50266910) +# svn: command not found # -# which results in, +# even though it is installed via Homebrew and available at the following +# path. # -# 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' +alias svn='/usr/local/bin/svn' ## Override certain other aliases @@ -46,5 +39,5 @@ ## Constants # -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 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 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 +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 129 234 235 418 420 435 444 445 701 702 703 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 2004 2005 2006 2007 2008 2010 2011 2012 2013 2020 2021 2051 2052 2053 2084 2085 2090 2091 2092 2101 2424 2425 3001:3300 3480 3481 4001:4100" # 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 ## Environment @@ -147,7 +140,4 @@ export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured - # Ensure that runme.py uses Python 3 interpreter - sed -i '' "s|/usr/bin/env python|/usr/local/bin/python3|g" ./runme.py - # Run tests, redirecting output to logfile and suppressing output to console ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 @@ -155,5 +145,5 @@ # Check that Python did not exit in error pythonExitCode=`echo $?` - pythonExitedInError=`grep -c -E "Error|Standard exception|Traceback|bad interpreter" python.log` + pythonExitedInError=`grep -c -E "Error|No such file or directory|Permission denied|Standard exception|Traceback|bad interpreter|syntax error" python.log` if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then @@ -190,7 +180,7 @@ 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 +# ${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/*.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 Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh (revision 28012) +++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh (revision 28013) @@ -8,12 +8,12 @@ # builds. # -# In order to replicate the requried Jenkins project configuration: +# In order to replicate the required 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). +# - Contact one of the members of the ISSM development team for credentials 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. +# 'Add Credentials' and enter the credentials from above. # - From the 'Dashboard', select 'New Item' -> 'Freestyle project'. # - Under 'Source Code Management', select 'Subversion'. @@ -24,5 +24,5 @@ # - The 'Local module directory' text field should be set to the same # value as the constant UNSIGNED_REPO_COPY (set below to './unsigned'). -# - Under 'Build Trigggers', check the box for 'Poll SCM' and set the +# - Under 'Build Triggers', 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 @@ -52,20 +52,13 @@ 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' +# NOTE: For some reason, calling svn from within the context of this script +# gives, +# +# svn: command not found +# +# even though it is installed via Homebrew and available at the following +# path. +# +alias svn='/usr/local/bin/svn' ## Override certain other aliases @@ -87,5 +80,4 @@ PASSWORD=${ISSM_BINARIES_PASS} PKG="ISSM-macOS-MATLAB" -PRIMARY_BUNDLE_ID="gov.nasa.jpl.issm.matlab" SIGNED_REPO_COPY="./signed" SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/signed" @@ -131,4 +123,5 @@ find ${PKG}/bin -type f -name *.exe; \ find ${PKG}/lib -type f -name *.mexmaci64; \ + find ${PKG}/test -type f -name *.pkg; \ ) @@ -157,16 +150,10 @@ # 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 notarization request response" -while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do - sleep 30 -done +xcrun notarytool submit ${COMPRESSED_PKG} --apple-id "$AD_USERNAME" --team-id "$TEAM_ID" --password "$NOTARY_PASSWORD" --wait &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} echo "Notarization 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 +HAS_UUID=$(grep 'id: ' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) if [ -z "${HAS_UUID}" ]; then echo "Notarization failed!" @@ -182,5 +169,5 @@ # Get UUID from notarization request response -UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*RequestUUID = //') +UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*id: //') echo "UUID: ${UUID}" @@ -194,51 +181,21 @@ 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 +xcrun notarytool log ${UUID} --apple-id "$AD_USERNAME" --team-id "$TEAM_ID" --password "$NOTARY_PASSWORD" &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} +STATUS=$(grep 'status: Accepted' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} | wc -l) + +if [[ ${STATUS} -gt 0 ]]; 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} + echo "Notarization successful!" + + # Set flag indicating notarization was successful + SUCCESS=1 else echo "Notarization failed!" Index: sm/trunk/packagers/mac/sign-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-2.sh (revision 28012) +++ (revision ) @@ -1,348 +1,0 @@ -#!/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/2/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. -# - The 'Local module directory' text field should be set to the same -# value as the constant UNSIGNED_REPO_COPY (set below to './unsigned'). -# - 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 aforementioned 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=$(which grep) - -## Constants -# -AD_IDENTITY="**********" # Apple Developer identity -AD_USERNAME="**********" # Apple Developer username -ALTOOL_PASSWORD="@keychain:**********" # altool password (assumed to be stored in keychain) -ASC_PROVIDER="**********" -MAX_SVN_ATTEMPTS=10 -NOTARIZATION_CHECK_ATTEMPTS=20 -NOTARIZATION_CHECK_PERIOD=60 -NOTARIZATION_LOGFILE="notarization.log" -NOTARIZATION_LOGFILE_PATH="." -PASSWORD=${ISSM_BINARIES_PASS} -PKG="ISSM-macOS-Python-2" -PRIMARY_BUNDLE_ID="gov.nasa.jpl.issm.python" -SIGNED_REPO_COPY="./signed" -SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/2/signed" -SIGNING_LOCK_FILE="signing.lock" -SUCCESS_LOGFILE="${SIGNED_REPO_COPY}/success.log" -UNSIGNED_REPO_COPY="./unsigned" -UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/2/unsigned" -USERNAME=${ISSM_BINARIES_USER} - -COMPRESSED_PKG="${PKG}.zip" -EXE_ENTITLEMENTS_PLIST="${PKG}/bin/entitlements.plist" - -# NOTE: Uncomment the following for local testing (Jenkins checks out copy of -# repository for unsigned packages to working directory) -# - -# # 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 ${COMPRESSED_PKG} ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${UNSIGNED_REPO_COPY} - -# # Check out copy of repository for unsigned packages -# echo "Checking out copy of repository for unsigned packages" -# svn checkout \ -# --trust-server-cert \ -# --non-interactive \ -# --username ${USERNAME} \ -# --password ${PASSWORD} \ -# ${UNSIGNED_REPO_URL} \ -# ${UNSIGNED_REPO_COPY} - -rm -rf ${PKG} ${SIGNED_REPO_COPY} - - -# 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 notarization request response" -while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do - sleep 30 -done - -echo "Notarization request response received" - -# Check if UUID exists in response -HAS_UUID=$(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 - -# Check out copy of repository for signed packages -echo "Checking out copy of repository for signed packages" -SVN_ATTEMPT=0 -SVN_SUCCESS=0 -while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do - rm -rf ${SIGNED_REPO_COPY} - svn checkout \ - --trust-server-cert \ - --non-interactive \ - --username ${USERNAME} \ - --password ${PASSWORD} \ - ${SIGNED_REPO_URL} \ - ${SIGNED_REPO_COPY} > /dev/null 2>&1 - if [ $? -eq 0 ]; then - SVN_SUCCESS=1 - break - else - ((++SVN_ATTEMPT)) - sleep 5 - fi -done - -if [ ${SVN_SUCCESS} -eq 0 ]; then - echo "Checkout of repository for signed packages failed" - exit 1 -fi - -# 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} - -SVN_ATTEMPT=0 -SVN_SUCCESS=0 -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" - while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do - svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${USERNAME} \ - --password ${PASSWORD} \ - --message "CHG: New signed package (success)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 - if [ $? -eq 0 ]; then - SVN_SUCCESS=1 - break - else - ((++SVN_ATTEMPT)) - sleep 5 - fi - done - - if [ ${SVN_SUCCESS} -eq 0 ]; then - echo "Commit to repository for signed packages failed" - exit 1 - fi -else - # Commit changes - echo "Committing changes to repository for signed packages" - while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do - svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${USERNAME} \ - --password ${PASSWORD} \ - --message "CHG: New signed package (failure)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 - if [ $? -eq 0 ]; then - SVN_SUCCESS=1 - break - else - ((++SVN_ATTEMPT)) - sleep 5 - fi - done - - if [ ${SVN_SUCCESS} -eq 0 ]; then - echo "Commit to repository for signed packages failed" - exit 1 - fi - - exit 1 -fi Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-3.sh (revision 28012) +++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-3.sh (revision 28013) @@ -8,12 +8,12 @@ # new builds. # -# In order to replicate the requried Jenkins project configuration: +# In order to replicate the required 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). +# - Contact one of the members of the ISSM development team for credentials 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. +# 'Add Credentials' and enter the credentials from above. # - From the 'Dashboard', select 'New Item' -> 'Freestyle project'. # - Under 'Source Code Management', select 'Subversion'. @@ -24,5 +24,5 @@ # - The 'Local module directory' text field should be set to the same # value as the constant UNSIGNED_REPO_COPY (set below to './unsigned'). -# - Under 'Build Trigggers', check the box for 'Poll SCM' and set the +# - Under 'Build Triggers', 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 @@ -52,20 +52,13 @@ 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' +# NOTE: For some reason, calling svn from within the context of this script +# gives, +# +# svn: command not found +# +# even though it is installed via Homebrew and available at the following +# path. +# +alias svn='/usr/local/bin/svn' ## Override certain other aliases @@ -87,5 +80,4 @@ PASSWORD=${ISSM_BINARIES_PASS} PKG="ISSM-macOS-Python-3" -PRIMARY_BUNDLE_ID="gov.nasa.jpl.issm.python" SIGNED_REPO_COPY="./signed" SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/3/signed" @@ -120,5 +112,4 @@ rm -rf ${PKG} ${SIGNED_REPO_COPY} - # Extract package contents echo "Extracting package contents" @@ -132,4 +123,5 @@ find ${PKG}/bin -type f -name *.exe; \ find ${PKG}/bin -type f -name *.pyc; \ + find ${PKG}/test -type f -name *.pkg; \ ) @@ -167,16 +159,10 @@ # 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 notarization request response" -while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do - sleep 30 -done +xcrun notarytool submit ${COMPRESSED_PKG} --apple-id "$AD_USERNAME" --team-id "$TEAM_ID" --password "$NOTARY_PASSWORD" --wait &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} echo "Notarization 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 +HAS_UUID=$(grep 'id: = ' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) if [ -z "${HAS_UUID}" ]; then echo "Notarization failed!" @@ -192,5 +178,5 @@ # Get UUID from notarization request response -UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*RequestUUID = //') +UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*id: //') echo "UUID: ${UUID}" @@ -204,51 +190,21 @@ 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 +xcrun notarytool log ${UUID} --apple-id "$AD_USERNAME" --team-id "$TEAM_ID" --password "$NOTARY_PASSWORD" &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} +STATUS=$(grep 'status: Accepted' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} | wc -l) + +if [[ ${STATUS} -gt 0 ]]; 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} ${COMPRESSED_PKG} + echo "Notarization successful!" + + # Set flag indicating notarization was successful + SUCCESS=1 else echo "Notarization failed!" Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh (revision 28012) +++ /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh (revision 28013) @@ -10,7 +10,7 @@ ## Constants # -INSTALL_DIR=. -MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded -MATLAB_PATH="/Applications/MATLAB_R2018a.app" +INSTALL_DIR=${PWD} +MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,129,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2012,2013,2020,2021,2051,2052,2053,2084,2085,2090,2091,2092,2101,2424,2425,3001:3300,3480,3481,4001:4100]" # 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_R2022b.app" PKG="ISSM-macOS-MATLAB" @@ -34,5 +34,5 @@ # Check that MATLAB did not exit in error matlabExitCode=`echo $?` -matlabExitedInError=`grep -c -E "Activation cannot proceed|license|Error|Warning: Name is nonexistent or not a directory" matlab.log` +matlabExitedInError=`grep -c -E "Activation cannot proceed|Error in|Illegal|Invalid MEX-file|license|Warning: Name is nonexistent or not a directory" matlab.log` if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then Index: sm/trunk/packagers/mac/test-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/test-issm-mac-binaries-python-2.sh (revision 28012) +++ (revision ) @@ -1,54 +1,0 @@ -#!/bin/bash - -################################################################################ -# This script is intended to test ISSM macOS Python 2 binaries on an end-user -# machine after successful packaging and signing. -# -# NOTE: Tarball must already exist in INSTALL_DIR -################################################################################ - -## Constants -# -INSTALL_DIR=. -PKG="ISSM-macOS-Python-2" -PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded - -COMPRESSED_PKG="${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 -c -E "runme.py: error" python.log` - -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=`grep -c -E "FAILED|ERROR" python.log` - -if [[ ${numTestsFailed} -ne 0 ]]; then - echo "One or more tests FAILED" - cat python.log - exit 1 -else - echo "All tests PASSED" -fi Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/test-issm-mac-binaries-python-3.sh (revision 28012) +++ /issm/trunk/packagers/mac/test-issm-mac-binaries-python-3.sh (revision 28013) @@ -10,7 +10,7 @@ ## Constants # -INSTALL_DIR=. +INSTALL_DIR=${PWD} PKG="ISSM-macOS-Python-3" -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 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 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 +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 129 234 235 418 420 435 444 445 701 702 703 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 2004 2005 2006 2007 2008 2010 2011 2012 2013 2020 2021 2051 2052 2053 2084 2085 2090 2091 2092 2101 2424 2425 3001:3300 3480 3481 4001:4100" # 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" @@ -34,5 +34,5 @@ # Check that Python did not exit in error pythonExitCode=`echo $?` -pythonExitedInError=`grep -c -E "runme.py: error" python.log` +pythonExitedInError=`grep -c -E "Error|No such file or directory|Permission denied|Standard exception|Traceback|bad interpreter|syntax error" python.log` if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then Index: /issm/trunk/packagers/win/complete-issm-win-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/win/complete-issm-win-binaries-matlab.sh (revision 28013) +++ /issm/trunk/packagers/win/complete-issm-win-binaries-matlab.sh (revision 28013) @@ -0,0 +1,94 @@ +#!/bin/bash + +################################################################################ +# Wrapper script to build, package, and transfer to ISSM Web site ISSM +# distributable package for Windows with MATLAB API. +# +# Normally, we would put this directly into the project configuration under +# 'Build' -> 'Execute shell', but because it is a bit more involved, it is a +# good idea to version it. +# +# When no failures/errors occur, performs the following: +# - Builds ISSM according to configuration. +# - Packages executables and libraries. +# - Runs test suite against package. +# - Transmits package to ISSM Web site for distribution. +# +# Options: +# -b/--skipbuild Skip ISSM compilation. +# -s/--skiptests Skip ISSM compilation and testing during packaging +# step. Use if packaging fails for some reason but build +# is valid. +# -t/--transferonly Transfer package to ISSM Web site only. Use if transfer +# fails for some reason to skip building, packaging, and +# signing. +# +# NOTE: +# - Use only *one* of the above options at a time, and make sure it is removed +# again after a single run. +# - Builds will fail when any of the above options are used on a clean +# workspace. For example, if 'Source Code Management' -> 'Check-out Strategy' +# select menu is set to "Always check out a fresh copy". +################################################################################ + +## Constants +# +PKG="ISSM-Windows-MATLAB" # Name of directory to copy distributable files to + +COMPRESSED_PKG="${PKG}.tar.gz" + +## Environment +# +export COMPRESSED_PKG +export PKG + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +# NOTE: We could do this with binary switching (i.e. 0011 to sign and transfer, +# but the following is self-documenting). +# +build=1 +package=1 +transfer=1 + +if [ $# -eq 1 ]; then + case $1 in + -b|--skipbuild) build=0; shift ;; + -s|--skiptests) build=0; ;; + -t|--transferonly) build=0; package=0; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# Build +if [ ${build} -eq 1 ]; then + ./jenkins/jenkins.sh ./jenkins/ross-win-msys2-mingw-msmpi-binaries-matlab + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Package +if [ ${package} -eq 1 ]; then + ./packagers/win/package-issm-win-binaries-matlab.sh $1 + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Transfer distributable package to ISSM Web site +if [ ${transfer} -eq 1 ]; then + ./packagers/win/transfer-issm-win-binaries.sh + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + Index: /issm/trunk/packagers/win/package-issm-win-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/win/package-issm-win-binaries-matlab.sh (revision 28013) +++ /issm/trunk/packagers/win/package-issm-win-binaries-matlab.sh (revision 28013) @@ -0,0 +1,242 @@ +#!/bin/bash + +################################################################################ +# Packages and tests ISSM distributable package for Windows with MATLAB API. +# +# Options: +# -s/--skiptests Skip testing during packaging Use if packaging fails +# for some reason but build is valid. +# +# NOTE: +# - Assumes that the following constants are defined, +# +# COMPRESSED_PKG +# ISSM_DIR +# PKG +# +# See also: +# - packagers/win/complete-issm-win-binaries-matlab.sh +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +## Override certain aliases +# +alias grep=$(which grep) + +## Constants +# +#LIBGFORTRAN="/usr/lib/x86_64-win-gnu/libgfortran.so.5.0.0" # Important that this is the library itself +#LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),125,126,129,435,701,702,703]" +#MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,129,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2012,2013,2020,2021,2051,2052,2053,2084,2085,2090,2091,2092,2101,2424,2425,3001:3300,3480,3481,4001:4100]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded +MATLAB_PATH=$(cygpath -u $(cygpath -ms "/c/Program Files/MATLAB/R2019b")) +MSMPI_ROOT="${ISSM_DIR}/externalpackages/msmpi/install" + +## 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 + +if [ $# -eq 1 ]; then + case $1 in + -s|--skiptests) skip_tests=1; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# 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 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 system and MinGW libraries to bin/" +cp /c/msys64/mingw64/bin/libgcc_s_seh-1.dll . +cp /c/msys64/mingw64/bin/libstdc++-6.dll . +cp /c/msys64/mingw64/bin/libwinpthread-1.dll . +cp /c/msys64/mingw64/bin/libgfortran-5.dll . +cp /c/msys64/mingw64/bin/libquadmath-0.dll . + +echo "Moving MSMPI binaries and libraries to bin/" +if [ -f ${MSMPI_ROOT}/bin/mpiexec.exe ]; then + cp ${MSMPI_ROOT}/bin/* . + cp ${MSMPI_ROOT}/lib/libmsmpi.dll . + cp ${MSMPI_ROOT}/lib/msmpi.dll . +else + echo "MSMPI not found" + exit 1 +fi + +echo "Moving MEX-files to bin/" +mv ${ISSM_DIR}/lib/*.mexw64 . + +# 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 + +cd ${ISSM_DIR}/lib + +# echo "Moving libgfortran to lib/" +# cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null + +# echo "Moving GSHHG assets to share/" +# if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then +# mkdir ${ISSM_DIR}/share 2> /dev/null +# cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share +# else +# echo "GSHHG not found" +# exit 1 +# fi + +# echo "Moving PROJ assets to share/" +# if [ -d ${ISSM_DIR}/externalpackages/proj/install/share/proj ]; then +# mkdir ${ISSM_DIR}/share 2> /dev/null +# cp -R ${ISSM_DIR}/externalpackages/proj/install/share/proj ${ISSM_DIR}/share +# else +# echo "PROJ not found" +# exit 1 +# fi + +# Run tests +if [ ${skip_tests} -eq 0 ]; then + echo "Running tests" + cd ${ISSM_DIR}/test/NightlyRun + rm matlab.log 2> /dev/null + + # Run tests, redirecting output to logfile and suppressing output to console + export ISSM_DIR_WIN=$(cygpath -w "${ISSM_DIR}") + ${MATLAB_PATH}/bin/matlab -nodesktop -nosplash -nojvm -r "try, addpath ${ISSM_DIR_WIN}/bin ${ISSM_DIR_WIN}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log & + + # Wait for MATLAB to exit + # + # TODO: + # - Replace by adding -wait option to above calls to matlab? + # + sleep 5; + echo "Waiting for MATLAB to exit" + pid=$(ps -W | grep MATLAB | awk '{print $1}') + echo '-----------------------------' + echo "pid: ${pid}" + echo '-----------------------------' + + # Time out after $max_time seconds because sometimes multiple MATLAB processes get locked in race condition + timer=0 + max_time=7200 + while [[ $timer -lt $max_time && -n "${pid}" ]]; do + pid=$(ps -W | grep MATLAB | awk '{print $1}') + timer=$((timer + 1)) + sleep 1; + done + + # Check if timer hit $max_time + if [ $timer -eq $max_time ]; then + echo "Testing timed out at ${timer} seconds" + # Kill MATLAB processes + pid=$(ps -W | grep MATLAB | awk '{print $1}') + echo "${pid}" | xargs /bin/kill -f + exit 1 + fi + + # Filter out Windows characters + cat matlab.log | tr -cd '\11\12\40-\176' > matlab.log2 && mv matlab.log2 matlab.log + + # Check that MATLAB did not exit in error + matlabExitedInError=`grep -c -E "Activation cannot proceed|Error in|Illegal|Invalid MEX-file|license|Warning: Name is nonexistent or not a directory" matlab.log` + + if [ ${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 + sed -i "/FAILED TO establish the default connection to the WindowServer/d" matlab.log # First, need to remove WindowServer error message + numTestsFailed=`grep -c -E "FAILED|ERROR" matlab.log` + + if [ ${numTestsFailed} -ne 0 ]; then + echo "One or more tests FAILED" + cat matlab.log + 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}" +# NOTE: We do not copy lib directory to package as MATLAB seems to perform differently under Windows and so we package all DDL's and MEX-files in bin directory +cp -rf bin examples scripts share 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 -rf ${PKG}/test/SandBox # Remove testing sandbox from package + +# Compress package +echo "Compressing package" +tar -czf ${COMPRESSED_PKG} ${PKG} Index: /issm/trunk/packagers/win/transfer-issm-win-binaries.sh =================================================================== --- /issm/trunk/packagers/win/transfer-issm-win-binaries.sh (revision 28013) +++ /issm/trunk/packagers/win/transfer-issm-win-binaries.sh (revision 28013) @@ -0,0 +1,24 @@ +#!/bin/bash + +################################################################################ +# Transfers ISSM distributable package for Windows to ISSM website. +# +# NOTE: +# - Assumes that the following constants are defined, +# +# COMPRESSED_PKG +# +# See also: +# - packagers/win/complete-issm-win-binaries-matlab.sh +# - packagers/win/complete-issm-win-binaries-python-2.sh +# - packagers/win/complete-issm-win-binaries-python-3.sh +################################################################################ + +# Transfer package to ISSM Web site +echo "Transferring package to ISSM Web site" +scp -i ~/.ssh/windows_10-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 (with -t/--transferonly option to skip building and packaging)." + exit 1 +fi Index: /issm/trunk/scripts/BinRead.py =================================================================== --- /issm/trunk/scripts/BinRead.py (revision 28012) +++ /issm/trunk/scripts/BinRead.py (revision 28013) @@ -1,3 +1,3 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 import numpy as np from os import environ, path @@ -6,113 +6,113 @@ from argparse import ArgumentParser -def BinRead(filin, filout='', verbose=0): #{{{ +def BinRead(infile, outfile='', verbose=0): #{{{ - print("reading binary file.") - f = open(filin, 'rb') + print('reading binary file') + f = open(infile, 'rb') - if filout: - sys.stdout = open(filout, 'w') + if outfile: + sys.stdout = open(outfile, 'w') while True: try: - #Step 1: read size of record name + # 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)) + print('probable EOF: {}'.format(e)) break - print("============================================================================ ") + print('============================================================================') if verbose > 2: - print("\n recordnamesize = {}".format(recordnamesize)) - recordname = struct.unpack('{}s'.format(recordnamesize), f.read(recordnamesize))[0] - print("field: {}".format(recordname)) + print('\n recordnamesize = {}'.format(recordnamesize)) + recordname = struct.unpack('{}s'.format(recordnamesize), f.read(recordnamesize))[0].decode('ASCII') + print('field: {}'.format(recordname)) - #Step 2: read the data itself. - #first read length of record + # Step 2: Read the data itself + # First read length of record #reclen = struct.unpack('i', f.read(struct.calcsize('i')))[0] reclen = struct.unpack('q', f.read(struct.calcsize('q')))[0] if verbose > 1: - print("reclen = {}".format(reclen)) + print('reclen = {}'.format(reclen)) - #read data code: + # Read data code code = struct.unpack('i', f.read(struct.calcsize('i')))[0] - print("Format = {} (code {})".format(CodeToFormat(code), code)) + print('Format = {} (code {})'.format(CodeToFormat(code), code)) if code == FormatToCode('Boolean'): bval = struct.unpack('i', f.read(reclen - struct.calcsize('i')))[0] - print("value = {}".format(bval)) + print('value = {}'.format(bval)) elif code == FormatToCode('Integer'): ival = struct.unpack('i', f.read(reclen - struct.calcsize('i')))[0] - print("value = {}".format(ival)) + print('value = {}'.format(ival)) elif code == FormatToCode('Double'): dval = struct.unpack('d', f.read(reclen - struct.calcsize('i')))[0] - print("value = {}".format(dval)) + print('value = {}'.format(dval)) elif code == FormatToCode('String'): strlen = struct.unpack('i', f.read(struct.calcsize('i')))[0] if verbose > 1: - print("strlen = {}".format(strlen)) + print('strlen = {}'.format(strlen)) sval = struct.unpack('{}s'.format(strlen), f.read(strlen))[0] - print("value = '{}'".format(sval)) + print('value = {}'.format(sval)) elif code == FormatToCode('BooleanMat'): - #read matrix type: + # Read matrix type mattype = struct.unpack('i', f.read(struct.calcsize('i')))[0] - print("mattype = {}".format(mattype)) + print('mattype = {}'.format(mattype)) - #now read matrix + # Read matrix s = [0, 0] s[0] = struct.unpack('i', f.read(struct.calcsize('i')))[0] s[1] = struct.unpack('i', f.read(struct.calcsize('i')))[0] - print("size = [{}x{}]".format(s[0], s[1])) + 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 + data[i][j] = struct.unpack('d', f.read(struct.calcsize('d')))[0] if verbose > 2: - print("data[{}, {}] = {}".format(i, j, data[i][j])) + print('data[{}, {}] = {}'.format(i, j, data[i][j])) elif code == FormatToCode('IntMat'): - #read matrix type: + # Read matrix type mattype = struct.unpack('i', f.read(struct.calcsize('i')))[0] - print("mattype = {}".format(mattype)) + print('mattype = {}'.format(mattype)) - #now read matrix + # Read matrix s = [0, 0] s[0] = struct.unpack('i', f.read(struct.calcsize('i')))[0] s[1] = struct.unpack('i', f.read(struct.calcsize('i')))[0] - print("size = [{}x{}]".format(s[0], s[1])) + 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 + data[i][j] = struct.unpack('d', f.read(struct.calcsize('d')))[0] if verbose > 2: - print("data[{}, {}] = {}".format(i, j, data[i][j])) + print('data[{}, {}] = {}'.format(i, j, data[i][j])) elif code == FormatToCode('DoubleMat'): - #read matrix type: + # Read matrix type mattype = struct.unpack('i', f.read(struct.calcsize('i')))[0] - print("mattype = {}".format(mattype)) + print('mattype = {}'.format(mattype)) - #now read matrix + # Read matrix s = [0, 0] s[0] = struct.unpack('i', f.read(struct.calcsize('i')))[0] s[1] = struct.unpack('i', f.read(struct.calcsize('i')))[0] - print("size = [{}x{}]".format(s[0], s[1])) + 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 + data[i][j] = struct.unpack('d', f.read(struct.calcsize('d')))[0] if verbose > 2: - print("data[{}, {}] = {}".format(i, j, data[i][j])) + print('data[{}, {}] = {}'.format(i, j, data[i][j])) elif code == FormatToCode('MatArray'): f.seek(reclen - 4, 1) - print("skipping {} bytes for code {}.".format(code, reclen - 4)) + print('skipping {} bytes for code {}'.format(code, reclen - 4)) elif code == FormatToCode('StringArray'): f.seek(reclen - 4, 1) - print("skipping {} bytes for code {}.".format(code, reclen - 4)) + print('skipping {} bytes for code {}'.format(code, reclen - 4)) else: @@ -123,8 +123,7 @@ 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. + """This routine takes the format string and converts it into an integer, + which is passed along with the record in order to identify the nature of + the data being sent. """ @@ -154,8 +153,6 @@ 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. + """This routine takes a datatype code and converts it to the corresponding + string in order to identify the nature of the data retrieved. """ @@ -186,9 +183,9 @@ if __name__ == '__main__': #{{{ parser = ArgumentParser(description='BinRead - 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('-f', '--infile', help='name of binary input file', default='') + parser.add_argument('-o', '--outfile', help='optional name of text output file', default='') parser.add_argument('-v', '--verbose', help='optional level of output', default=0) args = parser.parse_args() - BinRead(args.filin, args.filout, args.verbose) + BinRead(args.infile, args.outfile, args.verbose) #}}} Index: /issm/trunk/scripts/DownloadExamplesDatasets.sh =================================================================== --- /issm/trunk/scripts/DownloadExamplesDatasets.sh (revision 28012) +++ /issm/trunk/scripts/DownloadExamplesDatasets.sh (revision 28013) @@ -25,7 +25,13 @@ fi -# Get content of page that hosts datasets, reduce to just datasets list, then +# Get content of page that hosts datasets, reduce to just datasets list, then # parse out dataset links +# +# NOTE: Clear DYLD_LIBRARY_PATH in case we have installed our own copy of cURL +# and $ISSM_DIR/etc/environment.sh has been sourced as there may be a +# conflict between versions of cURL executable and libcurl +# dataset_urls=$(\ + DYLD_LIBRARY_PATH=""; \ curl -Ls ${DATASETS_URL} |\ sed '//,// !d' |\ @@ -34,5 +40,7 @@ # Get datasets -wget --no-clobber --directory-prefix="${DIRECTORY_PREFIX}" -i - <<< "${dataset_urls}" +# +echo "Downloading examples datasets..." +wget --quiet --no-clobber --directory-prefix="${DIRECTORY_PREFIX}" -i - <<< "${dataset_urls}" # Expand zip files Index: /issm/trunk/scripts/ol.m =================================================================== --- /issm/trunk/scripts/ol.m (revision 28012) +++ /issm/trunk/scripts/ol.m (revision 28013) @@ -3,5 +3,10 @@ options=pairoptions(varargin{:}); - range=getfieldvalue(options,'<',Inf); + %recover steps in calling workspace: will be used to highlight current step. + steps= evalin('base', 'steps'); + + mmin=getfieldvalue(options,'>',1); + mmax=getfieldvalue(options,'<',Inf); + file=getfieldvalue(options,'file','runme.m'); @@ -20,6 +25,14 @@ return; end - disp(sprintf('%2i: %s',count,tline(16:lastchar))); - if count>range, + if ismember(count,steps), + disp(sprintf('%2i: *%s',count,tline(17:lastchar-1))); + else + if count>=mmin & count <= mmax, + disp(sprintf('%2i: %s',count,tline(17:lastchar-1))); + else + %do nothing. + end + end + if count>mmax, break; end Index: /issm/trunk/scripts/ola.m =================================================================== --- /issm/trunk/scripts/ola.m (revision 28013) +++ /issm/trunk/scripts/ola.m (revision 28013) @@ -0,0 +1,40 @@ +function ola(varargin) + + options=pairoptions(varargin{:}); + + %recover steps in calling workspace: will be used to highlight current step. + steps= evalin('base', 'steps'); + + r=getfieldvalue(options,'r',10); + range=(min(steps)-r):(max(steps)+r); + + file=getfieldvalue(options,'file','runme.m'); + + %Open runme.m file and read line by line + fid=fopen(file,'r'); + + tline = fgets(fid); + count=1; + while ischar(tline) + tline = fgets(fid); + if strncmpi(tline,'if perform(org,',14), + lastchar = strfind(tline,')'); + lastchar = lastchar(end)-1; + string=tline(17:lastchar-1); + if strcmpi(string,'End'), + return; + end + if ismember(count,range), + if ismember(count,steps), + disp(sprintf('%2i: *%s',count,tline(17:lastchar-1))); + else + disp(sprintf('%2i: %s',count,tline(17:lastchar-1))); + end + end + if count>range(end), + break; + end + count=count+1; + end + end + fclose(fid); Index: /issm/trunk/scripts/py_to_pyc.sh =================================================================== --- /issm/trunk/scripts/py_to_pyc.sh (revision 28012) +++ /issm/trunk/scripts/py_to_pyc.sh (revision 28013) @@ -14,8 +14,8 @@ echo "Compiling Python source files" -python -m compileall -q ${TARGET} > ${COMPILE_LOG} +python3 -m compileall -f -q -b ${TARGET} if [ -s ${COMPILE_LOG} ]; then - echo "Error(s) occured while compiling Python scripts!" + echo "Error(s) occurred while compiling Python scripts!" echo "--------------- start: ${COMPILE_LOG} ---------------" cat ${COMPILE_LOG} Index: /issm/trunk/scripts/svn_repo_authors.sh =================================================================== --- /issm/trunk/scripts/svn_repo_authors.sh (revision 28012) +++ /issm/trunk/scripts/svn_repo_authors.sh (revision 28013) @@ -38,5 +38,5 @@ function display_help_mac { - echo " -h diplay help" + echo " -h display help" echo " -a sort output by author name" echo " -c sort output by number of commits" @@ -45,5 +45,5 @@ function display_help_linux { - echo " -h | --help diplay help" + echo " -h | --help display help" echo " -a | --authors sort output by author name" echo " -c | --commits sort output by number of commits" Index: /issm/trunk/src/c/Makefile.am =================================================================== --- /issm/trunk/src/c/Makefile.am (revision 28012) +++ /issm/trunk/src/c/Makefile.am (revision 28013) @@ -7,5 +7,4 @@ # Library declaration {{{ -if !WINDOWS lib_LTLIBRARIES = libISSMCore.la if !MSYS2 @@ -14,10 +13,4 @@ if WRAPPERS lib_LTLIBRARIES += libISSMModules.la -endif -else -noinst_LTLIBRARIES = libISSMCore.la libISSMOverload.la -if WRAPPERS -noinst_LTLIBRARIES += libISSMModules.la -endif endif #}}} @@ -89,5 +82,9 @@ ./classes/Misfit.cpp \ ./classes/Cfsurfacesquare.cpp \ + ./classes/Cfsurfacesquaretransient.cpp \ ./classes/Cfdragcoeffabsgrad.cpp \ + ./classes/Cfdragcoeffabsgradtransient.cpp \ + ./classes/Cfrheologybbarabsgrad.cpp \ + ./classes/Cfrheologybbarabsgradtransient.cpp \ ./classes/Cfsurfacelogvel.cpp \ ./classes/Cflevelsetmisfit.cpp \ @@ -129,4 +126,5 @@ ./classes/Params/Parameters.cpp \ ./classes/Params/BoolParam.cpp \ + ./classes/Params/ControlParam.cpp \ ./classes/Params/IntParam.cpp \ ./classes/Params/IntVecParam.cpp \ @@ -487,4 +485,7 @@ issm_sources += ./analyses/HydrologyDCEfficientAnalysis.cpp endif +if HYDROLOGYARMAPW +issm_sources += ./analyses/HydrologyArmapwAnalysis.cpp +endif if L2PROJECTIONEPL issm_sources += ./analyses/L2ProjectionEPLAnalysis.cpp @@ -598,4 +599,5 @@ if FORTRAN issm_sources += ./modules/SurfaceMassBalancex/run_semic.f90 +issm_sources += ./modules/SurfaceMassBalancex/run_semic_transient.f90 endif endif @@ -715,10 +717,15 @@ libISSMCore_la_FFLAGS = $(AM_FFLAGS) -if !WINDOWS +libISSMCore_LIB_ADD = $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) +if FORTRAN +libISSMCore_LIB_ADD += $(FLIBS) $(FORTRANLIB) +endif +libISSMCore_LIB_ADD += $(OSLIBS) + +if MSYS2 +libISSMCore_la_LIBADD = ${libISSMCore_LIB_ADD} +else if !STANDALONE_LIBRARIES -libISSMCore_la_LIBADD = $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(OSLIBS) -if FORTRAN -libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB) -endif +libISSMCore_la_LIBADD = ${libISSMCore_LIB_ADD} endif endif @@ -739,13 +746,16 @@ libISSMModules_la_CXXFLAGS = $(ALL_CXXFLAGS) -if !WINDOWS -if STANDALONE_LIBRARIES + +libISSMModules_LIB_ADD = $(TRIANGLELIB) $(CHACOLIB) $(BLASLAPACKLIB) $(OSLIBS) libISSMModules_la_LIBADD = ./libISSMCore.la -else -libISSMModules_la_LIBADD = ./libISSMCore.la $(TRIANGLELIB) $(CHACOLIB) $(BLASLAPACKLIB) $(OSLIBS) -endif -endif -endif - + +if MSYS2 +libISSMModules_la_LIBADD += ${libISSMModules_LIB_ADD} +else +if !STANDALONE_LIBRARIES +libISSMModules_la_LIBADD += ${libISSMModules_LIB_ADD} +endif +endif +endif AM_LDFLAGS = @@ -760,5 +770,5 @@ # will be linked to, whether we like it or not, if no static version is # available. -# - On macOC, static linking of binaries is not supported. +# - On macOS, static linking of binaries is not supported. # if STANDALONE_EXECUTABLES @@ -766,5 +776,15 @@ AM_LDFLAGS += -Wl,-rpath,'@loader_path/../lib' else -AM_LDFLAGS += -static -Wl,--disable-new-dtags -Wl,-rpath,'$$ORIGIN/../lib' +if MSYS2 +AM_LDFLAGS += -Wl,-static +else +AM_LDFLAGS += -Wl,--disable-new-dtags -Wl,-rpath,'$$ORIGIN/../lib' +endif +endif +else +if MAC +if HAVE_FORTRANDIR +AM_LDFLAGS += -Wl,-rpath,$(FORTRANDIR) +endif endif endif @@ -783,7 +803,9 @@ if STANDALONE_LIBRARIES +if !MSYS2 libISSMCore_la_LDFLAGS += -static if WRAPPERS libISSMModules_la_LDFLAGS += -static +endif endif endif @@ -802,5 +824,7 @@ if STANDALONE_LIBRARIES +if !MSYS2 libISSMOverload_la_LDFLAGS += -static +endif endif endif @@ -833,9 +857,9 @@ # External packages -LDADD += $(SEMICLIB) $(M1QN3LIB) $(CHACOLIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS) - +LDADD += $(DAKOTALIB) $(SEMICLIB) $(M1QN3LIB) $(CHACOLIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) if FORTRAN LDADD += $(FLIBS) $(FORTRANLIB) endif +LDADD += $(OSLIBS) issm_SOURCES = main/issm.cpp @@ -844,5 +868,4 @@ issm_slc_SOURCES = main/issm_slc.cpp issm_slc_CXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS) -issm_slc_LDADD = $(DAKOTALIB) $(LDADD) if OCEAN @@ -862,5 +885,4 @@ issm_dakota_SOURCES = main/issm_dakota.cpp issm_dakota_CXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) -issm_dakota_LDADD = $(DAKOTALIB) $(LDADD) bin_PROGRAMS += issm_post issm_post_SOURCES = main/issm_post.cpp Index: /issm/trunk/src/c/analyses/AdjointHorizAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/AdjointHorizAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/AdjointHorizAnalysis.cpp (revision 28013) @@ -2391,4 +2391,6 @@ case 2: case 11: + case 13: + case 14: dragcoefficient_input = basalelement->GetInput(FrictionCEnum); _assert_(dragcoefficient_input); break; @@ -2484,4 +2486,5 @@ case 2: case 11: + case 14: dragcoeff_input = element->GetInput(FrictionCEnum); _assert_(dragcoeff_input); break; @@ -2593,4 +2596,5 @@ case 2: case 11: + case 14: dragcoeff_input = element->GetInput(FrictionCEnum); _assert_(dragcoeff_input); break; @@ -2714,4 +2718,5 @@ case 2: case 11: + case 14: dragcoeff_input = basalelement->GetInput(FrictionCEnum); _assert_(dragcoeff_input); break; @@ -2832,4 +2837,6 @@ case 2: case 11: + case 13: + case 14: dragcoeff_input = basalelement->GetInput(FrictionCEnum); _assert_(dragcoeff_input); break; Index: /issm/trunk/src/c/analyses/AgeAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/AgeAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/AgeAnalysis.cpp (revision 28013) @@ -92,68 +92,4 @@ }/*}}}*/ ElementMatrix* AgeAnalysis::CreateKMatrix(Element* element){/*{{{*/ - - _error_("STOP"); - /* Check if ice in element */ - if(!element->IsIceInElement()) return NULL; - - /*compute all stiffness matrices for this element*/ - ElementMatrix* Ke1=CreateKMatrixVolume(element); - ElementMatrix* Ke2=CreateKMatrixShelf(element); - ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2); - - /*clean-up and return*/ - delete Ke1; - delete Ke2; - return Ke; -}/*}}}*/ -ElementMatrix* AgeAnalysis::CreateKMatrixShelf(Element* element){/*{{{*/ - - /* Check if ice in element */ - if(!element->IsIceInElement()) return NULL; - - /*Initialize Element matrix and return if necessary*/ - if(!element->IsOnBase() || !element->IsAllFloating()) return NULL; - - IssmDouble dt,Jdet,D; - IssmDouble *xyz_list_base = NULL; - - /*Get basal element*/ - if(!element->IsOnBase() || !element->IsAllFloating()) return NULL; - - /*Fetch number of nodes for this finite element*/ - int numnodes = element->GetNumberOfNodes(); - - /*Initialize vectors*/ - ElementMatrix* Ke = element->NewElementMatrix(); - IssmDouble* basis = xNew(numnodes); - - /*Retrieve all inputs and parameters*/ - element->GetVerticesCoordinatesBase(&xyz_list_base); - element->FindParam(&dt,TimesteppingTimeStepEnum); - IssmDouble gravity = element->FindParam(ConstantsGEnum); - IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum); - IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); - IssmDouble heatcapacity = element->FindParam(MaterialsHeatcapacityEnum); - IssmDouble mixed_layer_capacity= element->FindParam(MaterialsMixedLayerCapacityEnum); - - /* Start looping on the number of gaussian points: */ - Gauss* gauss=element->NewGaussBase(4); - while(gauss->next()){ - - element->JacobianDeterminantBase(&Jdet,xyz_list_base,gauss); - element->NodalFunctions(basis,gauss); - - D=gauss->weight*Jdet*rho_water*mixed_layer_capacity/(heatcapacity*rho_ice); - if(reCast(dt)) D=dt*D; - for(int i=0;ivalues[i*numnodes+j] += D*basis[i]*basis[j]; - } - - /*Clean up and return*/ - delete gauss; - xDelete(basis); - xDelete(xyz_list_base); - return Ke; -}/*}}}*/ -ElementMatrix* AgeAnalysis::CreateKMatrixVolume(Element* element){/*{{{*/ /* Check if ice in element */ @@ -303,135 +239,7 @@ if(!element->IsIceInElement()) return NULL; - /*compute all load vectors for this element*/ - ElementVector* pe1=CreatePVectorVolume(element); - ElementVector* pe2=CreatePVectorSheet(element); - ElementVector* pe3=CreatePVectorShelf(element); - ElementVector* pe =new ElementVector(pe1,pe2,pe3); - - /*clean-up and return*/ - delete pe1; - delete pe2; - delete pe3; - return pe; -}/*}}}*/ -ElementVector* AgeAnalysis::CreatePVectorSheet(Element* element){/*{{{*/ - - /* Check if ice in element */ - if(!element->IsIceInElement()) return NULL; - - /* Geothermal flux on ice sheet base and basal friction */ - if(!element->IsOnBase() || element->IsAllFloating()) return NULL; - - IssmDouble dt,Jdet,geothermalflux,vx,vy,vz; - IssmDouble alpha2,scalar,basalfriction,heatflux; - IssmDouble *xyz_list_base = NULL; - - /*Fetch number of nodes for this finite element*/ - int numnodes = element->GetNumberOfNodes(); - - /*Initialize vectors*/ - ElementVector* pe = element->NewElementVector(); - IssmDouble* basis = xNew(numnodes); - - /*Retrieve all inputs and parameters*/ - element->GetVerticesCoordinatesBase(&xyz_list_base); - element->FindParam(&dt,TimesteppingTimeStepEnum); - Input* vx_input = element->GetInput(VxEnum); _assert_(vx_input); - Input* vy_input = element->GetInput(VyEnum); _assert_(vy_input); - Input* vz_input = element->GetInput(VzEnum); _assert_(vz_input); - Input* geothermalflux_input = element->GetInput(BasalforcingsGeothermalfluxEnum); _assert_(geothermalflux_input); - IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); - IssmDouble heatcapacity = element->FindParam(MaterialsHeatcapacityEnum); - - /*Build friction element, needed later: */ - Friction* friction=new Friction(element,3); - - /* Start looping on the number of gaussian points: */ - Gauss* gauss = element->NewGaussBase(4); - while(gauss->next()){ - - element->JacobianDeterminantBase(&Jdet,xyz_list_base,gauss); - element->NodalFunctions(basis,gauss); - - geothermalflux_input->GetInputValue(&geothermalflux,gauss); - friction->GetAlpha2(&alpha2,gauss); - vx_input->GetInputValue(&vx,gauss); - vy_input->GetInputValue(&vy,gauss); - vz_input->GetInputValue(&vz,gauss); - vz = 0.;//FIXME - basalfriction = alpha2*(vx*vx + vy*vy + vz*vz); - heatflux = (basalfriction+geothermalflux)/(rho_ice*heatcapacity); - - scalar = gauss->weight*Jdet*heatflux; - if(dt!