Index: /issm/trunk-jpl/externalpackages/autotools/install-win.sh =================================================================== --- /issm/trunk-jpl/externalpackages/autotools/install-win.sh (revision 23392) +++ /issm/trunk-jpl/externalpackages/autotools/install-win.sh (revision 23393) @@ -2,47 +2,79 @@ set -eu -rm -rf install +AUTOCONF_VER="2.69" +AUTOMAKE_MIN_VER="1.16" +AUTOMAKE_BUILD_VER="${AUTOMAKE_MIN_VER}.1" +LIBTOOL_VER="2.4.2" +M4_VER="1.4.17" + +AUTOCONF="autoconf-${AUTOCONF_VER}" +AUTOMAKE="automake-${AUTOMAKE_BUILD_VER}" +LIBTOOL="libtool-${LIBTOOL_VER}" +M4="m4-${M4_VER}" + +AUTOCONF_TARBALL="${AUTOCONF}.tar.gz" +AUTOMAKE_TARBALL="${AUTOMAKE}.tar.gz" +LIBTOOL_TARBALL="${LIBTOOL}.tar.gz" +M4_TARBALL="${M4}.tar.gz" + +# Clean up existing assets +rm -rf install src + +# Set up for installation mkdir install - export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH" -#install autoconf -echo " === INSTALLING AUTOCONF ==" -rm -rf src -$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="$ISSM_DIR/externalpackages/autotools/install" -make +# Install m4 +echo " === INSTALLING M4 ==" +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${M4_TARBALL}" $M4_TARBALL +tar -zxvf $M4_TARBALL +rm -f $M4_TARBALL +mv $M4 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make make install cd .. -#install automake -echo " === INSTALLING AUTOMAKE ==" +# Install autoconf +echo " === INSTALLING AUTOCONF ==" 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 +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${AUTOCONF_TARBALL}" $AUTOCONF_TARBALL +tar -zxvf $AUTOCONF_TARBALL +rm -f $AUTOCONF_TARBALL +mv $AUTOCONF src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make make install cd .. -#install libtool -echo " === INSTALLING LIBTOOL ==" +# Install automake +echo " === INSTALLING AUTOMAKE ==" 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 +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${AUTOMAKE_TARBALL}" $AUTOMAKE_TARBALL +tar -zxvf $AUTOMAKE_TARBALL +rm -f $AUTOMAKE_TARBALL +mv $AUTOMAKE src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make make install cd .. -# This patch takes care of removing options passed to the linker that casuse +# Install libtool +echo " === INSTALLING LIBTOOL ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${LIBTOOL_TARBALL}" $LIBTOOL_TARBALL +tar -zxvf $LIBTOOL_TARBALL +rm -f $LIBTOOL_TARBALL +mv $LIBTOOL src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +# This patch takes care of removing options passed to the linker that causes # the build to fail, as well as changing some flags to match up to Microsoft # compilers. @@ -54,5 +86,5 @@ # This patch is for ar-lib, and removes carriage return characters that cause -# commands to overwrite themselves and be misinterpreted during linking on +# commands to overwrite themselves and be misinterpreted during linking on # Cygwin Windows. -patch ./install/share/automake-1.14/ar-lib < ./patches/ar-lib.patch +patch ./install/share/automake-${AUTOMAKE_MIN_VER}/ar-lib < ./patches/ar-lib.patch Index: /issm/trunk-jpl/externalpackages/gmsh/install-mac-precompiled.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-mac-precompiled.sh (revision 23393) +++ /issm/trunk-jpl/externalpackages/gmsh/install-mac-precompiled.sh (revision 23393) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +# Set gmsh version +GMSH_VER="3.0.5" + +# Set tarball name +GMSH_TARBALL_NAME="gmsh-${GMSH_VER}-mac-precompiled" + +# Clean up from previous installation +rm -f $GMSH_TARBALL_NAME.tar.gz +rm -rf install src + +# Download Mac precompiled gmsh from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${GMSH_TARBALL_NAME}.tar.gz" "${GMSH_TARBALL_NAME}.tar.gz" + +# Untar gmsh +tar -xvzf $GMSH_TARBALL_NAME.tar.gz + +# Copy gmsh to path expected by packager +mkdir install +cp gmsh install +rm gmsh Index: /issm/trunk-jpl/externalpackages/gmsh/install-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-static.sh (revision 23392) +++ /issm/trunk-jpl/externalpackages/gmsh/install-static.sh (revision 23393) @@ -27,5 +27,5 @@ #Configure cd install -cmake ../src -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/gmsh/install" -DENABLE_MPI=0 -DENABLE_METIS=0 +cmake ../src -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/gmsh/install" -DENABLE_METIS=0 #Compile and install Index: /issm/trunk-jpl/externalpackages/gmsh/install-win64-precompiled.