Index: /issm/trunk/configs/config-arm-linux.sh =================================================================== --- /issm/trunk/configs/config-arm-linux.sh (revision 13974) +++ /issm/trunk/configs/config-arm-linux.sh (revision 13975) @@ -6,6 +6,8 @@ --host="arm-linux-androideabi" \ --enable-shared \ + --with-android=jni\ --without-fortran \ - --without-modules \ + --without-wrappers \ + --without-kriging \ --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 13974) +++ /issm/trunk/configs/config-discover.sh (revision 13975) @@ -22,5 +22,5 @@ --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ --with-graphics-lib=/usr/lib64/libX11.so \ - --with-cxxoptflags="-O3 -xS" \ + --with-cxxoptflags="-O3 -xS -DMPICH_IGNORE_CXX_SEEK" \ --with-vendor=intel-discover Index: /issm/trunk/configs/config-greenplanet.sh =================================================================== --- /issm/trunk/configs/config-greenplanet.sh (revision 13974) +++ /issm/trunk/configs/config-greenplanet.sh (revision 13975) @@ -6,5 +6,5 @@ ./configure \ --prefix=$ISSM_DIR \ - --with-modules=no \ + --with-wrappers=no \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ Index: /issm/trunk/configs/config-linux64-ad.sh =================================================================== --- /issm/trunk/configs/config-linux64-ad.sh (revision 13974) +++ /issm/trunk/configs/config-linux64-ad.sh (revision 13975) @@ -3,5 +3,5 @@ ./configure \ --prefix=$ISSM_DIR \ - --without-modules\ + --without-wrappers\ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ --without-thermal \ Index: sm/trunk/configs/config-linux64-astrid-python.sh =================================================================== --- /issm/trunk/configs/config-linux64-astrid-python.sh (revision 13974) +++ (revision ) @@ -1,25 +1,0 @@ -#!/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-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ - --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich " \ - --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/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-linux64-astrid.sh =================================================================== --- /issm/trunk/configs/config-linux64-astrid.sh (revision 13974) +++ /issm/trunk/configs/config-linux64-astrid.sh (revision 13975) @@ -13,5 +13,4 @@ --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-tao-dir=$ISSM_DIR/externalpackages/tao/install \ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ Index: /issm/trunk/configs/config-linux64-cloud.sh =================================================================== --- /issm/trunk/configs/config-linux64-cloud.sh (revision 13975) +++ /issm/trunk/configs/config-linux64-cloud.sh (revision 13975) @@ -0,0 +1,20 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.1 or 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_DIR \ + --without-wrappers \ + --with-triangle-dir=$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-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-cxxoptflags=" -O2 -fpermissive" Index: /issm/trunk/configs/config-linux64-murdo-ad.sh =================================================================== --- /issm/trunk/configs/config-linux64-murdo-ad.sh (revision 13974) +++ /issm/trunk/configs/config-linux64-murdo-ad.sh (revision 13975) @@ -2,36 +2,9 @@ ./configure \ - --prefix=$ISSM_DIR \ - --with-serial=no\ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ - --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ - --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/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-ml-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-graphics-lib=/usr/lib64/libX11.so \ - --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -lg2c /usr/lib/gcc/x86_64-redhat-linux/4.1.1/libgfortran.a" \ - --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ ---with-numthreads=24 \ - --without-thermal \ - --without-control \ - --without-hydrology \ - --without-diagnostic \ - --without-balanced \ - --without-responses \ - --without-slope \ - --without-rifts \ - --without-steadystate \ - --without-transient \ - --without-3d \ - --without-groundingline - -#--without-prognostic \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --without-kml \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install Index: /issm/trunk/configs/config-linux64-murdo.sh =================================================================== --- /issm/trunk/configs/config-linux64-murdo.sh (revision 13974) +++ /issm/trunk/configs/config-linux64-murdo.sh (revision 13975) @@ -1,26 +1,27 @@ #!/bin/sh +#petsc 3.2 +#mpich 1.4 + ./configure \ - --prefix=$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=$ISSM_DIR/externalpackages/mpich2/install/include \ - --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ - --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/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="$ISSM_DIR/externalpackages/chaco/install" \ - --with-graphics-lib=/usr/lib64/libX11.so \ - --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ - --with-numthreads=18 \ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --enable-debugging - - + --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-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-petsc-arch=$ISSM_ARCH \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-numthreads=18 \ + --enable-debugging Index: /issm/trunk/configs/config-macosx-snowleopard-bothapis.sh =================================================================== --- /issm/trunk/configs/config-macosx-snowleopard-bothapis.sh (revision 13974) +++ /issm/trunk/configs/config-macosx-snowleopard-bothapis.sh (revision 13975) @@ -3,11 +3,4 @@ #petsc 3.2 #mpich 1.4 - -#export FCFLAGS=" -m32" -#export FFLAGS=" -m32" -#export CFLAGS=" -arch i386" -#export CXXFLAGS=" -arch i386" - -pythonversion=2.7 ./configure \ @@ -16,6 +9,5 @@ --with-matlab-dir=$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$pythonversion/site-packages/numpy/core/include/numpy\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy\ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ Index: /issm/trunk/configs/config-macosx-snowleopard-python.sh =================================================================== --- /issm/trunk/configs/config-macosx-snowleopard-python.sh (revision 13974) +++ /issm/trunk/configs/config-macosx-snowleopard-python.sh (revision 13975) @@ -4,12 +4,9 @@ #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$pythonversion/site-packages/numpy/core/include/numpy\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy\ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ Index: /issm/trunk/configs/config-macosx64-ad.sh =================================================================== --- /issm/trunk/configs/config-macosx64-ad.sh (revision 13974) +++ /issm/trunk/configs/config-macosx64-ad.sh (revision 13975) @@ -3,5 +3,5 @@ ./configure \ --prefix=$ISSM_DIR \ - --without-modules\ + --without-wrappers\ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ --without-thermal \ Index: /issm/trunk/configs/config-macosx64-chris-bothapis.sh =================================================================== --- /issm/trunk/configs/config-macosx64-chris-bothapis.sh (revision 13974) +++ /issm/trunk/configs/config-macosx64-chris-bothapis.sh (revision 13975) @@ -4,18 +4,15 @@ #mpich 1.4 -pythonversion=2.7 - ./configure \ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy\ --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=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy\ --with-metis-dir=$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 $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ - --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ @@ -28,6 +25,3 @@ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-numthreads=8 - #--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ - #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ + #--with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ Index: /issm/trunk/configs/config-macosx64-chris-python.sh =================================================================== --- /issm/trunk/configs/config-macosx64-chris-python.sh (revision 13974) +++ /issm/trunk/configs/config-macosx64-chris-python.sh (revision 13975) @@ -4,12 +4,9 @@ #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=$ISSM_DIR/externalpackages/python/install/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ @@ -24,11 +21,6 @@ --with-petsc-arch=$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/ \ --with-numthreads=8 - #--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ - #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ Index: /issm/trunk/configs/config-macosx64-gsl.sh =================================================================== --- /issm/trunk/configs/config-macosx64-gsl.sh (revision 13974) +++ /issm/trunk/configs/config-macosx64-gsl.sh (revision 13975) @@ -3,5 +3,5 @@ ./configure \ --prefix=$ISSM_DIR \ - --without-modules\ + --without-wrappers\ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install #--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install Index: /issm/trunk/configs/config-macosx64-larour-ad.sh =================================================================== --- /issm/trunk/configs/config-macosx64-larour-ad.sh (revision 13974) +++ /issm/trunk/configs/config-macosx64-larour-ad.sh (revision 13975) @@ -1,3 +1,5 @@ #!/bin/sh + +pythonversion=2.7 ./configure \ @@ -8,4 +10,6 @@ --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: sm/trunk/configs/config-macosx64-larour-bothapis.sh =================================================================== --- /issm/trunk/configs/config-macosx64-larour-bothapis.sh (revision 13974) +++ (revision ) @@ -1,33 +1,0 @@ -#!/bin/sh - -#petsc 3.2 -#mpich 1.4 - -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 $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ - --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ - --with-fortran-lib="/usr/local/gfortran/lib/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 x86_64 -mmacosx-version-min=10.5 -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/ - #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ Index: /issm/trunk/configs/config-macosx64-larour-nopetsc.sh =================================================================== --- /issm/trunk/configs/config-macosx64-larour-nopetsc.sh (revision 13974) +++ /issm/trunk/configs/config-macosx64-larour-nopetsc.sh (revision 13975) @@ -1,5 +1,3 @@ #!/bin/sh - -pythonversion=3.2 ./configure \ @@ -7,6 +5,5 @@ --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-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-math-lib="/usr/lib/libm.dylib" \ Index: /issm/trunk/configs/config-macosx64-larour-python.sh =================================================================== --- /issm/trunk/configs/config-macosx64-larour-python.sh (revision 13974) +++ /issm/trunk/configs/config-macosx64-larour-python.sh (revision 13975) @@ -4,12 +4,9 @@ #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=$ISSM_DIR/externalpackages/python/install/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ Index: /issm/trunk/configs/config-macosx64-larour.sh =================================================================== --- /issm/trunk/configs/config-macosx64-larour.sh (revision 13974) +++ /issm/trunk/configs/config-macosx64-larour.sh (revision 13975) @@ -4,7 +4,11 @@ #mpich 1.4 +pythonversion=2.7 + ./configure \ --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ @@ -20,6 +24,4 @@ --with-petsc-arch=$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=$ISSM_DIR/externalpackages/petsc/install/ \ Index: /issm/trunk/configs/config-macosx64-lion-helene.sh =================================================================== --- /issm/trunk/configs/config-macosx64-lion-helene.sh (revision 13974) +++ /issm/trunk/configs/config-macosx64-lion-helene.sh (revision 13975) @@ -3,6 +3,4 @@ #petsc 3.2 #mpich 1.4 - -pythonversion=2.7 ./configure \ @@ -11,6 +9,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-python-dir=$ISSM_DIR/externalpackages/python/install\ - --with-python-version=$pythonversion \ - --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ Index: /issm/trunk/configs/config-macosx64-mlion-mathieu.sh =================================================================== --- /issm/trunk/configs/config-macosx64-mlion-mathieu.sh (revision 13975) +++ /issm/trunk/configs/config-macosx64-mlion-mathieu.sh (revision 13975) @@ -0,0 +1,25 @@ +#!/bin/sh + +#mpich 1.5 +#petsc 3.3 +#python 2.7 + +./configure \ + --prefix="$ISSM_DIR" \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir="$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-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 $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-graphics-lib="-L/usr/X11R6/lib -lX11" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-petsc-arch="$ISSM_ARCH" \ + --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-blacs-dir="$ISSM_DIR/externalpackages/petsc/install/" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/src/externalpackages/metis-5.0.2-p3" \ + --with-numthreads=16 Index: /issm/trunk/configs/config-pleiades-petsc2.sh =================================================================== --- /issm/trunk/configs/config-pleiades-petsc2.sh (revision 13974) +++ /issm/trunk/configs/config-pleiades-petsc2.sh (revision 13975) @@ -3,5 +3,5 @@ ./configure \ --prefix=$ISSM_DIR \ - --with-modules=no \ + --with-wrappers=no \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ Index: /issm/trunk/configs/config-pleiades-petsc3.3.sh =================================================================== --- /issm/trunk/configs/config-pleiades-petsc3.3.sh (revision 13975) +++ /issm/trunk/configs/config-pleiades-petsc3.3.sh (revision 13975) @@ -0,0 +1,21 @@ +#!/bin/csh + +./configure \ + --prefix=$ISSM_DIR \ + --with-wrappers=no \ + --with-triangle-dir=$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=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=/nasa/sgi/mpt/2.06a67/include \ + --with-mpi-lib="-L/nasa/sgi/mpt/2.06a67/lib/ -lmpi -lpthread -lgfortran " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3" \ + --with-vendor=intel-pleiades Index: /issm/trunk/configs/config-pleiades-petscdev.sh =================================================================== --- /issm/trunk/configs/config-pleiades-petscdev.sh (revision 13974) +++ /issm/trunk/configs/config-pleiades-petscdev.sh (revision 13975) @@ -3,5 +3,5 @@ ./configure \ --prefix=$ISSM_DIR \ - --with-modules=no \ + --with-wrappers=no \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/src/externalpackages/metis-5.0.2-p3 \ @@ -13,6 +13,4 @@ --with-dakota-dir=$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/ \ @@ -20,9 +18,8 @@ --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-cxxoptflags="-O3" \ --with-vendor=intel-pleiades Index: /issm/trunk/configs/config-pleiades.sh =================================================================== --- /issm/trunk/configs/config-pleiades.sh (revision 13974) +++ /issm/trunk/configs/config-pleiades.sh (revision 13975) @@ -3,5 +3,5 @@ ./configure \ --prefix=$ISSM_DIR \ - --with-modules=no \ + --with-wrappers=no \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 13974) +++ /issm/trunk/configure.ac (revision 13975) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([ISSM],[4.2.2],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([ISSM],[4.2.3],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 @@ -36,7 +36,9 @@ src/Makefile src/c/Makefile - src/modules/Makefile - src/modules/python/Makefile - src/modules/matlab/Makefile + src/wrappers/Makefile + src/wrappers/python/Makefile + src/wrappers/matlab/Makefile + src/android/Makefile + src/android/ISSM/Makefile src/m/Makefile]) Index: /issm/trunk/etc/environment.csh =================================================================== --- /issm/trunk/etc/environment.csh (revision 13974) +++ /issm/trunk/etc/environment.csh (revision 13975) @@ -88,5 +88,5 @@ set CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install" if (-d $CMAKE_DIR) then - setenv PATH {$PATH}:{$CMAKE_DIR}/bin + setenv PATH {$CMAKE_DIR}/bin:{$PATH} endif Index: /issm/trunk/etc/environment.