Index: /issm/trunk/configs/config-discover-intel11.sh =================================================================== --- /issm/trunk/configs/config-discover-intel11.sh (revision 20500) +++ /issm/trunk/configs/config-discover-intel11.sh (revision 20500) @@ -0,0 +1,24 @@ +#!/bin/csh + +#PETSc 3.2 +#MPI /usr/local/intel/mpi/4.0.3.008/lib64/ + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mkl-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-mpi-include="/usr/local/intel/mpi/4.0.3.008/include64/" \ + --with-mpi-libflags="-L/usr/local/intel/mpi/4.0.3.008/lib64/ -lmpi -lmpiif" \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-scalapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-blas-lapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -xS -DMPICH_IGNORE_CXX_SEEK" \ + --with-vendor=intel-discover + Index: /issm/trunk/configs/config-discover-intel13.sh =================================================================== --- /issm/trunk/configs/config-discover-intel13.sh (revision 20500) +++ /issm/trunk/configs/config-discover-intel13.sh (revision 20500) @@ -0,0 +1,23 @@ +#!/bin/csh + +#PETSc 3.2 +#MPI /usr/local/other/SLES11.1/mvapich2/1.8.1/intel-13.1.2.183/lib + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mkl-dir="/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/" \ + --with-mpi-include="/usr/local/other/SLES11.1/mvapich2/1.8.1/intel-13.1.2.183/include" \ + --with-mpi-libflags="-L/usr/local/other/SLES11.1/mvapich2/1.8.1/intel-13.1.2.183/lib -lmpich -lopa -lmpl -lfmpich -lmpichcxx -lmpichf90 -lpthread -lrdmacm -libverbs -libumad -lrt -lnuma" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blacs-dir="/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/" \ + --with-blas-lapack-dir="/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-cxxoptflags="-O3 -xS -DMPICH_IGNORE_CXX_SEEK" \ + --with-vendor=intel-discover + + # --with-esmf-dir=$ESMF_INSTALL_DIRECTORY \ + Index: sm/trunk/configs/config-discover.sh =================================================================== --- /issm/trunk/configs/config-discover.sh (revision 20499) +++ (revision ) @@ -1,24 +1,0 @@ -#!/bin/csh - -#PETSc 3.2 -#MPI /usr/local/intel/mpi/4.0.3.008/lib64/ - -./configure \ - --prefix=$ISSM_DIR \ - --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ - --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mkl-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ - --with-mpi-include="/usr/local/intel/mpi/4.0.3.008/include64/" \ - --with-mpi-libflags="-L/usr/local/intel/mpi/4.0.3.008/lib64/ -lmpi -lmpiif" \ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --with-scalapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ - --with-blas-lapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ - --with-graphics-lib=/usr/lib64/libX11.so \ - --with-cxxoptflags="-O3 -xS -DMPICH_IGNORE_CXX_SEEK" \ - --with-vendor=intel-discover - Index: sm/trunk/configs/config-greenplanet.sh =================================================================== --- /issm/trunk/configs/config-greenplanet.sh (revision 20499) +++ (revision ) @@ -1,23 +1,0 @@ -#!/bin/sh - -#PETSc 3.2 -#MPI /sopt/mpi/openmpi-1.5.4_psm/intel - -./configure \ - --prefix=$ISSM_DIR \ - --with-wrappers=no \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ - --with-mpi-include="/sopt/mpi/openmpi-1.5.4_psm/intel/include/" \ - --with-mpi-libflags="-L/sopt/mpi/openmpi-1.5.4_psm/intel/lib/ -lmpi -lmpi_f77" \ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --with-mkl-dir=/opt/intel/mkl/10.2.4.032/ \ - --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-graphics-lib=/usr/lib64/libX11.so \ - --with-cxxoptflags="-O3" \ - --with-vendor=intel-linux Index: sm/trunk/configs/config-hoffman2.sh =================================================================== --- /issm/trunk/configs/config-hoffman2.sh (revision 20499) +++ (revision ) @@ -1,16 +1,0 @@ -.//config-greenplanet.sh:21: #!/bin/csh - -./configure \ - --prefix=$ISSM_DIR \ - --with-wrappers=no \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mpi-include=/u/local/intel/11.1/openmpi/1.4.5/include \ - --with-mpi-libflags="-L/u/local/intel/11.1/openmpi/1.4.5/include -lmpi" \ - --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-graphics-lib=/usr/lib64/libX11.so \ - --with-cxxoptflags="-O3 -L/u/local/intel/11.1/openmpi/1.4.5/lib -lmpi -lmpi_f77 -lmpi_cxx" Index: sm/trunk/configs/config-linux64-ad.sh =================================================================== --- /issm/trunk/configs/config-linux64-ad.sh (revision 20499) +++ (revision ) @@ -1,20 +1,0 @@ -#!/bin/sh - -./configure \ - --prefix=$ISSM_DIR \ - --without-wrappers\ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ - --without-thermal \ - --without-control \ - --without-hydrology \ - --without-stressbalance \ - --without-balanced \ - --without-responses \ - --without-slope \ - --without-rifts \ - --without-steadystate \ - --without-transient \ - --without-3d \ - --without-groundingline \ - --without-kriging \ - --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install Index: sm/trunk/configs/config-linux64-cmake.sh =================================================================== --- /issm/trunk/configs/config-linux64-cmake.sh (revision 20499) +++ (revision ) @@ -1,2 +1,0 @@ -rm $ISSM_DIR/CMakeCache.txt -cmake -D GSL_DIR=${GSL_DIR} ${ISSM_DIR} Index: /issm/trunk/configs/config-linux64-cyclone.sh =================================================================== --- /issm/trunk/configs/config-linux64-cyclone.sh (revision 20500) +++ /issm/trunk/configs/config-linux64-cyclone.sh (revision 20500) @@ -0,0 +1,22 @@ +#!/bin/sh + +#Default configuration script +#automake 1.14 +#petsc 3.6 +#mpich 3.0 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \ + --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \ + --with-fortran-lib="-L/opt/intel/intelcompiler-12.04/composerxe-2011.4.191/compiler/lib/intel64 -lifport -lifcore -limf -lsvml -lintlc "\ + --enable-development \ + CC=mpicc \ + CXX=mpic++ Index: /issm/trunk/configs/config-linux64-hexagon.sh =================================================================== --- /issm/trunk/configs/config-linux64-hexagon.sh (revision 20500) +++ /issm/trunk/configs/config-linux64-hexagon.sh (revision 20500) @@ -0,0 +1,14 @@ +#!/bin/sh + +#need to swap to GNU environment +#need to change the petsc libflag to lcraypetsc... +./configure \ + --prefix=/work/bfl022/issm_install \ + --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ + --with-petsc-dir=$PETSC_DIR \ + --with-metis-dir=$CRAY_TPSL_PREFIX_DIR \ + --with-mumps-dir=$CRAY_TPSL_PREFIX_DIR \ + --with-mpi-include="$CRAY_MPICH2_DIR/include" \ + --with-mpi-libflags="-L$CRAY_MPICH2_DIR/lib -lmpich -lmpl -lfmpich -lmpichcxx -lmpichf90" \ + --with-gsl-dir="/work/apps/gsl/1.16-gnu/" \ + --enable-development Index: sm/trunk/configs/config-linux64-larsen-ad.sh =================================================================== --- /issm/trunk/configs/config-linux64-larsen-ad.sh (revision 20499) +++ (revision ) @@ -1,11 +1,0 @@ -#!/bin/sh - -./configure \ - --prefix=$ISSM_DIR \ - --without-kriging \ - --without-kml \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ - --with-adolc-version=3 \ - --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: sm/trunk/configs/config-linux64-larsen-gia.sh =================================================================== --- /issm/trunk/configs/config-linux64-larsen-gia.sh (revision 20499) +++ (revision ) @@ -1,31 +1,0 @@ -#!/bin/sh - -#External packages versions: -#petsc 3.4 -#mpich 3.0 - -./configure \ - --prefix=$ISSM_DIR \ - --with-matlab-dir=$ISSM_DIR/externalpackages/matlab/install \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-python-dir=$ISSM_DIR/externalpackages/python/install\ - --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl " \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ - --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ - --with-math77-dir="$ISSM_DIR/externalpackages/math77/install" \ - --with-gia="yes"\ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.6/ -lgfortran" \ - --with-graphics-lib="/usr/lib/x86_64-linux-gnu/libX11.so" \ - --with-cxxoptflags="-march=opteron -O2" \ - --with-numthreads=16 \ - --enable-debugging Index: sm/trunk/configs/config-linux64-larsen.sh =================================================================== --- /issm/trunk/configs/config-linux64-larsen.sh (revision 20499) +++ (revision ) @@ -1,27 +1,0 @@ -#!/bin/sh - -#External packages versions: -#petsc 3.4 -#mpich 3.0 - -./configure \ - --prefix=$ISSM_DIR \ - --with-matlab-dir=$ISSM_DIR/externalpackages/matlab/install \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-python-dir=$ISSM_DIR/externalpackages/python/install\ - --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl " \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.6/ -lgfortran" \ - --with-graphics-lib="/usr/lib/x86_64-linux-gnu/libX11.so" \ - --with-cxxoptflags="-march=opteron -O2" \ - --with-numthreads=16 \ - --enable-debugging Index: sm/trunk/configs/config-linux64-murdo-nopetsc.sh =================================================================== --- /issm/trunk/configs/config-linux64-murdo-nopetsc.sh (revision 20499) +++ (revision ) @@ -1,16 +1,0 @@ -#!/bin/sh -./configure \ - --prefix=$ISSM_DIR\ - --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \ - --with-graphics-lib="/usr/lib/x86_64-linux-gnu/libX11.so" \ - --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-numthreads=18 \ - --enable-debugging Index: sm/trunk/configs/config-linux64-murdo.sh =================================================================== --- /issm/trunk/configs/config-linux64-murdo.sh (revision 20499) +++ (revision ) @@ -1,24 +1,0 @@ -#!/bin/sh - -#petsc 3.2 -#mpich 1.4 - -./configure \ - --prefix=$ISSM_DIR \ - --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \ - --with-petsc-dir=$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=$ISSM_DIR/externalpackages/tao/install \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ - --with-graphics-lib="/usr/lib/x86_64-linux-gnu/libX11.so" \ - --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ - --with-numthreads=18 \ - --enable-debugging Index: sm/trunk/configs/config-linux64-ubuntu64.sh =================================================================== --- /issm/trunk/configs/config-linux64-ubuntu64.sh (revision 20499) +++ (revision ) @@ -1,23 +1,0 @@ -#!/bin/sh - -./configure \ - --prefix=$ISSM_DIR \ - --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mpi-include="/usr/lib/mpich/include" \ - --with-mpi-libflags="-L/usr/lib/mpich/lib -lmpich -lmpl -ldl" \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ - --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.7/ -lgfortran"\ - --with-numthreads=8 \ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --enable-debugging - - Index: /issm/trunk/configs/config-macosx64-dakota.sh =================================================================== --- /issm/trunk/configs/config-macosx64-dakota.sh (revision 20500) +++ /issm/trunk/configs/config-macosx64-dakota.sh (revision 20500) @@ -0,0 +1,26 @@ +#!