Index: /issm/trunk/configs/config-arm-linux.sh =================================================================== --- /issm/trunk/configs/config-arm-linux.sh (revision 12706) +++ /issm/trunk/configs/config-arm-linux.sh (revision 12707) @@ -3,11 +3,8 @@ ./configure \ --prefix=$ISSM_DIR \ - --host="arm-linux" \ + --build="i386-apple-darwin10.8.0" \ + --host="arm-linux-androideabi" \ + --without-fortran \ --without-modules \ - CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc \ - GCC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc \ - CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-g++ \ - --with-vendor=arm-linux \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ - --without-fortran-lib + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install Index: /issm/trunk/configs/config-discover.sh =================================================================== --- /issm/trunk/configs/config-discover.sh (revision 12706) +++ /issm/trunk/configs/config-discover.sh (revision 12707) @@ -2,23 +2,26 @@ #PETSc 3.2 -#MPI /usr/local/intel/mpi/3.2.2.006/lib64/ +#MPI /usr/local/intel/mpi/4.0.3.008/lib64/ ./configure \ --prefix=$ISSM_DIR \ - --with-modules=no \ + --with-matlab-dir=$MATLAB_DIR \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mpi-include="/usr/local/intel/mpi/3.2.2.006/include64/" \ - --with-mpi-lib="-L/usr/local/intel/mpi/3.2.2.006/lib64/ -lmpi -lmpi_ilp64 -lmpiif" \ + --with-mkl-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-mpi-include="/usr/local/intel/mpi/4.0.3.008/include64/" \ + --with-mpi-lib="-L/usr/local/intel/mpi/4.0.3.008/lib64/ -lmpi -lmpiif" \ --with-petsc-arch=$ISSM_ARCH \ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --with-mkl-dir=/usr/local/intel/mkl/10.1.2.024/ \ + --with-scalapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-blacs-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blas-lapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-graphics-lib=/usr/lib64/libX11.so \ --with-cxxoptflags="-O3 -xS" \ - --with-vendor=intel-linux + --with-vendor=intel-discover + Index: /issm/trunk/configs/config-greenplanet.sh =================================================================== --- /issm/trunk/configs/config-greenplanet.sh (revision 12706) +++ /issm/trunk/configs/config-greenplanet.sh (revision 12707) @@ -10,4 +10,5 @@ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ --with-mpi-include="/sopt/mpi/openmpi-1.5.4_psm/intel/include/" \ --with-mpi-lib="-L/sopt/mpi/openmpi-1.5.4_psm/intel/lib/ -lmpi -lmpi_f77" \ Index: /issm/trunk/configs/config-linux64-ad.sh =================================================================== --- /issm/trunk/configs/config-linux64-ad.sh (revision 12706) +++ /issm/trunk/configs/config-linux64-ad.sh (revision 12707) @@ -16,3 +16,5 @@ --without-transient \ --without-3d \ - --without-groundingline + --without-groundingline \ + --without-kriging \ + --with-adolc-dir=$ADOLC_DIR Index: /issm/trunk/configs/config-linux64-astrid-petscdev.sh =================================================================== --- /issm/trunk/configs/config-linux64-astrid-petscdev.sh (revision 12707) +++ /issm/trunk/configs/config-linux64-astrid-petscdev.sh (revision 12707) @@ -0,0 +1,37 @@ +#!/bin/sh + +#External packages versions: +#petsc Dev: FH trying out +#mpich 1.4 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/src/externalpackages/metis-5.0.2-p3 \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-spai-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-prometheus-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-superlu-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-spooles-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-pastix-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2" \ + --with-numthreads=32 \ + --enable-debugging Index: /issm/trunk/configs/config-linux64-astrid-python.sh =================================================================== --- /issm/trunk/configs/config-linux64-astrid-python.sh (revision 12707) +++ /issm/trunk/configs/config-linux64-astrid-python.sh (revision 12707) @@ -0,0 +1,34 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.1 or 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-python-version=2.7\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2 -lutil" \ + --with-numthreads=32 \ + --enable-debugging Index: /issm/trunk/configs/config-macosx-snowleopard-bothapis.sh =================================================================== --- /issm/trunk/configs/config-macosx-snowleopard-bothapis.sh (revision 12707) +++ /issm/trunk/configs/config-macosx-snowleopard-bothapis.sh (revision 12707) @@ -0,0 +1,35 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +#export FCFLAGS=" -m32" +#export FFLAGS=" -m32" +#export CFLAGS=" -arch i386" +#export CXXFLAGS=" -arch i386" + +pythonversion=2.7 + +./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch i386 -DMX_COMPAT_32 -O3 -DNDEBUG -w "\ + --with-numthreads=8 \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ Index: /issm/trunk/configs/config-macosx-snowleopard-python.sh =================================================================== --- /issm/trunk/configs/config-macosx-snowleopard-python.sh (revision 12707) +++ /issm/trunk/configs/config-macosx-snowleopard-python.sh (revision 12707) @@ -0,0 +1,29 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +pythonversion=2.7 + +./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -fexceptions -O3 -DNDEBUG -w "\ + --with-numthreads=8 \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ Index: /issm/trunk/configs/config-macosx64-chris.sh =================================================================== --- /issm/trunk/configs/config-macosx64-chris.sh (revision 12707) +++ /issm/trunk/configs/config-macosx64-chris.sh (revision 12707) @@ -0,0 +1,28 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -fexceptions -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 Index: /issm/trunk/configs/config-macosx64-larour-ad.sh =================================================================== --- /issm/trunk/configs/config-macosx64-larour-ad.sh (revision 12706) +++ /issm/trunk/configs/config-macosx64-larour-ad.sh (revision 12707) @@ -1,23 +1,7 @@ #!/bin/sh -#petsc 3.2 -#mpich 1.4 - ./configure \ - --with-serial=no\ --prefix=$ISSM_DIR \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ - --without-blas-lapack-dir \ - --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ - --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --with-math-lib="/usr/lib/libm.dylib" \ - --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ - --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ - --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ - --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install/ \ - --with-numthreads=8 \ + --without-modules\ --without-thermal \ --without-control \ @@ -31,13 +15,6 @@ --without-transient \ --without-3d \ - --without-groundingline - -#--without-prognostic \ -#--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ -#--with-petsc-arch=$ISSM_ARCH \ -#--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ -#--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ -#--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ -#--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ -#--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ -#--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --without-groundingline \ + --without-kriging \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install + #--with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install\ Index: /issm/trunk/configs/config-pleiades-petscdev.sh =================================================================== --- /issm/trunk/configs/config-pleiades-petscdev.sh (revision 12707) +++ /issm/trunk/configs/config-pleiades-petscdev.sh (revision 12707) @@ -0,0 +1,28 @@ +#!/bin/csh + +./configure \ + --prefix=$ISSM_DIR \ + --with-modules=no \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/src/externalpackages/metis-5.0.2-p3 \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=/nasa/sgi/mpt/2.04/include \ + --with-mpi-lib="-L/nasa/sgi/mpt/2.04/lib/ -lmpi -lpthread -lgfortran" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/src/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-spai-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-prometheus-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-superlu-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-spooles-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-pastix-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -xS" \ + --with-vendor=intel-pleiades Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 12706) +++ /issm/trunk/configure.ac (revision 12707) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([ISSM],[4.2],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([ISSM],[4.2.1],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 Index: /issm/trunk/etc/environment.csh =================================================================== --- /issm/trunk/etc/environment.csh (revision 12706) +++ /issm/trunk/etc/environment.csh (revision 12707) @@ -127,2 +127,14 @@ setenv VALGRIND_DIR {$VALGRIND_DIR} setenv PATH {$PATH}:{$VALGRIND_DIR} + +#MERCURIAL +#setenv PYTHONPATH {$PYTHONPATH}:{$MERCURIAL_DIR}/mercurial/pure/ +setenv PYTHONPATH {$MERCURIAL_DIR}/mercurial/pure/ +setenv PATH {$PATH}:{$MERCURIAL_DIR} + +#GSL +setenv GSL_DIR {$GSL_DIR} +setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GSL_DIR}/lib + +#CMAKE +setenv PATH {$PATH}:{$CMAKE_DIR}/bin Index: /issm/trunk/etc/environment.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 12706) +++ /issm/trunk/etc/environment.sh (revision 12707) @@ -262,5 +262,5 @@ export PATH="$PYTHON_DIR/bin:$PATH" export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/src/modules/python" -export LD_LIBRARY_PATH=$ISSM_DIR/src/modules/python:$LD_LIBRARY_PATH +export LD_LIBRARY_PATH=$ISSM_DIR/src/modules/python:$ISSM_DIR/externalpackages/python/install/lib:$LD_LIBRARY_PATH export PYTHONSTARTUP @@ -270,2 +270,26 @@ #GIT export PATH="$PATH:$GIT_DIR/install/bin" + +#NCVIEW +export PATH="$PATH:$NCVIEW_DIR/install" + +#TCLX +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$TCLX_DIR" +export LD_RUN_PATH="$LD_RUN_PATH:$TCLX_DIR" + + +#ASPELL +export PATH="$ASPELL_DIR/install/bin:$PATH" + + +#ESMF +export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf +export ESMF_COMPILER=gfortran +export ESMF_COMM=mpich2 + +#HDF5 +export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HDF5_DIR/lib" +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HDF5_DIR/lib" +export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib" +export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include" + Index: /issm/trunk/etc/environment_variables.csh =================================================================== --- /issm/trunk/etc/environment_variables.csh (revision 12706) +++ /issm/trunk/etc/environment_variables.csh (revision 12707) @@ -81,4 +81,13 @@ set SSH_DIR={$ISSM_DIR}/externalpackages/ssh +#mercurial +set MERCURIAL_DIR={$ISSM_DIR}/externalpackages/mercurial/install + #valgrind set VALGRIND_DIR={$ISSM_DIR}/externalpackages/valgrind/install/bin + +#gsl +set GSL_DIR={$ISSM_DIR}/externalpackages/gsl/install + +#cmake +set CMAKE_DIR={$ISSM_DIR}/externalpackages/cmake/install Index: /issm/trunk/etc/environment_variables.sh =================================================================== --- /issm/trunk/etc/environment_variables.sh (revision 12706) +++ /issm/trunk/etc/environment_variables.sh (revision 12707) @@ -201,2 +201,14 @@ #GIT GIT_DIR="$ISSM_DIR/externalpackages/git" + +#NCVIEW +NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview" + +#TCLX +TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4" + +#ASPELL +ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/" + +#HDF5 +export HDF5_DIR=$ISSM_DIR/externalpackages/hdf5/install Index: /issm/trunk/externalpackages/adolc/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-macosx64.sh (revision 12707) +++ /issm/trunk/externalpackages/adolc/install-macosx64.sh (revision 12707) @@ -0,0 +1,61 @@ +#!