Index: sm/trunk-jpl/packagers/ubuntu/README =================================================================== --- /issm/trunk-jpl/packagers/ubuntu/README (revision 18435) +++ (revision ) @@ -1,60 +1,0 @@ -TARBALL INSTALLATION: - -To install ISSM, untar ISSM-Ubuntu32.tar.gz -You will get an ISSM directory. - -You then need to setup the following environment variable in your -.bashrc or .cshrc: - -in your .bashrc: -export ISSM_TIER='path_to_untarred_ISSM/bin' - -or in your .cshrc: -setenv ISSM_TIER 'path_to_untarred_ISSM' - -Once this is done, fireup matlab from inside the ISSM directory: -matlab -nojvm -r "startup;" - - -UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION -------------------------------------------------------------------------------- - OR THE RIGHT WAY.... -DPKG/DEB INSTALLATION: - -To install from deb archives (*.deb), use: - - > sudo dpkg --install - -That's it! But not really. Do make sure that you install petsc and metis first. -When you first try to install issm, dpkg will tell you that you are missing -dependencies. Just: - - > sudo apt-get install -f - -to fix the dependencies and complete the install. When apt-get is done, you -should see something that says that ISSM is installed correctly on your -machine. That's it! For real this time. - -Uninstalling is simple too: - - > sudo apt-get remove - -That'll do all the work for you. This won't delete any configuration or user -defined environment stuff. Just swap "remove" out for "purge" and that'll -delete everything. And apt-get might ask you to remove unneeded dependencies, -so you should probably do that to keep your system clean. - -To create your own custom debian archive, see the README in issmpkg. - -------------------------------------------------------------------------------- - -APT-GET INSTALLATION: (this doesnot work yet) - -To install from apt-get: - - > sudo add-apt-repository - > sudo apt-get install - -Just say yes to everything apt asks you, and you're good. - -UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION Index: /issm/trunk-jpl/packagers/ubuntu/install.sh =================================================================== --- /issm/trunk-jpl/packagers/ubuntu/install.sh (revision 18436) +++ /issm/trunk-jpl/packagers/ubuntu/install.sh (revision 18436) @@ -0,0 +1,127 @@ +#!/bin/bash + +# ISSM_DIR and MATLAB_DIR must be set correctly. +# {{{ +if [ "${ISSM_DIR}x" == "x" ]; then + echo "ISSM_DIR is not set!" >&2 + exit 1; +elif [ -d ${ISSM_DIR} ]; then + echo "ISSM_DIR: ${ISSM_DIR}" +else + echo "ISSM_DIR: ${ISSM_DIR} does not exist!" >&2 + exit 1; +fi + +if [ "${MATLAB_DIR}x" == "x" ]; then + echo "MATLAB_DIR is not set!" + exit 1; +elif [ -d ${MATLAB_DIR} ]; then + echo "MATLAB_DIR: ${MATLAB_DIR}" +else + echo "MATLAB_DIR: ${MATLAB_DIR} does not exist!" >&2 + exit 1; +fi +# }}} + +#List of external pakages to be installed and their installation scripts +EXTERNALPACKAGES="autotools install.sh + cmake install.sh + petsc install-3.5-linux64-static.sh + triangle install-linux64.sh " + +# Install Externalpackages +# {{{ + +#Files source environment to make sure installed packages are in PATH +source $ISSM_DIR/etc/environment.sh + +#number of packages: +NUMPACKAGES=$(($(echo $EXTERNALPACKAGES | wc -w )/2)) + +for ((i=1;i<=$NUMPACKAGES;i++)) +do + NUM1=$((2*$i-1)) + NUM2=$((2*$i)) + PACKAGENAME=$(echo $EXTERNALPACKAGES | cut -d " " -f $NUM1-$NUM1) + PACKAGEINST=$(echo $EXTERNALPACKAGES | cut -d " " -f $NUM2-$NUM2) + + cd $ISSM_DIR/externalpackages/$PACKAGENAME + + if [[ $PACKAGEINST -nt install ]]; then + #go ahead and reinstall. + echo "Triggering new install of $PACKAGENAME" + install_test=1 + else + #ok, we want to skip, unless the package is not installed: + if [ -d install ]; then + #could be empty, signaling a failed previous install: + if [ "$(ls -A install)" ];then + echo "and install directory exists, so skipping install of $PACKAGENAME" + install_test=0; + else + echo "and install directory exists, however, it is empty, so triggering install of $PACKAGENAME" + install_test=1; + fi + else + echo "However, install directory does not exist, so triggering install of $PACKAGENAME" + install_test=1; + fi + fi + + if [[ $install_test == 1 ]]; then + echo "======================================================"; + echo " Installing $PACKAGENAME "; + echo "======================================================"; + ./$PACKAGEINST | tee compil.log + if [ $? -ne 0 ]; then + echo "======================================================"; + echo " ERROR: installation of $PACKAGENAME failed "; + echo "======================================================"; + #erase install directory, so that next time, we still try and compile this! + rm -rf install + fi + source $ISSM_DIR/etc/environment.sh + else + echo "======================================================"; + echo " Skipping install of $PACKAGENAME "; + echo "======================================================"; + fi + cd .. +done +# }}} + +# Compile ISSM +#{{{ +cd $ISSM_DIR +echo "Aureconf..." +autoreconf -if +echo "Configuring..." +./configure \ + --prefix=$ISSM_DIR \ + --disable-static \ + --enable-standalone-executables \ + --enable-standalone-libraries \ + --with-matlab-dir="/Applications/MATLAB_R2011b.app/" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/petsc/install/include \ + --with-mpi-libflags=" -L$ISSM_DIR/externalpackages/petsc/install/lib -lmpich -lmpl " \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.6/ -lgfortran" \ + --enable-debugging \ + --with-numthreads=4 + + +if [ $? -ne 0 ]; then echo "FAILED TO CONFIGURE!" && exit 1; fi + +echo "Building..." +make -j 8 +if [ $? -ne 0 ]; then echo "FAILED TO BUILD!" && exit 1; fi + +echo "Installing..." +make install +if [ $? -ne 0 ]; then echo "FAILED TO INSTALL!" && exit 1; fi +#}}} Index: /issm/trunk-jpl/packagers/ubuntu/package.sh =================================================================== --- /issm/trunk-jpl/packagers/ubuntu/package.sh (revision 18435) +++ /issm/trunk-jpl/packagers/ubuntu/package.sh (revision 18436) @@ -1,15 +1,31 @@ -#/bin/bash +#!/bin/bash -#Just tar gz the bin/ directory and test/ directory and put a startup.m file. +echo "modify generic" +cd $ISSM_DIR/bin +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 . -rm -rf ISSM ISSM-Ubuntu32.tar.gz +#Check that test101 runs +cd $ISSM_DIR/test/NightlyRun +rm matlab.log +$MATLAB_DIR/bin/matlab -nojvm -nosplash -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log -mkdir ISSM -cd ISSM -ln -s $ISSM_TIER/bin ./bin -ln -s $ISSM_TIER/test ./test -cp ../startup.m ./ -cp ../README.m ./ -cd .. -tar zcvfh ISSM-Ubuntu32.tar.gz --exclude='.svn' ./ISSM -rm -rf ISSM +if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then + echo "test101 FAILED" + exit 1; +else + echo "test101 passed" +fi + +tarball_name='issm-ubuntu-static_build.tar.gz' + +echo "Cleanup first" +cd $ISSM_DIR +rm $tarball_name + +echo "Creating tarball: ${tarball_name}" +cd $ISSM_DIR +tar -czf $tarball_name ./bin ./lib ./test ./examples +ls -lah $tarball_name Index: sm/trunk-jpl/packagers/ubuntu/startup.m =================================================================== --- /issm/trunk-jpl/packagers/ubuntu/startup.m (revision 18435) +++ (revision ) @@ -1,40 +1,0 @@ -%STARTUP - Matlab startup script -% -% startup.m is a script run by matlab at the beginning of a session, just -% before handing over the prompt to the user. This delivery startup.m script -% has been customized here for the ISSM code. This startup script should be -% run by users before trying to use ISSM. The best way to do that is to put -% the startup file in the location where Matlab starts and established its -% root directory. - -% clear the last warning to focus on the warnings of the ISSM path -lastwarn(''); - -%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN -ISSM_TIER=getenv('ISSM_TIER'); - -if (isempty(ISSM_TIER)), - error('issmdir error message: ''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); -end - -%Now add all issm code paths necessary to run issm smoothly. -%We capture the error output, so that we can warn the user to update -%the variable ISSM_TIER in this file, in case it is not correctly setup. - -%ISSM path -addpath(ISSM_TIER); -addpath([ISSM_TIER '/bin']); - -%Check on any warning messages that might indicate that the paths were not correct. -if ~isempty(lastwarn), - fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n'); - fprintf(' ''ISSM'' will not work at all until this is resolved\n\n'); -else - fprintf('\n To get started with ISSM, type issmdoc at the command prompt.\n\n'); -end - -%disable matlab bell! -beep off; - -% no warning if we try to plot while in nojvm (will not be supported in future releases) -warning off MATLAB:HandleGraphics:noJVM