=0.) scalar=dt*scalar; - - for(int i=0;ivalues[i]+=scalar*basis[i]; - } - - /*Clean up and return*/ - delete gauss; - delete friction; - xDelete(basis); - xDelete(xyz_list_base); - return pe; -}/*}}}*/ -ElementVector* AgeAnalysis::CreatePVectorShelf(Element* element){/*{{{*/ - - /* Check if ice in element */ - if(!element->IsIceInElement()) return NULL; - - IssmDouble t_pmp,dt,Jdet,scalar_ocean,pressure; - IssmDouble *xyz_list_base = NULL; - - /*Get basal element*/ - if(!element->IsOnBase() || !element->IsAllFloating()) return NULL; - - /*Fetch number of nodes for this finite element*/ - int numnodes = element->GetNumberOfNodes(); - - /*Initialize vectors*/ - ElementVector* pe = element->NewElementVector(); - IssmDouble* basis = xNew(numnodes); - - /*Retrieve all inputs and parameters*/ - element->GetVerticesCoordinatesBase(&xyz_list_base); - element->FindParam(&dt,TimesteppingTimeStepEnum); - Input* pressure_input=element->GetInput(PressureEnum); _assert_(pressure_input); - IssmDouble gravity = element->FindParam(ConstantsGEnum); - IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum); - IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); - IssmDouble heatcapacity = element->FindParam(MaterialsHeatcapacityEnum); - IssmDouble mixed_layer_capacity= element->FindParam(MaterialsMixedLayerCapacityEnum); - - /* Start looping on the number of gaussian points: */ - Gauss* gauss=element->NewGaussBase(4); - while(gauss->next()){ - - element->JacobianDeterminantBase(&Jdet,xyz_list_base,gauss); - element->NodalFunctions(basis,gauss); - - pressure_input->GetInputValue(&pressure,gauss); - t_pmp=element->TMeltingPoint(pressure); - - scalar_ocean=gauss->weight*Jdet*rho_water*mixed_layer_capacity*(t_pmp)/(heatcapacity*rho_ice); - if(reCast(dt)) scalar_ocean=dt*scalar_ocean; - - for(int i=0;ivalues[i]+=scalar_ocean*basis[i]; - } - - /*Clean up and return*/ - delete gauss; - xDelete(basis); - xDelete(xyz_list_base); - return pe; -}/*}}}*/ -ElementVector* AgeAnalysis::CreatePVectorVolume(Element* element){/*{{{*/ - - /* Check if ice in element */ - if(!element->IsIceInElement()) return NULL; - /*Intermediaries*/ int stabilization; - IssmDouble Jdet,phi,dt; + IssmDouble Jdet,dt; IssmDouble temperature; IssmDouble tau_parameter,diameter,hx,hy,hz; @@ -451,8 +259,4 @@ /*Retrieve all inputs and parameters*/ element->GetVerticesCoordinates(&xyz_list); - IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); - IssmDouble heatcapacity = element->FindParam(MaterialsHeatcapacityEnum); - IssmDouble thermalconductivity = 1.; - IssmDouble kappa = thermalconductivity/(rho_ice*heatcapacity); element->FindParam(&dt,TimesteppingTimeStepEnum); element->FindParam(&stabilization,AgeStabilizationEnum); @@ -469,7 +273,6 @@ element->JacobianDeterminant(&Jdet,xyz_list,gauss); element->NodalFunctions(basis,gauss); - element->ViscousHeating(&phi,xyz_list,gauss,vx_input,vy_input,vz_input); - - scalar_def=phi/(rho_ice*heatcapacity)*Jdet*gauss->weight; + + scalar_def=1.*Jdet*gauss->weight; if(reCast(dt)) scalar_def=scalar_def*dt; @@ -490,5 +293,5 @@ vz_input->GetInputValue(&w,gauss); - tau_parameter=element->StabilizationParameter(u,v,w,diameter,kappa); + tau_parameter=element->StabilizationParameter(u,v,w,diameter,1.e-15); //assume very small conductivity to get tau for(int i=0;ivalues[i]+=tau_parameter*scalar_def*(u*dbasis[0*numnodes+i]+v*dbasis[1*numnodes+i]+w*dbasis[2*numnodes+i]); @@ -504,5 +307,5 @@ vy_input->GetInputValue(&v,gauss); vz_input->GetInputValue(&w,gauss); - element->StabilizationParameterAnisotropic(&tau_parameter_anisotropic[0],u,v,w,hx,hy,hz,kappa); + element->StabilizationParameterAnisotropic(&tau_parameter_anisotropic[0],u,v,w,hx,hy,hz,1.e-15); //assume very small conductivity to get tau tau_parameter_hor=tau_parameter_anisotropic[0]; tau_parameter_ver=tau_parameter_anisotropic[1]; @@ -518,5 +321,4 @@ delete gauss; return pe; - }/*}}}*/ void AgeAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/ @@ -533,5 +335,39 @@ void AgeAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ SetActiveNodesLSMx(femmodel); - _error_("Should also automatically constrain surface/basal nodes where we have inflow"); -}/*}}}*/ + + /*Constrain all nodes that are grounded and unconstrain the ones that float*/ + for(Object* & object : femmodel->elements->objects){ + Element *element = xDynamicCast(object); + + if(element->IsOnSurface()){ + element = element->SpawnTopElement(); + int numnodes = element->GetNumberOfNodes(); + IssmDouble *mask = xNew(numnodes); + IssmDouble *bed = xNew(numnodes); + IssmDouble *ls_active = xNew(numnodes); + + element->GetInputListOnNodes(&mask[0],MaskOceanLevelsetEnum); + element->GetInputListOnNodes(&bed[0],BaseEnum); + element->GetInputListOnNodes(&ls_active[0],IceMaskNodeActivationEnum); + + for(int in=0;inGetNode(in); + if(mask[in]<0. && ls_active[in]==1.){ + node->Activate(); + } + else{ + node->Deactivate(); + node->ApplyConstraint(0,bed[in]); + } + } + xDelete(mask); + xDelete(bed); + xDelete(ls_active); + } + else if(element->IsOnBase()){ + element = element->SpawnBasalElement(); + _error_("not supported"); + } + } +}/*}}}*/ Index: /issm/trunk/src/c/analyses/AgeAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/AgeAnalysis.h (revision 28012) +++ /issm/trunk/src/c/analyses/AgeAnalysis.h (revision 28013) @@ -26,10 +26,5 @@ ElementMatrix* CreateJacobianMatrix(Element* element); ElementMatrix* CreateKMatrix(Element* element); - ElementMatrix* CreateKMatrixShelf(Element* element); - ElementMatrix* CreateKMatrixVolume(Element* element); ElementVector* CreatePVector(Element* element); - ElementVector* CreatePVectorSheet(Element* element); - ElementVector* CreatePVectorShelf(Element* element); - ElementVector* CreatePVectorVolume(Element* element); void GetSolutionFromInputs(Vector* solution,Element* element); void GradientJ(Vector* gradient,Element* element,int control_type,int control_interp,int control_index); Index: /issm/trunk/src/c/analyses/DebrisAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/DebrisAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/DebrisAnalysis.cpp (revision 28013) @@ -10,4 +10,5 @@ #define FINITEELEMENT P1Enum +#define EPS 1e-14 /*Model processing*/ @@ -52,5 +53,5 @@ } - /*free ressources: */ + /*free resources: */ iomodel->DeleteData(vertex_pairing,"md.debris.vertex_pairing"); iomodel->DeleteData(nodeonsurface,"md.mesh.vertexonsurface"); @@ -59,5 +60,5 @@ if(iomodel->domaintype!=Domain2DhorizontalEnum) iomodel->FetchData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); - ::CreateNodes(nodes,iomodel,DebrisAnalysisEnum,FINITEELEMENT); + ::CreateNodes(nodes,iomodel,DebrisAnalysisEnum,FINITEELEMENT,isamr); iomodel->DeleteData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); @@ -127,85 +128,9 @@ void DebrisAnalysis::Core(FemModel* femmodel){/*{{{*/ - - Element* element= NULL; - for(Object* & object : femmodel->elements->objects){ - element=xDynamicCast(object); - - - int numvertices = element->GetNumberOfNodes(); - - IssmDouble* vx = xNew(numvertices); - IssmDouble* debristhickness = xNew(numvertices); - IssmDouble* slopex = xNew(numvertices); - IssmDouble* onsurface = xNew(numvertices); - IssmDouble* icethickness = xNew(numvertices); - - element->GetInputListOnVertices(&debristhickness[0],DebrisThicknessEnum); - element->GetInputListOnVertices(&vx[0],VxEnum); - element->GetInputListOnVertices(&slopex[0],SurfaceSlopeXEnum); - element->GetInputListOnVertices(&onsurface[0],MeshVertexonsurfaceEnum); - element->GetInputListOnVertices(&icethickness[0],ThicknessEnum); - - IssmDouble slope,rad2deg=180./M_PI; //=57.2958 - IssmDouble vslipx,rhod=1900.; - IssmDouble gravity=element->FindParam(ConstantsGEnum); - IssmDouble slope_threshold=element->FindParam(DebrisRemovalSlopeThresholdEnum); - IssmDouble iceminthickness=element->FindParam(MasstransportMinThicknessEnum); - - int step; - IssmDouble dt, maxv; - IssmDouble yts=31536000.; - femmodel->parameters->FindParam(&step,StepEnum); - femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); - - bool isminthicknessinelement=false; - for(int i=0;i.5){ - slope=fabs(slopex[i]); - if((atan(slope)*rad2deg)>25.){ - //if(debristhickness[i]>0.01){ - vslipx=slope_threshold/yts; - //maxv=10.0/2./dt; - //vslipx=-slope_threshold*rhod*gravity*debristhickness[i]*slopex[i]/yts; - vx[i]=vx[i]+vslipx; - //debristhickness[i]=debristhickness[i]; - //if(vx[i]>maxv) vx[i]=maxv; - //} - } - //} - } - } - //if(step%100==0) - element->AddInput(VxDebrisEnum,vx,P1Enum); - //element->AddInput(DebrisThicknessEnum,debristhickness,P1Enum); - - /* Free resources */ - xDelete(debristhickness); - xDelete(icethickness); - xDelete(vx); - xDelete(slopex); - xDelete(onsurface); - } - - //if(step%7==0) //PreProcessing(femmodel); //femmodel->parameters->SetParam(VxDebrisEnum,InputToExtrudeEnum); //extrudefromtop_core(femmodel); - femmodel->SetCurrentConfiguration(DebrisAnalysisEnum); solutionsequence_linear(femmodel); - - int step; - femmodel->parameters->FindParam(&step,StepEnum); - //if(step%7==0) PreProcessing(femmodel); PostProcessing(femmodel); @@ -230,5 +155,6 @@ IssmDouble Jdet,D_scalar,dt,h; IssmDouble vel,vx,vy,dvxdx,dvydy; - IssmDouble xi,tau; + IssmDouble yts=31536000.; + IssmDouble tau; IssmDouble dvx[2],dvy[2]; Element* topelement = NULL; @@ -271,5 +197,5 @@ Input* vy_input=NULL; if(dim>1){vy_input = topelement->GetInput(VyDebrisEnum); _assert_(vy_input);} - h = topelement->CharacteristicLength(); + h=topelement->CharacteristicLength(); /* Start looping on the number of gaussian points: */ @@ -302,6 +228,5 @@ } } - } - else{ + }else{ dvxdx=dvx[0]; for(int i=0;iFindParam(&step,StepEnum); - IssmDouble slope_threshold; - topelement->FindParam(&slope_threshold,DebrisRemovalSlopeThresholdEnum); - IssmDouble kappa,f,smb,debristhickness,slopex; - IssmDouble Diff,fraction,M=1,C; - IssmDouble rad2deg=180./M_PI; - Diff=3.2/3e7; - Input* slopex_input=topelement->GetInput(SurfaceSlopeXEnum); _assert_(slopex_input); - Input* smb_input=topelement->GetInput(SmbMassBalanceEnum); _assert_(smb_input); - Input* debristhickness_input=topelement->GetInput(DebrisThicknessEnum); _assert_(debristhickness_input); - - if(isdisplacement){ - - slopex_input->GetInputValue(&slopex, gauss); - smb_input->GetInputValue(&smb, gauss); - debristhickness_input->GetInputValue(&debristhickness, gauss); - if((atan(fabs(slopex))*rad2deg)>30.){ - f=1.; - }else{ - f=0.; - } - //f=1; - //kappa=-5.6e16*smb*debristhickness*f; - //kappa=debristhickness/h*4e9*f; - //kappa=14.2809e8*f; // 25° - kappa=slope_threshold*1e8*f; - if(dim==2){ - for(int i=0;ivalues[i*numnodes+j] += D_scalar*kappa*( - dbasis[0*numnodes+j]*dbasis[0*numnodes+i] + dbasis[1*numnodes+j]*dbasis[1*numnodes+i] + dbasis[2*numnodes+j]*dbasis[2*numnodes+i] - ); - } - } - }else{ - for(int i=0;ivalues[i*numnodes+j] += D_scalar*kappa*(dbasis[0*numnodes+j]*dbasis[0*numnodes+i]); - } - } - } - } - - /*******************************************************************/ - IssmDouble rho; if(FINITEELEMENT==P1Enum){ - rho=2; + rho=2.; }else if(FINITEELEMENT==P2Enum){ rho=4.; } - if(stabilization==2){ + + for(int i=0;i<(dim*dim);i++) D[i]=0.; + if(stabilization==1){ + /*SSA*/ + if(dim==1){ + vx_input->GetInputValue(&vx,gauss); + D[0]=h/rho*fabs(vx); + }else{ + vx_input->GetInputValue(&vx,gauss); + vy_input->GetInputValue(&vy,gauss); + vel=sqrt(vx*vx+vy*vy); + D[0*dim+0]=h/rho*fabs(vx); + D[1*dim+1]=h/rho*fabs(vy); + } + }else if(stabilization==2){ /*Streamline upwinding*/ if(dim==1){ vx_input->GetInputValue(&vx,gauss); - vel=fabs(vx)+1.e-10; + vel=fabs(vx)+EPS; D[0] = h/(rho*vel)*vx*vx; - } - else{ - vx_input->GetInputAverage(&vx); - vy_input->GetInputAverage(&vy); - vel=sqrt(vx*vx+vy*vy)+1.e-10; + }else{ + vx_input->GetInputValue(&vx,gauss); + vy_input->GetInputValue(&vy,gauss); + vel=sqrt(vx*vx+vy*vy)+EPS; D[0*dim+0]=h/(rho*vel)*vx*vx; D[1*dim+0]=h/(rho*vel)*vy*vx; D[0*dim+1]=h/(rho*vel)*vx*vy; D[1*dim+1]=h/(rho*vel)*vy*vy; - } - } - else if(stabilization==1){ - /*SSA*/ - if(dim==1){ - vx_input->GetInputAverage(&vx); - D[0]=h/rho*fabs(vx); - } - else{ - vx_input->GetInputAverage(&vx); - vy_input->GetInputAverage(&vy); - D[0*dim+0]=h/rho*fabs(vx); - D[1*dim+1]=h/rho*fabs(vy); - } - } - else if(stabilization==3){ + } + }else if(stabilization==3){ /*SUPG*/ if(dim==1){ - vx_input->GetInputAverage(&vx); - tau=h/(rho*fabs(vx)+1e-10); - } - else{ - vx_input->GetInputAverage(&vx); - vy_input->GetInputAverage(&vy); - tau=1*h/(rho*sqrt(vx*vx+vy*vy)+1e-10); - } - } + vx_input->GetInputValue(&vx,gauss); + tau=h/(rho*max(fabs(vx),EPS)); + }else{ + vx_input->GetInputValue(&vx,gauss); + vy_input->GetInputValue(&vy,gauss); + tau=h/(rho*sqrt(vx*vx+vy*vy)+EPS); + } + } + if(stabilization==1 || stabilization==2){ for(int i=0;ivalues[i*numnodes+j] += ( dbasis[0*numnodes+i] *(D[0*dim+0]*dbasis[0*numnodes+j] + D[0*dim+1]*dbasis[1*numnodes+j]) + - dbasis[1*numnodes+i] *(D[1*dim+0]*dbasis[0*numnodes+j] + D[1*dim+1]*dbasis[1*numnodes+j]) - ); + dbasis[1*numnodes+i] *(D[1*dim+0]*dbasis[0*numnodes+j] + D[1*dim+1]*dbasis[1*numnodes+j])); } } - } - else{ + }else{ for(int i=0;ivalues[i*numnodes+j] += dbasis[0*numnodes+i]*D[0]*dbasis[0*numnodes+j]; } }else if(stabilization==3){ - /*Mass matrix - part 2*/ if(dim==1){ + /*Mass matrix - part 2*/ for(int i=0;ivalues[i*numnodes+j]+=dt*gauss->weight*Jdet*tau*(basis[j]*dvxdx+basis[j]*dvydy)*(basis[i]*dvxdx); + Ke->values[i*numnodes+j]+=dt*gauss->weight*Jdet*tau*(basis[j]*dvxdx)*(basis[i]*dvxdx);; + } + } + }else if(dim==2){ + /*Mass matrix - part 2*/ + for(int i=0;ivalues[i*numnodes+j]+=gauss->weight*Jdet*tau*basis[j]*(vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i]); + } + } + /*Mass matrix - part 3*/ + for(int i=0;ivalues[i*numnodes+j]+=gauss->weight*Jdet*tau*basis[j]*(basis[i]*dvxdx+basis[i]*dvydy); + } + } + + /*Advection matrix - part 2, A*/ + for(int i=0;ivalues[i*numnodes+j]+=dt*gauss->weight*Jdet*tau*(vx*dbasis[0*numnodes+j]+vy*dbasis[1*numnodes+j])*(vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i]); + } + } + /*Advection matrix - part 3, A*/ + for(int i=0;ivalues[i*numnodes+j]+=dt*gauss->weight*Jdet*tau*(vx*dbasis[0*numnodes+j]+vy*dbasis[1*numnodes+j])*(basis[i]*dvxdx+basis[i]*dvydy); + } + } + + /*Advection matrix - part 2, B*/ + for(int i=0;ivalues[i*numnodes+j]+=dt*gauss->weight*Jdet*tau*(basis[j]*dvxdx+basis[j]*dvydy)*(vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i]); + } + } + /*Advection matrix - part 3, B*/ + for(int i=0;ivalues[i*numnodes+j]+=dt*gauss->weight*Jdet*tau*(basis[j]*dvxdx+basis[j]*dvydy)*(basis[i]*dvxdx+basis[i]*dvydy); } } @@ -487,6 +400,7 @@ int stabilization,dim,domaintype; IssmDouble Jdet,dt; - IssmDouble smb,thickness; - IssmDouble vx,vy,vel,dvxdx,dvydy,xi,h,tau,pf; + IssmDouble smb,thickness,psi; + IssmDouble vx,vy,vel,dvxdx,dvydy,h,tau,pf; + IssmDouble yts=31536000.; IssmDouble dvx[2],dvy[2]; IssmDouble* xyz_list = NULL; @@ -533,4 +447,5 @@ vy_input=topelement->GetInput(VyDebrisEnum); _assert_(vy_input); } + h=topelement->CharacteristicLength(); IssmDouble rho; @@ -550,35 +465,46 @@ smb_input->GetInputValue(&smb,gauss); thickness_input->GetInputValue(&thickness,gauss); - if(smb>0.){ - for(int i=0;ivalues[i]+=Jdet*gauss->weight*(thickness-0.*dt*smb*pf)*basis[i]; - } else { - for(int i=0;ivalues[i]+=Jdet*gauss->weight*(thickness-dt*smb*pf)*basis[i]; // take the negative of melt, because it is a debris production term here - } + psi=thickness-0.*dt*smb*pf; + }else{ + psi=thickness-dt*smb*pf; + } + + for(int i=0;ivalues[i]+=Jdet*gauss->weight*psi*basis[i]; if(stabilization==3){ /*SUPG*/ topelement->NodalFunctionsDerivatives(dbasis,xyz_list,gauss); + vx_input->GetInputDerivativeValue(&dvx[0],xyz_list,gauss); + dvxdx=dvx[0]; if(dim==1){ - vx_input->GetInputValue(&vx,gauss); - vx_input->GetInputDerivativeValue(&dvx[0],xyz_list,gauss); - dvxdx=dvx[0]; - tau=h/(rho*fabs(vx)+1e-10); - IssmDouble psi; - if(smb>0.){ - psi=thickness; - } else { - psi=thickness-dt*smb*pf; - } + tau=h/(rho*max(fabs(vx),EPS)); + /*Force vector - part 2*/ for(int i=0;ivalues[i]+=Jdet*gauss->weight*psi*tau*(vx*dbasis[0*numnodes+i]); + pe->values[i]+=Jdet*gauss->weight*psi*tau*vx*dbasis[0*numnodes+i]; } /*Force vector - part 3*/ for(int i=0;ivalues[i]+=Jdet*gauss->weight*psi*tau*(basis[i]*dvxdx); - } - + pe->values[i]+=Jdet*gauss->weight*psi*tau*basis[i]*dvxdx; + } + + }else if(dim==2){ + vx_input->GetInputValue(&vx,gauss); + vy_input->GetInputValue(&vy,gauss); + vy_input->GetInputDerivativeValue(&dvy[0],xyz_list,gauss); + vel=sqrt(vx*vx+vy*vy); + dvydy=dvy[1]; + tau=h/(rho*vel+EPS); + + /*Force vector - part 2*/ + for(int i=0;ivalues[i]+=Jdet*gauss->weight*psi*tau*(vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i]); + } + /*Force vector - part 3*/ + for(int i=0;ivalues[i]+=Jdet*gauss->weight*psi*tau*(basis[i]*dvxdx+basis[i]*dvydy); + } } } @@ -600,22 +526,12 @@ }/*}}}*/ void DebrisAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ - //element->InputUpdateFromSolutionOneDof(solution,DebrisThicknessEnum); - int* ddoflist=NULL; + + int *ddoflist=NULL; int numnodes = element->GetNumberOfNodes(); - IssmDouble* thickness = xNew(numnodes); - IssmDouble* thicknessold = xNew(numnodes); IssmDouble* newthickness = xNew(numnodes); - IssmDouble* icethickness = xNew(numnodes); - IssmDouble* bedslopex = xNew(numnodes); - IssmDouble* surfaceslopex = xNew(numnodes); /*Use the dof list to index into the solution vector: */ IssmDouble minthickness = element->FindParam(DebrisMinThicknessEnum); - IssmDouble iceminthickness = element->FindParam(MasstransportMinThicknessEnum); - element->GetInputListOnVertices(&thickness[0],DebrisThicknessEnum); - element->GetInputListOnVertices(&icethickness[0],ThicknessEnum); - element->GetInputListOnVertices(&bedslopex[0],BedSlopeXEnum); - element->GetInputListOnVertices(&surfaceslopex[0],SurfaceSlopeXEnum); element->GetDofListLocal(&ddoflist,NoneApproximationEnum,GsetEnum); @@ -625,26 +541,50 @@ if(xIsInf(newthickness[i])) _error_("Inf found in solution vector"); - /* check for thicknessAddInput(DebrisThicknessEnum,newthickness,P1Enum); - /* Free resources */ + // Free resources xDelete(newthickness); - xDelete(thickness); - xDelete(icethickness); - xDelete(bedslopex); - xDelete(surfaceslopex); xDelete(ddoflist); + //*/ }/*}}}*/ void DebrisAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ - // return; - SetActiveNodesLSMx(femmodel); + //SetActiveNodesLSMx(femmodel); + + // Update active elements based on ice levelset and ocean levelset*/ + GetMaskOfIceVerticesLSMx(femmodel,false,true); //FIXME? + SetActiveNodesLSMx(femmodel,false,true); //FIXME? + + /*Constrain all nodes that are grounded and unconstrain the ones that float*/ + for(Object* & object : femmodel->elements->objects){ + Element *element = xDynamicCast(object); + int numnodes = element->GetNumberOfNodes(); + IssmDouble *mask = xNew(numnodes); + IssmDouble *ls_active = xNew(numnodes); + + element->GetInputListOnNodes(&mask[0],MaskOceanLevelsetEnum); + element->GetInputListOnNodes(&ls_active[0],DebrisMaskNodeActivationEnum); + + for(int in=0;inGetNode(in); + if(mask[in]>0. && ls_active[in]==1.){ + // Do nothing + node->Activate(); //Not sure if we need this! + } + else{ + IssmDouble phi=0; + node->Deactivate();// Not sure if we need this + node->ApplyConstraint(0,phi); + } + } + xDelete(mask); + xDelete(ls_active); + } + //*/ + return; }/*}}}*/ void DebrisAnalysis::PostProcessing(FemModel* femmodel){/*{{{*/ @@ -676,7 +616,10 @@ IssmDouble* slopey = xNew(numnodes); IssmDouble* onsurface = xNew(numnodes); + IssmDouble* ls_active = xNew(numnodes); element->GetInputListOnNodes(debristhickness,DebrisThicknessEnum); element->GetInputListOnNodes(icethickness,ThicknessEnum); element->GetInputListOnNodes(onsurface,MeshVertexonsurfaceEnum); + element->GetInputListOnNodes(ls_active,DebrisMaskNodeActivationEnum); + dim=1; element->GetInputListOnNodes(slopex,SurfaceSlopeXEnum); @@ -688,4 +631,5 @@ bool isminthicknessinelement=false; bool remove_debris=false; + bool isactive=false; IssmDouble iceminthickness=element->FindParam(MasstransportMinThicknessEnum); @@ -693,72 +637,71 @@ switch(removalmodel){ case 1:{ - IssmDouble slope_threshold=element->FindParam(DebrisRemovalSlopeThresholdEnum); - - for(k=0; k0.5){ - slope=fabs(slopex[k]); - if(dim==2) slope=pow(pow(slopex[k],2)+pow(slopey[k],2),0.5); - if((atan(slope)*rad2deg)>slope_threshold) debristhickness[k]=remove_debris=true; - } - } - if(remove_debris){ - for(k=0; kGetElementType(); - //element->AddInput(DebrisThicknessEnum,debristhickness,FINITEELEMENT); - element->AddInput(DebrisThicknessEnum,debristhickness,P1Enum); - - xDelete(debristhickness); - xDelete(icethickness); - xDelete(slopex); - xDelete(slopey); - break; - } + IssmDouble slope_threshold=element->FindParam(DebrisRemovalSlopeThresholdEnum); + int kk=0; + for(k=0; kslope_threshold) remove_debris=true; + //if((atan(slope)*rad2deg)>slope_threshold) debristhickness[k]=0.; + } + //if((atan(slope_mean)*rad2deg)>slope_threshold) remove_debris=true; + if(remove_debris){ + for(k=0; kAddInput(DebrisThicknessEnum,debristhickness,P1Enum); + + xDelete(debristhickness); + xDelete(icethickness); + xDelete(slopex); + xDelete(slopey); + break; + } case 2:{ - IssmDouble stress_threshold = element->FindParam(DebrisRemovalStressThresholdEnum); - IssmDouble gravity = element->FindParam(ConstantsGEnum); - IssmDouble stress,rhod=1900.; - - for(k=0; k0.5){ - slope=fabs(slopex[k]); - if(dim==2) slope=pow(pow(slopex[k],2)+pow(slopey[k],2),0.5); - stress=rhod*gravity*debristhickness[k]*slope;//pow(slope*slope/(slope*slope+1),0.5);//sin(slope/rad2deg); - if(stress>stress_threshold) debristhickness[k]=0.; - //kk++; - } - } - /*if((stress/double(kk))>stress_threshold) remove_debris=true; - if(remove_debris){ - for(k=0; kGetElementType(); - //element->AddInput(DebrisThicknessEnum,debristhickness,FINITEELEMENT); - element->AddInput(DebrisThicknessEnum,debristhickness,P1Enum); - - xDelete(debristhickness); - xDelete(icethickness); - xDelete(slopex); - xDelete(slopey); - break; - } + IssmDouble stress_threshold = element->FindParam(DebrisRemovalStressThresholdEnum); + IssmDouble gravity = element->FindParam(ConstantsGEnum); + IssmDouble stress,rhod=1900.; + int kk=0; + for(k=0; kstress_threshold) remove_debris=true; + //if(stress>stress_threshold) debristhickness[k]=0.; + } + //if((stress_sum/double(kk))>stress_threshold) remove_debris=true; + if(remove_debris){ + for(k=0; kAddInput(DebrisThicknessEnum,debristhickness,P1Enum); + + xDelete(debristhickness); + xDelete(icethickness); + xDelete(slopex); + xDelete(slopey); + xDelete(ls_active); + break; + } default: _error_("removalmodel "<parameters->FindParam(&domaintype,DomainTypeEnum); - //femmodel->parameters->FindParam(&displacementmodel,DebrisDisplacementmodelEnum); Element* element= NULL; - IssmDouble *xyz_list = NULL; - //IssmDouble top_normal[2]; - - if(isdebrisdisplacement){ - - //if(displacementmodel==0){ - // no displacement, do nothing - //}else{ - // deterministic or random displacement - - for(Object* & object : femmodel->elements->objects){ - element=xDynamicCast(object); - - numnodes=element->GetNumberOfNodes(); - IssmDouble* debristhickness= xNew(numnodes); - IssmDouble* icethickness= xNew(numnodes); - IssmDouble* slopex = xNew(numnodes); - IssmDouble* slopey = xNew(numnodes); - IssmDouble* vx = xNew(numnodes); - IssmDouble* vy = xNew(numnodes); - IssmDouble* surface = xNew(numnodes); - IssmDouble* onsurface = xNew(numnodes); - element->GetInputListOnNodes(vx,VxDebrisEnum); - element->GetInputListOnNodes(debristhickness,DebrisThicknessEnum); - element->GetInputListOnNodes(icethickness,ThicknessEnum); - element->GetInputListOnNodes(surface,SurfaceEnum); - element->GetInputListOnNodes(onsurface,MeshVertexonsurfaceEnum); - element->GetVerticesCoordinates(&xyz_list); - - dim=1; - element->GetInputListOnNodes(slopex,SurfaceSlopeXEnum); - if(domaintype!=Domain2DverticalEnum){ - element->GetInputListOnNodes(slopey,SurfaceSlopeYEnum); - element->GetInputListOnNodes(vy,VyDebrisEnum); - dim=2; - } - IssmDouble slope,rad2deg=180./M_PI; //=57.2958 - IssmDouble h=10.,f; - IssmDouble debrissum; - IssmDouble dt = element->FindParam(TimesteppingTimeStepEnum); - bool displacedebris; - - switch(displacementmodel){ - case 1:{ - IssmDouble slope_threshold = element->FindParam(DebrisRemovalSlopeThresholdEnum); - IssmDouble iceminthickness=element->FindParam(MasstransportMinThicknessEnum); - - bool isminthicknessinelement=false; - for(k=0; k.5){ - slope=pow(slopex[k]*slopex[k],0.5); - if(dim==2) slope=pow(pow(slopex[k],2)+pow(slopey[k],2),0.5); - if((atan(slope)*rad2deg)>30.){ - f=0.5; - test=test+0; - debrissum=debrissum+debristhickness[k]*f; - //displacedebris=true; - //if(debristhickness[k]>1.e-6) vx[k]=vx[k]+10./31536000.;//*vx[k]/pow(pow(vx[k],2),0.5); - //debristhickness[k]=debristhickness[k]*(1.-f); - } - } - } - if(test>1){ - test=test; - }else{ - test=1; - } - //if(displacedebris){ - int index=-1; - IssmDouble min=1e14; - for(k=0; k.5){ - if(surface[k].5){ - if(k==index){ - debristhickness[k]=debristhickness[k]+debrissum; - }else{ - debristhickness[k]=debristhickness[k]-debrissum; - if(debristhickness[k]<=0) debristhickness[k]=0; - } - //if(debristhickness[k]>10.) debristhickness[k]=10.; - } - } - //} - } - - int finite_element = element->GetElementType(); - //element->AddInput(DebrisThicknessEnum,debristhickness,finite_element); - //element->AddInput(VxDebrisEnum,vx,P1Enum); - element->AddInput(DebrisThicknessEnum,debristhickness,P1Enum); - - xDelete(debristhickness); - xDelete(icethickness); - xDelete(vx); - xDelete(vy); - xDelete(slopex); - xDelete(slopey); - xDelete(surface); - break; - } - case 2: - // Do nothing - - default: _error_("Debris displacement model "<elements->objects){ + element=xDynamicCast(object); + + int numvertices = element->GetNumberOfVertices(); + + IssmDouble* vx = xNew(numvertices); + IssmDouble* debristhickness = xNew(numvertices); + IssmDouble* slopex = xNew(numvertices); + IssmDouble* onsurface = xNew(numvertices); + IssmDouble* icethickness = xNew(numvertices); + + element->GetInputListOnVertices(&debristhickness[0],DebrisThicknessEnum); + element->GetInputListOnVertices(&vx[0],VxDebrisEnum); + element->GetInputListOnVertices(&slopex[0],SurfaceSlopeXEnum); + element->GetInputListOnVertices(&onsurface[0],MeshVertexonsurfaceEnum); + element->GetInputListOnVertices(&icethickness[0],ThicknessEnum); + + IssmDouble slope,rad2deg=180./M_PI; //=57.2958 + IssmDouble vslipx,rhod=1900.; + IssmDouble gravity=element->FindParam(ConstantsGEnum); + IssmDouble slope_threshold=element->FindParam(DebrisRemovalSlopeThresholdEnum); + IssmDouble iceminthickness=element->FindParam(MasstransportMinThicknessEnum); + + int step; + IssmDouble dt, maxv; + IssmDouble yts=31536000.; + femmodel->parameters->FindParam(&step,StepEnum); + femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + + bool isminthicknessinelement=false; + for(int i=0;i.5){ + slope=fabs(slopex[i]); + //if((atan(slope)*rad2deg)>25.){ + //if(debristhickness[i]>0.01){ + vslipx=1.0/yts; + //maxv=10.0/2./dt; + //vslipx=-slope_threshold*rhod*gravity*debristhickness[i]*slopex[i]/yts; + vx[i]=vx[i]+vslipx; + //debristhickness[i]=debristhickness[i]; + //if(vx[i]>maxv) vx[i]=maxv; + //} + //} + //} + } + } + //if(step%100==0) + element->AddInput(VxDebrisEnum,vx,P1Enum); + + /* Free resources */ + xDelete(debristhickness); + xDelete(icethickness); + xDelete(vx); + xDelete(slopex); + xDelete(onsurface); + } + +}/*}}}*/ Index: /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp (revision 28013) @@ -102,6 +102,5 @@ bool dakota_analysis,ismovingfront,isenthalpy; - int frictionlaw,basalforcing_model,materialstype; - int FrictionCoupling; + int basalforcing_model,materialstype; /*Now, is the model 3d? otherwise, do nothing: */ @@ -131,5 +130,4 @@ iomodel->FindConstant(&dakota_analysis,"md.qmu.isdakota"); iomodel->FindConstant(&ismovingfront,"md.transient.ismovingfront"); - iomodel->FindConstant(&frictionlaw,"md.friction.law"); iomodel->FindConstant(&materialstype,"md.materials.type"); @@ -191,73 +189,6 @@ } - /*Friction law variables*/ - switch(frictionlaw){ - case 1: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if (FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 2: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - break; - case 3: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.As",FrictionAsEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if (FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 4: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - break; - case 5: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.water_layer",FrictionWaterLayerEnum); - break; - case 6: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - break; - case 7: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficientcoulomb",FrictionCoefficientcoulombEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if (FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 9: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.pressure_adjusted_temperature",FrictionPressureAdjustedTemperatureEnum); - InputUpdateFromConstantx(inputs,elements,1.,FrictionPEnum); - InputUpdateFromConstantx(inputs,elements,1.,FrictionQEnum); - break; - default: - _error_("friction law not supported"); - } + /*Friction*/ + FrictionUpdateInputs(elements, inputs, iomodel); /*Free data: */ @@ -277,5 +208,4 @@ parameters->AddObject(iomodel->CopyConstantObject("md.thermal.isdrainicecolumn",ThermalIsdrainicecolumnEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.thermal.watercolumn_upperlimit",ThermalWatercolumnUpperlimitEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.law",FrictionLawEnum)); iomodel->FindConstant(&requestedoutputs,&numoutputs,"md.thermal.requested_outputs"); @@ -284,24 +214,6 @@ iomodel->DeleteData(&requestedoutputs,numoutputs,"md.thermal.requested_outputs"); - /*Deal with friction parameters*/ - int frictionlaw; - iomodel->FindConstant(&frictionlaw,"md.friction.law"); - if(frictionlaw==6){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - } - if(frictionlaw==4){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - } - if(frictionlaw==1 || frictionlaw==3 || frictionlaw==7){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - } - if(frictionlaw==9){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - parameters->AddObject(new IntParam(FrictionCouplingEnum,0)); - } + /*Friction*/ + FrictionUpdateParameters(parameters, iomodel); }/*}}}*/ Index: /issm/trunk/src/c/analyses/EnumToAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/EnumToAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/EnumToAnalysis.cpp (revision 28013) @@ -74,4 +74,7 @@ case GLheightadvectionAnalysisEnum : return new GLheightadvectionAnalysis(); #endif + #ifdef _HAVE_HYDROLOGYARMAPW_ + case HydrologyArmapwAnalysisEnum : return new HydrologyArmapwAnalysis(); + #endif #ifdef _HAVE_HYDROLOGYDCEFFICIENT_ case HydrologyDCEfficientAnalysisEnum : return new HydrologyDCEfficientAnalysis(); Index: /issm/trunk/src/c/analyses/HydrologyArmapwAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyArmapwAnalysis.cpp (revision 28013) +++ /issm/trunk/src/c/analyses/HydrologyArmapwAnalysis.cpp (revision 28013) @@ -0,0 +1,170 @@ +#include "./HydrologyArmapwAnalysis.h" +#include "../toolkits/toolkits.h" +#include "../classes/classes.h" +#include "../shared/shared.h" +#include "../modules/modules.h" + +/*Model processing*/ +void HydrologyArmapwAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/ + + return; + +}/*}}}*/ +void HydrologyArmapwAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/ + /*No loads*/ +}/*}}}*/ +void HydrologyArmapwAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel,bool isamr){/*{{{*/ + + return; + +}/*}}}*/ +int HydrologyArmapwAnalysis::DofsPerNode(int** doflist,int domaintype,int approximation){/*{{{*/ + return 0; +}/*}}}*/ +void HydrologyArmapwAnalysis::UpdateElements(Elements* elements,Inputs* inputs,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ + + /*Fetch data needed: */ + int hydrology_model,frictionlaw; + iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); + + /*Now, do we really want armapw?*/ + if(hydrology_model!=HydrologyarmapwEnum) return; + + /*Add input to elements*/ + iomodel->FetchDataToInput(inputs,elements,"md.mask.ice_levelset",MaskIceLevelsetEnum); + iomodel->FetchDataToInput(inputs,elements,"md.mask.ocean_levelset",MaskOceanLevelsetEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.hydrology.basin_id",HydrologyBasinsIdEnum); + iomodel->FetchDataToInput(inputs,elements,"md.initialization.watercolumn",WatercolumnEnum,0.); + +}/*}}}*/ +void HydrologyArmapwAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ + + /*retrieve some parameters: */ + int hydrology_model; + int numoutputs; + char** requestedoutputs = NULL; + iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); + + /*Now, do we really want Armapw?*/ + if(hydrology_model!=HydrologyarmapwEnum) return; + + parameters->AddObject(new IntParam(HydrologyModelEnum,hydrology_model)); + /*Requested outputs*/ + iomodel->FindConstant(&requestedoutputs,&numoutputs,"md.hydrology.requested_outputs"); + parameters->AddObject(new IntParam(HydrologyNumRequestedOutputsEnum,numoutputs)); + if(numoutputs)parameters->AddObject(new StringArrayParam(HydrologyRequestedOutputsEnum,requestedoutputs,numoutputs)); + iomodel->DeleteData(&requestedoutputs,numoutputs,"md.hydrology.requested_outputs"); + +}/*}}}*/ + +/*Finite Element Analysis*/ +void HydrologyArmapwAnalysis::Core(FemModel* femmodel){/*{{{*/ + _error_("not implemented"); +}/*}}}*/ +void HydrologyArmapwAnalysis::PreCore(FemModel* femmodel){/*{{{*/ + _error_("not implemented"); +}/*}}}*/ +ElementVector* HydrologyArmapwAnalysis::CreateDVector(Element* element){/*{{{*/ + /*Default, return NULL*/ + return NULL; +}/*}}}*/ +ElementMatrix* HydrologyArmapwAnalysis::CreateJacobianMatrix(Element* element){/*{{{*/ + _error_("Not implemented"); +}/*}}}*/ +ElementMatrix* HydrologyArmapwAnalysis::CreateKMatrix(Element* element){/*{{{*/ + _error_("Not implemented"); +}/*}}}*/ +ElementVector* HydrologyArmapwAnalysis::CreatePVector(Element* element){/*{{{*/ + _error_("Not implemented"); +}/*}}}*/ +void HydrologyArmapwAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/ + _error_("Not implemented"); +}/*}}}*/ +void HydrologyArmapwAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_interp,int control_index){/*{{{*/ + _error_("Not implemented"); +}/*}}}*/ +void HydrologyArmapwAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ + _error_("Not implemented"); +}/*}}}*/ +void HydrologyArmapwAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ + _error_("Not implemented"); +}/*}}}*/ + +/*Additional methods*/ +void HydrologyArmapwAnalysis::UpdateSubglacialWaterPressure(FemModel* femmodel){/*{{{*/ + + /*Get time parameters*/ + IssmDouble time,dt,starttime,tstep_arma; + femmodel->parameters->FindParam(&time,TimeEnum); + femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + femmodel->parameters->FindParam(&starttime,TimesteppingStartTimeEnum); + femmodel->parameters->FindParam(&tstep_arma,HydrologyarmaTimestepEnum); + + /*Determine if this is a time step for the ARMA model*/ + bool isstepforarma = false; + + #ifndef _HAVE_AD_ + if((fmod(time,tstep_arma)parameters->FindParam(&numbasins,HydrologyNumBasinsEnum); + femmodel->parameters->FindParam(&numparams,HydrologyarmaNumParamsEnum); + femmodel->parameters->FindParam(&numbreaks,HydrologyarmaNumBreaksEnum); + femmodel->parameters->FindParam(&arorder,HydrologyarmaarOrderEnum); + femmodel->parameters->FindParam(&maorder,HydrologyarmamaOrderEnum); + IssmDouble* datebreaks = NULL; + IssmDouble* arlagcoefs = NULL; + IssmDouble* malagcoefs = NULL; + IssmDouble* monthlyfactors = NULL; + IssmDouble* polyparams = NULL; + + femmodel->parameters->FindParam(&datebreaks,&M,&N,HydrologyarmadatebreaksEnum); _assert_(M==numbasins); _assert_(N==max(numbreaks,1)); + femmodel->parameters->FindParam(&polyparams,&M,&N,HydrologyarmapolyparamsEnum); _assert_(M==numbasins); _assert_(N==(numbreaks+1)*numparams); + femmodel->parameters->FindParam(&arlagcoefs,&M,&N,HydrologyarmaarlagcoefsEnum); _assert_(M==numbasins); _assert_(N==arorder); + femmodel->parameters->FindParam(&malagcoefs,&M,&N,HydrologyarmamalagcoefsEnum); _assert_(M==numbasins); _assert_(N==maorder); + femmodel->parameters->FindParam(&monthlyfactors,&M,&N,HydrologyarmaMonthlyFactorsEnum); _assert_(M==numbasins); _assert_(N==12); + + femmodel->parameters->FindParam(&isstochastic,StochasticForcingIsStochasticForcingEnum); + if(isstochastic){ + int numstochasticfields; + int* stochasticfields; + femmodel->parameters->FindParam(&numstochasticfields,StochasticForcingNumFieldsEnum); + femmodel->parameters->FindParam(&stochasticfields,&N,StochasticForcingFieldsEnum); _assert_(N==numstochasticfields); + for(int i=0;i(stochasticfields); + } + + /*Check if seasonality is imposed*/ + bool isseasonality = false; + for(int i=0;ielements->objects){ + Element* element = xDynamicCast(object); + /*Compute ARMA perturbation values*/ + element->ArmaProcess(isstepforarma,arorder,maorder,numparams,numbreaks,tstep_arma,polyparams,arlagcoefs,malagcoefs,datebreaks,ispwstochastic,HydrologyarmapwEnum); + /*Compute subglacial water pressure with the ARMA perturbation*/ + element->SubglacialWaterPressure(FrictionWaterPressureEnum); + /*Scale with monthly factors*/ + if(isseasonality) element->MonthlyFactorBasin(monthlyfactors,HydrologyarmapwEnum); + } + + /*Cleanup*/ + xDelete(arlagcoefs); + xDelete(malagcoefs); + xDelete(polyparams); + xDelete(datebreaks); + xDelete(monthlyfactors); +}/*}}}*/ + Index: /issm/trunk/src/c/analyses/HydrologyArmapwAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/HydrologyArmapwAnalysis.h (revision 28013) +++ /issm/trunk/src/c/analyses/HydrologyArmapwAnalysis.h (revision 28013) @@ -0,0 +1,37 @@ +/*! \file HydrologyArmapwAnalysis.h + * \brief: header file for generic external result object + */ + +#ifndef _HydrologyArmapwAnalysis_ +#define _HydrologyArmapwAnalysis_ + +/*Headers*/ +#include "./Analysis.h" + +class HydrologyArmapwAnalysis: public Analysis{ + + public: + /*Model processing*/ + void CreateConstraints(Constraints* constraints,IoModel* iomodel); + void CreateLoads(Loads* loads, IoModel* iomodel); + void CreateNodes(Nodes* nodes,IoModel* iomodel,bool isamr=false); + int DofsPerNode(int** doflist,int domaintype,int approximation); + void UpdateElements(Elements* elements,Inputs* inputs,IoModel* iomodel,int analysis_counter,int analysis_type); + void UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum); + + /*Finite element Analysis*/ + void Core(FemModel* femmodel); + void PreCore(FemModel* femmodel); + ElementVector* CreateDVector(Element* element); + ElementMatrix* CreateJacobianMatrix(Element* element); + ElementMatrix* CreateKMatrix(Element* element); + ElementVector* CreatePVector(Element* element); + void GetSolutionFromInputs(Vector* solution,Element* element); + void GradientJ(Vector* gradient,Element* element,int control_type,int control_interp,int control_index); + void InputUpdateFromSolution(IssmDouble* solution,Element* element); + void UpdateConstraints(FemModel* femmodel); + + /*Intermediaries*/ + void UpdateSubglacialWaterPressure(FemModel* femmodel); +}; +#endif Index: /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 28013) @@ -297,7 +297,8 @@ IssmDouble dt,scalar,water_head; IssmDouble water_load,transfer,runoff_value; - IssmDouble epl_storing,epl_transmitivity; + IssmDouble epl_storing; //,epl_transmitivity; IssmDouble Jdet,time; IssmDouble residual,connectivity; + IssmDouble active_node; IssmDouble *xyz_list = NULL; @@ -313,4 +314,5 @@ ElementVector* pe = basalelement->NewElementVector(); IssmDouble* basis = xNew(numnodes); + /*Retrieve all inputs and parameters*/ @@ -353,6 +355,6 @@ basalelement ->JacobianDeterminant(&Jdet,xyz_list,gauss); basalelement ->NodalFunctions(basis,gauss); + //epl_transmitivity = EplTransmitivity(basalelement,gauss,epl_thick_input); epl_storing = EplStoring(basalelement,gauss,epl_thick_input); - epl_transmitivity = EplTransmitivity(basalelement,gauss,epl_thick_input); /*Loading term*/ @@ -362,6 +364,14 @@ scalar = Jdet*gauss->weight*(water_load+runoff_value); if(dt!=0.) scalar = scalar*dt; - for(int i=0;ivalues[i]+=scalar*basis[i]; - + for(int i=0;ivalues[i]+=scalar*basis[i]; + //This is the noded version + /* basalelement->GetInputValue(&active_node,basalelement->nodes[i],HydrologydcMaskEplactiveNodeEnum); */ + /* if(!reCast(active_node)){ */ + /* pe->values[i]+=scalar*basis[i]; */ + //} + //if(basalelement->nodes[i]->Sid()==42)_printf_("EPL uni Input "<GaussVertex(iv); - epl_transmitivity = EplTransmitivity(basalelement,gauss,epl_thick_input); + //epl_transmitivity = EplTransmitivity(basalelement,gauss,epl_thick_input); connectivity = IssmDouble(basalelement->VertexConnectivity(iv)); residual_input->GetInputValue(&residual,gauss); Index: /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 28013) @@ -326,10 +326,11 @@ /*Intermediaries */ bool active_element,isefficientlayer; - int smb_model,smbsubstepping; - int hydrologysubstepping,smb_averaging; - IssmDouble dt,scalar,sediment_storing; - IssmDouble water_head,sediment_transmitivity; + int smb_model,smb_averaging; + int smbsubstepping, hydrologysubstepping; + IssmDouble dt,scalar,water_head; + IssmDouble sediment_storing,sediment_transmitivity; IssmDouble water_load,runoff_value,transfer; IssmDouble Jdet,time; + IssmDouble active_node; IssmDouble *xyz_list = NULL; @@ -401,7 +402,5 @@ scalar = Jdet*gauss->weight*(water_load+runoff_value); if(dt!=0.) scalar = scalar*dt; - for(int i=0;ivalues[i]+=scalar*basis[i]; - } + for(int i=0;ivalues[i]+=scalar*basis[i]; } else{ @@ -414,5 +413,12 @@ if(dt!=0.) scalar = scalar*dt; for(int i=0;ivalues[i]+=scalar*basis[i]; + //This is the noded version + /* basalelement->GetInputValue(&active_node,basalelement->nodes[i],HydrologydcMaskEplactiveNodeEnum); */ + /* if(!reCast(active_node)){ */ + /* pe->values[i]+=scalar*basis[i]; */ + /* //if(basalelement->nodes[i]->Sid()==42)_printf_("IDS uni Input "<domaintype!=Domain2DhorizontalEnum && iomodel->domaintype!=Domain3DsurfaceEnum) iomodel->FetchData(1,"md.mesh.vertexonbase"); for(int i=0;inumberofvertices;i++){ if (iomodel->domaintype!=Domain3DEnum){ @@ -110,7 +111,9 @@ /*Fetch data needed: */ - int hydrology_model,frictionlaw; + int hydrology_model; iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); - + int meltflag; + iomodel->FindConstant(&meltflag,"md.hydrology.melt_flag"); + /*Now, do we really want GlaDS?*/ if(hydrology_model!=HydrologyGlaDSEnum) return; @@ -132,4 +135,7 @@ iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.geothermalflux",BasalforcingsGeothermalfluxEnum); iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); + if(meltflag==2){ + iomodel->FetchDataToInput(inputs,elements,"md.smb.runoff",SmbRunoffEnum); + } if(iomodel->domaintype!=Domain2DhorizontalEnum){ iomodel->FetchDataToInput(inputs,elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum); @@ -140,4 +146,5 @@ iomodel->FetchDataToInput(inputs,elements,"md.hydrology.bump_height",HydrologyBumpHeightEnum); iomodel->FetchDataToInput(inputs,elements,"md.hydrology.sheet_conductivity",HydrologySheetConductivityEnum); + iomodel->FetchDataToInput(inputs,elements,"md.hydrology.channel_conductivity",HydrologyChannelConductivityEnum); iomodel->FetchDataToInput(inputs,elements,"md.hydrology.neumannflux",HydrologyNeumannfluxEnum); iomodel->FetchDataToInput(inputs,elements,"md.hydrology.moulin_input",HydrologyMoulinInputEnum); @@ -149,116 +156,13 @@ iomodel->FetchDataToInput(inputs,elements,"md.initialization.vx",VxBaseEnum); iomodel->FetchDataToInput(inputs,elements,"md.initialization.vy",VyBaseEnum); - iomodel->FindConstant(&frictionlaw,"md.friction.law"); } else{ iomodel->FetchDataToInput(inputs,elements,"md.initialization.vx",VxEnum); iomodel->FetchDataToInput(inputs,elements,"md.initialization.vy",VyEnum); - iomodel->FindConstant(&frictionlaw,"md.friction.law"); - } - - /*Friction law variables*/ - int FrictionCoupling; - switch(frictionlaw){ - case 1: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 2: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - break; - case 3: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.As",FrictionAsEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 4: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - break; - case 5: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.water_layer",FrictionWaterLayerEnum); - break; - case 6: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - break; - case 7: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficientcoulomb",FrictionCoefficientcoulombEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - - } - break; - case 9: - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.pressure_adjusted_temperature",FrictionPressureAdjustedTemperatureEnum); - InputUpdateFromConstantx(inputs,elements,1.,FrictionPEnum); - InputUpdateFromConstantx(inputs,elements,1.,FrictionQEnum); - break; - case 10: - iomodel->FetchDataToInput(inputs,elements,"md.friction.till_friction_angle",FrictionTillFrictionAngleEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.sediment_compressibility_coefficient",FrictionSedimentCompressibilityCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.hydrology.watercolumn_max",HydrologyWatercolumnMaxEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.watercolumn",WatercolumnEnum,0.); - break; - case 11: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.Cmax",FrictionCmaxEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 12: - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.f",FrictionfEnum); - break; - case 13: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - default: - _error_("friction law "<< frictionlaw <<" not supported"); - } + } + + /*Friction*/ + FrictionUpdateInputs(elements, inputs, iomodel); + }/*}}}*/ void HydrologyGlaDSAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ @@ -274,71 +178,19 @@ parameters->AddObject(new IntParam(HydrologyModelEnum,hydrology_model)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.law",FrictionLawEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.pressure_melt_coefficient",HydrologyPressureMeltCoefficientEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.cavity_spacing",HydrologyCavitySpacingEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.ischannels",HydrologyIschannelsEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.melt_flag",HydrologyMeltFlagEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.channel_conductivity",HydrologyChannelConductivityEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.channel_sheet_width",HydrologyChannelSheetWidthEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.channel_alpha",HydrologyChannelAlphaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.channel_beta",HydrologyChannelBetaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.sheet_alpha",HydrologySheetAlphaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.sheet_beta",HydrologySheetBetaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.omega",HydrologyOmegaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.istransition",HydrologyIsTransitionEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.englacial_void_ratio",HydrologyEnglacialVoidRatioEnum)); - /*Deal with friction parameters*/ - int frictionlaw; - iomodel->FindConstant(&frictionlaw,"md.friction.law"); - switch(frictionlaw){ - case 1: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 2: - break; - case 3: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 4: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 5: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.f",FrictionFEnum)); - break; - case 6: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - break; - case 7: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 8: - break; - case 9: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - parameters->AddObject(new IntParam(FrictionCouplingEnum,0)); - break; - case 10: - parameters->AddObject(new IntParam(FrictionCouplingEnum,2)); /*comment this line to use effective pressure from Beuler and Pelt (2015)*/ - parameters->AddObject(new DoubleParam(FrictionEffectivePressureLimitEnum,0.)