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 13974) +++ /issm/trunk/etc/environment.sh (revision 13975) @@ -3,5 +3,5 @@ pathprepend(){ #{{{ if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then - PATH="$1:$PATH" + export PATH="$1:$PATH" fi } #}}} @@ -66,7 +66,9 @@ MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install" -export MPI_DIR -pathprepend "$MPI_DIR/bin" -libpathappend "$MPI_DIR/lib" +if [ -d "$MPI_DIR" ]; then + export MPI_DIR + pathprepend "$MPI_DIR/bin" + libpathappend "$MPI_DIR/lib" +fi PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" @@ -102,5 +104,5 @@ GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install" -pathprepend "$GDAL_DIR/bin:$PATH" +pathprepend "$GDAL_DIR/bin" libpathappend "$GDAL_DIR/lib" @@ -187,8 +189,11 @@ pathappend "$PACKAGEMAKER_DIR" -ANDROID_NDK_DIR="$ISSM_DIR/externalpackages/android-ndk/install" -pathappend "$ANDROID_NDK_DIR/" - -ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install-sdk" +#android-dev-dir +export ANDROID_DIR="$ISSM_DIR/externalpackages/android" + +export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install" +pathappend "$ANDROID_NDK_DIR/arm-linux-android-install/bin" + +export ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install" pathappend "$ANDROID_SDK_DIR/" @@ -212,5 +217,5 @@ GIT_DIR="$ISSM_DIR/externalpackages/git/install" -pathappend "$GIT_DIR/bin" +pathprepend "$GIT_DIR/bin" NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview/install" Index: /issm/trunk/externalpackages/adolc/install-2.2.0.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-2.2.0.sh (revision 13975) +++ /issm/trunk/externalpackages/adolc/install-2.2.0.sh (revision 13975) @@ -0,0 +1,60 @@ +#!/bin/bash +set -eu + +#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. + +#Some cleanup +rm -rf install ADOL-C-2.2.0 src trunk + +#Create install directories +mkdir install src + +#Download from ISSM server +$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' + +#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 [ $# -eq 0 ]; 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 [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/adolc/install-dev.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-dev.sh (revision 13974) +++ /issm/trunk/externalpackages/adolc/install-dev.sh (revision 13975) @@ -3,10 +3,10 @@ #Some cleanup -rm -rf install adolc_v220_issm +rm -rf install adolc*issm -git clone -b 2.3.x_ISSM git://gitorious.org/~utke/adol-c/adolc_v220_issm.git +git clone -b 2.3.x_ISSM git://git.mcs.anl.gov/adol-c.git adolc_issm #Compile ADOL-C -cd adolc_v220_issm +cd adolc_issm autoreconf -f -i Index: /issm/trunk/externalpackages/adolc/install-update-dev.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-update-dev.sh (revision 13975) +++ /issm/trunk/externalpackages/adolc/install-update-dev.sh (revision 13975) @@ -0,0 +1,26 @@ +#!/bin/bash +set -eu + +#This script is very specific to the larour larsen nightly using adolc. +#It relies on just an update of adolc, and symlink to an existing adolc +#repo. + +#Some cleanup +rm -rf install adolc_issm + +#symlink: +ln -s /u/astrid-r1b/larour/issm-uci/trunk-jpl/externalpackages/adolc/adolc_issm ./adolc_issm + +#update and compile +cd adolc_issm +git pull + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: sm/trunk/externalpackages/adolc/install.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install.sh (revision 13974) +++ (revision ) @@ -1,60 +1,0 @@ -#!/bin/bash -set -eu - -#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. - -#Some cleanup -rm -rf install ADOL-C-2.2.0 src trunk - -#Create install directories -mkdir install src - -#Download from ISSM server -$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' - -#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 [ $# -eq 0 ]; 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 [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk/externalpackages/adolc/update.sh =================================================================== --- /issm/trunk/externalpackages/adolc/update.sh (revision 13975) +++ /issm/trunk/externalpackages/adolc/update.sh (revision 13975) @@ -0,0 +1,14 @@ +#!/bin/bash + +cd adolc_issm +git pull + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/android/android-ndk/install.sh =================================================================== --- /issm/trunk/externalpackages/android/android-ndk/install.sh (revision 13974) +++ /issm/trunk/externalpackages/android/android-ndk/install.sh (revision 13975) @@ -1,4 +1,3 @@ #!/bin/bash -set -eu # This installs the Android NDK (Native Development Kit) @@ -29,4 +28,4 @@ # Note: API-14 corresponds to Android 4.0. if [[ $step == "2" || $step == "0" ]]; then - $ANDROID_NDK_DIR/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/arm-linux-android-4.0 + $ANDROID_DIR/android-ndk/install/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/android-ndk/install/arm-linux-android-install fi Index: /issm/trunk/externalpackages/android/android-sdk/install.sh =================================================================== --- /issm/trunk/externalpackages/android/android-sdk/install.sh (revision 13974) +++ /issm/trunk/externalpackages/android/android-sdk/install.sh (revision 13975) @@ -1,4 +1,3 @@ #!/bin/bash -set -eu # This installs the Android SDK (Software Development Kit) Index: /issm/trunk/externalpackages/android/android_aux.sh =================================================================== --- /issm/trunk/externalpackages/android/android_aux.sh (revision 13974) +++ /issm/trunk/externalpackages/android/android_aux.sh (revision 13975) @@ -16,5 +16,9 @@ j=1; +echo "" +echo "This install script utilizes 'android_aux.sh' to allow for options." +echo "For usage information enter: '--help'" echo Number of arguments is: $# + for arg in $* do @@ -22,9 +26,18 @@ step=${BASH_REMATCH[1]}; echo "Setting step to: " $step - elif [[ "$arg" =~ -j=([1-9]+[0-9]*) || "$arg" =~ ([1-9]+[0-9]*) ]]; then + elif [[ "$arg" == "--help" ]]; then + echo "" + echo "USAGE: $ install.sh [--step=#] [-j#]" + echo "" + echo "Where '#' is some integer." + echo "To check the number of steps check the install script." + echo "" + exit 1; + elif [[ "$arg" =~ -j=([1-9]+[0-9]*) ]]; then j=${BASH_REMATCH[1]}; echo "Number of jobs set to: " $j else echo "Option not recognized" + exit 1; fi done Index: /issm/trunk/externalpackages/chaco/install.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install.sh (revision 13974) +++ /issm/trunk/externalpackages/chaco/install.sh (revision 13975) @@ -10,4 +10,5 @@ #Download from ISSM server $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf' # Untar Index: /issm/trunk/externalpackages/dakota/install-linux64-cloud.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-linux64-cloud.sh (revision 13975) +++ /issm/trunk/externalpackages/dakota/install-linux64-cloud.sh (revision 13975) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C ./NonDSampling.C.patch +patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/usr/lib/libblas.so \ + --with-lapack=/usr/lib/liblapack.so +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dakota/install-pleiades-petsc3.3.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-pleiades-petsc3.3.sh (revision 13975) +++ /issm/trunk/externalpackages/dakota/install-pleiades-petsc3.3.sh (revision 13975) @@ -0,0 +1,103 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C ./NonDSampling.C.patch +patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ +--with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " + +#--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ +#--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +#--with-blas="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" \ +#--with-lapack="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" + +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/ec2ami/install.sh =================================================================== --- /issm/trunk/externalpackages/ec2ami/install.sh (revision 13975) +++ /issm/trunk/externalpackages/ec2ami/install.sh (revision 13975) @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf ec2-api-tools.zip +rm -rf ec2-api-tools-1.4.0.7 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ec2-api-tools.zip' 'ec2-api-tools.zip' + +#Untar +unzip ec2-api-tools.zip Index: /issm/trunk/externalpackages/ec2api/install.sh =================================================================== --- /issm/trunk/externalpackages/ec2api/install.sh (revision 13975) +++ /issm/trunk/externalpackages/ec2api/install.sh (revision 13975) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf ec2-api-tools.zip +rm -rf ec2-api-tools-1.6.3.1 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ec2-api-tools.zip' 'ec2-api-tools.zip' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ec2-ug.pdf' 'ec2-ug.pdf' + +#Untar +unzip ec2-api-tools.zip Index: /issm/trunk/externalpackages/esmf/install.sh =================================================================== --- /issm/trunk/externalpackages/esmf/install.sh (revision 13974) +++ /issm/trunk/externalpackages/esmf/install.sh (revision 13975) @@ -1,10 +1,4 @@ #!/bin/bash set -eu - -#0: cleanup -#1: install -#2: test - -install=2 export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf @@ -12,40 +6,33 @@ export ESMF_COMM=mpich2 -if [[ $install == "0" ]]; then - #Some cleanup - rm -rf esmf_5_2_0rp2 - rm -rf esmf +#Some cleanup +rm -rf esmf_5_2_0rp2 +rm -rf esmf + +#Download from ISSM server +$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' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ESMF_refdoc.pdf' 'ESMF_refdoc.pdf' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ESMF_usrdoc.pdf' 'ESMF_usrdoc.pdf' + +#Untar +tar -zxvf esmf_5_2_0rp2_src.tar.gz + + +#Configure esmf +cd esmf + +#Compile and install esmf +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install 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 [ $# -eq 0 ]; then - make - make install - else - make -j $1 - make -j $1 install - fi +cd esmf +if [ $# -eq 0 ]; then + make all_tests +else + make -j $1 all_tests fi - -if [[ $install == "2" ]]; then - cd esmf - if [ $# -eq 0 ]; then - make all_tests - else - make -j $1 all_tests - fi -fi Index: /issm/trunk/externalpackages/gdal/GDALmake.opt.patch.astrid =================================================================== --- /issm/trunk/externalpackages/gdal/GDALmake.opt.patch.astrid (revision 13975) +++ /issm/trunk/externalpackages/gdal/GDALmake.opt.patch.astrid (revision 13975) @@ -0,0 +1,8 @@ +31c31 +< LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib -lexpat -ljpeg -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +--- +> LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib64 -lexpat -ljpeg -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +225c225 +< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz +--- +> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: /issm/trunk/externalpackages/gdal/install-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-linux64-astrid.sh (revision 13975) +++ /issm/trunk/externalpackages/gdal/install-linux64-astrid.sh (revision 13975) @@ -0,0 +1,41 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --without-png \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --with-unix-stdio-64=no \ + --with-expat-lib=/usr/lib64/libexpat.so + +#Patch GDALmake.opt +patch GDALmake.opt ../GDALmake.opt.patch.astrid + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/gdal/install-linux64-murdo.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-linux64-murdo.sh (revision 13975) +++ /issm/trunk/externalpackages/gdal/install-linux64-murdo.sh (revision 13975) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --without-png \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --with-unix-stdio-64=no + +#Patch GDALmake.opt +patch GDALmake.opt ../GDALmake.opt.patch + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/gdal/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-macosx64.sh (revision 13975) +++ /issm/trunk/externalpackages/gdal/install-macosx64.sh (revision 13975) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --without-png \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --with-unix-stdio-64=no \ + --with-expat-lib=/usr/lib64/libexpat.so + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: sm/trunk/externalpackages/gdal/install-murdo.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-murdo.sh (revision 13974) +++ (revision ) @@ -1,39 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src -rm -rf install -rm -rf gdal-1.6.0 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' - -#Untar -tar -zxvf gdal-1.6.0.tar.gz - -#Move gdal into src directory -mv gdal-1.6.0/* src -rm -rf gdal-1.6.0 - -#Configure gdal -cd src -./configure --prefix="$ISSM_DIR/externalpackages/gdal/install" \ - --without-python \ - --without-png \ - --with-netcdf=no \ - --with-jasper=no \ - --without-ld-shared \ - --with-unix-stdio-64=no - -#Patch GDALmake.opt -patch GDALmake.opt ../GDALmake.opt.patch - -#Compile and install gdal -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk/externalpackages/gdal/install.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install.sh (revision 13974) +++ (revision ) @@ -1,41 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src -rm -rf install -rm -rf gdal-1.6.0 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' - -#Untar -tar -zxvf gdal-1.6.0.tar.gz - -#Move gdal into src directory -mv gdal-1.6.0/* src -rm -rf gdal-1.6.0 - -#Configure gdal -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/gdal/install" \ - --without-python \ - --without-png \ - --with-netcdf=no \ - --with-jasper=no \ - --without-ld-shared \ - --with-unix-stdio-64=no \ - --with-expat-lib=/usr/lib64/libexpat.so - -#Patch GDALmake.opt -patch GDALmake.opt ../GDALmake.opt.patch - -#Compile and install gdal -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk/externalpackages/git/install-nopython.sh =================================================================== --- /issm/trunk/externalpackages/git/install-nopython.sh (revision 13974) +++ (revision ) @@ -1,23 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src install git-1.7.10.2 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/git-1.7.10.2.tar.gz' 'git-1.7.10.2.tar.gz' - -#Untar -tar -zxvf git-1.7.10.2.tar.gz - -#Move git into install directory -mv git-1.7.10.2/* src -rm -rf git-1.7.10.2 - -#install -cd src -./configure --prefix="$ISSM_DIR/externalpackages/git/install" - -#Compile -make install Index: /issm/trunk/externalpackages/git/install.sh =================================================================== --- /issm/trunk/externalpackages/git/install.sh (revision 13974) +++ /issm/trunk/externalpackages/git/install.sh (revision 13975) @@ -18,5 +18,6 @@ #install cd src -./configure --prefix="$ISSM_DIR/externalpackages/git/install" --with-python="$ISSM_DIR/externalpackages/python/install/bin/python" +./configure --prefix="$ISSM_DIR/externalpackages/git/install" +#--with-python="$ISSM_DIR/externalpackages/python/install/bin/python" #Do we really need this line? #Compile Index: /issm/trunk/externalpackages/gmp/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/gmp/install-linux64.sh (revision 13975) +++ /issm/trunk/externalpackages/gmp/install-linux64.sh (revision 13975) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gmp-5.0.5 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gmp-5.0.5.tar.bz2' 'gmp-5.0.5.tar.bz2' + +#Untar +bunzip2 gmp-5.0.5.tar.bz2 +tar -xvf gmp-5.0.5.tar + +#Move gmp into install directory +mv gmp-5.0.5/* src +rm -rf gmp-5.0.5 + +#install +cd src +./configure --prefix="$ISSM_DIR/externalpackages/gmp/install" + +#Compile and install gmp +if [ $# -eq 0 ]; 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 13974) +++ /issm/trunk/externalpackages/gsl/install-android.sh (revision 13975) @@ -24,6 +24,8 @@ if [[ $step == "2" || $step == "0" ]]; then cd src + + patch Makefile.am < Makefile.am.patch - autoreconf -iv --force -I $LIBTOOL_DIR/share/aclocal/ + autoreconf -iv --force -I $ISSM_DIR/externalpackages/autotools/install/share/aclocal ./configure \ @@ -36,4 +38,5 @@ #Compile gsl if [[ $step == "3" || $step == "0" ]]; then + cd src if [ $# -eq 0 ]; then make $j @@ -44,2 +47,3 @@ make install fi + Index: /issm/trunk/externalpackages/hdf5/install.