/bin/bash + +#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. + +#Some cleanup +rm -rf install ADOL-C-2.2.0 src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' + +#Create install directories +mkdir install src + +#Untar +tar -zxvf ADOL-C-2.2.0.tar.gz + +#Move ADOL-C into install directory +mv ADOL-C-2.2.0/* src +rm -rf ADOL-C-2.2.0 + +#Compile ADOL-C +cd src + +#export CC=gcc +#export CXX=g++ +#export CFLAGS="-arch x86_64" +#export CXXFLAGS="-arch x86_64" + +./configure \ + --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --enable-sparse \ + --enable-docexa \ + --enable-addexa \ + --disable-shave + +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + + +#Ok, bug with libtool: replace all LIBTOOL= by LIBTOOL=libtool +#in all Makefiles +for i in `find ./ -name Makefile ` +do + echo $i + cat $i | sed 's/LIBTOOL =/LIBTOOL = libtool/g' > $i.bak + mv $i.bak $i +done + +#remake: +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + + Index: /issm/trunk/externalpackages/adolc/install.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install.sh (revision 12706) +++ /issm/trunk/externalpackages/adolc/install.sh (revision 12707) @@ -22,4 +22,9 @@ cd src +export CC=gcc +export CXX=g++ +export CFLAGS="-arch x86_64" +export CXXFLAGS="-arch x86_64" + ./configure \ --prefix=$ISSM_DIR/externalpackages/adolc/install \ Index: /issm/trunk/externalpackages/android/android-ndk/install.sh =================================================================== --- /issm/trunk/externalpackages/android/android-ndk/install.sh (revision 12706) +++ /issm/trunk/externalpackages/android/android-ndk/install.sh (revision 12707) @@ -3,22 +3,25 @@ #native architecture of the Android device. -#The android-ndk-r7b-darwin-x86.tar.bz2 dummy.tar.bz2 file was downloaded +#The android-ndk-r8-darwin-x86.tar.bz2 ndk.tar.bz2 file was downloaded #from the android developer website: +source $ANDROID_DIR/android_variables.sh #Cleanup the install rm -rf install -rm -rf $ANDROID_DIR/arm-linux-android-4.0 +rm -rf $ANDROID_DIR/arm-linux-android-${default_droid} #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-ndk-r7b-darwin-x86.tar.bz2' 'dummy.tar.bz2' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-ndk-r'${ndk_rev}'-darwin-x86.tar.bz2' 'ndk.tar.bz2' # Install Android SDK and NDK. -bunzip2 dummy.tar.bz2 -tar -xvf dummy.tar -rm -rf dummy.tar dummy.tar.bz2 +bunzip2 ndk.tar.bz2 +tar -xvf ndk.tar +rm -rf ndk.tar ndk.tar.bz2 #Move to install -mv android-ndk-r7b install +mv android-ndk-r${ndk_rev} install #Create Standalone Development Directory -$ANDROID_NDK_DIR/build/tools/make-standalone-toolchain.sh --platform=android-5 --install-dir=$ANDROID_DIR/arm-linux-android-4.0 +#Note: API-14 corresponds to Android 4.0 although we are +#calling our toolchain 4.1 to agree with our device. +$ANDROID_NDK_DIR/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/arm-linux-android-4.0 Index: /issm/trunk/externalpackages/android/android-sdk/install.sh =================================================================== --- /issm/trunk/externalpackages/android/android-sdk/install.sh (revision 12706) +++ /issm/trunk/externalpackages/android/android-sdk/install.sh (revision 12707) @@ -1,6 +1,7 @@ #This installs the Android SDK (Software Development Kit) #which is needed for the compilation of the Java project. +source $ANDROID_DIR/android_variables.sh -step=3; +step=1; #Different steps here. @@ -11,23 +12,27 @@ present_dir=`pwd`; -default_droid="Android-4.0" sd_card="issm-sdcard" + +((tmp=$1 )) + +if [[ $tmp -ge "1" && $tmp -le "4" ]]; then + step=$1 +else + echo "Using default step: " $step +fi if [[ $step == "1" ]]; then #Cleanup the install - rm -rf install-sdk install-ant + rm -rf install-sdk #Download from ISSM server - $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-sdk-r16-macosx.zip' 'android-sdk-r16-macosx.zip' - $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/apache-ant-1.8.2-bin.zip' 'apache-ant-1.8.2-bin.zip' + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-sdk_r'$sdk_rev'-macosx.zip' 'android-sdk_r'${sdk_rev}'-macosx.zip' # Install Android SDK and NDK. - unzip -o android-sdk-r16-macosx.zip - unzip -o apache-ant-1.8.2-bin.zip + unzip -o android-sdk_r${sdk_rev}-macosx.zip #Move to install - mv android-sdk-macosx install-sdk - mv apache-ant-1.8.2 install-ant + mv -f android-sdk-macosx install-sdk #Post_install configuration: @@ -37,8 +42,8 @@ #For now, we need to install: #android sdk platform tools - #and a specific android api: API 15 - #Note: API 15 corresponds to Android 4.0.3 + #and a specific android api: API 16, API 15 and API 14 + #Note: API 16, API 15 and 14 correspond to Android 4.1, 4.0.3 and 4.0 respectively. - cd install-sdk/tools/ && source ./android update sdk -t platform-tools,android-15,android-14,system-image --no-ui + cd install-sdk/tools/ && source ./android update sdk -t platform-tool,${api_levels},system-image --no-ui fi @@ -76,12 +81,13 @@ cd ../platform-tools - ./adb wait-for-device shell mount -o rw,remount -t yaffs2 /dev/block/mtdblock1 /system + ./adb wait-for-device shell + #./adb wait-for-device shell mount -o rw,remount -t yaffs2 /dev/block/mtdblock1 /system #./adb wait-for-device shell - ./adb push $ISSM_TIER/src/c/issm.exe /data/issm.exe - ./adb shell chmod 777 /data/issm.exe - ./adb shell /data/issm.exe + #./adb push $ISSM_TIER/src/c/issm.exe /data/issm.exe + #./adb shell chmod 777 /data/issm.exe + #./adb shell /data/issm.exe fi if [[ $step == "4" ]]; then - rm -rf install-sdk install-ant + rm -rf install-sdk fi Index: /issm/trunk/externalpackages/android/android_variables.sh =================================================================== --- /issm/trunk/externalpackages/android/android_variables.sh (revision 12707) +++ /issm/trunk/externalpackages/android/android_variables.sh (revision 12707) @@ -0,0 +1,5 @@ +sdk_rev=20 +ndk_rev=8 +api_levels="android-14,android-15,android-16" +host_triplet="arm-linux-androideabi" +default_droid="android-4.1" Index: /issm/trunk/externalpackages/aspell/install.sh =================================================================== --- /issm/trunk/externalpackages/aspell/install.sh (revision 12707) +++ /issm/trunk/externalpackages/aspell/install.sh (revision 12707) @@ -0,0 +1,61 @@ +#!/bin/bash + +#0: cleanup +#1: install aspell +#2: install en dictionary +step=0 + + +#Some cleanup +if [[ $step == "0" ]]; then + rm -rf src install dicts + rm -rf aspell-0.50.5 + rm -rf aspell5-en-6.0.0 +fi + +#install aspell +if [[ $step == "1" ]]; then + + mkdir src install dicts + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/aspell-0.50.5.tar.gz' 'aspell-0.50.5.tar.gz' + + #Untar + tar -zxvf aspell-0.50.5.tar.gz + + #Move aspell into src directory + mv aspell-0.50.5/* src + rm -rf aspell-0.50.5 + + #Configure aspell + cd src + ./configure \ + --prefix="$ISSM_DIR/externalpackages/aspell/install" \ + + #Compile and install aspell + if [ -z $1 ]; then + make + else + make -j $1 + fi + make install +fi + +#languages +if [[ $step == "2" ]]; then + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/aspell5-en-6.0.0.tar.gz' 'aspell5-en-6.0.0.tar.gz' + + #Untar + tar -zxvf aspell5-en-6.0.0.tar.gz + + #Move aspell into src directory + mv aspell5-en-6.0.0 dicts + + #install + cd dicts/aspell5-en-6.0.0 + ./configure + make install +fi Index: /issm/trunk/externalpackages/dakota/install-discover.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-discover.sh (revision 12706) +++ /issm/trunk/externalpackages/dakota/install-discover.sh (revision 12707) @@ -36,6 +36,6 @@ --with-pic \ --disable-mpi \ ---with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ ---with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +--with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" \ +--with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" cd .. Index: /issm/trunk/externalpackages/esmf/install.sh =================================================================== --- /issm/trunk/externalpackages/esmf/install.sh (revision 12707) +++ /issm/trunk/externalpackages/esmf/install.sh (revision 12707) @@ -0,0 +1,50 @@ +#!/bin/bash + +#0: cleanup +#1: install +#2: test + +install=2 + +export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf +export ESMF_COMPILER=gfortran +export ESMF_COMM=mpich2 + +if [[ $install == "0" ]]; then + #Some cleanup + rm -rf esmf_5_2_0rp2 + rm -rf esmf +fi + +if [[ $install == "1" ]]; then + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/esmf_5_2_0rp2_src.tar.gz' 'esmf_5_2_0rp2_src.tar.gz' + + #Untar + tar -zxvf esmf_5_2_0rp2_src.tar.gz + + + #Configure esmf + cd esmf + + + + #Compile and install esmf + if [ -z $1 ]; then + make + make install + else + make -j $1 + make -j $1 install + fi +fi + +if [[ $install == "2" ]]; then + cd esmf + if [ -z $1 ]; then + make all_tests + else + make -j $1 all_tests + fi +fi Index: /issm/trunk/externalpackages/export_fig/export_fig.m =================================================================== --- /issm/trunk/externalpackages/export_fig/export_fig.m (revision 12706) +++ /issm/trunk/externalpackages/export_fig/export_fig.m (revision 12707) @@ -16,4 +16,5 @@ % export_fig ... - % export_fig ... -append +% export_fig ... -bookmark % export_fig(..., handle) % @@ -120,4 +121,6 @@ % exists, the figure is to be appended as a new page, instead % of being overwritten (default). +% -bookmark - option to indicate that a bookmark with the name of the +% figure is to be created in the output file (pdf only). % handle - The handle of the figure or axes (can be an array of handles % of several axes, but these must be in the same figure) to be @@ -159,4 +162,8 @@ % 14/03/12: Fix bug in fixing the axes limits (thanks to Tobias Lamour for % reporting it). +% 02/05/12: Incorporate patch of Petr Nechaev (many thanks), enabling +% bookmarking of figures in pdf files. +% 09/05/12: Incorporate patch of Arcelia Arrieta (many thanks), to keep +% tick marks fixed. function [im alpha] = export_fig(varargin) @@ -194,11 +201,14 @@ Hlims = findall(fig, 'Type', 'axes'); if ~cls - % Record the old axes limit modes + % Record the old axes limit and tick modes Xlims = make_cell(get(Hlims, 'XLimMode')); Ylims = make_cell(get(Hlims, 'YLimMode')); Zlims = make_cell(get(Hlims, 'ZLimMode')); -end -% Set all axes limit modes to manual, so the limits can't change -set(Hlims, 'XLimMode', 'manual', 'YLimMode', 'manual', 'ZLimMode', 'manual'); + Xtick = make_cell(get(Hlims, 'XTickMode')); + Ytick = make_cell(get(Hlims, 'YTickMode')); + Ztick = make_cell(get(Hlims, 'ZTickMode')); +end +% Set all axes limit and tick modes to manual, so the limits and ticks can't change +set(Hlims, 'XLimMode', 'manual', 'YLimMode', 'manual', 'ZLimMode', 'manual', 'XTickMode', 'manual', 'YTickMode', 'manual', 'ZTickMode', 'manual'); % Set to print exactly what is there set(fig, 'InvertHardcopy', 'off'); @@ -403,4 +413,12 @@ eps_remove_background(tmp_nam); end + % Add a bookmark to the PDF if desired + if options.bookmark + fig_nam = get(fig, 'Name'); + if isempty(fig_nam) + warning('export_fig:EmptyBookmark', 'Bookmark requested for figure with no name. Bookmark will be empty.'); + end + add_bookmark(tmp_nam, fig_nam); + end % Generate a pdf eps2pdf(tmp_nam, pdf_nam, 1, options.append, options.colourspace==2, options.quality); @@ -435,7 +453,7 @@ % Reset the hardcopy mode set(fig, 'InvertHardcopy', old_mode); - % Reset the axes limit modes + % Reset the axes limit and tick modes for a = 1:numel(Hlims) - set(Hlims(a), 'XLimMode', Xlims{a}, 'YLimMode', Ylims{a}, 'ZLimMode', Zlims{a}); + set(Hlims(a), 'XLimMode', Xlims{a}, 'YLimMode', Ylims{a}, 'ZLimMode', Zlims{a}, 'XTickMode', Xtick{a}, 'YTickMode', Ytick{a}, 'ZTickMode', Ztick{a}); end end @@ -462,4 +480,5 @@ 'aa_factor', 3, ... 