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.pseudoplasticity_exponent",FrictionPseudoplasticityExponentEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.threshold_speed",FrictionThresholdSpeedEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.delta",FrictionDeltaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.void_ratio",FrictionVoidRatioEnum)); - break; - case 11: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 12: - parameters->AddObject(new IntParam(FrictionCouplingEnum,2)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 13: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - default: _error_("Friction law "<FindParam(&istransition,HydrologyIsTransitionEnum); + IssmDouble alpha = element->FindParam(HydrologySheetAlphaEnum); + IssmDouble beta = element->FindParam(HydrologySheetBetaEnum); + IssmDouble omega = element->FindParam(HydrologyOmegaEnum); IssmDouble dt = element->FindParam(TimesteppingTimeStepEnum); IssmDouble rho_water = element->FindParam(MaterialsRhoFreshwaterEnum); + IssmDouble mu_water = element->FindParam(MaterialsMuWaterEnum); IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); IssmDouble g = element->FindParam(ConstantsGEnum); IssmDouble e_v = element->FindParam(HydrologyEnglacialVoidRatioEnum); + Input* hr_input = element->GetInput(HydrologyBumpHeightEnum);_assert_(hr_input); Input* k_input = element->GetInput(HydrologySheetConductivityEnum);_assert_(k_input); Input* phi_input = element->GetInput(HydraulicPotentialEnum); _assert_(phi_input); @@ -416,12 +272,27 @@ B_input->GetInputValue(&B,gauss); n_input->GetInputValue(&n,gauss); + hr_input->GetInputValue(&h_r,gauss); b_input->GetInputValue(&b,gauss); H_input->GetInputValue(&H,gauss); + /*Hard code B*/ + B = Cuffey(273.15-2); + /*Get norm of gradient of hydraulic potential and make sure it is >0*/ IssmDouble normgradphi = sqrt(dphi[0]*dphi[0] + dphi[1]*dphi[1]); if(normgradphi < AEPS) normgradphi = AEPS; - - IssmDouble coeff = k*pow(h,alpha)*pow(normgradphi,beta-2.); + + /*Use transition model if specified*/ + IssmDouble nu = mu_water/rho_water; + IssmDouble coeff; + if(istransition==1 && omega>=AEPS){ + IssmDouble hratio = fabs(h/h_r); + IssmDouble coarg = 1. + 4.*pow(hratio,3-2*alpha)*omega*k*pow(h,3)*normgradphi/nu; + coeff = nu/2./omega*pow(hratio,2*alpha-3) * (-1 + pow(coarg, 0.5))/normgradphi; + } + else { + /*If omega is zero, use standard model, otherwise transition model*/ + coeff = k*pow(h,alpha)*pow(normgradphi,beta-2.); + } /*Diffusive term*/ @@ -469,7 +340,7 @@ /*Intermediaries */ - bool meltflag; + int meltflag; IssmDouble Jdet,w,v2,vx,vy,ub,h,h_r; - IssmDouble G,m,frictionheat,alpha2; + IssmDouble G,m,melt,RO,frictionheat,alpha2; IssmDouble A,B,n,phi_old,phi,phi_0; IssmDouble H,b; @@ -498,5 +369,6 @@ Input* b_input = element->GetInput(BedEnum); _assert_(b_input); Input* G_input = element->GetInput(BasalforcingsGeothermalfluxEnum);_assert_(G_input); - Input* m_input = element->GetInput(BasalforcingsGroundediceMeltingRateEnum);_assert_(m_input); + Input* melt_input = element->GetInput(BasalforcingsGroundediceMeltingRateEnum);_assert_(melt_input); + Input* RO_input = NULL; Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); @@ -523,4 +395,8 @@ b_input->GetInputValue(&b,gauss); H_input->GetInputValue(&H,gauss); + melt_input->GetInputValue(&melt,gauss); + + /*Hard code B*/ + B = Cuffey(273.15-2); /*Get basal velocity*/ @@ -537,9 +413,14 @@ /*Compute melt (if necessary)*/ - if(!meltflag){ + if(meltflag == 0){ m = (G + frictionheat)/(rho_ice*L); } + else if(meltflag == 1){ + m = melt; + } else{ - m_input->GetInputValue(&m,gauss); + Input* RO_input = element->GetInput(SmbRunoffEnum);_assert_(RO_input); + RO_input->GetInputValue(&melt,gauss); + m = melt + RO; } @@ -580,10 +461,7 @@ /*Intermediaries*/ IssmDouble dphi[3],h,k,phi; + IssmDouble h_r; IssmDouble oceanLS,iceLS; IssmDouble* xyz_list = NULL; - - /*Hard coded coefficients*/ - const IssmPDouble alpha = 5./4.; - const IssmPDouble beta = 3./2.; /*Fetch number vertices for this element*/ @@ -606,7 +484,15 @@ /*Retrieve all inputs and parameters*/ + bool istransition; + element->FindParam(&istransition,HydrologyIsTransitionEnum); + IssmDouble alpha = element->FindParam(HydrologySheetAlphaEnum); + IssmDouble beta = element->FindParam(HydrologySheetBetaEnum); + IssmDouble omega = element->FindParam(HydrologyOmegaEnum); element->GetVerticesCoordinates(&xyz_list); + IssmDouble rho_water = element->FindParam(MaterialsRhoFreshwaterEnum); + IssmDouble mu_water = element->FindParam(MaterialsMuWaterEnum); Input *k_input = element->GetInput(HydrologySheetConductivityEnum); _assert_(k_input); Input *phi_input = element->GetInput(HydraulicPotentialEnum); _assert_(phi_input); + Input *hr_input = element->GetInput(HydrologyBumpHeightEnum); _assert_(hr_input); Input *h_input = element->GetInput(HydrologySheetThicknessEnum); _assert_(h_input); Input *oceanLS_input = element->GetInput(MaskOceanLevelsetEnum); _assert_(oceanLS_input); @@ -622,4 +508,5 @@ phi_input->GetInputValue(&phi,gauss); h_input->GetInputValue(&h,gauss); + hr_input->GetInputValue(&h_r,gauss); k_input->GetInputValue(&k,gauss); oceanLS_input->GetInputValue(&oceanLS,gauss); @@ -636,6 +523,17 @@ IssmDouble normgradphi = sqrt(dphi[0]*dphi[0] + dphi[1]*dphi[1]); if(normgradphi < AEPS) normgradphi = AEPS; - - IssmDouble coeff = k*pow(h,alpha)*pow(normgradphi,beta-2.)/max(AEPS,h); // divide by h to get speed instead of discharge + + /*If omega is zero, use standard model, otherwise transition model*/ + IssmDouble nu = mu_water/rho_water; + IssmDouble coeff; + if(istransition==1 && omega>=AEPS){ + IssmDouble hratio = fabs(h/h_r); + IssmDouble coarg = 1. + 4.*pow(hratio,3-2*alpha)*omega*k*pow(h,3)*normgradphi/nu; + coeff = nu/2./omega*pow(hratio,2*alpha-3) * (-1 + pow(coarg, 0.5))/normgradphi/max(AEPS,h); // divide by h to get speed instead of discharge + } + else { + coeff = k*pow(h,alpha)*pow(normgradphi,beta-2.)/max(AEPS,h); // divide by h to get speed instead of discharge + } + vx[iv] = -coeff*dphi[0]; @@ -674,5 +572,5 @@ element->GetInputListOnNodes(&mask[0],MaskOceanLevelsetEnum); element->GetInputListOnNodes(&bed[0],BaseEnum); - element->GetInputListOnNodes(&thickness[0],BaseEnum); + element->GetInputListOnNodes(&thickness[0],ThicknessEnum); element->GetInputListOnNodes(&ls_active[0],HydrologyMaskNodeActivationEnum); @@ -779,4 +677,7 @@ iceLS_input->GetInputValue(&iceLS,gauss); + /*Hard code B*/ + B = Cuffey(273.15-2); + /*Set sheet thickness to zero if floating or no ice*/ if(oceanLS<0. || iceLS>0.){ @@ -793,5 +694,5 @@ /*Get A from B and n*/ - A=pow(B,-n); + A = pow(B,-n); /*Define alpha and beta*/ @@ -812,9 +713,4 @@ } } - - /*Force floating ice to have zero sheet thickness*/ - /*if(!element->IsAllGrounded() || !element->IsIceInElement()){ - for(int iv=0;ivAddInput(HydrologySheetThicknessEnum,h_new,P1Enum); @@ -878,5 +774,5 @@ p_i = rho_ice*g*H; - /*Copmute overburden potential*/ + /*Compute overburden potential*/ phi_0 = phi_m + p_i; Index: /issm/trunk/src/c/analyses/HydrologyShaktiAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyShaktiAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/HydrologyShaktiAnalysis.cpp (revision 28013) @@ -34,4 +34,5 @@ /*Create discrete loads for Moulins*/ CreateSingleNodeToElementConnectivity(iomodel); + if(iomodel->domaintype!=Domain2DhorizontalEnum && iomodel->domaintype!=Domain3DsurfaceEnum) iomodel->FetchData(1,"md.mesh.vertexonbase"); for(int i=0;inumberofvertices;i++){ if (iomodel->domaintype!=Domain3DEnum){ @@ -52,8 +53,17 @@ int M,N; int *segments = NULL; - iomodel->FetchData(&segments,&M,&N,"md.mesh.segments"); + if(iomodel->domaintype==Domain3DEnum){ + iomodel->FetchData(&segments,&M,&N,"md.mesh.segments2d"); + } + else if(iomodel->domaintype==Domain2DhorizontalEnum){ + iomodel->FetchData(&segments,&M,&N,"md.mesh.segments"); + } + else{ + _error_("mesh type not supported yet"); + } /*Check that the size seem right*/ _assert_(N==3); _assert_(M>=3); + for(int i=0;imy_elements[segments[i*3+2]-1]){ @@ -123,19 +133,7 @@ iomodel->FetchDataToInput(inputs,elements,"md.initialization.vy",VyBaseEnum); } - iomodel->FindConstant(&frictionlaw,"md.friction.law"); - - /*Friction law variables*/ - switch(frictionlaw){ - case 1: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - break; - case 8: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - break; - default: - _error_("Friction law "<< frictionlaw <<" not supported"); - } + + /*Friction*/ + FrictionUpdateInputs(elements, inputs, iomodel); }/*}}}*/ void HydrologyShaktiAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ @@ -151,28 +149,6 @@ parameters->AddObject(new IntParam(HydrologyModelEnum,hydrology_model)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.law",FrictionLawEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.relaxation",HydrologyRelaxationEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.storage",HydrologyStorageEnum)); - - /*Deal with friction parameters*/ - int frictionlaw; - iomodel->FindConstant(&frictionlaw,"md.friction.law"); - if(frictionlaw==6){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - } - if(frictionlaw==4){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - } - if(frictionlaw==1 || frictionlaw==3 || frictionlaw==7){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - } - if(frictionlaw==9){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - parameters->AddObject(new IntParam(FrictionCouplingEnum,0)); - } /*Requested outputs*/ @@ -181,4 +157,7 @@ if(numoutputs)parameters->AddObject(new StringArrayParam(HydrologyRequestedOutputsEnum,requestedoutputs,numoutputs)); iomodel->DeleteData(&requestedoutputs,numoutputs,"md.hydrology.requested_outputs"); + + /*Friction*/ + FrictionUpdateParameters(parameters, iomodel); }/*}}}*/ @@ -198,4 +177,9 @@ }/*}}}*/ ElementMatrix* HydrologyShaktiAnalysis::CreateKMatrix(Element* element){/*{{{*/ + + /* Check if ice in element */ + if(element->IsAllFloating() || !element->IsIceInElement()) return NULL; + if(!element->IsOnBase()) return NULL; + Element* basalelement = element->SpawnBasalElement(); /*Intermediaries */ @@ -205,57 +189,55 @@ /*Fetch number of nodes and dof for this finite element*/ - int numnodes = element->GetNumberOfNodes(); + int numnodes = basalelement->GetNumberOfNodes(); /*Initialize Element vector and other vectors*/ - ElementMatrix* Ke = element->NewElementMatrix(); + ElementMatrix* Ke = basalelement->NewElementMatrix(); IssmDouble* dbasis = xNew(2*numnodes); IssmDouble* basis = xNew(numnodes); /*Retrieve all inputs and parameters*/ - element->GetVerticesCoordinates(&xyz_list); + basalelement->GetVerticesCoordinates(&xyz_list); /*Get conductivity from inputs*/ - IssmDouble conductivity = GetConductivity(element); + IssmDouble conductivity = GetConductivity(basalelement); /*Get englacial storage coefficient*/ IssmDouble storage,dt; - element->FindParam(&storage,HydrologyStorageEnum); - element->FindParam(&dt,TimesteppingTimeStepEnum); - - /*Get all inputs and parameters*/ - element->FindParam(&rho_water,MaterialsRhoFreshwaterEnum); - element->FindParam(&rho_ice,MaterialsRhoIceEnum); - element->FindParam(&g,ConstantsGEnum); - Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); - Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); - Input* gap_input = element->GetInput(HydrologyGapHeightEnum); _assert_(gap_input); - Input* thickness_input = element->GetInput(ThicknessEnum); _assert_(thickness_input); - Input* head_input = element->GetInput(HydrologyHeadEnum); _assert_(head_input); - Input* base_input = element->GetInput(BaseEnum); _assert_(base_input); + basalelement->FindParam(&storage,HydrologyStorageEnum); + basalelement->FindParam(&dt,TimesteppingTimeStepEnum); + + /*Get all inputs and parameters*/ + basalelement->FindParam(&rho_water,MaterialsRhoFreshwaterEnum); + basalelement->FindParam(&rho_ice,MaterialsRhoIceEnum); + basalelement->FindParam(&g,ConstantsGEnum); + Input* B_input = basalelement->GetInput(MaterialsRheologyBEnum); _assert_(B_input); + Input* n_input = basalelement->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + Input* gap_input = basalelement->GetInput(HydrologyGapHeightEnum); _assert_(gap_input); + Input* thickness_input = basalelement->GetInput(ThicknessEnum); _assert_(thickness_input); + Input* head_input = basalelement->GetInput(HydrologyHeadEnum); _assert_(head_input); + Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); /* Start looping on the number of gaussian points: */ - Gauss* gauss=element->NewGauss(1); + Gauss* gauss=basalelement->NewGauss(1); while(gauss->next()){ - element->JacobianDeterminant(&Jdet,xyz_list,gauss); - element->NodalFunctionsDerivatives(dbasis,xyz_list,gauss); - element->NodalFunctions(basis,gauss); - - base_input->GetInputValue(&bed,gauss); - thickness_input->GetInputValue(&thickness,gauss); - gap_input->GetInputValue(&gap,gauss); - head_input->GetInputValue(&head,gauss); - - /*Get ice A parameter*/ - B_input->GetInputValue(&B,gauss); - n_input->GetInputValue(&n,gauss); - A=pow(B,-n); - - /*Get water and ice pressures*/ - IssmDouble pressure_ice = rho_ice*g*thickness; _assert_(pressure_ice>0.); - IssmDouble pressure_water = rho_water*g*(head-bed); - if(pressure_water>pressure_ice) pressure_water = pressure_ice; - - + basalelement->JacobianDeterminant(&Jdet,xyz_list,gauss); + basalelement->NodalFunctionsDerivatives(dbasis,xyz_list,gauss); + basalelement->NodalFunctions(basis,gauss); + + base_input->GetInputValue(&bed,gauss); + thickness_input->GetInputValue(&thickness,gauss); + gap_input->GetInputValue(&gap,gauss); + head_input->GetInputValue(&head,gauss); + + /*Get ice A parameter*/ + B_input->GetInputValue(&B,gauss); + n_input->GetInputValue(&n,gauss); + A=pow(B,-n); + + /*Get water and ice pressures*/ + IssmDouble pressure_ice = rho_ice*g*thickness; _assert_(pressure_ice>0.); + IssmDouble pressure_water = rho_water*g*(head-bed); + if(pressure_water>pressure_ice) pressure_water = pressure_ice; for(int i=0;ivalues[i*numnodes+j] += conductivity*gauss->weight*Jdet*(dbasis[0*numnodes+i]*dbasis[0*numnodes+j] + dbasis[1*numnodes+i]*dbasis[1*numnodes+j]) + gauss->weight*Jdet*storage/dt*basis[i]*basis[j] - +gauss->weight*Jdet*A*(n)*(pow(fabs(pressure_ice-pressure_water),(n-1))*rho_water*g)*gap*basis[i]*basis[j]; + +gauss->weight*Jdet*A*(n)*(pow(fabs(pressure_ice-pressure_water),(n-1))*rho_water*g)*gap*basis[i]*basis[j]; } } @@ -273,4 +255,5 @@ xDelete(dbasis); delete gauss; + if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; return Ke; }/*}}}*/ @@ -278,5 +261,7 @@ /*Skip if water or ice shelf element*/ - if(element->IsAllFloating()) return NULL; + if(element->IsAllFloating() || !element->IsIceInElement()) return NULL; + if(!element->IsOnBase()) return NULL; + Element* basalelement = element->SpawnBasalElement(); /*Intermediaries */ @@ -289,45 +274,45 @@ /*Fetch number of nodes and dof for this finite element*/ - int numnodes = element->GetNumberOfNodes(); + int numnodes = basalelement->GetNumberOfNodes(); /*Initialize Element vector and other vectors*/ - ElementVector* pe = element->NewElementVector(); + ElementVector* pe = basalelement->NewElementVector(); IssmDouble* basis = xNew(numnodes); /*Retrieve all inputs and parameters*/ - element->GetVerticesCoordinates(&xyz_list); - IssmDouble latentheat = element->FindParam(MaterialsLatentheatEnum); - IssmDouble g = element->FindParam(ConstantsGEnum); - IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); - IssmDouble rho_water = element->FindParam(MaterialsRhoFreshwaterEnum); - Input* geothermalflux_input = element->GetInput(BasalforcingsGeothermalfluxEnum);_assert_(geothermalflux_input); - Input* head_input = element->GetInput(HydrologyHeadEnum); _assert_(head_input); - Input* gap_input = element->GetInput(HydrologyGapHeightEnum); _assert_(gap_input); - Input* thickness_input = element->GetInput(ThicknessEnum); _assert_(thickness_input); - Input* base_input = element->GetInput(BaseEnum); _assert_(base_input); - Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); - Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); - Input* englacial_input = element->GetInput(HydrologyEnglacialInputEnum); _assert_(englacial_input); - Input* lr_input = element->GetInput(HydrologyBumpSpacingEnum); _assert_(lr_input); - Input* br_input = element->GetInput(HydrologyBumpHeightEnum); _assert_(br_input); - Input* headold_input = element->GetInput(HydrologyHeadOldEnum); _assert_(headold_input); + basalelement->GetVerticesCoordinates(&xyz_list); + IssmDouble latentheat = basalelement->FindParam(MaterialsLatentheatEnum); + IssmDouble g = basalelement->FindParam(ConstantsGEnum); + IssmDouble rho_ice = basalelement->FindParam(MaterialsRhoIceEnum); + IssmDouble rho_water = basalelement->FindParam(MaterialsRhoFreshwaterEnum); + Input* geothermalflux_input = basalelement->GetInput(BasalforcingsGeothermalfluxEnum);_assert_(geothermalflux_input); + Input* head_input = basalelement->GetInput(HydrologyHeadEnum); _assert_(head_input); + Input* gap_input = basalelement->GetInput(HydrologyGapHeightEnum); _assert_(gap_input); + Input* thickness_input = basalelement->GetInput(ThicknessEnum); _assert_(thickness_input); + Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); + Input* B_input = basalelement->GetInput(MaterialsRheologyBEnum); _assert_(B_input); + Input* n_input = basalelement->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + Input* englacial_input = basalelement->GetInput(HydrologyEnglacialInputEnum); _assert_(englacial_input); + Input* lr_input = basalelement->GetInput(HydrologyBumpSpacingEnum); _assert_(lr_input); + Input* br_input = basalelement->GetInput(HydrologyBumpHeightEnum); _assert_(br_input); + Input* headold_input = basalelement->GetInput(HydrologyHeadOldEnum); _assert_(headold_input); /*Get conductivity from inputs*/ - IssmDouble conductivity = GetConductivity(element); + IssmDouble conductivity = GetConductivity(basalelement); /*Get englacial storage coefficient*/ IssmDouble storage,dt; - element->FindParam(&storage,HydrologyStorageEnum); - element->FindParam(&dt,TimesteppingTimeStepEnum); - - /*Build friction element, needed later: */ - Friction* friction=new Friction(element,2); + basalelement->FindParam(&storage,HydrologyStorageEnum); + basalelement->FindParam(&dt,TimesteppingTimeStepEnum); + + /*Build friction basalelement, needed later: */ + Friction* friction=new Friction(basalelement,2); /* Start looping on the number of gaussian points: */ - Gauss* gauss=element->NewGauss(2); + Gauss* gauss=basalelement->NewGauss(2); while(gauss->next()){ - element->JacobianDeterminant(&Jdet,xyz_list,gauss); - element->NodalFunctions(basis,gauss); + basalelement->JacobianDeterminant(&Jdet,xyz_list,gauss); + basalelement->NodalFunctions(basis,gauss); geothermalflux_input->GetInputValue(&G,gauss); base_input->GetInputValue(&bed,gauss); @@ -368,21 +353,21 @@ /*Compute change in sensible heat due to changes in pressure melting point*/ - dpressure_water[0] = rho_water*g*(dh[0] - dbed[0]); + dpressure_water[0] = rho_water*g*(dh[0] - dbed[0]); dpressure_water[1] = rho_water*g*(dh[1] - dbed[1]); - meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1])); - - for(int i=0;ivalues[i]+=Jdet*gauss->weight* - ( - meltrate*(1/rho_water-1/rho_ice) - +A*pow(fabs(pressure_ice - pressure_water),n-1)*(pressure_ice + rho_water*g*bed)*gap - +(n-1)*A*pow(fabs(pressure_ice - pressure_water),n-1)*(rho_water*g*head)*gap - -beta*sqrt(vx*vx+vy*vy) - +ieb - +storage*head_old/dt - )*basis[i]; - - - } + meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1])); + + for(int i=0;ivalues[i]+=Jdet*gauss->weight* + ( + meltrate*(1/rho_water-1/rho_ice) + +A*pow(fabs(pressure_ice - pressure_water),n-1)*(pressure_ice + rho_water*g*bed)*gap + +(n-1)*A*pow(fabs(pressure_ice - pressure_water),n-1)*(rho_water*g*head)*gap + -beta*sqrt(vx*vx+vy*vy) + +ieb + +storage*head_old/dt + )*basis[i]; + + } + /*Clean up and return*/ xDelete(xyz_list); @@ -390,4 +375,5 @@ delete friction; delete gauss; + if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; return pe; }/*}}}*/ @@ -399,4 +385,7 @@ }/*}}}*/ void HydrologyShaktiAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ + + /*Only update if on base*/ + if(!element->IsOnBase()) return; /*Intermediary*/ @@ -441,5 +430,5 @@ /*Add input to the element: */ - element->AddInput(HydrologyHeadEnum,values,element->GetElementType()); + element->AddBasalInput(HydrologyHeadEnum,values,element->GetElementType()); /*Update reynolds number according to new solution*/ @@ -454,5 +443,5 @@ IssmDouble reynolds = conductivity*sqrt(dh[0]*dh[0]+dh[1]*dh[1])/NU; - element->AddInput(HydrologyReynoldsEnum,&reynolds,P0Enum); + element->AddBasalInput(HydrologyReynoldsEnum,&reynolds,P0Enum); /*Compute new effective pressure*/ @@ -468,5 +457,48 @@ }/*}}}*/ void HydrologyShaktiAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ - /*Default, do nothing*/ + /*Update active elements based on ice levelset and ocean levelset*/ + GetMaskOfIceVerticesLSMx(femmodel,true); + SetActiveNodesLSMx(femmodel,true); + + IssmDouble rho_ice = femmodel->parameters->FindParam(MaterialsRhoIceEnum); + IssmDouble rho_water = femmodel->parameters->FindParam(MaterialsRhoFreshwaterEnum); + IssmDouble g = femmodel->parameters->FindParam(ConstantsGEnum); + + /*Constrain all nodes that are grounded and unconstrain the ones that float*/ + for(Object* & object : femmodel->elements->objects){ + + /*Get current element and return if not on base*/ + Element *element = xDynamicCast(object); + if(!element->IsOnBase()) continue; + + int numnodes = element->GetNumberOfNodes(); + IssmDouble *mask = xNew(numnodes); + IssmDouble *bed = xNew(numnodes); + IssmDouble *thickness = xNew(numnodes); + IssmDouble *ls_active = xNew(numnodes); + + element->GetInputListOnNodes(&mask[0],MaskOceanLevelsetEnum); + element->GetInputListOnNodes(&bed[0],BaseEnum); + element->GetInputListOnNodes(&thickness[0],ThicknessEnum); + element->GetInputListOnNodes(&ls_active[0],HydrologyMaskNodeActivationEnum); + + //for(int in=0;inGetNode(in); + if(mask[in]>0. && ls_active[in]==1.){ + node->Activate(); //Not sure if we need this! + } + else{ + IssmDouble phi = rho_ice*g*thickness[in] + rho_water*g*bed[in]; //FIXME this is correct! + node->Deactivate();// Not sure if we need this + node->ApplyConstraint(0,phi); + } + } + xDelete(mask); + xDelete(bed); + xDelete(thickness); + xDelete(ls_active); + } + return; }/*}}}*/ @@ -505,39 +537,41 @@ /*Skip if water or ice shelf element*/ - if(element->IsAllFloating()) return; + if(element->IsAllFloating() || !element->IsIceInElement()) return; + if(!element->IsOnBase()) return; + Element* basalelement = element->SpawnBasalElement(); /*Intermediaries */ - IssmDouble newgap = 0.; - IssmDouble Jdet,meltrate,G,dh[2],B,A,n,dt; + IssmDouble newgap = 0.; + IssmDouble Jdet,meltrate,G,dh[3],B,A,n,dt; IssmDouble gap,bed,thickness,head; IssmDouble lr,br,vx,vy,beta,lc; IssmDouble alpha2,frictionheat; IssmDouble* xyz_list = NULL; - IssmDouble dpressure_water[2],dbed[2],PMPheat,dissipation; + IssmDouble dpressure_water[3],dbed[3],PMPheat,dissipation; IssmDouble q = 0.; - IssmDouble channelization = 0.; + IssmDouble channelization = 0.; /*Retrieve all inputs and parameters*/ - element->GetVerticesCoordinates(&xyz_list); - element->FindParam(&dt,TimesteppingTimeStepEnum); - IssmDouble latentheat = element->FindParam(MaterialsLatentheatEnum); - IssmDouble g = element->FindParam(ConstantsGEnum); - IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); - IssmDouble rho_water = element->FindParam(MaterialsRhoFreshwaterEnum); - Input* geothermalflux_input = element->GetInput(BasalforcingsGeothermalfluxEnum);_assert_(geothermalflux_input); - Input* head_input = element->GetInput(HydrologyHeadEnum); _assert_(head_input); - Input* gap_input = element->GetInput(HydrologyGapHeightEnum); _assert_(gap_input); - Input* thickness_input = element->GetInput(ThicknessEnum); _assert_(thickness_input); - Input* base_input = element->GetInput(BaseEnum); _assert_(base_input); - Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); - Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); - Input* lr_input = element->GetInput(HydrologyBumpSpacingEnum); _assert_(lr_input); - Input* br_input = element->GetInput(HydrologyBumpHeightEnum); _assert_(br_input); + basalelement->GetVerticesCoordinates(&xyz_list); + basalelement->FindParam(&dt,TimesteppingTimeStepEnum); + IssmDouble latentheat = basalelement->FindParam(MaterialsLatentheatEnum); + IssmDouble g = basalelement->FindParam(ConstantsGEnum); + IssmDouble rho_ice = basalelement->FindParam(MaterialsRhoIceEnum); + IssmDouble rho_water = basalelement->FindParam(MaterialsRhoFreshwaterEnum); + Input* geothermalflux_input = basalelement->GetInput(BasalforcingsGeothermalfluxEnum);_assert_(geothermalflux_input); + Input* head_input = basalelement->GetInput(HydrologyHeadEnum); _assert_(head_input); + Input* gap_input = basalelement->GetInput(HydrologyGapHeightEnum); _assert_(gap_input); + Input* thickness_input = basalelement->GetInput(ThicknessEnum); _assert_(thickness_input); + Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); + Input* B_input = basalelement->GetInput(MaterialsRheologyBEnum); _assert_(B_input); + Input* n_input = basalelement->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + Input* lr_input = basalelement->GetInput(HydrologyBumpSpacingEnum); _assert_(lr_input); + Input* br_input = basalelement->GetInput(HydrologyBumpHeightEnum); _assert_(br_input); /*Get conductivity from inputs*/ - IssmDouble conductivity = GetConductivity(element); - - /*Build friction element, needed later: */ - Friction* friction=new Friction(element,2); + IssmDouble conductivity = GetConductivity(basalelement); + + /*Build friction basalelement, needed later: */ + Friction* friction=new Friction(basalelement,2); /*Keep track of weights*/ @@ -545,8 +579,8 @@ /* Start looping on the number of gaussian points: */ - Gauss* gauss=element->NewGauss(2); + Gauss* gauss=basalelement->NewGauss(2); while(gauss->next()){ - element->JacobianDeterminant(&Jdet,xyz_list,gauss); + basalelement->JacobianDeterminant(&Jdet,xyz_list,gauss); geothermalflux_input->GetInputValue(&G,gauss); @@ -581,6 +615,6 @@ if(pressure_water>pressure_ice) pressure_water = pressure_ice; - /* Compute change in sensible heat due to changes in pressure melting point*/ - dpressure_water[0] = rho_water*g*(dh[0] - dbed[0]); + /* Compute change in sensible heat due to changes in pressure melting point*/ + dpressure_water[0] = rho_water*g*(dh[0] - dbed[0]); dpressure_water[1] = rho_water*g*(dh[1] - dbed[1]); dissipation=rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1]); @@ -588,15 +622,14 @@ meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1])); - element->AddInput(DummyEnum,&meltrate,P0Enum); - element->AddInput(EsaEmotionEnum,&frictionheat,P0Enum); - element->AddInput(EsaNmotionEnum,&dissipation,P0Enum); - element->AddInput(EsaUmotionEnum,&PMPheat,P0Enum); - + //element->AddBasalInput(DummyEnum,&meltrate,P0Enum); + //element->AddBasalInput(EsaEmotionEnum,&frictionheat,P0Enum); + //element->AddBasalInput(EsaNmotionEnum,&dissipation,P0Enum); + //element->AddBasalInput(EsaUmotionEnum,&PMPheat,P0Enum); newgap += gauss->weight*Jdet*(gap+dt*( - meltrate/rho_ice - -A*pow(fabs(pressure_ice-pressure_water),n-1)*(pressure_ice-pressure_water)*gap - +beta*sqrt(vx*vx+vy*vy) - )); + meltrate/rho_ice + -A*pow(fabs(pressure_ice-pressure_water),n-1)*(pressure_ice-pressure_water)*gap + +beta*sqrt(vx*vx+vy*vy) + )); @@ -604,5 +637,5 @@ /* Compute basal water flux */ - q += gauss->weight*Jdet*(conductivity*sqrt(dh[0]*dh[0]+dh[1]*dh[1])); + q += gauss->weight*Jdet*(conductivity*sqrt(dh[0]*dh[0]+dh[1]*dh[1])); /* Compute "degree of channelization" (ratio of melt opening to opening by sliding) */ @@ -620,13 +653,13 @@ /*Add new gap as an input*/ - element->AddInput(HydrologyGapHeightEnum,&newgap,P0Enum); + element->AddBasalInput(HydrologyGapHeightEnum,&newgap,P0Enum); /*Divide by connectivity, add basal flux as an input*/ q = q/totalweights; - element->AddInput(HydrologyBasalFluxEnum,&q,P0Enum); + element->AddBasalInput(HydrologyBasalFluxEnum,&q,P0Enum); /* Divide by connectivity, add degree of channelization as an input */ channelization = channelization/totalweights; - element->AddInput(DegreeOfChannelizationEnum,&channelization,P0Enum); + element->AddBasalInput(DegreeOfChannelizationEnum,&channelization,P0Enum); /*Clean up and return*/ @@ -634,4 +667,5 @@ delete friction; delete gauss; + if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; }/*}}}*/ void HydrologyShaktiAnalysis::UpdateEffectivePressure(FemModel* femmodel){/*{{{*/ @@ -646,5 +680,6 @@ /*Skip if water or ice shelf element*/ - if(element->IsAllFloating()) return; + if(element->IsAllFloating() || !element->IsIceInElement()) return; + if(!element->IsOnBase()) return; /*Intermediaries*/ @@ -663,5 +698,4 @@ Input* base_input = element->GetInput(BaseEnum); _assert_(base_input); - Gauss* gauss=element->NewGauss(); for (int i=0;iAddInput(EffectivePressureEnum,N,element->GetElementType()); + element->AddBasalInput(EffectivePressureEnum,N,element->GetElementType()); /*Clean up and return*/ Index: /issm/trunk/src/c/analyses/HydrologyShreveAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyShreveAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/HydrologyShreveAnalysis.cpp (revision 28013) @@ -14,5 +14,5 @@ if(hydrology_model!=HydrologyshreveEnum) return; - IoModelToConstraintsx(constraints,iomodel,"md.hydrologyshreve.spcwatercolumn",HydrologyShreveAnalysisEnum,P1Enum); + IoModelToConstraintsx(constraints,iomodel,"md.hydrology.spcwatercolumn",HydrologyShreveAnalysisEnum,P1Enum); }/*}}}*/ Index: /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 28013) @@ -107,4 +107,8 @@ iomodel->FetchDataToInput(inputs,elements,"md.geometry.bed",BedEnum); break; + case CalvingVonmisesADEnum: + iomodel->FetchDataToInput(inputs,elements,"md.calving.basin_id",CalvingBasinIdEnum); + iomodel->FetchDataToInput(inputs,elements,"md.geometry.bed",BedEnum); + break; case CalvingDev2Enum: iomodel->FetchDataToInput(inputs,elements,"md.calving.stress_threshold_groundedice",CalvingStressThresholdGroundediceEnum); @@ -115,4 +119,6 @@ case CalvingParameterizationEnum: iomodel->FetchDataToInput(inputs,elements,"md.geometry.bed",BedEnum); + break; + case CalvingCalvingMIPEnum: break; @@ -146,5 +152,5 @@ case FrontalForcingsDefaultEnum: iomodel->FetchDataToInput(inputs,elements,"md.frontalforcings.meltingrate",CalvingMeltingrateEnum); - if (calvinglaw == CalvingParameterizationEnum) { + if ((calvinglaw == CalvingParameterizationEnum) || (calvinglaw == CalvingCalvingMIPEnum)) { iomodel->FetchDataToInput(inputs,elements,"md.frontalforcings.ablationrate",CalvingAblationrateEnum); } @@ -153,9 +159,13 @@ /*Retrieve thermal forcing only in the case of non-arma FrontalForcingsRignot*/ iomodel->FetchDataToInput(inputs,elements,"md.frontalforcings.thermalforcing",ThermalForcingEnum); - /* Do not break here, still retrieve basin_ID,subglacial_discharge, etc.*/ - case FrontalForcingsRignotarmaEnum: iomodel->FetchDataToInput(inputs,elements,"md.frontalforcings.basin_id",FrontalForcingsBasinIdEnum); iomodel->FetchDataToInput(inputs,elements,"md.frontalforcings.subglacial_discharge",FrontalForcingsSubglacialDischargeEnum); - break; + break; + case FrontalForcingsRignotarmaEnum: + bool isdischargearma; + iomodel->FindConstant(&isdischargearma,"md.frontalforcings.isdischargearma"); + iomodel->FetchDataToInput(inputs,elements,"md.frontalforcings.basin_id",FrontalForcingsBasinIdEnum); + if(isdischargearma==false) iomodel->FetchDataToInput(inputs,elements,"md.frontalforcings.subglacial_discharge",FrontalForcingsSubglacialDischargeEnum); + break; default: _error_("Frontal forcings"<AddObject(iomodel->CopyConstantObject("md.calving.min_thickness",CalvingMinthicknessEnum)); + break; + case CalvingVonmisesADEnum: + parameters->AddObject(iomodel->CopyConstantObject("md.calving.min_thickness",CalvingMinthicknessEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.calving.num_basins",CalvingNumberofBasinsEnum)); + + iomodel->FetchData(&transparam,&M,&N,"md.calving.stress_threshold_groundedice"); + _assert_(M>=1 && N>=1); + parameters->AddObject(new DoubleVecParam(CalvingADStressThresholdGroundediceEnum,transparam,M)); + xDelete(transparam); + + iomodel->FetchData(&transparam,&M,&N,"md.calving.stress_threshold_floatingice"); + _assert_(M>=1 && N>=1); + parameters->AddObject(new DoubleVecParam(CalvingADStressThresholdFloatingiceEnum,transparam,M)); + xDelete(transparam); + break; case CalvingMinthicknessEnum: @@ -234,4 +259,8 @@ parameters->AddObject(iomodel->CopyConstantObject("md.calving.rc",CalvingRcEnum)); break; + case CalvingCalvingMIPEnum: + parameters->AddObject(iomodel->CopyConstantObject("md.calving.experiment",CalvingUseParamEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.calving.min_thickness",CalvingMinthicknessEnum)); + break; default: _error_("Calving law "<AddObject(iomodel->CopyConstantObject("md.frontalforcings.num_basins",FrontalForcingsNumberofBasinsEnum)); + /*Retrieve thermal forcing parameters*/ parameters->AddObject(iomodel->CopyConstantObject("md.frontalforcings.num_params",FrontalForcingsNumberofParamsEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.frontalforcings.num_breaks",FrontalForcingsNumberofBreaksEnum)); @@ -273,5 +303,31 @@ parameters->AddObject(new DoubleMatParam(FrontalForcingsARMAmonthtrendsEnum,transparam,M,N)); xDelete(transparam); - /*Do not break here, generic FrontalForcingsRignot parameters still to be retrieved*/ + parameters->AddObject(iomodel->CopyConstantObject("md.frontalforcings.isdischargearma",FrontalForcingsIsDischargeARMAEnum)); + /*Retrieve subglacial discharge parameters */ + bool isdischargearma; + parameters->FindParam(&isdischargearma,FrontalForcingsIsDischargeARMAEnum); + if(isdischargearma==true){ + parameters->AddObject(iomodel->CopyConstantObject("md.frontalforcings.sd_num_params",FrontalForcingsSdNumberofParamsEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.frontalforcings.sd_num_breaks",FrontalForcingsSdNumberofBreaksEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.frontalforcings.sd_ar_order",FrontalForcingsSdarOrderEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.frontalforcings.sd_ma_order",FrontalForcingsSdmaOrderEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.frontalforcings.sd_arma_timestep",FrontalForcingsSdARMATimestepEnum)); + iomodel->FetchData(&transparam,&M,&N,"md.frontalforcings.sd_polynomialparams"); + parameters->AddObject(new DoubleMatParam(FrontalForcingsSdpolyparamsEnum,transparam,M,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.frontalforcings.sd_datebreaks"); + parameters->AddObject(new DoubleMatParam(FrontalForcingsSddatebreaksEnum,transparam,M,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.frontalforcings.sd_arlag_coefs"); + parameters->AddObject(new DoubleMatParam(FrontalForcingsSdarlagcoefsEnum,transparam,M,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.frontalforcings.sd_malag_coefs"); + parameters->AddObject(new DoubleMatParam(FrontalForcingsSdmalagcoefsEnum,transparam,M,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.frontalforcings.sd_monthlyfrac"); + parameters->AddObject(new DoubleMatParam(FrontalForcingsSdMonthlyFracEnum,transparam,M,N)); + xDelete(transparam); + } + break; case FrontalForcingsRignotEnum: parameters->AddObject(iomodel->CopyConstantObject("md.frontalforcings.num_basins",FrontalForcingsNumberofBasinsEnum)); @@ -698,5 +754,5 @@ /*Apply minimum thickness criterion*/ - if(calvinglaw==CalvingMinthicknessEnum || calvinglaw==CalvingVonmisesEnum || calvinglaw==CalvingParameterizationEnum){ + if(calvinglaw==CalvingMinthicknessEnum || calvinglaw==CalvingVonmisesEnum || calvinglaw==CalvingParameterizationEnum || calvinglaw==CalvingVonmisesADEnum || calvinglaw==CalvingCalvingMIPEnum){ IssmDouble mig_max = femmodel->parameters->FindParam(MigrationMaxEnum); Index: /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 28013) @@ -118,6 +118,6 @@ bool isgroundingline; bool ismovingfront; - bool isoceancoupling; bool issmb; + int isoceancoupling; int grdmodel; @@ -170,4 +170,5 @@ case FloatingMeltRateEnum: iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.perturbation_melting_rate",BasalforcingsPerturbationMeltingRateEnum,0.); if(isstochastic){ iomodel->FetchDataToInput(inputs,elements,"md.stochasticforcing.default_id",StochasticForcingDefaultIdEnum); @@ -208,5 +209,5 @@ if(iomodel->domaintype!=Domain2DhorizontalEnum && !element->IsOnBase()) continue; for(int kk=0;kkDatasetInputAdd(BasalforcingsIsmip6TfEnum,array3d[kk],inputs,iomodel,Ms[kk],Ns[kk],1,BasalforcingsIsmip6TfEnum,7,kk); + element->DatasetInputAdd(BasalforcingsIsmip6TfEnum,array3d[kk],inputs,iomodel,Ms[kk],Ns[kk],1,BasalforcingsIsmip6TfEnum,kk); } } @@ -622,5 +623,5 @@ IssmDouble fraction1,fraction2; IssmDouble Jdet,dt; - IssmDouble ms,mb,gmb,fmb,thickness; + IssmDouble ms,mb,gmb,fmb,thickness,fmb_pert; IssmDouble vx,vy,vel,dvxdx,dvydy,xi,h,tau; IssmDouble dvx[2],dvy[2]; @@ -653,4 +654,5 @@ Input* gmb_input = element->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(gmb_input); Input* fmb_input = element->GetInput(BasalforcingsFloatingiceMeltingRateEnum); _assert_(fmb_input); + //Input* fmb_pert_input = element->GetInput(BasalforcingsPerturbationMeltingRateEnum); _assert_(fmb_pert_input); Input* gllevelset_input = element->GetInput(MaskOceanLevelsetEnum); _assert_(gllevelset_input); Input* ms_input = element->GetInput(SmbMassBalanceEnum); _assert_(ms_input); @@ -659,9 +661,4 @@ Input* vyaverage_input = element->GetInput(VyAverageEnum); _assert_(vyaverage_input); -// if(element->Id()==9){ -// gmb_input->Echo(); -// _error_("S"); -// } - h=element->CharacteristicLength(); @@ -685,4 +682,5 @@ gmb_input->GetInputValue(&gmb,gauss); fmb_input->GetInputValue(&fmb,gauss); + //fmb_pert_input->GetInputValue(&fmb_pert,gauss); gllevelset_input->GetInputValue(&gllevelset,gauss); thickness_input->GetInputValue(&thickness,gauss); @@ -697,5 +695,7 @@ } else if(melt_style==NoMeltOnPartiallyFloatingEnum){ - if (phi<0.00000001) mb=fmb; + if (phi<0.00000001){ + mb=fmb;//+fmb_pert; + } else mb=gmb; } Index: /issm/trunk/src/c/analyses/SealevelchangeAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/SealevelchangeAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/SealevelchangeAnalysis.cpp (revision 28013) @@ -470,5 +470,5 @@ *with steps equal to timeacc:*/ if(viscous){ - nt=reCast((final_time-start_time)/timeacc)+1; + nt=reCast((final_time-start_time)/timeacc)+1; #ifdef _HAVE_AD_ G_viscoelastic_interpolated=xNew(M*nt,"t"); Index: /issm/trunk/src/c/analyses/SmbAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 28013) @@ -206,5 +206,7 @@ break; case SMBsemicEnum: - iomodel->FetchDataToInput(inputs,elements,"md.thermal.spctemperature",ThermalSpctemperatureEnum); + int ismethod; + //if(VerboseSolution()) _printf0_(" smb semic: UpdateElements.\n"); + //iomodel->FetchDataToInput(inputs,elements,"md.thermal.spctemperature",ThermalSpctemperatureEnum); iomodel->FetchDataToInput(inputs,elements,"md.smb.s0gcm",SmbS0gcmEnum); iomodel->FetchDataToInput(inputs,elements,"md.smb.dailysnowfall",SmbDailysnowfallEnum); @@ -217,8 +219,44 @@ iomodel->FetchDataToInput(inputs,elements,"md.smb.dailyairhumidity",SmbDailyairhumidityEnum); iomodel->FetchDataToInput(inputs,elements,"md.smb.dailytemperature",SmbDailytemperatureEnum); - break; - case SMBdebrisMLEnum: - iomodel->FetchDataToInput(inputs,elements,"md.initialization.debris",DebrisThicknessEnum); - break; + // assign initial SEMIC temperature from initialization class. + if(VerboseSolution()) _printf0_(" smb semic: UpdateElements - temperature.\n"); + iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); + + iomodel->FindConstant(&ismethod,"md.smb.ismethod"); + if (ismethod == 1){ + if(VerboseSolution()) _printf0_(" smb semic: UpdateElements - albedo.\n"); + iomodel->FetchDataToInput(inputs,elements,"md.smb.albedo",SmbAlbedoInitEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.albedo_snow",SmbAlbedoSnowInitEnum); + if(VerboseSolution()) _printf0_(" smb semic: UpdateElements - Hice/Hsnow.\n"); + iomodel->FetchDataToInput(inputs,elements,"md.smb.hice",SmbHIceInitEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.hsnow",SmbHSnowInitEnum); + + // initial Temperature amplitude. + if(VerboseSolution()) _printf0_(" smb semic: UpdateElements - Tamp.\n"); + iomodel->FetchDataToInput(inputs,elements,"md.smb.Tamp",SmbTampEnum); + + // assign masking + iomodel->FetchDataToInput(inputs,elements,"md.smb.mask",SmbMaskEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.qmr",SmbSemicQmrInitEnum); + if(VerboseSolution()) _printf0_(" smb semic: UpdateElements - done.\n"); + } + break; + case SMBdebrisEvattEnum: + iomodel->FetchDataToInput(inputs,elements,"md.initialization.debris",DebrisThicknessEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.s0t",SmbS0tEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.snowheight",SmbSnowheightEnum); + iomodel->FetchDataToDatasetInput(inputs,elements,"md.smb.temperature",SmbMonthlytemperaturesEnum); + iomodel->FetchDataToDatasetInput(inputs,elements,"md.smb.precipitation",SmbPrecipitationEnum); + iomodel->FetchDataToDatasetInput(inputs,elements,"md.smb.dsradiation",SmbMonthlydsradiationEnum); + iomodel->FetchDataToDatasetInput(inputs,elements,"md.smb.dlradiation",SmbMonthlydlradiationEnum); + iomodel->FetchDataToDatasetInput(inputs,elements,"md.smb.windspeed",SmbMonthlywindspeedEnum); + iomodel->FetchDataToDatasetInput(inputs,elements,"md.smb.airhumidity",SmbMonthlyairhumidityEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.precipitation_anomaly",SmbPrecipitationsAnomalyEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.temperature_anomaly",SmbTemperaturesAnomalyEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.dsradiation_anomaly",SmbDsradiationAnomalyEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.dlradiation_anomaly",SmbDlradiationAnomalyEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.windspeed_anomaly",SmbWindspeedAnomalyEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.airhumidity_anomaly",SmbAirhumidityAnomalyEnum); + break; default: _error_("Surface mass balance model "<FindParam(&ismethod,SmbSemicMethodEnum); + if (ismethod == 1){ + parameters->AddObject(iomodel->CopyConstantObject("md.smb.desfacElevation",SmbDesfacElevEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.hcrit",SmbSemicHcritEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.rcrit",SmbSemicRcritEnum)); + /*Define albedo parameters.