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-win64-precompiled.sh (revision 23393) +++ /issm/trunk-jpl/externalpackages/gmsh/install-win64-precompiled.sh (revision 23393) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +# Set gmsh version +VER="3.0.5" + +# Set tarball name +TARBALL_NAME="gmsh-${VER}-win64-precompiled" +TARBALL=${TARBALL_NAME}.tar.gz + +# Clean up from previous installation +rm -rf install + +# Download Windows 64-bit precompiled gmsh from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${TARBALL}" "${TARBALL}" + +# Untar gmsh +tar -xvzf $TARBALL + +# Rename untarred dir +mv $TARBALL_NAME install + +# Clean up +rm -f $TARBALL Index: /issm/trunk-jpl/externalpackages/gmt/install-mac-precompiled.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-mac-precompiled.sh (revision 23393) +++ /issm/trunk-jpl/externalpackages/gmt/install-mac-precompiled.sh (revision 23393) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +# Set gmt version +VER="5.4.4" + +# Set tarball name +TARBALL_NAME="gmt-${VER}-mac-precompiled" +TARBALL=${TARBALL_NAME}.tar.gz + +# Clean up from previous installation +rm -rf install + +# Download Mac precompiled gmsh from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${TARBALL}" "${TARBALL}" + +# Untar gmt +tar -xvzf $TARBALL + +# Rename untarred dir +mv $TARBALL_NAME install + +# Clean up +rm -f $TARBALL Index: /issm/trunk-jpl/externalpackages/gmt/install-win64-precompiled.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-win64-precompiled.sh (revision 23393) +++ /issm/trunk-jpl/externalpackages/gmt/install-win64-precompiled.sh (revision 23393) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +# Set gmt version +VER="5.4.4" + +# Set tarball name +TARBALL_NAME="gmt-${VER}-win64-precompiled" +TARBALL=${TARBALL_NAME}.tar.gz + +# Clean up from previous installation +rm -rf install + +# Download Windows 64-bit precompiled gmsh from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${TARBALL}" "${TARBALL}" + +# Untar gmt +tar -xvzf $TARBALL + +# Rename untarred dir +mv $TARBALL_NAME install + +# Clean up +rm -f $TARBALL Index: /issm/trunk-jpl/externalpackages/mpich/install-3.2-linux64-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/mpich/install-3.2-linux64-static.sh (revision 23392) +++ /issm/trunk-jpl/externalpackages/mpich/install-3.2-linux64-static.sh (revision 23393) @@ -9,5 +9,5 @@ $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.2.tar.gz' 'mpich-3.2.tar.gz' -#Untar +#Untar tar -zxvf mpich-3.2.tar.gz @@ -19,5 +19,9 @@ cd src ./configure \ - --prefix="$ISSM_DIR/externalpackages/mpich/install" + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --disable-shared \ + --enable-strict=all \ + --enable-fast \ + --with-pic #Compile mpich (this new version supports parallel make) @@ -27,3 +31,4 @@ make -j $1 fi -make install + +make install Index: /issm/trunk-jpl/externalpackages/mpich/install-3.2-linux64.sh =================================================================== --- /issm/trunk-jpl/externalpackages/mpich/install-3.2-linux64.sh (revision 23392) +++ /issm/trunk-jpl/externalpackages/mpich/install-3.2-linux64.sh (revision 23393) @@ -9,5 +9,5 @@ $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.2.tar.gz' 'mpich-3.2.tar.gz' -#Untar +#Untar tar -zxvf mpich-3.2.tar.gz @@ -28,3 +28,3 @@ make -j $1 fi -make install +make install Index: /issm/trunk-jpl/externalpackages/petsc/install-3.7-linux64-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.7-linux64-static.sh (revision 23392) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.7-linux64-static.sh (revision 23393) @@ -18,16 +18,18 @@ ./config/configure.py \ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-single-library=1 \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-shared-libraries=0 \ + --with-debugging=0 \ --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-shared-libraries=0 \ + --download-fblaslapack=1 \ --download-metis=1 \ --download-parmetis=1 \ + --with-x=0 \ + --download-scalapack=1 \ --download-mumps=1 \ - --download-fblaslapack=1 \ - --download-scalapack=1 \ + --with-ssl=0 \ + --with-valgrind=0 \ + --with-pic=1 \ --COPTFLAGS="-fPIC" \ --CXXOPTFLAGS="-fPIC" \ Index: /issm/trunk-jpl/jenkins/linux64_ross_static =================================================================== --- /issm/trunk-jpl/jenkins/linux64_ross_static (revision 23392) +++ /issm/trunk-jpl/jenkins/linux64_ross_static (revision 23393) @@ -7,22 +7,22 @@ MATLAB_PATH="/usr/local/MATLAB/R2015a" -#ISSM CONFIGURATION +#ISSM CONFIGURATION ISSM_CONFIG='--prefix=$ISSM_DIR \ - --disable-static \ --enable-standalone-executables \ + --enable-standalone-modules \ --enable-standalone-libraries \ - --enable-standalone-modules \ --with-matlab-dir=$MATLAB_PATH \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpifort" \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mpi-libflags="$ISSM_DIR/externalpackages/mpich/install/lib/libmpifort.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpi.a -lrt -lpthread" \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \ + --with-pic \ --with-numthreads=4' @@ -52,8 +52,8 @@ #number of cpus used in ISSM installation and compilation (one is usually #safer as some packages are very sensitive to parallel compilation) -NUMCPUS_INSTALL=4 +NUMCPUS_INSTALL=10 #number of cpus used in the nightly runs. -NUMCPUS_RUN=2 +NUMCPUS_RUN=10 #Nightly run options. The matlab routine runme.m will be called @@ -61,5 +61,5 @@ #by Matlab and runme.m #ex: "'id',[101 102 103]" -## FS +## FS #PYTHON_NROPTIONS="--exclude_name 'Dakota'" #MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]" Index: /issm/trunk-jpl/jenkins/macosx_pine-island_static =================================================================== --- /issm/trunk-jpl/jenkins/macosx_pine-island_static (revision 23392) +++ /issm/trunk-jpl/jenkins/macosx_pine-island_static (revision 23393) @@ -14,5 +14,5 @@ --with-matlab-dir=$MATLAB_PATH \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich -lmpl -lpmpich" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -23,6 +23,5 @@ --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \ - --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a /usr/local/gfortran/lib/libquadmath.a /usr/local/gfortran/lib/gcc/x86_64-apple-darwin14/5.2.0/libgcc.a" \ - --with-numthreads=4' + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a /usr/local/gfortran/lib/libquadmath.a /usr/local/gfortran/lib/gcc/x86_64-apple-darwin14/5.2.0/libgcc.a"' #PYTHON and MATLAB testing @@ -35,13 +34,14 @@ #List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES="autotools install.sh - cmake install.sh - mpich install-3.0-macosx64-static.sh - m1qn3 install.sh - petsc install-3.6-macosx64-static.sh - triangle install-macosx64.sh - math77 install.sh - gmsh install-static.sh - shell2junit install.sh" +EXTERNALPACKAGES="autotools install.sh + cmake install.sh + mpich install-3.0-macosx64-static.sh + m1qn3 install.sh + petsc install-3.6-macosx64-static.sh + triangle install-macosx64.sh + math77 install.sh + gmt install-mac-precompiled.sh + gmsh install-mac-precompiled.sh + shell2junit install.sh" #for SLR we need gmsh to mesh, math77, and gmt (which itself needs gdal and netcdf...) @@ -62,4 +62,4 @@ #ex: "'id',[101 102 103]" ## bamg mesh FS -#PYTHON_NROPTIONS="--exclude_name 'Dakota'" -#MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,435,IdFromString('Dakota')]" +#PYTHON_NROPTIONS="" +#MATLAB_NROPTIONS="" Index: /issm/trunk-jpl/jenkins/windows =================================================================== --- /issm/trunk-jpl/jenkins/windows (revision 23392) +++ /issm/trunk-jpl/jenkins/windows (revision 23393) @@ -7,5 +7,5 @@ MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a/" -#ISSM CONFIGURATION +#ISSM CONFIGURATION ISSM_CONFIG='--prefix=$ISSM_DIR \ --with-vendor=MSVC-Win64 \ @@ -41,5 +41,5 @@ petsc install-3.6-win10.sh