/bin/sh + +#petsc 3.6 +#mpich 3.0 yosemite +#boost 1.55 yosemite +#dakota 5.3.1 yosemite +export F77='/usr/local/gfortran/bin/gfortran' +export CC=/usr/local/gfortran/bin/gcc +export CXX=/usr/local/gfortran/bin/g++ + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags=" $ISSM_DIR/externalpackages/mpich/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpl.a " \ + --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-numthreads=8 + Index: sm/trunk/configs/config-macosx64-static.sh =================================================================== --- /issm/trunk/configs/config-macosx64-static.sh (revision 20499) +++ (revision ) @@ -1,19 +1,0 @@ -#!/bin/sh - -./configure \ - --prefix=$ISSM_DIR \ - --disable-static \ - --enable-standalone-executables \ - --enable-standalone-libraries \ - --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags=" -L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich -lpmpich" \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-fortran-lib="/usr/local/lib/libgfortran.a" \ - --enable-debugging \ - --with-numthreads=4 Index: sm/trunk/configs/config-win7-32.sh =================================================================== --- /issm/trunk/configs/config-win7-32.sh (revision 20499) +++ (revision ) @@ -1,14 +1,0 @@ -#!/bin/sh - -#get configure.sh to pick up the win7 Visual Studio compiler -./configure --prefix=$ISSM_DIR \ - --disable-static \ - --with-vendor=intel-win7-32 \ - --with-matlab-dir=""$ISSM_DIR/externalpackages/matlab/install"" \ - --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ - --with-metis-dir="$ISSM_DIR/externalpackages/metis/install" \ - --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mpi-libdir="$ISSM_DIR/externalpackages/petsc/install/lib" \ - --with-mpi-libflags="-Wl,libpetsc.lib" \ - --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include/mpiuni" Index: sm/trunk/configs/config-win7-64-parallel.sh =================================================================== --- /issm/trunk/configs/config-win7-64-parallel.sh (revision 20499) +++ (revision ) @@ -1,16 +1,0 @@ -#!/bin/sh - -#Dos style path needed for the windows sdk 7.1 cl compiler: -ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"` - -#get configure.sh to pick up the win7 Visual Studio compiler -./configure --prefix=$ISSM_DIR \ - --with-vendor=intel-win7-64 \ - --with-matlab-dir="C:/MATLAB/R2012b/"\ - --with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \ - --with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \ - --with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \ - --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install/lib" \ - --with-mpi-include="C:/MPICH2/include" \ - --with-mpi-libflags="-LC:/MPICH2/lib mpi.lib" - Index: sm/trunk/configs/config-win7-64.sh =================================================================== --- /issm/trunk/configs/config-win7-64.sh (revision 20499) +++ (revision ) @@ -1,14 +1,0 @@ -#!/bin/sh - -#get configure.sh to pick up the win7 Visual Studio compiler -./configure --prefix=$ISSM_DIR \ - --disable-static \ - --with-vendor=intel-win7-64 \ - --with-matlab-dir=""$ISSM_DIR/externalpackages/matlab/install"" \ - --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ - --with-metis-dir="$ISSM_DIR/externalpackages/metis/install" \ - --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ - --with-mpi-libflags-dir="$ISSM_DIR/externalpackages/petsc/install/lib" \ - --with-mpi-libflagss="-Wl,libpetsc.lib" \ - --with-mpi-include-dir="$ISSM_DIR/externalpackages/petsc/install/include/mpiuni" Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 20499) +++ /issm/trunk/configure.ac (revision 20500) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([Ice Sheet System Model (ISSM)],[4.9],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([Ice Sheet System Model (ISSM)],[4.10],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 @@ -11,7 +11,7 @@ #Compilers -AC_PROG_CC([icc cccl cl icl gcc]) +AC_PROG_CC([icc cl icl gcc]) AC_PROG_CPP -AC_PROG_CXX([icpc cccl cl icl g++]) +AC_PROG_CXX([icpc cl icl g++]) AC_PROG_F77([ifort g77 gfortran]) @@ -37,4 +37,5 @@ src/wrappers/python/Makefile src/wrappers/matlab/Makefile + src/wrappers/javascript/Makefile src/mobile/Makefile src/mobile/native/Makefile Index: /issm/trunk/etc/environment.csh =================================================================== --- /issm/trunk/etc/environment.csh (revision 20499) +++ /issm/trunk/etc/environment.csh (revision 20500) @@ -109,2 +109,8 @@ setenv PATH {$SHELL2JUNIT_DIR}/install:{$PATH} endif + +#GMT +set GMT_DIR="$ISSM_DIR/externalpackages/gmt" +if (-d $GMT_DIR) then + setenv PATH {$GMT_DIR}/install/bin/:{$PATH} +endif Index: /issm/trunk/etc/environment.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 20499) +++ /issm/trunk/etc/environment.sh (revision 20500) @@ -96,6 +96,8 @@ PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" -export PETSC_DIR -libpathappend "$PETSC_DIR/lib" +if [ -d "$PETSC_DIR" ]; then + export PETSC_DIR + libpathappend "$PETSC_DIR/lib" +fi SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install" @@ -282,4 +284,7 @@ libpathappend "$SVN_DIR/lib" +CVS_DIR="$ISSM_DIR/externalpackages/cvs/install" +pathprepend "$CVS_DIR/bin" + APR_DIR="$ISSM_DIR/externalpackages/apr/install" pathappend "$APR_DIR/bin" @@ -312,4 +317,7 @@ libpathprepend "$ISSM_DIR/externalpackages/expat/install" dylibpathprepend "$ISSM_DIR/externalpackages/expat/install" + +#GMSH +pathappend "$ISSM_DIR/externalpackages/gmsh/install" #CURL @@ -317,2 +325,5 @@ dylibpathprepend "$ISSM_DIR/externalpackages/curl/install/lib" pathprepend "$ISSM_DIR/externalpackages/curl/install/bin" + +#GMT +pathprepend "$ISSM_DIR/externalpackages/gmt/install/bin" Index: /issm/trunk/examples/Greenland/CheatSheet.m =================================================================== --- /issm/trunk/examples/Greenland/CheatSheet.m (revision 20499) +++ /issm/trunk/examples/Greenland/CheatSheet.m (revision 20500) @@ -10,5 +10,5 @@ %Save surface mass balance, by looping through 200 years, or 1000 steps surfmb=[]; for i=1:1000; surfmb=[surfmb ... - md.results.TransientSolution(i).SurfaceforcingsMassBalance]; end + md.results.TransientSolution(i).SmbMassBalance]; end %Plot surface mass balance time series in first subplot Index: /issm/trunk/examples/Greenland/Greenland.par =================================================================== --- /issm/trunk/examples/Greenland/Greenland.par (revision 20499) +++ /issm/trunk/examples/Greenland/Greenland.par (revision 20500) @@ -40,6 +40,6 @@ disp(' Interpolating surface mass balance'); -md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); -md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; +md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; disp(' Construct basal friction parameters'); Index: /issm/trunk/examples/Greenland/runme.m =================================================================== --- /issm/trunk/examples/Greenland/runme.m (revision 20499) +++ /issm/trunk/examples/Greenland/runme.m (revision 20500) @@ -1,4 +1,4 @@ clear all; -steps=[1]; +steps=[1 2 3 4 5]; %Location of SeaRISE dataset @@ -92,5 +92,5 @@ smb = smb*md.materials.rho_freshwater/md.materials.rho_ice; smb = [smb smb smb-1.0]; - md.surfaceforcings.mass_balance = [smb;1 10 20]; + md.smb.mass_balance = [smb;1 10 20]; %Set transient options, run for 20 years, saving every timestep @@ -102,5 +102,5 @@ md.inversion.iscontrol=0; md.transient.requested_outputs={'IceVolume','TotalSmb', ... - 'SurfaceforcingsMassBalance'}; + 'SmbMassBalance'}; md.verbose=verbose('solution',true,'module',true,'convergence',true); @@ -117,12 +117,5 @@ %Planview plots - plotmodel(md,'data',md.results.TransientSolution(end).Vel,'caxis',[1e-1 6000],... - 'log', 10, 'title', 'Velocity (m/y)','gridded',1, ... - 'data', md.results.TransientSolution(1).SurfaceforcingsMassBalance, ... - 'title', 'Surface mass balance (m/y)', 'gridded',1,... - 'data',md.results.TransientSolution(end).Thickness,... - 'title','Thickness (m)', 'gridded',1, ... - 'data',md.results.TransientSolution(end).Surface, ... - 'title', 'Surface (m)', 'gridded',1); + plotmodel(md,'data',md.results.TransientSolution(end).Vel,'caxis',[1e-1 6000],'log', 10, 'title', 'Velocity (m/y)','gridded',11); %Line Plots @@ -131,5 +124,5 @@ %Plot surface mass balance surfmb=[]; for i=1:100; surfmb=[surfmb ... - md.results.TransientSolution(i).SurfaceforcingsMassBalance]; end + md.results.TransientSolution(i).SmbMassBalance]; end subplot(3,1,1); plot([0.2:0.2:20],mean(surfmb)); title('Mean Surface mass balance'); @@ -188,5 +181,5 @@ smb_mo = InterpFromMeshToMesh2d(index,x1(:),y1(:),smbmean(:),xi,yi); smb = smb_mo*12/1000*md.materials.rho_freshwater/md.materials.rho_ice; - md.surfaceforcings.mass_balance = [smb;1 ]; + md.smb.mass_balance = [smb;1 ]; %Set transient options, run for 20 years, saving every timestep @@ -198,5 +191,5 @@ md.inversion.iscontrol=0; md.transient.requested_outputs={'IceVolume','TotalSmb', ... - 'SurfaceforcingsMassBalance'}; + 'SmbMassBalance'}; md.verbose=verbose('solution',true,'module',true); @@ -279,5 +272,5 @@ end end - md.surfaceforcings.mass_balance = ... + md.smb.mass_balance = ... [smb*12/1000*md.materials.rho_freshwater/md.materials.rho_ice; ... [1/24:1/12:length(years_of_simulation)]]; @@ -291,5 +284,5 @@ md.inversion.iscontrol=0; md.transient.requested_outputs={'IceVolume','TotalSmb', ... - 'SurfaceforcingsMassBalance'}; + 'SmbMassBalance'}; md.verbose=verbose('solution',true,'module',true); Index: /issm/trunk/examples/Pig/Pig.par =================================================================== --- /issm/trunk/examples/Pig/Pig.par (revision 20499) +++ /issm/trunk/examples/Pig/Pig.par (revision 20500) @@ -99,6 +99,6 @@ %Forcings disp(' Interpolating surface mass balance'); -md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); -md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; +md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; clear smb; Index: /issm/trunk/externalpackages/adolc/install-withampi-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi-macosx64.sh (revision 20499) +++ /issm/trunk/externalpackages/adolc/install-withampi-macosx64.sh (revision 20500) @@ -5,5 +5,6 @@ rm -rf install src -git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +git clone https://gitlab.com/adol-c/adol-c.git src +#git clone -b ampi git://git.mcs.anl.gov/adol-c.git src #git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad Index: /issm/trunk/externalpackages/adolc/install-withampi.