*/ + parameters->AddObject(iomodel->CopyConstantObject("md.smb.albedo_scheme",SmbAlbedoSchemeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.alb_smax",SmbAlbedoSnowMaxEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.alb_smin",SmbAlbedoSnowMinEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.albi",SmbAlbedoIceEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.albl",SmbAlbedoLandEnum)); + + //albedo parameter - slatter + parameters->AddObject(iomodel->CopyConstantObject("md.smb.tmin",SmbSemicTmaxEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.tmax",SmbSemicTminEnum)); + + //albedo parameter - isba & denby + parameters->AddObject(iomodel->CopyConstantObject("md.smb.mcrit",SmbSemicMcritEnum)); + //albedo parameter - isba + parameters->AddObject(iomodel->CopyConstantObject("md.smb.tau_a",SmbSemicTauAEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.tau_f",SmbSemicTauFEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.wcrit",SmbSemicWcritEnum)); + //albedo parameter - alex + parameters->AddObject(iomodel->CopyConstantObject("md.smb.tmid",SmbSemicTmidEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.afac",SmbSemicAfacEnum)); + } /*Nothing to add to parameters*/ break; - case SMBdebrisMLEnum: + case SMBdebrisEvattEnum: /*Nothing to add to parameters*/ break; @@ -514,14 +579,16 @@ case SMBsemicEnum: #ifdef _HAVE_SEMIC_ - if(VerboseSolution())_printf0_(" call smb SEMIC module\n"); - SmbSemicx(femmodel); + if(VerboseSolution())_printf0_(" call smb SEMIC module\n"); + int ismethod; + femmodel->parameters->FindParam(&ismethod,SmbSemicMethodEnum); + SmbSemicx(femmodel,ismethod); #else _error_("SEMIC not installed"); #endif //_HAVE_SEMIC_ break; - case SMBdebrisMLEnum: - if(VerboseSolution())_printf0_(" call smb debris Mayer & Liculli module\n"); - SmbDebrisMLx(femmodel); - break; + case SMBdebrisEvattEnum: + if(VerboseSolution())_printf0_(" call smb Evatt debris module\n"); + SmbDebrisEvattx(femmodel); + break; default: _error_("Surface mass balance model "<FindConstant(&materials_type,"md.materials.type"); iomodel->FindConstant(&ismovingfront,"md.transient.ismovingfront"); - iomodel->FindConstant(&frictionlaw,"md.friction.law"); /*return if no processing required*/ @@ -876,111 +874,6 @@ } - /*Friction law variables*/ - switch(frictionlaw){ - case 1: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 2: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - break; - case 3: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.As",FrictionAsEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 4: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - break; - case 5: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.water_layer",FrictionWaterLayerEnum); - break; - case 6: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - break; - case 7: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficientcoulomb",FrictionCoefficientcoulombEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - - } - break; - case 9: - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.pressure_adjusted_temperature",FrictionPressureAdjustedTemperatureEnum); - InputUpdateFromConstantx(inputs,elements,1.,FrictionPEnum); - InputUpdateFromConstantx(inputs,elements,1.,FrictionQEnum); - break; - case 10: - iomodel->FetchDataToInput(inputs,elements,"md.friction.till_friction_angle",FrictionTillFrictionAngleEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.sediment_compressibility_coefficient",FrictionSedimentCompressibilityCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.hydrology.watercolumn_max",HydrologyWatercolumnMaxEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.watercolumn",WatercolumnEnum,0.); - break; - case 11: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.Cmax",FrictionCmaxEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 12: - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.f",FrictionfEnum); - break; - case 13: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - if(FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - default: - _error_("friction law "<< frictionlaw <<" not supported"); - } - -#ifdef _HAVE_ANDROID_ - inputs->DuplicateInput(FrictionCoefficientEnum,AndroidFrictionCoefficientEnum); -#endif + /*Friction*/ + FrictionUpdateInputs(elements, inputs, iomodel); /*Free data: */ @@ -1014,5 +907,4 @@ parameters->AddObject(iomodel->CopyConstantObject("md.stressbalance.FSreconditioning",StressbalanceFSreconditioningEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.stressbalance.shelf_dampening",StressbalanceShelfDampeningEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.law",FrictionLawEnum)); /*XTH LATH parameters*/ @@ -1037,62 +929,6 @@ iomodel->DeleteData(&requestedoutputs,numoutputs,"md.stressbalance.requested_outputs"); - /*Deal with friction parameters*/ - int frictionlaw; - iomodel->FindConstant(&frictionlaw,"md.friction.law"); - switch(frictionlaw){ - case 1: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 2: - break; - case 3: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 4: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 5: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.f",FrictionFEnum)); - break; - case 6: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - break; - case 7: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 8: - break; - case 9: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - parameters->AddObject(new IntParam(FrictionCouplingEnum,0)); - break; - case 10: - parameters->AddObject(new IntParam(FrictionCouplingEnum,2)); /*comment this line to use effective pressure from Beuler and Pelt (2015)*/ - parameters->AddObject(new DoubleParam(FrictionEffectivePressureLimitEnum,0.)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.pseudoplasticity_exponent",FrictionPseudoplasticityExponentEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.threshold_speed",FrictionThresholdSpeedEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.delta",FrictionDeltaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.void_ratio",FrictionVoidRatioEnum)); - break; - case 11: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 12: - parameters->AddObject(new IntParam(FrictionCouplingEnum,2)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - case 13: - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - break; - default: _error_("Friction law "<FindConstant(&isSIA,"md.flowequation.isSIA"); iomodel->FindConstant(&ismovingfront,"md.transient.ismovingfront"); - iomodel->FindConstant(&frictionlaw,"md.friction.law"); /*Now, is the flag SIA on? otherwise, do nothing: */ @@ -140,25 +138,4 @@ iomodel->DeleteData(1,"md.flowequation.element_equation"); - /*Friction law variables*/ - switch(frictionlaw){ - case 1: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - break; - case 2: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - break; - case 6: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - break; - default: - _error_("not supported"); - } - iomodel->FetchDataToInput(inputs,elements,"md.geometry.thickness",ThicknessEnum); iomodel->FetchDataToInput(inputs,elements,"md.mask.ocean_levelset",MaskOceanLevelsetEnum); @@ -168,8 +145,12 @@ } + /*Friction*/ + FrictionUpdateInputs(elements, inputs, iomodel); + }/*}}}*/ void StressbalanceSIAAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ - /*No specific parameters*/ + /*Friction*/ + FrictionUpdateParameters(parameters, iomodel); }/*}}}*/ Index: /issm/trunk/src/c/analyses/ThermalAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/ThermalAnalysis.cpp (revision 28012) +++ /issm/trunk/src/c/analyses/ThermalAnalysis.cpp (revision 28013) @@ -106,6 +106,6 @@ void ThermalAnalysis::UpdateElements(Elements* elements,Inputs* inputs,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ - int frictionlaw,basalforcing_model,materialstype; - int FrictionCoupling; + int basalforcing_model,materialstype; + /*Now, is the model 3d? otherwise, do nothing: */ if(iomodel->domaintype==Domain2DhorizontalEnum)return; @@ -127,5 +127,4 @@ iomodel->FindConstant(&dakota_analysis,"md.qmu.isdakota"); iomodel->FindConstant(&ismovingfront,"md.transient.ismovingfront"); - iomodel->FindConstant(&frictionlaw,"md.friction.law"); iomodel->FindConstant(&materialstype,"md.materials.type"); @@ -183,73 +182,7 @@ break; } - /*Friction law variables*/ - switch(frictionlaw){ - case 1: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if (FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 2: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - break; - case 3: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.As",FrictionAsEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if (FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 4: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - break; - case 5: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.water_layer",FrictionWaterLayerEnum); - break; - case 6: - iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); - iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); - break; - case 7: - iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficientcoulomb",FrictionCoefficientcoulombEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); - if (FrictionCoupling==3){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} - else if(FrictionCoupling==4){ - iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); - } - break; - case 9: - iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); - iomodel->FetchDataToInput(inputs,elements,"md.friction.pressure_adjusted_temperature",FrictionPressureAdjustedTemperatureEnum); - InputUpdateFromConstantx(inputs,elements,1.,FrictionPEnum); - InputUpdateFromConstantx(inputs,elements,1.,FrictionQEnum); - break; - default: - _error_("friction law not supported"); - } + + /*Friction*/ + FrictionUpdateInputs(elements, inputs, iomodel); }/*}}}*/ void ThermalAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ @@ -265,5 +198,4 @@ parameters->AddObject(iomodel->CopyConstantObject("md.thermal.isenthalpy",ThermalIsenthalpyEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.thermal.isdynamicbasalspc",ThermalIsdynamicbasalspcEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.law",FrictionLawEnum)); iomodel->FindConstant(&requestedoutputs,&numoutputs,"md.thermal.requested_outputs"); @@ -272,25 +204,6 @@ iomodel->DeleteData(&requestedoutputs,numoutputs,"md.thermal.requested_outputs"); - /*Deal with friction parameters*/ - int frictionlaw; - iomodel->FindConstant(&frictionlaw,"md.friction.law"); - if(frictionlaw==6){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - } - if(frictionlaw==4){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - } - if(frictionlaw==1 || frictionlaw==3 || frictionlaw==7){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - } - if(frictionlaw==9){ - parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); - parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); - parameters->AddObject(new IntParam(FrictionCouplingEnum,0)); - } - + /*Friction*/ + FrictionUpdateParameters(parameters, iomodel); }/*}}}*/ Index: /issm/trunk/src/c/analyses/analyses.h =================================================================== --- /issm/trunk/src/c/analyses/analyses.h (revision 28012) +++ /issm/trunk/src/c/analyses/analyses.h (revision 28013) @@ -28,4 +28,5 @@ #include "./LoveAnalysis.h" #include "./EsaAnalysis.h" +#include "./HydrologyArmapwAnalysis.h" #include "./HydrologyDCEfficientAnalysis.h" #include "./HydrologyDCInefficientAnalysis.h" Index: /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.cpp (revision 28013) @@ -29,9 +29,9 @@ this->definitionenum = -1; this->name = NULL; - this->weights_enum = UNDEF; - this->timepassedflag = false; -} -/*}}}*/ -Cfdragcoeffabsgrad::Cfdragcoeffabsgrad(char* in_name, int in_definitionenum, int in_weights_enum, bool in_timepassedflag){/*{{{*/ + this->J = 0.; + this->firsttimepassed = false; +} +/*}}}*/ +Cfdragcoeffabsgrad::Cfdragcoeffabsgrad(char* in_name, int in_definitionenum){/*{{{*/ this->definitionenum=in_definitionenum; @@ -40,6 +40,28 @@ xMemCpy(this->name,in_name,strlen(in_name)+1); - this->weights_enum=in_weights_enum; - this->timepassedflag=in_timepassedflag; + this->J = 0.; + this->firsttimepassed = false; +} +/*}}}*/ +Cfdragcoeffabsgrad::Cfdragcoeffabsgrad(char* in_name, int in_definitionenum, IssmDouble in_J){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->J = in_J; + this->firsttimepassed = false; +} +/*}}}*/ +Cfdragcoeffabsgrad::Cfdragcoeffabsgrad(char* in_name, int in_definitionenum, IssmDouble in_J, bool in_firsttimepassed){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->J = in_J; + this->firsttimepassed = in_firsttimepassed; } /*}}}*/ @@ -50,5 +72,5 @@ /*Object virtual function resolutoin: */ Object* Cfdragcoeffabsgrad::copy() {/*{{{*/ - Cfdragcoeffabsgrad* mf = new Cfdragcoeffabsgrad(this->name,this->definitionenum, this->weights_enum,this->timepassedflag); + Cfdragcoeffabsgrad* mf = new Cfdragcoeffabsgrad(this->name,this->definitionenum, this->J, this->firsttimepassed); return (Object*) mf; } @@ -60,6 +82,4 @@ void Cfdragcoeffabsgrad::Echo(void){/*{{{*/ _printf_(" Cfdragcoeffabsgrad: " << name << " " << this->definitionenum << "\n"); - _printf_(" weights_enum: " << weights_enum << " " << EnumToStringx(weights_enum) << "\n"); - _printf_(" timepassedflag: "<call(this->definitionenum); marshallhandle->call(this->name); - marshallhandle->call(this->weights_enum); - marshallhandle->call(this->timepassedflag); + marshallhandle->call(this->J); + marshallhandle->call(this->firsttimepassed); } /*}}}*/ @@ -99,22 +119,24 @@ /*recover parameters: */ - IssmDouble J=0.; + IssmDouble J_part=0.; IssmDouble J_sum=0.; - for(Object* & object : femmodel->elements->objects){ - Element* element=xDynamicCast(object); - J+=this->Cfdragcoeffabsgrad_Calculation(element,weights_enum); - } - - ISSM_MPI_Allreduce ( (void*)&J,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); - ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); - J=J_sum; - - timepassedflag = true; - return J; + if (!this->firsttimepassed){ + for(Object* & object : femmodel->elements->objects){ + Element* element=xDynamicCast(object); + J_part+=this->Cfdragcoeffabsgrad_Calculation(element); + } + + ISSM_MPI_Allreduce ( (void*)&J_part,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + this->J=J_sum; + + this->firsttimepassed = true; + } + return this->J; }/*}}}*/ -IssmDouble Cfdragcoeffabsgrad::Cfdragcoeffabsgrad_Calculation(Element* element, int weights_enum){/*{{{*/ - - int domaintype,numcomponents; +IssmDouble Cfdragcoeffabsgrad::Cfdragcoeffabsgrad_Calculation(Element* element){/*{{{*/ + + int domaintype,numcomponents,frictionlaw; IssmDouble Jelem=0.; IssmDouble Jdet; @@ -145,5 +167,19 @@ /*Get input if it already exists*/ DatasetInput *datasetinput = basalelement->GetDatasetInput(definitionenum); _assert_(datasetinput); - Input *drag_input = basalelement->GetInput(FrictionCoefficientEnum); _assert_(drag_input); + Input *drag_input = NULL; + + /* get the friction law: if 2-Weertman, 11-Schoof, 14-RegularizedCoulomb 15-RegularizedCoulomb2, which has a different names of C */ + element->FindParam(&frictionlaw, FrictionLawEnum); + switch(frictionlaw) { + case 2: + case 11: + case 14: + case 15: + drag_input = basalelement->GetInput(FrictionCEnum); _assert_(drag_input); + break; + default: + drag_input = basalelement->GetInput(FrictionCoefficientEnum); _assert_(drag_input); + } + /* Start looping on the number of gaussian points: */ Index: /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.h =================================================================== --- /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.h (revision 28012) +++ /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.h (revision 28013) @@ -17,26 +17,28 @@ int definitionenum; - char* name; - int weights_enum; - bool timepassedflag; + char *name; + bool firsttimepassed; + IssmDouble J; /*Cfdragcoeffabsgrad constructors, destructors :*/ Cfdragcoeffabsgrad(); - Cfdragcoeffabsgrad(char* in_name, int in_definitionenum, int in_weights_enum, bool timepassedflag); + Cfdragcoeffabsgrad(char* in_name, int in_definitionenum); + Cfdragcoeffabsgrad(char* in_name, int in_definitionenum, IssmDouble in_J); + Cfdragcoeffabsgrad(char* in_name, int in_definitionenum, IssmDouble in_J, bool in_firsttimepassed); ~Cfdragcoeffabsgrad(); /*Object virtual function resolutoin: */ - Object* copy(); - void DeepEcho(void); - void Echo(void); - int Id(void); - void Marshall(MarshallHandle* marshallhandle); - int ObjectEnum(void); + Object *copy(); + void DeepEcho(void); + void Echo(void); + int Id(void); + void Marshall(MarshallHandle *marshallhandle); + int ObjectEnum(void); /*Definition virtual function resolutoin: */ - int DefinitionEnum(); - char* Name(); - IssmDouble Response(FemModel* femmodel); - IssmDouble Cfdragcoeffabsgrad_Calculation(Element* element, int weights_enum); + int DefinitionEnum(); + char *Name(); + IssmDouble Response(FemModel *femmodel); + IssmDouble Cfdragcoeffabsgrad_Calculation(Element *element); }; #endif /* _CFDRAGCOEFFABSGRAD_H_ */ Index: /issm/trunk/src/c/classes/Cfdragcoeffabsgradtransient.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfdragcoeffabsgradtransient.cpp (revision 28013) +++ /issm/trunk/src/c/classes/Cfdragcoeffabsgradtransient.cpp (revision 28013) @@ -0,0 +1,243 @@ +/*!\file Cfdragcoeffabsgradtransient.cpp + * \brief: Cfdragcoeffabsgradtransient Object + */ + +/*Headers:*/ +/*{{{*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "./classes.h" +#include "./ExternalResults/ExternalResult.h" +#include "./ExternalResults/Results.h" +#include "../datastructures/datastructures.h" +#include "./Elements/Element.h" +#include "./Elements/Elements.h" +#include "./FemModel.h" +#include "../modules/SurfaceAreax/SurfaceAreax.h" +#include "../classes/Params/Parameters.h" +#include "../classes/gauss/Gauss.h" +#include "./Inputs/DatasetInput.h" +/*}}}*/ + +/*Cfdragcoeffabsgradtransient constructors, destructors :*/ +Cfdragcoeffabsgradtransient::Cfdragcoeffabsgradtransient(){/*{{{*/ + + this->definitionenum = -1; + this->name = NULL; + this->datatimes = NULL; + this->passedflags = NULL; + this->J = 0.; +} +/*}}}*/ +Cfdragcoeffabsgradtransient::Cfdragcoeffabsgradtransient(char* in_name, int in_definitionenum, int in_num_datatimes, IssmDouble* in_datatimes, bool* in_passedflags, IssmDouble in_J){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->num_datatimes = in_num_datatimes; + + /*Allocate arrays*/ + _assert_(this->num_datatimes>0); + this->datatimes = xNew(this->num_datatimes); + this->passedflags = xNew(this->num_datatimes); + xMemCpy(this->datatimes,in_datatimes,this->num_datatimes); + xMemCpy(this->passedflags,in_passedflags,this->num_datatimes); + + this->J = in_J; +} +/*}}}*/ +Cfdragcoeffabsgradtransient::Cfdragcoeffabsgradtransient(char* in_name, int in_definitionenum, int in_num_datatimes, IssmDouble* in_datatimes){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->num_datatimes = in_num_datatimes; + + /*Allocate arrays*/ + _assert_(this->num_datatimes>0); + this->datatimes = xNew(this->num_datatimes); + this->passedflags = xNew(this->num_datatimes); + xMemCpy(this->datatimes,in_datatimes,this->num_datatimes); + + /*initialize passedtimes to false*/ + for(int i=0;inum_datatimes;i++) this->passedflags[i]= false; + this->J = 0; +} +/*}}}*/ +Cfdragcoeffabsgradtransient::~Cfdragcoeffabsgradtransient(){/*{{{*/ + if(this->name)xDelete(this->name); + if(this->datatimes) xDelete(this->datatimes); + if(this->passedflags) xDelete(this->passedflags); +} +/*}}}*/ +/*Object virtual function resolutoin: */ +Object* Cfdragcoeffabsgradtransient::copy() {/*{{{*/ + Cfdragcoeffabsgradtransient* mf = new Cfdragcoeffabsgradtransient(this->name,this->definitionenum, this->num_datatimes, this->datatimes,this->passedflags, this->J); + return (Object*) mf; +} +/*}}}*/ +void Cfdragcoeffabsgradtransient::DeepEcho(void){/*{{{*/ + this->Echo(); +} +/*}}}*/ +void Cfdragcoeffabsgradtransient::Echo(void){/*{{{*/ + _printf_(" Cfdragcoeffabsgradtransient: " << name << " " << this->definitionenum << "\n"); + _error_("not implemented yet"); +} +/*}}}*/ +int Cfdragcoeffabsgradtransient::Id(void){/*{{{*/ + return -1; +} +/*}}}*/ +void Cfdragcoeffabsgradtransient::Marshall(MarshallHandle* marshallhandle){/*{{{*/ + + /*ok, marshall operations: */ + int object_enum=CfdragcoeffabsgradtransientEnum; + marshallhandle->call(object_enum); + + marshallhandle->call(this->definitionenum); + marshallhandle->call(this->name); + marshallhandle->call(this->num_datatimes); + marshallhandle->call(this->datatimes,this->num_datatimes); + marshallhandle->call(this->passedflags,this->num_datatimes); + marshallhandle->call(this->J); +} +/*}}}*/ +int Cfdragcoeffabsgradtransient::ObjectEnum(void){/*{{{*/ + return CfdragcoeffabsgradtransientEnum; +} +/*}}}*/ +/*Definition virtual function resolutoin: */ +int Cfdragcoeffabsgradtransient::DefinitionEnum(){/*{{{*/ + return this->definitionenum; +} +/*}}}*/ +char* Cfdragcoeffabsgradtransient::Name(){/*{{{*/ + char* name2=xNew(strlen(this->name)+1); + xMemCpy(name2,this->name,strlen(this->name)+1); + + return name2; +} +/*}}}*/ +IssmDouble Cfdragcoeffabsgradtransient::Response(FemModel* femmodel){/*{{{*/ + + /*recover time parameters: */ + IssmDouble time; + femmodel->parameters->FindParam(&time,TimeEnum); + + /*Find closest datatime that is less than time*/ + int pos=-1; + for(int i=0;inum_datatimes;i++){ + if(this->datatimes[i]<=time){ + pos = i; + } + else{ + break; + } + } + + /*if pos=-1, time is earlier than the first data observation in this dataset*/ + if(pos==-1){ + _assert_(this->J==0.); + return 0.; + } + + /*Check that we have not yet calculated this cost function*/ + if(this->passedflags[pos]){ + return this->J; + } + + /*Calculate cost function for this time slice*/ + IssmDouble J_part=0.; + IssmDouble J_sum=0.; + + for(Object* & object : femmodel->elements->objects){ + Element* element=xDynamicCast(object); + J_part+=this->Cfdragcoeffabsgradtransient_Calculation(element); + } + + ISSM_MPI_Allreduce ( (void*)&J_part,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + + this->passedflags[pos]= true; + this->J += J_sum; + + return this->J; +}/*}}}*/ +IssmDouble Cfdragcoeffabsgradtransient::Cfdragcoeffabsgradtransient_Calculation(Element* element){/*{{{*/ + + int domaintype,numcomponents,frictionlaw; + IssmDouble Jelem=0.; + IssmDouble Jdet; + IssmDouble dp[2],weight; + IssmDouble* xyz_list = NULL; + + /*Get basal element*/ + if(!element->IsOnBase()) return 0.; + + /*If on water, return 0: */ + if(!element->IsIceInElement()) return 0.; + + /*Get problem dimension*/ + element->FindParam(&domaintype,DomainTypeEnum); + switch(domaintype){ + case Domain2DverticalEnum: numcomponents = 1; break; + case Domain3DEnum: numcomponents = 2; break; + case Domain2DhorizontalEnum: numcomponents = 2; break; + default: _error_("not supported yet"); + } + + /*Spawn surface element*/ + Element* basalelement = element->SpawnBasalElement(); + + /* Get node coordinates*/ + basalelement->GetVerticesCoordinates(&xyz_list); + + /*Get input if it already exists*/ + DatasetInput *datasetinput = basalelement->GetDatasetInput(definitionenum); _assert_(datasetinput); + Input *drag_input = NULL; + + /* get the friction law: if 2-Weertman, 11-Schoof, 14-RegularizedCoulomb 15-RegularizedCoulomb2, which has a different names of C */ + element->FindParam(&frictionlaw, FrictionLawEnum); + switch(frictionlaw) { + case 2: + case 11: + case 14: + case 15: + drag_input = basalelement->GetInput(FrictionCEnum); _assert_(drag_input); + break; + default: + drag_input = basalelement->GetInput(FrictionCoefficientEnum); _assert_(drag_input); + } + + + /* Start looping on the number of gaussian points: */ + Gauss* gauss=basalelement->NewGauss(2); + while(gauss->next()){ + + /* Get Jacobian determinant: */ + basalelement->JacobianDeterminant(&Jdet,xyz_list,gauss); + + /*Get all parameters at gaussian point*/ + datasetinput->GetInputValue(&weight,gauss,WeightsSurfaceObservationEnum); + drag_input->GetInputDerivativeValue(&dp[0],xyz_list,gauss); + + /*Add to cost function*/ + Jelem+=weight*.5*dp[0]*dp[0]*Jdet*gauss->weight; + if(numcomponents==2) Jelem+=weight*.5*dp[1]*dp[1]*Jdet*gauss->weight; + } + + /*clean up and Return: */ + if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; + xDelete(xyz_list); + delete gauss; + return Jelem; +}/*}}}*/ Index: /issm/trunk/src/c/classes/Cfdragcoeffabsgradtransient.h =================================================================== --- /issm/trunk/src/c/classes/Cfdragcoeffabsgradtransient.h (revision 28013) +++ /issm/trunk/src/c/classes/Cfdragcoeffabsgradtransient.h (revision 28013) @@ -0,0 +1,45 @@ +/*!\file Cfdragcoeffabsgradtransient.h + * \brief: header file for Cfdragcoeffabsgradtransient object + */ + +#ifndef _CFDRAGCOEFFABSGRADTRANSIENT_H_ +#define _CFDRAGCOEFFABSGRADTRANSIENT_H_ + +/*Headers:*/ +#include "./Definition.h" +class FemModel; + +IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); + +class Cfdragcoeffabsgradtransient: public Object, public Definition{ + + public: + + int definitionenum; + char *name; + int num_datatimes; + IssmDouble *datatimes; + bool *passedflags; + IssmDouble J; + + /*Cfdragcoeffabsgradtransient constructors, destructors :*/ + Cfdragcoeffabsgradtransient(); + Cfdragcoeffabsgradtransient(char* in_name, int in_definitionenum, int num_datatimes, IssmDouble* in_datatime); + Cfdragcoeffabsgradtransient(char* in_name, int in_definitionenum, int num_datatimes, IssmDouble* in_datatime, bool* in_timepassedflag, IssmDouble in_J); + ~Cfdragcoeffabsgradtransient(); + + /*Object virtual function resolutoin: */ + Object *copy(); + void DeepEcho(void); + void Echo(void); + int Id(void); + void Marshall(MarshallHandle *marshallhandle); + int ObjectEnum(void); + + /*Definition virtual function resolutoin: */ + int DefinitionEnum(); + char *Name(); + IssmDouble Response(FemModel *femmodel); + IssmDouble Cfdragcoeffabsgradtransient_Calculation(Element *element); +}; +#endif /* _CFDRAGCOEFFABSGRADTRANSIENT_H_ */ Index: /issm/trunk/src/c/classes/Cflevelsetmisfit.cpp =================================================================== --- /issm/trunk/src/c/classes/Cflevelsetmisfit.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Cflevelsetmisfit.cpp (revision 28013) @@ -30,11 +30,10 @@ this->name = NULL; this->model_enum = UNDEF; - this->observation_enum = UNDEF; - this->weights_enum = UNDEF; this->datatime=0.; this->timepassedflag = false; -} -/*}}}*/ -Cflevelsetmisfit::Cflevelsetmisfit(char* in_name, int in_definitionenum, int in_model_enum, int in_observation_enum, int in_weights_enum, IssmDouble in_datatime, bool in_timepassedflag){/*{{{*/ + this->J = 0.; +} +/*}}}*/ +Cflevelsetmisfit::Cflevelsetmisfit(char* in_name, int in_definitionenum, int in_model_enum, IssmDouble in_datatime){/*{{{*/ this->definitionenum=in_definitionenum; @@ -44,8 +43,20 @@ this->model_enum=in_model_enum; - this->observation_enum=in_observation_enum; - this->weights_enum=in_weights_enum; + this->datatime=in_datatime; + this->timepassedflag=false; + this->J = 0.; +} +/*}}}*/ +Cflevelsetmisfit::Cflevelsetmisfit(char* in_name, int in_definitionenum, int in_model_enum, IssmDouble in_datatime, bool in_timepassedflag, IssmDouble in_J){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->model_enum=in_model_enum; this->datatime=in_datatime; this->timepassedflag=in_timepassedflag; + this->J = in_J; } /*}}}*/ @@ -56,5 +67,5 @@ /*Object virtual function resolutoin: */ Object* Cflevelsetmisfit::copy() {/*{{{*/ - Cflevelsetmisfit* mf = new Cflevelsetmisfit(this->name,this->definitionenum, this->model_enum,this->observation_enum,this->weights_enum,this->datatime,this->timepassedflag); + Cflevelsetmisfit* mf = new Cflevelsetmisfit(this->name,this->definitionenum, this->model_enum,this->datatime,this->timepassedflag, this->J); return (Object*) mf; } @@ -67,6 +78,4 @@ _printf_(" Cflevelsetmisfit: " << name << " " << this->definitionenum << "\n"); _printf_(" model_enum: " << model_enum << " " << EnumToStringx(model_enum) << "\n"); - _printf_(" observation_enum: " << observation_enum << " " << EnumToStringx(observation_enum) << "\n"); - _printf_(" weights_enum: " << weights_enum << " " << EnumToStringx(weights_enum) << "\n"); _printf_(" datatime: " << datatime << "\n"); _printf_(" timepassedflag: "<call(this->model_enum); marshallhandle->call(this->name); - marshallhandle->call(this->observation_enum); - marshallhandle->call(this->weights_enum); marshallhandle->call(this->datatime); marshallhandle->call(this->timepassedflag); + marshallhandle->call(this->J); } /*}}}*/ @@ -114,25 +122,24 @@ /*recover time parameters: */ femmodel->parameters->FindParam(&time,TimeEnum); - - IssmDouble J=0.; - IssmDouble J_sum=0.; - if(datatime<=time && !timepassedflag){ + + IssmDouble J_part = 0.; + IssmDouble J_sum = 0.; + for(Object* & object : femmodel->elements->objects){ Element* element=xDynamicCast(object); - J+=this->Cflevelsetmisfit_Calculation(element,model_enum,observation_enum,weights_enum); + J_part+=this->Cflevelsetmisfit_Calculation(element,model_enum); } - ISSM_MPI_Allreduce ( (void*)&J,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + ISSM_MPI_Allreduce ( (void*)&J_part,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); - J=J_sum; - - timepassedflag = true; - return J; + + this->timepassedflag = true; + this->J = J_sum; } - else return J; - } - /*}}}*/ -IssmDouble Cflevelsetmisfit::Cflevelsetmisfit_Calculation(Element* element, int model_enum, int observation_enum, int weights_enum){/*{{{*/ + + return this->J; + }/*}}}*/ +IssmDouble Cflevelsetmisfit::Cflevelsetmisfit_Calculation(Element* element, int model_enum){/*{{{*/ int domaintype,numcomponents; Index: /issm/trunk/src/c/classes/Cflevelsetmisfit.h =================================================================== --- /issm/trunk/src/c/classes/Cflevelsetmisfit.h (revision 28012) +++ /issm/trunk/src/c/classes/Cflevelsetmisfit.h (revision 28013) @@ -18,13 +18,13 @@ int definitionenum; int model_enum; - char* name; - int observation_enum; - int weights_enum; - IssmDouble datatime; - bool timepassedflag; + char *name; + IssmDouble datatime; + bool timepassedflag; + IssmDouble J; /*Cflevelsetmisfit constructors, destructors :*/ Cflevelsetmisfit(); - Cflevelsetmisfit(char* in_name, int in_definitionenum, int in_model_enum, int in_observation_enum, int in_weights_enum, IssmDouble in_datatime, bool timepassedflag); + Cflevelsetmisfit(char* in_name, int in_definitionenum, int in_model_enum, IssmDouble in_datatime); + Cflevelsetmisfit(char* in_name, int in_definitionenum, int in_model_enum, IssmDouble in_datatime, bool timepassedflag, IssmDouble in_J); ~Cflevelsetmisfit(); @@ -41,5 +41,5 @@ char* Name(); IssmDouble Response(FemModel* femmodel); - IssmDouble Cflevelsetmisfit_Calculation(Element* element, int model_enum, int observation_enum, int weights_enum); + IssmDouble Cflevelsetmisfit_Calculation(Element* element, int model_enum); IssmDouble Heaviside(IssmDouble x); }; Index: /issm/trunk/src/c/classes/Cfrheologybbarabsgrad.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfrheologybbarabsgrad.cpp (revision 28013) +++ /issm/trunk/src/c/classes/Cfrheologybbarabsgrad.cpp (revision 28013) @@ -0,0 +1,192 @@ +/*!\file Cfrheologybbarabsgrad.cpp + * \brief: Cfrheologybbarabsgrad Object + */ + +/*Headers:*/ +/*{{{*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "./classes.h" +#include "./ExternalResults/ExternalResult.h" +#include "./ExternalResults/Results.h" +#include "../datastructures/datastructures.h" +#include "./Elements/Element.h" +#include "./Elements/Elements.h" +#include "./FemModel.h" +#include "../modules/SurfaceAreax/SurfaceAreax.h" +#include "../classes/Params/Parameters.h" +#include "../classes/gauss/Gauss.h" +#include "./Inputs/DatasetInput.h" +/*}}}*/ + +/*Cfrheologybbarabsgrad constructors, destructors :*/ +Cfrheologybbarabsgrad::Cfrheologybbarabsgrad(){/*{{{*/ + + this->definitionenum = -1; + this->name = NULL; + this->J = 0.; + this->firsttimepassed = false; +} +/*}}}*/ +Cfrheologybbarabsgrad::Cfrheologybbarabsgrad(char* in_name, int in_definitionenum){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->J=0; + this->firsttimepassed = false; +} +/*}}}*/ +Cfrheologybbarabsgrad::Cfrheologybbarabsgrad(char* in_name, int in_definitionenum, IssmDouble in_J){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->J=in_J; + this->firsttimepassed = false; +} +/*}}}*/ +Cfrheologybbarabsgrad::Cfrheologybbarabsgrad(char* in_name, int in_definitionenum, IssmDouble in_J, bool in_firsttimepassed){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->J=in_J; + this->firsttimepassed = in_firsttimepassed; +} +/*}}}*/ +Cfrheologybbarabsgrad::~Cfrheologybbarabsgrad(){/*{{{*/ + if(this->name)xDelete(this->name); +} +/*}}}*/ +/*Object virtual function resolutoin: */ +Object* Cfrheologybbarabsgrad::copy() {/*{{{*/ + Cfrheologybbarabsgrad* mf = new Cfrheologybbarabsgrad(this->name,this->definitionenum, this->J, this->firsttimepassed); + return (Object*) mf; +} +/*}}}*/ +void Cfrheologybbarabsgrad::DeepEcho(void){/*{{{*/ + this->Echo(); +} +/*}}}*/ +void Cfrheologybbarabsgrad::Echo(void){/*{{{*/ + _printf_(" Cfrheologybbarabsgrad: " << name << " " << this->definitionenum << "\n"); +} +/*}}}*/ +int Cfrheologybbarabsgrad::Id(void){/*{{{*/ + return -1; +} +/*}}}*/ +void Cfrheologybbarabsgrad::Marshall(MarshallHandle* marshallhandle){/*{{{*/ + + /*ok, marshall operations: */ + int object_enum=CfrheologybbarabsgradEnum; + marshallhandle->call(object_enum); + + marshallhandle->call(this->definitionenum); + marshallhandle->call(this->name); + marshallhandle->call(this->J); + marshallhandle->call(this->firsttimepassed); +} +/*}}}*/ +int Cfrheologybbarabsgrad::ObjectEnum(void){/*{{{*/ + return CfrheologybbarabsgradEnum; +} +/*}}}*/ +/*Definition virtual function resolutoin: */ +int Cfrheologybbarabsgrad::DefinitionEnum(){/*{{{*/ + return this->definitionenum; +} +/*}}}*/ +char* Cfrheologybbarabsgrad::Name(){/*{{{*/ + char* name2=xNew(strlen(this->name)+1); + xMemCpy(name2,this->name,strlen(this->name)+1); + + return name2; +} +/*}}}*/ +IssmDouble Cfrheologybbarabsgrad::Response(FemModel* femmodel){/*{{{*/ + + /*recover parameters: */ + IssmDouble J_part=0.; + IssmDouble J_sum=0.; + + if (!this->firsttimepassed){ + for(Object* & object : femmodel->elements->objects){ + Element* element=xDynamicCast(object); + J_part+=this->Cfrheologybbarabsgrad_Calculation(element); + } + + ISSM_MPI_Allreduce( (void*)&J_part,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + this->J = J_sum; + + this->firsttimepassed = true; + } + return this->J; +}/*}}}*/ +IssmDouble Cfrheologybbarabsgrad::Cfrheologybbarabsgrad_Calculation(Element* element){/*{{{*/ + + int domaintype,numcomponents; + IssmDouble Jelem=0.; + IssmDouble Jdet; + IssmDouble dp[2],weight; + IssmDouble* xyz_list = NULL; + + /*Get basal element*/ + if(!element->IsOnBase()) return 0.; + + /*If on water, return 0: */ + if(!element->IsIceInElement()) return 0.; + + /*Get problem dimension*/ + element->FindParam(&domaintype,DomainTypeEnum); + switch(domaintype){ + case Domain2DverticalEnum: numcomponents = 1; break; + case Domain3DEnum: numcomponents = 2; break; + case Domain2DhorizontalEnum: numcomponents = 2; break; + default: _error_("not supported yet"); + } + + /*Spawn surface element*/ + Element* basalelement = element->SpawnBasalElement(); + + /* Get node coordinates*/ + basalelement->GetVerticesCoordinates(&xyz_list); + + /*Get input if it already exists*/ + DatasetInput *datasetinput = basalelement->GetDatasetInput(definitionenum); _assert_(datasetinput); + Input* rheologyb_input=basalelement->GetInput(MaterialsRheologyBbarEnum); _assert_(rheologyb_input); + + /* Start looping on the number of gaussian points: */ + Gauss* gauss=basalelement->NewGauss(2); + while(gauss->next()){ + + /* Get Jacobian determinant: */ + basalelement->JacobianDeterminant(&Jdet,xyz_list,gauss); + + /*Get all parameters at gaussian point*/ + datasetinput->GetInputValue(&weight,gauss,WeightsSurfaceObservationEnum); + rheologyb_input->GetInputDerivativeValue(&dp[0],xyz_list,gauss); + + /*Add to cost function*/ + Jelem+=weight*.5*dp[0]*dp[0]*Jdet*gauss->weight; + if(numcomponents==2) Jelem+=weight*.5*dp[1]*dp[1]*Jdet*gauss->weight; + } + + /*clean up and Return: */ + if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; + xDelete(xyz_list); + delete gauss; + return Jelem; +}/*}}}*/ Index: /issm/trunk/src/c/classes/Cfrheologybbarabsgrad.h =================================================================== --- /issm/trunk/src/c/classes/Cfrheologybbarabsgrad.h (revision 28013) +++ /issm/trunk/src/c/classes/Cfrheologybbarabsgrad.h (revision 28013) @@ -0,0 +1,45 @@ +/*!\file Cfrheologybbarabsgrad.h + * \brief: header file for Cfrheologybbarabsgrad object + */ + +#ifndef _CFRHEOLOGYBBARABSGRAD_H_ +#define _CFRHEOLOGYBBARABSGRAD_H_ + +/*Headers:*/ +#include "./Definition.h" +#include "./FemModel.h" + +IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); +void GetVectorFromInputsx( IssmDouble** pvector, int* pvector_size, FemModel* femmodel,int name); + +class Cfrheologybbarabsgrad: public Object, public Definition{ + + public: + + int definitionenum; + char* name; + bool firsttimepassed; + IssmDouble J; + + /*Cfrheologybbarabsgrad constructors, destructors :*/ + Cfrheologybbarabsgrad(); + Cfrheologybbarabsgrad(char* in_name, int in_definitionenum); + Cfrheologybbarabsgrad(char* in_name, int in_definitionenum, IssmDouble in_J); + Cfrheologybbarabsgrad(char* in_name, int in_definitionenum, IssmDouble in_J, bool in_firsttimepassed); + ~Cfrheologybbarabsgrad(); + + /*Object virtual function resolutoin: */ + Object* copy(); + void DeepEcho(void); + void Echo(void); + int Id(void); + void Marshall(MarshallHandle* marshallhandle); + int ObjectEnum(void); + + /*Definition virtual function resolutoin: */ + int DefinitionEnum(); + char* Name(); + IssmDouble Response(FemModel* femmodel); + IssmDouble Cfrheologybbarabsgrad_Calculation(Element* element); +}; +#endif /* _CFRHEOLOGYBBARABSGRAD_H_ */ Index: /issm/trunk/src/c/classes/Cfrheologybbarabsgradtransient.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfrheologybbarabsgradtransient.cpp (revision 28013) +++ /issm/trunk/src/c/classes/Cfrheologybbarabsgradtransient.cpp (revision 28013) @@ -0,0 +1,227 @@ +/*!\file Cfrheologybbarabsgradtransient.cpp + * \brief: Cfrheologybbarabsgradtransient Object + */ + +/*Headers:*/ +/*{{{*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "./classes.h" +#include "./ExternalResults/ExternalResult.h" +#include "./ExternalResults/Results.h" +#include "../datastructures/datastructures.h" +#include "./Elements/Element.h" +#include "./Elements/Elements.h" +#include "./FemModel.h" +#include "../modules/SurfaceAreax/SurfaceAreax.h" +#include "../classes/Params/Parameters.h" +#include "../classes/gauss/Gauss.h" +#include "./Inputs/DatasetInput.h" +/*}}}*/ + +/*Cfrheologybbarabsgradtransient constructors, destructors :*/ +Cfrheologybbarabsgradtransient::Cfrheologybbarabsgradtransient(){/*{{{*/ + + this->definitionenum = -1; + this->name = NULL; + this->datatimes = NULL; + this->passedflags = NULL; + this->J = 0.; +} +/*}}}*/ +Cfrheologybbarabsgradtransient::Cfrheologybbarabsgradtransient(char* in_name, int in_definitionenum, int in_num_datatimes, IssmDouble* in_datatimes, bool* in_passedflags, IssmDouble in_J){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->num_datatimes = in_num_datatimes; + + /*Allocate arrays*/ + _assert_(this->num_datatimes>0); + this->datatimes = xNew(this->num_datatimes); + this->passedflags = xNew(this->num_datatimes); + xMemCpy(this->datatimes,in_datatimes,this->num_datatimes); + xMemCpy(this->passedflags,in_passedflags,this->num_datatimes); + + this->J = in_J; +} +/*}}}*/ +Cfrheologybbarabsgradtransient::Cfrheologybbarabsgradtransient(char* in_name, int in_definitionenum, int in_num_datatimes, IssmDouble* in_datatimes){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->num_datatimes = in_num_datatimes; + + /*Allocate arrays*/ + _assert_(this->num_datatimes>0); + this->datatimes = xNew(this->num_datatimes); + this->passedflags = xNew(this->num_datatimes); + xMemCpy(this->datatimes,in_datatimes,this->num_datatimes); + + /*initialize passedtimes to false*/ + for(int i=0;inum_datatimes;i++) this->passedflags[i]= false; + this->J = 0; +} +/*}}}*/ +Cfrheologybbarabsgradtransient::~Cfrheologybbarabsgradtransient(){/*{{{*/ + if(this->name)xDelete(this->name); +} +/*}}}*/ +/*Object virtual function resolutoin: */ +Object* Cfrheologybbarabsgradtransient::copy() {/*{{{*/ + Cfrheologybbarabsgradtransient* mf = new Cfrheologybbarabsgradtransient(this->name,this->definitionenum, this->num_datatimes, this->datatimes, this->passedflags, this->J); + return (Object*) mf; +} +/*}}}*/ +void Cfrheologybbarabsgradtransient::DeepEcho(void){/*{{{*/ + this->Echo(); +} +/*}}}*/ +void Cfrheologybbarabsgradtransient::Echo(void){/*{{{*/ + _printf_(" Cfrheologybbarabsgradtransient: " << name << " " << this->definitionenum << "\n"); + _error_("not implemented yet"); +} +/*}}}*/ +int Cfrheologybbarabsgradtransient::Id(void){/*{{{*/ + return -1; +} +/*}}}*/ +void Cfrheologybbarabsgradtransient::Marshall(MarshallHandle* marshallhandle){/*{{{*/ + + /*ok, marshall operations: */ + int object_enum=CfrheologybbarabsgradtransientEnum; + marshallhandle->call(object_enum); + + marshallhandle->call(this->definitionenum); + marshallhandle->call(this->name); + marshallhandle->call(this->num_datatimes); + marshallhandle->call(this->datatimes,this->num_datatimes); + marshallhandle->call(this->passedflags,this->num_datatimes); + marshallhandle->call(this->J); +} +/*}}}*/ +int Cfrheologybbarabsgradtransient::ObjectEnum(void){/*{{{*/ + return CfrheologybbarabsgradtransientEnum; +} +/*}}}*/ +/*Definition virtual function resolutoin: */ +int Cfrheologybbarabsgradtransient::DefinitionEnum(){/*{{{*/ + return this->definitionenum; +} +/*}}}*/ +char* Cfrheologybbarabsgradtransient::Name(){/*{{{*/ + char* name2=xNew(strlen(this->name)+1); + xMemCpy(name2,this->name,strlen(this->name)+1); + + return name2; +} +/*}}}*/ +IssmDouble Cfrheologybbarabsgradtransient::Response(FemModel* femmodel){/*{{{*/ + + /*recover time parameters: */ + IssmDouble time; + femmodel->parameters->FindParam(&time,TimeEnum); + + /*Find closest datatime that is less than time*/ + int pos=-1; + for(int i=0;inum_datatimes;i++){ + if(this->datatimes[i]<=time){ + pos = i; + } + else{ + break; + } + } + + /*if pos=-1, time is earlier than the first data observation in this dataset*/ + if(pos==-1){ + _assert_(this->J==0.); + return 0.; + } + + /*Check that we have not yet calculated this cost function*/ + if(this->passedflags[pos]){ + return this->J; + } + + /*Calculate cost function for this time slice*/ + IssmDouble J_part=0.; + IssmDouble J_sum=0.; + + for(Object* & object : femmodel->elements->objects){ + Element* element=xDynamicCast(object); + J_part+=this->Cfrheologybbarabsgradtransient_Calculation(element); + } + + ISSM_MPI_Allreduce( (void*)&J_part,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + + this->passedflags[pos]= true; + this->J += J_sum; + + return this->J; +}/*}}}*/ +IssmDouble Cfrheologybbarabsgradtransient::Cfrheologybbarabsgradtransient_Calculation(Element* element){/*{{{*/ + + int domaintype,numcomponents; + IssmDouble Jelem=0.; + IssmDouble Jdet; + IssmDouble dp[2],weight; + IssmDouble* xyz_list = NULL; + + /*Get basal element*/ + if(!element->IsOnBase()) return 0.; + + /*If on water, return 0: */ + if(!element->IsIceInElement()) return 0.; + + /*Get problem dimension*/ + element->FindParam(&domaintype,DomainTypeEnum); + switch(domaintype){ + case Domain2DverticalEnum: numcomponents = 1; break; + case Domain3DEnum: numcomponents = 2; break; + case Domain2DhorizontalEnum: numcomponents = 2; break; + default: _error_("not supported yet"); + } + + /*Spawn surface element*/ + Element* basalelement = element->SpawnBasalElement(); + + /* Get node coordinates*/ + basalelement->GetVerticesCoordinates(&xyz_list); + + /*Get input if it already exists*/ + DatasetInput *datasetinput = basalelement->GetDatasetInput(definitionenum); _assert_(datasetinput); + Input* rheologyb_input=basalelement->GetInput(MaterialsRheologyBbarEnum); _assert_(rheologyb_input); + + /* Start looping on the number of gaussian points: */ + Gauss* gauss=basalelement->NewGauss(2); + while(gauss->next()){ + + /* Get Jacobian determinant: */ + basalelement->JacobianDeterminant(&Jdet,xyz_list,gauss); + + /*Get all parameters at gaussian point*/ + datasetinput->GetInputValue(&weight,gauss,WeightsSurfaceObservationEnum); + rheologyb_input->GetInputDerivativeValue(&dp[0],xyz_list,gauss); + + /*Add to cost function*/ + Jelem+=weight*.5*dp[0]*dp[0]*Jdet*gauss->weight; + if(numcomponents==2) Jelem+=weight*.5*dp[1]*dp[1]*Jdet*gauss->weight; + } + + /*clean up and Return: */ + if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; + xDelete(xyz_list); + delete gauss; + return Jelem; +}/*}}}*/ Index: /issm/trunk/src/c/classes/Cfrheologybbarabsgradtransient.h =================================================================== --- /issm/trunk/src/c/classes/Cfrheologybbarabsgradtransient.h (revision 28013) +++ /issm/trunk/src/c/classes/Cfrheologybbarabsgradtransient.h (revision 28013) @@ -0,0 +1,45 @@ +/*!\file Cfrheologybbarabsgradtransient.h + * \brief: header file for Cfrheologybbarabsgradtransient object + */ + +#ifndef _CFRHEOLOGYBBARABSGRADTRANSIENT_H_ +#define _CFRHEOLOGYBBARABSGRADTRANSIENT_H_ + +/*Headers:*/ +#include "./Definition.h" +class FemModel; + +IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); + +class Cfrheologybbarabsgradtransient: public Object, public Definition{ + + public: + + int definitionenum; + char *name; + int num_datatimes; + IssmDouble *datatimes; + bool *passedflags; + IssmDouble J; + + /*Cfrheologybbarabsgradtransient constructors, destructors :*/ + Cfrheologybbarabsgradtransient(); + Cfrheologybbarabsgradtransient(char* in_name, int in_definitionenum, int num_datatimes, IssmDouble* in_datatime); + Cfrheologybbarabsgradtransient(char* in_name, int in_definitionenum, int num_datatimes, IssmDouble* in_datatime, bool* in_timepassedflag, IssmDouble in_J); + ~Cfrheologybbarabsgradtransient(); + + /*Object virtual function resolutoin: */ + Object* copy(); + void DeepEcho(void); + void Echo(void); + int Id(void); + void Marshall(MarshallHandle* marshallhandle); + int ObjectEnum(void); + + /*Definition virtual function resolutoin: */ + int DefinitionEnum(); + char* Name(); + IssmDouble Response(FemModel* femmodel); + IssmDouble Cfrheologybbarabsgradtransient_Calculation(Element* element); +}; +#endif /* _CFRHEOLOGYBBARABSGRADTRANSIENT_H_ */ Index: /issm/trunk/src/c/classes/Cfsurfacelogvel.