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install.sh (revision 13974) +++ /issm/trunk/externalpackages/hdf5/install.sh (revision 13975) @@ -22,6 +22,7 @@ if [ $# -eq 0 ]; then make + make install else make -j $1 + make -j $1 install fi -make install Index: /issm/trunk/externalpackages/mpich2/install-1.0.2-altix64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 13974) +++ /issm/trunk/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 13975) @@ -30,10 +30,6 @@ patch -R ./src/include/mpicxx.h ../configs/1.0.2/altix64/mpicxx.h.patch -#Compile mpich2 -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi +#Compile mpich2 (parallel make not supported) +make make install Index: /issm/trunk/externalpackages/mpich2/install-1.0.2-linux64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 13974) +++ /issm/trunk/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 13975) @@ -30,9 +30,5 @@ patch -R ./src/include/mpicxx.h ../configs/1.0.2/linux64/mpicxx.h.patch -#Compile mpich2 -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi +#Compile mpich2 (parallel make not supported) +make make install Index: /issm/trunk/externalpackages/mpich2/install-1.0.2-macosx32.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 13974) +++ /issm/trunk/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 13975) @@ -29,10 +29,6 @@ patch -R ./src/include/mpicxx.h ../configs/1.0.2/macosx32/mpicxx.h.patch -#Compile mpich2 -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi +#Compile mpich2 (parallel make not supported) +make make install Index: /issm/trunk/externalpackages/mpich2/install-1.0.2-win32.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.0.2-win32.sh (revision 13974) +++ /issm/trunk/externalpackages/mpich2/install-1.0.2-win32.sh (revision 13975) @@ -27,10 +27,6 @@ patch -R ./src/include/mpicxx.h ../configs/1.0.2/win32/mpicxx.h.patch -#Compile mpich2 -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi +#Compile mpich2 (parallel make not supported) +make make install Index: /issm/trunk/externalpackages/mpich2/install-1.3.1-linux64-berg.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.3.1-linux64-berg.sh (revision 13974) +++ /issm/trunk/externalpackages/mpich2/install-1.3.1-linux64-berg.sh (revision 13975) @@ -36,13 +36,5 @@ fi -#Compile mpich2 -if [ $# -eq 0 ]; -then - make -else - make -j $1 -fi +#Compile mpich2 (parallel make not supported) +make make install - -cd ../install/lib -rm -rf *.so Index: /issm/trunk/externalpackages/mpich2/install-1.4-linux64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.4-linux64.sh (revision 13974) +++ /issm/trunk/externalpackages/mpich2/install-1.4-linux64.sh (revision 13975) @@ -26,9 +26,5 @@ --enable-f91=gfortran -#Compile mpich2 -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi +#Compile mpich2 (parallel make not supported) +make make install Index: /issm/trunk/externalpackages/mpich2/install-1.4-macosx32.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.4-macosx32.sh (revision 13974) +++ /issm/trunk/externalpackages/mpich2/install-1.4-macosx32.sh (revision 13975) @@ -28,9 +28,5 @@ --enable-fc -#Compile mpich2 -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi +#Compile mpich2 (parallel make not supported) +make make install Index: /issm/trunk/externalpackages/mpich2/install-1.4-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.4-macosx64.sh (revision 13974) +++ /issm/trunk/externalpackages/mpich2/install-1.4-macosx64.sh (revision 13975) @@ -28,9 +28,5 @@ --enable-fc -#Compile mpich2 -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi +#Compile mpich2 (parallel make not supported) +make make install Index: /issm/trunk/externalpackages/mpich2/install-1.5-linux64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.5-linux64.sh (revision 13975) +++ /issm/trunk/externalpackages/mpich2/install-1.5-linux64.sh (revision 13975) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich2-1.5 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.5.tar.gz' 'mpich2-1.5.tar.gz' + +#Untar +tar -zxvf mpich2-1.5.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.5/* src +rm -rf mpich2-1.5 + +#Configure mpich2 +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ + --enable-shared \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran + +#Compile mpich2 (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/mpich2/install-1.5-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.5-macosx64.sh (revision 13975) +++ /issm/trunk/externalpackages/mpich2/install-1.5-macosx64.sh (revision 13975) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich2-1.5 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.5.tar.gz' 'mpich2-1.5.tar.gz' + +#Untar +tar -zxvf mpich2-1.5.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.5/* src +rm -rf mpich2-1.5 + +#Configure mpich2 +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ + --enable-shared \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran + +#Compile mpich2 (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/mpich2/install-1.5-walgreen.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.5-walgreen.sh (revision 13975) +++ /issm/trunk/externalpackages/mpich2/install-1.5-walgreen.sh (revision 13975) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich2-1.5 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.5.tar.gz' 'mpich2-1.5.tar.gz' + +#Untar +tar -zxvf mpich2-1.5.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.5/* src +rm -rf mpich2-1.5 + +#Configure mpich2 +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ + --enable-shared \ + --with-device=ch3:sock\ + --with-atomic-primitives=no + + #--with-device=ch_p4 \ + +#Compile mpich2 (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: sm/trunk/externalpackages/netcdf/install-4.0.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.0.sh (revision 13974) +++ (revision ) @@ -1,27 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src install netcdf-4.0.1 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netcdf-4.0.1.tar.gz" "netcdf-4.0.1.tar.gz" - -#Untar -tar -zxvf netcdf-4.0.1.tar.gz - -#Move netcdf to install directory -rm -rf src/* -mv netcdf-4.0.1/* src/ -rm -rf netcdf-4.0.1 - -#Configure and compile -cd src -./configure --prefix="$ISSM_DIR/externalpackages/netcdf/install" -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk/externalpackages/netcdf/install-4.2.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.2.sh (revision 13974) +++ (revision ) @@ -1,30 +1,0 @@ -#!/bin/bash -set -eu -#you need hdf5 compiled - -#Some cleanup -rm -rf src install netcdf-4.2 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netcdf-4.2.tar.gz" "netcdf-4.2.tar.gz" - -#Untar -tar -zxvf netcdf-4.2.tar.gz - -#Move netcdf to install directory -rm -rf src/* -mv netcdf-4.2/* src/ -rm -rf netcdf-4.2 - -#Configure and compile -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/netcdf/install" \ - --disable-doxygen -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk/externalpackages/netcdf/install.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install.sh (revision 13975) +++ /issm/trunk/externalpackages/netcdf/install.sh (revision 13975) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu +#you need hdf5 compiled + +#Some cleanup +rm -rf src install netcdf-4.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netcdf-4.2.tar.gz" "netcdf-4.2.tar.gz" + +#Untar +tar -zxvf netcdf-4.2.tar.gz + +#Move netcdf to install directory +rm -rf src/* +mv netcdf-4.2/* src/ +rm -rf netcdf-4.2 + +#Configure and compile +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/netcdf/install" \ + --disable-doxygen +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/numpy/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/numpy/install-linux64.sh (revision 13974) +++ /issm/trunk/externalpackages/numpy/install-linux64.sh (revision 13975) @@ -10,11 +10,14 @@ #clean up rm -rf numpy +rm -rf numpy-1.7.0b2 #download numpy first -export GIT_SSL_NO_VERIFY=true -git clone https://github.com/numpy/numpy.git +#export GIT_SSL_NO_VERIFY=true +#git clone https://github.com/numpy/numpy.git +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/numpy-1.7.0b2.tar.gz' 'numpy-1.7.0b2.tar.gz' #install numpy -cd numpy +tar -zxvf numpy-1.7.0b2.tar.gz +cd numpy-1.7.0b2 python setup.py build python setup.py install Index: /issm/trunk/externalpackages/numpy/install-macosx-lion.sh =================================================================== --- /issm/trunk/externalpackages/numpy/install-macosx-lion.sh (revision 13974) +++ /issm/trunk/externalpackages/numpy/install-macosx-lion.sh (revision 13975) @@ -6,9 +6,19 @@ export FFLAGS=-ff2c +#clean up +rm -rf numpy +rm -rf numpy-1.7.0b2 + #download numpy first -git clone https://github.com/numpy/numpy.git +#export GIT_SSL_NO_VERIFY=true +#git clone https://github.com/numpy/numpy.git +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/numpy-1.7.0b2.tar.gz' 'numpy-1.7.0b2.tar.gz' #install numpy -cd numpy +tar -zxvf numpy-1.7.0b2.tar.gz +cd numpy-1.7.0b2 python setup.py build python setup.py install +cd .. +python -c "import numpy; print 'Installed NumPy', numpy.__version__" +python -c "import numpy; numpy.test()" Index: /issm/trunk/externalpackages/numpy/install-macosx-mlion.sh =================================================================== --- /issm/trunk/externalpackages/numpy/install-macosx-mlion.sh (revision 13975) +++ /issm/trunk/externalpackages/numpy/install-macosx-mlion.sh (revision 13975) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +export CC=gcc +export CXX=g++ +export FFLAGS=-ff2c + +#clean up +rm -rf numpy +rm -rf numpy-1.7.0b2 + +#download numpy first +#export GIT_SSL_NO_VERIFY=true +#git clone https://github.com/numpy/numpy.git +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/numpy-1.7.0b2.tar.gz' 'numpy-1.7.0b2.tar.gz' + +#install numpy +tar -zxvf numpy-1.7.0b2.tar.gz +cd numpy-1.7.0b2 +python setup.py build +python setup.py install +cd .. +python -c "import numpy; print 'Installed NumPy', numpy.__version__" +python -c "import numpy; numpy.test()" Index: /issm/trunk/externalpackages/openssl/install.sh =================================================================== --- /issm/trunk/externalpackages/openssl/install.sh (revision 13975) +++ /issm/trunk/externalpackages/openssl/install.sh (revision 13975) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +#Download latest version +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/openssl-0.9.8x.tar.gz' 'openssl-0.9.8x.tar.gz' + +#Untar +tar -xzf openssl-0.9.8x.tar.gz +mv openssl-0.9.8x src +mkdir install + +#Configure openssl +cd src +./config --prefix="$ISSM_DIR/externalpackages/openssl/install" +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/petsc/install-3.2-greenplanet.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.2-greenplanet.sh (revision 13974) +++ /issm/trunk/externalpackages/petsc/install-3.2-greenplanet.sh (revision 13975) @@ -22,5 +22,5 @@ --with-batch=1 \ --with-debugging=0 \ - --with-shared-libraries=0 \ + --with-shared-libraries=1 \ --known-mpi-shared-libraries=1 \ --with-mpi-dir=/sopt/mpi/openmpi-1.5.4_psm/intel/ \ Index: /issm/trunk/externalpackages/petsc/install-3.3-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.3-pleiades.sh (revision 13975) +++ /issm/trunk/externalpackages/petsc/install-3.3-pleiades.sh (revision 13975) @@ -0,0 +1,66 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.3-p2 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p2.tar.gz' 'petsc-3.3-p2.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.3-p2.tar.gz +mv petsc-3.3-p2/* src/ +rm -rf petsc-3.3-p2 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-lib=/nasa/sgi/mpt/2.06a67/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/2.06a67/include \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=no \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-hypre=yes \ + --with-cxx=icc \ + --with-fc=ifort \ + --COPTFLAGS="-lmpi -O3" \ + --FOPTFLAGS="-lmpi -O3" \ + --CXXOPTFLAGS="-lmpi -O3" + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l select=1:ncpus=1:model=wes +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e + +. /usr/share/modules/init/bash +module load comp-intel/2012.0.032 +module load mpi-sgi/mpt.2.06a67 +module load math/intel_mkl_64_10.0.011 + +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== qsub -q devel script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/trunk/externalpackages/petsc/install-3.3-walgreen.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.3-walgreen.sh (revision 13975) +++ /issm/trunk/externalpackages/petsc/install-3.3-walgreen.sh (revision 13975) @@ -0,0 +1,42 @@ +#!/bin/bash + +##Some cleanup +#rm -rf install petsc-3.3-p2 src +#mkdir install src +# +##Download from ISSM server +#$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p2.tar.gz' 'petsc-3.3-p2.tar.gz' +# +##Untar and move petsc to install directory +#tar -zxvf petsc-3.3-p2.tar.gz +#mv petsc-3.3-p2/* src/ +#rm -rf petsc-3.3-p2 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --with-blas-lapack-dir=/opt/intel/mkl/10.0.1.014/ \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --download-mumps=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-parmetis=yes \ + --download-metis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-spai=yes \ + --download-superlu=yes \ + --download-hypre=yes \ + --download-prometheus=yes \ + --with-cc=/opt/mpich/ch-p4/bin/mpicc \ + --with-cxx=/opt/mpich/ch-p4/bin/mpicxx \ + --with-fc=/opt/mpich/ch-p4/bin/mpif90 \ + --COPTFLAGS="-I/opt/mpich/ch-p4/include/ -lmpich -O3" \ + --FOPTFLAGS="-I/opt/mpich/ch-p4/include/ -lmpich -O3" \ + --CXXOPTFLAGS="-I/opt/mpich/ch-p4/include/ -lmpich -O3" Index: /issm/trunk/externalpackages/petsc/install-dev-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-dev-linux64.sh (revision 13974) +++ /issm/trunk/externalpackages/petsc/install-dev-linux64.sh (revision 13975) @@ -1,4 +1,3 @@ #!/bin/bash -set -eu STEP=2 @@ -19,9 +18,12 @@ # hg pull -u - # configure script -# Note: using metis from externalpackages did not work... -# -for now download new metis -# -rename metis in externalpackages to metis2 +# Note: +# Metis: -using metis from externalpackages did not work... +# -for now download new metis +# -rename metis in externalpackages to metis2 +# +# SuperLU: -If download-..-=yes does not work try downloading from +# --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ @@ -38,5 +40,4 @@ --with-shared-libraries=1 \ --download-mumps=yes \ - --download-plapack=yes \ --download-scalapack=yes \ --download-blacs=yes \ @@ -47,12 +48,10 @@ --download-trilinos=yes \ --download-euclid=yes \ - --download-pastix=yes \ - --download-ptscotch=yes \ --download-spooles=yes \ --download-spai=yes \ - --download-superlu=yes \ + --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ --download-hypre=yes \ - --download-prometheus=yes \ - --with-pic=1 + --download-c2html=yes +# --with-pic=1 #Compile petsc and install it Index: /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh (revision 13974) +++ /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh (revision 13975) @@ -1,7 +1,6 @@ #!