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi.sh (revision 20499) +++ /issm/trunk/externalpackages/adolc/install-withampi.sh (revision 20500) @@ -5,5 +5,5 @@ rm -rf install src -git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +git clone https://gitlab.com/adol-c/adol-c.git src #git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad Index: /issm/trunk/externalpackages/adolc/install.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install.sh (revision 20499) +++ /issm/trunk/externalpackages/adolc/install.sh (revision 20500) @@ -5,5 +5,5 @@ rm -rf install src -git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +git clone https://gitlab.com/adol-c/adol-c.git src #git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad Index: /issm/trunk/externalpackages/autotools/install-discover.sh =================================================================== --- /issm/trunk/externalpackages/autotools/install-discover.sh (revision 20500) +++ /issm/trunk/externalpackages/autotools/install-discover.sh (revision 20500) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + +rm -rf install +mkdir install + +export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH" + +#install m4 +echo " === INSTALLING M4 ==" +rm -rf src +wget http://ftp.gnu.org/gnu/m4/m4-latest.tar.gz +tar zxvf m4* +rm m4-latest.tar.gz +mv m4-* src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd ../ + +#install autoconf +echo " === INSTALLING AUTOCONF ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.69.tar.gz' 'autoconf-2.69.tar.gz' +tar -zxvf autoconf-2.69.tar.gz +mv autoconf-2.69 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install automake +echo " === INSTALLING AUTOMAKE ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.14.tar.gz' 'automake-1.14.tar.gz' +tar -zxvf automake-1.14.tar.gz +mv automake-1.14 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install libtool +echo " === INSTALLING LIBTOOL ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool-2.4.2.tar.gz' 'libtool-2.4.2.tar.gz' +tar -zxvf libtool-2.4.2.tar.gz +rm libtool-2.4.2.tar.gz +mv libtool-2.4.2 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. Index: /issm/trunk/externalpackages/autotools/install-win.sh =================================================================== --- /issm/trunk/externalpackages/autotools/install-win.sh (revision 20499) +++ /issm/trunk/externalpackages/autotools/install-win.sh (revision 20500) @@ -10,7 +10,7 @@ echo " === INSTALLING AUTOCONF ==" rm -rf src -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.68.tar.gz' 'autoconf-2.68.tar.gz' -tar -zxvf autoconf-2.68.tar.gz -mv autoconf-2.68 src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.69.tar.gz' 'autoconf-2.69.tar.gz' +tar -zxvf autoconf-2.69.tar.gz +mv autoconf-2.69 src cd src ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" @@ -22,7 +22,7 @@ echo " === INSTALLING AUTOMAKE ==" rm -rf src -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.11.3.tar.gz' 'automake-1.11.3.tar.gz' -tar -zxvf automake-1.11.3.tar.gz -mv automake-1.11.3 src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.14.tar.gz' 'automake-1.14.tar.gz' +tar -zxvf automake-1.14.tar.gz +mv automake-1.14 src cd src ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" @@ -44,3 +44,10 @@ cd .. +# This patch takes care of removing options passed to the linker that casuse +# the build to fail, as well as changing some flags to match up to Microsoft +# compilers. patch ./install/share/aclocal/libtool.m4 < ./patches/libtool.m4.patch + +# Small change to Automake in order to get the right flags for Microsoft's +# compiler. +patch ./install/bin/automake < ./patches/automake.patch Index: /issm/trunk/externalpackages/autotools/patches/automake.patch =================================================================== --- /issm/trunk/externalpackages/autotools/patches/automake.patch (revision 20500) +++ /issm/trunk/externalpackages/autotools/patches/automake.patch (revision 20500) @@ -0,0 +1,13 @@ +--- ./externalpackages/autotools/install/bin/automake 2015-09-24 19:26:11.796659200 -0700 ++++ /home/daeden/tmp/automake 2015-09-25 11:32:53.557609300 -0700 +@@ -702,8 +702,8 @@ + 'compile' => "\$(CXX) @cpplike_flags \$(AM_CXXFLAGS) \$(CXXFLAGS)", + 'ccer' => 'CXX', + 'compiler' => 'CXXCOMPILE', +- 'compile_flag' => '-c', +- 'output_flag' => '-o', ++ 'compile_flag' => '/c', ++ 'output_flag' => '/Fo:', + 'libtool_tag' => 'CXX', + 'lder' => 'CXXLD', + 'ld' => '$(CXX)', Index: /issm/trunk/externalpackages/autotools/patches/libtool.m4.patch =================================================================== --- /issm/trunk/externalpackages/autotools/patches/libtool.m4.patch (revision 20499) +++ /issm/trunk/externalpackages/autotools/patches/libtool.m4.patch (revision 20500) @@ -1,4 +1,22 @@ ---- m4/libtool.m4 2013-06-19 22:19:27.313488900 -0700 -+++ m4/libtool.m4.bak 2013-06-18 18:45:55.766285300 -0700 +--- ./install/share/aclocal/libtool.m4 2015-09-25 15:51:40.870862200 -0700 ++++ /home/daeden/tmp/libtool.m4 2015-09-25 15:42:15.385935100 -0700 +@@ -2382,7 +2382,7 @@ + # Native MSVC + libname_spec='$name' + soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}' +- library_names_spec='${libname}.dll.lib' ++ library_names_spec='${libname}${shrext_cmds}' + + case $build_os in + mingw*) +@@ -3142,7 +3142,7 @@ + case $host_os in + cygwin* | mingw* | pw32* | cegcc*) + if test "$GCC" != yes; then +- reload_cmds=false ++ reload_cmds='lib /OUT:$output$reload_objs' + fi + ;; + darwin*) @@ -4752,7 +4752,7 @@ _LT_TAGVAR(exclude_expsyms, $1)=['[_]+GLOBAL_OFFSET_TABLE_|[_]+GLOBAL__[FID]_.*|[_]+head_[A-Za-z0-9_]+_dll|[A-Za-z0-9_]+_dll_iname'] @@ -6,5 +24,5 @@ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then - _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' -+ _LT_TAGVAR(archive_cmds, $1)='$CC /LD $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib ' ++ _LT_TAGVAR(archive_cmds, $1)='$CC /LD $libobjs $deplibs $compiler_flags /OUT:$output_objdir/$soname ' # If the export-symbols file already is a .def file (1st line # is EXPORTS), use it as is; otherwise, prepend... @@ -15,8 +33,26 @@ fi~ - $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' -+ $CC /LD $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib ' ++ $CC /LD $output_objdir/$soname.def $libobjs $deplibs $compiler_flags /OUT:$output_objdir/$soname ' else _LT_TAGVAR(ld_shlibs, $1)=no fi +@@ -5136,7 +5136,7 @@ + else + sed -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; + fi~ +- $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ ++ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs~ + linknames=' + # The linker will not automatically build a static lib if we build a DLL. + # _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' +@@ -6135,7 +6135,7 @@ + else + $SED -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; + fi~ +- $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ ++ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs~ + linknames=' + # The linker will not automatically build a static lib if we build a DLL. + # _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' @@ -6168,7 +6168,7 @@ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes @@ -24,5 +60,5 @@ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then - _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' -+ _LT_TAGVAR(archive_cmds, $1)='$CC /LD -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib ' ++ _LT_TAGVAR(archive_cmds, $1)='$CC /LD -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags /OUT:$output_objdir/$soname ' # If the export-symbols file already is a .def file (1st line # is EXPORTS), use it as is; otherwise, prepend... @@ -33,5 +69,5 @@ fi~ - $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' -+ $CC /LD -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib ' ++ $CC /LD -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags /OUT:$output_objdir/$soname ' else _LT_TAGVAR(ld_shlibs, $1)=no Index: /issm/trunk/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch =================================================================== --- /issm/trunk/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch (revision 20500) +++ /issm/trunk/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch (revision 20500) @@ -0,0 +1,7 @@ +33,34c33,35 +< || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +< ) +--- +> ) +> // || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +> // ) Index: /issm/trunk/externalpackages/boost/configs/1.55/adl.hpp.patch =================================================================== --- /issm/trunk/externalpackages/boost/configs/1.55/adl.hpp.patch (revision 20500) +++ /issm/trunk/externalpackages/boost/configs/1.55/adl.hpp.patch (revision 20500) @@ -0,0 +1,7 @@ +33,34c33,35 +< || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +< ) +--- +> ) +> // || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +> // ) Index: /issm/trunk/externalpackages/boost/install-1.49-linux.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.49-linux.sh (revision 20499) +++ /issm/trunk/externalpackages/boost/install-1.49-linux.sh (revision 20500) @@ -25,5 +25,5 @@ ./bootstrap.sh \ --prefix="$ISSM_DIR/externalpackages/boost/install" \ - --with-python=python3.2 \ + --with-python=python2.7 \ --with-python-root="$ISSM_DIR/externalpackages/python/install" Index: /issm/trunk/externalpackages/boost/install-1.49-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.49-macosx-snowleopard.sh (revision 20500) +++ /issm/trunk/externalpackages/boost/install-1.49-macosx-snowleopard.sh (revision 20500) @@ -0,0 +1,35 @@ +#!/bin/bash + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_49_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz' + +#Untar +tar -zxvf boost_1_49_0.tar.gz + +#Move boost into install directory +mv boost_1_49_0/* src +rm -rf boost_1_49_0 +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +#./b2 address-model=32 architecture=x86 cxxflags="-arch i386" variant=release threading=multi install +./b2 toolset=darwin address-model=32 architecture=x86 variant=release threading=multi install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk/externalpackages/boost/install-1.55-discover.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-discover.sh (revision 20500) +++ /issm/trunk/externalpackages/boost/install-1.55-discover.sh (revision 20500) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk/externalpackages/boost/install-1.55-linux.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-linux.sh (revision 20500) +++ /issm/trunk/externalpackages/boost/install-1.55-linux.sh (revision 20500) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk/externalpackages/boost/install-1.55-lonestar.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-lonestar.sh (revision 20500) +++ /issm/trunk/externalpackages/boost/install-1.55-lonestar.sh (revision 20500) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.lonestar.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk/externalpackages/boost/install-1.55-macosx-el_capitan.