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacelogvel.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Cfsurfacelogvel.cpp (revision 28013) @@ -31,8 +31,9 @@ this->datatime=0.; this->timepassedflag = false; - -} -/*}}}*/ -Cfsurfacelogvel::Cfsurfacelogvel(char* in_name, int in_definitionenum, IssmDouble in_datatime, bool in_timepassedflag){/*{{{*/ + this->J = 0.; + +} +/*}}}*/ +Cfsurfacelogvel::Cfsurfacelogvel(char* in_name, int in_definitionenum, IssmDouble in_datatime){/*{{{*/ this->definitionenum=in_definitionenum; @@ -42,5 +43,20 @@ this->datatime=in_datatime; + + this->timepassedflag=false; + this->J=0.; + +} +/*}}}*/ +Cfsurfacelogvel::Cfsurfacelogvel(char* in_name, int in_definitionenum, IssmDouble in_datatime, bool in_timepassedflag,IssmDouble in_J){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->datatime=in_datatime; this->timepassedflag=in_timepassedflag; + this->J=in_J; } @@ -52,5 +68,5 @@ /*Object virtual function resolutoin: */ Object* Cfsurfacelogvel::copy() {/*{{{*/ - Cfsurfacelogvel* mf = new Cfsurfacelogvel(this->name,this->definitionenum,this->datatime,this->timepassedflag); + Cfsurfacelogvel* mf = new Cfsurfacelogvel(this->name,this->definitionenum,this->datatime,this->timepassedflag, this->J); return (Object*) mf; } @@ -64,4 +80,5 @@ _printf_(" datatime: " << datatime << "\n"); _printf_(" timepassedflag: "<call(this->datatime); marshallhandle->call(this->timepassedflag); + marshallhandle->call(this->J); } /*}}}*/ @@ -104,22 +122,20 @@ if(this->datatime<=time && !this->timepassedflag){ - IssmDouble J=0.; + IssmDouble J_part=0.; IssmDouble J_sum=0.; for(Object* & object : femmodel->elements->objects){ Element* element=xDynamicCast(object); - J+=this->Cfsurfacelogvel_Calculation(element,definitionenum); - } - - ISSM_MPI_Allreduce ( (void*)&J,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + J_part+=this->Cfsurfacelogvel_Calculation(element,definitionenum); + } + + ISSM_MPI_Allreduce ( (void*)&J_part,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); - J=J_sum; this->timepassedflag = true; - return J_sum; - } - else{ - return 0.; - } + this->J = J_sum; + } + + return this->J; }/*}}}*/ IssmDouble Cfsurfacelogvel::Cfsurfacelogvel_Calculation(Element* element, int definitionenum){/*{{{*/ Index: /issm/trunk/src/c/classes/Cfsurfacelogvel.h =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacelogvel.h (revision 28012) +++ /issm/trunk/src/c/classes/Cfsurfacelogvel.h (revision 28013) @@ -20,17 +20,19 @@ IssmDouble datatime; bool timepassedflag; + IssmDouble J; /*Cfsurfacelogvel constructors, destructors :*/ Cfsurfacelogvel(); - Cfsurfacelogvel(char* in_name, int in_definitionenum, IssmDouble in_datatime, bool timepassedflag); + Cfsurfacelogvel(char* in_name, int in_definitionenum, IssmDouble in_datatime); + Cfsurfacelogvel(char* in_name, int in_definitionenum, IssmDouble in_datatime, bool timepassedflag, IssmDouble in_J); ~Cfsurfacelogvel(); /*Object virtual function resolutoin: */ - Object* copy(); - void DeepEcho(void); - void Echo(void); - int Id(void); - void Marshall(MarshallHandle* marshallhandle); - int ObjectEnum(void); + Object *copy(); + void DeepEcho(void); + void Echo(void); + int Id(void); + void Marshall(MarshallHandle *marshallhandle); + int ObjectEnum(void); /*Definition virtual function resolutoin: */ Index: /issm/trunk/src/c/classes/Cfsurfacesquare.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacesquare.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Cfsurfacesquare.cpp (revision 28013) @@ -30,11 +30,10 @@ this->name = NULL; this->model_enum = UNDEF; - this->observation_enum = UNDEF; - this->weights_enum = UNDEF; this->datatime = 0.; this->timepassedflag = false; -} -/*}}}*/ -Cfsurfacesquare::Cfsurfacesquare(char* in_name, int in_definitionenum, int in_model_enum, int in_observation_enum, int in_weights_enum, IssmDouble in_datatime, bool in_timepassedflag){/*{{{*/ + this->J = 0.; +} +/*}}}*/ +Cfsurfacesquare::Cfsurfacesquare(char* in_name, int in_definitionenum, int in_model_enum, IssmDouble in_datatime){/*{{{*/ this->definitionenum=in_definitionenum; @@ -44,8 +43,20 @@ this->model_enum=in_model_enum; - this->observation_enum=in_observation_enum; - this->weights_enum=in_weights_enum; + this->datatime=in_datatime; + this->timepassedflag=false; + this->J=0.; +} +/*}}}*/ +Cfsurfacesquare::Cfsurfacesquare(char* in_name, int in_definitionenum, int in_model_enum, IssmDouble in_datatime, bool in_timepassedflag, IssmDouble in_J){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->model_enum=in_model_enum; this->datatime=in_datatime; this->timepassedflag=in_timepassedflag; + this->J=in_J; } /*}}}*/ @@ -57,5 +68,5 @@ /*Object virtual function resolutoin: */ Object* Cfsurfacesquare::copy() {/*{{{*/ - Cfsurfacesquare* mf = new Cfsurfacesquare(this->name,this->definitionenum, this->model_enum,this->observation_enum,this->weights_enum,this->datatime,this->timepassedflag); + Cfsurfacesquare* mf = new Cfsurfacesquare(this->name,this->definitionenum, this->model_enum,this->datatime,this->timepassedflag,this->J); return (Object*) mf; } @@ -68,8 +79,7 @@ _printf_(" Cfsurfacesquare: " << name << " " << this->definitionenum << "\n"); _printf_(" model_enum: " << model_enum << " " << EnumToStringx(model_enum) << "\n"); - _printf_(" observation_enum: " << observation_enum << " " << EnumToStringx(observation_enum) << "\n"); - _printf_(" weights_enum: " << weights_enum << " " << EnumToStringx(weights_enum) << "\n"); _printf_(" datatime: " << datatime << "\n"); _printf_(" timepassedflag: "<call(this->definitionenum); - marshallhandle->call(this->local); marshallhandle->call(this->model_enum); marshallhandle->call(this->name); - marshallhandle->call(this->observation_enum); - marshallhandle->call(this->weights_enum); marshallhandle->call(this->datatime); marshallhandle->call(this->timepassedflag); + marshallhandle->call(this->J); } /*}}}*/ @@ -119,24 +127,23 @@ if(this->datatime<=time && !this->timepassedflag){ - IssmDouble J=0.; + IssmDouble J_part=0.; IssmDouble J_sum=0.; for(Object* & object : femmodel->elements->objects){ Element* element=xDynamicCast(object); - J+=this->Cfsurfacesquare_Calculation(element,model_enum,observation_enum,weights_enum); + J_part+=this->Cfsurfacesquare_Calculation(element,model_enum); } - ISSM_MPI_Allreduce ( (void*)&J,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + ISSM_MPI_Allreduce ( (void*)&J_part,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); this->timepassedflag = true; - return J_sum; + this->J = J_sum; } - else{ - return 0.; - } -} -/*}}}*/ -IssmDouble Cfsurfacesquare::Cfsurfacesquare_Calculation(Element* element, int model_enum, int observation_enum, int weights_enum){/*{{{*/ + + return this->J; +} +/*}}}*/ +IssmDouble Cfsurfacesquare::Cfsurfacesquare_Calculation(Element* element, int model_enum){/*{{{*/ int domaintype,numcomponents; Index: /issm/trunk/src/c/classes/Cfsurfacesquare.h =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacesquare.h (revision 28012) +++ /issm/trunk/src/c/classes/Cfsurfacesquare.h (revision 28013) @@ -17,30 +17,29 @@ int definitionenum; - int local; int model_enum; - char* name; - int observation_enum; - int weights_enum; - IssmDouble datatime; - bool timepassedflag; + char *name; + IssmDouble datatime; + bool timepassedflag; + IssmDouble J; /*Cfsurfacesquare constructors, destructors :*/ Cfsurfacesquare(); - Cfsurfacesquare(char* in_name, int in_definitionenum, int in_model_enum, int in_observation_enum, int in_weights_enum, IssmDouble in_datatime, bool timepassedflag); + Cfsurfacesquare(char* in_name, int in_definitionenum, int in_model_enum, IssmDouble in_datatime); + Cfsurfacesquare(char* in_name, int in_definitionenum, int in_model_enum, IssmDouble in_datatime, bool timepassedflag, IssmDouble in_J); ~Cfsurfacesquare(); /*Object virtual function resolutoin: */ - Object* copy(); - void DeepEcho(void); - void Echo(void); - int Id(void); - void Marshall(MarshallHandle* marshallhandle); - int ObjectEnum(void); + Object *copy(); + void DeepEcho(void); + void Echo(void); + int Id(void); + void Marshall(MarshallHandle *marshallhandle); + int ObjectEnum(void); /*Definition virtual function resolutoin: */ - int DefinitionEnum(); - char* Name(); - IssmDouble Response(FemModel* femmodel); - IssmDouble Cfsurfacesquare_Calculation(Element* element, int model_enum, int observation_enum, int weights_enum); + int DefinitionEnum(); + char *Name(); + IssmDouble Response(FemModel *femmodel); + IssmDouble Cfsurfacesquare_Calculation(Element *element, int model_enum); }; #endif /* _CFSURFACESQUARE_H_ */ Index: /issm/trunk/src/c/classes/Cfsurfacesquaretransient.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacesquaretransient.cpp (revision 28013) +++ /issm/trunk/src/c/classes/Cfsurfacesquaretransient.cpp (revision 28013) @@ -0,0 +1,235 @@ +/*!\file Cfsurfacesquaretransient.cpp + * \brief: Cfsurfacesquaretransient Object + */ + +/*Headers:*/ +/*{{{*/ +#ifdef HAVE_CONFIG_H +#include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "./classes.h" +#include "./ExternalResults/ExternalResult.h" +#include "./ExternalResults/Results.h" +#include "../datastructures/datastructures.h" +#include "./Elements/Element.h" +#include "./Elements/Elements.h" +#include "./FemModel.h" +#include "../modules/SurfaceAreax/SurfaceAreax.h" +#include "../classes/Params/Parameters.h" +#include "../classes/gauss/Gauss.h" +#include "./Inputs/DatasetInput.h" +/*}}}*/ + +/*Cfsurfacesquaretransient constructors, destructors :*/ +Cfsurfacesquaretransient::Cfsurfacesquaretransient(){/*{{{*/ + + this->definitionenum = -1; + this->name = NULL; + this->model_enum = UNDEF; + this->datatimes = NULL; + this->passedflags = NULL; + this->J = 0.; +} +/*}}}*/ +Cfsurfacesquaretransient::Cfsurfacesquaretransient(char* in_name, int in_definitionenum, int in_model_enum, int in_num_datatimes, IssmDouble* in_datatimes, bool* in_passedflags, IssmDouble in_J){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->model_enum=in_model_enum; + this->num_datatimes = in_num_datatimes; + + /*Allocate arrays*/ + _assert_(this->num_datatimes>0); + this->datatimes = xNew(this->num_datatimes); + this->passedflags = xNew(this->num_datatimes); + xMemCpy(this->datatimes,in_datatimes,this->num_datatimes); + xMemCpy(this->passedflags,in_passedflags,this->num_datatimes); + + this->J = in_J; +} +/*}}}*/ +Cfsurfacesquaretransient::Cfsurfacesquaretransient(char* in_name, int in_definitionenum, int in_model_enum, int in_num_datatimes, IssmDouble* in_datatimes){/*{{{*/ + + this->definitionenum=in_definitionenum; + + this->name = xNew(strlen(in_name)+1); + xMemCpy(this->name,in_name,strlen(in_name)+1); + + this->model_enum=in_model_enum; + this->num_datatimes = in_num_datatimes; + + /*Allocate arrays*/ + _assert_(this->num_datatimes>0); + this->datatimes = xNew(this->num_datatimes); + this->passedflags = xNew(this->num_datatimes); + xMemCpy(this->datatimes,in_datatimes,this->num_datatimes); + + /*initialize passedtimes to false*/ + for(int i=0;inum_datatimes;i++) this->passedflags[i]= false; + this->J = 0; +} +/*}}}*/ +Cfsurfacesquaretransient::~Cfsurfacesquaretransient(){/*{{{*/ + if(this->name) xDelete(this->name); + if(this->datatimes) xDelete(this->datatimes); + if(this->passedflags) xDelete(this->passedflags); +} +/*}}}*/ + +/*Object virtual function resolutoin: */ +Object* Cfsurfacesquaretransient::copy() {/*{{{*/ + Cfsurfacesquaretransient* output = new Cfsurfacesquaretransient(this->name,this->definitionenum, this->model_enum, this->num_datatimes, this->datatimes,this->passedflags, this->J); + return (Object*)output; +} +/*}}}*/ +void Cfsurfacesquaretransient::DeepEcho(void){/*{{{*/ + this->Echo(); +} +/*}}}*/ +void Cfsurfacesquaretransient::Echo(void){/*{{{*/ + _printf_(" Cfsurfacesquaretransient: " << name << " " << this->definitionenum << "\n"); + _printf_(" model_enum: " << model_enum << " " << EnumToStringx(model_enum) << "\n"); + _error_("not implemented yet"); +} +/*}}}*/ +int Cfsurfacesquaretransient::Id(void){/*{{{*/ + return -1; +} +/*}}}*/ +void Cfsurfacesquaretransient::Marshall(MarshallHandle* marshallhandle){/*{{{*/ + + int object_enum=CfsurfacesquaretransientEnum; + marshallhandle->call(object_enum); + + marshallhandle->call(this->definitionenum); + marshallhandle->call(this->model_enum); + marshallhandle->call(this->name); + marshallhandle->call(this->num_datatimes); + marshallhandle->call(this->datatimes,this->num_datatimes); + marshallhandle->call(this->passedflags,this->num_datatimes); + marshallhandle->call(this->J); +} +/*}}}*/ +int Cfsurfacesquaretransient::ObjectEnum(void){/*{{{*/ + return CfsurfacesquaretransientEnum; +} +/*}}}*/ + +/*Definition virtual function resolutoin: */ +int Cfsurfacesquaretransient::DefinitionEnum(){/*{{{*/ + return this->definitionenum; +} +/*}}}*/ +char* Cfsurfacesquaretransient::Name(){/*{{{*/ + char* name2=xNew(strlen(this->name)+1); + xMemCpy(name2,this->name,strlen(this->name)+1); + + return name2; +} +/*}}}*/ +IssmDouble Cfsurfacesquaretransient::Response(FemModel* femmodel){/*{{{*/ + + /*recover model time parameters: */ + IssmDouble time; + femmodel->parameters->FindParam(&time,TimeEnum); + + /*Find closest datatime that is less than time*/ + int pos=-1; + for(int i=0;inum_datatimes;i++){ + if(this->datatimes[i]<=time){ + pos = i; + } + else{ + break; + } + } + + /*if pos=-1, time is earlier than the first data observation in this dataset*/ + if(pos==-1){ + _assert_(this->J==0.); + return 0.; + } + + /*Check that we have not yet calculated this cost function*/ + if(this->passedflags[pos]){ + return this->J; + } + + /*Calculate cost function for this time slice*/ + IssmDouble J_part=0.; + for(Object* & object : femmodel->elements->objects){ + Element* element=xDynamicCast(object); + J_part+=this->Cfsurfacesquaretransient_Calculation(element,model_enum); + } + + /*Sum across partition*/ + IssmDouble J_sum; + ISSM_MPI_Allreduce((void*)&J_part,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + + /*Record this cost function so that we do not recalculate it later*/ + this->passedflags[pos]= true; + this->J += J_sum; + + /*Return full cost function this far*/ + return this->J; +}/*}}}*/ +IssmDouble Cfsurfacesquaretransient::Cfsurfacesquaretransient_Calculation(Element* element, int model_enum){/*{{{*/ + + IssmDouble Jelem=0.; + IssmDouble misfit,Jdet; + IssmDouble model,obs,weight; + IssmDouble* xyz_list = NULL; + + /*Get basal element*/ + if(!element->IsOnSurface()) return 0.; + + /*If on water, return 0: */ + if(!element->IsIceInElement()) return 0.; + + /*Spawn surface element*/ + Element* topelement = element->SpawnTopElement(); + + /* Get node coordinates*/ + topelement->GetVerticesCoordinates(&xyz_list); + + /*Retrieve all inputs we will be needing: */ + DatasetInput *datasetinput = topelement->GetDatasetInput(definitionenum); _assert_(datasetinput); + Input *model_input = topelement->GetInput(model_enum); _assert_(model_input); + + /* Start looping on the number of gaussian points: */ + Gauss* gauss=topelement->NewGauss(2); + while(gauss->next()){ + + /* Get Jacobian determinant: */ + topelement->JacobianDeterminant(&Jdet,xyz_list,gauss); + + /*Get all parameters at gaussian point*/ + datasetinput->GetInputValue(&weight,gauss,WeightsSurfaceObservationEnum); + datasetinput->GetInputValue(&obs,gauss,SurfaceObservationEnum); + model_input->GetInputValue(&model,gauss); + + /*Compute Misfit + * + * 1 [ 2 ] + * J = --- | (x - x ) | + * 2 [ obs ] + **/ + misfit=0.5*(model-obs)*(model-obs); + + /*Add to cost function*/ + Jelem+=misfit*weight*Jdet*gauss->weight; + } + + /*clean up and Return: */ + if(topelement->IsSpawnedElement()){topelement->DeleteMaterials(); delete topelement;}; + xDelete(xyz_list); + delete gauss; + return Jelem; +}/*}}}*/ Index: /issm/trunk/src/c/classes/Cfsurfacesquaretransient.h =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacesquaretransient.h (revision 28013) +++ /issm/trunk/src/c/classes/Cfsurfacesquaretransient.h (revision 28013) @@ -0,0 +1,46 @@ +/*!\file Cfsurfacesquaretransient.h + * \brief: header file for Cfsurfacesquaretransient object + */ + +#ifndef _CFSURFACESQUARETRANSIENT_H_ +#define _CFSURFACESQUARETRANSIENT_H_ + +/*Headers:*/ +#include "./Definition.h" +class FemModel; + +IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); + +class Cfsurfacesquaretransient: public Object, public Definition{ + + public: + + int definitionenum; + int model_enum; + char *name; + int num_datatimes; + IssmDouble *datatimes; + bool *passedflags; + IssmDouble J; + + /*Cfsurfacesquaretransient constructors, destructors :*/ + Cfsurfacesquaretransient(); + Cfsurfacesquaretransient(char* in_name, int in_definitionenum, int in_model_enum,int num_datatimes, IssmDouble* in_datatime); + Cfsurfacesquaretransient(char* in_name, int in_definitionenum, int in_model_enum,int num_datatimes, IssmDouble* in_datatime, bool* in_timepassedflag, IssmDouble in_J); + ~Cfsurfacesquaretransient(); + + /*Object virtual function resolutoin: */ + Object *copy(); + void DeepEcho(void); + void Echo(void); + int Id(void); + void Marshall(MarshallHandle *marshallhandle); + int ObjectEnum(void); + + /*Definition virtual function resolutoin: */ + int DefinitionEnum(); + char *Name(); + IssmDouble Response(FemModel *femmodel); + IssmDouble Cfsurfacesquaretransient_Calculation(Element *element, int model_enum); +}; +#endif /* _CFSURFACESQUARE_H_ */ Index: /issm/trunk/src/c/classes/DependentObject.cpp =================================================================== --- /issm/trunk/src/c/classes/DependentObject.cpp (revision 28012) +++ /issm/trunk/src/c/classes/DependentObject.cpp (revision 28013) @@ -16,19 +16,16 @@ DependentObject::DependentObject(){/*{{{*/ this->name=NULL; - this->index=-1; this->response_value=0.; } /*}}}*/ -DependentObject::DependentObject(char* in_name,int in_index){/*{{{*/ +DependentObject::DependentObject(char* in_name){/*{{{*/ this->name=xNew(strlen(in_name)+1); xMemCpy(this->name,in_name,strlen(in_name)+1); - this->index=in_index; this->response_value=0.; }/*}}}*/ -DependentObject::DependentObject(char* in_name,int in_index,IssmDouble in_response){/*{{{*/ +DependentObject::DependentObject(char* in_name,IssmDouble in_response){/*{{{*/ this->name=xNew(strlen(in_name)+1); xMemCpy(this->name,in_name,strlen(in_name)+1); - this->index=in_index; this->response_value=in_response; @@ -40,5 +37,5 @@ /*Object virtual functions definitions:*/ Object* DependentObject::copy(void) { /*{{{*/ - return new DependentObject(name,index,response_value); + return new DependentObject(name,response_value); } /*}}}*/ void DependentObject::DeepEcho(void){/*{{{*/ @@ -50,5 +47,4 @@ _printf_("DependentObject:\n"); _printf_(" name: " << this->name << "\n"); - if(this->index>=0) _printf_(" index: " << this->index << "\n"); _printf_(" response_value: " << this->response_value<< "\n"); } @@ -70,16 +66,17 @@ marshallhandle->call(this->name); - marshallhandle->call(this->index); marshallhandle->call(this->response_value); }/*}}}*/ /*DependentObject methods: */ -void DependentObject::Responsex(IssmDouble* poutput_value,FemModel* femmodel){/*{{{*/ +void DependentObject::RecordResponsex(FemModel* femmodel){/*{{{*/ /*Is this some special type of response for which we need to go in the output definitions? :*/ if (StringToEnumx(this->name,false)==-1){ - *poutput_value=OutputDefinitionsResponsex(femmodel,this->name); + this->response_value = OutputDefinitionsResponsex(femmodel,this->name); } - else femmodel->Responsex(poutput_value,this->name); + else{ + femmodel->Responsex(&this->response_value, this->name); + } } /*}}}*/ @@ -88,8 +85,4 @@ } /*}}}*/ -void DependentObject::AddValue(IssmDouble in_value){/*{{{*/ - this->response_value+=in_value; -} -/*}}}*/ void DependentObject::ResetResponseValue(){/*{{{*/ this->response_value=0.; Index: /issm/trunk/src/c/classes/DependentObject.h =================================================================== --- /issm/trunk/src/c/classes/DependentObject.h (revision 28012) +++ /issm/trunk/src/c/classes/DependentObject.h (revision 28013) @@ -18,11 +18,10 @@ char* name; - int index; /*0: scalar, 1: vertex*/ IssmDouble response_value; /*DependentObject constructors, destructors */ DependentObject(); - DependentObject(char* name,int index); - DependentObject(char* name,int index,IssmDouble in_response); + DependentObject(char* name); + DependentObject(char* name, IssmDouble in_response); ~DependentObject(); @@ -36,7 +35,6 @@ /*DependentObject methods: */ - void Responsex(IssmDouble *poutput_value,FemModel*femmodel); + void RecordResponsex(FemModel*femmodel); IssmDouble GetValue(void); - void AddValue(IssmDouble in_value); void ResetResponseValue(void); Index: /issm/trunk/src/c/classes/Elements/Element.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Element.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Elements/Element.cpp (revision 28013) @@ -30,4 +30,17 @@ extern "C" void run_semic_(IssmDouble *sf_in, IssmDouble *rf_in, IssmDouble *swd_in, IssmDouble *lwd_in, IssmDouble *wind_in, IssmDouble *sp_in, IssmDouble *rhoa_in, IssmDouble *qq_in, IssmDouble *tt_in, IssmDouble *tsurf_out, IssmDouble *smb_out, IssmDouble *saccu_out, IssmDouble *smelt_out); + +extern "C" void run_semic_transient_(int *nx, int *ntime, int *nloop, + IssmDouble *sf_in, IssmDouble *rf_in, IssmDouble *swd_in, + IssmDouble *lwd_in, IssmDouble *wind_in, IssmDouble *sp_in, IssmDouble *rhoa_in, + IssmDouble *qq_in, IssmDouble *tt_in, IssmDouble *tsurf_in, IssmDouble *qmr_in, + IssmDouble *tstic, + IssmDouble *hcrit, IssmDouble *rcrit, + IssmDouble *mask, IssmDouble *hice, IssmDouble *hsnow, + IssmDouble *albedo_in, IssmDouble *albedo_snow_in, + int *alb_scheme, IssmDouble *alb_smax, IssmDouble *alb_smin, IssmDouble *albi, IssmDouble *albl, + IssmDouble *Tamp, + IssmDouble *tmin, IssmDouble *tmax, IssmDouble *tmid, IssmDouble *mcrit, IssmDouble *wcrit, IssmDouble *tau_a, IssmDouble* tau_f, IssmDouble *afac, bool *verbose, + IssmDouble *tsurf_out, IssmDouble *smb_out, IssmDouble *smbi_out, IssmDouble *smbs_out, IssmDouble *saccu_out, IssmDouble *smelt_out, IssmDouble *refr_out, IssmDouble *albedo_out, IssmDouble *albedo_snow_out, IssmDouble *hsnow_out, IssmDouble *hice_out, IssmDouble *qmr_out); #endif // _HAVE_SEMIC_ @@ -99,5 +112,19 @@ outenum_type = BasalforcingsSpatialDeepwaterMeltingRateEnum; break; - } + case(FrontalForcingsSubglacialDischargearmaEnum): + arenum_type = SubglacialdischargeValuesAutoregressionEnum; + maenum_type = SubglacialdischargeValuesMovingaverageEnum; + basinenum_type = FrontalForcingsBasinIdEnum; + noiseenum_type = SubglacialdischargeARMANoiseEnum; + outenum_type = FrontalForcingsSubglacialDischargeEnum; + break; + case(HydrologyarmapwEnum): + arenum_type = WaterPressureValuesAutoregressionEnum; + maenum_type = WaterPressureValuesMovingaverageEnum; + basinenum_type = HydrologyBasinsIdEnum; + noiseenum_type = FrictionWaterPressureNoiseEnum; + outenum_type = WaterPressureArmaPerturbationEnum; + break; + } /*Get time parameters*/ @@ -126,13 +153,14 @@ indperiod = 0; for(int i=0;idatebreaks_basin[i]) indperiod = i+1; + if(tatstep>=datebreaks_basin[i]) indperiod = i+1; } /*Compute polynomial with parameters of indperiod*/ - if(indperiod==0) telapsed_break = tatstep; + if(indperiod==0) telapsed_break = tatstep-starttime; else telapsed_break = tatstep-datebreaks_basin[indperiod-1]; for(int j=0;j(numvertices*arorder); @@ -911,5 +944,5 @@ /*Get material parameters :*/ - IssmDouble rho_water = this->FindParam(MaterialsRhoSeawaterEnum); + IssmDouble rho_water = this->FindParam(MaterialsRhoFreshwaterEnum); IssmDouble rho_ice = this->FindParam(MaterialsRhoIceEnum); @@ -1218,4 +1251,50 @@ /*Return: */ return this->FloatingArea(scaled); +} +/*}}}*/ +void Element::FrictionAlpha2CreateInput(void){/*{{{*/ + + /*Return if element is inactive*/ + if(this->IsAllFloating() || !this->IsIceInElement()) return; + + /*Intermediaries*/ + int domaintype, dim; + Element* basalelement = NULL; + + /*Get basal element*/ + this->FindParam(&domaintype,DomainTypeEnum); + switch(domaintype){ + case Domain2DhorizontalEnum: + basalelement = this; + dim = 2; + break; + case Domain3DEnum: case Domain2DverticalEnum: + if(!this->IsOnBase()) return; + basalelement = this->SpawnBasalElement(true); + dim = 2; + break; + default: _error_("mesh "<GetNumberOfVertices(); + + /*build friction object, used later on: */ + Friction* friction=new Friction(basalelement,dim); + IssmDouble alpha2_list[MAXVERTICES]; + IssmDouble alpha2; + + Gauss* gauss=basalelement->NewGauss(); + for(int i=0;iGaussVertex(i); + + friction->GetAlpha2(&alpha2,gauss); + alpha2_list[i] = alpha2; + } + + /*Clean up and return*/ + delete gauss; + delete friction; + if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; + this->AddBasalInput(FrictionAlpha2Enum,&alpha2_list[0],P1Enum); } /*}}}*/ @@ -1870,8 +1949,11 @@ /*Are we in transient or static? */ if(M==1){ - values[0]=vector[0]; + if(N!=1) _error_("Size of Input "<SetElementInput(inputs,vector_enum,vector[0]); } + else if(M==iomodel->numberofvertices){ + if(N!=1) _error_("Size of Input "<SetElementInput(inputs,NUM_VERTICES,vertexlids,values,vector_enum); @@ -1912,5 +1994,5 @@ } else{ - _error_("Patch interpolation not supported yet"); + _error_("Size of Input "<(evalues); @@ -1918,13 +2000,34 @@ } else{ - _error_("nodal vector is either numberofvertices or numberofvertices+1 long. Field provided (" << EnumToStringx(vector_enum) << ") is " << M << " long"); + _error_("Size of Input "<numberofelements){ + if(M==1){ + if(N!=1) _error_("Size of Input "<SetElementInput(inputs,vector_enum,vector[0]); + } + else if(M==2){ + /*create transient input: */ + IssmDouble* times = xNew(N); + for(int t=0;tSetTransientInput(vector_enum,times,N); + TransientInput* transientinput = inputs->GetTransientInput(vector_enum); + + for(int t=0;tObjectEnum()){ + case TriaEnum: transientinput->AddTriaTimeInput( t,1,&(this->lid),&value,P0Enum); break; + case PentaEnum: transientinput->AddPentaTimeInput(t,1,&(this->lid),&value,P0Enum); break; + default: _error_("Not implemented yet"); + } + } + xDelete(times); + } + else if(M==iomodel->numberofelements){ + if(N!=1) _error_("Size of Input "<SetBoolInput(inputs,vector_enum,reCast(vector[this->Sid()])); @@ -1945,5 +2048,5 @@ TransientInput* transientinput = inputs->GetTransientInput(vector_enum); for(int t=0;tSid()+t]; + IssmDouble value=vector[N*this->Sid()+t]; switch(this->ObjectEnum()){ case TriaEnum: transientinput->AddTriaTimeInput( t,1,&(this->lid),&value,P0Enum); break; @@ -1954,24 +2057,8 @@ xDelete(times); } - else if(M==1 || M==2){ - /*create transient input: */ - IssmDouble* times = xNew(N); - if(M==1)times[0]=0; - if(M==2)for(int t=0;tSetTransientInput(vector_enum,times,N); - TransientInput* transientinput = inputs->GetTransientInput(vector_enum); - - for(int t=0;tObjectEnum()){ - case TriaEnum: transientinput->AddTriaTimeInput( t,1,&(this->lid),&value,P0Enum); break; - case PentaEnum: transientinput->AddPentaTimeInput(t,1,&(this->lid),&value,P0Enum); break; - default: _error_("Not implemented yet"); - } - } - xDelete(times); - } - else _error_("element vector is either numberofelements or numberofelements+1 long. Field provided (" << EnumToStringx(vector_enum) << ") is " << M << " long"); + + else{ + _error_("Size of Input "<(layers); } - else _error_("element vector is either numberofelements or numberofelements+1 long. Field provided (" << EnumToStringx(vector_enum) << ") is " << M << " long"); - } - else _error_("Cannot add input for vector type " << vector_type << " (not supported)"); + else{ + _error_("Size of Input "<numberofelements){ - if (code==5){ //boolean - _error_("not implemented"); - //datasetinput->AddInput(new BoolInput(input_enum,reCast(vector[this->Sid()])),input_id); - } - else if (code==6){ //integer - _error_("not implemented"); - //datasetinput->AddInput(new IntInput(input_enum,reCast(vector[this->Sid()])),input_id); - } - else if (code==7){ //IssmDouble - _error_("not implemented"); - //datasetinput->AddInput(new DoubleInput(input_enum,vector[this->Sid()]),input_id); - } - else _error_("could not recognize nature of vector from code " << code); + _error_("not implemented"); } else if(M==iomodel->numberofelements+1){ _error_("not supported"); - ///*create transient input: */ - //IssmDouble* times = xNew(N); - //for(t=0;tSid()+t]; - // switch(this->ObjectEnum()){ - // case TriaEnum: transientinput->AddTimeInput(new TriaInput( input_enum,&value,P0Enum)); break; - // case PentaEnum: transientinput->AddTimeInput(new PentaInput(input_enum,&value,P0Enum)); break; - // case TetraEnum: transientinput->AddTimeInput(new TetraInput(input_enum,&value,P0Enum)); break; - // default: _error_("Not implemented yet"); - // } - //} - //xDelete(times); } else _error_("element vector is either numberofelements or numberofelements+1 long. Field provided (" << EnumToStringx(input_enum) << ") is " << M << " long"); @@ -2340,4 +2403,17 @@ Input* input=this->GetInput(MaskOceanLevelsetEnum); _assert_(input); return (input->GetInputMax()<=0.); +} +/*}}}*/ +bool Element::IsAllMinThicknessInElement(){/*{{{*/ + + IssmDouble minthickness = this->FindParam(MasstransportMinThicknessEnum); + + Input* input=this->GetInput(ThicknessEnum); _assert_(input); + if(input->GetInputMax()<=(minthickness+0.00000001)){ + return true; + } + else{ + return false; + } } /*}}}*/ @@ -2411,12 +2487,23 @@ const int numvertices = this->GetNumberOfVertices(); bool isadjustsmb = false; - int basinid,bb1,bb2; - IssmDouble ela,refelevation_b; + int basinid,bb1,bb2,mindex; + IssmDouble ela,refelevation_b,time,dt,fracyear,yts; + IssmDouble monthsteps[12] = {0.,1./12,2./12,3./12,4./12,5./12,6./12,7./12,8./12,9./12,10./12,11./12}; IssmDouble* surfacelist = xNew(numvertices); IssmDouble* smblist = xNew(numvertices); - /* numelevbins values of lapse rates */ + /* numelevbins values of lapse rates at current month */ IssmDouble* lapserates_b = xNew(numelevbins); - /* (numelevbins-1) limits between elevation bins (be cautious with indexing) */ + /* (numelevbins-1) limits between elevation bins at current month (be cautious with indexing) */ IssmDouble* elevbins_b = xNew(numelevbins-1); + + /*Find month of current time step*/ + this->parameters->FindParam(&yts,ConstantsYtsEnum); + this->parameters->FindParam(&time,TimeEnum); + this->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + fracyear = time/yts-floor(time/yts); + for(int i=1;i<12;i++){ + if(fracyear>=monthsteps[i-1]) mindex = i-1; + } + if(fracyear>=monthsteps[11]) mindex = 11; /*Retrieve SMB values non-adjusted for SMB lapse rate*/ @@ -2427,21 +2514,24 @@ this->GetInputValue(&basinid,SmbBasinsIdEnum); refelevation_b = refelevation[basinid]; - for(int ii=0;ii<(numelevbins-1);ii++) elevbins_b[ii] = elevbins[basinid*(numelevbins-1)+ii]; + /*Retrieve bins and laps rates for this basin at this month*/ + for(int ii=0;ii<(numelevbins-1);ii++) elevbins_b[ii] = elevbins[basinid*(numelevbins-1)*12+mindex*(numelevbins-1)+ii]; for(int ii=0;ii=elevbins_b[ii]) bb1 = ii+1; + if(refelevation_b>=elevbins_b[ii]) bb2 = ii+1; } - /*Check for elevations above highest bin limit */ - if(surfacelist[v]>elevbins_b[numelevbins-1-1]) bb1 = numelevbins-1; - if(refelevation_b>elevbins_b[numelevbins-1-1]) bb2 = numelevbins-1; + /*Vertex and Reference elevation in same elevation bin*/ if(bb1==bb2){ @@ -2478,4 +2568,5 @@ IssmDouble deepwaterel,upperwaterel,deepwatermelt,upperwatermelt; IssmDouble base[MAXVERTICES]; + IssmDouble perturbation[MAXVERTICES]; IssmDouble values[MAXVERTICES]; IssmDouble time; @@ -2489,4 +2580,5 @@ this->GetInputListOnVertices(&base[0],BaseEnum); + this->GetInputListOnVertices(&perturbation[0],BasalforcingsPerturbationMeltingRateEnum); for(int i=0;i=upperwaterel){ @@ -2500,4 +2592,7 @@ values[i]=deepwatermelt*alpha+(1.-alpha)*upperwatermelt; } + + /*Add perturbation*/ + values[i] += perturbation[i]; } @@ -2717,4 +2812,86 @@ }/*}}}*/ +void Element::MonthlyFactorBasin(IssmDouble* monthlyfac,int enum_type){/*{{{*/ + + /*Variable declaration*/ + bool ratevariable; + const int numvertices = this->GetNumberOfVertices(); + int basinid,mindex,mindexnext,basinenum_type,varenum_type,indperiod; + IssmDouble time,dt,fracyear,fracyearnext,fracmonth,fracmonthnext,yts; + IssmDouble monthsteps[12] = {0.,1./12,2./12,3./12,4./12,5./12,6./12,7./12,8./12,9./12,10./12,11./12}; + IssmDouble* monthlyfac_b = xNew(12); + IssmDouble* monthlyrate_b = xNew(12); + IssmDouble* fracdtinmonth = xNew(12); + IssmDouble* rateinmonth = xNew(numvertices*12); + IssmDouble* varlistinput = xNew(numvertices); + IssmDouble* varlist = xNewZeroInit(numvertices); + + /*Get field-specific enums*/ + switch(enum_type){ + case(FrontalForcingsSubglacialDischargearmaEnum): + basinenum_type = FrontalForcingsBasinIdEnum; + varenum_type = FrontalForcingsSubglacialDischargeEnum; + ratevariable = true; + break; + case(HydrologyarmapwEnum): + basinenum_type = HydrologyBasinsIdEnum; + varenum_type = FrictionWaterPressureEnum; + ratevariable = false; + break; + } + + /*Evaluate the month index now and at (now-timestepjump)*/ + this->parameters->FindParam(&yts,ConstantsYtsEnum); + this->parameters->FindParam(&time,TimeEnum); + this->parameters->FindParam(&dt,TimesteppingTimeStepEnum); _assert_(dt=monthsteps[i-1]) mindex = i-1; + if(fracyearnext>=monthsteps[i-1]) mindexnext = i-1; + } + if(fracyear>=monthsteps[11]) mindex = 11; + if(fracyearnext>=monthsteps[11]) mindexnext = 11; + + /*Calculate fraction of the time step spent in each month*/ + for(int i=0;i<12;i++){ + if(mindexi) fracdtinmonth[i] = 1.0/dt*yts/12.0; + else if(mindexi && mindexnexti) fracdtinmonth[i] = 1.0/dt*yts/12.0; + else if(mindex>i && mindexnextGetInputValue(&basinid,basinenum_type); + for(int i=0;i<12;i++) monthlyfac_b[i] = monthlyfac[basinid*12+i]; + + /*Retrieve input*/ + this->GetInputListOnVertices(varlistinput,varenum_type); + + /*Calculate monthly rate for each month and weight-average it for application over dt*/ + for(int v=0;vAddInput(varenum_type,varlist,P1DGEnum); + + /*Clean-up*/ + xDelete(fracdtinmonth); + xDelete(rateinmonth); + xDelete(monthlyfac_b); + xDelete(monthlyrate_b); + xDelete(varlist); + xDelete(varlistinput); +}/*}}}*/ void Element::MonthlyPiecewiseLinearEffectBasin(int nummonthbreaks,IssmDouble* monthlyintercepts,IssmDouble* monthlytrends,IssmDouble* monthlydatebreaks,int enum_type){/*{{{*/ @@ -2726,6 +2903,6 @@ IssmDouble monthsteps[12] = {0.,1./12,2./12,3./12,4./12,5./12,6./12,7./12,8./12,9./12,10./12,11./12}; IssmDouble* datebreaks_b = xNew(nummonthbreaks); - IssmDouble* intercepts_b = xNew(nummonthbreaks*12); - IssmDouble* trends_b = xNew(nummonthbreaks*12); + IssmDouble* intercepts_b = xNew(numperiods*12); + IssmDouble* trends_b = xNew(numperiods*12); IssmDouble* varlist = xNew(numvertices); @@ -3610,4 +3787,340 @@ } /*}}}*/ +void Element::SmbDebrisEvatt(){/*{{{*/ + + const int NUM_VERTICES = this->GetNumberOfVertices(); + const int NUM_VERTICES_DAYS_PER_YEAR = NUM_VERTICES * 365; // 365 FIXME + + int i,vertexlids[MAXVERTICES];; + IssmDouble* smb=xNew(NUM_VERTICES); + IssmDouble* melt=xNew(NUM_VERTICES); + IssmDouble* summermelt=xNew(NUM_VERTICES); + IssmDouble* albedo=xNew(NUM_VERTICES); + IssmDouble* summeralbedo=xNew(NUM_VERTICES); + IssmDouble* accu=xNew(NUM_VERTICES); + + // climate inputs + IssmDouble* temperature=xNew(NUM_VERTICES_DAYS_PER_YEAR); + IssmDouble* precip=xNew(NUM_VERTICES_DAYS_PER_YEAR); + IssmDouble* lw=xNew(NUM_VERTICES_DAYS_PER_YEAR); + IssmDouble* sw=xNew(NUM_VERTICES_DAYS_PER_YEAR); + IssmDouble* wind=xNew(NUM_VERTICES_DAYS_PER_YEAR); + IssmDouble* humidity=xNew(NUM_VERTICES_DAYS_PER_YEAR); + IssmDouble* yearlytemperatures=xNew(NUM_VERTICES); memset(yearlytemperatures, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* p_ampl=xNew(NUM_VERTICES); + IssmDouble* t_ampl=xNew(NUM_VERTICES); + IssmDouble* lw_ampl=xNew(NUM_VERTICES); + IssmDouble* sw_ampl=xNew(NUM_VERTICES); + IssmDouble* wind_ampl=xNew(NUM_VERTICES); + IssmDouble* humidity_ampl=xNew(NUM_VERTICES); + + IssmDouble* surface=xNew(NUM_VERTICES); + IssmDouble* s0t=xNew(NUM_VERTICES); + IssmDouble* snowheight=xNew(NUM_VERTICES); + IssmDouble* debriscover=xNew(NUM_VERTICES); + IssmDouble rho_water,rho_ice,Tf,debris,debris_here; + IssmDouble qlaps,rlaps,dsgrad,dlgrad,windspeedgrad,humiditygrad,Tm; + IssmDouble inv_twelve=1./365.; + IssmDouble time,yts,time_yr,lambda; + IssmDouble DailyMelt,CleanIceDailyMelt, CumDailyMelt=0,CleanIceMelt,CumDailySummerMelt=0; + IssmDouble MeanAlbedo=0, MeanSummerAlbedo=0; + bool isdebris,isAnderson,iscryokarst; + this->parameters->FindParam(&isdebris,TransientIsdebrisEnum); + this->parameters->FindParam(&isAnderson,SmbDebrisIsAndersonEnum); + this->parameters->FindParam(&iscryokarst,SmbDebrisIsCryokarstEnum); + IssmDouble PhiD=0.,p; + IssmDouble icealbedo=this->FindParam(SmbIcealbedoEnum); + IssmDouble snowalbedo=this->FindParam(SmbSnowalbedoEnum); + IssmDouble debrisalbedo=this->FindParam(SmbDebrisalbedoEnum); + IssmDouble Lm=this->FindParam(MaterialsLatentheatEnum); + IssmDouble D0=this->FindParam(SmbDebrisAndersonD0Enum); + int step; + this->FindParam(&step,StepEnum); + + // cryokarst + int dim=1,domaintype; + this->parameters->FindParam(&domaintype,DomainTypeEnum); + if(domaintype!=Domain2DverticalEnum){ + dim=2; + } + IssmDouble taud_plus=110e3, taud_minus=60e3; + IssmDouble taud, slope, gravity, taudx, taudy; + this->parameters->FindParam(&gravity,ConstantsGEnum); + IssmDouble* slopex = xNew(NUM_VERTICES); + IssmDouble* slopey = xNew(NUM_VERTICES); + IssmDouble* icethickness = xNew(NUM_VERTICES); + + /*Get material parameters :*/ + rho_water=this->FindParam(MaterialsRhoSeawaterEnum); + rho_ice=this->FindParam(MaterialsRhoIceEnum); + IssmDouble sconv=(rho_water/rho_ice); + Tf=this->FindParam(MaterialsMeltingpointEnum); + + /*Get parameters for height corrections*/ + qlaps=this->FindParam(SmbDesfacEnum); // comment MR; on alpine galciers we dont have the desertification effect + rlaps=this->FindParam(SmbRlapsEnum); + dsgrad=this->FindParam(SmbSWgradEnum); + dlgrad=this->FindParam(SmbLWgradEnum); + windspeedgrad=this->FindParam(SmbWindspeedgradEnum); + humiditygrad=this->FindParam(SmbHumiditygradEnum); + + /* Get time */ + this->parameters->FindParam(&time,TimeEnum); + this->parameters->FindParam(&yts,ConstantsYtsEnum); + time_yr=floor(time/yts)*yts; + + /*Get inputs*/ + DatasetInput* tempday =this->GetDatasetInput(SmbMonthlytemperaturesEnum); _assert_(tempday); + DatasetInput* precipday =this->GetDatasetInput(SmbPrecipitationEnum); _assert_(precipday); + DatasetInput* lwday =this->GetDatasetInput(SmbMonthlydlradiationEnum); _assert_(lwday); + DatasetInput* swday =this->GetDatasetInput(SmbMonthlydsradiationEnum); _assert_(swday); + DatasetInput* windday =this->GetDatasetInput(SmbMonthlywindspeedEnum); _assert_(windday); + DatasetInput* humidityday =this->GetDatasetInput(SmbMonthlyairhumidityEnum); _assert_(humidityday); + + /*loop over vertices: */ + Gauss* gauss=this->NewGauss(); + for(int month=0;month<365;month++){ + for(int iv=0;ivGaussVertex(iv); + tempday->GetInputValue(&temperature[iv*365+month],gauss,month); + temperature[iv*365+month]=temperature[iv*365+month]-Tf; // conversion from Kelvin to celcius for PDD module + precipday->GetInputValue(&precip[iv*365+month],gauss,month); + precip[iv*365+month]=precip[iv*365+month]*yts; // from m/s to m/a + lwday->GetInputValue(&lw[iv*365+month],gauss,month); + swday->GetInputValue(&sw[iv*365+month],gauss,month); + windday->GetInputValue(&wind[iv*365+month],gauss,month); + humidityday->GetInputValue(&humidity[iv*365+month],gauss,month); + } + } + + /*Recover info at the vertices: */ + GetInputListOnVertices(&surface[0],SurfaceEnum); + GetInputListOnVertices(&s0t[0],SmbS0tEnum); + GetInputListOnVertices(&snowheight[0],SmbSnowheightEnum); + GetInputListOnVertices(&debriscover[0],DebrisThicknessEnum); + GetInputListOnVertices(&t_ampl[0],SmbTemperaturesAnomalyEnum); + GetInputListOnVertices(&p_ampl[0],SmbPrecipitationsAnomalyEnum); + GetInputListOnVertices(&lw_ampl[0],SmbDsradiationAnomalyEnum); + GetInputListOnVertices(&sw_ampl[0],SmbDlradiationAnomalyEnum); + GetInputListOnVertices(&wind_ampl[0],SmbWindspeedAnomalyEnum); + GetInputListOnVertices(&humidity_ampl[0],SmbAirhumidityAnomalyEnum); + if(iscryokarst){ + GetInputListOnVertices(&slopex[0],SurfaceSlopeXEnum); + GetInputListOnVertices(&icethickness[0],ThicknessEnum); + if(dim==2){ + GetInputListOnVertices(&slopey[0],SurfaceSlopeYEnum); + } + taudx=rho_ice*gravity*icethickness[i]*slopex[i]; + if(dim==2) taudy=rho_ice*gravity*icethickness[i]*slopey[i]; + taud=sqrt(taudx*taudx+taudy*taudy); + } + IssmDouble Alphaeff,Alphaeff_cleanice; + + /*measure the surface mass balance*/ + for (int iv = 0; iv i.e + + /*Partition of precip in solid and liquid parts */ + IssmDouble temp_plus=1; + IssmDouble temp_minus=-1.; + IssmDouble frac_solid; + if(Tm>=temp_plus){ + frac_solid=0; + }else if(Tm<=temp_minus){ + frac_solid=1; + }else{ + frac_solid=1*(1-cos(PI*(temp_plus-Tm)/(temp_plus-temp_minus)))/2; + } + + /*Get yearly temperatures and accumulation */ + yearlytemperatures[iv]=yearlytemperatures[iv]+((temperature[iv*365+iday]-rlaps*st+Tf+t_ampl[iv]))/365; // Has to be in Kelvin + accu[iv]=accu[iv]+P*frac_solid; + if(yearlytemperatures[iv]>Tf) yearlytemperatures[iv]=Tf; + + CleanIceDailyMelt=((In-(Eps*Sigma*(Tf*Tf*Tf*Tf))+ + Q*(1.-Alphaeff)+ + (Rhoaa*Ca*Ustar*Ustar)/(Um-Ustar*(2.-(exp(Gamma*Xr))))*Tm)/((1-PhiD)*rho_ice*Lm)/(1.+ + ((Rhoaa*Ca*Ustar*Ustar)/(Um-Ustar*(2.-(exp(Gamma*Xr))))+4.*Eps*Sigma*(Tf*Tf*Tf))/ + K*debris)-(Lv*Ustar*Ustar*((Humidity))*(exp(-Gamma*Xr)))/((1.-PhiD)* + rho_ice*Lm*Ustar)/(((Um + -2.*Ustar)*exp(-Gamma*Xr))/Ustar+exp(Gamma*debris))); + if(CleanIceDailyMelt<0) CleanIceDailyMelt=0.; + DailyMelt=CleanIceDailyMelt; + + if(ismb==1){ + + //snowheight[iv]=snowheight[iv]+(P-CleanIceDailyMelt*yts/365); + IssmDouble sn_prev; + sn_prev=snowheight[iv]; + snowheight[iv]=sn_prev+(-CleanIceDailyMelt*yts/365);//P + + if(snowheight[iv]<=0) snowheight[iv]=0.; + if(snowheight[iv]<=0.0001){ + p=debris_here*PhiD/(2*0.2*0.01); //Eq. 51 from Evatt et al 2015 without source term g*t + if(p>1.) p=1.; + if(p>=0.999){ + Alphaeff=debrisalbedo; + } else { + Alphaeff=Alphaeff_cleanice+p*(debrisalbedo-Alphaeff_cleanice); + } + debris=debris_here; + DailyMelt=((In-(Eps*Sigma*(Tf*Tf*Tf*Tf))+ + Q*(1.-Alphaeff)+ + (Rhoaa*Ca*Ustar*Ustar)/(Um-Ustar*(2.-(exp(Gamma*Xr))))*Tm)/((1-PhiD)*rho_ice*Lm)/(1.+ + ((Rhoaa*Ca*Ustar*Ustar)/(Um-Ustar*(2.-(exp(Gamma*Xr))))+4.*Eps*Sigma*(Tf*Tf*Tf))/ + K*debris)-(Lv*Ustar*Ustar*((Humidity))*(exp(-Gamma*Xr)))/((1.-PhiD)* + rho_ice*Lm*Ustar)/(((Um-2.*Ustar)*exp(-Gamma*Xr))/Ustar+exp(Gamma*debris))); + if(DailyMelt<0) DailyMelt=0.; + MeanSummerAlbedo=MeanSummerAlbedo+Alphaeff; + CumDailySummerMelt=CumDailySummerMelt+DailyMelt/365; + } + } + CumDailyMelt=CumDailyMelt+DailyMelt/365; + } + MeanAlbedo=MeanAlbedo+Alphaeff; + if(ismb==0) CleanIceMelt=CumDailyMelt; + } + + if(iscryokarst){ + if(taud>=taud_plus){ + lambda=0; + }else if(taud>=taud_minus & taudAddInput(SmbMassBalanceEnum,smb,P1Enum); + this->AddInput(SmbAccumulationEnum,accu,P1Enum); + this->AddInput(SmbMeltEnum,melt,P1Enum); + this->AddInput(SmbSummerMeltEnum,summermelt,P1Enum); + this->AddInput(SmbSnowheightEnum,snowheight,P1Enum); + this->AddInput(SmbAlbedoEnum,albedo,P1Enum); + this->AddInput(SmbSummerAlbedoEnum,summeralbedo,P1Enum); + this->AddInput(TemperaturePDDEnum,yearlytemperatures,P1Enum); // TemperaturePDD is wrong here, but don't want to create new Enum ... + + /*clean-up*/ + xDelete(temperature); + xDelete(precip); + xDelete(lw); + xDelete(sw); + xDelete(wind); + xDelete(humidity); + xDelete(smb); + xDelete(surface); + xDelete(melt); + xDelete(summermelt); + xDelete(albedo); + xDelete(summeralbedo); + xDelete(accu); + xDelete(yearlytemperatures); + xDelete(s0t); + xDelete(snowheight); + xDelete(debriscover); + xDelete(t_ampl); + xDelete(p_ampl); + xDelete(lw_ampl); + xDelete(sw_ampl); + xDelete(humidity_ampl); + xDelete(wind_ampl); + xDelete(slopex); + xDelete(slopey); + xDelete(icethickness); +} +/*}}}*/ void Element::ResultInterpolation(int* pinterpolation,int* pnodesperelement,int* parray_size, int output_enum){/*{{{*/ @@ -3615,4 +4128,5 @@ switch(output_enum){ case ViscousHeatingEnum: this->ViscousHeatingCreateInput(); break; + case FrictionAlpha2Enum: this->FrictionAlpha2CreateInput(); break; case StressMaxPrincipalEnum: this->StressMaxPrincipalCreateInput(); break; case StressTensorxxEnum: @@ -3666,4 +4180,7 @@ this->CalvingRateVonmises(); break; + case CalvingVonmisesADEnum: + this->CalvingRateVonmisesAD(); + break; case CalvingCrevasseDepthEnum: this->CalvingCrevasseDepth(); @@ -3671,4 +4188,7 @@ case CalvingParameterizationEnum: this->CalvingRateParameterization(); + break; + case CalvingCalvingMIPEnum: + this->CalvingRateCalvingMIP(); break; case CalvingTestEnum: @@ -3837,12 +4357,12 @@ /* Start looping on the number of vertices: */ - GaussTria gauss; + Gauss* gauss=this->NewGauss(); for(int iv=0;ivGaussVertex(iv); /* Get variables */ - bed_input->GetInputValue(&bed,&gauss); - qsg_input->GetInputValue(&qsg,&gauss); - TF_input->GetInputValue(&TF,&gauss); + bed_input->GetInputValue(&bed,gauss); + qsg_input->GetInputValue(&qsg,gauss); + TF_input->GetInputValue(&TF,gauss); if(basin_icefront_area[basinid]==0.) meltrates[iv]=0.; @@ -3863,5 +4383,6 @@ /*Cleanup and return*/ - xDelete(basin_icefront_area); + delete gauss; + xDelete(basin_icefront_area); } /*}}}*/ @@ -4082,4 +4603,321 @@ xDelete(st); xDelete(s0gcm); +} +/*}}}*/ +void Element::SmbSemicTransient(){/*{{{*/ + + bool isverbose=VerboseSmb(); + if(isverbose && this->Sid()==0){ + _printf0_("smb core: initialize.