/bin/bash -set -eu #Step 0: download #Step 1: install and write script -STEP=0 +STEP=1 if [ $STEP -eq 0 ]; then @@ -24,7 +23,10 @@ # for now downloading new metis # -then rename metis in externalpackages to metis2 +# +# --download-prometheus=yes \ +#--download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ +# --download-plapack=yes \ + if [ $STEP -eq 1 ]; then - - mkdir install #configure @@ -36,11 +38,9 @@ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ - --with-shared-libraries=0 \ + --with-shared-libraries=1 \ --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 \ + --with-mpi=1 \ --download-mumps=yes \ - --download-plapack=yes \ --download-scalapack=yes \ --download-blacs=yes \ @@ -51,29 +51,21 @@ --download-trilinos=yes \ --download-euclid=yes \ - --download-pastix=yes \ - --download-ptscotch=yes \ - --download-spooles=yes \ --download-spai=yes \ - --download-superlu=yes \ + --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ --download-hypre=yes \ - --download-prometheus=yes \ - --FFLAGS=-I/usr/include \ - --with-cxx=icpc \ - --with-cc=icc \ - --with-fc=ifort \ - --COPTFLAGS=" -O3 -xS" \ - --FOPTFLAGS=" -O3 -xS" \ - --CXXOPTFLAGS=" -O3 -xS" \ - --with-pic=1 + --with-cxx=/nasa/sgi/mpt/2.06a67/bin/mpicxx \ + --with-fc=/nasa/sgi/mpt/2.06a67/bin/mpif90 \ + --COPTFLAGS="-lmpi -O3" \ + --FOPTFLAGS="-lmpi -O3" \ + --CXXOPTFLAGS="-lmpi -O3" cat > script.queue << EOF #PBS -S /bin/bash -#PBS -q debug -#PBS -l select=1:ncpus=1:model=har +#PBS -l select=1:ncpus=1:model=wes #PBS -l walltime=200 #PBS -W group_list=s1010 #PBS -m e . /usr/share/modules/init/bash -module load comp-intel/11.1.046 -module load mpi-sgi/mpt.2.04 #DEFINES MPI_Type_create_indexed_block +module load comp-intel/2012.0.032 +module load mpi-sgi/mpt.2.06a67 module load math/intel_mkl_64_10.0.011 export PATH="$PATH:." @@ -81,4 +73,6 @@ mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py EOF - echo "== Follow PETSc's instructions" + echo "== Now: cd src/ " + echo "== qsub -q devel script.queue " + echo "== Then run reconfigure script generated by PETSc and follow instructions" fi Index: /issm/trunk/externalpackages/python/install-2.7.3-macosx-mlion.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2.7.3-macosx-mlion.sh (revision 13975) +++ /issm/trunk/externalpackages/python/install-2.7.3-macosx-mlion.sh (revision 13975) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure and compile +cd src +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install + +#get rid of bin, because it's just a copy of +#Library/Frameworks/Python.framework/Versions/2.7/bin, and will not reflect +#new changes being made +rm -rf bin +ln -s Library/Frameworks/Python.framework/Headers include +ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib +ln -s Library/Frameworks/Python.framework/Versions/2.7/bin bin + +#Patch pyport.h: +cd include +patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: /issm/trunk/externalpackages/readline/install.sh =================================================================== --- /issm/trunk/externalpackages/readline/install.sh (revision 13974) +++ /issm/trunk/externalpackages/readline/install.sh (revision 13975) @@ -17,5 +17,5 @@ rm -rf readline-6.2.2 -$install +#install cd src python setup.py install Index: /issm/trunk/externalpackages/scipy/install-macosx-mlion.sh =================================================================== --- /issm/trunk/externalpackages/scipy/install-macosx-mlion.sh (revision 13975) +++ /issm/trunk/externalpackages/scipy/install-macosx-mlion.sh (revision 13975) @@ -0,0 +1,20 @@ +#!/bin/bash +set -eu + +export CC=gcc +export CXX=g++ +export FFLAGS=-ff2c + +#download scipy +git clone https://github.com/scipy/scipy.git + +#install scipy +cd scipy +export BLAS_SRC=$ISSM_DIR/externalpackages/blas/install/lib +export BLAS=$ISSM_DIR/externalpackages/blas/install/lib +export LAPACK_SRC=$ISSM_DIR/externalpackages/lapack/install/lib +export LAPACK=$ISSM_DIR/externalpackages/lapack/install/lib + +#install scipy +python setup.py build +python setup.py install Index: /issm/trunk/externalpackages/scotch/install.sh =================================================================== --- /issm/trunk/externalpackages/scotch/install.sh (revision 13974) +++ /issm/trunk/externalpackages/scotch/install.sh (revision 13975) @@ -12,4 +12,6 @@ #Download from ISSM server $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/scotch_5.1.6.tar.gz' 'scotch_5.1.6.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ptscotch_user5.1.pdf' 'ptscotch_user5.1.pdf' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/scotch_user5.1.pdf' 'scotch_user5.1.pdf' # Untar Index: /issm/trunk/externalpackages/shapelib/install.sh =================================================================== --- /issm/trunk/externalpackages/shapelib/install.sh (revision 13974) +++ /issm/trunk/externalpackages/shapelib/install.sh (revision 13975) @@ -10,5 +10,6 @@ #Download from ISSM server $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shapelib-1.2.10.tar.gz' 'shapelib-1.2.10.tar.gz' -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shape_eg_data.zip' 'shape_eg_data.zip' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shape_eg_data.zip' 'shape_eg_data.zip' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/shapefile.pdf' 'shapefile.pdf' # Untar Index: /issm/trunk/externalpackages/starcluster/install.sh =================================================================== --- /issm/trunk/externalpackages/starcluster/install.sh (revision 13975) +++ /issm/trunk/externalpackages/starcluster/install.sh (revision 13975) @@ -0,0 +1,7 @@ +#/bin/bash + +git clone git://github.com/jtriley/StarCluster.git + +cd StarCluster +python distribute_setup.py +python setup.py install Index: /issm/trunk/externalpackages/vim/addons/vim/colors/issm_black.vim =================================================================== --- /issm/trunk/externalpackages/vim/addons/vim/colors/issm_black.vim (revision 13974) +++ /issm/trunk/externalpackages/vim/addons/vim/colors/issm_black.vim (revision 13975) @@ -1,227 +1,86 @@ -" ir_black color scheme -" More at: http://blog.infinitered.com/entries/show/8 +" issm_black color scheme +" table http://www.calmar.ws/vim/256-xterm-24bit-rgb-color-chart.html - -" ******************************************************************************** -" Standard colors used in all ir_black themes: -" Note, x:x:x are RGB values -" -" normal: #f6f3e8 -" -" string: #A8FF60 168:255:96 -" string inner (punc, code, etc): #00A0A0 0:160:160 -" number: #FF73FD 255:115:253 -" comments: #7C7C7C 124:124:124 -" keywords: #96CBFE 150:203:254 -" operators: white -" class: #FFFFB6 255:255:182 -" method declaration name: #FFD2A7 255:210:167 -" regular expression: #E9C062 233:192:98 -" regexp alternate: #FF8000 255:128:0 -" regexp alternate 2: #B18A3D 177:138:61 -" variable: #C6C5FE 198:197:254 -" -" Misc colors: -" red color (used for whatever): #FF6C60 255:108:96 -" light red: #FFB6B0 255:182:176 -" -" brown: #E18964 good for special -" -" lightpurpleish: #FFCCFF -" -" Interface colors: -" background color: black -" cursor (where underscore is used): #FFA560 255:165:96 -" cursor (where block is used): white -" visual selection: #1D1E2C -" current line: #151515 21:21:21 -" search selection: #07281C 7:40:28 -" line number: #3D3D3D 61:61:61 - - -" ******************************************************************************** -" The following are the preferred 16 colors for your terminal -" Colors Bright Colors -" Black #4E4E4E #7C7C7C -" Red #FF6C60 #FFB6B0 -" Green #A8FF60 #CEFFAB -" Yellow #FFFFB6 #FFFFCB -" Blue #96CBFE #FFFFCB -" Magenta #FF73FD #FF9CFE -" Cyan #C6C5FE #DFDFFE -" White #EEEEEE #FFFFFF - - -" ******************************************************************************** +"Set up coloring hi clear - if exists("syntax_on") syntax reset endif syntax on - let colors_name = "issm_black" -" GUI not used in terminal mode forground background style (reverse,bold,..) -"hi Example guifg=NONE guibg=NONE gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE +"preferred colors: +" 0 : black +" 9 : red +" 15 : white +" 69 : blue +" 87 : cyan +" 129 : dark purple +" 202 : orange +" 214 : light orange +" 227 : yellow +" 234 : very dark gray +" 241 : dark gray +" 244 : gray +" 255 : light gray +" forground background style (reverse,bold,..) " General colors -hi Normal guifg=#f6f3e8 guibg=black gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE -hi NonText guifg=#070707 guibg=black gui=NONE ctermfg=129 ctermbg=NONE cterm=NONE "214 =orange - -hi Cursor guifg=black guibg=white gui=NONE ctermfg=NONE ctermbg=NONE cterm=reverse "cursor (mouse) -hi LineNr guifg=#3D3D3D guibg=black gui=NONE ctermfg=249 ctermbg=232 cterm=NONE "line numbering gray/blak - -hi VertSplit guifg=#202020 guibg=#202020 gui=NONE ctermfg=241 ctermbg=241 cterm=NONE "vertical split -hi StatusLine guifg=#CCCCCC guibg=#202020 gui=italic ctermfg=241 ctermbg=87 cterm=NONE "87 = cyan -hi StatusLineNC guifg=black guibg=#202020 gui=NONE ctermfg=87 ctermbg=241 cterm=NONE "241 = dark gray - -hi Folded guifg=#a0a8b0 guibg=#384048 gui=NONE ctermfg=135 ctermbg=234 cterm=NONE "folded 129 = violet ,234 Gray -hi Title guifg=#f6f3e8 guibg=NONE gui=bold ctermfg=NONE ctermbg=NONE cterm=NONE -hi Visual guifg=NONE guibg=#262D51 gui=NONE ctermfg=NONE ctermbg=NONE cterm=reverse "visual 255 = white - -hi SpecialKey guifg=#808080 guibg=#343434 gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE - -hi WildMenu guifg=green guibg=yellow gui=NONE ctermfg=black ctermbg=yellow cterm=NONE "????? -hi PmenuSbar guifg=black guibg=white gui=NONE ctermfg=black ctermbg=magenta cterm=NONE "???? -"hi Ignore guifg=gray guibg=black gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE - -hi Error guifg=white guibg=NONE gui=none ctermfg=255 ctermbg=129 cterm=NONE -hi ErrorMsg guifg=white guibg=#FF6C60 gui=BOLD ctermfg=255 ctermbg=129 cterm=NONE " 196 = red -hi WarningMsg guifg=white guibg=#FF6C60 gui=BOLD ctermfg=255 ctermbg=201 cterm=NONE "201 = magenta +hi Normal ctermfg=NONE ctermbg=NONE cterm=NONE +hi NonText ctermfg=129 ctermbg=NONE cterm=NONE +hi Cursor ctermfg=NONE ctermbg=NONE cterm=reverse +hi LineNr ctermfg=15 ctermbg=241 cterm=NONE +hi VertSplit ctermfg=241 ctermbg=241 cterm=NONE +hi StatusLine ctermfg=241 ctermbg=87 cterm=NONE +hi StatusLineNC ctermfg=87 ctermbg=241 cterm=NONE +hi Folded ctermfg=141 ctermbg=236 cterm=NONE +hi Title ctermfg=NONE ctermbg=NONE cterm=NONE +hi Visual ctermfg=NONE ctermbg=NONE cterm=reverse +hi SpecialKey ctermfg=NONE ctermbg=NONE cterm=NONE +hi WildMenu ctermfg=0 ctermbg=227 cterm=NONE +hi PmenuSbar ctermfg=0 ctermbg=129 cterm=NONE +hi Error ctermfg=15 ctermbg=129 cterm=NONE +hi ErrorMsg ctermfg=15 ctermbg=129 cterm=NONE +hi WarningMsg ctermfg=15 ctermbg=129 cterm=NONE " Message displayed in lower left, such as --INSERT-- -hi ModeMsg guifg=black guibg=#C6C5FE gui=BOLD ctermfg=241 ctermbg=87 cterm=BOLD - +hi ModeMsg ctermfg=0 ctermbg=87 cterm=BOLD if version >= 700 " Vim 7.x specific colors - hi CursorLine guifg=NONE guibg=#121212 gui=NONE ctermfg=NONE ctermbg=NONE cterm=BOLD - hi CursorColumn guifg=NONE guibg=#121212 gui=NONE ctermfg=NONE ctermbg=NONE cterm=BOLD - hi MatchParen guifg=#f6f3e8 guibg=#857b6f gui=BOLD ctermfg=87 ctermbg=241 cterm=BOLD,reverse "matching parenthesis - hi Pmenu guifg=#f6f3e8 guibg=#444444 gui=NONE ctermfg=black ctermbg=white cterm=NONE "auto completion panel - hi PmenuSel guifg=#000000 guibg=#cae682 gui=NONE ctermfg=255 ctermbg=darkgray cterm=NONE - hi Search guifg=NONE guibg=NONE gui=underline ctermfg=black ctermbg=220 cterm=NONE "227 = yellow + hi CursorLine ctermfg=NONE ctermbg=NONE cterm=BOLD + hi CursorColumn ctermfg=NONE ctermbg=NONE cterm=BOLD + hi MatchParen ctermfg=87 ctermbg=241 cterm=reverse "matching parenthesis + hi Pmenu ctermfg=0 ctermbg=15 cterm=NONE "auto completion panel + hi PmenuSel ctermfg=255 ctermbg=241 cterm=NONE + hi Search ctermfg=0 ctermbg=220 cterm=NONE endif " Syntax highlighting -hi Comment guifg=#7C7C7C guibg=NONE gui=NONE ctermfg=243 ctermbg=NONE cterm=NONE -hi String guifg=#A8FF60 guibg=NONE gui=NONE ctermfg=120 ctermbg=NONE cterm=NONE -hi Number guifg=#FF73FD guibg=NONE gui=NONE ctermfg=201 ctermbg=NONE cterm=NONE +hi Comment ctermfg=244 ctermbg=NONE cterm=NONE +hi String ctermfg=120 ctermbg=NONE cterm=NONE +hi Number ctermfg=201 ctermbg=NONE cterm=NONE +hi Keyword ctermfg=9 ctermbg=NONE cterm=NONE " matlab function +hi PreProc ctermfg=9 ctermbg=NONE cterm=NONE " def undef include +hi Conditional ctermfg=220 ctermbg=NONE cterm=NONE " if else end +hi Todo ctermfg=214 ctermbg=NONE cterm=NONE +hi Constant ctermfg=196 ctermbg=NONE cterm=NONE +hi Identifier ctermfg=9 ctermbg=NONE cterm=NONE +hi Function ctermfg=69 ctermbg=NONE cterm=NONE "functions 69 = pastel blue +hi Type ctermfg=87 ctermbg=NONE cterm=NONE "cterm matlab global +hi Statement ctermfg=69 ctermbg=NONE cterm=NONE "cd ls sed mv +hi Special ctermfg=202 ctermbg=NONE cterm=NONE " matlab '...' +hi Delimiter ctermfg=NONE ctermbg=NONE cterm=NONE " [ ] +hi Operator ctermfg=202 ctermbg=NONE cterm=NONE " == & +hi Directory ctermfg=87 ctermbg=NONE cterm=NONE " == & -hi Keyword guifg=#96CBFE guibg=NONE gui=NONE ctermfg=red ctermbg=NONE cterm=NONE " matlab function -hi PreProc guifg=#96CBFE guibg=NONE gui=NONE ctermfg=red ctermbg=NONE cterm=NONE " def undef include -hi Conditional guifg=#6699CC guibg=NONE gui=NONE ctermfg=220 ctermbg=NONE cterm=NONE " if else end - -hi Todo guifg=#8f8f8f guibg=NONE gui=NONE ctermfg=214 ctermbg=NONE cterm=NONE -hi Constant guifg=#99CC99 guibg=NONE gui=NONE ctermfg=196 ctermbg=NONE cterm=NONE - -hi Identifier guifg=#C6C5FE guibg=NONE gui=NONE ctermfg=red ctermbg=NONE cterm=NONE -hi Function guifg=#FFD2A7 guibg=NONE gui=NONE ctermfg=69 ctermbg=NONE cterm=NONE "functions 69 = pastel blue -hi Type guifg=#FFFFB6 guibg=NONE gui=NONE ctermfg=87 ctermbg=NONE cterm=NONE "cterm matlab global -hi Statement guifg=#6699CC guibg=NONE gui=NONE ctermfg=69 ctermbg=NONE cterm=NONE " cd ls sed mv - -hi Special guifg=#E18964 guibg=NONE gui=NONE ctermfg=202 ctermbg=NONE cterm=NONE " ; 202 = orange -hi Delimiter guifg=#00A0A0 guibg=NONE gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE " [ ] -hi Operator guifg=white guibg=NONE gui=NONE ctermfg=202 ctermbg=NONE cterm=NONE " == & 178 = darkyellow - -hi Directory guifg=white guibg=NONE gui=NONE ctermfg=87 ctermbg=NONE cterm=NONE " == & 178 = darkyellow - - "Specific for diff - hi DiffAdd guifg=#ffff33 guibg=#404010 gui=bold term=none cterm=none ctermfg=black ctermbg=119 - hi DiffChange guibg=#202020 gui=bold term=none cterm=none ctermfg=black ctermbg=228 - hi DiffText guifg=#3333ff guibg=#100040 gui=bold term=none cterm=none ctermfg=black ctermbg=178 - hi DiffDelete guifg=#ff0000 guibg=#401010 gui=bold term=none cterm=none ctermfg=black ctermbg=197 - hi diffLine guifg=#444444 guibg=bg gui=bold term=none cterm=bold ctermfg=darkgrey - hi diffOldLine guifg=#444444 guibg=bg gui=none term=none cterm=none ctermfg=darkgrey - hi diffOldFile guifg=#444444 guibg=bg gui=none term=none cterm=none ctermfg=darkgrey - hi diffNewFile guifg=#444444 guibg=bg gui=none term=none cterm=none ctermfg=darkgrey - hi diffAdded guifg=#80ff80 guibg=bg gui=none term=none cterm=none - hi diffRemoved guifg=#ff0000 guibg=bg gui=none term=none cterm=none ctermfg=red - hi diffChanged guifg=#0000ff guibg=bg gui=none term=none cterm=none ctermfg=blue - -hi link Character Constant -hi link Boolean Constant -hi link Float Number -hi link Repeat Statement -hi link Label Statement -hi link Exception Statement -hi link Include PreProc -hi link Define PreProc -hi link Macro PreProc -hi link PreCondit PreProc -hi link StorageClass Type -hi link Structure Type -hi link Typedef Type -hi link Tag Special -hi link SpecialChar Special -hi link SpecialComment Special -hi link Debug Special - - -" Special for Ruby -hi rubyRegexp guifg=#B18A3D guibg=NONE gui=NONE ctermfg=brown ctermbg=NONE cterm=NONE -hi rubyRegexpDelimiter guifg=#FF8000 guibg=NONE gui=NONE ctermfg=brown ctermbg=NONE cterm=NONE -hi rubyEscape guifg=white guibg=NONE gui=NONE ctermfg=cyan ctermbg=NONE cterm=NONE -hi rubyInterpolationDelimiter guifg=#00A0A0 guibg=NONE gui=NONE ctermfg=blue ctermbg=NONE cterm=NONE -hi rubyControl guifg=#6699CC guibg=NONE gui=NONE ctermfg=blue ctermbg=NONE cterm=NONE "and break, etc -"hi rubyGlobalVariable guifg=#FFCCFF guibg=NONE gui=NONE ctermfg=lightblue ctermbg=NONE cterm=NONE "yield -hi rubyStringDelimiter guifg=#336633 guibg=NONE gui=NONE ctermfg=lightgreen ctermbg=NONE cterm=NONE -"rubyInclude -"rubySharpBang -"rubyAccess -"rubyPredefinedVariable -"rubyBoolean -"rubyClassVariable -"rubyBeginEnd -"rubyRepeatModifier -"hi link rubyArrayDelimiter Special " [ , , ] -"rubyCurlyBlock { , , } - -hi link rubyClass Keyword -hi link rubyModule Keyword -hi link rubyKeyword Keyword -hi link rubyOperator Operator -hi link rubyIdentifier Identifier -hi link rubyInstanceVariable Identifier -hi link rubyGlobalVariable Identifier -hi link rubyClassVariable Identifier -hi link rubyConstant Type - - -" Special for Java -" hi link javaClassDecl Type -hi link javaScopeDecl Identifier -hi link javaCommentTitle javaDocSeeTag -hi link javaDocTags javaDocSeeTag -hi link javaDocParam javaDocSeeTag -hi link javaDocSeeTagParam javaDocSeeTag - -hi javaDocSeeTag guifg=#CCCCCC guibg=NONE gui=NONE ctermfg=darkgray ctermbg=NONE cterm=NONE -hi javaDocSeeTag guifg=#CCCCCC guibg=NONE gui=NONE ctermfg=darkgray ctermbg=NONE cterm=NONE -"hi javaClassDecl guifg=#CCFFCC guibg=NONE gui=NONE ctermfg=white ctermbg=NONE cterm=NONE - - -" Special for XML -hi link xmlTag Keyword -hi link xmlTagName Conditional -hi link xmlEndTag Identifier - - -" Special for HTML -hi link htmlTag Keyword -hi link htmlTagName Conditional -hi link htmlEndTag Identifier - - -" Special for Javascript -hi link javaScriptNumber Number - - -" Special for Python -"hi link pythonEscape Keyword - - -" Special for CSharp -hi link csXmlTag Keyword - - -" Special for PHP +"Specific for diff +hi DiffAdd cterm=none ctermfg=0 ctermbg=119 +hi DiffChange cterm=none ctermfg=0 ctermbg=228 +hi DiffText cterm=none ctermfg=0 ctermbg=178 +hi DiffDelete cterm=none ctermfg=0 ctermbg=197 +hi diffLine cterm=bold ctermfg=241 +hi diffOldLine cterm=none ctermfg=241 +hi diffOldFile cterm=none ctermfg=241 +hi diffNewFile cterm=none ctermfg=241 +hi diffAdded cterm=none +hi diffRemoved cterm=none ctermfg=9 +hi diffChanged cterm=none ctermfg=69 Index: /issm/trunk/externalpackages/vim/addons/vim/colors/issm_white.vim =================================================================== --- /issm/trunk/externalpackages/vim/addons/vim/colors/issm_white.vim (revision 13974) +++ /issm/trunk/externalpackages/vim/addons/vim/colors/issm_white.vim (revision 13975) @@ -1,212 +1,86 @@ -" ir_black color scheme -" More at: http://blog.infinitered.com/entries/show/8 +" issm_white scheme +" table http://www.calmar.ws/vim/256-xterm-24bit-rgb-color-chart.html - -" ******************************************************************************** -" Standard colors used in all ir_black themes: -" Note, x:x:x are RGB values -" -" normal: #f6f3e8 -" -" string: #A8FF60 168:255:96 -" string inner (punc, code, etc): #00A0A0 0:160:160 -" number: #FF73FD 255:115:253 -" comments: #7C7C7C 124:124:124 -" keywords: #96CBFE 150:203:254 -" operators: white -" class: #FFFFB6 255:255:182 -" method declaration name: #FFD2A7 255:210:167 -" regular expression: #E9C062 233:192:98 -" regexp alternate: #FF8000 255:128:0 -" regexp alternate 2: #B18A3D 177:138:61 -" variable: #C6C5FE 198:197:254 -" -" Misc colors: -" red color (used for whatever): #FF6C60 255:108:96 -" light red: #FFB6B0 255:182:176 -" -" brown: #E18964 good for special -" -" lightpurpleish: #FFCCFF -" -" Interface colors: -" background color: black -" cursor (where underscore is used): #FFA560 255:165:96 -" cursor (where block is used): white -" visual selection: #1D1E2C -" current line: #151515 21:21:21 -" search selection: #07281C 7:40:28 -" line number: #3D3D3D 61:61:61 - - -" ******************************************************************************** -" The following are the preferred 16 colors for your terminal -" Colors Bright Colors -" Black #4E4E4E #7C7C7C -" Red #FF6C60 #FFB6B0 -" Green #A8FF60 #CEFFAB -" Yellow #FFFFB6 #FFFFCB -" Blue #96CBFE #FFFFCB -" Magenta #FF73FD #FF9CFE -" Cyan #C6C5FE #DFDFFE -" White #EEEEEE #FFFFFF - - -" ******************************************************************************** +"Set up coloring hi clear - if exists("syntax_on") syntax reset endif syntax on +let colors_name = "issm_black" -let colors_name = "issm_white" +"preferred colors: +" 0 : black +" 9 : red +" 15 : white +" 20 : blue +" 33 : cyan +" 129 : dark purple +" 202 : orange +" 204 : light orange +" 227 : yellow +" 234 : very dark gray +" 241 : dark gray +" 244 : gray +" 255 : light gray -" GUI not used in terminal mode forground background style (reverse,bold,..) -"hi Example guifg=NONE guibg=NONE gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE - +" forground background style (reverse,bold,..) " General colors -hi Normal guifg=#f6f3e8 guibg=black gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE -hi NonText guifg=#070707 guibg=black gui=NONE ctermfg=129 ctermbg=NONE cterm=NONE "214 =orange - -hi Cursor guifg=black guibg=white gui=NONE ctermfg=NONE ctermbg=NONE cterm=reverse "cursor (mouse) -hi LineNr guifg=#3D3D3D guibg=black gui=NONE ctermfg=249 ctermbg=232 cterm=NONE "line numbering gray/blak - -hi VertSplit guifg=#202020 guibg=#202020 gui=NONE ctermfg=241 ctermbg=241 cterm=NONE "vertical split -hi StatusLine guifg=#CCCCCC guibg=#202020 gui=italic ctermfg=241 ctermbg=87 cterm=NONE "87 = cyan -hi StatusLineNC guifg=black guibg=#202020 gui=NONE ctermfg=87 ctermbg=241 cterm=NONE "241 = dark gray - -hi Folded guifg=#a0a8b0 guibg=#384048 gui=NONE ctermfg=NONE ctermbg=129 cterm=NONE "folded 129 = violet -hi Title guifg=#f6f3e8 guibg=NONE gui=bold ctermfg=NONE ctermbg=NONE cterm=NONE -hi Visual guifg=NONE guibg=#262D51 gui=NONE ctermbg=255 cterm=bold,reverse "visual 255 = white - -hi SpecialKey guifg=#808080 guibg=#343434 gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE - -hi WildMenu guifg=green guibg=yellow gui=NONE ctermfg=black ctermbg=yellow cterm=NONE "????? -hi PmenuSbar guifg=black guibg=white gui=NONE ctermfg=black ctermbg=magenta cterm=NONE "???? -"hi Ignore guifg=gray guibg=black gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE - -hi Error guifg=NONE guibg=black gui=NONE ctermfg=255 ctermbg=129 cterm=NONE -hi ErrorMsg guifg=white guibg=#FF6C60 gui=BOLD ctermfg=255 ctermbg=129 cterm=NONE " 196 = red -hi WarningMsg guifg=white guibg=#FF6C60 gui=BOLD ctermfg=255 ctermbg=201 cterm=NONE "201 = magenta +hi Normal ctermfg=NONE ctermbg=NONE cterm=NONE +hi NonText ctermfg=129 ctermbg=NONE cterm=NONE +hi Cursor ctermfg=NONE ctermbg=NONE cterm=reverse +hi LineNr ctermfg=15 ctermbg=241 cterm=NONE +hi VertSplit ctermfg=241 ctermbg=241 cterm=NONE +hi StatusLine ctermfg=241 ctermbg=33 cterm=NONE +hi StatusLineNC ctermfg=33 ctermbg=241 cterm=NONE +hi Folded ctermfg=93 ctermbg=254 cterm=NONE +hi Title ctermfg=NONE ctermbg=NONE cterm=NONE +hi Visual ctermfg=NONE ctermbg=NONE cterm=reverse +hi SpecialKey ctermfg=NONE ctermbg=NONE cterm=NONE +hi WildMenu ctermfg=0 ctermbg=227 cterm=NONE +hi PmenuSbar ctermfg=0 ctermbg=129 cterm=NONE +hi Error ctermfg=15 ctermbg=129 cterm=NONE +hi ErrorMsg ctermfg=15 ctermbg=129 cterm=NONE +hi WarningMsg ctermfg=15 ctermbg=129 cterm=NONE " Message displayed in lower left, such as --INSERT-- -hi ModeMsg guifg=black guibg=#C6C5FE gui=BOLD ctermfg=241 ctermbg=87 cterm=BOLD - +hi ModeMsg ctermfg=0 ctermbg=33 cterm=BOLD if version >= 700 " Vim 7.x specific colors - hi CursorLine guifg=NONE guibg=#121212 gui=NONE ctermfg=NONE ctermbg=NONE cterm=BOLD - hi CursorColumn guifg=NONE guibg=#121212 gui=NONE ctermfg=NONE ctermbg=NONE cterm=BOLD - hi MatchParen guifg=#f6f3e8 guibg=#857b6f gui=BOLD ctermfg=87 ctermbg=241 cterm=BOLD,reverse "matching parenthesis - hi Pmenu guifg=#f6f3e8 guibg=#444444 gui=NONE ctermfg=232 ctermbg=254 cterm=NONE "auto completion panel - hi PmenuSel guifg=#000000 guibg=#cae682 gui=NONE ctermfg=255 ctermbg=201 cterm=NONE - hi Search guifg=NONE guibg=NONE gui=underline ctermfg=NONE ctermbg=227 cterm=NONE "227 = yellow + hi CursorLine ctermfg=NONE ctermbg=NONE cterm=BOLD + hi CursorColumn ctermfg=NONE ctermbg=NONE cterm=BOLD + hi MatchParen ctermfg=33 ctermbg=241 cterm=reverse "matching parenthesis + hi Pmenu ctermfg=0 ctermbg=15 cterm=NONE "auto completion panel + hi PmenuSel ctermfg=255 ctermbg=241 cterm=NONE + hi Search ctermfg=0 ctermbg=220 cterm=NONE endif " Syntax highlighting -hi Comment guifg=#7C7C7C guibg=NONE gui=NONE ctermfg=243 ctermbg=NONE cterm=NONE -hi String guifg=#A8FF60 guibg=NONE gui=NONE ctermfg=40 ctermbg=NONE cterm=NONE -hi Number guifg=#FF73FD guibg=NONE gui=NONE ctermfg=201 ctermbg=NONE cterm=NONE +hi Comment ctermfg=241 ctermbg=NONE cterm=NONE +hi String ctermfg=28 ctermbg=NONE cterm=NONE +hi Number ctermfg=201 ctermbg=NONE cterm=NONE +hi Keyword ctermfg=9 ctermbg=NONE cterm=NONE " matlab function +hi PreProc ctermfg=9 ctermbg=NONE cterm=NONE " def undef include +hi Conditional ctermfg=220 ctermbg=NONE cterm=NONE " if else end +hi Todo ctermfg=204 ctermbg=NONE cterm=NONE +hi Constant ctermfg=196 ctermbg=NONE cterm=NONE +hi Identifier ctermfg=9 ctermbg=NONE cterm=NONE +hi Function ctermfg=20 ctermbg=NONE cterm=NONE "functions 20 = pastel blue +hi Type ctermfg=33 ctermbg=NONE cterm=NONE "cterm matlab global +hi Statement ctermfg=20 ctermbg=NONE cterm=NONE "cd ls sed mv +hi Special ctermfg=202 ctermbg=NONE cterm=NONE " matlab '...' +hi Delimiter ctermfg=NONE ctermbg=NONE cterm=NONE " [ ] +hi Operator ctermfg=202 ctermbg=NONE cterm=NONE " == & +hi Directory ctermfg=33 ctermbg=NONE cterm=NONE " == & -hi Keyword guifg=#96CBFE guibg=NONE gui=NONE ctermfg=196 ctermbg=NONE cterm=NONE " matlab function -hi PreProc guifg=#96CBFE guibg=NONE gui=NONE ctermfg=196 ctermbg=NONE cterm=NONE " def undef include -hi Conditional guifg=#6699CC guibg=NONE gui=NONE ctermfg=93 ctermbg=NONE cterm=NONE " if else end - -hi Todo guifg=#8f8f8f guibg=NONE gui=NONE ctermfg=18 ctermbg=NONE cterm=NONE -hi Constant guifg=#99CC99 guibg=NONE gui=NONE ctermfg=21 ctermbg=NONE cterm=NONE - -hi Identifier guifg=#C6C5FE guibg=NONE gui=NONE ctermfg=21 ctermbg=NONE cterm=NONE -hi Function guifg=#FFD2A7 guibg=NONE gui=NONE ctermfg=69 ctermbg=NONE cterm=NONE "functions 69 = pastel blue -hi Type guifg=#FFFFB6 guibg=NONE gui=NONE ctermfg=165 ctermbg=NONE cterm=NONE -hi Statement guifg=#6699CC guibg=NONE gui=NONE ctermfg=69 ctermbg=NONE cterm=NONE " cd ls sed mv - -hi Special guifg=#E18964 guibg=NONE gui=NONE ctermfg=43 ctermbg=NONE cterm=NONE " ; 202 = orange -hi Delimiter guifg=#00A0A0 guibg=NONE gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE " [ ] -hi Operator guifg=white guibg=NONE gui=NONE ctermfg=43 ctermbg=NONE cterm=NONE " == & 178 = darkyellow - -hi link Character Constant -hi link Boolean Constant -hi link Float Number -hi link Repeat Statement -hi link Label Statement -hi link Exception Statement -hi link Include PreProc -hi link Define PreProc -hi link Macro PreProc -hi link PreCondit PreProc -hi link StorageClass Type -hi link Structure Type -hi link Typedef Type -hi link Tag Special -hi link SpecialChar Special -hi link SpecialComment Special -hi link Debug Special - - -" Special for Ruby -hi rubyRegexp guifg=#B18A3D guibg=NONE gui=NONE ctermfg=brown ctermbg=NONE cterm=NONE -hi rubyRegexpDelimiter guifg=#FF8000 guibg=NONE gui=NONE ctermfg=brown ctermbg=NONE cterm=NONE -hi rubyEscape guifg=white guibg=NONE gui=NONE ctermfg=cyan ctermbg=NONE cterm=NONE -hi rubyInterpolationDelimiter guifg=#00A0A0 guibg=NONE gui=NONE ctermfg=blue ctermbg=NONE cterm=NONE -hi rubyControl guifg=#6699CC guibg=NONE gui=NONE ctermfg=blue ctermbg=NONE cterm=NONE "and break, etc -"hi rubyGlobalVariable guifg=#FFCCFF guibg=NONE gui=NONE ctermfg=lightblue ctermbg=NONE cterm=NONE "yield -hi rubyStringDelimiter guifg=#336633 guibg=NONE gui=NONE ctermfg=lightgreen ctermbg=NONE cterm=NONE -"rubyInclude -"rubySharpBang -"rubyAccess -"rubyPredefinedVariable -"rubyBoolean -"rubyClassVariable -"rubyBeginEnd -"rubyRepeatModifier -"hi link rubyArrayDelimiter Special " [ , , ] -"rubyCurlyBlock { , , } - -hi link rubyClass Keyword -hi link rubyModule Keyword -hi link rubyKeyword Keyword -hi link rubyOperator Operator -hi link rubyIdentifier Identifier -hi link rubyInstanceVariable Identifier -hi link rubyGlobalVariable Identifier -hi link rubyClassVariable Identifier -hi link rubyConstant Type - - -" Special for Java -" hi link javaClassDecl Type -hi link javaScopeDecl Identifier -hi link javaCommentTitle javaDocSeeTag -hi link javaDocTags javaDocSeeTag -hi link javaDocParam javaDocSeeTag -hi link javaDocSeeTagParam javaDocSeeTag - -hi javaDocSeeTag guifg=#CCCCCC guibg=NONE gui=NONE ctermfg=darkgray ctermbg=NONE cterm=NONE -hi javaDocSeeTag guifg=#CCCCCC guibg=NONE gui=NONE ctermfg=darkgray ctermbg=NONE cterm=NONE -"hi javaClassDecl guifg=#CCFFCC guibg=NONE gui=NONE ctermfg=white ctermbg=NONE cterm=NONE - - -" Special for XML -hi link xmlTag Keyword -hi link xmlTagName Conditional -hi link xmlEndTag Identifier - - -" Special for HTML -hi link htmlTag Keyword -hi link htmlTagName Conditional -hi link htmlEndTag Identifier - - -" Special for Javascript -hi link javaScriptNumber Number - - -" Special for Python -"hi link pythonEscape Keyword - - -" Special for CSharp -hi link csXmlTag Keyword - - -" Special for PHP +"Specific for diff +hi DiffAdd cterm=none ctermfg=0 ctermbg=119 +hi DiffChange cterm=none ctermfg=0 ctermbg=228 +hi DiffText cterm=none ctermfg=0 ctermbg=178 +hi DiffDelete cterm=none ctermfg=0 ctermbg=197 +hi diffLine cterm=bold ctermfg=241 +hi diffOldLine cterm=none ctermfg=241 +hi diffOldFile cterm=none ctermfg=241 +hi diffNewFile cterm=none ctermfg=241 +hi diffAdded cterm=none +hi diffRemoved cterm=none ctermfg=9 +hi diffChanged cterm=none ctermfg=20 Index: /issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim =================================================================== --- /issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim (revision 13974) +++ /issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim (revision 13975) @@ -569,7 +569,24 @@ "ISSM's objects end "ISSM's Enums begin -syn keyword cConstant AutodiffForwardEnum syn keyword cConstant AutodiffIsautodiffEnum -syn keyword cConstant AutodiffReverseEnum +syn keyword cConstant AutodiffNumDependentsEnum +syn keyword cConstant AutodiffNumDependentObjectsEnum +syn keyword cConstant AutodiffDependentObjectNamesEnum +syn keyword cConstant AutodiffDependentObjectTypesEnum +syn keyword cConstant AutodiffDependentObjectIndicesEnum +syn keyword cConstant AutodiffDependentObjectsEnum +syn keyword cConstant AutodiffNumIndependentsEnum +syn keyword cConstant AutodiffNumIndependentObjectsEnum +syn keyword cConstant AutodiffIndependentObjectNamesEnum +syn keyword cConstant AutodiffIndependentObjectTypesEnum +syn keyword cConstant AutodiffIndependentObjectsEnum +syn keyword cConstant AutodiffJacobianEnum +syn keyword cConstant AutodiffXpEnum +syn keyword cConstant AutodiffDriverEnum +syn keyword cConstant AutodiffFosForwardIndexEnum +syn keyword cConstant AutodiffFovForwardIndicesEnum +syn keyword cConstant AutodiffFosReverseIndexEnum +syn keyword cConstant AutodiffMassFluxSegmentsPresentEnum +syn keyword cConstant AutodiffKeepEnum syn keyword cConstant BalancethicknessSpcthicknessEnum syn keyword cConstant BalancethicknessStabilizationEnum @@ -583,4 +600,5 @@ syn keyword cConstant ConstantsReferencetemperatureEnum