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-macosx-el_capitan.sh (revision 20500) +++ /issm/trunk/externalpackages/boost/install-1.55-macosx-el_capitan.sh (revision 20500) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +python2.7 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +# export CC=/usr/local/gfortan/bin/gcc +# export CXX=/usr/local/gfortran/bin/g++ +./bjam toolset=darwin link=static install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk/externalpackages/boost/install-1.55-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-macosx-snowleopard.sh (revision 20500) +++ /issm/trunk/externalpackages/boost/install-1.55-macosx-snowleopard.sh (revision 20500) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +./bjam toolset=darwin-std0x link=static install + +#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk/externalpackages/boost/install-1.55-macosx-yosemite.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-macosx-yosemite.sh (revision 20500) +++ /issm/trunk/externalpackages/boost/install-1.55-macosx-yosemite.sh (revision 20500) @@ -0,0 +1,46 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +python2.7 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +#./bjam toolset=darwin-std0x link=static install + +export CC=/usr/local/gfortan/bin/gcc +export CXX=/usr/local/gfortran/bin/g++ +./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 architecture=x86 variant=release link=static threading=multi install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk/externalpackages/boost/install-1.55-pleiades_dakota6.2.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-pleiades_dakota6.2.sh (revision 20500) +++ /issm/trunk/externalpackages/boost/install-1.55-pleiades_dakota6.2.sh (revision 20500) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.lonestar.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: sm/trunk/externalpackages/boost/install-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-macosx-snowleopard.sh (revision 20499) +++ (revision ) @@ -1,35 +1,0 @@ -#!/bin/bash - -#Note of caution: stop after boostrap phase, and run -#bjam --debug-configuration, to figure out which paths boost is using to include -#python. make sure everyone of these paths is covered by python. If not, just make -#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY -#to get the boost library to include python support without doing that. - -#Some cleanup -rm -rf install boost_1_49_0 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz' - -#Untar -tar -zxvf boost_1_49_0.tar.gz - -#Move boost into install directory -mv boost_1_49_0/* src -rm -rf boost_1_49_0 -#Configure and compile -cd src -./bootstrap.sh \ - --prefix="$ISSM_DIR/externalpackages/boost/install" \ - --with-python=python2.7 \ - --with-python-root="$ISSM_DIR/externalpackages/python/install" - -#Compile boost -#./b2 address-model=32 architecture=x86 cxxflags="-arch i386" variant=release threading=multi install -./b2 toolset=darwin address-model=32 architecture=x86 variant=release threading=multi install - -#put bjam into install also: -mkdir ../install/bin -cp bjam ../install/bin Index: /issm/trunk/externalpackages/chaco/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install-macosx64.sh (revision 20500) +++ /issm/trunk/externalpackages/chaco/install-macosx64.sh (revision 20500) @@ -0,0 +1,55 @@ +#!/bin/bash +set -eu + +# Some cleanup +rm -rf Chaco-2.2 +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf' + +# Untar +tar -xvzf Chaco-2.2.tar.gz + +# Move chaco to src directory +mv Chaco-2.2/* src +rm -rf Chaco-2.2 + +# Apply patches (all at once) +# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch) +patch -R -p0 < chaco.patch + +# Patch src/code/Makefile +patch ./src/code/Makefile ./patches/Makefile.patch + + +# Build chaco +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Populate install directory +cp -p src/exec/README install +cp -p src/exec/User_Params install +cp -p src/exec/*.coords install +cp -p src/exec/*.graph install +mkdir install/include +cp -p src/code/main/defs.h install/include/defs.h +cp -p src/code/main/params.h install/include/params.h +cp -p chaco.h install/include/chaco.h +mkdir install/lib +mv src/code/chaco.a install/lib/libchaco.a +mv src/code/chacominusblas.a install/lib/libchacominusblas.a +mkdir install/exec +mv src/exec/chaco install/exec Index: /issm/trunk/externalpackages/chaco/patches/Makefile.patch =================================================================== --- /issm/trunk/externalpackages/chaco/patches/Makefile.patch (revision 20500) +++ /issm/trunk/externalpackages/chaco/patches/Makefile.patch (revision 20500) @@ -0,0 +1,11 @@ +--- ./src/code/Makefile 2016-02-16 19:39:30.000000000 -0800 ++++ ./Makefile 2016-02-16 19:37:49.000000000 -0800 +@@ -6,7 +6,7 @@ + #CFLAGS = -O2 + #OFLAGS = -O2 + #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +-CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g ++CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/include/malloc + #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB + OFLAGS = -O2 + #AR = /usr/ccs/bin/ar rcv # for solaris 2 Index: /issm/trunk/externalpackages/cmake/install-macosx64-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/cmake/install-macosx64-snowleopard.sh (revision 20500) +++ /issm/trunk/externalpackages/cmake/install-macosx64-snowleopard.sh (revision 20500) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu +VER="2.8.11.2" + +#Some cleanup +rm -rf install cmake-$VER +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/cmake-$VER.tar.gz" "cmake-$VER.tar.gz" + +#Untar +tar -zxvf cmake-$VER.tar.gz + +#Move cmake into install directory +mv cmake-$VER/* install +rm -rf cmake-$VER + +LDFLAGS="-L/usr/lib/ -lstdc++ -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/ -lgfortran" +F77="/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran" + +#Compile cmake +cd install +./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install +if [ $# -eq 0 ]; then + make +else + make -j $1; +fi +make install Index: /issm/trunk/externalpackages/cmake/install.sh =================================================================== --- /issm/trunk/externalpackages/cmake/install.sh (revision 20499) +++ /issm/trunk/externalpackages/cmake/install.sh (revision 20500) @@ -1,18 +1,19 @@ #!/bin/bash set -eu +VER="3.3.1" #Some cleanup -rm -rf install cmake-2.8.11.2 +rm -rf install cmake-$VER mkdir install #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cmake-2.8.11.2.tar.gz' 'cmake-2.8.11.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/cmake-$VER.tar.gz" "cmake-$VER.tar.gz" #Untar -tar -zxvf cmake-2.8.11.2.tar.gz +tar -zxvf cmake-$VER.tar.gz #Move cmake into install directory -mv cmake-2.8.11.2/* install -rm -rf cmake-2.8.11.2 +mv cmake-$VER/* install +rm -rf cmake-$VER #Compile cmake Index: /issm/trunk/externalpackages/cvs/install.sh =================================================================== --- /issm/trunk/externalpackages/cvs/install.sh (revision 20500) +++ /issm/trunk/externalpackages/cvs/install.sh (revision 20500) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf cvs-1.11.23 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cvs-1.11.23.tar.gz' 'cvs-1.11.23.tar.gz' + +#Untar +tar -zxvf cvs-1.11.23.tar.gz + +#Move subversion into src directory +mv cvs-1.11.23/* src +rm -rf cvs-1.11.23 + +#Patch getline +cd src +cat lib/getline.c | sed -e "s/getline /get_line /" > BACK && mv BACK lib/getline.c +cat lib/getline.h | sed -e "s/getline /get_line /" > BACK && mv BACK lib/getline.h + +#Configure +./configure --prefix="$ISSM_DIR/externalpackages/cvs/install" + +#Compile and install subversion +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/cython/install-22.sh =================================================================== --- /issm/trunk/externalpackages/cython/install-22.sh (revision 20500) +++ /issm/trunk/externalpackages/cython/install-22.sh (revision 20500) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.22 + +#download numpy first +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Cython-0.22.tar.gz' 'cython.tar.gz' + +#install numpy +tar -zxvf cython.tar.gz +cd Cython-0.22 +python setup.py install Index: /issm/trunk/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch (revision 20500) @@ -0,0 +1,26 @@ +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "/nasa/boost/1.50.0" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch (revision 20500) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/trunk/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 20499) +++ /issm/trunk/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 20500) @@ -3,4 +3,4 @@ --- > # TODO: Can't this be integrated into the following logic? -> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") -> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") +> set(BLAS_LIBS "-L/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm") +> set(LAPACK_LIBS "-L/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm") Index: /issm/trunk/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.mac.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.mac.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.mac.patch (revision 20500) @@ -0,0 +1,14 @@ +64,65c64,65 +< #set( DAKOTA_HAVE_MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE_MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.patch (revision 20500) @@ -0,0 +1,26 @@ +64,65c64,65 +< #set( DAKOTA_HAVE_MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE_MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk/externalpackages/dakota/configs/6.1/CMakeLists.txt.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/CMakeLists.txt.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/CMakeLists.txt.patch (revision 20500) @@ -0,0 +1,4 @@ +47a48,50 +> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE) +> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE) +> Index: /issm/trunk/externalpackages/dakota/configs/6.1/CMakeLists.txt.pfe.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/CMakeLists.txt.pfe.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/CMakeLists.txt.pfe.patch (revision 20500) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") +> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") Index: /issm/trunk/externalpackages/dakota/configs/6.1/DakotaDev.cmake.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/DakotaDev.cmake.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/DakotaDev.cmake.patch (revision 20500) @@ -0,0 +1,16 @@ +4,8c4,8 +< set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +< "Enable DAKOTA specification maintenance mode?") +< set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +--- +> #set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +> # "Enable DAKOTA specification maintenance mode?") +> #set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +14c14 +< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) +--- +> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) Index: /issm/trunk/externalpackages/dakota/configs/6.1/NonDLocalReliability.cpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/NonDLocalReliability.cpp.