\n"); + } + /*only compute SMB at the surface: */ + if (!IsOnSurface()) return; + + const int NUM_VERTICES = this->GetNumberOfVertices(); + + // daily forcing inputs + IssmDouble* dailyrainfall =xNew(NUM_VERTICES); + IssmDouble* dailysnowfall =xNew(NUM_VERTICES); + IssmDouble* dailydlradiation=xNew(NUM_VERTICES); + IssmDouble* dailydsradiation=xNew(NUM_VERTICES); + IssmDouble* dailywindspeed =xNew(NUM_VERTICES); + IssmDouble* dailypressure =xNew(NUM_VERTICES); + IssmDouble* dailyairdensity =xNew(NUM_VERTICES); + IssmDouble* dailyairhumidity=xNew(NUM_VERTICES); + IssmDouble* dailytemperature=xNew(NUM_VERTICES); + + // inputs: geometry + IssmDouble* s=xNew(NUM_VERTICES); + IssmDouble* s0gcm=xNew(NUM_VERTICES); + IssmDouble* st=xNew(NUM_VERTICES); + + // inputs + IssmDouble* tsurf_in =xNew(NUM_VERTICES); + IssmDouble* mask_in =xNew(NUM_VERTICES); + IssmDouble* Tamp_in =xNew(NUM_VERTICES); + IssmDouble* albedo_in =xNew(NUM_VERTICES); + IssmDouble* albedo_snow_in =xNew(NUM_VERTICES); + IssmDouble* hice_in =xNew(NUM_VERTICES); + IssmDouble* hsnow_in =xNew(NUM_VERTICES); + IssmDouble* qmr_in =xNew(NUM_VERTICES); + + // outputs + IssmDouble* tsurf_out =xNew(NUM_VERTICES); memset(tsurf_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* smb_out =xNew(NUM_VERTICES); memset(smb_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* smbi_out =xNew(NUM_VERTICES); memset(smb_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* smbs_out =xNew(NUM_VERTICES); memset(smb_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* saccu_out =xNew(NUM_VERTICES); memset(saccu_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* smelt_out =xNew(NUM_VERTICES); memset(smelt_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* refr_out =xNew(NUM_VERTICES); memset(refr_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* albedo_out =xNew(NUM_VERTICES); memset(albedo_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* albedo_snow_out =xNew(NUM_VERTICES); memset(albedo_snow_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* hsnow_out =xNew(NUM_VERTICES); memset(hsnow_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* hice_out =xNew(NUM_VERTICES); memset(hice_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + IssmDouble* qmr_out =xNew(NUM_VERTICES); memset(qmr_out, 0., NUM_VERTICES*sizeof(IssmDouble)); + + IssmDouble rho_water,rho_ice,desfac,desfacElev,rlaps,rdl; + IssmDouble alb_smax, alb_smin, albi, albl; + IssmDouble hcrit, rcrit; // parameters for ? and refreezing. + int alb_scheme; + // albedo parameters - slatter + IssmDouble tmin, tmax; + // albedo parameters - isba + IssmDouble mcrit, tau_a, tau_f, wcrit; + // albedo parameters - alex + IssmDouble tmid, afac; + + IssmDouble tstart, time,yts,time_yr,dt; + + /* Get time: */ + this->parameters->FindParam(&time,TimeEnum); + this->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + this->parameters->FindParam(&yts,ConstantsYtsEnum); + this->parameters->FindParam(&tstart,TimesteppingStartTimeEnum); + time_yr=floor(time/yts)*yts; + //dt = dt * yts; + + /*Get material parameters :*/ + rho_water=this->FindParam(MaterialsRhoFreshwaterEnum); + rho_ice=this->FindParam(MaterialsRhoIceEnum); + desfac=this->FindParam(SmbDesfacEnum); + desfacElev=this->FindParam(SmbDesfacElevEnum); + rlaps=this->FindParam(SmbRlapsEnum); + rdl=this->FindParam(SmbRdlEnum); + + this->FindParam(&alb_scheme,SmbAlbedoSchemeEnum); + this->FindParam(&hcrit,SmbSemicHcritEnum); + this->FindParam(&rcrit,SmbSemicRcritEnum); + alb_smax=this->FindParam(SmbAlbedoSnowMaxEnum); + alb_smin=this->FindParam(SmbAlbedoSnowMinEnum); + albi=this->FindParam(SmbAlbedoIceEnum); + albl=this->FindParam(SmbAlbedoLandEnum); + + // albedo parameters + this->FindParam(&tmid,SmbSemicTmidEnum); + this->FindParam(&tmin,SmbSemicTminEnum); + this->FindParam(&tmax,SmbSemicTmaxEnum); + this->FindParam(&mcrit,SmbSemicMcritEnum); + this->FindParam(&wcrit,SmbSemicWcritEnum); + this->FindParam(&tau_a,SmbSemicTauAEnum); + this->FindParam(&tau_f,SmbSemicTauFEnum); + this->FindParam(&afac,SmbSemicAfacEnum); + + /* Recover info at the vertices: */ + GetInputListOnVertices(&s[0],SurfaceEnum); + GetInputListOnVertices(&s0gcm[0],SmbS0gcmEnum); + + if(isverbose && this->Sid()==0){ + _printf0_("smb core: allocate inputs.\n"); + _printf0_("smb core: time_yr : " << time_yr/yts <<"\n"); + _printf0_("smb core: time : " << time <<"\n"); + _printf0_("smb core: dt : " << dt <<"\n"); + } + /* loop over vertices and days */ + Gauss* gauss=this->NewGauss(); + /* Retrieve inputs: */ + Input* dailysnowfall_input = this->GetInput(SmbDailysnowfallEnum,time); _assert_(dailysnowfall_input); + Input* dailyrainfall_input = this->GetInput(SmbDailyrainfallEnum,time); _assert_(dailyrainfall_input); + Input* dailydlradiation_input = this->GetInput(SmbDailydlradiationEnum,time); _assert_(dailydlradiation_input); + Input* dailydsradiation_input = this->GetInput(SmbDailydsradiationEnum,time); _assert_(dailydsradiation_input); + Input* dailywindspeed_input = this->GetInput(SmbDailywindspeedEnum,time); _assert_(dailywindspeed_input); + Input* dailypressure_input = this->GetInput(SmbDailypressureEnum,time); _assert_(dailypressure_input); + Input* dailyairdensity_input = this->GetInput(SmbDailyairdensityEnum,time); _assert_(dailyairdensity_input); + Input* dailyairhumidity_input = this->GetInput(SmbDailyairhumidityEnum,time); _assert_(dailyairhumidity_input); + Input* dailytemperature_input = this->GetInput(SmbDailytemperatureEnum,time); _assert_(dailytemperature_input); + + /*temporal Enum depending on time*/ + int enum_temp =TemperatureSEMICEnum; + int enum_hice =SmbHIceEnum; + int enum_hsnow =SmbHSnowEnum; + int enum_albedo =SmbAlbedoEnum; + int enum_albedo_snow=SmbAlbedoSnowEnum; + int enum_qmr =SmbSemicQmrEnum; + if (tstart+dt == time) { + /* Load inital value at first time step*/ + enum_temp=TemperatureEnum; + enum_hice=SmbHIceInitEnum; + enum_hsnow=SmbHSnowInitEnum; + enum_albedo=SmbAlbedoInitEnum; + enum_albedo_snow=SmbAlbedoSnowInitEnum; + enum_qmr =SmbSemicQmrInitEnum; + } + //if(isverbose && this->Sid()==0)_printf0_("smb core: assign temp.\n"); + Input* tsurf_input = this->GetInput(enum_temp); _assert_(tsurf_in); + //if(isverbose && this->Sid()==0)_printf0_("smb core: assign mask.\n"); + Input* mask_input = this->GetInput(SmbMaskEnum); _assert_(mask_input); + //if(isverbose && this->Sid()==0)_printf0_("smb core: assign Tamp.\n"); + Input* Tamp_input = this->GetInput(SmbTampEnum); _assert_(Tamp_input); + //if(isverbose && this->Sid()==0)_printf0_("smb core: assign albedo.\n"); + Input* albedo_input = this->GetInput(enum_albedo); _assert_(albedo_input); + Input* albedo_snow_input = this->GetInput(enum_albedo_snow); _assert_(albedo_snow_input); + Input* hice_input = this->GetInput(enum_hice); _assert_(hice_input); + Input* hsnow_input = this->GetInput(enum_hsnow); _assert_(hsnow_input); + Input* qmr_input = this->GetInput(enum_qmr); _assert_(qmr_input); + + if(isverbose && this->Sid()==0)_printf0_("smb core: assign inputs done....\n"); + for(int iv=0;ivGaussVertex(iv); + /* get forcing */ + dailyrainfall_input->GetInputValue(&dailyrainfall[iv],gauss); + dailysnowfall_input->GetInputValue(&dailysnowfall[iv],gauss); + dailydlradiation_input->GetInputValue(&dailydlradiation[iv],gauss); + dailydsradiation_input->GetInputValue(&dailydsradiation[iv],gauss); + dailywindspeed_input->GetInputValue(&dailywindspeed[iv],gauss); + dailypressure_input->GetInputValue(&dailypressure[iv],gauss); + dailyairdensity_input->GetInputValue(&dailyairdensity[iv],gauss); + dailyairhumidity_input->GetInputValue(&dailyairhumidity[iv],gauss); + dailytemperature_input->GetInputValue(&dailytemperature[iv],gauss); + tsurf_input->GetInputValue(&tsurf_in[iv],gauss); + + /* Get Albedo information */ + albedo_input->GetInputValue(&albedo_in[iv],gauss); + albedo_snow_input->GetInputValue(&albedo_snow_in[iv],gauss); + mask_input->GetInputValue(&mask_in[iv],gauss); + Tamp_input->GetInputValue(&Tamp_in[iv],gauss); + + hsnow_input->GetInputValue(&hsnow_in[iv],gauss); + hice_input->GetInputValue(&hice_in[iv],gauss); + qmr_input->GetInputValue(&qmr_in[iv],gauss); + + /* Surface temperature correction */ + st[iv]=(s[iv]-s0gcm[iv])/1000.; + dailytemperature[iv]=dailytemperature[iv]-rlaps *st[iv]; + + /* Precipitation correction (Vizcaino et al. 2010) */ + if (s0gcm[iv] < desfacElev) { + dailysnowfall[iv] = dailysnowfall[iv]*exp(desfac*(max(s[iv],desfacElev)-desfacElev)); + dailyrainfall[iv] = dailyrainfall[iv]*exp(desfac*(max(s[iv],desfacElev)-desfacElev)); + }else{ + dailysnowfall[iv] = dailysnowfall[iv]*exp(desfac*(max(s[iv],desfacElev)-s0gcm[iv])); + dailyrainfall[iv] = dailyrainfall[iv]*exp(desfac*(max(s[iv],desfacElev)-s0gcm[iv])); + } + + /* downward longwave radiation correction (Marty et al. 2002) */ + st[iv]=(s[iv]-s0gcm[iv])/1000.; + dailydlradiation[iv]=dailydlradiation[iv]+rdl*st[iv]; + } + if(isverbose && this->Sid()==0){ + _printf0_("smb core: assign tsurf_in :" << tsurf_in[0] << "\n"); + _printf0_("smb core: assign dailytemperature:" << dailytemperature[0] << "\n"); + _printf0_("smb core: assign hsnow :" << hsnow_in[0] << "\n"); + _printf0_("smb core: assign hice :" << hice_in[0] << "\n"); + _printf0_("smb core: assign mask :" << mask_in[0] << "\n"); + _printf0_("smb core: assign Tamp :" << Tamp_in[0] << "\n"); + _printf0_("smb core: assign albedo :" << albedo_in[0] << "\n"); + _printf0_("smb core: assign albedo_snow :" << albedo_snow_in[0] << "\n"); + _printf0_("smb core: assign albedo_scheme :" << alb_scheme << "\n"); + _printf0_("smb core: assign qmr :" << qmr_in[0] << "\n"); + } + + if(isverbose && this->Sid()==0)_printf0_("smb core: call run_semic_transient module.\n"); + /* call semic */ + int nx=NUM_VERTICES, ntime=1, nloop=1; + bool semic_verbose=false; //VerboseSmb(); + run_semic_transient_(&nx, &ntime, &nloop, + dailysnowfall, dailyrainfall, dailydsradiation, dailydlradiation, + dailywindspeed, dailypressure, dailyairdensity, dailyairhumidity, dailytemperature, tsurf_in, qmr_in, + &dt, + &hcrit, &rcrit, + mask_in, hice_in, hsnow_in, + albedo_in, albedo_snow_in, + &alb_scheme, &alb_smax, &alb_smin, &albi, &albl, + Tamp_in, + &tmin, &tmax, &tmid, &mcrit, &wcrit, &tau_a, &tau_f, &afac, &semic_verbose, + tsurf_out, smb_out, smbi_out, smbs_out, saccu_out, smelt_out, refr_out, albedo_out, albedo_snow_out, hsnow_out, hice_out, qmr_out); + + for (int iv = 0; iv ice + w.e. : water equivalenet. + */ + smb_out[iv] = smb_out[iv]*yts; // w.e. m/sec -> m/yr + smbi_out[iv] = smbi_out[iv]*rho_water/rho_ice; // w.e. m/sec -> ice m/yr + smbs_out[iv] = smbs_out[iv]*yts; // w.e. m/sec -> m/yr + saccu_out[iv] = saccu_out[iv]*yts; // w.e. m/sec -> m/yr + smelt_out[iv] = smelt_out[iv]*rho_water/rho_ice; // w.e. m/sec -> ice m/yr + refr_out[iv] = refr_out[iv]*rho_water/rho_ice; // w.e. m/sec -> ice m/yr + } + + if(isverbose && this->Sid()==0){ + _printf0_("smb core: tsurf_out " << tsurf_out[0] << " " << tsurf_out[1] << " " << tsurf_out[2] << "\n"); + _printf0_("smb core: hice_out " << hice_out[0] << " " << hice_out[1] << " " << hice_out[2] << "\n"); + _printf0_("smb core: hsnow_out " << hsnow_out[0] << "\n"); + _printf0_("smb core: smb_ice " << smbi_out[0]*yts << "\n"); + _printf0_("smb core: smb_ice " << albedo_out[0] <<" "<ObjectEnum()){ + case TriaEnum: + this->AddInput(TemperatureSEMICEnum, &tsurf_out[0],P1DGEnum); + // SMBout = SMB_ice + SMB_snow values. + //this->AddInput(SmbMassBalanceTotalEnum,&smb_out[0],P1DGEnum); + // water equivalent SMB ice to ice equivalent. + this->AddInput(SmbMassBalanceEnum, &smbi_out[0],P1DGEnum); + this->AddInput(SmbMassBalanceIceEnum, &smbi_out[0],P1DGEnum); + this->AddInput(SmbMassBalanceSnowEnum, &smbs_out[0],P1DGEnum); + this->AddInput(SmbMassBalanceSemicEnum,&smb_out[0],P1DGEnum); + //this->AddInput(SmbMassBalanceSnowEnum,&smbs_out[0],P1DGEnum); + // saccu - accumulation of snow. + this->AddInput(SmbAccumulationEnum,&saccu_out[0],P1DGEnum); + // smelt + this->AddInput(SmbMeltEnum, &smelt_out[0],P1DGEnum); + this->AddInput(SmbRefreezeEnum, &refr_out[0],P1DGEnum); + this->AddInput(SmbAlbedoEnum, &albedo_out[0],P1DGEnum); + this->AddInput(SmbAlbedoSnowEnum, &albedo_snow_out[0],P1DGEnum); + this->AddInput(SmbHSnowEnum, &hsnow_out[0],P1DGEnum); + this->AddInput(SmbHIceEnum, &hice_out[0],P1DGEnum); + this->AddInput(SmbSemicQmrEnum, &qmr_out[0],P1DGEnum); + break; + case PentaEnum: + // TODO + break; + case TetraEnum: + // TODO + break; + default: _error_("Not implemented yet"); + } + + /*clean-up {{{*/ + delete gauss; + xDelete(dailysnowfall); + xDelete(dailyrainfall); + xDelete(dailydlradiation); + xDelete(dailydsradiation); + xDelete(dailywindspeed); + xDelete(dailypressure); + xDelete(dailyairdensity); + xDelete(dailyairhumidity); + xDelete(dailypressure); + xDelete(dailytemperature); + + /*for outputs*/ + xDelete(tsurf_out); + xDelete(smb_out); + xDelete(smbi_out); + xDelete(smbs_out); + xDelete(saccu_out); + xDelete(smelt_out); + xDelete(refr_out); + xDelete(albedo_out); + xDelete(albedo_snow_out); + xDelete(hsnow_out); + xDelete(hice_out); + xDelete(qmr_out); + + /*for inputs*/ + xDelete(hsnow_in); + xDelete(hice_in); + xDelete(mask_in); + xDelete(Tamp_in); + xDelete(albedo_in); + xDelete(albedo_snow_in); + xDelete(tsurf_in); + xDelete(qmr_in); + + /* for inputs:geometry */ + xDelete(s); + xDelete(st); + xDelete(s0gcm); + /*}}}*/ } /*}}}*/ @@ -4626,4 +5464,32 @@ } /*}}}*/ +void Element::SubglacialWaterPressure(int output_enum){/*{{{*/ + + bool ispwHydroArma; + int M; + int numvertices = this->GetNumberOfVertices(); + IssmDouble p_water[numvertices]; + IssmDouble* perturbationvalues = xNew(numvertices); + Gauss* gauss=this->NewGauss(); + Friction* friction = new Friction(this); + /*Calculate subglacial water pressure*/ + for(int i=0;iGaussVertex(i); + p_water[i] = friction->SubglacialWaterPressure(gauss); + } + /*Add perturbation in water pressure if HydrologyIsWaterPressureArmaEnum is true*/ + this->parameters->FindParam(&ispwHydroArma,HydrologyIsWaterPressureArmaEnum); + if(ispwHydroArma){ + this->GetInputListOnVertices(perturbationvalues,WaterPressureArmaPerturbationEnum); + for(int i=0;iAddInput(output_enum,p_water,P1DGEnum); + /*Clean-up*/ + delete gauss; + delete friction; + xDelete(perturbationvalues); + +}/*}}}*/ void Element::StrainRateESA(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ @@ -4933,4 +5799,30 @@ } /*}}}*/ +IssmDouble Element::TotalSmbMelt(IssmDouble* mask, bool scaled){/*{{{*/ + + /*Retrieve values of the mask defining the element: */ + for(int i=0;iGetNumberOfVertices();i++){ + if(mask[this->vertices[i]->Sid()]<=0.){ + return 0.; + } + } + + /*Return: */ + return this->TotalSmbMelt(scaled); +} +/*}}}*/ +IssmDouble Element::TotalSmbRefreeze(IssmDouble* mask, bool scaled){/*{{{*/ + + /*Retrieve values of the mask defining the element: */ + for(int i=0;iGetNumberOfVertices();i++){ + if(mask[this->vertices[i]->Sid()]<=0.){ + return 0.; + } + } + + /*Return: */ + return this->TotalSmbRefreeze(scaled); +} +/*}}}*/ void Element::TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,int transformenum){/*{{{*/ Index: /issm/trunk/src/c/classes/Elements/Element.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Element.h (revision 28012) +++ /issm/trunk/src/c/classes/Elements/Element.h (revision 28013) @@ -140,5 +140,5 @@ void InputCreateP1FromConstant(Inputs* inputs,IoModel* iomodel,IssmDouble value,int vector_enum); void ControlInputCreate(IssmDouble* doublearray,IssmDouble* independents_min,IssmDouble* independents_max,Inputs*inputs,IoModel* iomodel,int M,int N,IssmDouble scale,int input_enum,int id); - void DatasetInputAdd(int enum_type,IssmDouble* vector,Inputs* inputs,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code,int input_enum); + void DatasetInputAdd(int enum_type,IssmDouble* vector,Inputs* inputs,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int input_enum); void InputUpdateFromConstant(IssmDouble constant, int name); void InputUpdateFromConstant(int constant, int name); @@ -155,4 +155,5 @@ bool IsOceanInElement(); bool IsOceanOnlyInElement(); + bool IsAllMinThicknessInElement(); bool IsLandInElement(); void Ismip6FloatingiceMeltingRate(); @@ -164,4 +165,5 @@ void MigrateGroundingLine(IssmDouble* sheet_ungrounding); void MismipFloatingiceMeltingRate(); + void MonthlyFactorBasin(IssmDouble* monthlyfac,int enum_type); void MonthlyPiecewiseLinearEffectBasin(int nummonthbreaks,IssmDouble* monthlyintercepts,IssmDouble* monthlytrends,IssmDouble* monthlydatebreaks,int enum_type); void BeckmannGoosseFloatingiceMeltingRate(); @@ -175,4 +177,5 @@ void PositiveDegreeDay(IssmDouble* pdds,IssmDouble* pds,IssmDouble signorm,bool ismungsm,bool issetpddfac); void PositiveDegreeDaySicopolis(bool isfirnwarming); + void SmbDebrisEvatt(); void RignotMeltParameterization(); void ResultInterpolation(int* pinterpolation,int*nodesperelement,int* parray_size, int output_enum); @@ -185,4 +188,5 @@ void SetIntInput(Inputs* inputs,int enum_in,int value); void SmbSemic(); + void SmbSemicTransient(); int Sid(); void SmbGemb(IssmDouble timeinputs, int count); @@ -195,7 +199,10 @@ void StrainRateSSA1d(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input); void StressMaxPrincipalCreateInput(void); + void SubglacialWaterPressure(int output_enum); IssmDouble TotalFloatingBmb(IssmDouble* mask, bool scaled); IssmDouble TotalGroundedBmb(IssmDouble* mask, bool scaled); IssmDouble TotalSmb(IssmDouble* mask, bool scaled); + IssmDouble TotalSmbMelt(IssmDouble* mask, bool scaled); + IssmDouble TotalSmbRefreeze(IssmDouble* mask, bool scaled); void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,int cs_enum); void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum); @@ -218,4 +225,5 @@ void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array); void TransformStiffnessMatrixCoord(ElementMatrix* Ke,int numnodes,int* transformenum_list){_error_("not implemented yet");};/*Tiling only*/ + void FrictionAlpha2CreateInput(void); void ViscousHeatingCreateInput(void); void ThermalToEnthalpy(IssmDouble * penthalpy,IssmDouble temperature,IssmDouble waterfraction,IssmDouble pressure); @@ -234,5 +242,7 @@ virtual void BasalNodeIndices(int* pnumindices,int** pindices,int finiteelement){_error_("not implemented yet");}; virtual void CalvingRateParameterization(void){_error_("not implemented yet");}; + virtual void CalvingRateCalvingMIP(void){_error_("not implemented yet");}; virtual void CalvingRateVonmises(void){_error_("not implemented yet");}; + virtual void CalvingRateVonmisesAD(void){_error_("not implemented yet");}; virtual void CalvingRateTest(void){_error_("not implemented yet");}; virtual void CalvingCrevasseDepth(void){_error_("not implemented yet");}; @@ -381,4 +391,6 @@ virtual IssmDouble TotalGroundedBmb(bool scaled)=0; virtual IssmDouble TotalSmb(bool scaled)=0; + virtual IssmDouble TotalSmbMelt(bool scaled)=0; + virtual IssmDouble TotalSmbRefreeze(bool scaled)=0; virtual void Update(Inputs* inputs,int index, IoModel* iomodel,int analysis_counter,int analysis_type,int finite_element)=0; virtual void UpdateConstraintsExtrudeFromBase(void)=0; Index: /issm/trunk/src/c/classes/Elements/Penta.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Penta.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Elements/Penta.cpp (revision 28013) @@ -177,5 +177,13 @@ } } - else _error_("not implemented yet"); + else if(interpolation_enum==P0Enum){ + Penta* penta=this; + for(;;){ + penta->AddInput(input_enum,&values[0],interpolation_enum); + if (penta->IsOnSurface()) break; + penta=penta->GetUpperPenta(); _assert_(penta->Id()!=this->id); + } + } + else _error_("Interpolation "<GetInput(VxEnum); _assert_(vx_input); - Input* vy_input=this->GetInput(VyEnum); _assert_(vy_input); - Input* vz_input=this->GetInput(VzEnum); _assert_(vz_input); + Input* vx_input=this->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input=this->GetInput(VyEnum); _assert_(vy_input); + Input* vz_input=this->GetInput(VzEnum); _assert_(vz_input); /* Start looping on the number of vertices: */ @@ -1443,103 +1451,15 @@ IssmDouble Penta::GetIcefrontArea(){/*{{{*/ - IssmDouble bed[NUMVERTICES]; //basinId[NUMVERTICES]; - IssmDouble Haverage,frontarea; - IssmDouble x1,y1,x2,y2,distance; - IssmDouble lsf[NUMVERTICES], Haux[NUMVERTICES], surfaces[NUMVERTICES], bases[NUMVERTICES]; - int* indices=NULL; - IssmDouble* H=NULL;; - int nrfrontbed,numiceverts; - + /*We need to be on base and cross the levelset*/ + if(!IsZeroLevelset(MaskIceLevelsetEnum)) return 0; if(!this->IsOnBase()) return 0; - if(!IsZeroLevelset(MaskIceLevelsetEnum)) return 0; - - /*Retrieve all inputs and parameters*/ - Element::GetInputListOnVertices(&bed[0],BedEnum); - Element::GetInputListOnVertices(&surfaces[0],SurfaceEnum); - Element::GetInputListOnVertices(&bases[0],BaseEnum); - Element::GetInputListOnVertices(&lsf[0],MaskIceLevelsetEnum); - - nrfrontbed=0; - for(int i=0;iGetLevelsetIntersectionBase(&indices, &numiceverts,&s[0],MaskIceLevelsetEnum,0.); - _assert_(numiceverts); - - /*3 Write coordinates*/ - IssmDouble xyz_list[NUMVERTICES][3]; - ::GetVerticesCoordinates(&xyz_list[0][0],this->vertices,NUMVERTICES); - int counter = 0; - if((numiceverts>0) && (numiceverts(numthk); - for(int iv=0;iv(indices); - xDelete(H); - - _assert_(frontarea>0); + + /*Spawn Tria element from the base of the Penta: */ + Tria* tria=(Tria*)SpawnTria(0,1,2); + IssmDouble frontarea = tria->GetIcefrontArea(); + delete tria->material; delete tria; + return frontarea; -} -/*}}}*/ +}/*}}}*/ void Penta::GetIcefrontCoordinates(IssmDouble** pxyz_front,IssmDouble* xyz_list,int levelsetenum){/*{{{*/ @@ -3474,4 +3394,19 @@ } /*}}}*/ +void Penta::SetElementInput(int enum_in,IssmDouble value,int type){/*{{{*/ + + if(type==P0Enum){ + this->inputs->SetPentaInput(enum_in,P0Enum,this->lid,value); + } + else if(type==P1Enum){ + IssmDouble values[6]; + for(int i=0;i<6;i++)values[i]=value; + int lidlist[6]; + this->GetVerticesLidList(&lidlist[0]); + this->inputs->SetPentaInput(enum_in,P1Enum,6,&lidlist[0],&values[0]); + } + else _error_("interpolation type not supported yet"); +} +/*}}}*/ void Penta::SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index,int offset, int M, int N){/*{{{*/ @@ -3490,7 +3425,4 @@ if(!IsOnBase()) return; } - - /*Get out if this is not an element input*/ - if(!IsInputEnum(control_enum)) return; /*Prepare index list*/ @@ -4353,4 +4285,140 @@ /*Return: */ return Total_Smb; +} +/*}}}*/ +IssmDouble Penta::TotalSmbMelt(bool scaled){/*{{{*/ + + /*The smbmelt[Gt yr-1] of one element is area[m2] * smb [ m ice yr^-1] * rho_ice [kg m-3] / 1e+10^12 */ + IssmDouble base,smbmelt,rho_ice,scalefactor; + IssmDouble Total_SmbMelt=0; + IssmDouble lsf[NUMVERTICES]; + IssmDouble xyz_list[NUMVERTICES][3]; + + /*Get material parameters :*/ + rho_ice=FindParam(MaterialsRhoIceEnum); + + if(!IsIceInElement() || !IsOnSurface()) return 0.; + + ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + + /*First calculate the area of the base (cross section triangle) + * http://en.wikipedia.org/wiki/Triangle + * base = 1/2 abs((xA-xC)(yB-yA)-(xA-xB)(yC-yA))*/ + base = 1./2. * fabs((xyz_list[0][0]-xyz_list[2][0])*(xyz_list[1][1]-xyz_list[0][1]) - (xyz_list[0][0]-xyz_list[1][0])*(xyz_list[2][1]-xyz_list[0][1])); + + /*Now get the average SMB over the element*/ + Element::GetInputListOnVertices(&lsf[0],MaskIceLevelsetEnum); + if(lsf[0]*lsf[1]<=0 || lsf[0]*lsf[2]<=0 || lsf[1]*lsf[2]<=0){ + /*Partially ice-covered element*/ + bool mainlyice; + int point; + IssmDouble* smbmelt_vertices = xNew(NUMVERTICES); + IssmDouble weights[NUMVERTICES2D]; + IssmDouble lsf2d[NUMVERTICES2D]; + IssmDouble f1,f2,phi; + Element::GetInputListOnVertices(&smbmelt_vertices[0],SmbMeltEnum); + for(int i=0;i(NUMVERTICES); + Element::GetInputListOnVertices(&scalefactor_vertices[0],MeshScaleFactorEnum); + /*Compute loop only over lower vertices: i(scalefactor_vertices); + } + else scalefactor = 1.0; + + /*Cleanup*/ + xDelete(smbmelt_vertices); + } + + else{ + /*Fully ice-covered element*/ + Input* smbmelt_input = this->GetInput(SmbMeltEnum); _assert_(smbmelt_input); + smbmelt_input->GetInputAverage(&smbmelt); + + if(scaled==true){ + Input* scalefactor_input = this->GetInput(MeshScaleFactorEnum); _assert_(scalefactor_input); + scalefactor_input->GetInputAverage(&scalefactor);// average scalefactor on element + } + else scalefactor=1.0; + } + + Total_SmbMelt=rho_ice*base*smbmelt*scalefactor;// smbmelt on element in kg s-1 + + /*Return: */ + return Total_SmbMelt; +} +/*}}}*/ +IssmDouble Penta::TotalSmbRefreeze(bool scaled){/*{{{*/ + + /*The smbrefreeze[Gt yr-1] of one element is area[m2] * smb [ m ice yr^-1] * rho_ice [kg m-3] / 1e+10^12 */ + IssmDouble base,smbrefreeze,rho_ice,scalefactor; + IssmDouble Total_SmbRefreeze=0; + IssmDouble lsf[NUMVERTICES]; + IssmDouble xyz_list[NUMVERTICES][3]; + + /*Get material parameters :*/ + rho_ice=FindParam(MaterialsRhoIceEnum); + + if(!IsIceInElement() || !IsOnSurface()) return 0.; + + ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + + /*First calculate the area of the base (cross section triangle) + * http://en.wikipedia.org/wiki/Triangle + * base = 1/2 abs((xA-xC)(yB-yA)-(xA-xB)(yC-yA))*/ + base = 1./2. * fabs((xyz_list[0][0]-xyz_list[2][0])*(xyz_list[1][1]-xyz_list[0][1]) - (xyz_list[0][0]-xyz_list[1][0])*(xyz_list[2][1]-xyz_list[0][1])); + + /*Now get the average SMB over the element*/ + Element::GetInputListOnVertices(&lsf[0],MaskIceLevelsetEnum); + if(lsf[0]*lsf[1]<=0 || lsf[0]*lsf[2]<=0 || lsf[1]*lsf[2]<=0){ + /*Partially ice-covered element*/ + bool mainlyice; + int point; + IssmDouble* smbrefreeze_vertices = xNew(NUMVERTICES); + IssmDouble weights[NUMVERTICES2D]; + IssmDouble lsf2d[NUMVERTICES2D]; + IssmDouble f1,f2,phi; + Element::GetInputListOnVertices(&smbrefreeze_vertices[0],SmbRefreezeEnum); + for(int i=0;i(NUMVERTICES); + Element::GetInputListOnVertices(&scalefactor_vertices[0],MeshScaleFactorEnum); + /*Compute loop only over lower vertices: i(scalefactor_vertices); + } + else scalefactor = 1.0; + + /*Cleanup*/ + xDelete(smbrefreeze_vertices); + } + + else{ + /*Fully ice-covered element*/ + Input* smbrefreeze_input = this->GetInput(SmbRefreezeEnum); _assert_(smbrefreeze_input); + smbrefreeze_input->GetInputAverage(&smbrefreeze); + + if(scaled==true){ + Input* scalefactor_input = this->GetInput(MeshScaleFactorEnum); _assert_(scalefactor_input); + scalefactor_input->GetInputAverage(&scalefactor);// average scalefactor on element + } + else scalefactor=1.0; + } + + Total_SmbRefreeze=rho_ice*base*smbrefreeze*scalefactor;// smbrefreeze on element in kg s-1 + + /*Return: */ + return Total_SmbRefreeze; } /*}}}*/ Index: /issm/trunk/src/c/classes/Elements/Penta.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Penta.h (revision 28012) +++ /issm/trunk/src/c/classes/Elements/Penta.h (revision 28013) @@ -64,4 +64,5 @@ void ComputeSigmaNN(){_error_("not implemented yet");}; void ComputeStressTensor(); + //void ComputeMeanEla(IssmDouble* paltitude, int* pcounter); void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters,Inputs* inputsin); void ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index,int offset,int M,int N,int interp); @@ -175,5 +176,5 @@ void ResetHooks(); void SetElementInput(int enum_in,IssmDouble value); - void SetElementInput(int enum_in,IssmDouble value,int type){_error_("not implemented yet");}; + void SetElementInput(int enum_in,IssmDouble value,int type); void SetElementInput(Inputs* inputs,int enum_in,IssmDouble value); void SetElementInput(Inputs* inputs,int enum_in,IssmDouble value,int type){_error_("not implemented yet");}; @@ -200,4 +201,6 @@ IssmDouble TotalGroundedBmb(bool scaled); IssmDouble TotalSmb(bool scaled); + IssmDouble TotalSmbMelt(bool scaled); + IssmDouble TotalSmbRefreeze(bool scaled); void Update(Inputs* inputs,int index, IoModel* iomodel,int analysis_counter,int analysis_type,int finitelement); void UpdateConstraintsExtrudeFromBase(void); Index: /issm/trunk/src/c/classes/Elements/PentaRef.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/PentaRef.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Elements/PentaRef.cpp (revision 28013) @@ -307,4 +307,5 @@ basis[6]=27.*gauss->coord1*gauss->coord2*gauss->coord3*(1.+zeta)*(1.-zeta); return; + #ifndef _HAVE_AD_ case P2xP1Enum: /*Corner nodes*/ @@ -459,4 +460,5 @@ basis[14]=gauss->coord3*(-8./3.)*(zeta-1.0)*zeta*(zeta+0.5)*(zeta+1.); return; + #endif default: _error_("Element type "<coord1*gauss->coord2*gauss->coord3*zeta; return; + #ifndef _HAVE_AD_ case P2xP1Enum: /*Nodal function 1*/ @@ -1057,4 +1060,5 @@ return; + #endif default: _error_("Element type "<GetInputValue(&sigma_max_floating,&gauss); smax_gr_input->GetInputValue(&sigma_max_grounded,&gauss); + sl_input->GetInputValue(&sealevel,&gauss); + + /*Tensile stress threshold*/ + if(groundedice<0) + sigma_max = sigma_max_floating; + else + sigma_max = sigma_max_grounded; + + /*Assign values*/ + if(bed>sealevel){ + calvingrate[iv] = 0.; + } + else{ + calvingrate[iv] = sqrt(vx*vx+vy*vy)*sigma_vm/sigma_max; + } + } + + /*Add input*/ + this->AddInput(CalvingCalvingrateEnum,&calvingrate[0],P1DGEnum); + this->CalvingRateToVector(); +} +/*}}}*/ +void Tria::CalvingRateVonmisesAD(){/*{{{*/ + + /*First, compute Von Mises Stress*/ + this->ComputeSigmaVM(); + + /*Now compute calving rate*/ + IssmDouble calvingrate[NUMVERTICES]; + IssmDouble sigma_vm,vx,vy; + IssmDouble sigma_max,sigma_max_floating,sigma_max_grounded,n; + IssmDouble groundedice,bed,sealevel; + int M; + int basinid; + IssmDouble* sigma_max_floating_basin=NULL; + IssmDouble* sigma_max_grounded_basin=NULL; + + /*Retrieve all inputs and parameters we will need*/ + Input* vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input* gr_input = this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); + Input* bs_input = this->GetInput(BaseEnum); _assert_(bs_input); + Input* sl_input = this->GetInput(SealevelEnum); _assert_(sl_input); + Input* sigma_vm_input = this->GetInput(SigmaVMEnum); _assert_(sigma_vm_input); + + this->Element::GetInputValue(&basinid,CalvingBasinIdEnum); + + parameters->FindParam(&sigma_max_floating_basin,&M,CalvingADStressThresholdFloatingiceEnum); + parameters->FindParam(&sigma_max_grounded_basin,&M,CalvingADStressThresholdGroundediceEnum); + + sigma_max_floating = sigma_max_floating_basin[basinid]; + sigma_max_grounded = sigma_max_grounded_basin[basinid]; + + /* Start looping on the number of vertices: */ + GaussTria gauss; + for(int iv=0;ivGetInputValue(&sigma_vm,&gauss); + vx_input->GetInputValue(&vx,&gauss); + vy_input->GetInputValue(&vy,&gauss); + gr_input->GetInputValue(&groundedice,&gauss); + bs_input->GetInputValue(&bed,&gauss); sl_input->GetInputValue(&sealevel,&gauss); @@ -1054,4 +1118,84 @@ /*Clean up and return*/ delete gauss; +} +/*}}}*/ +void Tria::CalvingRateCalvingMIP(){/*{{{*/ + + IssmDouble calvingrate[NUMVERTICES]; + IssmDouble calvingratex[NUMVERTICES]; + IssmDouble calvingratey[NUMVERTICES]; + int experiment = 1; /* exp:1 by default */ + int dim, domaintype; + IssmDouble vx, vy, vel, c, wrate; + IssmDouble time, groundedice, yts; + + /*Get problem dimension and whether there is moving front or not*/ + this->FindParam(&domaintype,DomainTypeEnum); + this->FindParam(&time,TimeEnum); + this->FindParam(&yts,ConstantsYtsEnum); + + switch(domaintype){ + case Domain2DverticalEnum: dim = 1; break; + case Domain2DhorizontalEnum: dim = 2; break; + case Domain3DEnum: dim = 2; break; + default: _error_("mesh "<GetInput(VxEnum); _assert_(vx_input); + Input *vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input *wrate_input = this->GetInput(CalvingAblationrateEnum); _assert_(wrate_input); + Input* gr_input = this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); + + /* Use which experiment: use existing Enum */ + this->FindParam(&experiment, CalvingUseParamEnum); + + /* Start looping on the number of vertices: */ + GaussTria gauss; + for(int iv=0;ivGetInputValue(&vx,&gauss); + vy_input->GetInputValue(&vy,&gauss); + vel=sqrt(vx*vx+vy*vy)+1.e-14; + + /* no calving for grounded ice in EXP4 */ + gr_input->GetInputValue(&groundedice,&gauss); + + switch (experiment) { + case 1: + case 3: + /* Exp 1 and 3: set c=v-wrate, wrate=0, so that w=0 */ + wrate = 0.0; + break; + case 2: + /* Exp 2: set c=v-wrate(given)*/ + wrate_input->GetInputValue(&wrate,&gauss); + break; + case 4: + /* Exp 4: set c=v-wrate(given), for the first 500 years, then c=0 for the second 500 years*/ + if((groundedice<0) && (time<=500.0*yts)) { + // wrate_input->GetInputValue(&wrate,&gauss); + wrate = -750*sin(2.0*M_PI*time/yts/1000)/yts; // m/a -> m/s + } + else { + /* no calving on the grounded ice*/ + wrate = vel; + } + break; + default: + _error_("The experiment is not supported yet!"); + } + + calvingrate[iv] = vel - wrate; + calvingratex[iv] = vx - wrate*vx/vel; + calvingratey[iv] = vy - wrate*vy/vel; + } + /*Add input*/ + this->AddInput(CalvingCalvingrateEnum,&calvingrate[0],P1DGEnum); + this->AddInput(CalvingratexEnum,&calvingratex[0],P1DGEnum); + this->AddInput(CalvingrateyEnum,&calvingratey[0],P1DGEnum); } /*}}}*/ @@ -2628,13 +2772,13 @@ IssmDouble Tria::GetIcefrontArea(){/*{{{*/ - IssmDouble bed[NUMVERTICES]; //basinId[NUMVERTICES]; + IssmDouble bed[NUMVERTICES]; IssmDouble Haverage,frontarea; IssmDouble x1,y1,x2,y2,distance; IssmDouble lsf[NUMVERTICES], Haux[NUMVERTICES], surfaces[NUMVERTICES], bases[NUMVERTICES]; int* indices=NULL; - IssmDouble* H=NULL;; - int nrfrontbed,numiceverts; - + + /*Return if no ice front present*/ if(!IsZeroLevelset(MaskIceLevelsetEnum)) return 0; + //if(!this->IsIcefront()) return 0.; /*Retrieve all inputs and parameters*/ @@ -2644,81 +2788,87 @@ Element::GetInputListOnVertices(&lsf[0],MaskIceLevelsetEnum); - nrfrontbed=0; - for(int i=0;iGetLevelsetIntersection(&indices, &numiceverts,&s[0],MaskIceLevelsetEnum,0.); - _assert_(numiceverts); - - /*3 Write coordinates*/ - IssmDouble xyz_list[NUMVERTICES][3]; - ::GetVerticesCoordinates(&xyz_list[0][0],this->vertices,NUMVERTICES); - int counter = 0; - if((numiceverts>0) && (numiceverts=0.) return 0.; + + /*2. Find coordinates of where levelset crosses 0*/ + int numiceverts; + IssmDouble s[2],x[2],y[2]; + this->GetLevelsetIntersection(&indices, &numiceverts, &s[0],MaskIceLevelsetEnum,0.); + _assert_(numiceverts); + if(numiceverts>2){ + Input* ls_input = this->GetInput(MaskIceLevelsetEnum); + ls_input->Echo(); + } + + /*3 Write coordinates*/ + IssmDouble xyz_list[NUMVERTICES][3]; + ::GetVerticesCoordinates(&xyz_list[0][0],this->vertices,NUMVERTICES); + int counter = 0; + if((numiceverts>0) && (numiceverts(indices); + + switch(numiceverts){ + case 1: // average over triangle + H[0]=Haux[0]; + H[1]=Haux[0]+s[0]*(Haux[1]-Haux[0]); + H[2]=Haux[0]+s[1]*(Haux[2]-Haux[0]); + Haverage=(H[1]+H[2])/2; + break; + case 2: // average over quadrangle + H[0]=Haux[0]; + H[1]=Haux[1]; + H[2]=Haux[0]+s[0]*(Haux[2]-Haux[0]); + H[3]=Haux[1]+s[1]*(Haux[2]-Haux[1]); + Haverage=(H[2]+H[3])/2; + break; + case 3: + if(counter==1) distance = 0; //front has 0 width on this element because levelset is 0 at a single vertex + else if(counter==2){ //two vertices with levelset=0: averaging ice front depth over both + Haverage = 0; + for(int i=0;i(numthk); - for(int iv=0;iv(indices); - xDelete(H); + break; + default: + _error_("Number of ice covered vertices wrong in Tria::GetIceFrontArea(void)"); + break; + } + frontarea=distance*Haverage; _assert_(frontarea>0); @@ -4414,8 +4564,10 @@ case DefaultCalvingEnum: case CalvingVonmisesEnum: + case CalvingVonmisesADEnum: case CalvingLevermannEnum: case CalvingPollardEnum: case CalvingTestEnum: case CalvingParameterizationEnum: + case CalvingCalvingMIPEnum: calvingratex_input=this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); calvingratey_input=this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); @@ -4458,8 +4610,10 @@ case DefaultCalvingEnum: case CalvingVonmisesEnum: + case CalvingVonmisesADEnum: case CalvingTestEnum: case CalvingParameterizationEnum: case CalvingLevermannEnum: case CalvingPollardEnum: + case CalvingCalvingMIPEnum: calvingratex_input->GetInputValue(&c[0],&gauss); calvingratey_input->GetInputValue(&c[1],&gauss); @@ -4575,6 +4729,11 @@ /*Do we assume that the calving front does not move if MICI is not engaged?*/ - movingfrontvx[iv] = 0.; - movingfrontvy[iv] = 0.; + bool regrowth = false; + bool apply_as_retreat = true; + if(!regrowth){ + movingfrontvx[iv] = 0.; + movingfrontvy[iv] = 0.; + } + //movingfrontvx[iv] = -2000./(365*24*3600.)*dlsf[0]/norm_dlsf; //movingfrontvy[iv] = -2000./(365*24*3600.)*dlsf[1]/norm_dlsf; @@ -4588,4 +4747,8 @@ } else if (MICI==2 && Hc>135. && bed<0. && fabs(ls)<100.e3){ // Crawford et all + + /*if 1: RETREAT rate + *if 0: calving rate*/ + if(0) v[0]=0.; v[1]=0.; /*5C Bn (worst case scenario)*/ @@ -4597,4 +4760,10 @@ movingfrontvx[iv] = v[0] -C*dlsf[0]/norm_dlsf; movingfrontvy[iv] = v[1] -C*dlsf[1]/norm_dlsf; + + /*disable regrowth if calving rate is too low*/ + if(!regrowth && C(NUMVERTICES); + IssmDouble* smbmelt_vertices = xNew(NUMVERTICES); + IssmDouble f1,f2,phi; + + Element::GetInputListOnVertices(&smbmelt_vertices[0],SmbMeltEnum); + GetFractionGeometry(weights,&phi,&point,&f1,&f2,&mainlyice,lsf); + smbmelt = 0.0; + for(int i=0;i(NUMVERTICES); + Element::GetInputListOnVertices(&scalefactor_vertices[0],MeshScaleFactorEnum); + scalefactor = 0.0; + for(int i=0;i(scalefactor_vertices); + } + else scalefactor = 1.0; + + /*Cleanup*/ + xDelete(weights); + xDelete(smbmelt_vertices); + } + else{ + /*Fully ice-covered element*/ + Input* smbmelt_input = this->GetInput(SmbMeltEnum); _assert_(smbmelt_input); + smbmelt_input->GetInputAverage(&smbmelt); // average smbmelt on element in m ice s-1 + + if(scaled==true){ + Input* scalefactor_input = this->GetInput(MeshScaleFactorEnum); _assert_(scalefactor_input); + scalefactor_input->GetInputAverage(&scalefactor);// average scalefactor on element + } + else scalefactor=1.0; + } + + Total_Melt=rho_ice*base*smbmelt*scalefactor; // smbmelt on element in kg s-1 + + /*Return: */ + return Total_Melt; +} +/*}}}*/ +IssmDouble Tria::TotalSmbRefreeze(bool scaled){/*{{{*/ + + /*The smb[kg yr-1] of one element is area[m2] * smb [kg m^-2 yr^-1]*/ + IssmDouble base,smbrefreeze,rho_ice,scalefactor; + IssmDouble Total_Refreeze=0; + IssmDouble lsf[NUMVERTICES]; + IssmDouble xyz_list[NUMVERTICES][3]; + + /*Get material parameters :*/ + rho_ice=FindParam(MaterialsRhoIceEnum); + + if(!IsIceInElement())return 0; + + ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + + /*First calculate the area of the base (cross section triangle) + * http://en.wikipedia.org/wiki/Triangle + * base = 1/2 abs((xA-xC)(yB-yA)-(xA-xB)(yC-yA))*/ + base = 1./2. * fabs((xyz_list[0][0]-xyz_list[2][0])*(xyz_list[1][1]-xyz_list[0][1]) - (xyz_list[0][0]-xyz_list[1][0])*(xyz_list[2][1]-xyz_list[0][1])); // area of element in m2 + + /*Now get the average SMB over the element*/ + Element::GetInputListOnVertices(&lsf[0],MaskIceLevelsetEnum); + if(lsf[0]*lsf[1]<=0 || lsf[0]*lsf[2]<=0 || lsf[1]*lsf[2]<=0){ + /*Partially ice-covered element*/ + bool mainlyice; + int point; + IssmDouble* weights = xNew(NUMVERTICES); + IssmDouble* smbrefreeze_vertices = xNew(NUMVERTICES); + IssmDouble f1,f2,phi; + + Element::GetInputListOnVertices(&smbrefreeze_vertices[0],SmbRefreezeEnum); + GetFractionGeometry(weights,&phi,&point,&f1,&f2,&mainlyice,lsf); + smbrefreeze = 0.0; + for(int i=0;i(NUMVERTICES); + Element::GetInputListOnVertices(&scalefactor_vertices[0],MeshScaleFactorEnum); + scalefactor = 0.0; + for(int i=0;i(scalefactor_vertices); + } + else scalefactor = 1.0; + + /*Cleanup*/ + xDelete(weights); + xDelete(smbrefreeze_vertices); + } + else{ + /*Fully ice-covered element*/ + Input* smbrefreeze_input = this->GetInput(SmbRefreezeEnum); _assert_(smbrefreeze_input); + smbrefreeze_input->GetInputAverage(&smbrefreeze); // average smbrefreeze on element in m ice s-1 + + if(scaled==true){ + Input* scalefactor_input = this->GetInput(MeshScaleFactorEnum); _assert_(scalefactor_input); + scalefactor_input->GetInputAverage(&scalefactor);// average scalefactor on element + } + else scalefactor=1.0; + } + + Total_Refreeze=rho_ice*base*smbrefreeze*scalefactor; // smbrefreeze on element in kg s-1 + + /*Return: */ + return Total_Refreeze; } /*}}}*/ @@ -7215,5 +7513,5 @@ barycontrib->Set(this->Sid(),bslcice,bslchydro,bslcbp); - /*Free ressources*/ + /*Free resources*/ xDelete(areae); @@ -7590,5 +7888,5 @@ b=i*nt; c=av*nel; - for (int ae=0;aenactiveloads;ae++){ + for(ae=0;aenactiveloads;ae++){ e=loads->combined_loads_index[ae]; a=AlphaIndex[c+e]*viscousnumsteps; @@ -7695,5 +7993,5 @@ //get projection if (spatial_component==1){ //north - for (int ae=0;aenactiveloads;ae++){ + for(ae=0;aenactiveloads;ae++){ e=loads->combined_loads_index[ae]; horiz_projection[ae]=cos(2.0*M_PI*reCast(AzimIndex[av*nel+e])/65535.0); // 65535=2^16-1 = max value of 16 bits unsigned int @@ -7701,5 +7999,5 @@ for(l=0;lnbar[l]; - for (ae=0;aenactivesubloads[l];ae++){ + for(ae=0;aenactivesubloads[l];ae++){ e=loads->combined_subloads_index[l][ae]; horiz_projectionsub[l][ae]=cos(2.0*M_PI*reCast(AzimIndexsub[l][av*nbar+e])/65535.0); @@ -7708,5 +8006,5 @@ } else if (spatial_component==2){ //east - for (int ae=0;aenactiveloads;ae++){ + for(ae=0;aenactiveloads;ae++){ e=loads->combined_loads_index[ae]; horiz_projection[ae]=sin(2.0*M_PI*reCast(AzimIndex[av*nel+e])/65535.0); @@ -7714,5 +8012,5 @@ for(l=0;lnbar[l]; - for (ae=0;aenactivesubloads[l];ae++){ + for(ae=0;aenactivesubloads[l];ae++){ e=loads->combined_subloads_index[l][ae]; horiz_projectionsub[l][ae]=sin(2.0*M_PI*reCast(AzimIndexsub[l][av*nbar+e])/65535.0); @@ -7722,10 +8020,10 @@ //project load in the right direction - for (int ae=0;aenactiveloads;ae++){ + for (ae=0;aenactiveloads;ae++){ projected_loads[ae]=loads->combined_loads[ae]*horiz_projection[ae]; } for(l=0;lnbar[l]; - for (ae=0;aenactivesubloads[l];ae++){ + for(ae=0;aenactivesubloads[l];ae++){ projected_subloads[l][ae]=loads->combined_subloads[l][ae]*horiz_projectionsub[l][ae]; } @@ -7734,5 +8032,5 @@ //do the convolution c=av*nel; - for (int ae=0;aenactiveloads;ae++){ + for(ae=0;aenactiveloads;ae++){ e=loads->combined_loads_index[ae]; a=AlphaIndex[c+e]*viscousnumsteps; @@ -7744,5 +8042,5 @@ nbar=slgeom->nbar[l]; c=av*nbar; - for (ae=0;aenactivesubloads[l];ae++){ + for(ae=0;aenactivesubloads[l];ae++){ e=loads->combined_subloads_index[l][ae]; a=AlphaIndexsub[l][c+e]*viscousnumsteps; @@ -7757,5 +8055,4 @@ //free resources - xDelete(horiz_projection); xDelete(projected_loads); Index: /issm/trunk/src/c/classes/Elements/Tria.