'magnify', 1, ... + 'bookmark', false, ... 'quality', []); native = false; % Set resolution to native of an image @@ -504,4 +523,6 @@ case 'append' options.append = true; + case 'bookmark' + options.bookmark = true; case 'native' native = true; @@ -743,6 +764,40 @@ % Helper function function A = make_cell(A) - if ~iscell(A) - A = {A}; - end - +if ~iscell(A) + A = {A}; +end +return + +function add_bookmark(fname, bookmark_text) +% Adds a bookmark to the temporary EPS file after %%EndPageSetup +% Read in the file +fh = fopen(fname, 'r'); +if fh == -1 + error('File %s not found.', fname); +end +try + fstrm = fread(fh, '*char')'; +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); + +% Include standard pdfmark prolog to maximize compatibility +fstrm = strrep(fstrm, '%%BeginProlog', sprintf('%%%%BeginProlog\n/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse')); +% Add page bookmark +fstrm = strrep(fstrm, '%%EndPageSetup', sprintf('%%%%EndPageSetup\n[ /Title (%s) /OUT pdfmark',bookmark_text)); + +% Write out the updated file +fh = fopen(fname, 'w'); +if fh == -1 + error('Unable to open %s for writing.', fname); +end +try + fwrite(fh, fstrm, 'char*1'); +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); +return Index: /issm/trunk/externalpackages/export_fig/print2array.m =================================================================== --- /issm/trunk/externalpackages/export_fig/print2array.m (revision 12706) +++ /issm/trunk/externalpackages/export_fig/print2array.m (revision 12707) @@ -41,4 +41,7 @@ % 27/1/2012 Bug fix affecting painters rendering tall figures. Thanks to % Ken Campbell for reporting it. + +% 3/4/2012 Bug fix to median input. Thanks to Andy Matthews for reporting +% it. function [A bcol] = print2array(fig, res, renderer) @@ -119,5 +122,5 @@ end end - bcol = median([reshape(A(:,[l r],:), [], size(A, 3)); reshape(A([t b],:,:), [], size(A, 3))], 1); + bcol = uint8(median(single([reshape(A(:,[l r],:), [], size(A, 3)); reshape(A([t b],:,:), [], size(A, 3))]), 1)); for c = 1:size(A, 3) A(:,[1:l-1, r+1:end],c) = bcol(c); Index: /issm/trunk/externalpackages/export_fig/print2eps.m =================================================================== --- /issm/trunk/externalpackages/export_fig/print2eps.m (revision 12706) +++ /issm/trunk/externalpackages/export_fig/print2eps.m (revision 12707) @@ -45,4 +45,6 @@ % alias can lead to another font being swapped in. +% 10/4/2012 Make the font swapping case insensitive. + function print2eps(name, fig, varargin) options = {'-depsc2'}; @@ -57,33 +59,42 @@ end % Find all the used fonts in the figure -fonts = get(findall(fig, '-property', 'FontName'), 'FontName'); +font_handles = findall(fig, '-property', 'FontName'); +fonts = get(font_handles, 'FontName'); if ~iscell(fonts) fonts = {fonts}; end -fonts = unique(fonts); % Map supported font aliases onto the correct name +fontsl = lower(fonts); for a = 1:numel(fonts) - f = lower(fonts{a}); + f = fontsl{a}; f(f==' ') = []; switch f case {'times', 'timesnewroman', 'times-roman'} - fonts{a} = 'Times-Roman'; + fontsl{a} = 'times-roman'; case {'arial', 'helvetica'} - fonts{a} = 'Helvetica'; + fontsl{a} = 'helvetica'; case {'newcenturyschoolbook', 'newcenturyschlbk'} - fonts{a} = 'NewCenturySchlbk'; + fontsl{a} = 'newcenturyschlbk'; otherwise end end +fontslu = unique(fontsl); % Determine the font swap table matlab_fonts = {'Helvetica', 'Times-Roman', 'Palatino', 'Bookman', 'Helvetica-Narrow', 'Symbol', ... 'AvantGarde', 'NewCenturySchlbk', 'Courier', 'ZapfChancery', 'ZapfDingbats'}; -require_swap = find(~ismember(fonts, matlab_fonts)); -unused_fonts = find(~ismember(matlab_fonts, fonts)); -font_swap = min(numel(require_swap), numel(unused_fonts)); -font_swap = [reshape(matlab_fonts(unused_fonts(1:font_swap)), 1, font_swap); reshape(fonts(require_swap(1:font_swap)), 1, font_swap)]; +matlab_fontsl = lower(matlab_fonts); +require_swap = find(~ismember(fontslu, matlab_fontsl)); +unused_fonts = find(~ismember(matlab_fontsl, fontslu)); +font_swap = cell(3, 0); +for a = 1:min(numel(require_swap), numel(unused_fonts)) + ind = find(strcmp(fontslu{require_swap(a)}, fontsl)); + n = numel(ind); + font_swap(1,end+1:end+n) = reshape(mat2cell(font_handles(ind), ones(n, 1)), 1, []); + font_swap(2,end-n+1:end) = matlab_fonts(unused_fonts(a)); + font_swap(3,end-n+1:end) = reshape(fonts(ind), 1, []); +end % Swap the fonts for a = 1:size(font_swap, 2) - set(findall(fig, 'FontName', font_swap{2,a}), 'FontName', font_swap{1,a}); + set(font_swap{1,a}, 'FontName', font_swap{2,a}); end % Set paper size @@ -114,7 +125,8 @@ % Reset the font names in the figure for a = 1:size(font_swap, 2) - set(findall(fig, 'FontName', font_swap{1,a}), 'FontName', font_swap{2,a}); + set(font_swap{1,a}, 'FontName', font_swap{3,a}); end % Replace the font names in the eps file + font_swap = font_swap(2:3,:); try swap_fonts(name, font_swap{:}); Index: sm/trunk/externalpackages/gsl/install-android-4.0.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-android-4.0.sh (revision 12706) +++ (revision ) @@ -1,38 +1,0 @@ -#!/bin/bash - -#Some cleanup -rm -rf src install gsl-1.15 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' - -#Untar -tar -zxvf gsl-1.15.tar.gz - -#Move gsl into src directory -mv gsl-1.15/* src -rm -rf gsl-1.15 - -#Configure gsl -cd src - -./configure \ - CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc\ - LD=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ld\ - AR=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ar\ - RANLIB=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib\ - NM=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-nm\ - OBJ_EXT=o\ - LIB_EXT=a\ - --host="arm-linux"\ - --prefix="$ISSM_DIR/externalpackages/gsl/install" - -#Compile gsl -if [ -z $1 ]; then - make -else - make -j $1 -fi - -make install Index: /issm/trunk/externalpackages/gsl/install-android.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-android.sh (revision 12707) +++ /issm/trunk/externalpackages/gsl/install-android.sh (revision 12707) @@ -0,0 +1,33 @@ +#!/bin/bash +source $ANDROID_DIR/android_variables.sh + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + --build="i386-apple-darwin10.8.0" \ + --host=$host_triplet\ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ -z $1 ]; then + make +else + make -j $1 +fi + +make install Index: /issm/trunk/externalpackages/h5py/install.sh =================================================================== --- /issm/trunk/externalpackages/h5py/install.sh (revision 12707) +++ /issm/trunk/externalpackages/h5py/install.sh (revision 12707) @@ -0,0 +1,24 @@ +#!/bin/bash + +#needed further along +export HDF5_DIR=$ISSM_DIR/externalpackages/hdf5/install + +#Some cleanup +rm -rf install h5py-2.0.1 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/h5py-2.0.1.tar.gz' 'h5py-2.0.1.tar.gz' + +#Untar +tar -zxvf h5py-2.0.1.tar.gz + +#Move h5py to install directory +rm -rf install/* +mv h5py-2.0.1/* install/ +rm -rf h5py-2.0.1 + +#Configure and compile +cd install +python setup.py build –hdf5=$ISSM_DIR/externalpackages/hdf5/install +python setup.py install Index: /issm/trunk/externalpackages/hdf5/install.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install.sh (revision 12707) +++ /issm/trunk/externalpackages/hdf5/install.sh (revision 12707) @@ -0,0 +1,26 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install hdf5-1.8.9 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/hdf5-1.8.9.tar.gz' 'hdf5-1.8.9.tar.gz' + +#Untar +tar -zxvf hdf5-1.8.9.tar.gz + +#Move hdf5 to src directory +rm -rf src/* +mv hdf5-1.8.9/* src/ +rm -rf hdf5-1.8.9 + +#Configure and compile +cd src +./configure --prefix="$ISSM_DIR/externalpackages/hdf5/install" +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/matlab/install.sh =================================================================== --- /issm/trunk/externalpackages/matlab/install.sh (revision 12706) +++ /issm/trunk/externalpackages/matlab/install.sh (revision 12707) @@ -6,4 +6,5 @@ #Select or create a new simlink ln -s /usr/local/pkgs/matlab-7.6/ install +#ln -s /discover/vis/mathworks/matlab_r2011b/ install #ln -s /usr/local/matlab704/ install #ln -s /usr/local/matlab711/ install Index: /issm/trunk/externalpackages/modules/install.sh =================================================================== --- /issm/trunk/externalpackages/modules/install.sh (revision 12707) +++ /issm/trunk/externalpackages/modules/install.sh (revision 12707) @@ -0,0 +1,21 @@ +#!/bin/bash + +#Some cleanup +rm -rf install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/modules-3.2.9c.tar.gz modules-3.2.9c.tar.gz + +#Untar and move python into install directory +tar -zxvf modules-3.2.9c.tar.gz +mv modules-3.2.9 install + +#Configure doxygen +cd install +./configure \ + --prefix "$ISSM_DIR/externalpackages/modules/install" \ + --without-x + +#compile and install +make +make install Index: /issm/trunk/externalpackages/ncview/install.sh =================================================================== --- /issm/trunk/externalpackages/ncview/install.sh (revision 12706) +++ /issm/trunk/externalpackages/ncview/install.sh (revision 12707) @@ -18,5 +18,5 @@ cd install ./configure \ - --prefix "$ISSM_DIR/externalpackages/ncview/install" \ + --prefix="$ISSM_DIR/externalpackages/ncview/install" \ --x-libraries=/usr/X11/lib/ \ --x-includes=/usr/X11/include/ \ Index: /issm/trunk/externalpackages/netcdf-python/install.sh =================================================================== --- /issm/trunk/externalpackages/netcdf-python/install.sh (revision 12707) +++ /issm/trunk/externalpackages/netcdf-python/install.sh (revision 12707) @@ -0,0 +1,29 @@ +#!/bin/bash + +#Some cleanup +rm -rf install netCDF4-1.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netCDF4-1.0.tar.gz" "netCDF4-1.0.tar.gz" + +#Untar +tar -zxvf netCDF4-1.0.tar.gz + +#for later: +rm -rf ISSMDIR +echo $ISSM_DIR | sed 's/\//\\\//g' > ISSMDIR +ISSMDIR=`cat ISSMDIR` && rm -rf ISSMDIR + +#Move netCDF4 to install directory +rm -rf install/* +mv netCDF4-1.0/* install/ +rm -rf netCDF4-1.0 + +#Configur and compile +cd install +#edit setup.cfg to point to hdf5 and netcdf +cat setup.cfg.template | sed "s/\#netCDF4_dir = \/usr\/local/netCDF4_dir = $ISSMDIR\/externalpackages\/netcdf\/install/g" | sed "s/\#HDF5_dir = \/usr\/local/HDF5_DIR = $ISSMDIR\/externalpackages\/hdf5\/install/g" > setup.cfg + +python setup.py build +python setup.py install Index: /issm/trunk/externalpackages/netcdf/install.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install.sh (revision 12706) +++ /issm/trunk/externalpackages/netcdf/install.sh (revision 12707) @@ -1,22 +1,31 @@ #!/bin/bash +version=4.0.1 +#version=4.2 + +#for versions 4.2, you need hdf5 compiled, as well as doxygen for the +#documentation! + #Some cleanup -rm -rf install netcdf-4.0.1 -mkdir install +rm -rf src install netcdf-$version +mkdir install src #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/netcdf-4.0.1.tar.gz' 'netcdf-4.0.1.