metis install-4.0-win10.sh - triangle install-win10.sh + triangle install-win10.sh shell2junit install.sh" @@ -50,8 +50,8 @@ #number of cpus used in ISSM installation and compilation (one is usually #safer as some packages are very sensitive to parallel compilation) -NUMCPUS_INSTALL=6 +NUMCPUS_INSTALL=8 #number of cpus used in the nightly runs. -NUMCPUS_RUN=2 +NUMCPUS_RUN=8 #Nightly run options. The matlab routine runme.m will be called Index: /issm/trunk-jpl/jenkins/windows_static =================================================================== --- /issm/trunk-jpl/jenkins/windows_static (revision 23393) +++ /issm/trunk-jpl/jenkins/windows_static (revision 23393) @@ -0,0 +1,65 @@ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#MATLAB path +MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a/" + +#ISSM CONFIGURATION +ISSM_CONFIG='--prefix=$ISSM_DIR \ + --disable-static \ + --enable-standalone-executables \ + --enable-standalone-libraries \ + --with-matlab-dir=$MATLAB_PATH \ + --with-vendor=MSVC-Win64 \ + --with-fortran=no \ + --without-GiaIvins \ + --without-Love \ + --without-kriging \ + --without-kml \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib \ + --with-mpi-libdir=$ISSM_DIR/externalpackages/petsc/install/lib \ + --with-mpi-libflags="-Wl,libpetsc.lib" \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \ + --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include/petsc/mpiuni" \ + --with-cxxoptflags="-fp:strict"' + +#PYTHON and MATLAB testing +MATLAB_TEST=0 +PYTHON_TEST=0 + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#List of external pakages to be installed and their installation scripts +EXTERNALPACKAGES="autotools install-win.sh + petsc install-3.6-win10.sh + metis install-4.0-win10.sh + triangle install-win10.sh + math77 install.sh + gmt install-win64-precompiled.sh + gmsh install-win64-precompiled.sh + shell2junit install.sh" + +#-----------------# +# 4: test options # +#-----------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=8 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=8 + +#Nightly run options. The matlab routine runme.m will be called +#as follows: runme($MATLAB_NROPTIONS). The options must be understandable +#by Matlab and runme.m +#ex: "'id',[101 102 103]" +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk-jpl/packagers/macosx/package.sh =================================================================== --- /issm/trunk-jpl/packagers/macosx/package.sh (revision 23392) +++ /issm/trunk-jpl/packagers/macosx/package.sh (revision 23393) @@ -1,11 +1,28 @@ #!/bin/bash -echo "modify generic" +TARBALL_NAME='issm-mac-static_build' +TARBALL=$TARBALL_NAME.tar.gz + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd $ISSM_DIR +rm -rf trunk +mkdir trunk + +# Add/modify required binaries cd $ISSM_DIR/bin + +echo "Modifying generic" cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m -echo "move mpiexec to bin" -cp ../externalpackages/mpich/install/bin/mpiexec . -cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy . -echo "move gmsh to bin" + +echo "Moving mpiexec to bin" +if [ -f ../externalpackages/mpich/install/bin/mpiexec ]; then + cp ../externalpackages/mpich/install/bin/mpiexec . + cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "mpich not found" +fi + +echo "Moving gmsh to bin" if [ -f ../externalpackages/gmsh/install/gmsh ]; then cp ../externalpackages/gmsh/install/gmsh . @@ -14,5 +31,16 @@ fi -#Check that test101 runs +# Copy gmt to trunk +# NOTE: The following assumes the precompiled version of gmt +echo "Moving gmt to externalpackages" +if [ -f $ISSM_DIR/externalpackages/gmt/install/bin/gmt ]; then + mkdir $ISSM_DIR/trunk/externalpackages + mkdir $ISSM_DIR/trunk/externalpackages/gmt + cp -a $ISSM_DIR/externalpackages/gmt/install/. $ISSM_DIR/trunk/externalpackages/gmt +else + echo "gmt not found" +fi + +# Check that test101 runs cd $ISSM_DIR/test/NightlyRun rm matlab.log @@ -26,17 +54,19 @@ fi -tarball_name='issm-mac-static_build.tar.gz' +echo "Creating tarball: ${TARBALL_NAME}" +cd $ISSM_DIR +rm -f $TARBALL +cp -rf bin lib test examples