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/NonDLocalReliability.cpp.patch (revision 20500) @@ -0,0 +1,9 @@ +2645a2646 +> // add sensitivity output to importance factors (jes, 8/06/10) +2651c2652,2655 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/trunk/externalpackages/dakota/configs/6.1/NonDSampling.cpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/NonDSampling.cpp.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/NonDSampling.cpp.patch (revision 20500) @@ -0,0 +1,25 @@ +780,786c780,787 +< if (!subIteratorFlag) { +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +< // archive the correlations to the results DB +< nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels, +< div_labels, dsv_labels, drv_labels, +< iteratedModel.response_labels()); +< } +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) { +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +> // // archive the correlations to the results DB +> // nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels, +> // div_labels, dsv_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1277,1278c1278,1281 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +< drv_labels,iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +> // drv_labels,iteratedModel.response_labels()); Index: /issm/trunk/externalpackages/dakota/configs/6.1/ParallelLibrary.cpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/ParallelLibrary.cpp.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/ParallelLibrary.cpp.patch (revision 20500) @@ -0,0 +1,24 @@ +51a54,76 +> /** This constructor is provided for the ISSM software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> mpiManager(dummy_mpi_mgr), programOptions(dummy_prg_opt), +> outputManager(dummy_out_mgr), dummyFlag(true), outputTimings(false) +> { +> initialize_timers(); +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 6.1 MPI executable in serial mode on CPU 0 for ISSM." << std::endl; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 6.1 serial executable in serial mode for ISSM." << std::endl; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> increment_parallel_configuration(); +> } +> +> Index: /issm/trunk/externalpackages/dakota/configs/6.1/ParallelLibrary.hpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/ParallelLibrary.hpp.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/ParallelLibrary.hpp.patch (revision 20500) @@ -0,0 +1,3 @@ +475a476,477 +> /// library mode constructor, serial mode (for the ISSM software) +> ParallelLibrary(char* serial_mode); Index: /issm/trunk/externalpackages/dakota/configs/6.1/pecos_global_defs.hpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.1/pecos_global_defs.hpp.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.1/pecos_global_defs.hpp.patch (revision 20500) @@ -0,0 +1,4 @@ +25a26 +> #ifndef PI +26a28 +> #endif Index: /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch (revision 20500) @@ -0,0 +1,35 @@ +54,55c54,55 +< #set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} " +< # CACHE STRING "CXX Flags for my platform" ) +--- +> set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK" +> CACHE STRING "CXX Flags for my platform" ) +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.mac.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.mac.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.mac.patch (revision 20500) @@ -0,0 +1,8 @@ +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.patch (revision 20500) @@ -0,0 +1,29 @@ +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch (revision 20500) @@ -0,0 +1,29 @@ +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "/nasa/boost/1.50.0" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.yosemite.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.yosemite.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.yosemite.patch (revision 20500) @@ -0,0 +1,29 @@ +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.a" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch (revision 20500) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/usr/local/intel/Composer/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/usr/local/intel/Composer/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.lonestar.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.lonestar.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.lonestar.patch (revision 20500) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/opt/apps/intel/11.1/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/opt/apps/intel/11.1/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.patch (revision 20500) @@ -0,0 +1,4 @@ +47a48,50 +> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE) +> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE) +> Index: /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 20500) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") +> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") Index: /issm/trunk/externalpackages/dakota/configs/6.2/DakotaDev.cmake.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/DakotaDev.cmake.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/DakotaDev.cmake.patch (revision 20500) @@ -0,0 +1,14 @@ +5,8c5,8 +< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +< "Enable DAKOTA specification maintenance mode?") +< set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +--- +> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +> # "Enable DAKOTA specification maintenance mode?") +> #set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +14c14 +< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) +--- +> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) Index: /issm/trunk/externalpackages/dakota/configs/6.2/NonDLocalReliability.cpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/NonDLocalReliability.cpp.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/NonDLocalReliability.cpp.patch (revision 20500) @@ -0,0 +1,9 @@ +2645a2646 +> // add sensitivity output to importance factors (jes, 8/06/10) +2651c2652,2655 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/trunk/externalpackages/dakota/configs/6.2/NonDSampling.cpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/NonDSampling.cpp.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/NonDSampling.cpp.patch (revision 20500) @@ -0,0 +1,25 @@ +780,786c780,787 +< if (!subIteratorFlag) { +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +< // archive the correlations to the results DB +< nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels, +< div_labels, dsv_labels, drv_labels, +< iteratedModel.response_labels()); +< } +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) { +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +> // // archive the correlations to the results DB +> // nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels, +> // div_labels, dsv_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1277,1278c1278,1281 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +< drv_labels,iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +> // drv_labels,iteratedModel.response_labels()); Index: /issm/trunk/externalpackages/dakota/configs/6.2/pecos_global_defs.hpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/pecos_global_defs.hpp.patch (revision 20500) +++ /issm/trunk/externalpackages/dakota/configs/6.2/pecos_global_defs.hpp.patch (revision 20500) @@ -0,0 +1,4 @@ +24a25 +> #ifndef PI +25a27 +> #endif Index: /issm/trunk/externalpackages/dakota/install-5.2-linux64-caladan.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-5.2-linux64-caladan.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-5.2-linux64-caladan.sh (revision 20500) @@ -0,0 +1,48 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch +patch src/packages/teuchos/src/Teuchos_ConfigDefs.hpp configs/5.2/Teuchos_ConfigDefs.hpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas="$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a" \ + --with-lapack="$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a" + +#Compile and install dakota +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-5.3.1-linux64-caladan.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-5.3.1-linux64-caladan.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-5.3.1-linux64-caladan.sh (revision 20500) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +#patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC -DBLAS_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a -DLAPACK_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-5.3.1-linux64.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-5.3.1-linux64.sh (revision 20499) +++ /issm/trunk/externalpackages/dakota/install-5.3.1-linux64.sh (revision 20500) @@ -25,4 +25,5 @@ patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +#patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.patch #Apply patches Index: /issm/trunk/externalpackages/dakota/install-5.3.1-lonestar.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-5.3.1-lonestar.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-5.3.1-lonestar.sh (revision 20500) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.lonestar.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-5.3.1-macosx64-yosemite.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-5.3.1-macosx64-yosemite.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-5.3.1-macosx64-yosemite.sh (revision 20500) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -D CMAKE_C_COMPILER=/usr/local/gfortran/bin/gcc -D CMAKE_CXX_COMPILER=/usr/local/gfortran/bin/g++ -D CMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/gfortran -D LDFLAGS="-std=gnu++0x" -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-5.3.1-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-5.3.1-pleiades.sh (revision 20499) +++ /issm/trunk/externalpackages/dakota/install-5.3.1-pleiades.sh (revision 20500) @@ -23,5 +23,5 @@ export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake -patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.pfe.patch Index: /issm/trunk/externalpackages/dakota/install-6.2-intel15-discover.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-intel15-discover.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-6.2-intel15-discover.sh (revision 20500) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.discover.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.discover.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=mpicc \ + -D CMAKE_CXX_COMPILER=mpicxx \ + -D CMAKE_Fortran_COMPILER=/usr/bin/gfortran \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-linux64.