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netcdf-$version.tar.gz" "netcdf-$version.tar.gz" #Untar -tar -zxvf netcdf-4.0.1.tar.gz +tar -zxvf netcdf-$version.tar.gz #Move netcdf to install directory -rm -rf install/* -mv netcdf-4.0.1/* install/ -rm -rf netcdf-4.0.1 +rm -rf src/* +mv netcdf-$version/* src/ +rm -rf netcdf-$version #Configure and compile -cd install -./configure --prefix="$ISSM_DIR/externalpackages/netcdf/install" +cd src + +#version dependent: +./configure --prefix="$ISSM_DIR/externalpackages/netcdf/install" + if [ -z $1 ]; then make Index: /issm/trunk/externalpackages/petsc/install-3.2-discover.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.2-discover.sh (revision 12706) +++ /issm/trunk/externalpackages/petsc/install-3.2-discover.sh (revision 12707) @@ -23,9 +23,13 @@ --with-shared-libraries=0 \ --known-mpi-shared-libraries=1 \ - --with-mpi-dir=/usr/local/intel/mpi/3.2.2.006/lib64 \ + --with-mpi-dir=/usr/local/intel/mpi/4.0.3.008/lib64/ \ --with-blas-lapack-dir=/usr/local/intel/mkl/10.1.2.024/lib/64/ \ + --with-scalapack-lib=/usr/local/intel/mkl/10.1.2.024/lib/64/libmkl_scalapack_lp64.a \ + --with-scalapack-include=/usr/local/intel/mkl/10.1.2.024/include/ \ + --with-blacs-lib=/usr/local/intel/mkl/10.1.2.024/lib/64/libmkl_blacs_intelmpi_lp64.a \ + --with-blacs-include=/usr/local/intel/mkl/10.1.2.024/include/ \ --download-mumps=yes \ - --download-scalapack=yes \ - --download-blacs=yes \ + --download-scalapack=no \ + --download-blacs=no \ --download-plapack=yes \ --download-parmetis=yes \ Index: /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh (revision 12707) +++ /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh (revision 12707) @@ -0,0 +1,123 @@ +#!/bin/bash +#Step 0: download +#Step 1: install before plapack crasehs +#Step 2: After Plapack implodes +STEP=0 + +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 +if [ $STEP -eq 1 ]; then + + mkdir install + + #configure + cd src + ./config/configure.py \ + --prefix="$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=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --known-mpi-shared-libraries=1 \ + --with-mpi-lib=/nasa/sgi/mpt/2.04/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/2.04/include \ + --download-mumps=yes \ + --download-plapack=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-pastix=yes \ + --download-ptscotch=yes \ + --download-spooles=yes \ + --download-spai=yes \ + --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/documentation/faq/petsc32/) ==" + echo "== Then run STEP=2 ==" +fi +if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ + --prefix="$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=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --with-mpi-lib=/nasa/sgi/mpt/2.04/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/2.04/include \ + --known-mpi-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --with-f-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ + --download-parmetis=yes \ + --download-metis=yes \ + --with-cxx=icpc \ + --download-hypre=yes \ + --download-trilinos=yes \ + --download-prometheus=yes \ + --download-euclid=yes \ + --download-pastix=yes \ + --download-ptscotch=yes \ + --download-spooles=yes \ + --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ + --with-spai-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ + --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -q debug +#PBS -l select=1:ncpus=1:model=har +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e +. /usr/share/modules/init/bash +module load comp-intel/11.1.046 +module load mpi-sgi/mpt.2.04 #DEFINES MPI_Type_create_indexed_block +module load math/intel_mkl_64_10.0.011 +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + echo "== Follow PETSc's instructions" +fi Index: /issm/trunk/externalpackages/python/install-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/python/install-linux64-astrid.sh (revision 12706) +++ /issm/trunk/externalpackages/python/install-linux64-astrid.sh (revision 12707) @@ -21,7 +21,7 @@ rm -rf Python-$version -#Configure doxygen +#Configure python cd src -./configure --prefix="$ISSM_DIR/externalpackages/python/install" +./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-shared if [ -z $1 ]; then @@ -34,10 +34,15 @@ #Some modifications to be done in case version is 3.2: if [[ $version == "3.2.2" ]]; then - cd install/bin + cd ../install/bin ln -s python3.2 python cd ../ ln -s Python.framework/Versions/3.2/include/python3.2m include ln -s Python.framework/Versions/3.2/lib/ lib - - fi +if [[ $version == "2.7.2" ]]; then + cd ../install/include + cp python2.7/* ./ + cd ../lib + ln -s libpython2.7.so.1.0 libpython.so + +fi Index: /issm/trunk/externalpackages/python/install-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/python/install-macosx-snowleopard.sh (revision 12706) +++ /issm/trunk/externalpackages/python/install-macosx-snowleopard.sh (revision 12707) @@ -24,5 +24,7 @@ #Configure doxygen cd src -./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" --enable-universalsdk --with-universal-archs="32-bit" +# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory +# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include +./configure --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" if [ -z $1 ]; then make @@ -40,2 +42,9 @@ ln -s Python.framework/Versions/3.2/lib/ lib fi + +#Some modifications to be done in case version is 2.7 +if [[ $version == "2.7.2" ]]; then + cd ../install + ln -s Library/Frameworks/Python.framework/Headers include + ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib +fi Index: /issm/trunk/externalpackages/scipy/README =================================================================== --- /issm/trunk/externalpackages/scipy/README (revision 12706) +++ /issm/trunk/externalpackages/scipy/README (revision 12707) @@ -1,2 +1,9 @@ -You will find instructions on scipy at: +For OSX 10.7 (Lion), the instructions here can be followed: http://www.scipy.org/Installing_SciPy/Mac_OS_X + +For OSX 10.6 (Snow Leopard), the scipy folks recommend gcc and g++ version 4.0. +However, ISSM needs the gfortran version recommended in $ISSM_DIR/externalpackages/gfortran. +On the webpage listed above, make sure the "export CC" and "export CXX" commands point to the +binaries associated with this gfortran version (likely in /usr/local/gfortran/bin by default). +Once this gfortran is installed, the install script in this directory for Snow Leopard should +work. Index: /issm/trunk/externalpackages/scipy/install-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/scipy/install-macosx-snowleopard.sh (revision 12706) +++ /issm/trunk/externalpackages/scipy/install-macosx-snowleopard.sh (revision 12707) @@ -8,6 +8,8 @@ install=2 -export CC=/usr/bin/gcc-4.0 -export CXX=/usr/bin/g++-4.0 +# gfortran 4.6 (see ISSM_DIR/externalpackages/gfortran) is necessary for ISSM compilation. +# On OSX 10.6, this recommended version gets installed in /usr/local/gfortran +export CC=/usr/local/gfortran/bin/gcc +export CXX=/usr/local/gfortran/bin/g++ if [[ $install == "1" ]];then @@ -22,4 +24,5 @@ cd .. ${PYTHON} -c "import numpy; print 'Installed NumPy', numpy.__version__" + ${PYTHON} -c "import numpy; numpy.test()" elif [[ $install == "2" ]];then @@ -34,4 +37,5 @@ cd .. ${PYTHON} -c "import scipy; print 'Installed SciPy', scipy.__version__" + ${PYTHON} -c "import scipy; scipy.test()" elif [[ $install == "3" ]];then Index: /issm/trunk/externalpackages/triangle/configs/android/configure.make =================================================================== --- /issm/trunk/externalpackages/triangle/configs/android/configure.make (revision 12707) +++ /issm/trunk/externalpackages/triangle/configs/android/configure.make (revision 12707) @@ -0,0 +1,17 @@ +# This makefile configures build process to cross-compile to the android platform. +# The binary tools referenced below are specifically configuered to target armeabi-v7a. +# Furthermore, the compilers (which are simply wrappers around GNU GCC) are set to +# produce binaries that are EABI complient. +# +# Note that the AAPCS standard defines 'EABI' as a moniker used to specify +# a _family_ of similar but distinct ABIs. Android follows the little-endian +# ARM GNU/Linux ABI as documented in the following document: +# +# http://www.codesourcery.com/gnu_toolchains/arm/arm_gnu_linux_abi.pdf +CC=${toolchain_path}-gcc +AR=${toolchain_path}-ar +RANLIB=${toolchain_path}-ranlib +CSWITCHES = $(CFLAGS) +TRILIBDEFS = -DTRILIBRARY +OBJ_EXT=o +LIB_EXT=a Index: sm/trunk/externalpackages/triangle/install-android-4.0.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-android-4.0.sh (revision 12706) +++ (revision ) @@ -1,33 +1,0 @@ -#!/bin/bash - -#use matlab? -matlab=0 - -#Some cleanup -rm -rf install triangle -mkdir install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' - -#Untar -cd install -cp ../triangle.zip ./ -unzip triangle.zip - -#copy new makefile -cp ../configs/android/android-4.0/configure.make ./ -cp ../makefile ./ - -#Patch triangle.c -if [[ $matlab == "1" ]];then - patch triangle.c ../triangle.c.patch.matlab -else - patch triangle.c ../triangle.c.patch.python -fi - -#Compile triangle -make - -#Patch triangle.h -patch triangle.h ../triangle.h.patch Index: /issm/trunk/externalpackages/triangle/install-android.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-android.sh (revision 12707) +++ /issm/trunk/externalpackages/triangle/install-android.sh (revision 12707) @@ -0,0 +1,35 @@ +#!/bin/bash +source $ANDROID_DIR/android_variables.sh +export toolchain_path + +#use matlab? +matlab=0 + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs//android/configure.make ./ +cp ../makefile ./ + +#Patch triangle.c +if [[ $matlab == "1" ]];then + patch triangle.c ../triangle.c.patch.matlab +else + patch triangle.c ../triangle.c.patch.python +fi + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/trunk/externalpackages/triangle/install-discover.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-discover.sh (revision 12707) +++ /issm/trunk/externalpackages/triangle/install-discover.sh (revision 12707) @@ -0,0 +1,26 @@ +#!