scripts trunk/ -echo "Cleanup first" +# Create link to gmt from bin +# NOTE: It is important that we are in the destination dir when sym linking so that the path is relative +if [ -f $ISSM_DIR/trunk/externalpackages/gmt/bin/gmt ]; then + cd $ISSM_DIR/trunk/bin + ln -s ../externalpackages/gmt/bin/gmt ./gmt +fi + cd $ISSM_DIR -rm $tarball_name - -echo "Creating tarball: ${tarball_name}" -cd $ISSM_DIR -rm -rf trunk -mkdir trunk -cp -rf bin lib test examples scripts trunk/ -tar -czf $tarball_name trunk -ls -lah $tarball_name +tar -czf $TARBALL trunk +ls -lah $TARBALL echo "Shipping binaries to website" @@ -56,5 +86,5 @@ ssh-add ~/.ssh/macosx-bins_richese-to-ross -scp $tarball_name ross.ics.uci.edu:/var/www/html/$tarball_name +scp $TARBALL ross.ics.uci.edu:/var/www/html/$TARBALL if [ $? -ne 0 ]; then Index: /issm/trunk-jpl/packagers/win10/package64.sh =================================================================== --- /issm/trunk-jpl/packagers/win10/package64.sh (revision 23393) +++ /issm/trunk-jpl/packagers/win10/package64.sh (revision 23393) @@ -0,0 +1,106 @@ +#!/bin/bash + +TARBALL_NAME='ISSM-Win10-64' +TARBALL=$TARBALL_NAME.tar.gz +MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a" + +# Source Windows environment +source $ISSM_DIR/externalpackages/windows/windows_environment.sh + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd $ISSM_DIR +rm -rf trunk +mkdir trunk + +# Add/modify required binaries +cd $ISSM_DIR/bin + +echo "Making generic_static.m work like generic.m" +cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m + +echo "Copying scripts from /src to /bin" +rm $ISSM_DIR/bin/*.m +find $ISSM_DIR/src/m -name '*.m' | xargs cp -t $ISSM_DIR/bin + +echo "Copying gmsh to bin" +if [ -f ../externalpackages/gmsh/install/gmsh.exe ]; then + cp ../externalpackages/gmsh/install/gmsh.exe . +else + echo "gmsh not found" +fi + +# Copy gmt to trunk +# NOTE: The following assumes the precompiled version of gmt +echo "Moving gmt to externalpackages" +if [ -f $ISSM_DIR/externalpackages/gmt/install/bin/gmt ]; then + mkdir $ISSM_DIR/trunk/externalpackages + mkdir $ISSM_DIR/trunk/externalpackages/gmt + cp -a $ISSM_DIR/externalpackages/gmt/install/. $ISSM_DIR/trunk/externalpackages/gmt +else + echo "gmt not found" +fi + +# Check that test 101 runs +cd $ISSM_DIR/test/NightlyRun +rm matlab.log +$MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "try, addpath $ISSM_DIR_WIN/bin $ISSM_DIR_WIN/lib; runme('id',101); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log + +# Wait until MATLAB closes +sleep 5 +pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}') +while [ -n "$pid" ] +do + pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}') + sleep 1 +done + +if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then + echo "test101 FAILED" + exit 1; +else + echo "test101 passed" +fi + +# Create tarball +echo "Creating tarball: ${TARBALL_NAME}" +cd $ISSM_DIR +rm -f $TARBALL +cp -rf bin lib test examples scripts trunk/ + +# Create link to gmt from bin +# NOTE: It is important that we are in the destination dir when sym linking so that the path is relative +if [ -f $ISSM_DIR/trunk/externalpackages/gmt/bin/gmt ]; then + cd $ISSM_DIR/trunk/bin + ln -s ../externalpackages/gmt/bin/gmt.exe ./gmt +fi + +cd $ISSM_DIR +tar -czf $TARBALL trunk +ls -lah $TARBALL + +# Ship binaries to website +echo "Shipping binaries to website" + +# We're using public key authentication method to upload the tarball The +# following lines check to see if the SSH Agent is running. If not, then it is +# started and relevant information is forwarded to a script. +pgrep "ssh-agent" > /dev/null + +if [ $? -ne 0 ]; then + echo "SSH agent is not running. Starting it..." + ssh-agent > ~/.ssh/agent.sh +else + echo "SSH agent is running..." +fi + +source ~/.ssh/agent.sh +ssh-add ~/.ssh/win_bins-geidi_prime_to_ross + +scp $TARBALL jenkins@ross.ics.uci.edu:/var/www/html/$TARBALL + +if [ $? -ne 0 ]; then + echo "The upload failed." + echo "Perhaps the SSH agent was started by some other means." + echo "Try killing the agent and running again." +fi Index: /issm/trunk-jpl/scripts/DownloadExternalPackage.py =================================================================== --- /issm/trunk-jpl/scripts/DownloadExternalPackage.py (revision 23392) +++ /issm/trunk-jpl/scripts/DownloadExternalPackage.py (revision 23393) @@ -1,139 +1,37 @@ #!