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-linux64.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-6.2-linux64.sh (revision 20500) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ + -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-lonestar.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-lonestar.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-6.2-lonestar.sh (revision 20500) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=/opt/cray/mpt/default/gni/mpich-intel/14.0/ +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.lonestar.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=/opt/apps/intel16/cray_mpich/7.3.0/bin/mpicc \ + -D CMAKE_CXX_COMPILER=/opt/apps/intel16/cray_mpich/7.3.0/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=/opt/apps/intel16/cray_mpich/7.3.0/bin/mpif77 \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-macosx64-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-snowleopard.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-6.2-macosx64-snowleopard.sh (revision 20500) @@ -0,0 +1,67 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.mac.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install + +#Configure dakota +# Set your local gcc compiler here +cd $DAK_BUILD +cmake -DBoost_NO_BOOST_CMAKE=TRUE \ + -DBoost_NO_SYSTEM_PATHS=TRUE \ + -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ + -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \ + -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ + -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ + -D LDFLAGS="-L/usr/lib/ -lstdc++ -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/ -lgfortran" \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +# Snowleopard: Mpi should be made with these compilers +#-DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CC_COMPILER=/usr/bin/gcc \ +#-DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran \ + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-macosx64-yosemite.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-yosemite.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-6.2-macosx64-yosemite.sh (revision 20500) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.yosemite.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ + -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ + -D LDFLAGS="-std=gnu++0x" \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-macosx64.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-6.2-macosx64.sh (revision 20500) @@ -0,0 +1,69 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.mac.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install + +#Configure dakota +# Set your local gcc compiler here +cd $DAK_BUILD +cmake -DBoost_NO_BOOST_CMAKE=TRUE \ + -DBoost_NO_SYSTEM_PATHS=TRUE \ + -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ + -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \ + -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ + -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ + -D CMAKE_CXX_FLAGS=-fdelayed-template-parsing \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +# Snowleopard: Mpi should be made with these compilers +#-DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CC_COMPILER=/usr/bin/gcc \ +#-DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran \ + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-pleiades.sh (revision 20500) +++ /issm/trunk/externalpackages/dakota/install-6.2-pleiades.sh (revision 20500) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.pfe.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=mpicc \ + -D CMAKE_CXX_COMPILER=mpicxx \ + -D CMAKE_Fortran_COMPILER=/usr/bin/gfortran \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk/externalpackages/dakota/tests/test.in =================================================================== --- /issm/trunk/externalpackages/dakota/tests/test.in (revision 20500) +++ /issm/trunk/externalpackages/dakota/tests/test.in (revision 20500) @@ -0,0 +1,36 @@ +method, + nond_sampling + seed = 1234 + rng rnum2 + samples = 2000 + sample_type lhs + distribution cumulative + num_probability_levels = 9 + probability_levels = + 0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 + 0.9999 + +model, + single + +variables, + normal_uncertain = 2 + nuv_means = + 1 1 + nuv_std_deviations = + 0.1 0.1 + nuv_descriptors = + 'x1' 'x2' + +interface, + direct + analysis_driver = 'plugin_text_book' + evaluation_scheduling master + processors_per_evaluation = 3 + +responses, + num_response_functions = 1 + response_descriptors = + 'MaxVel' + no_gradients + no_hessians Index: /issm/trunk/externalpackages/dakota/tests/test2.in =================================================================== --- /issm/trunk/externalpackages/dakota/tests/test2.in (revision 20500) +++ /issm/trunk/externalpackages/dakota/tests/test2.in (revision 20500) @@ -0,0 +1,36 @@ +method, + nond_sampling + seed = 1234 + rng rnum2 + samples = 3 + sample_type lhs + distribution cumulative + num_probability_levels = 9 + probability_levels = + 0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 + 0.9999 + +model, + single + +variables, + normal_uncertain = 2 + nuv_means = + 1 1 + nuv_std_deviations = + 0.1 0.1 + nuv_descriptors = + 'x1' 'x2' + +interface, + direct + analysis_driver = 'plugin_text_book' + evaluation_scheduling master + processors_per_evaluation = 1 + +responses, + num_response_functions = 1 + response_descriptors = + 'MaxVel' + no_gradients + no_hessians Index: /issm/trunk/externalpackages/esmf/install.sh =================================================================== --- /issm/trunk/externalpackages/esmf/install.sh (revision 20499) +++ /issm/trunk/externalpackages/esmf/install.sh (revision 20500) @@ -3,19 +3,19 @@ export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf +export ESMF_INSTALL_PREFIX=$ISSM_DIR/externalpackages/esmf/install export ESMF_COMPILER=gfortran export ESMF_COMM=mpich2 #Some cleanup -rm -rf esmf_5_2_0rp2 +rm -rf esmf_6_3_0rp1 rm -rf esmf #Download from ISSM server -$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/esmf_6_3_0rp1_src.tar.gz' 'esmf_6_3_0rp1_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 - +tar -zxvf esmf_6_3_0rp1_src.tar.gz #Configure esmf @@ -30,9 +30,2 @@ make -j $1 install fi - -cd esmf -if [ $# -eq 0 ]; then - make all_tests -else - make -j $1 all_tests -fi Index: /issm/trunk/externalpackages/gdal/install-1.10-linux64.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.10-linux64.sh (revision 20499) +++ /issm/trunk/externalpackages/gdal/install-1.10-linux64.sh (revision 20500) @@ -20,4 +20,7 @@ rm -rf gdal-1.10.0 +export CFLAGS=-D_HAVE_STRNDUP +export CXXFLAGS=-D_HAVE_STRNDUP + #Configure gdal cd src Index: /issm/trunk/externalpackages/geocode/install.sh =================================================================== --- /issm/trunk/externalpackages/geocode/install.sh (revision 20500) +++ /issm/trunk/externalpackages/geocode/install.sh (revision 20500) @@ -0,0 +1,2 @@ +#/bin/bash +unzip geoCode.zip Index: /issm/trunk/externalpackages/gmsh/install.sh =================================================================== --- /issm/trunk/externalpackages/gmsh/install.sh (revision 20499) +++ /issm/trunk/externalpackages/gmsh/install.sh (revision 20500) @@ -7,5 +7,5 @@ #Download latest version -svn --username gmsh --password gmsh co https://geuz.org/svn/gmsh/trunk src +svn co --username gmsh --password gmsh https://geuz.org/svn/gmsh/trunk src #Configure Index: /issm/trunk/externalpackages/gmt/configs/ConfigUser.cmake-jenkins =================================================================== --- /issm/trunk/externalpackages/gmt/configs/ConfigUser.cmake-jenkins (revision 20500) +++ /issm/trunk/externalpackages/gmt/configs/ConfigUser.cmake-jenkins (revision 20500) @@ -0,0 +1,240 @@ +# +# $Id: ConfigUserTemplate.cmake 12904 2014-02-17 20:52:35Z fwobbe $ +# +# Copyright (c) 1991-2014 by P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis and F. Wobbe +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License +# for more details. +# +# Contact info: gmt.soest.hawaii.edu +# ---------------------------------------------------------------------------- + +# Use this file to override variables in 'ConfigDefault.cmake' on a per-user +# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then +# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled +# (currently listed in svn:ignore property) +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## Section 1: Installation paths +## + +# ============================================================================ +# Basic setup begins here. All settings are optional. In most cases, setting +# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with +# reasonable defaults enabled. +# ============================================================================ + +# Installation path (usually defaults to /usr/local) [auto]: +set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") + +# Set install name suffix used for directories and gmt executables +# [undefined]: +#set (GMT_INSTALL_NAME_SUFFIX "suffix") + +# Install into traditional directory structure. Disable to install a +# distribution type directory structure (doc and share separated) [on]: +#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) + +# Install convenience links for GMT modules. Disable to install only the main +# gmt program and access modules as "gmt modulename options" [TRUE]: +#set (GMT_INSTALL_MODULE_LINKS FALSE) + +# Make executables relocatable on supported platforms (relative RPATH) [TRUE]: +#set (GMT_INSTALL_RELOCATABLE FALSE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new PDF and HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") + +# Copy GSHHG files to $/coast [FALSE]: +#set (COPY_GSHHG TRUE) + +# Set path to DCW Digital Chart of the World for GMT [auto]: +#set (DCW_ROOT "dcw-gmt_path") + +# Copy DCW files to $/dcw [FALSE]: +#set (COPY_DCW TRUE) + +# Set location of NetCDF (can be root directory, path to header file or path +# to nc-config) [auto]: +set (NETCDF_ROOT "/") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +#set (ZLIB_ROOT "zlib_install_prefix") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# Enable building of shared libraries [TRUE] (disable to use static libraries; +# not recommended): +#set (BUILD_SHARED_LIBS FALSE) + +# Build GMT shared lib with supplemental modules [TRUE]: +#set (BUILD_SUPPLEMENTS FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#set (DO_EXAMPLES TRUE) +#set (DO_TESTS TRUE) +# Number of parallel test jobs with "make check": +#set (N_TEST_JOBS 4) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmtextension project). +#set (EXTRA_BUILD_DIRS apidemo) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel +# [Release]: +#set (CMAKE_BUILD_TYPE