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Tria.h (revision 28012) +++ /issm/trunk/src/c/classes/Elements/Tria.h (revision 28013) @@ -55,4 +55,5 @@ void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part); void CalvingRateVonmises(); + void CalvingRateVonmisesAD(); void CalvingRateTest(); void CalvingCrevasseDepth(); @@ -62,4 +63,5 @@ void CalvingMeltingFluxLevelset(); void CalvingRateParameterization(); + void CalvingRateCalvingMIP(); IssmDouble CharacteristicLength(void); void ComputeBasalStress(void); @@ -156,4 +158,6 @@ IssmDouble TotalGroundedBmb(bool scaled); IssmDouble TotalSmb(bool scaled); + IssmDouble TotalSmbMelt(bool scaled); + IssmDouble TotalSmbRefreeze(bool scaled); void Update(Inputs* inputs,int index, IoModel* iomodel,int analysis_counter,int analysis_type,int finitelement); int UpdatePotentialUngrounding(IssmDouble* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,IssmDouble* nodes_on_iceshelf); Index: /issm/trunk/src/c/classes/FemModel.cpp =================================================================== --- /issm/trunk/src/c/classes/FemModel.cpp (revision 28012) +++ /issm/trunk/src/c/classes/FemModel.cpp (revision 28013) @@ -347,4 +347,7 @@ #endif + /*Cleanup toolkit*/ + ToolkitOptions::Delete(); + /*Clean up*/ xDelete(lockfilename); @@ -793,4 +796,7 @@ analyses_temp[numanalyses++]=L2ProjectionEPLAnalysisEnum; analyses_temp[numanalyses++]=L2ProjectionBaseAnalysisEnum; + } + if(hydrology_model==HydrologyarmapwEnum){ + analyses_temp[numanalyses++]=HydrologyArmapwAnalysisEnum; } } @@ -915,4 +921,7 @@ } if(isdebris){ + analyses_temp[numanalyses++]=L2ProjectionBaseAnalysisEnum; + analyses_temp[numanalyses++]=SmbAnalysisEnum; + analyses_temp[numanalyses++]=ExtrudeFromTopAnalysisEnum; analyses_temp[numanalyses++]=DebrisAnalysisEnum; } @@ -1445,19 +1454,20 @@ /*Now send and receive vector for vertices on partition edge*/ - #ifdef _HAVE_AD_ - IssmDouble* buffer = xNew(this->vertices->Size(),"t"); //only one alloc, "t" is required by adolc - #else - IssmDouble* buffer = xNew(this->vertices->Size()); - #endif + IssmDouble **send_buffers = xNewZeroInit(num_procs); + IssmDouble *recv_buffer = xNewZeroInit(this->vertices->Size()); + ISSM_MPI_Request *send_requests = xNew(num_procs); + for (int rank = 0;rankvertices->common_send[rank]){ int numids = this->vertices->common_send[rank]; + send_buffers[rank] = xNew(numids,"t"); //only one alloc, "t" is required by adolc for(int i=0;ivertices->common_send_ids[rank][i]; Vertex* vertex=xDynamicCast(this->vertices->GetObjectByOffset(master_lid)); _assert_(!vertex->clone); - buffer[i] = local_vector[vertex->lid]; - } - ISSM_MPI_Send(buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm()); + send_buffers[rank][i] = local_vector[vertex->lid]; + } + ISSM_MPI_Isend(send_buffers[rank],numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&send_requests[rank]); } } @@ -1465,14 +1475,20 @@ if(this->vertices->common_recv[rank]){ int numids = this->vertices->common_recv[rank]; - ISSM_MPI_Recv(buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); + ISSM_MPI_Recv(recv_buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); for(int i=0;ivertices->common_recv_ids[rank][i]; Vertex* vertex=xDynamicCast(this->vertices->GetObjectByOffset(master_lid)); _assert_(vertex->clone); - local_vector[vertex->lid] = buffer[i]; - } - } - } - xDelete(buffer); + local_vector[vertex->lid] = recv_buffer[i]; + } + } + } + xDelete(recv_buffer); + for(int rank=0;rankvertices->common_send[rank]) ISSM_MPI_Wait(&send_requests[rank],&status); + xDelete(send_buffers[rank]); + } + xDelete(send_buffers); + xDelete(send_requests); }/*}}}*/ void FemModel::SyncLocalVectorWithClonesVerticesAdd(IssmDouble* local_vector){/*{{{*/ @@ -1484,9 +1500,8 @@ /*Now send and receive vector for vertices on partition edge*/ - #ifdef _HAVE_AD_ - IssmDouble* buffer = xNew(this->vertices->Size(),"t"); //only one alloc, "t" is required by adolc - #else - IssmDouble* buffer = xNew(this->vertices->Size()); - #endif + IssmDouble **send_buffers = xNewZeroInit(num_procs); + IssmDouble *recv_buffer = xNewZeroInit(this->vertices->Size()); + ISSM_MPI_Request *send_requests = xNew(num_procs); + for (int rank = 0;rankvertices->common_recv[rank]){ int numids = this->vertices->common_recv[rank]; + send_buffers[rank] = xNew(numids,"t"); //only one alloc, "t" is required by adolc for(int i=0;ivertices->common_recv_ids[rank][i]; Vertex* vertex=xDynamicCast(this->vertices->GetObjectByOffset(master_lid)); _assert_(vertex->clone); - buffer[i] = local_vector[vertex->lid]; - } - ISSM_MPI_Send(buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm()); + send_buffers[rank][i] = local_vector[vertex->lid]; + } + ISSM_MPI_Isend(send_buffers[rank],numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&send_requests[rank]); } } @@ -1506,12 +1522,17 @@ if(this->vertices->common_send[rank]){ int numids = this->vertices->common_send[rank]; - ISSM_MPI_Recv(buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); + ISSM_MPI_Recv(recv_buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); for(int i=0;ivertices->common_send_ids[rank][i]; Vertex* vertex=xDynamicCast(this->vertices->GetObjectByOffset(master_lid)); _assert_(!vertex->clone); - local_vector[vertex->lid] += buffer[i]; - } - } + local_vector[vertex->lid] += recv_buffer[i]; + } + } + } + + /*Wait until MPI is done*/ + for(int rank=0;rankvertices->common_send[rank]) ISSM_MPI_Wait(&send_requests[rank],&status); } @@ -1520,11 +1541,13 @@ if(this->vertices->common_send[rank]){ int numids = this->vertices->common_send[rank]; + xDelete(send_buffers[rank]); + send_buffers[rank] = xNew(numids,"t"); //only one alloc, "t" is required by adolc for(int i=0;ivertices->common_send_ids[rank][i]; Vertex* vertex=xDynamicCast(this->vertices->GetObjectByOffset(master_lid)); _assert_(!vertex->clone); - buffer[i] = local_vector[vertex->lid]; - } - ISSM_MPI_Send(buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm()); + send_buffers[rank][i] = local_vector[vertex->lid]; + } + ISSM_MPI_Isend(send_buffers[rank],numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&send_requests[rank]); } } @@ -1532,14 +1555,21 @@ if(this->vertices->common_recv[rank]){ int numids = this->vertices->common_recv[rank]; - ISSM_MPI_Recv(buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); + ISSM_MPI_Recv(recv_buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); + for(int i=0;ivertices->common_recv_ids[rank][i]; Vertex* vertex=xDynamicCast(this->vertices->GetObjectByOffset(master_lid)); _assert_(vertex->clone); - local_vector[vertex->lid] = buffer[i]; - } - } - } - xDelete(buffer); + local_vector[vertex->lid] = recv_buffer[i]; + } + } + } + xDelete(recv_buffer); + for(int rank=0;rankvertices->common_send[rank]) ISSM_MPI_Wait(&send_requests[rank],&status); + xDelete(send_buffers[rank]); + } + xDelete(send_buffers); + xDelete(send_requests); }/*}}}*/ void FemModel::GetLocalVectorWithClonesNodes(IssmDouble** plocal_vector,Vector *vector){/*{{{*/ @@ -1567,19 +1597,20 @@ /*Now send and receive vector for nodes on partition edge*/ - #ifdef _HAVE_AD_ - IssmDouble* buffer = xNew(this->nodes->Size(),"t"); //only one alloc, "t" is required by adolc - #else - IssmDouble* buffer = xNew(this->nodes->Size()); - #endif + IssmDouble **send_buffers = xNewZeroInit(num_procs); + IssmDouble *recv_buffer = xNewZeroInit(this->nodes->Size(),"t"); //only one alloc, "t" is required by adolc + ISSM_MPI_Request *send_requests = xNew(num_procs); + for (int rank = 0;ranknodes->common_send[rank]){ int numids = this->nodes->common_send[rank]; + send_buffers[rank] = xNew(numids,"t"); //only one alloc, "t" is required by adolc for(int i=0;inodes->common_send_ids[rank][i]; Node* vertex=xDynamicCast(this->nodes->GetObjectByOffset(master_lid)); _assert_(!vertex->clone); - buffer[i] = local_vector[vertex->lid]; - } - ISSM_MPI_Send(buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm()); + send_buffers[rank][i] = local_vector[vertex->lid]; + } + ISSM_MPI_Isend(send_buffers[rank],numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&send_requests[rank]); } } @@ -1587,14 +1618,21 @@ if(this->nodes->common_recv[rank]){ int numids = this->nodes->common_recv[rank]; - ISSM_MPI_Recv(buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); + ISSM_MPI_Recv(recv_buffer,numids,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); for(int i=0;inodes->common_recv_ids[rank][i]; Node* vertex=xDynamicCast(this->nodes->GetObjectByOffset(master_lid)); _assert_(vertex->clone); - local_vector[vertex->lid] = buffer[i]; - } - } - } - xDelete(buffer); + local_vector[vertex->lid] = recv_buffer[i]; + } + } + } + + xDelete(recv_buffer); + for(int rank=0;ranknodes->common_send[rank]) ISSM_MPI_Wait(&send_requests[rank],&status); + xDelete(send_buffers[rank]); + } + xDelete(send_buffers); + xDelete(send_requests); /*Assign output pointer*/ @@ -1638,5 +1676,5 @@ basin_icefront_area[basin]=total_icefront_area; } - + this->parameters->AddObject(new DoubleVecParam(FrontalForcingsBasinIcefrontAreaEnum,basin_icefront_area,numbasins)); @@ -2297,21 +2335,16 @@ void FemModel::RequestedDependentsx(void){/*{{{*/ - bool isautodiff = false; - IssmDouble output_value; - - int num_dependents; - IssmPDouble *dependents; - DataSet* dependent_objects=NULL; - int my_rank=IssmComm::GetRank(); - /*AD mode on?: */ + bool isautodiff; parameters->FindParam(&isautodiff,AutodiffIsautodiffEnum); if(isautodiff){ #ifdef _HAVE_AD_ + int num_dependents; + DataSet* dependent_objects=NULL; parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); parameters->FindParam(&dependent_objects,AutodiffDependentObjectsEnum); if(num_dependents){ - dependents=xNew(num_dependents); + IssmPDouble* dependents=xNew(num_dependents); #if defined(_HAVE_CODIPACK_) @@ -2326,8 +2359,10 @@ /*Go through our dependent variables, and compute the response:*/ + int my_rank=IssmComm::GetRank(); int i = 0; for(Object* & object : dependent_objects->objects){ DependentObject* dep=(DependentObject*)object; - dep->Responsex(&output_value,this); + dep->RecordResponsex(this); + IssmDouble output_value = dep->GetValue(); if (my_rank==0) { #if defined(_HAVE_CODIPACK_) @@ -2347,7 +2382,7 @@ i++; } + xDelete(dependents); } delete dependent_objects; - if(num_dependents)xDelete(dependents); #else _error_("Should not be requesting dependents when an AD library is not available!"); @@ -2437,4 +2472,6 @@ case TotalGroundedBmbScaledEnum: this->TotalGroundedBmbx(&double_result,true); break; case TotalSmbEnum: this->TotalSmbx(&double_result,false); break; + case TotalSmbMeltEnum: this->TotalSmbMeltx(&double_result,false); break; + case TotalSmbRefreezeEnum: this->TotalSmbRefreezex(&double_result,false); break; case TotalSmbScaledEnum: this->TotalSmbx(&double_result,true); break; @@ -2509,4 +2546,11 @@ InputDuplicatex(this,DamageDbarEnum,DamageDbarOldEnum); this->ElementOperationx(&Element::ComputeNewDamage); + } + else if(output_enum==FrictionAlpha2Enum){ + for(Object* & object : this->elements->objects){ + Element* element=xDynamicCast(object); + element->SetElementInput(FrictionAlpha2Enum,0.,P1Enum); + } + this->ElementOperationx(&Element::FrictionAlpha2CreateInput); } @@ -2702,4 +2746,6 @@ case TotalGroundedBmbScaledEnum: this->TotalGroundedBmbx(responses, true); break; case TotalSmbEnum: this->TotalSmbx(responses, false); break; + case TotalSmbMeltEnum: this->TotalSmbMeltx(responses, false); break; + case TotalSmbRefreezeEnum: this->TotalSmbRefreezex(responses, false); break; case TotalSmbScaledEnum: this->TotalSmbx(responses, true); break; case MaterialsRheologyBbarEnum: this->ElementResponsex(responses,MaterialsRheologyBbarEnum); break; @@ -3092,4 +3138,36 @@ /*Assign output pointers: */ *pSmb=total_smb; + +}/*}}}*/ +void FemModel::TotalSmbMeltx(IssmDouble* pSmbMelt, bool scaled){/*{{{*/ + + IssmDouble local_smbmelt = 0; + IssmDouble total_smbmelt; + + for(Object* & object : this->elements->objects){ + Element* element = xDynamicCast(object); + local_smbmelt+=element->TotalSmbMelt(scaled); + } + ISSM_MPI_Reduce(&local_smbmelt,&total_smbmelt,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); + ISSM_MPI_Bcast(&total_smbmelt,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + + /*Assign output pointers: */ + *pSmbMelt=total_smbmelt; + +}/*}}}*/ +void FemModel::TotalSmbRefreezex(IssmDouble* pSmbRefreeze, bool scaled){/*{{{*/ + + IssmDouble local_smbrefreeze = 0; + IssmDouble total_smbrefreeze; + + for(Object* & object : this->elements->objects){ + Element* element = xDynamicCast(object); + local_smbrefreeze+=element->TotalSmbRefreeze(scaled); + } + ISSM_MPI_Reduce(&local_smbrefreeze,&total_smbrefreeze,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); + ISSM_MPI_Bcast(&total_smbrefreeze,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + + /*Assign output pointers: */ + *pSmbRefreeze=total_smbrefreeze; }/*}}}*/ @@ -4570,8 +4648,6 @@ void FemModel::DakotaResponsesx(double* d_responses,char** responses_descriptors,int numresponsedescriptors,int d_numresponses){/*{{{*/ - int i,j; - int my_rank; - /*intermediary: */ + int i,j; char root[50]; int index; @@ -4593,5 +4669,5 @@ /*retrieve my_rank: */ - my_rank=IssmComm::GetRank(); + int my_rank=IssmComm::GetRank(); /*save the d_responses pointer: */ Index: /issm/trunk/src/c/classes/FemModel.h =================================================================== --- /issm/trunk/src/c/classes/FemModel.h (revision 28012) +++ /issm/trunk/src/c/classes/FemModel.h (revision 28013) @@ -143,4 +143,6 @@ void TotalGroundedBmbx(IssmDouble* pGbmb, bool scaled); void TotalSmbx(IssmDouble* pSmb, bool scaled); + void TotalSmbMeltx(IssmDouble* pSmbMelt, bool scaled); + void TotalSmbRefreezex(IssmDouble* pSmbRefreeze, bool scaled); #ifdef _HAVE_DAKOTA_ void DakotaResponsesx(double* d_responses,char** responses_descriptors,int numresponsedescriptors,int d_numresponses); Index: /issm/trunk/src/c/classes/Inputs/ControlInput.cpp =================================================================== --- /issm/trunk/src/c/classes/Inputs/ControlInput.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Inputs/ControlInput.cpp (revision 28013) @@ -227,4 +227,8 @@ } /*}}}*/ +void ControlInput::AverageAndReplace(void){/*{{{*/ + this->values->AverageAndReplace(); +} +/*}}}*/ TriaInput* ControlInput::GetTriaInput(){/*{{{*/ Index: /issm/trunk/src/c/classes/Inputs/ControlInput.h =================================================================== --- /issm/trunk/src/c/classes/Inputs/ControlInput.h (revision 28012) +++ /issm/trunk/src/c/classes/Inputs/ControlInput.h (revision 28013) @@ -48,4 +48,5 @@ TriaInput* GetTriaInput(); PentaInput* GetPentaInput(); + void AverageAndReplace(void); }; #endif /* _CONTROLINPUT_H */ Index: /issm/trunk/src/c/classes/Inputs/Input.h =================================================================== --- /issm/trunk/src/c/classes/Inputs/Input.h (revision 28012) +++ /issm/trunk/src/c/classes/Inputs/Input.h (revision 28013) @@ -48,4 +48,5 @@ virtual void Pow(IssmDouble scale_factor){_error_("Not implemented yet");}; virtual void Scale(IssmDouble scale_factor){_error_("Not implemented yet");}; + virtual void AverageAndReplace(void){_error_("Not implemented yet");}; virtual int GetResultArraySize(void){_error_("Not implemented yet");}; Index: /issm/trunk/src/c/classes/Inputs/Inputs.cpp =================================================================== --- /issm/trunk/src/c/classes/Inputs/Inputs.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Inputs/Inputs.cpp (revision 28013) @@ -302,5 +302,5 @@ } /*}}}*/ -void Inputs::Shift(int xenum, IssmDouble alpha){/*{{{*/ +void Inputs::Shift(int xenum, IssmDouble alpha){/*{{{*/ _assert_(this); @@ -314,4 +314,15 @@ /*Shift: */ this->inputs[index_x]->Shift(alpha); +} +/*}}}*/ +void Inputs::AverageAndReplace(int inputenum){/*{{{*/ + + _assert_(this); + + /*Get indices from enums*/ + int index = EnumToIndex(inputenum); + if(!this->inputs[index]) _error_("Input "<inputs[index]->AverageAndReplace(); } /*}}}*/ Index: /issm/trunk/src/c/classes/Inputs/Inputs.h =================================================================== --- /issm/trunk/src/c/classes/Inputs/Inputs.h (revision 28012) +++ /issm/trunk/src/c/classes/Inputs/Inputs.h (revision 28013) @@ -50,4 +50,5 @@ void AXPY(IssmDouble alpha, int xenum, int yenum); void Shift(int inputenum, IssmDouble alpha); + void AverageAndReplace(int inputenum); void DeepEcho(void); void DeepEcho(int enum_in); Index: /issm/trunk/src/c/classes/Inputs/TransientInput.cpp =================================================================== --- /issm/trunk/src/c/classes/Inputs/TransientInput.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Inputs/TransientInput.cpp (revision 28013) @@ -435,4 +435,5 @@ /*First, recover current time from parameters: */ bool linear_interp,average,cycle; + int timestepping; IssmDouble dt; this->parameters->FindParam(&linear_interp,TimesteppingInterpForcingEnum); @@ -440,16 +441,20 @@ this->parameters->FindParam(&cycle,TimesteppingCycleForcingEnum); this->parameters->FindParam(&dt,TimesteppingTimeStepEnum); /*transient core time step*/ - - /*Change input time if we cycle through the forcing*/ - IssmDouble time0 = this->timesteps[0]; - IssmDouble time1 = this->timesteps[this->numtimesteps - 1]; - - /*We need the end time to be the last timestep that would be taken*/ - /* i.e., the case where GEMB has time stamps (finer timestep) after the last timestep */ - IssmDouble nsteps = reCast(time1/dt); - if (reCast(nsteps)parameters->FindParam(×tepping,TimesteppingTypeEnum); if(cycle){ + + /*Change input time if we cycle through the forcing*/ + IssmDouble time0 = this->timesteps[0]; + IssmDouble time1 = this->timesteps[this->numtimesteps - 1]; + + if(timestepping!=AdaptiveTimesteppingEnum){ + /*We need the end time to be the last timestep that would be taken*/ + /* i.e., the case where GEMB has time stamps (finer timestep) after the last timestep */ + /* warning: this assumes dt = constant!!*/ + IssmDouble nsteps = reCast(time1/dt); + if (reCast(nsteps)M!=this->numberofelements_local) _error_("not implemented for P1"); + + /*Get local sum and local size*/ + IssmDouble sum = 0.; + int weight; + for(int i=0;iM*this->N;i++) sum += this->values[i]; + weight = this->M*this->N; + + /*Get sum across all procs*/ + IssmDouble all_sum; + int all_weight; + ISSM_MPI_Allreduce((void*)&sum,(void*)&all_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + ISSM_MPI_Allreduce((void*)&weight,(void*)&all_weight,1,ISSM_MPI_INT,ISSM_MPI_SUM,IssmComm::GetComm()); + + /*Divide by number of procs*/ + IssmDouble newvalue = all_sum/reCast(all_weight); + + /*Now replace existing input*/ + this->Reset(P0Enum); + for(int i=0;iM*this->N;i++) this->values[i] = newvalue; +} +/*}}}*/ /*Object functions*/ Index: /issm/trunk/src/c/classes/Inputs/TriaInput.h =================================================================== --- /issm/trunk/src/c/classes/Inputs/TriaInput.h (revision 28012) +++ /issm/trunk/src/c/classes/Inputs/TriaInput.h (revision 28013) @@ -41,4 +41,5 @@ void AXPY(Input* xinput,IssmDouble scalar); void Shift(IssmDouble scalar); + void AverageAndReplace(void); void PointWiseMult(Input* xinput); void Serve(int numindices,int* indices); Index: /issm/trunk/src/c/classes/IoModel.cpp =================================================================== --- /issm/trunk/src/c/classes/IoModel.cpp (revision 28012) +++ /issm/trunk/src/c/classes/IoModel.cpp (revision 28013) @@ -480,7 +480,6 @@ this->FetchData(&num_independent_objects,"md.autodiff.num_independent_objects"); if(num_independent_objects){ - this->FetchData(&names,&temp,"md.autodiff.independent_object_names"); - _assert_(temp==num_independent_objects); - this->FetchData(&types,NULL,NULL,"md.autodiff.independent_object_types"); + this->FetchMultipleData(&names,&temp,"md.autodiff.independent_name"); _assert_(temp==num_independent_objects); + this->FetchMultipleData(&types,NULL,"md.autodiff.independent_type"); /*create independent objects, and at the same time, fetch the corresponding independent variables, @@ -1023,4 +1022,33 @@ } /*}}}*/ +void IoModel::FetchData(IssmDouble** pscalar, const char* data_name){/*{{{*/ + + /*output: */ + IssmPDouble *scalar = NULL; + int code = 0; + + /*recover my_rank:*/ + int my_rank=IssmComm::GetRank(); + + /*Set file pointer to beginning of the data: */ + fid=this->SetFilePointerToData(&code,NULL,data_name); + if(code!=3)_error_("expecting a IssmDouble for \""<(1); + if(my_rank==0) if(fread(scalar,sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix "); + ISSM_MPI_Bcast(scalar,1,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + + _printf0_("scalar: " << *scalar << "\n"); + *pscalar=xNew(1); + *pscalar[0]=scalar[0]; + xDelete(scalar); +} +/*}}}*/ void IoModel::FetchData(char** pstring,const char* data_name){/*{{{*/ @@ -1122,4 +1150,69 @@ *pstrings = strings; if(pnumstrings) *pnumstrings = numstrings; +} +/*}}}*/ +void IoModel::FetchData(bool** pmatrix,int* pM,int* pN,const char* data_name){/*{{{*/ + + /*output: */ + int M,N; + IssmPDouble* matrix=NULL; + bool* bool_matrix=NULL; + int code=0; + + /*recover my_rank:*/ + int my_rank=IssmComm::GetRank(); + + /*Set file pointer to beginning of the data: */ + fid=this->SetFilePointerToData(&code,NULL,data_name); + + if(code!=5 && code!=6 && code!=7)_error_("expecting a IssmDouble, integer or boolean matrix for \""<(M*N); + + /*Read matrix on node 0, then broadcast: */ + if(my_rank==0){ + if(fread(matrix,M*N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix "); + } + + ISSM_MPI_Bcast(matrix,M*N,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + } + + /*Now cast to bool: */ + if(M*N){ + bool_matrix=xNew(M*N); + for(int i=0;i(matrix); + + /*Assign output pointers: */ + *pmatrix=bool_matrix; + if (pM)*pM=M; + if (pN)*pN=N; + } /*}}}*/ @@ -1361,4 +1454,30 @@ if(pM) *pM=M; if(pN) *pN=N; +} +/*}}}*/ +void IoModel::FetchData(IssmPDouble** pscalar,const char* data_name){/*{{{*/ + + /*output: */ + IssmPDouble *scalar = NULL; + int code; + + /*recover my_rank:*/ + int my_rank=IssmComm::GetRank(); + + /*Set file pointer to beginning of the data: */ + fid=this->SetFilePointerToData(&code,NULL,data_name); + + if(code!=3)_error_("expecting a IssmDouble for \""<(1); + if(my_rank==0){ + if(fread(scalar,sizeof(IssmPDouble),1,fid)!=1)_error_("could not read scalar "); + } + ISSM_MPI_Bcast(scalar,1,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + + + /*Assign output pointers: */ + *pscalar=scalar; } /*}}}*/ @@ -2266,5 +2385,5 @@ /*Assign output pointers: */ *pstrings=strings; - *pnumstrings=num_instances; + if(pnumstrings) *pnumstrings=num_instances; } /*}}}*/ @@ -2278,7 +2397,7 @@ /*intermediary: */ - int integer; - int *codes = NULL; - int code; + int integer; + int *codes = NULL; + int code; /*recover my_rank:*/ @@ -2319,5 +2438,5 @@ /*Assign output pointers: */ *pvector=vector; - *pnum_instances=num_instances; + if(pnum_instances) *pnum_instances=num_instances; } /*}}}*/ @@ -2473,5 +2592,7 @@ xDelete(ndims); } - *pnumrecords=num_instances; + if(pnumrecords){ + *pnumrecords=num_instances; + } } /*}}}*/ Index: /issm/trunk/src/c/classes/IoModel.h =================================================================== --- /issm/trunk/src/c/classes/IoModel.h (revision 28012) +++ /issm/trunk/src/c/classes/IoModel.h (revision 28013) @@ -133,10 +133,13 @@ void FetchData(int* pinteger,const char* data_name); void FetchData(IssmDouble* pscalar,const char* data_name); + void FetchData(IssmDouble** pscalar, const char* data_name); void FetchData(char** pstring,const char* data_name); void FetchData(char*** pstrings,int* pnumstrings,const char* data_name); void FetchData(int** pmatrix,int* pM,int* pN,const char* data_name); + void FetchData(bool** pboolmatrix,int* pM,int* pN,const char* data_name); void FetchData(IssmDouble** pscalarmatrix,int* pM,int* pN,const char* data_name); #if _HAVE_AD_ && !defined(_WRAPPERS_) void FetchData(IssmPDouble** pscalarmatrix,int* pM,int* pN,const char* data_name); + void FetchData(IssmPDouble** pscalar,const char* data_name); #endif void FetchData(IssmDouble*** pmatrixarray,int** pmdims,int** pndims, int* pnumrecords,const char* data_name); @@ -151,5 +154,5 @@ void FetchMultipleData(int*** pmatrices,int** pmdims,int** pndims, int* pnumrecords,const char* data_name); void FetchMultipleData(int** pvector, int* pnum_instances,const char* data_name); - void FetchMultipleData(IssmDouble** pvector, int* pnum_instances,const char* data_name); + void FetchMultipleData(IssmDouble** pvector, int* pM,const char* data_name); fpos_t* SetFilePointersToData(int** pcodes,int** pvector_types, int* pnum_instances, const char* data_name); FILE* SetFilePointerToData(int* pcode,int* pvector_type, const char* data_name); Index: /issm/trunk/src/c/classes/Loads/Channel.cpp =================================================================== --- /issm/trunk/src/c/classes/Loads/Channel.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Loads/Channel.cpp (revision 28013) @@ -20,9 +20,4 @@ #define C_W 4.22e3 /*specific heat capacity of water (J/kg/K)*/ -#define ALPHA_C 5./4. -#define BETA_C 3./2. -/*Make sure these are the same as in HydrologyGlaDSAnalysis::CreateKMatrix*/ -#define ALPHA_S 5./4. -#define BETA_S 3./2. #define AEPS 2.2204460492503131E-015 @@ -366,5 +361,6 @@ /*Intermediaries */ IssmDouble Jdet,v1,qc,fFactor,Afactor,Bfactor,Xifactor; - IssmDouble A,B,n,phi_old,phi,phi_0,dPw,ks,Ngrad; + IssmDouble A,B,n,phi_old,phi,phi_0,dPw,ks,kc,Ngrad; + IssmDouble h_r; IssmDouble H,h,b,dphi[2],dphids,dphimds,db[2],dbds; IssmDouble xyz_list[NUMVERTICES][3]; @@ -382,19 +378,28 @@ GetVerticesCoordinates(&xyz_list_tria[0][0],tria->vertices,3); + bool istransition; + element->FindParam(&istransition,HydrologyIsTransitionEnum); IssmDouble L = element->FindParam(MaterialsLatentheatEnum); + IssmDouble mu_water = element->FindParam(MaterialsMuWaterEnum); IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); IssmDouble rho_water = element->FindParam(MaterialsRhoFreshwaterEnum); IssmDouble g = element->FindParam(ConstantsGEnum); - IssmDouble kc = element->FindParam(HydrologyChannelConductivityEnum); IssmDouble lc = element->FindParam(HydrologyChannelSheetWidthEnum); IssmDouble c_t = element->FindParam(HydrologyPressureMeltCoefficientEnum); - - Input* h_input = element->GetInput(HydrologySheetThicknessEnum);_assert_(h_input); - Input* H_input = element->GetInput(ThicknessEnum); _assert_(H_input); - Input* b_input = element->GetInput(BedEnum); _assert_(b_input); - Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); - Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); - Input* ks_input = element->GetInput(HydrologySheetConductivityEnum); _assert_(ks_input); - Input* phi_input = element->GetInput(HydraulicPotentialEnum); _assert_(phi_input); + IssmDouble alpha_c = element->FindParam(HydrologyChannelAlphaEnum); + IssmDouble beta_c = element->FindParam(HydrologyChannelBetaEnum); + IssmDouble alpha_s = element->FindParam(HydrologySheetAlphaEnum); + IssmDouble beta_s = element->FindParam(HydrologySheetBetaEnum); + IssmDouble omega = element->FindParam(HydrologyOmegaEnum); + + Input* h_input = element->GetInput(HydrologySheetThicknessEnum); _assert_(h_input); + Input* H_input = element->GetInput(ThicknessEnum); _assert_(H_input); + Input* b_input = element->GetInput(BedEnum); _assert_(b_input); + Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); + Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + Input* ks_input = element->GetInput(HydrologySheetConductivityEnum); _assert_(ks_input); + Input* kc_input = element->GetInput(HydrologyChannelConductivityEnum); _assert_(kc_input); + Input* hr_input = element->GetInput(HydrologyBumpHeightEnum);_assert_(hr_input); + Input* phi_input = element->GetInput(HydraulicPotentialEnum); _assert_(phi_input); /*Get tangent vector*/ @@ -421,8 +426,13 @@ h_input->GetInputValue(&h,gauss); ks_input->GetInputValue(&ks,gauss); + kc_input->GetInputValue(&kc,gauss); + hr_input->GetInputValue(&h_r,gauss); B_input->GetInputValue(&B,gauss); n_input->GetInputValue(&n,gauss); b_input->GetInputValue(&b,gauss); H_input->GetInputValue(&H,gauss); + + /*Hard code B*/ + B = Cuffey(273.15-2); /*Get values for a few potentials*/ @@ -432,8 +442,19 @@ Ngrad = fabs(dphids); if(NgradS,ALPHA_C) * pow(Ngrad,BETA_C-2.); - IssmDouble Ks = ks * pow(h ,ALPHA_S) * pow(Ngrad,BETA_S-2.); + + /*Compute the effective conductivity Kc = k h^alpha |grad Phi|^{beta-2} (same for sheet) and use transition model if specified*/ + IssmDouble Kc; + IssmDouble Ks; + IssmDouble nu = mu_water/rho_water; + if(istransition==1 && omega>=AEPS){ + IssmDouble hratio = h/h_r; + IssmDouble coarg = 1. + 4.*omega*pow(hratio,3-2*alpha_s)*ks*pow(h,3)*Ngrad/nu; + Ks = nu/2./omega*pow(hratio,2*alpha_s-3) * (-1 + pow(coarg, 0.5))/Ngrad; + Kc = kc * pow(this->S,alpha_c) * pow(Ngrad,beta_c-2.); + } + else { + Ks = ks*pow(h,alpha_s)*pow(Ngrad,beta_s-2.); + Kc = kc * pow(this->S,alpha_c) * pow(Ngrad,beta_c-2.); + } /*Approx. discharge in the sheet flowing folwing in the direction of the channel ofver a width lc*/ @@ -499,5 +520,6 @@ IssmDouble Jdet,v2,Afactor,Bfactor,fFactor; IssmDouble A,B,n,phi_old,phi,phi_0,dphimds,dphi[2]; - IssmDouble H,h,b,db[2],dphids,qc,dPw,ks,Ngrad; + IssmDouble H,h,b,db[2],dphids,qc,dPw,ks,kc,Ngrad; + IssmDouble h_r; IssmDouble xyz_list[NUMVERTICES][3]; IssmDouble xyz_list_tria[3][3]; @@ -512,5 +534,8 @@ GetVerticesCoordinates(&xyz_list_tria[0][0],tria->vertices,3); + bool istransition; + element->FindParam(&istransition,HydrologyIsTransitionEnum); IssmDouble L = element->FindParam(MaterialsLatentheatEnum); + IssmDouble mu_water = element->FindParam(MaterialsMuWaterEnum); IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); IssmDouble rho_water = element->FindParam(MaterialsRhoFreshwaterEnum); @@ -518,12 +543,17 @@ IssmDouble lc = element->FindParam(HydrologyChannelSheetWidthEnum); IssmDouble c_t = element->FindParam(HydrologyPressureMeltCoefficientEnum); - - Input* h_input = element->GetInput(HydrologySheetThicknessEnum);_assert_(h_input); - Input* H_input = element->GetInput(ThicknessEnum); _assert_(H_input); - Input* b_input = element->GetInput(BedEnum); _assert_(b_input); - Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); - Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); - Input* ks_input = element->GetInput(HydrologySheetConductivityEnum); _assert_(ks_input); - Input* phi_input = element->GetInput(HydraulicPotentialEnum); _assert_(phi_input); + IssmDouble alpha_s = element->FindParam(HydrologySheetAlphaEnum); + IssmDouble beta_s = element->FindParam(HydrologySheetBetaEnum); + IssmDouble omega = element->FindParam(HydrologyOmegaEnum); + + Input* h_input = element->GetInput(HydrologySheetThicknessEnum); _assert_(h_input); + Input* H_input = element->GetInput(ThicknessEnum); _assert_(H_input); + Input* b_input = element->GetInput(BedEnum); _assert_(b_input); + Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); + Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + Input* ks_input = element->GetInput(HydrologySheetConductivityEnum); _assert_(ks_input); + Input* kc_input = element->GetInput(HydrologyChannelConductivityEnum); _assert_(kc_input); + Input* phi_input = element->GetInput(HydraulicPotentialEnum); _assert_(phi_input); + Input* hr_input = element->GetInput(HydrologyBumpHeightEnum);_assert_(hr_input); /*Get tangent vector*/ @@ -546,4 +576,5 @@ h_input->GetInputValue(&h,gauss); ks_input->GetInputValue(&ks,gauss); + kc_input->GetInputValue(&kc,gauss); B_input->GetInputValue(&B,gauss); n_input->GetInputValue(&n,gauss); @@ -551,5 +582,9 @@ b_input->GetInputValue(&b,gauss); H_input->GetInputValue(&H,gauss); - + hr_input->GetInputValue(&h_r,gauss); + + /*Hard code B*/ + B = Cuffey(273.15-2); + /*Get values for a few potentials*/ phi_0 = rho_water*g*b + rho_ice*g*H; @@ -559,6 +594,16 @@ if(Ngrad=AEPS){ + IssmDouble hratio = h/h_r; + IssmDouble nu = mu_water/rho_water; + IssmDouble coarg = 1. + 4.*omega*pow(hratio,3-2*alpha_s)*ks*pow(h,3)*Ngrad/nu; + Ks = nu/2./omega*pow(hratio,2*alpha_s-3) * (-1 + pow(coarg, 0.5))/Ngrad; + } + else { + Ks = ks * pow(h,alpha_s) * pow(Ngrad,beta_s-2.); + } /*Approx. discharge in the sheet flowing folwing in the direction of the channel ofver a width lc*/ @@ -626,5 +671,6 @@ /*Intermediaries */ - IssmDouble A,B,n,phi,phi_0,ks,Ngrad; + IssmDouble A,B,n,phi,phi_0,ks,kc,Ngrad; + IssmDouble h_r; IssmDouble H,h,b,dphi[2],dphids,dphimds,db[2],dbds; IssmDouble xyz_list[NUMVERTICES][3]; @@ -635,20 +681,29 @@ GetVerticesCoordinates(&xyz_list_tria[0][0],tria->vertices,3); + bool istransition; + element->FindParam(&istransition,HydrologyIsTransitionEnum); IssmDouble L = element->FindParam(MaterialsLatentheatEnum); IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); IssmDouble rho_water = element->FindParam(MaterialsRhoFreshwaterEnum); + IssmDouble mu_water = element->FindParam(MaterialsMuWaterEnum); IssmDouble g = element->FindParam(ConstantsGEnum); - IssmDouble kc = element->FindParam(HydrologyChannelConductivityEnum); IssmDouble lc = element->FindParam(HydrologyChannelSheetWidthEnum); IssmDouble c_t = element->FindParam(HydrologyPressureMeltCoefficientEnum); IssmDouble dt = element->FindParam(TimesteppingTimeStepEnum); - - Input* h_input = element->GetInput(HydrologySheetThicknessEnum);_assert_(h_input); - Input* H_input = element->GetInput(ThicknessEnum); _assert_(H_input); - Input* b_input = element->GetInput(BedEnum); _assert_(b_input); - Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); - Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); - Input* ks_input = element->GetInput(HydrologySheetConductivityEnum); _assert_(ks_input); - Input* phi_input = element->GetInput(HydraulicPotentialEnum); _assert_(phi_input); + IssmDouble alpha_c = element->FindParam(HydrologyChannelAlphaEnum); + IssmDouble beta_c = element->FindParam(HydrologyChannelBetaEnum); + IssmDouble alpha_s = element->FindParam(HydrologySheetAlphaEnum); + IssmDouble beta_s = element->FindParam(HydrologySheetBetaEnum); + IssmDouble omega = element->FindParam(HydrologyOmegaEnum); + + Input* h_input = element->GetInput(HydrologySheetThicknessEnum); _assert_(h_input); + Input* H_input = element->GetInput(ThicknessEnum); _assert_(H_input); + Input* b_input = element->GetInput(BedEnum); _assert_(b_input); + Input* B_input = element->GetInput(MaterialsRheologyBEnum); _assert_(B_input); + Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + Input* ks_input = element->GetInput(HydrologySheetConductivityEnum); _assert_(ks_input); + Input* kc_input = element->GetInput(HydrologyChannelConductivityEnum); _assert_(kc_input); + Input* phi_input = element->GetInput(HydraulicPotentialEnum); _assert_(phi_input); + Input* hr_input = element->GetInput(HydrologyBumpHeightEnum);_assert_(hr_input); /*Get tangent vector*/ @@ -664,4 +719,5 @@ h_input->GetInputValue(&h,gauss); ks_input->GetInputValue(&ks,gauss); + kc_input->GetInputValue(&kc,gauss); B_input->GetInputValue(&B,gauss); n_input->GetInputValue(&n,gauss); @@ -669,4 +725,9 @@ b_input->GetInputDerivativeValue(&db[0],&xyz_list_tria[0][0],gauss); H_input->GetInputValue(&H,gauss); + hr_input->GetInputValue(&h_r,gauss); + + + /*Hard code B*/ + B = Cuffey(273.15-2); /*Get values for a few potentials*/ @@ -680,6 +741,15 @@ IssmDouble dPw = dphids - dphimds; - /*Approx. discharge in the sheet flowing folwing in the direction of the channel ofver a width lc*/ - IssmDouble qc = - ks * pow(h,ALPHA_S) * pow(Ngrad,BETA_S-2.) * dphids; + /*Approx. discharge in the sheet flowing folwing in the direction of the channel ofver a width lc, use transition model if necessary*/ + IssmDouble qc; + if (istransition==1 && omega>=AEPS){ + IssmDouble hratio = h/h_r; + IssmDouble nu = mu_water/rho_water; + IssmDouble coarg = 1. + 4.*omega*pow(hratio,3-2*alpha_s)*ks*pow(h,3)*fabs(Ngrad)/nu; + qc = -nu/2./omega*pow(hratio,2*alpha_s-3) * (-1 + pow(coarg, 0.5))*dphids/Ngrad; + } + else { + qc = - ks * pow(h,alpha_s) * pow(Ngrad,beta_s-2.) * dphids; + } /*Ice rate factor*/ @@ -687,5 +757,5 @@ IssmDouble C = C_W*c_t*rho_water; - IssmDouble Qprime = -kc * pow(Ngrad,BETA_C-2.)*dphids; + IssmDouble Qprime = -kc * pow(Ngrad,beta_c-2.)*dphids; IssmDouble N = phi_0 - phi; @@ -704,6 +774,6 @@ IssmDouble alpha = 1./(rho_ice*L)*( - fabs(Qprime*pow(Snew,ALPHA_C-1.)*dphids) - + C*Qprime*pow(Snew,ALPHA_C-1.)*dPw + fabs(Qprime*pow(Snew,alpha_c-1.)*dphids) + + C*Qprime*pow(Snew,alpha_c-1.)*dPw ) - 2./pow(n,n)*A*pow(fabs(N),n-1.)*N; @@ -716,5 +786,8 @@ /*Constrain the cross section to be between 0 and 500 m^2*/ if(this->S<0.) this->S = 0.; - if(this->S>500.) this->S = 500.; + if(this->S>100.) this->S = 100.; + + /*Do not allow channels to grow in areas with no sheet thickness*/ + if(H<200.) this->S = 0.; count++; @@ -724,5 +797,5 @@ /*Compute new channel discharge for output only*/ - IssmDouble Kc = kc * pow(this->S,ALPHA_C) * pow(Ngrad,BETA_C-2.); + IssmDouble Kc = kc * pow(this->S,alpha_c) * pow(Ngrad,beta_c-2.); this->discharge = -Kc*dphids; Index: /issm/trunk/src/c/classes/Loads/Friction.cpp =================================================================== --- /issm/trunk/src/c/classes/Loads/Friction.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Loads/Friction.cpp (revision 28013) @@ -13,4 +13,5 @@ #include "../classes.h" #include "shared/shared.h" +#include "../../modules/InputUpdateFromConstantx/InputUpdateFromConstantx.h" /*}}}*/ @@ -18,10 +19,13 @@ Friction::Friction(){/*{{{*/ this->element=NULL; - this->law=0; - this->apply_dim = 1.; - this->domaintype=-1; + this->law = 0; + this->linearize = 0; + this->apply_dim = 1.; + this->domaintype = -1; this->vx_input=NULL; this->vy_input=NULL; this->vz_input=NULL; + this->alpha2_list=NULL; + this->alpha2_complement_list=NULL; } /*}}}*/ @@ -29,5 +33,10 @@ /* Determine the dimension according to the domain type automatically. * There are exceptions, e.g. HO, which needs the user to specify the dimension used in Friciton.*/ + + /*Intermediaries*/ + int linearization_type; + this->element=element_in; + this->linearize = 0; /* Load necessary parameters */ @@ -39,21 +48,53 @@ case Domain2DhorizontalEnum: this->apply_dim = 2.; - this->vx_input = element_in->GetInput(VxBaseEnum); _assert_(this->vx_input); - this->vy_input = element_in->GetInput(VyBaseEnum); _assert_(this->vy_input); + this->vx_input = element_in->GetInput(VxBaseEnum); _assert_(this->vx_input); + this->vy_input = element_in->GetInput(VyBaseEnum); _assert_(this->vy_input); this->vz_input = NULL; break; case Domain2DverticalEnum: this->apply_dim = 2.; - this->vx_input = element_in->GetInput(VxEnum); _assert_(this->vx_input); - this->vy_input = element_in->GetInput(VyEnum); _assert_(this->vy_input); + this->vx_input = element_in->GetInput(VxEnum); _assert_(this->vx_input); + this->vy_input = element_in->GetInput(VyEnum); _assert_(this->vy_input); this->vz_input = NULL; break; case Domain3DEnum: this->apply_dim = 3.; - this->vx_input = element_in->GetInput(VxEnum); _assert_(this->vx_input); - this->vy_input = element_in->GetInput(VyEnum); _assert_(this->vy_input); - this->vz_input = element_in->GetInput(VzEnum); _assert_(this->vz_input); + this->vx_input = element_in->GetInput(VxEnum); _assert_(this->vx_input); + this->vy_input = element_in->GetInput(VyEnum); _assert_(this->vy_input); + this->vz_input = element_in->GetInput(VzEnum); _assert_(this->vz_input); break; default: _error_("mesh "<law==1 || this->law==2){ + element_in->FindParam(&linearization_type,FrictionLinearizeEnum); + if(linearization_type==0){ + /*Don't do anything*/ + } + else if(linearization_type==1){ + int numvertices = this->element->GetNumberOfVertices(); + this->alpha2_list = xNew(numvertices); + this->alpha2_complement_list = xNew(numvertices); + Gauss* gauss=this->element->NewGauss(); + for(int iv=0;ivGaussVertex(iv); + this->GetAlpha2(&this->alpha2_list[iv], gauss); + this->GetAlphaComplement(&this->alpha2_complement_list[iv], gauss); + } + this->linearize = linearization_type; /*Change back, we are now all set!*/ + delete gauss; + } + else if(linearization_type==2){ + this->alpha2_list = xNew(1); + this->alpha2_complement_list = xNew(1); + Gauss* gauss=element->NewGauss(1); gauss->GaussPoint(0); + this->GetAlpha2(&this->alpha2_list[0], gauss); + this->GetAlphaComplement(&this->alpha2_complement_list[0], gauss); + this->linearize = linearization_type; /*Change back, we are now all set!*/ + delete gauss; + } + else{ + _error_("not supported yet"); + } } } @@ -68,7 +109,10 @@ /*}}}*/ Friction::~Friction(){/*{{{*/ + if(this->linearize){ + xDelete(this->alpha2_list); + xDelete(this->alpha2_complement_list); + } } /*}}}*/ - /*methods: */ @@ -80,22 +124,39 @@ void Friction::GetAlphaComplement(IssmDouble* palpha_complement, Gauss* gauss){/*{{{*/ - switch(this->law){ - case 1: - GetAlphaViscousComplement(palpha_complement,gauss); - break; - case 2: - GetAlphaWeertmanComplement(palpha_complement, gauss); - break; - case 3: - GetAlphaHydroComplement(palpha_complement,gauss); - break; - case 4: - GetAlphaTempComplement(palpha_complement,gauss); - break; - case 11: - GetAlphaSchoofComplement(palpha_complement,gauss); - break; - default: - _error_("not supported"); + if(this->linearize==0){ + switch(this->law){ + case 1: + GetAlphaViscousComplement(palpha_complement,gauss); + break; + case 2: + GetAlphaWeertmanComplement(palpha_complement, gauss); + break; + case 3: + GetAlphaHydroComplement(palpha_complement,gauss); + break; + case 4: + GetAlphaTempComplement(palpha_complement,gauss); + break; + case 11: + GetAlphaSchoofComplement(palpha_complement,gauss); + break; + case 13: + GetAlphaCoulomb2Complement(palpha_complement,gauss); + break; + case 14: + GetAlphaRegCoulombComplement(palpha_complement,gauss); + break; + default: + _error_("not supported"); + } + } + else if(this->linearize==1){ + this->element->ValueP1OnGauss(palpha_complement, this->alpha2_complement_list, gauss); + } + else if(this->linearize==2){ + *palpha_complement = this->alpha2_complement_list[0]; + } + else{ + _error_("not supported yet"); } @@ -266,48 +327,127 @@ *palpha_complement=alpha_complement; }/*}}}*/ +void Friction::GetAlphaRegCoulombComplement(IssmDouble* palpha_complement, Gauss* gauss){/*{{{*/ + + /* Compute the complement of regularised Coulombs law for inversion + * d alpha2 + * -------- = |u_b|^(1/m-1) * (|u_b|/u_0 + 1)^(-1/m) + * dC + */ + + /*diverse: */ + IssmDouble m, u0; + IssmDouble alpha_complement; + + /*Recover parameters: */ + element->GetInputValue(&m,gauss,FrictionMEnum); + element->parameters->FindParam(&u0,FrictionU0Enum); + + /*Get velocity magnitude*/ + IssmDouble ub = VelMag(gauss); + + /*Check to prevent dividing by zero if vmag==0*/ + if(ub==0.) { + alpha_complement=0.; + } + else { + /*Compute friction complement*/ + alpha_complement= (pow(ub,1./m-1.)) / pow(ub/u0 + 1.,1./m); + } + + /*Assign output pointers:*/ + *palpha_complement=alpha_complement; +}/*}}}*/ +void Friction::GetAlphaCoulomb2Complement(IssmDouble* palpha_complement, Gauss* gauss){/*{{{*/ + + /* Compute the complement of Cornford's friction law for inversion + * d alpha2 + * ------ = (C*N*v^m)/(C^(2/m)*v + (N/2)^(1/m))^m - (C^(2/m - 1)*C^2*N*v*v^m)/(C^(2/m)*v + (N/2)^(1/m))^(m + 1) + * dC + */ + + /*diverse: */ + IssmDouble m, C; + IssmDouble alpha_complement; + + /*Recover parameters: */ + element->GetInputValue(&C,gauss,FrictionCEnum); + element->GetInputValue(&m,gauss,FrictionMEnum); + + /*Get effective pressure and velocity magnitude*/ + IssmDouble N = EffectivePressure(gauss); + IssmDouble v = VelMag(gauss); + + /*Compute alpha*/ + if(v<1e-10){ + alpha_complement = 0.; + } + else{ + alpha_complement= pow(0.5*N,1./m+1)* pow(v,m-1.) * pow(v*pow(C,1./m) +pow(0.5*N,1./m) ,-m-1.); + } + + /*Assign output pointers:*/ + *palpha_complement=alpha_complement/2.; +}/*}}}*/ void Friction::GetAlpha2(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ - switch(this->law){ - case 1: - GetAlpha2Viscous(palpha2,gauss); - break; - case 2: - GetAlpha2Weertman(palpha2,gauss); - break; - case 3: - GetAlpha2Hydro(palpha2,gauss); - break; - case 4: - GetAlpha2Temp(palpha2,gauss); - break; - case 5: - GetAlpha2WaterLayer(palpha2,gauss); - break; - case 6: - GetAlpha2WeertmanTemp(palpha2,gauss); - break; - case 7: - GetAlpha2Coulomb(palpha2,gauss); - break; - case 8: - GetAlpha2Shakti(palpha2,gauss); - break; - case 9: - GetAlpha2Josh(palpha2,gauss); - break; - case 10: - GetAlpha2PISM(palpha2,gauss); - break; - case 11: - GetAlpha2Schoof(palpha2,gauss); - break; - case 12: - GetAlpha2Tsai(palpha2,gauss); - break; - case 13: - GetAlpha2Coulomb2(palpha2,gauss); - break; - default: - _error_("Friction law "<< this->law <<" not supported"); + if(this->linearize==0){ + switch(this->law){ + case 1: + GetAlpha2Viscous(palpha2,gauss); + break; + case 2: + GetAlpha2Weertman(palpha2,gauss); + break; + case 3: + GetAlpha2Hydro(palpha2,gauss); + break; + case 4: + GetAlpha2Temp(palpha2,gauss); + break; + case 5: + GetAlpha2WaterLayer(palpha2,gauss); + break; + case 6: + GetAlpha2WeertmanTemp(palpha2,gauss); + break; + case 7: + GetAlpha2Coulomb(palpha2,gauss); + break; + case 8: + GetAlpha2Shakti(palpha2,gauss); + break; + case 9: + GetAlpha2Josh(palpha2,gauss); + break; + case 10: + GetAlpha2PISM(palpha2,gauss); + break; + case 11: + GetAlpha2Schoof(palpha2,gauss); + break; + case 12: + GetAlpha2Tsai(palpha2,gauss); + break; + case 13: + GetAlpha2Coulomb2(palpha2,gauss); + break; + case 14: + GetAlpha2RegCoulomb(palpha2,gauss); + break; + case 15: + GetAlpha2RegCoulomb2(palpha2,gauss); + break; + default: + _error_("Friction law "<< this->law <<" not supported"); + } + } + else if(this->linearize==1){ + this->element->ValueP1OnGauss(palpha2, this->alpha2_list, gauss); + } + else if(this->linearize==2){ + *palpha2 = this->alpha2_list[0]; + } + else{ + _error_("not supported yet"); } @@ -344,19 +484,20 @@ /*Get effective pressure*/ - bool ispwStochastic; - IssmDouble Neff; - element->parameters->FindParam(&ispwStochastic,StochasticForcingIsWaterPressureEnum); - if(ispwStochastic){ - /*Retrieve stochastic water pressure and compute ice pressure*/ - IssmDouble p_ice,p_water,Neff_limit; - element->GetInputValue(&p_water,gauss,FrictionCoulombWaterPressureEnum); - element->parameters->FindParam(&Neff_limit,FrictionEffectivePressureLimitEnum); - p_ice = IcePressure(gauss); - Neff = max(Neff_limit*p_ice, p_ice - p_water); - } - else{ - /*Compute effective pressure directly*/ - Neff = EffectivePressure(gauss); - } + bool ispwHydro,ispwStochastic; + IssmDouble Neff; + element->parameters->FindParam(&ispwStochastic,StochasticForcingIsWaterPressureEnum); + element->parameters->FindParam(&ispwHydro,HydrologyIsWaterPressureArmaEnum); + if(ispwStochastic || ispwHydro){ + /*Retrieve pre-computed water pressure and compute ice pressure*/ + IssmDouble p_ice,p_water,Neff_limit; + element->GetInputValue(&p_water,gauss,FrictionWaterPressureEnum); + element->parameters->FindParam(&Neff_limit,FrictionEffectivePressureLimitEnum); + p_ice = IcePressure(gauss); + Neff = max(Neff_limit*p_ice, p_ice - p_water); + } + else{ + /*Compute effective pressure directly*/ + Neff = EffectivePressure(gauss); + } /*Get velocity magnitude*/ @@ -559,4 +700,221 @@ IssmDouble vmag = VelMag(gauss); + bool ispwHydro,ispwStochastic; + IssmDouble Neff; + element->parameters->FindParam(&ispwStochastic,StochasticForcingIsWaterPressureEnum); + element->parameters->FindParam(&ispwHydro,HydrologyIsWaterPressureArmaEnum); + if(ispwStochastic || ispwHydro){ + /*Retrieve pre-computed water pressure and compute ice pressure*/ + IssmDouble p_ice,p_water,Neff_limit; + element->GetInputValue(&p_water,gauss,FrictionWaterPressureEnum); + element->parameters->FindParam(&Neff_limit,FrictionEffectivePressureLimitEnum); + p_ice = IcePressure(gauss); + Neff = max(Neff_limit*p_ice, p_ice - p_water); + } + else{ + /*Compute effective pressure directly*/ + Neff = EffectivePressure(gauss); + } + + /*Check to prevent dividing by zero if vmag==0*/ + if(s==1.){ + /*This is to make AD happy and avoid 0^0*/ + alpha2=drag_coefficient*drag_coefficient*pow(Neff,r); + } + else{ + if(vmag==0. && (s-1.)