/usr/bin/env python # -*- coding: ISO-8859-1 -*- -# -# TODO: Improve upon extension recognition by checking for mismatches in found targets -# and specified local file. -# -# imports {{{ -import os,sys,re +import os,sys import urllib -from HTMLParser import HTMLParser -from urllib import FancyURLopener -# }}} -class MyHTMLParser(HTMLParser): #{{{ - def __init__(self, pattern): - HTMLParser.__init__(self) - self.matcher = re.compile(pattern) - self.targets = [] +#Check inputs +if(len(sys.argv)!=3): raise NameError('usage: ./DownloadExternalPackage.py URL localfile') - def handle_starttag(self, tag, attrs): - for i in attrs: - if "href" == i[0] and str(self.matcher.match(i[1])) != "None": - self.targets.append(i[1]) -#}}} -def main(argv=None): # {{{ - # Separates the URL into a directory and the file or pattern based on the - # last appearance of '/'. - if len(sys.argv) > 1: - pivot = sys.argv[1].rfind("/") - url = (sys.argv[1])[:pivot] - pivot += 1 - find = (sys.argv[1])[pivot:] - else: - print "******************************************************************************************************************************" - print "* Invalid input! *" - print "* *" - print "* Try: 'DownloadExternalPackage.py url [localFile]' *" - print "* *" - print "* Where 'URL' is the URL with an explicit package name or the URL followed by the truncated package name. And 'localFile' is *" - print "* the file name (including extension) that you would like to save as. *" - print "* *" - print "* Examples: *" - print "* *" - print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' *" - print "* *" - print "* This is the old style and the safest way to download a package. *" - print "* *" - print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool' 'libtool.tar.gz' *" - print "* *" - print "* This is the new style. For packages like 'Libtool', which we never expect to be using multiple versions, this will *" - print "* download the most recent version and save it as the generic 'libtool.tar.gz'. *" - print "* *" - print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.' 'gsl-1.15.tar.gz' *" - print "* *" - print "* This is the new style. This is a demonstration of how this script can be used to disambiguate a package name if there *" - print "* are more than once package matching 'gsl-'. *" - print "* *" - print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool' *" - print "* *" - print "* This is the new style. This will download a package with 'libtool' as a prefix and save it as its canonical name. *" - print "* *" - print "* *" - print "******************************************************************************************************************************" - - if len(sys.argv) > 2: - localFile=sys.argv[2] - print "Downloaded file will be saved as: " + localFile - else: - localFile = None - print "Downloaded file will saved with the same file name." - - - print "Looking for: " + find - - # As an extra precaution, if no extension is given for a particular package - # such as '.../libtool', then ensure that files found are of appropriate - # file extensions. - # - # WARNING: The external packages directory includes executable binaries with - # '.exe' extensions. As such, '.exe' is an acceptable suffix, but this is - # inherently dangerous since this script can be used to download from any - # valid website. Furthermore, if an individual attempts a "man-in-the-middle" - # attack, then the user would be capable of downloading executables from - # an untrusted source. - pattern = find + "[\w.