Debug) + +# Extra debugging for developers: +#add_definitions(-DDEBUG) +#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info +#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +#set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) + +# vim: textwidth=78 noexpandtab tabstop=2 softtabstop=2 shiftwidth=2 Index: /issm/trunk/externalpackages/gmt/install-jenkins.sh =================================================================== --- /issm/trunk/externalpackages/gmt/install-jenkins.sh (revision 20500) +++ /issm/trunk/externalpackages/gmt/install-jenkins.sh (revision 20500) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src gmt + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gmt-5.1.1.tar.gz' 'gmt-5.1.1.tar.gz' + +#install directory +mkdir src +tar -zxvf gmt-5.1.1.tar.gz +mv gmt-5.1.1/* src +rm -rf gmt-5.1.1 + +#configure: +cp configs/ConfigUser.cmake-jenkins ./src/cmake/ConfigUser.cmake + +cd src +mkdir build +cd build +cmake ../ + +#compile +if [ $# -eq 0 ]; then + make install +else + make -j $1 install +fi + +#come back: +cd ../../ Index: /issm/trunk/externalpackages/gshhg/install.sh =================================================================== --- /issm/trunk/externalpackages/gshhg/install.sh (revision 20499) +++ /issm/trunk/externalpackages/gshhg/install.sh (revision 20500) @@ -2,15 +2,15 @@ set -eu -rm -rf gssh-gmt-2.3.3.tar.gz src install +rm -rf gssh-gmt-2.3.4.tar.gz src install #get gssh database from noaa's website: http://www.ngdc.noaa.gov/mgg/shorelines/gshhs.html -curl http://www.ngdc.noaa.gov/mgg/shorelines/data/gshhg/latest/gshhg-gmt-2.3.3.tar.gz > gshhg-gmt-2.3.3.tar.gz +#curl http://www.ngdc.noaa.gov/mgg/shorelines/data/gshhg/latest/gshhg-gmt-2.3.4.tar.gz > gshhg-gmt-2.3.4.tar.gz #Download from ISSM server -#$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gshhg-gmt-2.3.3.tar.gz' 'gshhg-gmt-2.3.3.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gshhg-gmt-2.3.4.tar.gz' 'gshhg-gmt-2.3.4.tar.gz' #untar: -tar -zxvf gshhg-gmt-2.3.3.tar.gz +tar -zxvf gshhg-gmt-2.3.4.tar.gz #move: -mv gshhg-gmt-2.3.3 install +mv gshhg-gmt-2.3.4 install Index: /issm/trunk/externalpackages/javascript/src/gauge.min.js =================================================================== --- /issm/trunk/externalpackages/javascript/src/gauge.min.js (revision 20500) +++ /issm/trunk/externalpackages/javascript/src/gauge.min.js (revision 20500) @@ -0,0 +1,1 @@ +(function(){var a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q={}.hasOwnProperty,r=function(a,b){function c(){this.constructor=a}for(var d in b)q.call(b,d)&&(a[d]=b[d]);return c.prototype=b.prototype,a.prototype=new c,a.__super__=b.prototype,a};!function(){var a,b,c,d,e,f,g;for(g=["ms","moz","webkit","o"],c=0,e=g.length;e>c&&(f=g[c],!window.requestAnimationFrame);c++)window.requestAnimationFrame=window[f+"RequestAnimationFrame"],window.cancelAnimationFrame=window[f+"CancelAnimationFrame"]||window[f+"CancelRequestAnimationFrame"];return 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a?cancelAnimationFrame(AnimationUpdater.animId):AnimationUpdater.animId=requestAnimationFrame(AnimationUpdater.run)}},"function"==typeof window.define&&null!=window.define.amd?define(function(){return{Gauge:g,Donut:f,BaseDonut:d,TextRenderer:i}}):"undefined"!=typeof module&&null!=module.exports?module.exports={Gauge:g,Donut:f,BaseDonut:d,TextRenderer:i}:(window.Gauge=g,window.Donut=f,window.BaseDonut=d,window.TextRenderer=i)}).call(this); Index: /issm/trunk/externalpackages/javascript/src/gl-matrix-min.js =================================================================== --- /issm/trunk/externalpackages/javascript/src/gl-matrix-min.js (revision 20500) +++ /issm/trunk/externalpackages/javascript/src/gl-matrix-min.js (revision 20500) @@ -0,0 +1,29 @@ +/** + * @fileoverview gl-matrix - High performance matrix and vector operations + * @author Brandon Jones + * @author Colin MacKenzie IV + * @version 2.3.2 + */ + +/* Copyright (c) 2015, Brandon Jones, Colin MacKenzie IV. + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. */ + +!function(t,a){if("object"==typeof exports&&"object"==typeof module)module.exports=a();else if("function"==typeof define&&define.amd)define(a);else{var n=a();for(var r in n)("object"==typeof exports?exports:t)[r]=n[r]}}(this,function(){return function(t){function a(r){if(n[r])return n[r].exports;var o=n[r]={exports:{},id:r,loaded:!1};return t[r].call(o.exports,o,o.exports,a),o.loaded=!0,o.exports}var n={};return a.m=t,a.c=n,a.p="",a(0)}([function(t,a,n){a.glMatrix=n(1),a.mat2=n(2),a.mat2d=n(3),a.mat3=n(4),a.mat4=n(5),a.quat=n(6),a.vec2=n(9),a.vec3=n(7),a.vec4=n(8)},function(t,a){var n={};n.EPSILON=1e-6,n.ARRAY_TYPE="undefined"!=typeof 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r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=n[0],s=n[1];return t[0]=r*i,t[1]=o*i,t[2]=l*s,t[3]=u*s,t[4]=e,t[5]=M,t},o.translate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=n[0],s=n[1];return t[0]=r,t[1]=o,t[2]=l,t[3]=u,t[4]=r*i+l*s+e,t[5]=o*i+u*s+M,t},o.fromRotation=function(t,a){var n=Math.sin(a),r=Math.cos(a);return t[0]=r,t[1]=n,t[2]=-n,t[3]=r,t[4]=0,t[5]=0,t},o.fromScaling=function(t,a){return t[0]=a[0],t[1]=0,t[2]=0,t[3]=a[1],t[4]=0,t[5]=0,t},o.fromTranslation=function(t,a){return t[0]=1,t[1]=0,t[2]=0,t[3]=1,t[4]=a[0],t[5]=a[1],t},o.str=function(t){return"mat2d("+t[0]+", "+t[1]+", "+t[2]+", "+t[3]+", "+t[4]+", "+t[5]+")"},o.frob=function(t){return Math.sqrt(Math.pow(t[0],2)+Math.pow(t[1],2)+Math.pow(t[2],2)+Math.pow(t[3],2)+Math.pow(t[4],2)+Math.pow(t[5],2)+1)},t.exports=o},function(t,a,n){var r=n(1),o={};o.create=function(){var t=new r.ARRAY_TYPE(9);return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=1,t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.fromMat4=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[4],t[4]=a[5],t[5]=a[6],t[6]=a[8],t[7]=a[9],t[8]=a[10],t},o.clone=function(t){var a=new r.ARRAY_TYPE(9);return a[0]=t[0],a[1]=t[1],a[2]=t[2],a[3]=t[3],a[4]=t[4],a[5]=t[5],a[6]=t[6],a[7]=t[7],a[8]=t[8],a},o.copy=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t},o.identity=function(t){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=1,t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.transpose=function(t,a){if(t===a){var n=a[1],r=a[2],o=a[5];t[1]=a[3],t[2]=a[6],t[3]=n,t[5]=a[7],t[6]=r,t[7]=o}else t[0]=a[0],t[1]=a[3],t[2]=a[6],t[3]=a[1],t[4]=a[4],t[5]=a[7],t[6]=a[2],t[7]=a[5],t[8]=a[8];return t},o.invert=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=s*u-e*i,D=-s*l+e*M,S=i*l-u*M,I=n*c+r*D+o*S;return I?(I=1/I,t[0]=c*I,t[1]=(-s*r+o*i)*I,t[2]=(e*r-o*u)*I,t[3]=D*I,t[4]=(s*n-o*M)*I,t[5]=(-e*n+o*l)*I,t[6]=S*I,t[7]=(-i*n+r*M)*I,t[8]=(u*n-r*l)*I,t):null},o.adjoint=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8];return t[0]=u*s-e*i,t[1]=o*i-r*s,t[2]=r*e-o*u,t[3]=e*M-l*s,t[4]=n*s-o*M,t[5]=o*l-n*e,t[6]=l*i-u*M,t[7]=r*M-n*i,t[8]=n*u-r*l,t},o.determinant=function(t){var a=t[0],n=t[1],r=t[2],o=t[3],l=t[4],u=t[5],e=t[6],M=t[7],i=t[8];return a*(i*l-u*M)+n*(-i*o+u*e)+r*(M*o-l*e)},o.multiply=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=n[0],S=n[1],I=n[2],x=n[3],f=n[4],F=n[5],m=n[6],h=n[7],d=n[8];return t[0]=D*r+S*u+I*i,t[1]=D*o+S*e+I*s,t[2]=D*l+S*M+I*c,t[3]=x*r+f*u+F*i,t[4]=x*o+f*e+F*s,t[5]=x*l+f*M+F*c,t[6]=m*r+h*u+d*i,t[7]=m*o+h*e+d*s,t[8]=m*l+h*M+d*c,t},o.mul=o.multiply,o.translate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=n[0],S=n[1];return t[0]=r,t[1]=o,t[2]=l,t[3]=u,t[4]=e,t[5]=M,t[6]=D*r+S*u+i,t[7]=D*o+S*e+s,t[8]=D*l+S*M+c,t},o.rotate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=Math.sin(n),S=Math.cos(n);return t[0]=S*r+D*u,t[1]=S*o+D*e,t[2]=S*l+D*M,t[3]=S*u-D*r,t[4]=S*e-D*o,t[5]=S*M-D*l,t[6]=i,t[7]=s,t[8]=c,t},o.scale=function(t,a,n){var r=n[0],o=n[1];return t[0]=r*a[0],t[1]=r*a[1],t[2]=r*a[2],t[3]=o*a[3],t[4]=o*a[4],t[5]=o*a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t},o.fromTranslation=function(t,a){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=1,t[5]=0,t[6]=a[0],t[7]=a[1],t[8]=1,t},o.fromRotation=function(t,a){var n=Math.sin(a),r=Math.cos(a);return t[0]=r,t[1]=n,t[2]=0,t[3]=-n,t[4]=r,t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.fromScaling=function(t,a){return t[0]=a[0],t[1]=0,t[2]=0,t[3]=0,t[4]=a[1],t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.fromMat2d=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=0,t[3]=a[2],t[4]=a[3],t[5]=0,t[6]=a[4],t[7]=a[5],t[8]=1,t},o.fromQuat=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=n+n,e=r+r,M=o+o,i=n*u,s=r*u,c=r*e,D=o*u,S=o*e,I=o*M,x=l*u,f=l*e,F=l*M;return t[0]=1-c-I,t[3]=s-F,t[6]=D+f,t[1]=s+F,t[4]=1-i-I,t[7]=S-x,t[2]=D-f,t[5]=S+x,t[8]=1-i-c,t},o.normalFromMat4=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15],m=n*e-r*u,h=n*M-o*u,d=n*i-l*u,v=r*M-o*e,z=r*i-l*e,p=o*i-l*M,w=s*x-c*I,A=s*f-D*I,R=s*F-S*I,b=c*f-D*x,Y=c*F-S*x,q=D*F-S*f,y=m*q-h*Y+d*b+v*R-z*A+p*w;return y?(y=1/y,t[0]=(e*q-M*Y+i*b)*y,t[1]=(M*R-u*q-i*A)*y,t[2]=(u*Y-e*R+i*w)*y,t[3]=(o*Y-r*q-l*b)*y,t[4]=(n*q-o*R+l*A)*y,t[5]=(r*R-n*Y-l*w)*y,t[6]=(x*p-f*z+F*v)*y,t[7]=(f*d-I*p-F*h)*y,t[8]=(I*z-x*d+F*m)*y,t):null},o.str=function(t){return"mat3("+t[0]+", "+t[1]+", "+t[2]+", "+t[3]+", "+t[4]+", "+t[5]+", "+t[6]+", "+t[7]+", "+t[8]+")"},o.frob=function(t){return Math.sqrt(Math.pow(t[0],2)+Math.pow(t[1],2)+Math.pow(t[2],2)+Math.pow(t[3],2)+Math.pow(t[4],2)+Math.pow(t[5],2)+Math.pow(t[6],2)+Math.pow(t[7],2)+Math.pow(t[8],2))},t.exports=o},function(t,a,n){var r=n(1),o={scalar:{},SIMD:{}};o.create=function(){var t=new r.ARRAY_TYPE(16);return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=1,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=1,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},o.clone=function(t){var a=new r.ARRAY_TYPE(16);return a[0]=t[0],a[1]=t[1],a[2]=t[2],a[3]=t[3],a[4]=t[4],a[5]=t[5],a[6]=t[6],a[7]=t[7],a[8]=t[8],a[9]=t[9],a[10]=t[10],a[11]=t[11],a[12]=t[12],a[13]=t[13],a[14]=t[14],a[15]=t[15],a},o.copy=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t[9]=a[9],t[10]=a[10],t[11]=a[11],t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.identity=function(t){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=1,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=1,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},o.scalar.transpose=function(t,a){if(t===a){var n=a[1],r=a[2],o=a[3],l=a[6],u=a[7],e=a[11];t[1]=a[4],t[2]=a[8],t[3]=a[12],t[4]=n,t[6]=a[9],t[7]=a[13],t[8]=r,t[9]=l,t[11]=a[14],t[12]=o,t[13]=u,t[14]=e}else t[0]=a[0],t[1]=a[4],t[2]=a[8],t[3]=a[12],t[4]=a[1],t[5]=a[5],t[6]=a[9],t[7]=a[13],t[8]=a[2],t[9]=a[6],t[10]=a[10],t[11]=a[14],t[12]=a[3],t[13]=a[7],t[14]=a[11],t[15]=a[15];return t},o.SIMD.transpose=function(t,a){var n,r,o,l,u,e,M,i,s,c;return n=SIMD.Float32x4.load(a,0),r=SIMD.Float32x4.load(a,4),o=SIMD.Float32x4.load(a,8),l=SIMD.Float32x4.load(a,12),u=SIMD.Float32x4.shuffle(n,r,0,1,4,5),e=SIMD.Float32x4.shuffle(o,l,0,1,4,5),M=SIMD.Float32x4.shuffle(u,e,0,2,4,6),i=SIMD.Float32x4.shuffle(u,e,1,3,5,7),SIMD.Float32x4.store(t,0,M),SIMD.Float32x4.store(t,4,i),u=SIMD.Float32x4.shuffle(n,r,2,3,6,7),e=SIMD.Float32x4.shuffle(o,l,2,3,6,7),s=SIMD.Float32x4.shuffle(u,e,0,2,4,6),c=SIMD.Float32x4.shuffle(u,e,1,3,5,7),SIMD.Float32x4.store(t,8,s),SIMD.Float32x4.store(t,12,c),t},o.transpose=r.USE_SIMD?o.SIMD.transpose:o.scalar.transpose,o.scalar.invert=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15],m=n*e-r*u,h=n*M-o*u,d=n*i-l*u,v=r*M-o*e,z=r*i-l*e,p=o*i-l*M,w=s*x-c*I,A=s*f-D*I,R=s*F-S*I,b=c*f-D*x,Y=c*F-S*x,q=D*F-S*f,y=m*q-h*Y+d*b+v*R-z*A+p*w;return y?