syn keyword cConstant ConstantsYtsEnum +syn keyword cConstant DependentObjectEnum syn keyword cConstant DiagnosticAbstolEnum syn keyword cConstant DiagnosticIcefrontEnum @@ -607,4 +625,5 @@ syn keyword cConstant FlowequationElementEquationEnum syn keyword cConstant FlowequationIshutterEnum +syn keyword cConstant FlowequationIsl1l2Enum syn keyword cConstant FlowequationIsmacayealpattynEnum syn keyword cConstant FlowequationIsstokesEnum @@ -621,4 +640,5 @@ syn keyword cConstant HydrologySpcwatercolumnEnum syn keyword cConstant HydrologyStabilizationEnum +syn keyword cConstant IndependentObjectEnum syn keyword cConstant InversionControlParametersEnum syn keyword cConstant InversionCostFunctionEnum @@ -658,4 +678,6 @@ syn keyword cConstant MaterialsRheologyLawEnum syn keyword cConstant MaterialsRheologyNEnum +syn keyword cConstant MaterialsRheologyZEnum +syn keyword cConstant MaterialsRheologyZbarEnum syn keyword cConstant MaterialsRhoIceEnum syn keyword cConstant MaterialsRhoWaterEnum @@ -692,6 +714,10 @@ syn keyword cConstant PrognosticStabilizationEnum syn keyword cConstant PrognosticVertexPairingEnum +syn keyword cConstant PrognosticNumRequestedOutputsEnum +syn keyword cConstant PrognosticRequestedOutputsEnum syn keyword cConstant QmuIsdakotaEnum -syn keyword cConstant QmuMassFluxSegmentsEnum +syn keyword cConstant MassFluxSegmentsEnum +syn keyword cConstant MassFluxSegmentsPresentEnum +syn keyword cConstant QmuMassFluxSegmentsPresentEnum syn keyword cConstant QmuNumberofpartitionsEnum syn keyword cConstant QmuNumberofresponsesEnum @@ -728,4 +754,6 @@ syn keyword cConstant SurfaceforcingsMonthlytemperaturesEnum syn keyword cConstant SurfaceforcingsHcEnum +syn keyword cConstant SurfaceforcingsHrefEnum +syn keyword cConstant SurfaceforcingsSmbrefEnum syn keyword cConstant SurfaceforcingsSmbPosMaxEnum syn keyword cConstant SurfaceforcingsSmbPosMinEnum @@ -789,9 +817,10 @@ syn keyword cConstant TransientSolutionEnum syn keyword cConstant ApproximationEnum +syn keyword cConstant NoneApproximationEnum syn keyword cConstant HutterApproximationEnum syn keyword cConstant MacAyealApproximationEnum syn keyword cConstant MacAyealPattynApproximationEnum syn keyword cConstant MacAyealStokesApproximationEnum -syn keyword cConstant NoneApproximationEnum +syn keyword cConstant L1L2ApproximationEnum syn keyword cConstant PattynApproximationEnum syn keyword cConstant PattynStokesApproximationEnum @@ -804,4 +833,6 @@ syn keyword cConstant VerticesEnum syn keyword cConstant ResultsEnum +syn keyword cConstant GenericParamEnum +syn keyword cConstant AdolcParamEnum syn keyword cConstant BoolInputEnum syn keyword cConstant BoolParamEnum @@ -811,4 +842,5 @@ syn keyword cConstant DofIndexingEnum syn keyword cConstant DoubleInputEnum +syn keyword cConstant DataSetParamEnum syn keyword cConstant DoubleMatArrayParamEnum syn keyword cConstant DoubleMatParamEnum @@ -829,8 +861,10 @@ syn keyword cConstant MacAyeal3dIceFrontEnum syn keyword cConstant MaticeEnum +syn keyword cConstant MatdamageiceEnum syn keyword cConstant MatparEnum syn keyword cConstant NodeEnum syn keyword cConstant NumericalfluxEnum syn keyword cConstant ParamEnum +syn keyword cConstant L1L2IceFrontEnum syn keyword cConstant PattynIceFrontEnum syn keyword cConstant PengridEnum @@ -838,4 +872,5 @@ syn keyword cConstant PentaEnum syn keyword cConstant PentaP1InputEnum +syn keyword cConstant ProfilerEnum syn keyword cConstant MatrixParamEnum syn keyword cConstant VectorParamEnum @@ -903,4 +938,6 @@ syn keyword cConstant TemperatureOldEnum syn keyword cConstant TemperaturePicardEnum +syn keyword cConstant TemperatureSurfaceEnum +syn keyword cConstant TemperatureBasalEnum syn keyword cConstant ThicknessAbsMisfitEnum syn keyword cConstant TypeEnum @@ -924,4 +961,6 @@ syn keyword cConstant EnthalpyPicardEnum syn keyword cConstant ThicknessAbsGradientEnum +syn keyword cConstant ThicknessAlongGradientEnum +syn keyword cConstant ThicknessAcrossGradientEnum syn keyword cConstant StepResponsesEnum syn keyword cConstant IntMatParamEnum @@ -944,8 +983,4 @@ syn keyword cConstant StressTensoryzEnum syn keyword cConstant StressTensorzzEnum -syn keyword cConstant IceVolumeEnum -syn keyword cConstant TotalSmbEnum -syn keyword cConstant ThicknessAlongGradientEnum -syn keyword cConstant ThicknessAcrossGradientEnum syn keyword cConstant P0Enum syn keyword cConstant P1Enum @@ -981,4 +1016,6 @@ syn keyword cConstant MaxVzEnum syn keyword cConstant MaxAbsVzEnum +syn keyword cConstant IceVolumeEnum +syn keyword cConstant TotalSmbEnum syn keyword cConstant RelativeEnum syn keyword cConstant AbsoluteEnum @@ -1004,4 +1041,6 @@ syn keyword cConstant OldGradientEnum syn keyword cConstant OutputFilePointerEnum +syn keyword cConstant OutputFileNameEnum +syn keyword cConstant LockFileNameEnum syn keyword cConstant PetscOptionsAnalysesEnum syn keyword cConstant PetscOptionsStringsEnum @@ -1020,4 +1059,5 @@ syn keyword cConstant XYZPEnum syn keyword cConstant OptionEnum +syn keyword cConstant GenericOptionEnum syn keyword cConstant OptionCellEnum syn keyword cConstant OptionCharEnum Index: /issm/trunk/externalpackages/vim/addons/vimrc =================================================================== --- /issm/trunk/externalpackages/vim/addons/vimrc (revision 13974) +++ /issm/trunk/externalpackages/vim/addons/vimrc (revision 13975) @@ -1,4 +1,4 @@ -" General setup{{{1 +" General setup{{{ " ---------------------------------------------------------------------- " Use Vim settings, rather then Vi settings (much better!). @@ -18,5 +18,5 @@ set showmode "----------------------------------------------------------------------}}} -" Text-Formatting, Identing, Tabbing{{{1 +" Text-Formatting, Identing, Tabbing{{{ " ---------------------------------------------------------------------- " allow backspacing (to delete) over everything in insert mode @@ -39,5 +39,5 @@ set foldtext=IssmFoldText() " -----------------------------------------------------------}}} -" Backups {{{1 +" Backups {{{ " ----------------------------------------------------------- " updatecount number of characters typed to cause a swap file update (0->disable) @@ -46,5 +46,5 @@ set nobackup " -----------------------------------------------------------}}} -" Searching, Substituting {{{1 +" Searching, Substituting {{{ " ----------------------------------------------------------- " select case-insenitive search @@ -75,5 +75,5 @@ set su=.h,.bak,~,.o,.info,.swp,.obj " ----------------------------------------------------------------------}}} -" Colors and theme {{{1 +" Colors and theme {{{ " ---------------------------------------------------------------------- " use 256 colors @@ -88,5 +88,5 @@ " ----------------------------------------------------------------------}}} -" Mappings{{{1 +" Mappings{{{ " ---------------------------------------------------------------------- "stop highlightings when spce is pressed @@ -111,5 +111,5 @@ map Q gq " ----------------------------------------------------------------------}}} -" Autocommands {{{1 +" Autocommands {{{ " ---------------------------------------------------------------------- " Only do this part when compiled with support for autocommands. @@ -140,5 +140,5 @@ endif " has("autocmd") " ----------------------------------------------------------------------}}} -" Matlab special {{{1 +" Matlab special {{{ " ---------------------------------------------------------------------- "" associate *.par with matlab filetype @@ -146,5 +146,5 @@ au BufRead,BufNewFile *.tpl setfiletype html " ----------------------------------------------------------------------}}} -" C special{{{1 +" C special{{{ " ---------------------------------------------------------------------- "indenting for C-code @@ -153,5 +153,5 @@ set cinoptions={.5s,+.5s,t0,n-2,p2s,(03s,=.5s,>1s,=1s,:1s " ----------------------------------------------------------------------}}} -" TEX special{{{1 +" TEX special{{{ " ---------------------------------------------------------------------- au BufRead,BufNewFile *.tex,*.html set textwidth=100 "100 caracters max (See gq command) @@ -165,9 +165,9 @@ let g:tex_flavor='latex' " ----------------------------------------------------------------------}}} -" FORTRAN special{{{1 +" FORTRAN special{{{ " ---------------------------------------------------------------------- au BufRead,BufNewFile *.src setfiletype fortran " ----------------------------------------------------------------------}}} -" InsertTabWrapper{{{1 +" InsertTabWrapper{{{ " ---------------------------------------------------------------------- function! InsertTabWrapper(direction) @@ -192,5 +192,5 @@ " ----------------------------------------------------------------------}}} -" Abbreviations {{{1 +" Abbreviations {{{ " ---------------------------------------------------------------------- "func Eatchar(pat) @@ -225,5 +225,5 @@ "au BufRead,BufNewFile *.tex ab (()) \left( \right) "}}} -" Skeletons {{{1 +" Skeletons {{{ au BufNewFile letter.tex 0r ~/.vim/xtr/skeleton/letter.tex "}}} Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 13974) +++ /issm/trunk/m4/issm_options.m4 (revision 13975) @@ -14,5 +14,5 @@ dnl }}} - dnl shared build {{{ + dnl Shared build {{{ AC_ARG_ENABLE([sharedlibs], dnl feature AS_HELP_STRING([--enable-sharedlibs], [produce libISSM.so.0]), dnl help string @@ -21,6 +21,5 @@ AM_CONDITIONAL([SHAREDLIBS], [test x$enable_sharedlibs = xyes]) dnl }}} - - dnl shared build {{{ + dnl Version{{{ AC_ARG_ENABLE([version], dnl feature AS_HELP_STRING([--enable-version], [produce libISSM.so.0]), dnl help string @@ -29,12 +28,11 @@ AM_CONDITIONAL([VERSION], [test x$enable_VERSION = xyes]) dnl }}} - - dnl Modules build {{{ - AC_ARG_WITH([modules], - AS_HELP_STRING([--with-modules = value],[modules compilation. ]), - [MODULES_VALUE=$withval],[MODULES_VALUE="yes"]) - AC_MSG_CHECKING(for modules compilation) - AM_CONDITIONAL([MODULES], [test $MODULES_VALUE = yes]) - AC_MSG_RESULT($MODULES_VALUE) + dnl Wrappers build {{{ + AC_ARG_WITH([wrappers], + AS_HELP_STRING([--with-wrappers = value],[wrappers compilation. ]), + [WRAPPERS_VALUE=$withval],[WRAPPERS_VALUE="yes"]) + AC_MSG_CHECKING(for wrappers compilation) + AM_CONDITIONAL([WRAPPERS], [test x$WRAPPERS_VALUE = xyes]) + AC_MSG_RESULT($WRAPPERS_VALUE) dnl }}} dnl Extensions{{{ @@ -80,6 +78,6 @@ export CC=icc export CXX=icpc - export CXXFLAGS=" -O3 -D_INTEL_LINUX_ " - export CFLAGS=" -O3 -D_INTEL_LINUX_ " + export CXXFLAGS=" -O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK" + export CFLAGS=" -O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK" elif test $VENDOR = intel-pleiades; then export CC=icc @@ -94,5 +92,5 @@ AC_MSG_RESULT(done) dnl }}} - dnl Matlab{{{ + dnl matlab{{{ dnl 1. See if matlab has been provided @@ -113,69 +111,7 @@ AM_CONDITIONAL([MATLAB], [test x$HAVE_MATLAB = xyes]) - dnl 2. if matlab is provided, get version number + dnl 2. Get Matlab libraries if test x$HAVE_MATLAB = xyes; then - AC_MSG_CHECKING([for matlab version]) - MATLAB_VERSION="" - - dnl For Matlab R2008a and more, the version number is stored in .VERSION - if test -f "$MATLAB_ROOT/.VERSION" ; then - MATLAB_VERSION=$(cat $MATLAB_ROOT/.VERSION) - fi - dnl Otherwise find version in file stored in bin/util/mex/version.txt - if test -f "$MATLAB_ROOT/bin/util/mex/version.txt" ; then - MATLAB_VERSION=$(cat $MATLAB_ROOT/bin/util/mex/version.txt) - fi - - dnl check that we found the version - if test -z "$MATLAB_VERSION" ; then - AC_MSG_ERROR([Matlab version not found]) - fi - - case $MATLAB_VERSION in - @<:@1-9@:>@.@<:@0-9@:>@ | @<:@1-9@:>@@<:@0-9@:>@.@<:@0-9@:>@ | @<:@1-9@:>@.@<:@1-9@:>@@<:@0-9@:>@) - MATLAB_MAJOR=$(echo $MATLAB_VERSION | sed -e "s/^\(@<:@0-9@:>@*\)\.@<:@0-9@:>@*.*/\1/") - MATLAB_MINOR=$(echo $MATLAB_VERSION | sed -e "s/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/") - ;; - R2007a) - MATLAB_MAJOR=7 - MATLAB_MINOR=4 - ;; - R2008a) - MATLAB_MAJOR=7 - MATLAB_MINOR=6 - ;; - R2009a) - MATLAB_MAJOR=7 - MATLAB_MINOR=8 - ;; - R2010a) - MATLAB_MAJOR=7 - MATLAB_MINOR=10 - ;; - R2010b) - MATLAB_MAJOR=7 - MATLAB_MINOR=11 - ;; - R2011a) - MATLAB_MAJOR=7 - MATLAB_MINOR=12 - ;; - R2011b) - MATLAB_MAJOR=7 - MATLAB_MINOR=13 - ;; - R2012a) - MATLAB_MAJOR=7 - MATLAB_MINOR=14 - ;; - *) - AC_MSG_ERROR([can not determine Matlab version number]) - esac - AC_SUBST([MATLAB_VERSION]) - AC_SUBST([MATLAB_MAJOR]) - AC_SUBST([MATLAB_MINOR]) - AC_MSG_RESULT($MATLAB_VERSION ($MATLAB_MAJOR.$MATLAB_MINOR)) - - dnl 3. Get Matlab libraries + AC_MSG_CHECKING(for matlab headers and libraries in $MATLAB_ROOT) MATLABINCL=-I"$MATLAB_ROOT/extern/include"; @@ -185,42 +121,4 @@ MEXLIB=$( mex -v 2>&1 < /dev/null | grep CXXLIBS | sed -e "s/ CXXLIBS = //g") MEXEXT=$( mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/ LDEXTENSION = //g") - dnl dnl OS-dependent variables and checks (old stuff) - dnl case "${host_os}" in - dnl *linux*) - dnl if test "${host_cpu}" = "x86_64"; - dnl then - dnl MEXLIB="-Wl,-rpath-link,$MATLAB_ROOT/bin/glnxa64 -L$MATLAB_ROOT/bin/glnxa64/ -lmx -lmex -lmat -lm" - dnl MEXLINK="-pthread -shared -W2,--version-script,${MATLAB_ROOT}/extern/lib/glnxa64/mexFunction.map"; - dnl else - dnl MEXLIB=-L"$MATLAB_ROOT/bin/glnx86/ -lmex" - dnl MEXLINK="-pthread -shared -W2,--version-script,${MATLAB_ROOT}/extern/lib/glnx86/mexFunction.map"; - dnl fi - dnl MEXEXT=`$MATLAB_ROOT/bin/mexext` - dnl MEXEXT=".$MEXEXT" - dnl ;; - dnl *darwin*) - dnl dnl mex -v gives all the flags for compilation of mex files - dnl dnl if matlab version is 7.9 or more, we must use mexmaci64 (64 bits) - dnl MEXLINK="-O -Wl,-flat_namespace -undefined suppress -arch i386 -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci/mexFunction.map" - dnl MEXLIB=" -L$MATLAB_ROOT/bin/maci/ -lmx -lmex -lmat -lstdc++ -largeArrayDims" - dnl if test $MATLAB_MAJOR -ge 7; then - dnl if test $MATLAB_MINOR -ge 9; then - dnl MEXLINK="-O -Wl,-flat_namespace -undefined suppress -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci64/mexFunction.map" - dnl MEXLIB=" -L$MATLAB_ROOT/bin/maci64/ -lmx -lmex -lmat -lstdc++" - dnl fi - dnl fi - dnl MEXEXT=`$MATLAB_ROOT/bin/mexext` - dnl MEXEXT=".$MEXEXT" - dnl ;; - dnl *cygwin*) - dnl if test $VENDOR = intel-win7-32; then - dnl MEXLIB="-dll -export:mexFunction -LIBPATH:\"$MATLAB_ROOT\extern\lib\win32\microsoft\" libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib -NOLOGO -INCREMENTAL:NO -manifest" - dnl elif test $VENDOR = intel-win7-64; then - dnl MEXLIB="-dll -export:mexFunction -LIBPATH:\"$MATLAB_ROOT\extern\lib\win64\microsoft\" libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib -NOLOGO -INCREMENTAL:NO -manifest" - dnl fi - dnl MEXEXT=`$MATLAB_ROOT/bin/mexext.bat` - dnl MEXEXT=".$MEXEXT" - dnl ;; - dnl esac AC_MSG_RESULT(done) @@ -332,28 +230,35 @@ AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]), [PYTHON_ROOT=$withval],[PYTHON_ROOT=""]) + AC_MSG_CHECKING(for python) - if test -d "$PYTHON_ROOT"; then - dnl defaults - HAVE_PYTHON3="no" - HAVE_PYTHON=yes - - AC_ARG_WITH([python-version], - AS_HELP_STRING([--with-python-version = PYTHONVERSION],[python version.]), - [PYTHONVERSION=$withval],[PYTHONVERSION=""]) + HAVE_PYTHON="yes" + AC_DEFINE([_HAVE_PYTHON_],[1],[with Python in ISSM src]) + else + HAVE_PYTHON=no + fi + AC_MSG_RESULT($HAVE_PYTHON) + + dnl get python version + if test x$HAVE_PYTHON = xyes; then AC_MSG_CHECKING(for python version) + dnl Query Python for its version number.  Getting [:3] seems to be + dnl the best way to do this; it's what "site.py" does in the standard + dnl library. + PYTHON_VERSION=$($PYTHON_ROOT/bin/python -c "import sys; print sys.version[[:3]]") + AC_MSG_RESULT($PYTHON_VERSION) dnl recover major: - PYTHON_MAJOR=${PYTHONVERSION%.*} - + PYTHON_MAJOR=${PYTHON_VERSION%.