<0.) alpha2=0.; + else alpha2=drag_coefficient*drag_coefficient*pow(Neff,r)*pow(vmag,(s-1.)); + } + + /*Assign output pointers:*/ + *palpha2=alpha2; +}/*}}}*/ +void Friction::GetAlpha2WaterLayer(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + + /*This routine calculates the basal friction coefficient + alpha2= drag^2 * Neff ^r * | vel | ^(s-1), with Neff=rho_ice*g*thickness+rho_ice*g*base, r=q/p and s=1/p**/ + + /*diverse: */ + IssmDouble r,s; + IssmDouble drag_p, drag_q; + IssmDouble Neff,F; + IssmDouble thickness,base,sealevel; + IssmDouble drag_coefficient,water_layer; + IssmDouble alpha2; + + /*Recover parameters: */ + element->parameters->FindParam(&F,FrictionFEnum); + element->GetInputValue(&drag_p,gauss,FrictionPEnum); + element->GetInputValue(&drag_q,gauss,FrictionQEnum); + element->GetInputValue(&thickness, gauss,ThicknessEnum); + element->GetInputValue(&base, gauss,BaseEnum); + element->GetInputValue(&sealevel, gauss,SealevelEnum); + element->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum); + element->GetInputValue(&water_layer, gauss,FrictionWaterLayerEnum); + IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum); + IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); + IssmDouble gravity = element->FindParam(ConstantsGEnum); + + //compute r and q coefficients: */ + r=drag_q/drag_p; + s=1./drag_p; + + //From base and thickness, compute effective pressure when drag is viscous: + if(base>0) base=0; + if(water_layer==0) Neff=gravity*rho_ice*thickness+gravity*rho_water*(base-sealevel); + else if(water_layer>0) Neff=gravity*rho_ice*thickness*F; + else _error_("negative water layer thickness"); + if(Neff<0) Neff=0; + + IssmDouble vmag = VelMag(gauss); + + if(s==1.){ + /*This is to make AD happy and avoid 0^0*/ + alpha2=drag_coefficient*drag_coefficient*pow(Neff,r); + } + else{ + /*Check to prevent dividing by zero if vmag==0*/ + if(vmag==0. && (s-1.)<0.) alpha2=0.; + else alpha2=drag_coefficient*drag_coefficient*pow(Neff,r)*pow(vmag,(s-1.)); + } + + /*Assign output pointers:*/ + *palpha2=alpha2; +}/*}}}*/ +void Friction::GetAlpha2Weertman(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + + /*This routine calculates the basal friction coefficient alpha2= C^2 |v|^(1/m-1) */ + + /*diverse: */ + IssmDouble C,m; + IssmDouble alpha2; + + /*Recover parameters: */ + element->GetInputValue(&C,gauss,FrictionCEnum); + element->GetInputValue(&m,gauss,FrictionMEnum); + + /*Get velocity magnitude*/ + IssmDouble vmag = VelMag(gauss); + + /*Check to prevent dividing by zero if vmag==0*/ + if(vmag==0. && (1./m-1.)<0.) alpha2=0.; + else alpha2=C*C*pow(vmag,(1./m-1.)); + + /*Assign output pointers:*/ + *palpha2=alpha2; +}/*}}}*/ +void Friction::GetAlpha2WeertmanTemp(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + /*Here, we want to parameterize the friction as a function of temperature + * + * alpha2 = alpha2_weertman * 1/f(T) + * + * where f(T) = exp((T-Tpmp)/gamma) + */ + + /*Intermediaries: */ + IssmDouble f,T,pressure,Tpmp,gamma; + IssmDouble alpha2; + + /*Get viscous part*/ + this->GetAlpha2Weertman(&alpha2,gauss); + + /*Get pressure melting point (Tpmp) for local pressure and get current temperature*/ + element->GetInputValue(&T,gauss,TemperatureEnum); + element->GetInputValue(&pressure,gauss,PressureEnum); + Tpmp = element->TMeltingPoint(pressure); + + /*Compute scaling parameter*/ + element->parameters->FindParam(&gamma,FrictionGammaEnum); + alpha2 = alpha2 / exp((T-Tpmp)/gamma); + + /*Assign output pointers:*/ + *palpha2=alpha2; +}/*}}}*/ +void Friction::GetAlpha2PISM(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + /*Here, we want to parameterize the friction using a pseudoplastic friction law, + * computing the basal shear stress as + * + * alpha2 = tau_c (u_b/(abs(u_b)^(1-q)*u_0^q)) + * + * The yield stress tau_c is a function of the effective pressure N + * using a Mohr-Coloumb criterion, so that + * tau_c = tan(phi)*N, + * where phi is the till friction angle, representing sediment strength + * + * The effective pressure is given by Eq. (5) in Aschwanden et al. 2016: + * + * N = delta * P0 * 10^((e_0/Cc)(1-(W/Wmax))) + * + * W is calculated by a non-conserving hydrology model in HydrologyPismAnalysis.cpp + * + * see Aschwanden et al. 2016 and Bueler and Brown, 2009 for more details + */ + + /*compute ice overburden pressure P0*/ + IssmDouble thickness,base,P0; + element->GetInputValue(&thickness, gauss,ThicknessEnum); + element->GetInputValue(&base, gauss,BaseEnum); + //element->GetInputValue(&sealevel, gauss,SealevelEnum); + IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); + IssmDouble gravity = element->FindParam(ConstantsGEnum); + P0 = gravity*rho_ice*thickness; + + /*Compute effective pressure*/ + IssmDouble N,delta,W,Wmax,e0,Cc; + element->parameters->FindParam(&delta,FrictionDeltaEnum); + element->parameters->FindParam(&e0,FrictionVoidRatioEnum); + element->GetInputValue(&Cc,gauss,FrictionSedimentCompressibilityCoefficientEnum); + element->GetInputValue(&W,gauss,WatercolumnEnum); + element->GetInputValue(&Wmax,gauss,HydrologyWatercolumnMaxEnum); + + /*Check that water column height is within 0 and upper bound, correct if needed*/ + if(W>Wmax) W=Wmax; + if(W<0) W=0.; + + N = delta*P0*pow(10.,(e0/Cc)*(1.-W/Wmax)); + + /*Get till friction angles, defined by user [deg]*/ + IssmDouble phi; + element->GetInputValue(&phi,gauss,FrictionTillFrictionAngleEnum); + + /*Convert till friction angle from user-defined deg to rad, which Matlab uses*/ + phi = phi*PI/180.; + + /*Compute yield stress following a Mohr-Colomb criterion*/ + IssmDouble tau_c = N*tan(phi); + + /*Compute basal speed*/ + IssmDouble ub; + element->GetInputValue(&ub,gauss,VelEnum); + + /*now compute alpha^2*/ + IssmDouble u0,q; + element->parameters->FindParam(&u0,FrictionThresholdSpeedEnum); + element->parameters->FindParam(&q,FrictionPseudoplasticityExponentEnum); + IssmDouble alpha2 = tau_c/(pow(ub+1.e-10,1.-q)*pow(u0,q)); + + /*Assign output pointers:*/ + *palpha2=alpha2; +}/*}}}*/ +void Friction::GetAlpha2Schoof(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + + /*This routine calculates the basal friction coefficient + * + * C^2 |u_b|^(m-1) + * alpha2= __________________________ + * (1+(C^2/(Cmax Neff))^1/m |u_b| )^m + * + * */ + + /*diverse: */ + IssmDouble C,Cmax,m,alpha2; + + /*Recover parameters: */ + element->GetInputValue(&Cmax,gauss,FrictionCmaxEnum); + element->GetInputValue(&C,gauss,FrictionCEnum); + element->GetInputValue(&m,gauss,FrictionMEnum); + + + /*Get effective pressure*/ bool ispwStochastic; IssmDouble Neff; @@ -575,222 +933,4 @@ } - /*Check to prevent dividing by zero if vmag==0*/ - if(s==1.){ - /*This is to make AD happy and avoid 0^0*/ - alpha2=drag_coefficient*drag_coefficient*pow(Neff,r); - } - else{ - if(vmag==0. && (s-1.)<0.) alpha2=0.; - else alpha2=drag_coefficient*drag_coefficient*pow(Neff,r)*pow(vmag,(s-1.)); - } - - /*Assign output pointers:*/ - *palpha2=alpha2; -}/*}}}*/ -void Friction::GetAlpha2WaterLayer(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ - - /*This routine calculates the basal friction coefficient - alpha2= drag^2 * Neff ^r * | vel | ^(s-1), with Neff=rho_ice*g*thickness+rho_ice*g*base, r=q/p and s=1/p**/ - - /*diverse: */ - IssmDouble r,s; - IssmDouble drag_p, drag_q; - IssmDouble Neff,F; - IssmDouble thickness,base,sealevel; - IssmDouble drag_coefficient,water_layer; - IssmDouble alpha2; - - /*Recover parameters: */ - element->parameters->FindParam(&F,FrictionFEnum); - element->GetInputValue(&drag_p,gauss,FrictionPEnum); - element->GetInputValue(&drag_q,gauss,FrictionQEnum); - element->GetInputValue(&thickness, gauss,ThicknessEnum); - element->GetInputValue(&base, gauss,BaseEnum); - element->GetInputValue(&sealevel, gauss,SealevelEnum); - element->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum); - element->GetInputValue(&water_layer, gauss,FrictionWaterLayerEnum); - IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum); - IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); - IssmDouble gravity = element->FindParam(ConstantsGEnum); - - //compute r and q coefficients: */ - r=drag_q/drag_p; - s=1./drag_p; - - //From base and thickness, compute effective pressure when drag is viscous: - if(base>0) base=0; - if(water_layer==0) Neff=gravity*rho_ice*thickness+gravity*rho_water*(base-sealevel); - else if(water_layer>0) Neff=gravity*rho_ice*thickness*F; - else _error_("negative water layer thickness"); - if(Neff<0) Neff=0; - - IssmDouble vmag = VelMag(gauss); - - if(s==1.){ - /*This is to make AD happy and avoid 0^0*/ - alpha2=drag_coefficient*drag_coefficient*pow(Neff,r); - } - else{ - /*Check to prevent dividing by zero if vmag==0*/ - if(vmag==0. && (s-1.)<0.) alpha2=0.; - else alpha2=drag_coefficient*drag_coefficient*pow(Neff,r)*pow(vmag,(s-1.)); - } - - /*Assign output pointers:*/ - *palpha2=alpha2; -}/*}}}*/ -void Friction::GetAlpha2Weertman(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ - - /*This routine calculates the basal friction coefficient alpha2= C^2 |v|^(1/m-1) */ - - /*diverse: */ - IssmDouble C,m; - IssmDouble alpha2; - - /*Recover parameters: */ - element->GetInputValue(&C,gauss,FrictionCEnum); - element->GetInputValue(&m,gauss,FrictionMEnum); - - /*Get velocity magnitude*/ - IssmDouble vmag = VelMag(gauss); - - /*Check to prevent dividing by zero if vmag==0*/ - if(vmag==0. && (1./m-1.)<0.) alpha2=0.; - else alpha2=C*C*pow(vmag,(1./m-1.)); - - /*Assign output pointers:*/ - *palpha2=alpha2; -}/*}}}*/ -void Friction::GetAlpha2WeertmanTemp(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ - /*Here, we want to parameterize the friction as a function of temperature - * - * alpha2 = alpha2_weertman * 1/f(T) - * - * where f(T) = exp((T-Tpmp)/gamma) - */ - - /*Intermediaries: */ - IssmDouble f,T,pressure,Tpmp,gamma; - IssmDouble alpha2; - - /*Get viscous part*/ - this->GetAlpha2Weertman(&alpha2,gauss); - - /*Get pressure melting point (Tpmp) for local pressure and get current temperature*/ - element->GetInputValue(&T,gauss,TemperatureEnum); - element->GetInputValue(&pressure,gauss,PressureEnum); - Tpmp = element->TMeltingPoint(pressure); - - /*Compute scaling parameter*/ - element->parameters->FindParam(&gamma,FrictionGammaEnum); - alpha2 = alpha2 / exp((T-Tpmp)/gamma); - - /*Assign output pointers:*/ - *palpha2=alpha2; -}/*}}}*/ -void Friction::GetAlpha2PISM(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ - /*Here, we want to parameterize the friction using a pseudoplastic friction law, - * computing the basal shear stress as - * - * alpha2 = tau_c (u_b/(abs(u_b)^(1-q)*u_0^q)) - * - * The yield stress tau_c is a function of the effective pressure N - * using a Mohr-Coloumb criterion, so that - * tau_c = tan(phi)*N, - * where phi is the till friction angle, representing sediment strength - * - * The effective pressure is given by Eq. (5) in Aschwanden et al. 2016: - * - * N = delta * P0 * 10^((e_0/Cc)(1-(W/Wmax))) - * - * W is calculated by a non-conserving hydrology model in HydrologyPismAnalysis.cpp - * - * see Aschwanden et al. 2016 and Bueler and Brown, 2009 for more details - */ - - /*compute ice overburden pressure P0*/ - IssmDouble thickness,base,P0; - element->GetInputValue(&thickness, gauss,ThicknessEnum); - element->GetInputValue(&base, gauss,BaseEnum); - //element->GetInputValue(&sealevel, gauss,SealevelEnum); - IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); - IssmDouble gravity = element->FindParam(ConstantsGEnum); - P0 = gravity*rho_ice*thickness; - - /*Compute effective pressure*/ - IssmDouble N,delta,W,Wmax,e0,Cc; - element->parameters->FindParam(&delta,FrictionDeltaEnum); - element->parameters->FindParam(&e0,FrictionVoidRatioEnum); - element->GetInputValue(&Cc,gauss,FrictionSedimentCompressibilityCoefficientEnum); - element->GetInputValue(&W,gauss,WatercolumnEnum); - element->GetInputValue(&Wmax,gauss,HydrologyWatercolumnMaxEnum); - - /*Check that water column height is within 0 and upper bound, correct if needed*/ - if(W>Wmax) W=Wmax; - if(W<0) W=0.; - - N = delta*P0*pow(10.,(e0/Cc)*(1.-W/Wmax)); - - /*Get till friction angles, defined by user [deg]*/ - IssmDouble phi; - element->GetInputValue(&phi,gauss,FrictionTillFrictionAngleEnum); - - /*Convert till friction angle from user-defined deg to rad, which Matlab uses*/ - phi = phi*PI/180.; - - /*Compute yield stress following a Mohr-Colomb criterion*/ - IssmDouble tau_c = N*tan(phi); - - /*Compute basal speed*/ - IssmDouble ub; - element->GetInputValue(&ub,gauss,VelEnum); - - /*now compute alpha^2*/ - IssmDouble u0,q; - element->parameters->FindParam(&u0,FrictionThresholdSpeedEnum); - element->parameters->FindParam(&q,FrictionPseudoplasticityExponentEnum); - IssmDouble alpha2 = tau_c/(pow(ub+1.e-10,1.-q)*pow(u0,q)); - - /*Assign output pointers:*/ - *palpha2=alpha2; -}/*}}}*/ -void Friction::GetAlpha2Schoof(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ - - /*This routine calculates the basal friction coefficient - * - * C |u_b|^(m-1) - * alpha2= __________________________ - * (1+(C/(Cmax Neff))^1/m |u_b| )^m - * - * */ - - /*diverse: */ - IssmDouble C,coeff,Cmax,m,alpha2; - - /*Recover parameters: */ - element->GetInputValue(&Cmax,gauss,FrictionCmaxEnum); - element->GetInputValue(&coeff,gauss,FrictionCEnum); - element->GetInputValue(&m,gauss,FrictionMEnum); - - /* scale C for a better inversion */ - C = coeff*coeff; - - /*Get effective pressure*/ - bool ispwStochastic; - IssmDouble Neff; - element->parameters->FindParam(&ispwStochastic,StochasticForcingIsWaterPressureEnum); - if(ispwStochastic){ - /*Retrieve stochastic water pressure and compute ice pressure*/ - IssmDouble p_ice,p_water,Neff_limit; - element->GetInputValue(&p_water,gauss,FrictionSchoofWaterPressureEnum); - element->parameters->FindParam(&Neff_limit,FrictionEffectivePressureLimitEnum); - p_ice = IcePressure(gauss); - Neff = max(Neff_limit*p_ice, p_ice - p_water); - } - else{ - /*Compute effective pressure directly*/ - Neff = EffectivePressure(gauss); - } - /*Get velocity magnitude*/ IssmDouble ub = VelMag(gauss); @@ -801,5 +941,5 @@ } else{ - alpha2= (C*pow(ub,m-1.)) / pow(1.+ pow(C/(Cmax*Neff),1./m)*ub,m); + alpha2= (C*C*pow(ub,m-1.)) / pow(1.+ pow(C*C/(Cmax*Neff),1./m)*ub,m); } @@ -874,5 +1014,74 @@ *palpha2=alpha2; }/*}}}*/ - +void Friction::GetAlpha2RegCoulomb(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + + /*This routine calculates the basal friction coefficient + * + * C |u_b|^(1/m-1) + * alpha2= __________________________ + * (|u_b|/u0 + 1 )^(1/m) + * + * */ + + /*diverse: */ + IssmDouble C,coeff,u0,m,alpha2; + + /*Recover parameters: */ + element->GetInputValue(&coeff,gauss,FrictionCEnum); + element->GetInputValue(&m,gauss,FrictionMEnum); + element->parameters->FindParam(&u0,FrictionU0Enum); + + /* scale C for a better inversion */ + C = coeff*coeff; + + /*Get velocity magnitude*/ + IssmDouble ub = VelMag(gauss); + + /*Check to prevent dividing by zero if vmag==0*/ + if(ub==0.) { + alpha2=0.; + } + else { + /*Compute alpha^2*/ + alpha2= (C*pow(ub,1./m-1.)) / pow(ub/u0 + 1.,1./m); + } + + /*Assign output pointers:*/ + *palpha2=alpha2; +}/*}}}*/ +void Friction::GetAlpha2RegCoulomb2(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + + /*This routine calculates the basal friction coefficient + * + * C N |u_b|^(1/m-1) + * alpha2= __________________________ + * (|u_b| + K N^m )^(1/m) + * + * */ + + /*diverse: */ + IssmDouble C,K,m,alpha2; + + /*Recover parameters: */ + element->GetInputValue(&C,gauss,FrictionCEnum); + element->GetInputValue(&m,gauss,FrictionMEnum); + element->GetInputValue(&K,gauss,FrictionKEnum); + + /*Get velocity magnitude*/ + IssmDouble ub = VelMag(gauss); + IssmDouble Neff = EffectivePressure(gauss); + + /*Check to prevent dividing by zero if vmag==0*/ + if(ub==0. && (m-1.)<0) { + alpha2=0.; + } + else { + /*Compute alpha^2*/ + alpha2= (C*pow(ub,1./m-1.)) * Neff / pow((ub+pow(K*Neff,m)),1./m); + } + + /*Assign output pointers:*/ + *palpha2=alpha2; +}/*}}}*/ IssmDouble Friction::EffectivePressure(Gauss* gauss){/*{{{*/ /*Get effective pressure as a function of flag */ @@ -1044,2 +1253,207 @@ _assert_(!xIsInf(*pvz)); }/*}}}*/ + +/*IO*/ +void FrictionUpdateInputs(Elements* elements,Inputs* inputs,IoModel* iomodel){/*{{{*/ + + /*Intermediaries*/ + int frictionlaw; + int frictioncoupling; + + /*Friction law variables*/ + iomodel->FindConstant(&frictionlaw,"md.friction.law"); + switch(frictionlaw){ + case 1: + iomodel->FindConstant(&frictioncoupling,"md.friction.coupling"); + iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); + if(frictioncoupling==3){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} + else if(frictioncoupling==4){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); + } + break; + case 2: + iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); + break; + case 3: + iomodel->FindConstant(&frictioncoupling,"md.friction.coupling"); + iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.As",FrictionAsEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); + if(frictioncoupling==3){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} + else if(frictioncoupling==4){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); + } + break; + case 4: + iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); + iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); + iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); + iomodel->FindConstant(&frictioncoupling,"md.friction.coupling"); + break; + case 5: + iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.water_layer",FrictionWaterLayerEnum); + break; + case 6: + iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); + iomodel->FetchDataToInput(inputs,elements,"md.initialization.pressure",PressureEnum); + iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); + break; + case 7: + iomodel->FindConstant(&frictioncoupling,"md.friction.coupling"); + iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficientcoulomb",FrictionCoefficientcoulombEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.p",FrictionPEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.q",FrictionQEnum); + if(frictioncoupling==3){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} + else if(frictioncoupling==4){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); + + } + break; + case 8: + iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); + break; + case 9: + iomodel->FetchDataToInput(inputs,elements,"md.initialization.temperature",TemperatureEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.pressure_adjusted_temperature",FrictionPressureAdjustedTemperatureEnum); + InputUpdateFromConstantx(inputs,elements,1.,FrictionPEnum); + InputUpdateFromConstantx(inputs,elements,1.,FrictionQEnum); + break; + case 10: + iomodel->FetchDataToInput(inputs,elements,"md.friction.till_friction_angle",FrictionTillFrictionAngleEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.sediment_compressibility_coefficient",FrictionSedimentCompressibilityCoefficientEnum); + iomodel->FetchDataToInput(inputs,elements,"md.hydrology.watercolumn_max",HydrologyWatercolumnMaxEnum); + iomodel->FetchDataToInput(inputs,elements,"md.initialization.watercolumn",WatercolumnEnum,0.); + break; + case 11: + iomodel->FindConstant(&frictioncoupling,"md.friction.coupling"); + iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.Cmax",FrictionCmaxEnum); + if(frictioncoupling==3){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} + else if(frictioncoupling==4){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); + } + break; + case 12: + iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.f",FrictionfEnum); + break; + case 13: + iomodel->FindConstant(&frictioncoupling,"md.friction.coupling"); + iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); + if(frictioncoupling==3){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum);} + else if(frictioncoupling==4){ + iomodel->FetchDataToInput(inputs,elements,"md.friction.effective_pressure",EffectivePressureEnum); + } + break; + case 14: + iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); + break; + case 15: + iomodel->FetchDataToInput(inputs,elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.m",FrictionMEnum); + iomodel->FetchDataToInput(inputs,elements,"md.friction.K",FrictionKEnum); + break; + default: + _error_("friction law "<< frictionlaw <<" not supported"); + } + +#ifdef _HAVE_ANDROID_ + inputs->DuplicateInput(FrictionCoefficientEnum,AndroidFrictionCoefficientEnum); +#endif + +}/*}}}*/ +void FrictionUpdateParameters(Parameters* parameters,IoModel* iomodel){/*{{{*/ + + parameters->AddObject(iomodel->CopyConstantObject("md.friction.law",FrictionLawEnum)); + + /*Set default linearize parameter to 0 for now*/ + parameters->AddObject(new IntParam(FrictionLinearizeEnum,0)); + + int frictionlaw; + iomodel->FindConstant(&frictionlaw,"md.friction.law"); + switch(frictionlaw){ + case 1: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.linearize",FrictionLinearizeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); + break; + case 2: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.linearize",FrictionLinearizeEnum)); + break; + case 3: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); + break; + case 4: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); + break; + case 5: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.f",FrictionFEnum)); + break; + case 6: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); + break; + case 7: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); + break; + case 8: + break; + case 9: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); + parameters->AddObject(new IntParam(FrictionCouplingEnum,2));/*comment this line to use effective pressure from Beuler and Pelt (2015)*/ + break; + case 10: + parameters->AddObject(new IntParam(FrictionCouplingEnum,2)); /*comment this line to use effective pressure from Beuler and Pelt (2015)*/ + parameters->AddObject(new DoubleParam(FrictionEffectivePressureLimitEnum,0.)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.pseudoplasticity_exponent",FrictionPseudoplasticityExponentEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.threshold_speed",FrictionThresholdSpeedEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.delta",FrictionDeltaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.void_ratio",FrictionVoidRatioEnum)); + break; + case 11: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); + break; + case 12: + parameters->AddObject(new IntParam(FrictionCouplingEnum,2)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); + break; + case 13: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); + break; + case 14: + parameters->AddObject(iomodel->CopyConstantObject("md.friction.u0",FrictionU0Enum)); + break; + case 15: + parameters->AddObject(new IntParam(FrictionCouplingEnum,2)); + parameters->AddObject(iomodel->CopyConstantObject("md.friction.effective_pressure_limit",FrictionEffectivePressureLimitEnum)); + break; + default: _error_("Friction law "<DeepEcho(); + + _printf_("Moulin:\n"); + _printf_(" id: " << id << "\n"); + hnode->Echo(); + hvertex->Echo(); + helement->Echo(); + _printf_(" parameters\n"); + parameters->Echo(); + //this->DeepEcho(); } /*}}}*/ @@ -143,5 +151,5 @@ void Moulin::Configure(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){/*{{{*/ - /*Take care of hooking up all objects for this load, ie links the objects in the hooks to their respective + /*Take care of hooking up all objects for this load, ie links the objects in the hooks to their respective * datasets, using internal ids and offsets hidden in hooks: */ hnode->configure(nodesin); @@ -204,8 +212,8 @@ break; case HydrologyDCInefficientAnalysisEnum: - pe = CreatePVectorHydrologyDCInefficient(); + pe = this->CreatePVectorHydrologyDCInefficient(); break; case HydrologyDCEfficientAnalysisEnum: - pe = CreatePVectorHydrologyDCEfficient(); + pe = this->CreatePVectorHydrologyDCEfficient(); break; default: @@ -427,8 +435,7 @@ * mesh), don't add the moulin input a second time*/ if(node->IsClone()) return NULL; - bool isefficientlayer; + bool isefficientlayer, active_element; IssmDouble moulin_load,dt; IssmDouble epl_active; - /*Initialize Element matrix*/ ElementVector* pe=new ElementVector(&node,1,this->parameters); @@ -437,17 +444,25 @@ parameters->FindParam(&dt,TimesteppingTimeStepEnum); parameters->FindParam(&isefficientlayer,HydrologydcIsefficientlayerEnum); - // Test version input in EPL when active + + //Test version input in EPL when active if(isefficientlayer){ - this->element->GetInputValue(&epl_active,node,HydrologydcMaskEplactiveNodeEnum); - if(reCast(epl_active)){ - pe->values[0]=moulin_load*0.0; + this->element->GetInputValue(&active_element,HydrologydcMaskEplactiveEltEnum); + if(!active_element){ + /* this->element->GetInputValue(&epl_active,node,HydrologydcMaskEplactiveNodeEnum); */ + /* if(reCast(epl_active))pe->values[0]=0.0; */ + /* else { */ + pe->values[0]=moulin_load*dt; + /* if (moulin_load>0)_printf_("MoulinInput in Sed is "<values[0]<<"\n"); */ + /* if (moulin_load>0)pe->Echo(); */ + /* } */ + //if (node->Sid()==4)_printf_("MoulinInput in Sed is "<values[0]=moulin_load*dt; - } - } - else{ - pe->values[0]=moulin_load*dt; - } + else pe->values[0]=0.0; + } + else pe->values[0]=moulin_load*dt; + + //Test only input in sed + /* pe->values[0]=moulin_load*dt; */ + /*Clean up and return*/ return pe; @@ -458,14 +473,39 @@ /*If this node is not the master node (belongs to another partition of the * mesh), don't add the moulin input a second time*/ + if(node->IsClone()) return NULL; - if(!this->node->IsActive()) return NULL; - IssmDouble moulin_load,dt; ElementVector* pe=new ElementVector(&node,1,this->parameters); - this->element->GetInputValue(&moulin_load,node,HydrologydcBasalMoulinInputEnum); - parameters->FindParam(&dt,TimesteppingTimeStepEnum); - - pe->values[0]=moulin_load*dt; - /*Clean up and return*/ + //Test Input in epl if active + /* IssmDouble epl_active; */ + /* this->element->GetInputValue(&epl_active,node,HydrologydcMaskEplactiveNodeEnum); */ + /* //if(node->Sid()==4)_printf_("Activity is "<(epl_active)){ */ + /* IssmDouble moulin_load,dt; */ + /* this->element->GetInputValue(&moulin_load,node,HydrologydcBasalMoulinInputEnum); */ + /* parameters->FindParam(&dt,TimesteppingTimeStepEnum); */ + /* pe->values[0]=moulin_load*dt; */ + /* if (moulin_load>0)_printf_("MoulinInput in Epl is "<values[1]<<"\n"); */ + + /* } */ + /* else{ */ + /* pe->values[0]=0.0; */ + /* } */ + // Test element only test + bool active_element; + this->element->GetInputValue(&active_element,HydrologydcMaskEplactiveEltEnum); + if(active_element){ + IssmDouble moulin_load,dt; + this->element->GetInputValue(&moulin_load,node,HydrologydcBasalMoulinInputEnum); + parameters->FindParam(&dt,TimesteppingTimeStepEnum); + pe->values[0]=moulin_load*dt; + } + else pe->values[0]=0.0; + + + //Test only input is sed + /* pe->values[0]=0.0; */ + + //Clean up and return return pe; } Index: /issm/trunk/src/c/classes/Loads/Neumannflux.cpp =================================================================== --- /issm/trunk/src/c/classes/Loads/Neumannflux.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Loads/Neumannflux.cpp (revision 28013) @@ -352,5 +352,11 @@ /*Initialize Load Vector and return if necessary*/ - Tria* tria=(Tria*)element; + Tria* tria=NULL; + if(element->ObjectEnum()==TriaEnum){ + tria = (Tria*)this->element; + } + else if(element->ObjectEnum()==PentaEnum){ + tria = (Tria*)this->element->SpawnBasalElement(); + } _assert_(tria->FiniteElement()==P1Enum); if(!tria->IsIceInElement() || tria->IsAllFloating()) return NULL; @@ -380,4 +386,5 @@ /*Clean up and return*/ delete gauss; + if(tria->IsSpawnedElement()){tria->DeleteMaterials(); delete tria;}; return pe; } Index: /issm/trunk/src/c/classes/Materials/Matlitho.cpp =================================================================== --- /issm/trunk/src/c/classes/Materials/Matlitho.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Materials/Matlitho.cpp (revision 28013) @@ -14,25 +14,22 @@ /*Matlitho constructors and destructor*/ Matlitho::Matlitho(){/*{{{*/ - this->numlayers=0; - this->radius=NULL; - this->viscosity=NULL; - this->lame_lambda=NULL; - this->lame_mu=NULL; - this->burgers_viscosity=NULL; - this->burgers_mu=NULL; - this->ebm_alpha=NULL; - this->ebm_delta=NULL; - this->ebm_taul=NULL; - this->ebm_tauh=NULL; - this->density=NULL; - this->rheologymodel=NULL; - this->issolid=NULL; - return; -} -/*}}}*/ -Matlitho::Matlitho(int matlitho_mid, IoModel* iomodel){/*{{{*/ - - IssmDouble* rheologymodeld=NULL; - IssmDouble* issolidd=NULL; + this->numlayers = 0; + this->radius = NULL; + this->viscosity = NULL; + this->lame_lambda = NULL; + this->lame_mu = NULL; + this->burgers_viscosity = NULL; + this->burgers_mu = NULL; + this->ebm_alpha = NULL; + this->ebm_delta = NULL; + this->ebm_taul = NULL; + this->ebm_tauh = NULL; + this->density = NULL; + this->rheologymodel = NULL; + this->issolid = NULL; + return; +} +/*}}}*/ +Matlitho::Matlitho(int matlitho_mid, IoModel* iomodel, bool* issolid_in, int* rheo_in){/*{{{*/ this->mid=matlitho_mid; @@ -72,23 +69,9 @@ xMemCpy(this->density, iomodel->Data("md.materials.density"),this->numlayers); - this->rheologymodel=xNew(this->numlayers); - xMemCpy(this->rheologymodel, iomodel->Data("md.materials.rheologymodel"),this->numlayers); - - this->issolid=xNew(this->numlayers); - xMemCpy(this->issolid, iomodel->Data("md.materials.issolid"),this->numlayers); - - /*rheologymodeld= xNew(this->numlayers); - this->rheologymodel=xNew(this->numlayers); - xMemCpy(rheologymodeld, iomodel->Data("md.materials.rheologymodel"),this->numlayers); - for (int i=0;inumlayers;i++)this->rheologymodel[i]=reCast(rheologymodeld[i]); - - issolidd= xNew(this->numlayers); + this->rheologymodel=xNew(this->numlayers); + xMemCpy(this->rheologymodel, rheo_in, this->numlayers); + this->issolid=xNew(this->numlayers); - xMemCpy(issolidd, iomodel->Data("md.materials.issolid"),this->numlayers); - for (int i=0;inumlayers;i++)this->issolid[i]=reCast(issolidd[i]);*/ - - /*Free resources: */ - xDelete(rheologymodeld); - xDelete(issolidd); + xMemCpy(this->issolid, issolid_in, this->numlayers); } /*}}}*/ @@ -106,6 +89,6 @@ xDelete(ebm_tauh); xDelete(density); - xDelete(rheologymodel); - xDelete(issolid); + xDelete(rheologymodel); + xDelete(issolid); return; @@ -141,8 +124,6 @@ matlitho->ebm_tauh=xNew(this->numlayers); xMemCpy(matlitho->ebm_tauh, this->ebm_tauh,this->numlayers); matlitho->density=xNew(this->numlayers); xMemCpy(matlitho->density, this->density,this->numlayers); - matlitho->rheologymodel=xNew(this->numlayers); xMemCpy(matlitho->rheologymodel, this->rheologymodel,this->numlayers); - matlitho->issolid=xNew(this->numlayers); xMemCpy(matlitho->issolid, this->issolid,this->numlayers); - /*matlitho->rheologymodel=xNew(this->numlayers); for(int i=0;inumlayers;i++)matlitho->rheologymodel[i]=this->rheologymodel[i]; - matlitho->issolid=xNew(this->numlayers); for(int i=0;inumlayers;i++)matlitho->issolid[i]=this->issolid[i];*/ + matlitho->rheologymodel=xNew(this->numlayers); xMemCpy(matlitho->rheologymodel, this->rheologymodel,this->numlayers); + matlitho->issolid=xNew(this->numlayers); xMemCpy(matlitho->issolid, this->issolid,this->numlayers); } Index: /issm/trunk/src/c/classes/Materials/Matlitho.h =================================================================== --- /issm/trunk/src/c/classes/Materials/Matlitho.h (revision 28012) +++ /issm/trunk/src/c/classes/Materials/Matlitho.h (revision 28013) @@ -28,9 +28,9 @@ IssmDouble* ebm_tauh; IssmDouble* density; - IssmDouble* rheologymodel; - IssmDouble* issolid; + int* rheologymodel; + bool* issolid; Matlitho(); - Matlitho(int matlitho_id, IoModel* iomodel); + Matlitho(int matlitho_id, IoModel* iomodel, bool* issolid_in, int* rheo_in); ~Matlitho(); void SetMid(int matlitho_mid); Index: /issm/trunk/src/c/classes/Nodalvalue.cpp =================================================================== --- /issm/trunk/src/c/classes/Nodalvalue.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Nodalvalue.cpp (revision 28013) @@ -64,5 +64,12 @@ /*}}}*/ void Nodalvalue::Marshall(MarshallHandle* marshallhandle){/*{{{*/ - _error_("not implemented yet!"); + + int object_enum=NodalvalueEnum; + marshallhandle->call(object_enum); + + marshallhandle->call(this->definitionenum); + marshallhandle->call(this->model_enum); + marshallhandle->call(this->name); + marshallhandle->call(this->node); } /*}}}*/ Index: /issm/trunk/src/c/classes/Nodalvalue.h =================================================================== --- /issm/trunk/src/c/classes/Nodalvalue.h (revision 28012) +++ /issm/trunk/src/c/classes/Nodalvalue.h (revision 28013) @@ -30,10 +30,10 @@ /*Object virtual function resolutoin: */ - Object* copy(); - void DeepEcho(void); - void Echo(void); - int Id(void); - void Marshall(MarshallHandle* marshallhandle); - int ObjectEnum(void); + Object *copy(); + void DeepEcho(void); + void Echo(void); + int Id(void); + void Marshall(MarshallHandle *marshallhandle); + int ObjectEnum(void); /*Definition virtual function resolutoin: */ Index: /issm/trunk/src/c/classes/Node.cpp =================================================================== --- /issm/trunk/src/c/classes/Node.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Node.cpp (revision 28013) @@ -147,4 +147,6 @@ analysis_enum==HydrologyDCInefficientAnalysisEnum || analysis_enum==HydrologyDCEfficientAnalysisEnum || + analysis_enum==HydrologyShaktiAnalysisEnum || + analysis_enum==HydrologyGlaDSAnalysisEnum || analysis_enum==GLheightadvectionAnalysisEnum || analysis_enum==LevelsetAnalysisEnum Index: /issm/trunk/src/c/classes/Nodes.cpp =================================================================== --- /issm/trunk/src/c/classes/Nodes.cpp (revision 28012) +++ /issm/trunk/src/c/classes/Nodes.cpp (revision 28013) @@ -181,14 +181,19 @@ * object that is not a clone, tell them to show their dofs, so that later on, they can get picked * up by their clones: */ - int maxdofspernode = this->MaxNumDofs(GsetEnum); - int* truedofs = xNewZeroInit(this->Size()*maxdofspernode); //only one alloc + int maxdofspernode = this->MaxNumDofs(GsetEnum); + int **send_truedofs = xNewZeroInit(num_procs); + int *recv_truedofs = xNewZeroInit(this->Size()*maxdofspernode); + ISSM_MPI_Request *send_requests = xNew(num_procs); + for (int rank = 0;rankcommon_send[rank]){ int numids = this->common_send[rank]; + send_truedofs[rank] = xNew(numids*maxdofspernode); for(int i=0;i(this->GetObjectByOffset(this->common_send_ids[rank][i])); - node->ShowMasterDofs(&truedofs[i*maxdofspernode+0],setenum); - } - ISSM_MPI_Send(truedofs,numids*maxdofspernode,ISSM_MPI_INT,rank,0,IssmComm::GetComm()); + node->ShowMasterDofs(&send_truedofs[rank][i*maxdofspernode+0],setenum); + } + ISSM_MPI_Isend(send_truedofs[rank],numids*maxdofspernode,ISSM_MPI_INT,rank,0,IssmComm::GetComm(),&send_requests[rank]); } } @@ -196,12 +201,18 @@ if(this->common_recv[rank]){ int numids = this->common_recv[rank]; - ISSM_MPI_Recv(truedofs,numids*maxdofspernode,ISSM_MPI_INT,rank,0,IssmComm::GetComm(),&status); + ISSM_MPI_Recv(recv_truedofs,numids*maxdofspernode,ISSM_MPI_INT,rank,0,IssmComm::GetComm(),&status); for(int i=0;i(this->GetObjectByOffset(this->common_recv_ids[rank][i])); - node->UpdateCloneDofs(&truedofs[i*maxdofspernode+0],setenum); - } - } - } - xDelete(truedofs); + node->UpdateCloneDofs(&recv_truedofs[i*maxdofspernode+0],setenum); + } + } + } + xDelete(recv_truedofs); + for(int rank=0;rankcommon_send[rank]) ISSM_MPI_Wait(&send_requests[rank],&status); + xDelete(send_truedofs[rank]); + } + xDelete(send_truedofs); + xDelete(send_requests); /*Update indexingupdateflag*/ @@ -261,13 +272,17 @@ /* Share pids of masters and update pids of clones*/ - int* truepids = xNew(this->Size()); //only one alloc + int **send_truepids = xNewZeroInit(num_procs); + int *recv_truepids = xNewZeroInit(this->Size()); + ISSM_MPI_Request* send_requests = xNew(num_procs); + for(int rank=0;rankcommon_send[rank]){ int numids = this->common_send[rank]; + send_truepids[rank] = xNew(numids); for(int i=0;i(this->GetObjectByOffset(this->common_send_ids[rank][i])); - truepids[i] = node->pid; - } - ISSM_MPI_Send(truepids,numids,ISSM_MPI_INT,rank,0,IssmComm::GetComm()); + send_truepids[rank][i] = node->pid; + } + ISSM_MPI_Isend(send_truepids[rank],numids,ISSM_MPI_INT,rank,0,IssmComm::GetComm(),&send_requests[rank]); } } @@ -275,12 +290,18 @@ if(this->common_recv[rank]){ int numids = this->common_recv[rank]; - ISSM_MPI_Recv(truepids,numids,ISSM_MPI_INT,rank,0,IssmComm::GetComm(),&status); + ISSM_MPI_Recv(recv_truepids,numids,ISSM_MPI_INT,rank,0,IssmComm::GetComm(),&status); for(int i=0;i(this->GetObjectByOffset(this->common_recv_ids[rank][i])); - node->pid = truepids[i]; - } - } - } - xDelete(truepids); + node->pid = recv_truepids[i]; + } + } + } + xDelete(recv_truepids); + for(int rank=0;rankcommon_send[rank]) ISSM_MPI_Wait(&send_requests[rank],&status); + xDelete(send_truepids[rank]); + } + xDelete(send_truepids); + xDelete(send_requests); /*4. Distribute G dofs once for all*/ @@ -483,19 +504,20 @@ /*Now send and receive ug for nodes on partition edge*/ - #ifdef _HAVE_AD_ - IssmDouble* buffer = xNew(this->Size()*maxdofspernode,"t"); //only one alloc, "t" is required by adolc - #else - IssmDouble* buffer = xNew(this->Size()*maxdofspernode); - #endif + IssmDouble **send_buffers = xNewZeroInit(num_procs); + IssmDouble *recv_buffer = xNewZeroInit(this->Size()*maxdofspernode,"t"); + ISSM_MPI_Request *send_requests = xNew(num_procs); + for (int rank = 0;rankcommon_send[rank]){ int numids = this->common_send[rank]; + send_buffers[rank] = xNew(numids*maxdofspernode,"t"); //"t" is required by adolc for(int i=0;icommon_send_ids[rank][i]; Node* node=xDynamicCast(this->GetObjectByOffset(master_lid)); _assert_(!node->IsClone()); - for(int j=0;jgsize;j++) buffer[i*maxdofspernode+j]=local_ug[node->gdoflist_local[j]]; - } - ISSM_MPI_Send(buffer,numids*maxdofspernode,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm()); + for(int j=0;jgsize;j++) send_buffers[rank][i*maxdofspernode+j]=local_ug[node->gdoflist_local[j]]; + } + ISSM_MPI_Isend(send_buffers[rank],numids*maxdofspernode,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&send_requests[rank]); } } @@ -503,13 +525,20 @@ if(this->common_recv[rank]){ int numids = this->common_recv[rank]; - ISSM_MPI_Recv(buffer,numids*maxdofspernode,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); + ISSM_MPI_Recv(recv_buffer,numids*maxdofspernode,ISSM_MPI_DOUBLE,rank,0,IssmComm::GetComm(),&status); for(int i=0;icommon_recv_ids[rank][i]; Node* node=xDynamicCast(this->GetObjectByOffset(master_lid)); - for(int j=0;jgsize;j++) local_ug[node->gdoflist_local[j]] = buffer[i*maxdofspernode+j]; - } - } - } - xDelete(buffer); + for(int j=0;jgsize;j++) local_ug[node->gdoflist_local[j]] = recv_buffer[i*maxdofspernode+j]; + } + } + } + + xDelete(recv_buffer); + for(int rank=0;rankcommon_send[rank]) ISSM_MPI_Wait(&send_requests[rank],&status); + xDelete(send_buffers[rank]); + } + xDelete(send_buffers); + xDelete(send_requests); /*Assign output pointer*/ Index: /issm/trunk/src/c/classes/Params/BoolParam.h =================================================================== --- /issm/trunk/src/c/classes/Params/BoolParam.h (revision 28012) +++ /issm/trunk/src/c/classes/Params/BoolParam.h (revision 28013) @@ -49,4 +49,5 @@ void GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");} void GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");} + void GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, const char* data){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");} void GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");} void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} @@ -62,4 +63,5 @@ void SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");} void SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");} + void SetValue(IssmDouble* IssmDoublearray){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");} void SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");} void SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");} @@ -70,4 +72,5 @@ void SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");} void SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");} + void SetGradient(IssmDouble* poutput, int M, int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an IssmDouble");}; /*}}}*/ }; Index: /issm/trunk/src/c/classes/Params/ControlParam.cpp =================================================================== --- /issm/trunk/src/c/classes/Params/ControlParam.cpp (revision 28013) +++ /issm/trunk/src/c/classes/Params/ControlParam.cpp (revision 28013) @@ -0,0 +1,252 @@ +/*!\file ControlParam.c + * \brief: implementation of the ControlParam object + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../classes.h" +#include "shared/shared.h" + +/*ControlParam constructors and destructor*/ +ControlParam::ControlParam(){/*{{{*/ + return; +} +/*}}}*/ +ControlParam::ControlParam(IssmDouble* in_value, IssmDouble* in_minvalue, IssmDouble* in_maxvalue, int in_enum_type, int in_M,int in_N){/*{{{*/ + + this->enum_type=in_enum_type; + this->M=in_M; + this->N=in_N; + + /*Sanity check, can't hurt*/ + if(this->N<1) _error_("Parameter is empty"); + if(this->M<1) _error_("Parameter is empty"); + if(this->M>2) _error_("Cannot handle more than 2 rows (as a TransientParam)"); + + /*Assign value*/ + this->value=xNew(M*N); + xMemCpy(value,in_value,M*N); + + /*Assign other fields*/ + this->minvalue=xNew(N); + xMemCpy(minvalue,in_minvalue,N); + this->maxvalue=xNew(N); + xMemCpy(maxvalue,in_maxvalue,N); + this->gradient=xNewZeroInit(N); +} +/*}}}*/ +ControlParam::~ControlParam(){/*{{{*/ + xDelete(value); + xDelete(minvalue); + xDelete(maxvalue); + xDelete(gradient); + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +Param* ControlParam::copy() {/*{{{*/ + + ControlParam* output = new ControlParam(); + output->enum_type=this->enum_type; + output->M=this->M; + output->N=this->N; + if(value){ + output->value=xNew(this->M*this->N); + xMemCpy(output->value,this->value,this->M*this->N); + } + if(minvalue){ + output->minvalue=xNew(this->N); + xMemCpy(output->minvalue,this->minvalue,this->N); + } + if(maxvalue){ + output->maxvalue=xNew(this->N); + xMemCpy(output->maxvalue,this->maxvalue,this->N); + } + if(gradient){ + output->gradient=xNew(this->N); + xMemCpy(output->gradient,this->gradient,this->N); + } + return output; + +} +/*}}}*/ +void ControlParam::DeepEcho(void){/*{{{*/ + + _printf_(setw(22)<<" ControlParam "<enum_type)<<"\n "); + if (value) _printf_("---value: "); + for(int i=0;iM;i++) _printf_(" "<< this->value[i]); + _printf_("]\n"); + if (minvalue) _printf_("---minvalue: "); + for(int i=0;iM;i++) _printf_(" "<< this->minvalue[i]); + _printf_("]\n"); + if (maxvalue) _printf_("---maxvalue: "); + for(int i=0;iM;i++) _printf_(" "<< this->maxvalue[i]); + _printf_("]\n"); + if (gradient) _printf_("---gradient: " << this->gradient << "\n"); +} +/*}}}*/ +void ControlParam::Echo(void){/*{{{*/ + this->DeepEcho(); +} +/*}}}*/ +int ControlParam::Id(void){ return -1; }/*{{{*/ +/*}}}*/ +void ControlParam::Marshall(MarshallHandle* marshallhandle){ /*{{{*/ + + int object_enum = ControlParamEnum; + marshallhandle->call(object_enum); + marshallhandle->call(this->enum_type); + marshallhandle->call(this->M); + marshallhandle->call(this->N); + marshallhandle->call(this->value,this->M*this->N); + marshallhandle->call(this->minvalue,this->N); + marshallhandle->call(this->maxvalue,this->N); + marshallhandle->call(this->gradient,this->N); + +} +/*}}}*/ +int ControlParam::ObjectEnum(void){/*{{{*/ + + return ControlParamEnum; + +} +/*}}}*/ + +void ControlParam::GetParameterValue(IssmDouble** poutput,int* pN, const char* data){/*{{{*/ + + IssmDouble* output=xNew(N); + + if(strcmp(data,"value")==0){ + xMemCpy(output,value,N); + } + else if (strcmp(data,"lowerbound")==0){ + xMemCpy(output,minvalue,N); + } + else if (strcmp(data,"upperbound")==0){ + xMemCpy(output,maxvalue,N); + } + else if (strcmp(data,"gradient")==0){ + xMemCpy(output,gradient,N); + } + else{ + _error_("Data " << data << " not supported yet"); + } + + /*Assign output pointers:*/ + if(pN) *pN=N; + *poutput=output; +} +/*}}}*/ +void ControlParam::GetParameterValue(IssmDouble* poutput){/*{{{*/ + + /*Copy entire vector if M==1, or first row if M==2*/ + if(M==1){ + xMemCpy(poutput,value,N); + return; + } + + _error_("STOP"); + +} +/*}}}*/ +void ControlParam::GetParameterValue(IssmDouble* poutput, IssmDouble time){/*{{{*/ + + if(M==1){ + *poutput = value[0]; + return; + } + + IssmDouble *timesteps = &this->value[1*this->N+0]; + IssmDouble output; + bool found; + + /*Ok, we have the time, go through the timesteps, and figure out which interval we + *fall within. Then interpolate the values on this interval: */ + if(timevalue[0]; + found=true; + } + else if(time>timesteps[this->N-1]){ + /*get values for the last time: */ + output=this->value[this->N-1]; + found=true; + } + else{ + /*Find which interval we fall within: */ + for(int i=0;iN;i++){ + if(time==timesteps[i]){ + /*We are right on one step time: */ + output=this->value[i]; + found=true; + break; //we are done with the time interpolation. + } + else{ + if(timesteps[i]