(y=1/y,t[0]=(e*q-M*Y+i*b)*y,t[1]=(o*Y-r*q-l*b)*y,t[2]=(x*p-f*z+F*v)*y,t[3]=(D*z-c*p-S*v)*y,t[4]=(M*R-u*q-i*A)*y,t[5]=(n*q-o*R+l*A)*y,t[6]=(f*d-I*p-F*h)*y,t[7]=(s*p-D*d+S*h)*y,t[8]=(u*Y-e*R+i*w)*y,t[9]=(r*R-n*Y-l*w)*y,t[10]=(I*z-x*d+F*m)*y,t[11]=(c*d-s*z-S*m)*y,t[12]=(e*A-u*b-M*w)*y,t[13]=(n*b-r*A+o*w)*y,t[14]=(x*h-I*v-f*m)*y,t[15]=(s*v-c*h+D*m)*y,t):null},o.SIMD.invert=function(t,a){var n,r,o,l,u,e,M,i,s,c,D=SIMD.Float32x4.load(a,0),S=SIMD.Float32x4.load(a,4),I=SIMD.Float32x4.load(a,8),x=SIMD.Float32x4.load(a,12);return u=SIMD.Float32x4.shuffle(D,S,0,1,4,5),r=SIMD.Float32x4.shuffle(I,x,0,1,4,5),n=SIMD.Float32x4.shuffle(u,r,0,2,4,6),r=SIMD.Float32x4.shuffle(r,u,1,3,5,7),u=SIMD.Float32x4.shuffle(D,S,2,3,6,7),l=SIMD.Float32x4.shuffle(I,x,2,3,6,7),o=SIMD.Float32x4.shuffle(u,l,0,2,4,6),l=SIMD.Float32x4.shuffle(l,u,1,3,5,7),u=SIMD.Float32x4.mul(o,l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),e=SIMD.Float32x4.mul(r,u),M=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(SIMD.Float32x4.mul(r,u),e),M=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),M),M=SIMD.Float32x4.swizzle(M,2,3,0,1),u=SIMD.Float32x4.mul(r,o),u=SIMD.Float32x4.swizzle(u,1,0,3,2),e=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),e),s=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(e,SIMD.Float32x4.mul(l,u)),s=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),u=SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(r,2,3,0,1),l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),o=SIMD.Float32x4.swizzle(o,2,3,0,1),e=SIMD.Float32x4.add(SIMD.Float32x4.mul(o,u),e),i=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(e,SIMD.Float32x4.mul(o,u)),i=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),i),i=SIMD.Float32x4.swizzle(i,2,3,0,1),u=SIMD.Float32x4.mul(n,r),u=SIMD.Float32x4.swizzle(u,1,0,3,2),i=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),i),s=SIMD.Float32x4.sub(SIMD.Float32x4.mul(o,u),s),u=SIMD.Float32x4.swizzle(u,2,3,0,1),i=SIMD.Float32x4.sub(SIMD.Float32x4.mul(l,u),i),s=SIMD.Float32x4.sub(s,SIMD.Float32x4.mul(o,u)),u=SIMD.Float32x4.mul(n,l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),M=SIMD.Float32x4.sub(M,SIMD.Float32x4.mul(o,u)),i=SIMD.Float32x4.add(SIMD.Float32x4.mul(r,u),i),u=SIMD.Float32x4.swizzle(u,2,3,0,1),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(o,u),M),i=SIMD.Float32x4.sub(i,SIMD.Float32x4.mul(r,u)),u=SIMD.Float32x4.mul(n,o),u=SIMD.Float32x4.swizzle(u,1,0,3,2),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),M),s=SIMD.Float32x4.sub(s,SIMD.Float32x4.mul(r,u)),u=SIMD.Float32x4.swizzle(u,2,3,0,1),M=SIMD.Float32x4.sub(M,SIMD.Float32x4.mul(l,u)),s=SIMD.Float32x4.add(SIMD.Float32x4.mul(r,u),s),c=SIMD.Float32x4.mul(n,e),c=SIMD.Float32x4.add(SIMD.Float32x4.swizzle(c,2,3,0,1),c),c=SIMD.Float32x4.add(SIMD.Float32x4.swizzle(c,1,0,3,2),c),u=SIMD.Float32x4.reciprocalApproximation(c),c=SIMD.Float32x4.sub(SIMD.Float32x4.add(u,u),SIMD.Float32x4.mul(c,SIMD.Float32x4.mul(u,u))),(c=SIMD.Float32x4.swizzle(c,0,0,0,0))?(SIMD.Float32x4.store(t,0,SIMD.Float32x4.mul(c,e)),SIMD.Float32x4.store(t,4,SIMD.Float32x4.mul(c,M)),SIMD.Float32x4.store(t,8,SIMD.Float32x4.mul(c,i)),SIMD.Float32x4.store(t,12,SIMD.Float32x4.mul(c,s)),t):null},o.invert=r.USE_SIMD?o.SIMD.invert:o.scalar.invert,o.scalar.adjoint=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15];return t[0]=e*(D*F-S*f)-c*(M*F-i*f)+x*(M*S-i*D),t[1]=-(r*(D*F-S*f)-c*(o*F-l*f)+x*(o*S-l*D)),t[2]=r*(M*F-i*f)-e*(o*F-l*f)+x*(o*i-l*M),t[3]=-(r*(M*S-i*D)-e*(o*S-l*D)+c*(o*i-l*M)),t[4]=-(u*(D*F-S*f)-s*(M*F-i*f)+I*(M*S-i*D)),t[5]=n*(D*F-S*f)-s*(o*F-l*f)+I*(o*S-l*D),t[6]=-(n*(M*F-i*f)-u*(o*F-l*f)+I*(o*i-l*M)),t[7]=n*(M*S-i*D)-u*(o*S-l*D)+s*(o*i-l*M),t[8]=u*(c*F-S*x)-s*(e*F-i*x)+I*(e*S-i*c),t[9]=-(n*(c*F-S*x)-s*(r*F-l*x)+I*(r*S-l*c)),t[10]=n*(e*F-i*x)-u*(r*F-l*x)+I*(r*i-l*e),t[11]=-(n*(e*S-i*c)-u*(r*S-l*c)+s*(r*i-l*e)),t[12]=-(u*(c*f-D*x)-s*(e*f-M*x)+I*(e*D-M*c)),t[13]=n*(c*f-D*x)-s*(r*f-o*x)+I*(r*D-o*c),t[14]=-(n*(e*f-M*x)-u*(r*f-o*x)+I*(r*M-o*e)),t[15]=n*(e*D-M*c)-u*(r*D-o*c)+s*(r*M-o*e),t},o.SIMD.adjoint=function(t,a){var n,r,o,l,u,e,M,i,s,c,D,S,I,n=SIMD.Float32x4.load(a,0),r=SIMD.Float32x4.load(a,4),o=SIMD.Float32x4.load(a,8),l=SIMD.Float32x4.load(a,12);return s=SIMD.Float32x4.shuffle(n,r,0,1,4,5),e=SIMD.Float32x4.shuffle(o,l,0,1,4,5),u=SIMD.Float32x4.shuffle(s,e,0,2,4,6),e=SIMD.Float32x4.shuffle(e,s,1,3,5,7),s=SIMD.Float32x4.shuffle(n,r,2,3,6,7),i=SIMD.Float32x4.shuffle(o,l,2,3,6,7),M=SIMD.Float32x4.shuffle(s,i,0,2,4,6),i=SIMD.Float32x4.shuffle(i,s,1,3,5,7),s=SIMD.Float32x4.mul(M,i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),c=SIMD.Float32x4.mul(e,s),D=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(SIMD.Float32x4.mul(e,s),c),D=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),D),D=SIMD.Float32x4.swizzle(D,2,3,0,1),s=SIMD.Float32x4.mul(e,M),s=SIMD.Float32x4.swizzle(s,1,0,3,2),c=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),c),I=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(c,SIMD.Float32x4.mul(i,s)),I=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),I),I=SIMD.Float32x4.swizzle(I,2,3,0,1),s=SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,2,3,0,1),i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),M=SIMD.Float32x4.swizzle(M,2,3,0,1),c=SIMD.Float32x4.add(SIMD.Float32x4.mul(M,s),c),S=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(c,SIMD.Float32x4.mul(M,s)),S=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),S),S=SIMD.Float32x4.swizzle(S,2,3,0,1),s=SIMD.Float32x4.mul(u,e),s=SIMD.Float32x4.swizzle(s,1,0,3,2),S=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),S),I=SIMD.Float32x4.sub(SIMD.Float32x4.mul(M,s),I),s=SIMD.Float32x4.swizzle(s,2,3,0,1),S=SIMD.Float32x4.sub(SIMD.Float32x4.mul(i,s),S),I=SIMD.Float32x4.sub(I,SIMD.Float32x4.mul(M,s)),s=SIMD.Float32x4.mul(u,i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),D=SIMD.Float32x4.sub(D,SIMD.Float32x4.mul(M,s)),S=SIMD.Float32x4.add(SIMD.Float32x4.mul(e,s),S),s=SIMD.Float32x4.swizzle(s,2,3,0,1),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(M,s),D),S=SIMD.Float32x4.sub(S,SIMD.Float32x4.mul(e,s)),s=SIMD.Float32x4.mul(u,M),s=SIMD.Float32x4.swizzle(s,1,0,3,2),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),D),I=SIMD.Float32x4.sub(I,SIMD.Float32x4.mul(e,s)),s=SIMD.Float32x4.swizzle(s,2,3,0,1),D=SIMD.Float32x4.sub(D,SIMD.Float32x4.mul(i,s)),I=SIMD.Float32x4.add(SIMD.Float32x4.mul(e,s),I),SIMD.Float32x4.store(t,0,c),SIMD.Float32x4.store(t,4,D),SIMD.Float32x4.store(t,8,S),SIMD.Float32x4.store(t,12,I),t},o.adjoint=r.USE_SIMD?o.SIMD.adjoint:o.scalar.adjoint,o.determinant=function(t){var a=t[0],n=t[1],r=t[2],o=t[3],l=t[4],u=t[5],e=t[6],M=t[7],i=t[8],s=t[9],c=t[10],D=t[11],S=t[12],I=t[13],x=t[14],f=t[15],F=a*u-n*l,m=a*e-r*l,h=a*M-o*l,d=n*e-r*u,v=n*M-o*u,z=r*M-o*e,p=i*I-s*S,w=i*x-c*S,A=i*f-D*S,R=s*x-c*I,b=s*f-D*I,Y=c*f-D*x;return F*Y-m*b+h*R+d*A-v*w+z*p},o.SIMD.multiply=function(t,a,n){var r=SIMD.Float32x4.load(a,0),o=SIMD.Float32x4.load(a,4),l=SIMD.Float32x4.load(a,8),u=SIMD.Float32x4.load(a,12),e=SIMD.Float32x4.load(n,0),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,3,3,3,3),u))));SIMD.Float32x4.store(t,0,M);var i=SIMD.Float32x4.load(n,4),s=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,3,3,3,3),u))));SIMD.Float32x4.store(t,4,s);var c=SIMD.Float32x4.load(n,8),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,3,3,3,3),u))));SIMD.Float32x4.store(t,8,D);var S=SIMD.Float32x4.load(n,12),I=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,3,3,3,3),u))));return SIMD.Float32x4.store(t,12,I),t},o.scalar.multiply=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=a[9],S=a[10],I=a[11],x=a[12],f=a[13],F=a[14],m=a[15],h=n[0],d=n[1],v=n[2],z=n[3];return t[0]=h*r+d*e+v*c+z*x,t[1]=h*o+d*M+v*D+z*f,t[2]=h*l+d*i+v*S+z*F,t[3]=h*u+d*s+v*I+z*m,h=n[4],d=n[5],v=n[6],z=n[7],t[4]=h*r+d*e+v*c+z*x,t[5]=h*o+d*M+v*D+z*f,t[6]=h*l+d*i+v*S+z*F,t[7]=h*u+d*s+v*I+z*m,h=n[8],d=n[9],v=n[10],z=n[11],t[8]=h*r+d*e+v*c+z*x,t[9]=h*o+d*M+v*D+z*f,t[10]=h*l+d*i+v*S+z*F,t[11]=h*u+d*s+v*I+z*m,h=n[12],d=n[13],v=n[14],z=n[15],t[12]=h*r+d*e+v*c+z*x,t[13]=h*o+d*M+v*D+z*f,t[14]=h*l+d*i+v*S+z*F,t[15]=h*u+d*s+v*I+z*m,t},o.multiply=r.USE_SIMD?o.SIMD.multiply:o.scalar.multiply,o.mul=o.multiply,o.scalar.translate=function(t,a,n){var r,o,l,u,e,M,i,s,c,D,S,I,x=n[0],f=n[1],F=n[2];return a===t?(t[12]=a[0]*x+a[4]*f+a[8]*F+a[12],t[13]=a[1]*x+a[5]*f+a[9]*F+a[13],t[14]=a[2]*x+a[6]*f+a[10]*F+a[14],t[15]=a[3]*x+a[7]*f+a[11]*F+a[15]):(r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=a[9],S=a[10],I=a[11],t[0]=r,t[1]=o,t[2]=l,t[3]=u,t[4]=e,t[5]=M,t[6]=i,t[7]=s,t[8]=c,t[9]=D,t[10]=S,t[11]=I,t[12]=r*x+e*f+c*F+a[12],t[13]=o*x+M*f+D*F+a[13],t[14]=l*x+i*f+S*F+a[14],t[15]=u*x+s*f+I*F+a[15]),t},o.SIMD.translate=function(t,a,n){var r=SIMD.Float32x4.load(a,0),o=SIMD.Float32x4.load(a,4),l=SIMD.Float32x4.load(a,8),u=SIMD.Float32x4.load(a,12),e=SIMD.Float32x4(n[0],n[1],n[2],0);a!==t&&(t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t[9]=a[9],t[10]=a[10],t[11]=a[11]),r=SIMD.Float32x4.mul(r,SIMD.Float32x4.swizzle(e,0,0,0,0)),o=SIMD.Float32x4.mul(o,SIMD.Float32x4.swizzle(e,1,1,1,1)),l=SIMD.Float32x4.mul(l,SIMD.Float32x4.swizzle(e,2,2,2,2));var M=SIMD.Float32x4.add(r,SIMD.Float32x4.add(o,SIMD.Float32x4.add(l,u)));return SIMD.Float32x4.store(t,12,M),t},o.translate=r.USE_SIMD?o.SIMD.translate:o.scalar.translate,o.scalar.scale=function(t,a,n){var r=n[0],o=n[1],l=n[2];return t[0]=a[0]*r,t[1]=a[1]*r,t[2]=a[2]*r,t[3]=a[3]*r,t[4]=a[4]*o,t[5]=a[5]*o,t[6]=a[6]*o,t[7]=a[7]*o,t[8]=a[8]*l,t[9]=a[9]*l,t[10]=a[10]*l,t[11]=a[11]*l,t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.SIMD.scale=function(t,a,n){var r,o,l,u=SIMD.Float32x4(n[0],n[1],n[2],0);return r=SIMD.Float32x4.load(a,0),SIMD.Float32x4.store(t,0,SIMD.Float32x4.mul(r,SIMD.Float32x4.swizzle(u,0,0,0,0))),o=SIMD.Float32x4.load(a,4),SIMD.Float32x4.store(t,4,SIMD.Float32x4.mul(o,SIMD.Float32x4.swizzle(u,1,1,1,1))),l=SIMD.Float32x4.load(a,8),SIMD.Float32x4.store(t,8,SIMD.Float32x4.mul(l,SIMD.Float32x4.swizzle(u,2,2,2,2))),t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.scale=r.USE_SIMD?o.SIMD.scale:o.scalar.scale,o.rotate=function(t,a,n,o){var l,u,e,M,i,s,c,D,S,I,x,f,F,m,h,d,v,z,p,w,A,R,b,Y,q=o[0],y=o[1],E=o[2],g=Math.sqrt(q*q+y*y+E*E);return 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