*} if test x$PYTHON_MAJOR = x3; then dnl are we running python 3? HAVE_PYTHON3="yes" + else + HAVE_PYTHON3="no" fi AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major]) - AC_MSG_RESULT($PYTHON_MAJOR) PYTHONINCL=-I$PYTHON_ROOT/include - PYTHONLIB="-L$PYTHON_ROOT/lib -lpython$PYTHONVERSION" + PYTHONLIB="-L$PYTHON_ROOT/lib -lpython$PYTHON_VERSION" PYTHONEXT=.so @@ -370,5 +275,4 @@ esac - AC_DEFINE([_HAVE_PYTHON_],[1],[with Python in ISSM src]) AC_SUBST([PYTHONINCL]) AC_SUBST([PYTHONLIB]) @@ -376,11 +280,7 @@ AC_SUBST([PYTHONWRAPPEREXT]) AC_SUBST([PYTHONLINK]) - else - HAVE_PYTHON=no fi AM_CONDITIONAL([PYTHON], [test x$HAVE_PYTHON = xyes]) AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes]) - AC_MSG_RESULT($HAVE_PYTHON) - dnl }}} dnl python-numpy{{{ @@ -556,67 +456,4 @@ AM_CONDITIONAL([ROSE], [test x$HAVE_ROSE = xyes]) AC_MSG_RESULT($HAVE_ROSE) - dnl }}} - dnl metis{{{ - AC_ARG_WITH([metis-dir], - AS_HELP_STRING([--with-metis-dir=DIR],[metis root directory. necessary for serial build]), - [METIS_ROOT=$withval],[METIS_ROOT=""]) - - AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT) - - if test -d "$METIS_ROOT"; then - - dnl first figure out version of metis: does the VERSION file exist? - if test -e "$METIS_ROOT/VERSION"; then - METIS_VERSION=4 - else - METIS_VERSION=5 - fi - - dnl defaults - HAVE_METIS=yes - - if test "$METIS_VERSION" = "4" ; then - - METISINCL=-I"$METIS_ROOT/Lib" - case "${host_os}" in - *cygwin*) - METISLIB="-LIBPATH:\"$METIS_ROOT\" libmetis.lib" - ;; - *linux*) - METISLIB=-L"$METIS_ROOT/ -lmetis" - ;; - *darwin*) - METISLIB=-L"$METIS_ROOT/ -lmetis" - ;; - esac - - AC_DEFINE([_METIS_VERSION_],[4],[ Metis version number]) - fi - if test "$METIS_VERSION" = "5" ; then - - case "${host_os}" in - *cygwin*) - METISLIB="-LIBPATH:\"$METIS_ROOT\" libmetis.lib" - ;; - *linux*) - METISLIB=-L"$METIS_ROOT/lib -lmetis" - ;; - *darwin*) - METISLIB=-L"$METIS_ROOT/lib -lmetis" - ;; - esac - - METISINCL=-I"$METIS_ROOT/include" - AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number]) - fi - - AC_DEFINE([_HAVE_METIS_],[1],[with Metis in ISSM src]) - AC_SUBST([METISINCL]) - AC_SUBST([METISLIB]) - else - HAVE_METIS=no - fi - AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes]) - AC_MSG_RESULT($HAVE_METIS) dnl }}} dnl mpi{{{ @@ -681,34 +518,42 @@ if test -d "$PETSC_ROOT"; then - PETSCINCL="-I$PETSC_ROOT/$PETSC_ARCH/include -I$PETSC_ROOT/include/$PETSC_ARCH/ -I$PETSC_ROOT/include -I$PETSC_ROOT/ -I$PETSC_ROOT/bmake/$PETSC_ARCH -I$PETSC_ROOT/src/mat/impls/dense/mpi/plapack/" - - case "${host_os}" in + PETSCINCL=" -I$PETSC_ROOT/include" + dnl Add other location (maybe not needed anymore) + if test -d "$PETSC_ROOT/$PETSC_ARCH/include"; then + PETSCINCL+=" $PETSC_ROOT/$PETSC_ARCH/include" + fi + if test -d "$PETSC_ROOT/include/$PETSC_ARCH"; then + PETSCINCL+=" $PETSC_ROOT/include/$PETSC_ARCH" + fi + + case "${host_os}" in *cygwin*) - if test "$PETSC_MAJOR" = "2" ; then - PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetscksp.lib libpetscdm.lib libpetscmat.lib libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib" + if test $PETSC_MAJOR -lt 3 ; then + PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" libpetscksp.lib libpetscdm.lib libpetscmat.lib libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib" else - PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetsc.lib" + PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" libpetsc.lib" + if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" libmetis.lib"; fi fi ;; *linux*) - if test "$PETSC_MAJOR" = "2" ; then - PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -lpetscsnes -lpetscts" + if test $PETSC_MAJOR -lt 3 ; then + PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -lpetscsnes -lpetscts" else - PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc -ldl" + PETSCLIB="-L$PETSC_ROOT/lib -lpetsc -ldl" + if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" -lmetis"; fi fi ;; *darwin*) - if test "$PETSC_MAJOR" = "2" ; then - PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc" + if test $PETSC_MAJOR -lt 3 ; then + PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc" else - PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc" + PETSCLIB="-L$PETSC_ROOT/lib -lpetsc" + if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" -lmetis"; fi fi ;; esac - AC_DEFINE([_HAVE_PETSC_],[1],[with PETSc in ISSM src]) AC_SUBST([PETSCINCL]) AC_SUBST([PETSCLIB]) - HAVE_PETSC=yes else @@ -718,4 +563,75 @@ AM_CONDITIONAL([PETSC], [test x$HAVE_PETSC = xyes]) AC_MSG_RESULT($HAVE_PETSC) + dnl }}} + dnl metis{{{ + if test "$HAVE_PETSC" = "yes" && test "x$PETSC_MAJOR" = "x3" && test $PETSC_MINOR -ge 3; then + + dnl in petsc >=3.3, metis is provided + HAVE_METIS="yes" + AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number]) + AC_DEFINE([_HAVE_METIS_],[1],[with Metis in ISSM src]) + else + AC_ARG_WITH([metis-dir], + AS_HELP_STRING([--with-metis-dir=DIR],[metis root directory. necessary for serial build]), + [METIS_ROOT=$withval],[METIS_ROOT=""]) + + AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT) + + if test -d "$METIS_ROOT"; then + + dnl first figure out version of metis: does the VERSION file exist? + if test -e "$METIS_ROOT/VERSION"; then + METIS_VERSION=4 + else + METIS_VERSION=5 + fi + + dnl defaults + HAVE_METIS=yes + + if test "$METIS_VERSION" = "4" ; then + + METISINCL=-I"$METIS_ROOT/Lib" + case "${host_os}" in + *cygwin*) + METISLIB="-LIBPATH:\"$METIS_ROOT\" libmetis.lib" + ;; + *linux*) + METISLIB=-L"$METIS_ROOT/ -lmetis" + ;; + *darwin*) + METISLIB=-L"$METIS_ROOT/ -lmetis" + ;; + esac + + AC_DEFINE([_METIS_VERSION_],[4],[ Metis version number]) + fi + if test "$METIS_VERSION" = "5" ; then + + case "${host_os}" in + *cygwin*) + METISLIB="-LIBPATH:\"$METIS_ROOT\" libmetis.lib" + ;; + *linux*) + METISLIB=-L"$METIS_ROOT/lib -lmetis" + ;; + *darwin*) + METISLIB=-L"$METIS_ROOT/lib -lmetis" + ;; + esac + + METISINCL=-I"$METIS_ROOT/include" + AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number]) + fi + + AC_DEFINE([_HAVE_METIS_],[1],[with Metis in ISSM src]) + AC_SUBST([METISINCL]) + AC_SUBST([METISLIB]) + else + HAVE_METIS=no + fi + AC_MSG_RESULT($HAVE_METIS) + fi + AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes]) dnl }}} dnl tao{{{ @@ -1400,4 +1316,31 @@ AC_MSG_RESULT($HAVE_RIFTS) dnl }}} + dnl with-android{{{ + AC_ARG_WITH([android], + AS_HELP_STRING([--with-android = EXE], [compile with android capabilities (default is no, alternatives are exe and jni)]), + [ANDROID=$withval],[ANDROID=no]) + AC_MSG_CHECKING(for android capability compilation) + + if test "x$ANDROID" = "xjni"; then + + dnl defaults + HAVE_ANDROID=jni + + AC_DEFINE([_HAVE_ANDROID_],[1],[with android capability]) + elif test "x$ANDROID" = "xexe"; then + dnl defaults + HAVE_ANDROID=exe + + AC_DEFINE([_HAVE_ANDROID_],[1],[with android capability]) + elif test "x$ANDROID" = "xno"; then + HAVE_ANDROID=no + else + AC_MSG_ERROR([--with-android should be either no, exe or jni]) + fi + AM_CONDITIONAL([ANDROID], [test x$HAVE_ANDROID != xno]) + AM_CONDITIONAL([ANDROIDJNI], [test x$HAVE_ANDROID = xjni]) + AM_CONDITIONAL([ANDROIDEXE], [test x$HAVE_ANDROID = xexe]) + AC_MSG_RESULT($HAVE_ANDROID) + dnl }}} dnl with-3d{{{ AC_ARG_WITH([3d], @@ -1433,17 +1376,8 @@ fi - dnl check that we have python version if python compile is specified - if test "$HAVE_PYTHON" = "yes" && test "$PYTHONVERSION" = "" ; then - AC_MSG_ERROR([need python-version if python compile is required!]); - fi - dnl check that if we have MPI, we have metis if test "$HAVE_METIS" = "yes" && test "$HAVE_MPI" = "no" ; then AC_MSG_ERROR([need mpi if using the metis partitioner!]); fi - - - - AC_MSG_RESULT(done) @@ -1503,12 +1437,3 @@ 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/BinRead.py =================================================================== --- /issm/trunk/scripts/BinRead.py (revision 13975) +++ /issm/trunk/scripts/BinRead.py (revision 13975) @@ -0,0 +1,168 @@ +#! /usr/bin/env python + +import os +import sys +import numpy +import math +import struct + +def BinRead(filin,filout=''): + + from MatlabFuncs import * + from EnumDefinitions import * + from EnumToString import EnumToString + + print "reading binary file." + f=open(filin,'rb') + + if filout: + sys.stdout=open(filout,'w') + + while True: + try: + #Step 1: read the enum to identify this record uniquely + enum=struct.unpack('i',f.read(struct.calcsize('i')))[0] + except struct.error as e: + print "probable EOF: %s" % e + break + print "\nenum = %d (%s)" % (enum,EnumToString(enum)[0]) + + #Step 2: read the data itself. + #first read length of record + reclen=struct.unpack('i',f.read(struct.calcsize('i')))[0] + print "reclen = %d" % reclen + + #read data code: + code=struct.unpack('i',f.read(struct.calcsize('i')))[0] + print "code = %d" % code + + if code == FormatToCode('Boolean'): +# bval=struct.unpack('b',f.read(reclen-struct.calcsize('i')))[0] + bval=struct.unpack('i',f.read(reclen-struct.calcsize('i')))[0] + print "bval = %d" % bval + + elif code == FormatToCode('Integer'): + ival=struct.unpack('i',f.read(reclen-struct.calcsize('i')))[0] + print "ival = %d" % ival + + elif code == FormatToCode('Double'): + dval=struct.unpack('d',f.read(reclen-struct.calcsize('i')))[0] + print "dval = %f" % dval + + elif code == FormatToCode('String'): + strlen=struct.unpack('i',f.read(struct.calcsize('i')))[0] + print "strlen = %d" % strlen + sval=struct.unpack('%ds' % strlen,f.read(strlen))[0] + print "sval = '%s'" % sval + + elif code == FormatToCode('BooleanMat'): + #read matrix type: + mattype=struct.unpack('i',f.read(struct.calcsize('i')))[0] + print "mattype = %d" % mattype + + #now read matrix + s=[0,0] + s[0]=struct.unpack('i',f.read(struct.calcsize('i')))[0] + s[1]=struct.unpack('i',f.read(struct.calcsize('i')))[0] + print "s = [%dx%d]" % (s[0],s[1]) + data=numpy.zeros((s[0],s[1])) + for i in xrange(s[0]): + for j in xrange(s[1]): + data[i][j]=struct.unpack('d',f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose + print "data[%d,%d] = %f" % (i,j,data[i][j]) + + elif code == FormatToCode('IntMat'): + #read matrix type: + mattype=struct.unpack('i',f.read(struct.calcsize('i')))[0] + print "mattype = %d" % mattype + + #now read matrix + s=[0,0] + s[0]=struct.unpack('i',f.read(struct.calcsize('i')))[0] + s[1]=struct.unpack('i',f.read(struct.calcsize('i')))[0] + print "s = [%dx%d]" % (s[0],s[1]) + data=numpy.zeros((s[0],s[1])) + for i in xrange(s[0]): + for j in xrange(s[1]): + data[i][j]=struct.unpack('d',f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose + print "data[%d,%d] = %f" % (i,j,data[i][j]) + + elif code == FormatToCode('DoubleMat'): + #read matrix type: + mattype=struct.unpack('i',f.read(struct.calcsize('i')))[0] + print "mattype = %d" % mattype + + #now read matrix + s=[0,0] + s[0]=struct.unpack('i',f.read(struct.calcsize('i')))[0] + s[1]=struct.unpack('i',f.read(struct.calcsize('i')))[0] + print "s = [%dx%d]" % (s[0],s[1]) + data=numpy.zeros((s[0],s[1])) + for i in xrange(s[0]): + for j in xrange(s[1]): + data[i][j]=struct.unpack('d',f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose + print "data[%d,%d] = %f" % (i,j,data[i][j]) + + elif code == FormatToCode('MatArray'): + fid.seek(reclen-4,1) + print "skipping %d bytes for code %d." % (code, reclen-4) + + elif code == FormatToCode('StringArray'): + fid.seek(reclen-4,1) + print "skipping %d bytes for code %d." % (code, reclen-4) + + else: + raise TypeError('BinRead error message: data type: %d not supported yet! (%s)' % (code,EnumToString(enum)[0])) + + f.close() + +def FormatToCode(format): # {{{ + """ + This routine takes the format string, and hardcodes it into an integer, which + is passed along the record, in order to identify the nature of the dataset being + sent. + """ + + if strcmpi(format,'Boolean'): + code=1 + elif strcmpi(format,'Integer'): + code=2 + elif strcmpi(format,'Double'): + code=3 + elif strcmpi(format,'String'): + code=4 + elif strcmpi(format,'BooleanMat'): + code=5 + elif strcmpi(format,'IntMat'): + code=6 + elif strcmpi(format,'DoubleMat'): + code=7 + elif strcmpi(format,'MatArray'): + code=8 + elif strcmpi(format,'StringArray'): + code=9 + else: + raise InputError('FormatToCode error message: data type not supported yet!') + + return code +# }}} + +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='BinRead - function to read binary input file.') + parser.add_argument('-f','--filin', help='name of binary input file', default='') + args = parser.parse_args() + + BinRead(args.filin) + Index: /issm/trunk/scripts/mToPy.py =================================================================== --- /issm/trunk/scripts/mToPy.py (revision 13975) +++ /issm/trunk/scripts/mToPy.py (revision 13975) @@ -0,0 +1,52 @@ +#!/usr/bin/env python +#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +# +program = 'mToPy.py' +version = '1.0' +versionReleaseDate = '09/24/12' +origAuthor = 'Mike Pellegrin' +desc = '\nMain control unit for converting an matlab script file to python' +# +# Note: Output will be put in the same (absolute) location as the input. +#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +# History +# Date Developer Modification +#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +# 09/24/12 Michael Pellegrin Initial Release V1.0 +# +# +#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +import sys, os, shutil +import translateToPy +import mToPy # touch mToPy to assertain location of installation + +def convert ( inputFile ): + try: + if os.path.exists( inputFile + '.m') and os.path.isfile( inputFile + '.m'): + checkBackupOutputFile( inputFile ) + convertMToPy( inputFile ) + else: + print 'Specified input file: ' + inputFile + '.m doesn\'t appear to exist' + finally: + print '' + +def convertMToPy ( inputFileName ): + translateToPy.convertToPython ( inputFileName + '.m', inputFileName + '.py' ) + +def checkBackupOutputFile ( inputFile ): + mFile = inputFile + '.m' + pyFile = inputFile + '.py' + if os.path.exists( pyFile ): + i=1 + bkupName = pyFile + str(i) + while os.path.exists( bkupName ): + i+=1 + bkupName = pyFile + str(i) + os.rename( pyFile, bkupName ) + + shutil.copyfile(mFile, pyFile) + +if __name__ == "__main__": + convert( sys.argv[1]) + Index: /issm/trunk/scripts/report.sh =================================================================== --- /issm/trunk/scripts/report.sh (revision 13974) +++ /issm/trunk/scripts/report.sh (revision 13975) @@ -10,6 +10,6 @@ TABLE_STYLE='width="680px" rules=none bgcolor="#ffffdd" border=1 bordercolor="#000000" cellpadding="3"' TABLE_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px; font-weight: normal;" align="left"' -MATLAB_STYLE='width="700px" rules=none' -MATLAB_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:12px; font-weight: normal;" align="left"' +CODE_STYLE='width="700px" rules=none' +CODE_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:12px; font-weight: normal;" align="left"' BODY_STYLE='width="700px"' BODY_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px;"' @@ -104,5 +104,5 @@ $(if [ $CRASH_MATLAB -eq 0 ]; then -echo "" +echo "" else echo "" @@ -133,5 +133,5 @@
Status: all test desks have been run
Status: all tests have been run
Status: Matlab crashed
$(if [ $CRASH_PYTHON -eq 0 ]; then - echo "" + echo "" else echo "" @@ -215,5 +215,5 @@ - $(cat matlab_short.log | while read line + $(cat python_short.log | while read line do echo "" @@ -263,5 +263,5 @@ cat << END >> report.html
Status: all test desks have been run
Status: all tests have been run
Status: Python crashed
Field checked
Matlab errors
-
+
$(cat pythonerror.log)
+
+END + #}}} +fi if [ -s petscerror.log ]; then #PETSc{{{ cat << END >> report.html
PETSc errors
-
+
 0:
+				allParts += '\n'
+				numLines -= 1
+		res = allParts	
+
+		res = res.replace(';','')
+
+
+		res = convertFieldValues( res )
+		#print 'resulting line:' + str(res) + '\n'
+		output(res)
+
+def convertFieldValues ( currentLine ):
+	# before utilizing regex's {starting w/ eg. \([0-9]\) } for special case: ...(#)...
+	# i noticed what i'm looking for is only TransientSolution(*). So, ...