/bin/bash + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/pleiades/configure.make ./ +cp ../makefile ./ + +#Patch triangle.c +patch triangle.c ../triangle.c.patch + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim =================================================================== --- /issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim (revision 12706) +++ /issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim (revision 12707) @@ -404,9 +404,9 @@ """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" "ISSM containers: -syn keyword cType Constraints DataSet Elements Inputs Loads Materials Nodes Parameters Results Vertices +syn keyword cType Constraints DataSet Elements Inputs Loads Materials Nodes Parameters Results Vertices Options "Petsc -syn keyword cType Vec Mat +syn keyword cType Vec Mat SeqVec SeqMat "other ISSM's syntax -syn keyword cType mxArray ErrorException +syn keyword cType mxArray ErrorException QuadtreeBox IssmDouble IssmPDouble "ISSM's objects begin @@ -710,10 +710,10 @@ syn keyword cConstant SurfaceforcingsMonthlytemperaturesEnum syn keyword cConstant SurfaceforcingsHcEnum -syn keyword cConstant SurfaceforcingsSmb_pos_maxEnum -syn keyword cConstant SurfaceforcingsSmb_pos_minEnum -syn keyword cConstant SurfaceforcingsA_posEnum -syn keyword cConstant SurfaceforcingsB_posEnum -syn keyword cConstant SurfaceforcingsA_negEnum -syn keyword cConstant SurfaceforcingsB_negEnum +syn keyword cConstant SurfaceforcingsSmbPosMaxEnum +syn keyword cConstant SurfaceforcingsSmbPosMinEnum +syn keyword cConstant SurfaceforcingsAPosEnum +syn keyword cConstant SurfaceforcingsBPosEnum +syn keyword cConstant SurfaceforcingsANegEnum +syn keyword cConstant SurfaceforcingsBNegEnum syn keyword cConstant ThermalMaxiterEnum syn keyword cConstant ThermalPenaltyFactorEnum Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 12706) +++ /issm/trunk/m4/issm_options.m4 (revision 12707) @@ -60,4 +60,9 @@ export CFLAGS=" -D_INTEL_LINUX_" export CXXFLAGS=" -D_INTEL_LINUX_" + elif test $VENDOR = intel-discover; then + export CC=icc + export CXX=icpc + export CXXFLAGS=" -O3 -D_INTEL_LINUX_ " + export CFLAGS=" -O3 -D_INTEL_LINUX_ " elif test $VENDOR = intel-pleiades; then export CC=icc @@ -65,10 +70,4 @@ export CXXFLAGS=" -O3 -xS -D_INTEL_LINUX_ " export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ " - elif test $VENDOR = arm-linux; then - export CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc - export GCC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc - export CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-g++ - export AR=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ar - export RANLIB=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib else AC_MSG_ERROR([unknow compiler vendor!]) @@ -320,5 +319,16 @@ PYTHONLIB="-L$PYTHON_ROOT/lib -lpython$PYTHONVERSION" PYTHONEXT=.so - PYTHONLINK="-dynamiclib" + + case "${host_os}" in + *cygwin*) + PYTHONLINK="-shared" + ;; + *linux*) + PYTHONLINK="-shared" + ;; + *darwin*) + PYTHONLINK="-dynamiclib" + ;; + esac AC_DEFINE([_HAVE_PYTHON_],[1],[with Python in ISSM src]) @@ -429,5 +439,5 @@ dnl defaults HAVE_ADOLC=yes - ADOLCINCL="-I$ADOLC_ROOT/include/adolc -I$ADOLC_ROOT/include" + ADOLCINCL="-I$ADOLC_ROOT/include" ADOLCLIB="-L$ADOLC_ROOT/lib64 -ladolc" @@ -746,5 +756,9 @@ dnl defaults HAVE_SCALAPACK=yes - SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lscalapack" + if test x$VENDOR = xintel-discover; then + SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lmkl_scalapack_lp64" + else + SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lscalapack" + fi AC_DEFINE([_HAVE_SCALAPACK_],[1],[with Scalapack in ISSM src]) @@ -766,5 +780,8 @@ HAVE_BLASLAPACK=yes BLASLAPACKINCL="" - + + if test x$VENDOR = xintel-discover; then + BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lmkl_lapack -lmkl -lguide -lpthread" + else dnl: branch on whether we are running on windows or linux. case "${host_os}" in @@ -779,4 +796,5 @@ ;; esac + fi AC_DEFINE([_HAVE_BLASLAPACK_],[1],[with blas lapack in ISSM src]) @@ -853,4 +871,5 @@ MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps -lpord " else + dnl MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps -lmumps_common -lpord -lparmetis -lzmumps" MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps -lmumps_common -lpord -lparmetis" fi @@ -875,5 +894,9 @@ HAVE_BLACS=yes BLACSINCL="" - BLACSLIB=-L"$BLACS_ROOT/ -lblacs" + if test x$VENDOR = xintel-discover; then + BLACSLIB=-L"$BLACS_ROOT/ -lmkl_blacs_intelmpi_lp64" + else + BLACSLIB=-L"$BLACS_ROOT/ -lblacs" + fi AC_DEFINE([_HAVE_BLACS_],[1],[with Blacs in ISSM src]) @@ -896,5 +919,5 @@ HAVE_HYPRE=yes HYPREINCL="" - HYPRELIB=-L"$HYPRE_ROOT/ -lHYPRE" + HYPRELIB=-L"$HYPRE_ROOT/lib -lHYPRE" AC_DEFINE([_HAVE_HYPRE_],[1],[with Blacs in ISSM src]) @@ -906,4 +929,109 @@ AC_MSG_RESULT($HAVE_HYPRE) dnl }}} + dnl prometheus{{{ + AC_ARG_WITH([prometheus-dir], + AS_HELP_STRING([--with-prometheus-dir=DIR],[prometheus root directory]), + [PROMETHEUS_ROOT=$withval],[PROMETHEUS_ROOT=""]) + + AC_MSG_CHECKING(for prometheus headers and libraries in $PROMETHEUS_ROOT) + if test -d "$PROMETHEUS_ROOT"; then + + dnl defaults + HAVE_PROMETHEUS=yes + PROMETHEUSINCL=-I"$PROMETHEUS_ROOT/include" + PROMETHEUSLIB=-L"$PROMETHEUS_ROOT/lib -lpromfei -lprometheus -lparmetis" + + AC_DEFINE([_HAVE_PROMETHEUS_],[1],[with Prometheus in ISSM src]) + AC_SUBST([PROMETHEUSINCL]) + AC_SUBST([PROMETHEUSLIB]) + else + HAVE_PROMETHEUS=no + fi + AC_MSG_RESULT($HAVE_PROMETHEUS) + dnl }}} +dnl spai{{{ + AC_ARG_WITH([spai-dir], + AS_HELP_STRING([--with-spai-dir=DIR],[spai root directory]), + [SPAI_ROOT=$withval],[SPAI_ROOT=""]) + + AC_MSG_CHECKING(for spai headers and libraries in $SPAI_ROOT) + if test -d "$SPAI_ROOT"; then + + dnl defaults + HAVE_SPAI=yes + SPAIINCL=-I"$SPAI_ROOT/include" + SPAILIB=-L"$SPAI_ROOT/lib -lspai" + + AC_DEFINE([_HAVE_SPAI_],[1],[with Spai in ISSM src]) + AC_SUBST([SPAIINCL]) + AC_SUBST([SPAILIB]) + else + HAVE_SPAI=no + fi + AC_MSG_RESULT($HAVE_SPAI) + dnl }}} +dnl superlu{{{ + AC_ARG_WITH([superlu-dir], + AS_HELP_STRING([--with-superlu-dir=DIR],[superlu root directory]), + [SUPERLU_ROOT=$withval],[SUPERLU_ROOT=""]) + + AC_MSG_CHECKING(for superlu headers and libraries in $SUPERLU_ROOT) + if test -d "$SUPERLU_ROOT"; then + + dnl defaults + HAVE_SUPERLU=yes + SUPERLUINCL=-I"$SUPERLU_ROOT/include" + SUPERLULIB=-L"$SUPERLU_ROOT/lib -lsuperlu_4.3" + + AC_DEFINE([_HAVE_SUPERLU_],[1],[with Superlu in ISSM src]) + AC_SUBST([SUPERLUINCL]) + AC_SUBST([SUPERLULIB]) + else + HAVE_SUPERLU=no + fi + AC_MSG_RESULT($HAVE_SUPERLU) + dnl }}} +dnl spooles{{{ + AC_ARG_WITH([spooles-dir], + AS_HELP_STRING([--with-spooles-dir=DIR],[spooles root directory]), + [SPOOLES_ROOT=$withval],[SPOOLES_ROOT=""]) + + AC_MSG_CHECKING(for spooles headers and libraries in $SPOOLES_ROOT) + if test -d "$SPOOLES_ROOT"; then + + dnl defaults + HAVE_SPOOLES=yes + SPOOLESINCL=-I"$SPOOLES_ROOT/include" + SPOOLESLIB=-L"$SPOOLES_ROOT/lib -lspooles" + + AC_DEFINE([_HAVE_SPOOLES_],[1],[with Spooles in ISSM src]) + AC_SUBST([SPOOLESINCL]) + AC_SUBST([SPOOLESLIB]) + else + HAVE_SPOOLES=no + fi + AC_MSG_RESULT($HAVE_SPOOLES) + dnl }}} +dnl pastix{{{ + AC_ARG_WITH([pastix-dir], + AS_HELP_STRING([--with-pastix-dir=DIR],[pastix root directory]), + [PASTIX_ROOT=$withval],[PASTIX_ROOT=""]) + + AC_MSG_CHECKING(for pastix headers and libraries in $PASTIX_ROOT) + if test -d "$PASTIX_ROOT"; then + + dnl defaults + HAVE_PASTIX=yes + PASTIXINCL=-I"$PASTIX_ROOT/include" + PASTIXLIB=-L"$PASTIX_ROOT/lib -lpastix_XXbit_mpi_smp_nobubble_int32_simple_real_scotch_i686_pc_linux -lptscotch -lptscotcherr -lpastix" + + AC_DEFINE([_HAVE_PASTIX_],[1],[with Pastix in ISSM src]) + AC_SUBST([PASTIXINCL]) + AC_SUBST([PASTIXLIB]) + else + HAVE_PASTIX=no + fi + AC_MSG_RESULT($HAVE_PASTIX) + dnl }}} dnl ml{{{ AC_ARG_WITH([ml-dir], @@ -990,4 +1118,21 @@ fi AC_MSG_RESULT(done) + dnl }}} + + dnl Capabilities + dnl with-kriging{{{ + AC_ARG_WITH([kriging], + AS_HELP_STRING([--with-kriging = YES],[compile with kriging capabilities (default is yes)]), + [KRIGING=$withval],[KRIGING=yes]) + AC_MSG_CHECKING(for kriging capability compilation) + + if test "x$KRIGING" = "xyes"; then + HAVE_KRIGING=yes + AC_DEFINE([_HAVE_KRIGING_],[1],[with kriging capability]) + else + HAVE_KRIGING=no + fi + AM_CONDITIONAL([KRIGING], [test x$HAVE_KRIGING = xyes]) + AC_MSG_RESULT($HAVE_KRIGING) dnl }}} dnl with-steadystate{{{ @@ -1310,3 +1455,12 @@ AC_MSG_RESULT($USE_64BIT_INDICES) dnl }}} + dnl circular-dependency{{{ + AC_ARG_WITH([circular-dependency], + AS_HELP_STRING([--with-circular-dependency = bool],[do we look for circular dependencies, default "yes", ex: --with-circular-dependency="no"]), + [CIRCULAR_DEPENDENCIES=$withval],[CIRCULAR_DEPENDENCIES=yes]) + AC_MSG_CHECKING(for circular dependencies) + AM_CONDITIONAL([CIRCULAR_DEPENDENCIES], [test x$CIRCULAR_DEPENDENCIES = xyes]) + AC_MSG_RESULT($CIRCULAR_DEPENDENCIES) + + dnl }}} ]) Index: /issm/trunk/scripts/automakererun.sh =================================================================== --- /issm/trunk/scripts/automakererun.sh (revision 12706) +++ /issm/trunk/scripts/automakererun.sh (revision 12707) @@ -3,39 +3,9 @@ # archive. +# As it turns out, the autoreconf script provided by Autotools +# encompasses the functionality of this script. As such, the +# following two lines will replace the remainder of the script. +# If all goes well, then the script will be shortened in the future. - ACLOCAL="$ISSM_DIR/externalpackages/automake/install/bin/aclocal" -AUTOCONF="$ISSM_DIR/externalpackages/autoconf/install/bin/autoconf" -AUTOHEAD="$ISSM_DIR/externalpackages/autoconf/install/bin/autoheader" -AUTOMAKE="$ISSM_DIR/externalpackages/automake/install/bin/automake" - -echo "removing config.cach" -rm -rf config.cach -rm -rf aclocal.m4 - -if [ ! -f "$ACLOCAL" ] -then echo "issm aclocal not found, calling default aclocal" - aclocal -I m4 -else echo "Calling aclocal" - $ACLOCAL -I m4 -fi - -if [ ! -f "$AUTOCONF" ] -then echo "issm autoconf not found, calling default aclocal" - autoconf -else echo "Calling autoconf" - $AUTOCONF -fi - -if [ ! -f "$AUTOHEAD" ] -then echo "issm autoheader not found, calling default aclocal" - autoheader -else echo "Calling autoheader" - $AUTOHEAD -fi - -if [ ! -f "$AUTOMAKE" ] -then echo "issm automake not found, calling default aclocal" - automake -else echo "Calling automake " - $AUTOMAKE -a -fi +cd $ISSM_DIR +autoreconf -iv -I m4 Index: /issm/trunk/scripts/getloc.sh =================================================================== --- /issm/trunk/scripts/getloc.sh (revision 12706) +++ /issm/trunk/scripts/getloc.sh (revision 12707) @@ -1,5 +1,5 @@ #!/bin/bash #get number of lines of code -cloc-1.55.pl $ISSM_DIR/src $ISSM_DIR/m4 --exclude-dir=.svn --exclude-ext=exp --exclude-lang=make --out=temp +cloc-1.55.pl $ISSM_DIR/src $ISSM_DIR/m4 --exclude-dir=.svn --exclude-dir=ad --exclude-dir=android --exclude-ext=exp --exclude-lang=make --out=temp cat temp ./cloc2html.py Index: /issm/trunk/startup.py =================================================================== --- /issm/trunk/startup.py (revision 12706) +++ /issm/trunk/startup.py (revision 12707) @@ -22,4 +22,6 @@ #ISSM path. Go through src/py and load everything we find that looks like a python file for root,dirs,files in os.walk(ISSM_DIR+ '/src/py'): + if '.svn' in dirs: + dirs.remove('.svn') for file in files: if file.find(".py") != -1: @@ -31,4 +33,6 @@ for root,dirs,files in os.walk(ISSM_DIR+ '/src/m'): + if '.svn' in dirs: + dirs.remove('.svn') for file in files: if file.find(".py") != -1: @@ -77,6 +81,4 @@ from stokesoptions import * from generic import * -from none import * -from none import * from hydrology import * from miscellaneous import * Index: /issm/trunk/test/NightlyRun/IdFromString.m =================================================================== --- /issm/trunk/test/NightlyRun/IdFromString.m (revision 12706) +++ /issm/trunk/test/NightlyRun/IdFromString.m (revision 12707) @@ -22,5 +22,5 @@ %return if no test found if isempty(ids_raw), - disp(['No test matches ''' string '' ]); + disp(['No test matches ''' string '''' ]); return end Index: /issm/trunk/test/NightlyRun/IdFromString.py =================================================================== --- /issm/trunk/test/NightlyRun/IdFromString.py (revision 12707) +++ /issm/trunk/test/NightlyRun/IdFromString.py (revision 12707) @@ -0,0 +1,37 @@ +#! /usr/bin/env python +""" +IDFROMSTRING - output ids from a given string + + Usage: + ids=IdFromString(string) + + Examples: + ids=IdFromString('Parallel') + ids=IdFromString('79North') +""" + +from IdToName import IdToName + +def IdFromString(string): + + #Check input + if not isinstance(string,str): + raise TypeError('IdFromString error message: input argument is not a string.') + + #Get the dictionary and scan for matches + idnames=IdToName(0) + ids=[item[0] for item in idnames.iteritems() if string in item[1]] + + #Return if no test found + if not ids: + print "No test matches '%s'." % string + return ids + + #Display names + ids.sort() + print "%d tests match '%s':" % (len(ids),string) + for id in ids: + print " %d : %s" % (id,idnames[id]) + + return ids + Index: /issm/trunk/test/NightlyRun/IdToName.m =================================================================== --- /issm/trunk/test/NightlyRun/IdToName.m (revision 12706) +++ /issm/trunk/test/NightlyRun/IdToName.m (revision 12707) @@ -116,6 +116,6 @@ case 265, name='SquareShelfTranP3dForcTempSerial'; case 266, name='SquareShelfTranP3dForcTempParallel'; - case 267, name='SquareShelfTranForceNeg2dDakotaSamp'; - case 268, name='SquareShelfTranForceNeg2dDakotaLocal'; + case 268, name='SquareShelfTranForceNeg2dDakotaSamp'; + case 270, name='SquareShelfTranForceNeg2dDakotaLocal'; case 301, name='SquareSheetConstrainedDiagM2dSerial'; case 302, name='SquareSheetConstrainedDiagM2dParallel'; @@ -172,4 +172,6 @@ case 353, name='SquareSheetConstrainedTransP3dEnthSerial'; case 354, name='SquareSheetConstrainedTransP3dEnthParallel'; + case 356, name='SquareSheetConstrainedSmbGradients2dParallel'; + case 358, name='SquareSheetConstrainedSmbGradients3dParallel'; case 401, name='SquareSheetShelfDiagM2dSerial'; case 402, name='SquareSheetShelfDiagM2dParallel'; @@ -205,5 +207,5 @@ case 432, name='SquareSheetShelfCMDragSteaP3dParallel'; case 434, name='SquareSheetShelfDiadM3dDakotaSamp'; - case 435, name='SquareSheetShelfDiadM3dDakotaAreaAverage'; + case 436, name='SquareSheetShelfDiadM3dDakotaAreaAverage'; case 437, name='SquareSheetShelfDiagMP3dTilingSerial'; case 438, name='SquareSheetShelfDiagMP3dTilingParallel'; Index: /issm/trunk/test/NightlyRun/IdToName.py =================================================================== --- /issm/trunk/test/NightlyRun/IdToName.py (revision 12707) +++ /issm/trunk/test/NightlyRun/IdToName.py (revision 12707) @@ -0,0 +1,329 @@ +#! /usr/bin/env python +""" +IDTONAME- return name of test + + Usage: + name=IdToName(id) +""" + +def IdToName(id): + idname={ + 101 : 'SquareShelfConstrainedDiagM2dSerial', + 102 : 'SquareShelfConstrainedDiagM2dParallel', + 103 : 'SquareShelfConstrainedDiagM3dSerial', + 104 : 'SquareShelfConstrainedDiagM3dParallel', + 105 : 'SquareShelfConstrainedDiagP3dSerial', + 106 : 'SquareShelfConstrainedDiagP3dParallel', + 107 : 'SquareShelfConstrainedDiagS3dSerial', + 108 : 'SquareShelfConstrainedDiagS3dParallel', + 109 : 'SquareShelfConstrainedProg2dSerial', + 110 : 'SquareShelfConstrainedProg2dParallel', + 111 : 'SquareShelfConstrainedProg2dDGSerial', + 112 : 'SquareShelfConstrainedProg2dDGParallel', + 113 : 'SquareShelfConstrainedProg3dSerial', + 114 : 'SquareShelfConstrainedProg3dParallel', + 115 : 'SquareShelfConstrainedTherSteaSerial', + 116 : 'SquareShelfConstrainedTherSteaParallel', + 117 : 'SquareShelfConstrainedTherTranSerial', + 118 : 'SquareShelfConstrainedTherTranParallel', + 119 : 'SquareShelfConstrainedTranM2dSerial', + 120 : 'SquareShelfConstrainedTranM2dParallel', + 121 : 'SquareShelfConstrainedTranP3dSerial', + 122 : 'SquareShelfConstrainedTranP3dParallel', + 123 : 'SquareShelfConstrainedSurfSlop2dSerial', + 124 : 'SquareShelfConstrainedSurfSlop2dParallel', + 125 : 'SquareShelfConstrainedSurfSlop3dSerial', + 126 : 'SquareShelfConstrainedSurfSlope3dParallel', + 127 : 'SquareShelfConstrainedBedSlop2dSerial', + 128 : 'SquareShelfConstrainedBedSlop2dParallel', + 129 : 'SquareShelfConstrainedBedSlop3dSerial', + 130 : 'SquareShelfConstrainedBedSlop3dParallel', + 131 : 'SquareShelfConstrainedBalThic2dSerial', + 132 : 'SquareShelfConstrainedBalThic2dParallel', + 133 : 'SquareShelfConstrainedBalThic3dSerial', + 134 : 'SquareShelfConstrainedBalThic3dParallel', + 135 : 'SquareShelfConstrainedBalThic2dDGSerial', + 136 : 'SquareShelfConstrainedBalThic2dDGParallel', + 137 : 'SquareBamgMesh', + 139 : 'SquareShelfConstrainedEnthalpySteaSerial', + 140 : 'SquareShelfConstrainedEnthalpySteaParallel', + 141 : 'SquareShelfConstrainedEnthalpyTranSerial', + 142 : 'SquareShelfConstrainedEnthalpyTranParallel', + 143 : 'SquareShelfConstrainedTransP3dEnthSerial', + 144 : 'SquareShelfConstrainedTransP3dEnthParallel', + 201 : 'SquareShelfDiagM2dSerial', + 202 : 'SquareShelfDiagM2dParallel', + 203 : 'SquareShelfDiagM3dSerial', + 204 : 'SquareShelfDiagM3dParallel', + 205 : 'SquareShelfDiagP3dSerial', + 206 : 'SquareShelfDiagP3dParallel', + 207 : 'SquareShelfDiagS3dSerial', + 208 : 'SquareShelfDiagS3dParallel', + 209 : 'SquareShelfDiagMP3dPenaltiesSerial', + 210 : 'SquareShelfDiagMP3dPenaltiesParallel', + 211 : 'SquareShelfTherSteaSerial', + 212 : 'SquareShelfTherSteaParallel', + 213 : 'SquareShelfTherTranSerial', + 214 : 'SquareShelfTherTranParallel', + 215 : 'SquareShelfTranM2dSerial', + 216 : 'SquareShelfTranM2dParallel', + 217 : 'SquareShelfTranM3dSerial', + 218 : 'SquareShelfTranM3dParallel', + 219 : 'SquareShelfTranP3dSerial', + 220 : 'SquareShelfTranP3dParallel', + 221 : 'SquareShelfTranS3dSerial', + 222 : 'SquareShelfTranS3dParallel', + 223 : 'SquareShelfCMBM2dSerial', + 224 : 'SquareShelfCMBM2dParallel', + 225 : 'SquareShelfCMBM3dSerial', + 226 : 'SquareShelfCMBM3dParallel', + 227 : 'SquareShelfCMBP3dSerial', + 228 : 'SquareShelfCMBP3dParallel', + 229 : 'SquareShelfCMBS3dSerial', + 230 : 'SquareShelfCMBS3dParallel', + 231 : 'SquareShelfDiagM2dRiftSerial', + 232 : 'SquareShelfDiagM2dRiftParallel', + 233 : 'SquareShelfConstrainedSerial', + 234 : 'SquareShelfConstrainedParallel', + 235 : 'SquareShelfConstrainedDakotaBSerial', + 236 : 'SquareShelfConstrainedDakotaBParallel', + 237 : 'SquareShelfDiagMP3dTilingSerial', + 238 : 'SquareShelfDiagMP3dTilingParallel', + 239 : 'SquareShelfDiagPS3dTilingSerial', + 240 : 'SquareShelfDiagPS3dTilingParallel', + 241 : 'SquareShelfDiagMS3dTilingSerial', + 242 : 'SquareShelfDiagMS3dTilingParallel', + 243 : 'SquareShelfDiagM2dTransientIncrHydroSerial', + 244 : 'SquareShelfDiagM2dTransientIncrHydroParallel', + 245 : 'SquareShelfDiagM2dTransientIncrNonHydroSerial', + 246 : 'SquareShelfDiagM2dTransientIncrNonHydroParallel', + 247 : 'SquareShelfDiagP3dTransientIncrHydroSerial', + 248 : 'SquareShelfDiagP3dTransientIncrHydroParallel', + 249 : 'SquareShelfDiagP3dTransientIncrNonHydroSerial', + 250 : 'SquareShelfDiagP3dTransientIncrNonHydroParallel', + 251 : 'SquareShelfTranCflM2dSerial', + 252 : 'SquareShelfTranCflM2dParallel', + 253 : 'SquareShelfTranCflP3dSerial', + 254 : 'SquareShelfTranCflP3dParallel', + 255 : 'SquareShelfTranForceNeg2dSerial', + 256 : 'SquareShelfTranForceNeg2dParallel', + 257 : 'SquareShelfTranForcePos2dSerial', + 258 : 'SquareShelfTranForcePos2dParallel', + 259 : 'SquareShelfTranForceNeg3dSerial', + 260 : 'SquareShelfTranForceNeg3dParallel', + 261 : 'SquareShelfTranForcePos3dSerial', + 262 : 'SquareShelfTranForcePos3dParallel', + 263 : 'SquareShelfTherTranForcTempSerial', + 264 : 'SquareShelfTherTranForcTempParallel', + 265 : 'SquareShelfTranP3dForcTempSerial', + 266 : 'SquareShelfTranP3dForcTempParallel', + 267 : 'SquareShelfTranForceNeg2dDakotaSamp', + 268 : 'SquareShelfTranForceNeg2dDakotaLocal', + 301 : 'SquareSheetConstrainedDiagM2dSerial', + 302 : 'SquareSheetConstrainedDiagM2dParallel', + 303 : 'SquareSheetConstrainedDiagH2dSerial', + 304 : 'SquareSheetConstrainedDiagH2dParallel', + 305 : 'SquareSheetConstrainedDiagHM2dSerial', + 306 : 'SquareSheetConstrainedDiagHM2dParallel', + 307 : 'SquareSheetConstrainedDiagM3dSerial', + 308 : 'SquareSheetConstrainedDiagM3dParallel', + 309 : 'SquareSheetConstrainedDiagH3dSerial', + 310 : 'SquareSheetConstrainedDiagH3dParallel', + 311 : 'SquareSheetConstrainedDiagHM3dSerial', + 312 : 'SquareSheetConstrainedDiagHM3dParallel', + 313 : 'SquareSheetConstrainedDiagP3dSerial', + 314 : 'SquareSheetConstrainedDiagP3dParallel', + 315 : 'SquareSheetConstrainedDiagS3dSerial', + 316 : 'SquareSheetConstrainedDiagS3dParallel', + 317 : 'SquareSheetConstrainedProg2dSerial', + 318 : 'SquareSheetConstrainedProg2dParallel', + 319 : 'SquareSheetConstrainedProg2dDGSerial', + 320 : 'SquareSheetConstrainedProg2dDGParallel', + 321 : 'SquareSheetConstrainedProg3dSerial', + 322 : 'SquareSheetConstrainedProg3dParallel', + 323 : 'SquareSheetConstrainedTherSteaSerial', + 324 : 'SquareSheetConstrainedTherSteaParallel', + 325 : 'SquareSheetConstrainedTherTranSerial', + 326 : 'SquareSheetConstrainedTherTranParallel', + 327 : 'SquareSheetConstrainedTranH2dSerial', + 328 : 'SquareSheetConstrainedTranH2dParallel', + 329 : 'SquareSheetConstrainedTranH3dSerial', + 330 : 'SquareSheetConstrainedTranH3dParallel', + 331 : 'SquareSheetConstrainedTranM2dSerial', + 332 : 'SquareSheetConstrainedTranM2dParallel', + 333 : 'SquareSheetConstrainedTranP3dSerial', + 334 : 'SquareSheetConstrainedTranP3dParallel', + 335 : 'SquareSheetConstrainedSteaH3dSerial', + 336 : 'SquareSheetConstrainedSteaH3dParallel', + 337 : 'SquareSheetConstrainedCMDragM2dSerial', + 338 : 'SquareSheetConstrainedCMDragM2dParallel', + 339 : 'SquareSheetConstrainedCMDragM3dSerial', + 340 : 'SquareSheetConstrainedCMDragM3dParallel', + 341 : 'SquareSheetConstrainedCMDragP3dSerial', + 342 : 'SquareSheetConstrainedCMDragP3dParallel', + 343 : 'SquareSheetConstrainedCMDragS3dSerial', + 344 : 'SquareSheetConstrainedCMDragS3dParallel', + 345 : 'SquareSheetConstrainedTranCflM2dSerial', + 346 : 'SquareSheetConstrainedTranCflM2dParallel', + 347 : 'SquareSheetConstrainedTranCflH3dSerial', + 348 : 'SquareSheetConstrainedTranCflH3dParallel', + 349 : 'SquareSheetConstrainedEnthalpySteaSerial', + 350 : 'SquareSheetConstrainedEnthalpySteaParallel', + 351 : 'SquareSheetConstrainedEnthalpyTranSerial', + 352 : 'SquareSheetConstrainedEnthalpyTranParallel', + 353 : 'SquareSheetConstrainedTransP3dEnthSerial', + 354 : 'SquareSheetConstrainedTransP3dEnthParallel', + 401 : 'SquareSheetShelfDiagM2dSerial', + 402 : 'SquareSheetShelfDiagM2dParallel', + 403 : 'SquareSheetShelfDiagM3dSerial', + 404 : 'SquareSheetShelfDiagM3dParallel', + 405 : 'SquareSheetShelfDiagP3dSerial', + 406 : 'SquareSheetShelfDiagP3dParallel', + 407 : 'SquareSheetShelfDiagS3dSerial', + 408 : 'SquareSheetShelfDiagS3dParallel', + 409 : 'SquareSheetShelfDiagMP3dPenaltiesSerial', + 410 : 'SquareSheetShelfDiagMP3dPenaltiesParallel', + 411 : 'SquareSheetShelfTherSteaSerial', + 412 : 'SquareSheetShelfTherSteaParallel', + 413 : 'SquareSheetShelfTherTranSerial', + 414 : 'SquareSheetShelfTherTranParallel', + 415 : 'SquareSheetShelfTranM2dSerial', + 416 : 'SquareSheetShelfTranM2dParallel', + 417 : 'SquareSheetShelfTranMP3dPenaltiesSerial', + 418 : 'SquareSheetShelfTranMP3dPenaltiesParallel', + 419 : 'SquareSheetShelfSteaM3dSerial', + 420 : 'SquareSheetShelfSteaM3dParallel', + 421 : 'SquareSheetShelfSteaP3dSerial', + 422 : 'SquareSheetShelfSteaP3dParallel', + 423 : 'SquareSheetShelfDiadM3dDakotaSerial', + 424 : 'SquareSheetShelfDiadM3dDakotaParallel', + 425 : 'SquareSheetShelfDiadM3dDakotaPartSerial', + 426 : 'SquareSheetShelfDiadM3dDakotaPartParallel', + 427 : 'SquareSheetShelfDiadM3dDakotaMassFluxSerial', + 428 : 'SquareSheetShelfDiadM3dDakotaMassFluxParallel', + 429 : 'SquareSheetShelfCMDragSteaM3dSerial', + 430 : 'SquareSheetShelfCMDragSteaM3dParallel', + 431 : 'SquareSheetShelfCMDragSteaP3dSerial', + 432 : 'SquareSheetShelfCMDragSteaP3dParallel', + 434 : 'SquareSheetShelfDiadM3dDakotaSamp', + 435 : 'SquareSheetShelfDiadM3dDakotaAreaAverage', + 437 : 'SquareSheetShelfDiagMP3dTilingSerial', + 438 : 'SquareSheetShelfDiagMP3dTilingParallel', + 439 : 'SquareSheetShelfDakotaScaledResponse', + 440 : 'SquareSheetShelfDakotaScaledResponse', + 441 : 'SquareSheetShelfDiagPS3dTilingSerial', + 442 : 'SquareSheetShelfDiagPS3dTilingParallel', + 443 : 'SquareSheetShelfDiagMS3dTilingSerial', + 444 : 'SquareSheetShelfDiagMS3dTilingParallel', + 445 : 'RoundSheetShelfGLMigrationM2dSerial', + 446 : 'RoundSheetShelfGLMigrationM2dParallel', + 447 : 'SquareSheetShelfGroundingLine2dAgressiceSerial', + 448 : 'SquareSheetShelfGroundingLine2dAgressiceParallel', + 449 : 'SquareSheetShelfGroundingLine2dSoftSerial', + 450 : 'SquareSheetShelfGroundingLine2dSoftParallel', + 451 : 'SquareSheetShelfGroundingLine3dAgressiceSerial', + 452 : 'SquareSheetShelfGroundingLine3dAgressiceParallel', + 453 : 'SquareSheetShelfGroundingLine3dSoftSerial', + 454 : 