-]*(\.tar\.gz|tar\.gz2|tgz|zip|exe)?" - parser = MyHTMLParser(pattern) - - # Creates a 'FancyURL' which allows the script to fail gracefully by catching - # HTTP error codes 30X and several 40X(where 'X' is a natural number). - urlObject = FancyURLopener() - obj = urlObject.open(url) - parser.feed(obj.read()) - - # If a file pattern was used to describe the file that should be downloaded, - # then there is the potential for multiple file matches. Currently, the script - # will detect this ambiguity and print out all the matches, while informing - # the user that he must refine his search. - # - # TODO: Prompt the user to select from a list his/her preferred target. - if len(parser.targets) > 1: - print "Could not resolve your download due to the number of hits." - print "Refine your search." - for i in parser.targets: - print i - - elif len(parser.targets) == 1: - print "Found: " + parser.targets[0] - url += "/" + parser.targets[0] - - if localFile is None: - if os.path.exists(parser.targets[0]): - print "File " + parser.targets[0] + " already exists and will not be downloaded..." - else: - urllib.urlretrieve(url, parser.targets[0]) - print "File saved as: " + parser.targets[0] - else: - if os.path.exists(localFile): - print "File "+ localFile +" already exists and will not be downloaded..." - else: - if parser.targets[0] == localFile: - print "File found and destination match." - elif parser.matcher.match(localFile) != "None": - print "File found matches destination pattern." - else: - print "WARNING: the file found \'" + parser.targets[0] + "\' does not match \'" + localFile + "\'" - print "Ensure the downloaded version is suitable." - - urllib.urlretrieve(url, localFile) - print "File saved as: " + localFile - - else: - print "No matches found!" - - obj.close() -# End 'main' function. }}} +url=sys.argv[1]; +localFile=sys.argv[2] -if __name__ == "__main__": - main() +#Remove file if it already exists +if os.path.exists(localFile): + print "File "+ localFile +" already exists and will not be downloaded..." + sys.exit() + +#Try to download from url +httpfail=-1 +try: + print "Fetching %s" % localFile + urllib.urlretrieve(url,localFile) + httpfail=0 +except Exception, e: + httpfail=1 + +#Error message in case it failed +if (httpfail): + failureMessage = ''' +=========================================================================== +Unable to download package %s from: %s +* If URL specified manually - perhaps there is a typo? +* If your network is disconnected - please reconnect +* Alternatively, you can download the above URL manually +=========================================================================== +''' % (localFile,url) + raise RuntimeError(failureMessage) Index: sm/trunk-jpl/scripts/DownloadExternalPackage2.py =================================================================== --- /issm/trunk-jpl/scripts/DownloadExternalPackage2.py (revision 23392) +++ (revision ) @@ -1,37 +1,0 @@ -#!/usr/bin/env python -# -*- coding: ISO-8859-1 -*- - -import os,sys -import urllib - -#Check inputs -if(len(sys.argv)!=3): raise NameError('usage: ./DownloadExternalPackage.py URL localfile') - -url=sys.argv[1]; -localFile=sys.argv[2] - -#Remove file if it already exists -if os.path.exists(localFile): - print "File "+ localFile +" already exists and will not be downloaded..." - sys.exit() - -#Try to download from url -httpfail=-1 -try: - print "Fetching %s" % localFile - urllib.urlretrieve(url,localFile) - httpfail=0 -except Exception, e: - httpfail=1 - -#Error message in case it failed -if (httpfail): - failureMessage = ''' -=========================================================================== -Unable to download package %s from: %s -* If URL specified manually - perhaps there is a typo? -* If your network is disconnected - please reconnect -* Alternatively, you can download the above URL manually -=========================================================================== -''' % (localFile,url) - raise RuntimeError(failureMessage) Index: /issm/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp (revision 23392) +++ /issm/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp (revision 23393) @@ -80,5 +80,5 @@ /*launch the thread manager with InterpFromGridToMeshxt as a core: */ LaunchThread(InterpFromGridToMeshxt,(void*)&gate,_NUMTHREADS_); - _printf_("\r interpolation progress: "<