+
+	res = currentLine
+	if 'md.results' in currentLine:
+		res = res.replace('(md.results.','md.results[\'')
+
+		if 'TransientSolution(' in currentLine:		# got a TransientSolution([0-9..]) case
+			res = res.replace('TransientSolution(','TransientSolution\'][')
+			parts = res.split(')')
+			res = parts[0] + '][\'' + parts[1].replace('.','') + '\']' + parts[2]
+
+		else:				# handle the other cases for md.results
+			
+			res = res.replace('Solution.Vx)','Solution\'][1][\'Vx\']')
+			res = res.replace('Solution.Vy)','Solution\'][1][\'Vy\']')
+			res = res.replace('Solution.Vz)','Solution\'][1][\'Vz\']')
+			res = res.replace('Solution.Vel)','Solution\'][1][\'Vel\']')
+
+			res = res.replace('Solution.Pressure)','Solution\'][1][\'Pressure\']')
+
+			res = res.replace('Solution.StressTensorxx)','Solution\'][1][\'StressTensorxx\']')
+			res = res.replace('Solution.StressTensorxy)','Solution\'][1][\'StressTensorxy\']')
+			res = res.replace('Solution.StressTensoryy)','Solution\'][1][\'StressTensoryy\']')
+			res = res.replace('Solution.StressTensorzz)','Solution\'][1][\'StressTensorzz\']')
+			res = res.replace('Solution.StressTensorxz)','Solution\'][1][\'StressTensorxz\']')
+			res = res.replace('Solution.StressTensoryz)','Solution\'][1][\'StressTensoryz\']')
+
+			res = res.replace('Solution.FrictionCoefficient)','Solution\'][1][\'FrictionCoefficient\']')
+			res = res.replace('Solution.SurfaceforcingsMasBalance)','Solution\'][1][\'SurfaceforcingsMasBalance\']')
+			res = res.replace('Solution.MaskElementonfloatingice)','Solution\'][1][\'MaskElementonfloatingice\']')
+			res = res.replace('Solution.J)','Solution\'][1][\'J\']')
+			res = res.replace('Solution.BalancethicknessThickeningRate)','Solution\'][1][\'BalancethicknessThickeningRate\']')
+
+			res = res.replace('Solution.Gradient1)','Solution\'][1][\'Gradient1\']')
+			res = res.replace('Solution.Gradient2)','Solution\'][1][\'Gradient2\']')
+
+			res = res.replace('Solution.MaterialsRheologyZbar)','Solution\'][1][\'MaterialsRheologyZbar\']')
+			res = res.replace('Solution.MaterialsRheologyBbar)','Solution\'][1][\'MaterialsRheologyBbar\']')
+			res = res.replace('Solution.MaterialsRheologyB)','Solution\'][1][\'MaterialsRheologyB\']')
+
+			res = res.replace('Solution.Thickness)','Solution\'][1][\'Thickness\']')
+
+			res = res.replace('Solution.Temperature)','Solution\'][1][\'Temperature\']')
+
+			res = res.replace('Solution.BasalforcingsMeltingRate)','Solution\'][1][\'BasalforcingsMeltingRate\']')
+
+			res = res.replace('Solution.SurfaceSlopeX)','Solution\'][1][\'SurfaceSlopeX\']')
+			res = res.replace('Solution.SurfaceSlopeY)','Solution\'][1][\'SurfaceSlopeY\']')
+			res = res.replace('Solution.SurfaceSlopeZ)','Solution\'][1][\'SurfaceSlopeZ\']')
+
+			res = res.replace('Solution.BedSlopeX)','Solution\'][1][\'BedSlopeX\']')
+			res = res.replace('Solution.BedSlopeY)','Solution\'][1][\'BedSlopeY\']')
+			res = res.replace('Solution.BedSlopeZ)','Solution\'][1][\'BedSlopeZ\']')
+
+			res = res.replace('Solution.Enthalpy)','Solution\'][1][\'Enthalpy\']')
+			res = res.replace('Solution.Waterfraction)','Solution\'][1][\'Waterfraction\']')
+			res = res.replace('Solution.Temperature)','Solution\'][1][\'Temperature\']')
+
+			# special case
+			res = res.replace('.DiagnosticSolution.J','[\'DiagnosticSolution\'][1][\'J\']')
+
+	return res
+
+def output ( line ):
+	numTabs = indentLevel
+	while numTabs:
+		numTabs -= 1
+		print >> outputLocation, '\t',
+	print >> outputLocation, line
+
+def outputTopOfSript( inputFile ):
+
+	global indentLevel
+
+	output("\"\"\"")
+	output("== == == == == == == == == == == == == == == == == == ==")
+	output("Auto generated python script for ISSM:   %s" % (inputFile) )
+	output("Created on %s via %s Ver %s by %s" % ( datetime.date.today(), program, version, os.getlogin()))
+	output("== == == == == == == == == == == == == == == == == == ==")
+	#output("")
+	output(desc)
+	output("%s Author: Michael Pellegrin" % (program))
+	output("%s Date: %s" % (program, versionReleaseDate))
+	output("== == == == == == == == == == == == == == == == == == ==")
+	output("\"\"\"")
+	output("")
+
+def outputBottomOfScript():
+
+	global indentLevel
+
+	output("")
+	
+def genericImports ():
+	output("from MatlabFuncs import *")
+	output("from model import *")
+	output("from EnumDefinitions import *")
+	output("from numpy import *")
+
+def createImports ( inputFile ):
+	genericImports()
+
+	# cycle through eachline to assertain import needs
+	f = codecs.open( inputFile, encoding='utf-8' )
+	try:
+		for line in f:
+			# print "in: " +line
+
+			# toss blank lines
+			if len(line) == 1:
+				continue
+
+			asciiLine = unicodedata.normalize('NFKD', line).encode('ascii','ignore')
+			line = asciiLine
+
+			for il in importList:
+				if line.find(il) != -1:
+					output( "from %s import *" % (il) )
+					importList.remove(il)	# already got it
+
+	finally:
+		output("")
+		f.close()
+
+
+def initImportList ():
+	global importList
+	
+	importList = [ \
+		'triangle'	,\
+		'setmask'	,\
+		'parameterize'	,\
+		'setflowequation'	,\
+		'meshconvert'	,\
+		'solve'	,\
+		#'zeros'					# -> numpy
+		]
+	
+
+
+def convertToPython ( inFile, outFile = sys.stdout ):
+    #print ' in cnvrt to python w/ file:' + inFile
+    initImportList()
+    setupOutputLocation( outFile )
+    outputTopOfSript( inFile )
+    createImports( inFile )
+    translateFile( inFile )
+    #    outputBottomOfScript()
+
+	
+if __name__ == "__main__":
+    #print ' in main w/ arg:' + sys.argv[1]+' '+sys.argv[2]
+    if len(sys.argv)==2:
+        convertToPython( sys.argv[1], sys.argv[2] )
+    else:
+        convertToPython( sys.argv[1] )
+
+
+
Index: /issm/trunk/src/Makefile.am
===================================================================
--- /issm/trunk/src/Makefile.am	(revision 13974)
+++ /issm/trunk/src/Makefile.am	(revision 13975)
@@ -1,2 +1,5 @@
-EXTRA_DIST =  perl pro py
-SUBDIRS = c modules m
+EXTRA_DIST =  perl pro
+SUBDIRS = c m wrappers 
+if ANDROID
+SUBDIRS += android
+endif
Index: /issm/trunk/src/ad/todo
===================================================================
--- /issm/trunk/src/ad/todo	(revision 13974)
+++ /issm/trunk/src/ad/todo	(revision 13975)
@@ -57,2 +57,9 @@
 - make gdb wrapper.
 - think about ModelProcessor setup. need to keep track, before we partition, on cpu 0, of the independent declarations. 
+
+
+MPI: what's missing that equivalent of MPI.h -> no well defined api.  
+What's exposed is the internals of it.
+
+Wanted to look at changing the way for the matrices and vertices would be implemented.
+
Index: /issm/trunk/src/android/ISSM/.classpath
===================================================================
--- /issm/trunk/src/android/ISSM/.classpath	(revision 13975)
+++ /issm/trunk/src/android/ISSM/.classpath	(revision 13975)
@@ -0,0 +1,8 @@
+
+
+	
+	
+	
+	
+	
+
Index: /issm/trunk/src/android/ISSM/.project
===================================================================
--- /issm/trunk/src/android/ISSM/.project	(revision 13975)
+++ /issm/trunk/src/android/ISSM/.project	(revision 13975)
@@ -0,0 +1,33 @@
+
+
+	ISSM
+	
+	
+	
+	
+		
+			com.android.ide.eclipse.adt.ResourceManagerBuilder
+			
+			
+		
+		
+			com.android.ide.eclipse.adt.PreCompilerBuilder
+			
+			
+		
+		
+			org.eclipse.jdt.core.javabuilder
+			
+			
+		
+		
+			com.android.ide.eclipse.adt.ApkBuilder
+			
+			
+		
+	
+	
+		com.android.ide.eclipse.adt.AndroidNature
+		org.eclipse.jdt.core.javanature
+	
+
Index: /issm/trunk/src/android/ISSM/AndroidManifest.xml
===================================================================
--- /issm/trunk/src/android/ISSM/AndroidManifest.xml	(revision 13975)
+++ /issm/trunk/src/android/ISSM/AndroidManifest.xml	(revision 13975)
@@ -0,0 +1,25 @@
+
+
+    
+
+    
+        
+            
+                
+
+                
+            
+        
+    
+
+
Index: /issm/trunk/src/android/ISSM/Makefile.am
===================================================================
--- /issm/trunk/src/android/ISSM/Makefile.am	(revision 13975)
+++ /issm/trunk/src/android/ISSM/Makefile.am	(revision 13975)
@@ -0,0 +1,15 @@
+EXTRA_DIST =  AndroidManifest.xml  assets gen jni obj project.properties src Makefile.am bin ic_launcher-web.png libs proguard-project.txt res
+
+#Generate JNI library using the ndk-build capabilities:
+if SHAREDLIBS 	 	 
+deps = 	 	 
+else 	 	 
+deps = ../../c/libISSMCore.a 	 	 
+endif
+
+install-exec-am: all
+all: libs/armeabi/libIssmJni.so
+
+libs/armeabi/libIssmJni.so:  $(deps)
+	$(ANDROID_NDK_DIR)/ndk-build -C ./jni clean
+	$(ANDROID_NDK_DIR)/ndk-build -C ./jni
Index: /issm/trunk/src/android/ISSM/bin/AndroidManifest.xml
===================================================================
--- /issm/trunk/src/android/ISSM/bin/AndroidManifest.xml	(revision 13975)
+++ /issm/trunk/src/android/ISSM/bin/AndroidManifest.xml	(revision 13975)
@@ -0,0 +1,25 @@
+
+
+    
+
+    
+        
+            
+                
+
+                
+            
+        
+    
+
+
Index: /issm/trunk/src/android/ISSM/gen/com/example/issm/BuildConfig.java
===================================================================
--- /issm/trunk/src/android/ISSM/gen/com/example/issm/BuildConfig.java	(revision 13975)
+++ /issm/trunk/src/android/ISSM/gen/com/example/issm/BuildConfig.java	(revision 13975)
@@ -0,0 +1,6 @@
+/** Automatically generated file. DO NOT MODIFY */
+package com.example.issm;
+
+public final class BuildConfig {
+    public final static boolean DEBUG = true;
+}
Index: /issm/trunk/src/android/ISSM/gen/com/example/issm/R.java
===================================================================
--- /issm/trunk/src/android/ISSM/gen/com/example/issm/R.java	(revision 13975)
+++ /issm/trunk/src/android/ISSM/gen/com/example/issm/R.java	(revision 13975)
@@ -0,0 +1,43 @@
+/* AUTO-GENERATED FILE.  DO NOT MODIFY.
+ *
+ * This class was automatically generated by the
+ * aapt tool from the resource data it found.  It
+ * should not be modified by hand.
+ */
+
+package com.example.issm;
+
+public final class R {
+    public static final class attr {
+    }
+    public static final class dimen {
+        public static final int padding_large=0x7f040002;
+        public static final int padding_medium=0x7f040001;
+        public static final int padding_small=0x7f040000;
+    }
+    public static final class drawable {
+        public static final int ic_action_search=0x7f020000;
+        public static final int ic_launcher=0x7f020001;
+    }
+    public static final class id {
+        public static final int button1=0x7f080001;
+        public static final int input=0x7f080000;
+        public static final int menu_settings=0x7f080003;
+        public static final int output=0x7f080002;
+    }
+    public static final class layout {
+        public static final int activity_issm=0x7f030000;
+    }
+    public static final class menu {
+        public static final int activity_issm=0x7f070000;
+    }
+    public static final class string {
+        public static final int app_name=0x7f050000;
+        public static final int hello_world=0x7f050001;
+        public static final int menu_settings=0x7f050002;
+        public static final int title_activity_issm=0x7f050003;
+    }
+    public static final class style {
+        public static final int AppTheme=0x7f060000;
+    }
+}
Index: /issm/trunk/src/android/ISSM/jni/Android.mk
===================================================================
--- /issm/trunk/src/android/ISSM/jni/Android.mk	(revision 13975)
+++ /issm/trunk/src/android/ISSM/jni/Android.mk	(revision 13975)
@@ -0,0 +1,19 @@
+LOCAL_PATH:= $(call my-dir)
+my_LOCAL_PATH:=$(LOCAL_PATH)
+
+#include $(LOCAL_PATH)/issmlib\Android.mk
+include $(call all-subdir-makefiles)
+
+
+LOCAL_PATH := $(my_LOCAL_PATH)
+
+include $(CLEAR_VARS)
+LOCAL_PATH := $(my_LOCAL_PATH)
+LOCAL_ALLOW_UNDEFINED_SYMBOLS := true
+LOCAL_CFLAGS := -Wno-psabi
+LOCAL_LDLIBS := -llog -ldl
+LOCAL_MODULE := IssmJni
+LOCAL_SRC_FILES := Main.cpp 
+LOCAL_STATIC_LIBRARIES := libISSMCore
+
+include $(BUILD_SHARED_LIBRARY)
Index: /issm/trunk/src/android/ISSM/jni/Main.cpp
===================================================================
--- /issm/trunk/src/android/ISSM/jni/Main.cpp	(revision 13975)
+++ /issm/trunk/src/android/ISSM/jni/Main.cpp	(revision 13975)
@@ -0,0 +1,40 @@
+#include 
+#include "../../../c/android/fac.h"
+namespace com_example_issm
+{
+	static jlong factorial(JNIEnv *env, jclass clazz, jlong n)
+	{
+		fac *f = new fac();
+		jlong result = (jlong) (f->factorial(n));
+		delete(f);
+		return (jlong) result;
+	}
+//------------------------------------------------------------------------------------
+	static JNINativeMethod method_table[] = {
+			{"fac" ,"(J)J" , (void *) factorial},
+	};
+}
+
+using namespace com_example_issm;
+
+extern "C" jint JNI_OnLoad(JavaVM* vm, void* reserved)
+{
+    JNIEnv* env;
+    if (vm->GetEnv(reinterpret_cast(&env), JNI_VERSION_1_6) != JNI_OK) {
+        return -1;
+    }
+    else
+    {
+    	jclass clazz = env->FindClass("com/example/issm/IssmJni");
+    	if(clazz)
+    	{
+    		env->RegisterNatives(clazz, method_table, 1);
+    		env->DeleteLocalRef(clazz);
+    		return JNI_VERSION_1_6;
+    	}
+    	else return -1;
+    }
+
+    // Get jclass with env->FindClass.
+    // Register methods with env->RegisterNatives.
+}
Index: /issm/trunk/src/android/ISSM/jni/issmlib/Android.mk
===================================================================
--- /issm/trunk/src/android/ISSM/jni/issmlib/Android.mk	(revision 13975)
+++ /issm/trunk/src/android/ISSM/jni/issmlib/Android.mk	(revision 13975)
@@ -0,0 +1,6 @@
+LOCAL_PATH:= $(call my-dir)
+include $(CLEAR_VARS)
+LOCAL_MODULE    := libISSMCore
+LOCAL_SRC_FILES := ../../../../c/libISSMCore.a
+LOCAL_EXPORT_C_INCLUDES := ../../../../c/android/
+include $(PREBUILT_STATIC_LIBRARY)
Index: /issm/trunk/src/android/ISSM/proguard-project.txt
===================================================================
--- /issm/trunk/src/android/ISSM/proguard-project.txt	(revision 13975)
+++ /issm/trunk/src/android/ISSM/proguard-project.txt	(revision 13975)
@@ -0,0 +1,20 @@
+# To enable ProGuard in your project, edit project.properties
+# to define the proguard.config property as described in that file.
+#
+# Add project specific ProGuard rules here.
+# By default, the flags in this file are appended to flags specified
+# in ${sdk.dir}/tools/proguard/proguard-android.txt
+# You can edit the include path and order by changing the ProGuard
+# include property in project.properties.
+#
+# For more details, see
+#   http://developer.android.com/guide/developing/tools/proguard.html
+
+# Add any project specific keep options here:
+
+# If your project uses WebView with JS, uncomment the following
+# and specify the fully qualified class name to the JavaScript interface
+# class:
+#-keepclassmembers class fqcn.of.javascript.interface.for.webview {
+#   public *;
+#}
Index: /issm/trunk/src/android/ISSM/project.properties
===================================================================
--- /issm/trunk/src/android/ISSM/project.properties	(revision 13975)
+++ /issm/trunk/src/android/ISSM/project.properties	(revision 13975)
@@ -0,0 +1,14 @@
+# This file is automatically generated by Android Tools.
+# Do not modify this file -- YOUR CHANGES WILL BE ERASED!
+#
+# This file must be checked in Version Control Systems.
+#
+# To customize properties used by the Ant build system edit
+# "ant.properties", and override values to adapt the script to your
+# project structure.
+#
+# To enable ProGuard to shrink and obfuscate your code, uncomment this (available properties: sdk.dir, user.home):
+#proguard.config=${sdk.dir}/tools/proguard/proguard-android.txt:proguard-project.txt
+
+# Project target.
+target=android-15
Index: /issm/trunk/src/android/ISSM/res/layout/activity_issm.xml
===================================================================
--- /issm/trunk/src/android/ISSM/res/layout/activity_issm.xml	(revision 13975)
+++ /issm/trunk/src/android/ISSM/res/layout/activity_issm.xml	(revision 13975)
@@ -0,0 +1,33 @@
+
+
+    
+
+