'SquareSheetShelfGroundingLine3dSoftParallel', + 455 : 'SquareSheetShelfDiagM2dNewtonSerial', + 456 : 'SquareSheetShelfDiagM2dNewtonParallel', + 457 : 'SquareSheetShelfDiagP3dNewtonSerial', + 458 : 'SquareSheetShelfDiagP3dNewtonParallel', + 459 : 'SquareSheetShelfDiagS3dNewtonSerial', + 460 : 'SquareSheetShelfDiagS3dNewtonParallel', + 461 : 'SquareSheetShelfSteaEnthalpyM3dSerial', + 462 : 'SquareSheetShelfSteaEnthalpyM3dParallel', + 463 : 'SquareSheetShelfSteaEnthalpyP3dSerial', + 464 : 'SquareSheetShelfSteaEnthalpyP3dParallel', + 501 : 'PigDiagM2dSerial', + 502 : 'PigDiagM2dParallel', + 503 : 'PigDiagP3dSerial', + 504 : 'PigDiagP3dParallel', + 505 : 'PigDiagS3dSerial', + 506 : 'PigDiagS3dParallel', + 507 : 'PigTranM2dSerial', + 508 : 'PigTranM2dParallel', + 509 : 'PigTranM3dSerial', + 510 : 'PigTranM3dParallel', + 511 : 'PigTranP3dSerial', + 512 : 'PigTranP3dParallel', + 513 : 'PigTranS3dSerial', + 514 : 'PigTranS3dParallel', + 515 : 'PigSteaM3dSerial', + 516 : 'PigSteaM3dParallel', + 517 : 'PigSteaP3dSerial', + 518 : 'PigSteaP3dParallel', + 519 : 'PigSteaS3dSerial', + 520 : 'PigSteaS3dParallel', + 521 : 'PigCMBS3dSerial', + 522 : 'PigCMBS3dparallel', + 523 : 'PigCMDragP3dSerial', + 524 : 'PigCMDragP3dparallel', + 525 : 'PigCMDragSteaM3dSerial', + 526 : 'PigCMDragSteaM3dparallel', + 527 : 'PigBamgMesh', + 529 : 'PigTherTranSUPGSerial', + 530 : 'PigTherTranSUPGParallel', + 531 : 'PigTherSteaSUPGSerial', + 532 : 'PigTherSteaSUPGParallel', + 601 : '79NorthProg2dSerial', + 602 : '79NorthProg2dParallel', + 603 : '79NorthProg2dDGSerial', + 604 : '79NorthProg2dDGParallel', + 605 : '79NorthProg3dSerial', + 606 : '79NorthProg3dParallel', + 607 : '79NorthSurfSlop2dSerial', + 608 : '79NorthSurfSlop2dParallel', + 609 : '79NorthSurfSlop3dSerial', + 610 : '79NorthSurfSlop3dParallel', + 611 : '79NorthBedSlop2dSerial', + 612 : '79NorthBedSlop2dParallel', + 613 : '79NorthBedSlop3dSerial', + 614 : '79NorthBedSlop3dParallel', + 615 : '79NorthBalThic2dSerial', + 616 : '79NorthBalThic2dParallel', + 617 : '79NorthBalThic2dDGSerial', + 618 : '79NorthBalThic2dDGParallel', + 619 : '79NorthBalThic3dSerial', + 620 : '79NorthBalThic3dParallel', + 621 : '79NorthCMBalThic2dCGSerial', + 622 : '79NorthCMBalThic2dCGParallel', + 623 : '79NorthCMBalThic2dDGSerial', + 624 : '79NorthCMBalThic2dDGParallel', + 625 : '79NorthCMBalThicVxVyParallel', + 626 : '79NorthCMBalThicVxVySerial', + 1101 : 'ISMIPAPattyn', + 1102 : 'ISMIPAStokes', + 1103 : 'ISMIPBPattyn', + 1104 : 'ISMIPBStokes', + 1105 : 'ISMIPCPattyn', + 1106 : 'ISMIPCStokes', + 1107 : 'ISMIPDPattyn', + 1108 : 'ISMIPDStokes', + 1109 : 'ISMIPE', + 1110 : 'ISMIPF', + 1201 : 'EISMINTMassConservation', + 1202 : 'EISMINTDiag1', + 1203 : 'EISMINTDiag2', + 1204 : 'EISMINTTran2', + 1205 : 'EISMINTRoundIceSheetStaticHutter', + 1206 : 'EISMINTRoundIceSheetStaticPattyn', + 1207 : 'EISMINTRoundIceSheetStaticStokes', + 1208 : 'EISMINTA', + 1301 : 'ThermalMelting', + 1302 : 'ThermalAdvection', + 1303 : 'ThermalConduction', + 1304 : 'ThermalGeothermalFlux', + 1401 : 'AdaptiveMeshRefinement1', + 1402 : 'AdaptiveMeshRefinement2', + 1501 : 'SquareShelfTranSawTooth2d', + 1502 : 'SquareShelfTranSawTooth3d', + 1601 : 'SquareShelfM2dRotation', + 1602 : 'SquareSheetShelfP3dRotation', + } + + if not id == 0: + return idname.get(id,'N/A') + else: + return idname + Index: sm/trunk/test/NightlyRun/dak.m =================================================================== --- /issm/trunk/test/NightlyRun/dak.m (revision 12706) +++ (revision ) @@ -1,52 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=generic('name',oshostname(),'np',1); - -md.timestepping.time_step=1; -md.settings.output_frequency=1; -md.timestepping.final_time=4; - -%Set up transient -smb = ones(md.mesh.numberofvertices,1)*3.6; -smb=[ smb smb*-1 ]; - -md.surfaceforcings.mass_balance=smb; -md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; -md.transient.isthermal=0; - -%sigma_on_partition=AreaAverageOntoPartition(md,sigma); -%sigma_on_grids=sigma_on_partition(md.part+1); %just to check in case -%md.variables.thickness=normal_uncertain('scaled_Thickness',1,1); -%md.variables.thickness.stddev=sigma_on_partition; - -%Dakota inputs,outputs -md.qmu.variables.surface_mass_balance=normal_uncertain('scaled_SurfaceforcingsMassBalance',1,0.1); -md.qmu.responses.IceVolume=response_function('IceVolume',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); - -%% nond_sampling study -md.qmu.method =dakota_method('nond_samp'); -md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),... -'seed',1234,... -'samples',20,... -'sample_type','lhs'); - -%% a variety of parameters -md.qmu.params.evaluation_concurrency=1; -md.qmu.params.analysis_driver=''; -md.qmu.params.analysis_components=''; - -%partitioning -md.qmu.numberofpartitions=20; -md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); -md.qmu.partition=md.qmu.partition-1; -md.qmu.isdakota=1; - -md.transient.requested_outputs=IceVolumeEnum(); - -md.diagnostic.reltol=10^-5; %tighten for qmu analyses -%md.debug.valgrind=1; -%md.verbose.solution=true; -md=solve(md,TransientSolutionEnum,'overwrite','y'); Index: /issm/trunk/test/NightlyRun/runme.m =================================================================== --- /issm/trunk/test/NightlyRun/runme.m (revision 12706) +++ /issm/trunk/test/NightlyRun/runme.m (revision 12707) @@ -49,5 +49,5 @@ if ~ismember(benchmark,{'all','nightly','ismip','eismint','thermal','mesh','validation','tranforcing'}) disp('runme warning: benchmark not supported, defaulting to test ''nightly''') - benchmark='nighlty'; + benchmark='nightly'; end % }}} @@ -87,5 +87,5 @@ test_ids=intersect(test_ids,list_ids); % }}} -%GET exculde {{{1 +%GET exclude {{{1 exclude_ids=getfieldvalue(options,'exclude',[]); exclude_ids=[exclude_ids]; @@ -126,5 +126,5 @@ if ~strcmp(oshostname(),'larsen'); - error(['Nighlty run archives must be saved on "larsen" (hostname is "' oshostname() '")']); + error(['Nightly run archives must be saved on "larsen" (hostname is "' oshostname() '")']); end for k=1:length(field_names), @@ -135,5 +135,5 @@ disp(sprintf(['File ./../Archives/' archive_name ' saved\n'])); - %ELSE: CHECK TEST + %ELSE: CHECK TEST else, Index: /issm/trunk/test/NightlyRun/runme.py =================================================================== --- /issm/trunk/test/NightlyRun/runme.py (revision 12707) +++ /issm/trunk/test/NightlyRun/runme.py (revision 12707) @@ -0,0 +1,275 @@ +#! /usr/bin/env python +""" +RUNME - test deck for ISSM nightly runs + + In a test deck directory (tests/Vertification/NightlyRun for example) + The following command will launch all the existing tests: + >>> runme() + To run the tests 101 and 102: + >>> runme(id=[101,102]) + etc... + + Available options: + 'id' followed by the list of ids requested + 'exclude' ids to be excluded from the test + 'benchmark' 'nightly' (nightly run/ daily run) + 'ismip' : validation of ismip-hom tests + 'eismint': validation of eismint tests + 'thermal': validation of thermal tests + 'mesh' : validation of mesh tests + ... + 'procedure' 'check' : run the test (default) + 'update': update the archive + + Usage: + md=runme(varargin); + + Examples: + runme() + runme(exclude=101) + md=runme(id=102,procedure='update') +""" + +import os +import glob +import socket +import numpy +#import h5py +import netCDF4 +import sys + +def runme(id=None,exclude=None,benchmark='nightly',procedure='check',output='none',rank=1,numprocs=1): + + from parallelrange import parallelrange + from IdToName import IdToName + + #Get ISSM_DIR variable + ISSM_DIR=os.environ['ISSM_DIR'] + print 'ISSM_DIR =',ISSM_DIR + + #Process options + #GET benchmark {{{1 + if not benchmark.lower() in ['all','nightly','ismip','eismint','thermal','mesh','validation','tranforcing']: + print "runme warning: benchmark '%s' not supported, defaulting to test 'nightly'." % benchmark + benchmark='nightly' + # }}} + #GET procedure {{{1 + if not procedure.lower() in ['check','update']: + print "runme warning: procedure '%s' not supported, defaulting to test 'check'." % procedure + procedure='check' + # }}} + #GET output {{{1 + if not output.lower() in ['nightly','daily','none']: + print "runme warning: output '%s' not supported, defaulting to test 'none'." % output + output='none' + # }}} + #GET RANK and NUMPROCS for multithreaded runs {{{1 + if (numprocs %7.2g test id: %i test name: %s field: %s' % \ + (error_diff,tolerance,id,id_string,fieldname) + else: + print 'SUCCESS difference: %-7.2g < %7.2g test id: %i test name: %s field: %s' % \ + (error_diff,tolerance,id,id_string,fieldname) + + except Exception as me2: + + #something went wrong, print failure message: + directory=os.getcwd().split('/') # not used? + message=me2 + if output.lower() == 'nightly': + fid=open(os.path.join(ISSM_DIR,'nightlylog','matlaberror.log'), 'a') + fid.write('%s' % message) + fid.write('\n------------------------------------------------------------------\n') + fid.close() + print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,fieldname) + elif output.lower() == 'daily': + fid=open(os.path.join(ISSM_DIR,'dailylog','matlaberror.log'), 'a') + fid.write('%s' % message) + fid.write('\n------------------------------------------------------------------\n') + fid.close() + print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,fieldname) + else: + print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,fieldname) + raise RuntimeError(me2) + + f.close() + + except Exception as me: + + #something went wrong, print failure message: + directory=os.getcwd().split('/') # not used? + message=me + if output.lower() == 'nightly': + fid=open(os.path.join(ISSM_DIR+'nightlylog','matlaberror.log'), 'a') + fid.write('%s' % message) + fid.write('\n------------------------------------------------------------------\n') + fid.close() + print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,'N/A') + elif output.lower() == 'daily': + fid=open(os.path.join(ISSM_DIR+'dailylog','matlaberror.log'), 'a') + fid.write('%s' % message) + fid.write('\n------------------------------------------------------------------\n') + fid.close() + print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,'N/A') + else: + print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,'N/A') + raise RuntimeError(me) + +# #output md if requested +# if nargout==1 +# varargout{1}=md; +# end + + return + +if __name__ == '__main__': + if 'PYTHONSTARTUP' in os.environ: + PYTHONSTARTUP=os.environ['PYTHONSTARTUP'] + print 'PYTHONSTARTUP =',PYTHONSTARTUP + if os.path.exists(PYTHONSTARTUP): + try: + execfile(PYTHONSTARTUP) + except Exception as e: + print "PYTHONSTARTUP error: ",e + else: + print "PYTHONSTARTUP file '%s' does not exist." % PYTHONSTARTUP + + import argparse + parser = argparse.ArgumentParser(description='RUNME - test deck for ISSM nightly runs') + parser.add_argument('-i','--id', nargs='*', type=int, help='followed by the list of ids requested', default=[]) + parser.add_argument('-e','--exclude', nargs='*', type=int, help='ids to be excluded from the test', default=[]) + parser.add_argument('-b','--benchmark', help='nightly/ismip/eismint/thermal/mesh/...', default='nightly') + parser.add_argument('-p','--procedure', help='check/update', default='check') + parser.add_argument('-o','--output', help='nightly/daily/none', default='none') + parser.add_argument('-r','--rank', type=int, help='rank', default=1) + parser.add_argument('-n','--numprocs', type=int, help='numprocs', default=1) + args = parser.parse_args() + + md = runme(args.id, args.exclude, args.benchmark, args.procedure, args.output, args.rank, args.numprocs) + + exit(md) + Index: /issm/trunk/test/NightlyRun/test102.py =================================================================== --- /issm/trunk/test/NightlyRun/test102.py (revision 12706) +++ /issm/trunk/test/NightlyRun/test102.py (revision 12707) @@ -4,6 +4,21 @@ from parameterize import * -md=model(); -md=triangle(md,'../Exp/Square.exp',50000); -md=setmask(md,'all',''); +md=model() +md=triangle(md,'../Exp/Square.exp',50000) +md=setmask(md,'all','') md=parameterize(md,'../Par/SquareShelfConstrained.py') + +#Fields and tolerances to track changes +field_names =['Vx','Vy','Vel','Pressure',\ + 'StressTensorxx','StressTensoryy','StressTensorxy'] +field_tolerances=[1e-13,1e-13,1e-13,1e-13,\ + 1e-13,1e-13,1e-13] +field_values=[\ + [md.results.DiagnosticSolution.Vx],\ + [md.results.DiagnosticSolution.Vy],\ + [md.results.DiagnosticSolution.Vel],\ + [md.results.DiagnosticSolution.Pressure],\ + [md.results.DiagnosticSolution.StressTensorxx],\ + [md.results.DiagnosticSolution.StressTensoryy],\ + [md.results.DiagnosticSolution.StressTensorxy],\ + ] Index: /issm/trunk/test/NightlyRun/test268.m =================================================================== --- /issm/trunk/test/NightlyRun/test268.m (revision 12706) +++ /issm/trunk/test/NightlyRun/test268.m (revision 12707) @@ -23,5 +23,5 @@ %variables -md.qmu.variables.surface_mass_balance=normal_uncertain('scaled_SurfaceforcingsMassBalance',1,100); +md.qmu.variables.surface_mass_balance=normal_uncertain('scaled_SurfaceforcingsMassBalance',1,0.1); %responses @@ -39,6 +39,7 @@ md.qmu.mass_flux_profile_directory=pwd; -%method -md.qmu.method =dakota_method('nond_l'); +%% nond_sampling study +md.qmu.method=dakota_method('nond_samp'); +md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),'seed',1234,'samples',20,'sample_type','lhs'); %parameters @@ -48,5 +49,4 @@ md.qmu.params.evaluation_concurrency=1; md.qmu.params.interval_type='forward'; -md.qmu.params.fd_gradient_step_size='0.1'; md.qmu.isdakota=1; Index: /issm/trunk/test/NightlyRun/test270.m =================================================================== --- /issm/trunk/test/NightlyRun/test270.m (revision 12707) +++ /issm/trunk/test/NightlyRun/test270.m (revision 12707) @@ -0,0 +1,72 @@ +md=triangle(model,'../Exp/Square.exp',180000); +md=setmask(md,'all',''); +md=parameterize(md,'../Par/SquareShelf.par'); +md=setflowequation(md,'macayeal','all'); +md.cluster=generic('name',oshostname(),'np',3); + +md.timestepping.time_step=1; +md.settings.output_frequency=1; +md.timestepping.final_time=4; + +smb = ones(md.mesh.numberofvertices,1)*3.6; +smb=[ smb smb*-1 ]; + +md.surfaceforcings.mass_balance= smb; +md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; +md.transient.isthermal=0; +%Dakota options + +%partitioning +md.qmu.numberofpartitions=20; +md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); +md.qmu.partition=md.qmu.partition-1; + +%variables +md.qmu.variables.surface_mass_balance=normal_uncertain('scaled_SurfaceforcingsMassBalance',1,100); + +%responses +md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +md.qmu.responses.IceVolume=response_function('IceVolume',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +md.qmu.responses.MassFlux1=response_function('indexed_MassFlux_1',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +md.qmu.responses.MassFlux2=response_function('indexed_MassFlux_2',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +md.qmu.responses.MassFlux3=response_function('indexed_MassFlux_3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +md.qmu.responses.MassFlux4=response_function('indexed_MassFlux_4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +md.qmu.responses.MassFlux5=response_function('indexed_MassFlux_5',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +md.qmu.responses.massFlux6=response_function('indexed_MassFlux_6',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + +%mass flux profiles +md.qmu.mass_flux_profiles={'../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp'}; +md.qmu.mass_flux_profile_directory=pwd; + +%method +md.qmu.method =dakota_method('nond_l'); + +%parameters +md.qmu.params.direct=true; +md.qmu.params.analysis_driver=''; +md.qmu.params.analysis_components=''; +md.qmu.params.evaluation_concurrency=1; +md.qmu.params.interval_type='forward'; +md.qmu.params.fd_gradient_step_size='0.1'; +md.qmu.isdakota=1; + +md.diagnostic.reltol=10^-5; %tighten for qmu analyses +md.transient.requested_outputs=IceVolumeEnum(); + +%solve +md=solve(md,TransientSolutionEnum,'overwrite','y'); +md=tres(md,'dakota'); + +%Fields and tolerances to track changes +md.results.dakota.importancefactors=[]; +for i=1:8, + md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).mean]; +end +for i=1:8, + md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).stddev]; +end +field_names ={'importancefactors'}; +field_tolerances={1e-11}; +field_values={... + md.results.dakota.importancefactors,... + }; Index: /issm/trunk/test/NightlyRun/test356.m =================================================================== --- /issm/trunk/test/NightlyRun/test356.m (revision 12707) +++ /issm/trunk/test/NightlyRun/test356.m (revision 12707) @@ -0,0 +1,41 @@ +md=triangle(model,'../Exp/Square.exp',150000); +md=setmask(md,'',''); +md=parameterize(md,'../Par/SquareSheetConstrained.par'); +md=setflowequation(md,'macayeal','all'); +md.surfaceforcings.issmbgradients=1; +md.surfaceforcings.smb_pos_max=5000. - 0.00005*md.mesh.x + 0.0001*md.mesh.y; +md.surfaceforcings.smb_pos_min=1250. + 0.00005*md.mesh.x -0.0001*md.mesh.y; +md.surfaceforcings.a_pos=15000. - 0.000051*md.mesh.x + 0.00011*md.mesh.y; +md.surfaceforcings.b_pos=-100. + 0.00005*md.mesh.x - 0.0001*md.mesh.y; +md.surfaceforcings.a_neg=-20000. - 0.00005*md.mesh.x + 0.0001*md.mesh.y; +md.surfaceforcings.b_neg=250. + 0.000051*md.mesh.x - 0.00011*md.mesh.y; +md.surfaceforcings.hc=(md.surfaceforcings.a_pos-md.surfaceforcings.a_neg)./(md.surfaceforcings.b_neg-md.surfaceforcings.b_pos); +md.cluster=generic('name',oshostname(),'np',3); +md=solve(md,TransientSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx1','Vy1','Vel1','Bed1','Surface1','Thickness1','SMB1','Vx2','Vy2','Vel2','Bed2','Surface2','Thickness2','SMB2','Vx3','Vy3','Vel3','Bed3','Surface3','Thickness3','SMB3'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... + (md.results.TransientSolution(1).Vel),... + (md.results.TransientSolution(1).Bed),... + (md.results.TransientSolution(1).Surface),... + (md.results.TransientSolution(1).Thickness),... + (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... + (md.results.TransientSolution(2).Vx),... + (md.results.TransientSolution(2).Vy),... + (md.results.TransientSolution(2).Vel),... + (md.results.TransientSolution(2).Bed),... + (md.results.TransientSolution(2).Surface),... + (md.results.TransientSolution(2).Thickness),... + (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... + (md.results.TransientSolution(3).Vx),... + (md.results.TransientSolution(3).Vy),... + (md.results.TransientSolution(3).Vel),... + (md.results.TransientSolution(3).Bed),... + (md.results.TransientSolution(3).Surface),... + (md.results.TransientSolution(3).Thickness),... + (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... + }; Index: /issm/trunk/test/NightlyRun/test358.m =================================================================== --- /issm/trunk/test/NightlyRun/test358.m (revision 12707) +++ /issm/trunk/test/NightlyRun/test358.m (revision 12707) @@ -0,0 +1,51 @@ +md=triangle(model,'../Exp/Square.exp',150000); +md=setmask(md,'',''); +md=parameterize(md,'../Par/SquareSheetConstrained.par'); +md=extrude(md,3,1); +md=setflowequation(md,'pattyn','all'); +md.surfaceforcings.issmbgradients=1; +md.surfaceforcings.smb_pos_max=5000. - 0.00005*md.mesh.x + 0.0001*md.mesh.y; +md.surfaceforcings.smb_pos_min=1250. + 0.00005*md.mesh.x -0.0001*md.mesh.y; +md.surfaceforcings.a_pos=15000. - 0.000051*md.mesh.x + 0.00011*md.mesh.y; +md.surfaceforcings.b_pos=-100. + 0.00005*md.mesh.x - 0.0001*md.mesh.y; +md.surfaceforcings.a_neg=-20000. - 0.00005*md.mesh.x + 0.0001*md.mesh.y; +md.surfaceforcings.b_neg=250. + 0.000051*md.mesh.x - 0.00011*md.mesh.y; +md.surfaceforcings.hc=(md.surfaceforcings.a_pos-md.surfaceforcings.a_neg)./(md.surfaceforcings.b_neg-md.surfaceforcings.b_pos); +md.cluster=generic('name',oshostname(),'np',3); +md=solve(md,TransientSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx1','Vy1','Vz1','Vel1','Bed1','Surface1','Thickness1','Temperature1','SMB1','Vx2','Vy2','Vz2','Vel2','Bed2','Surface2','Thickness2','Temperature2','SMB2','Vx3','Vy3','Vz3','Vel3','Bed3','Surface3','Thickness3','Temperature3','SMB3'}; +field_tolerances={1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... + 1e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,... + 1e-09,5e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; + +field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... + (md.results.TransientSolution(1).Vz),... + (md.results.TransientSolution(1).Vel),... + (md.results.TransientSolution(1).Bed),... + (md.results.TransientSolution(1).Surface),... + (md.results.TransientSolution(1).Thickness),... + (md.results.TransientSolution(1).Temperature),... + (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... + (md.results.TransientSolution(2).Vx),... + (md.results.TransientSolution(2).Vy),... + (md.results.TransientSolution(2).Vz),... + (md.results.TransientSolution(2).Vel),... + (md.results.TransientSolution(2).Bed),... + (md.results.TransientSolution(2).Surface),... + (md.results.TransientSolution(2).Thickness),... + (md.results.TransientSolution(2).Temperature),... + (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... + (md.results.TransientSolution(3).Vx),... + (md.results.TransientSolution(3).Vy),... + (md.results.TransientSolution(3).Vz),... + (md.results.TransientSolution(3).Vel),... + (md.results.TransientSolution(3).Bed),... + (md.results.TransientSolution(3).Surface),... + (md.results.TransientSolution(3).Thickness),... + (md.results.TransientSolution(3).Temperature),... + (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... + }; Index: /issm/trunk/test/NightlyRun/test436.m =================================================================== --- /issm/trunk/test/NightlyRun/test436.m (revision 12707) +++ /issm/trunk/test/NightlyRun/test436.m (revision 12707) @@ -0,0 +1,21 @@ +%test partitioning, and partition averaging +md=triangle(model,'../Exp/Square.exp',30000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=setflowequation(md,'macayeal','all'); +md.cluster=generic('name',oshostname(),'np',3); + +%partitioning +md.qmu.numberofpartitions=100; +md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions); +md.qmu.partition=md.qmu.partition-1; + +vector=(1:1:md.mesh.numberofvertices)'; +vector_on_partition=AreaAverageOntoPartition(md,vector); +vector_on_nodes=vector_on_partition(md.qmu.partition+1); + +field_names ={'vector_on_nodes'}; +field_tolerances={1e-11}; +field_values={... + vector_on_nodes,... + }; Index: /issm/trunk/test/NightlyRun/test999.py =================================================================== --- /issm/trunk/test/NightlyRun/test999.py (revision 12707) +++ /issm/trunk/test/NightlyRun/test999.py (revision 12707) @@ -0,0 +1,27 @@ +#md=model() +#md=triangle(md,'../Exp/Square.exp',50000) +#md=setmask(md,'all','') +#md=parameterize(md,'../Par/SquareShelfConstrained.py') + +md1=[11,12,13] +md2=[21,22,23] +md3=[34,32,33] +md4=[41,44,43] +md5=[51,52,53] +md6=[61,62,63] +md7=[71,72,73] + +#Fields and tolerances to track changes +field_names =['Vx','Vy','Vel','Pressure',\ + 'StressTensorxx','StressTensoryy','StressTensorxy'] +field_tolerances=[1e-13,1e-13,1e-13,1e-13,\ + 1e-13,1e-13,1e-13] +field_values=[\ + [md1],\ + [md2],\ + [md3],\ + [md4],\ + [md5],\ + [md6],\ + [md7],\ + ]