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adding instructions for compiling "with-ocean"
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‎test/MITgcm/documents/READMEissm‎

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# In order to install ISSM, the Ice Sheet System Model,
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# download from the svn repository:
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svn co https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl
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# If you have an already existing trunk-jpl installation,
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# you can symlink to it:
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ln -s PATH_TO_TRUNK_JPL ./trunk-jpl
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# Then follow instructions in:
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# http://issm.jpl.nasa.gov/download/unix/
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# =========
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# Installation instructions on macOS Mojave 10.14.4
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* create an ISSM_DIR in you bashrc and source it
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export ISSM_DIR="/Users/XXX/issm/trunk-jpl/"
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source "$ISSM_DIR"/etc/environment.sh
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* checkout empty issm directory:
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svn co --username=username --depth=empty http://issm.ess.uci.edu/svn/issm/issm issm
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* get jpl trunk (development branch) in issm directory:
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svn update trunk-jpl
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* get xcode
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* install command line xcode
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xcode-select --install
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* install gfortran binaries: on https://gcc.gnu.org/wiki/GFortranBinaries#MacOS
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* use the first one on git (https://github.com/fxcoudert/gfortran-for-macOS/releases)
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* Install Matlab
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* In ~/matlab/startup.m add:
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% ISSM paths
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ISSM_DIR=getenv('ISSM_DIR');
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if length(ISSM_DIR)>0
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addpath([ISSM_DIR '/bin/']);
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addpath([ISSM_DIR '/lib/'],[ISSM_DIR '/scripts']);
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addpath([ISSM_DIR '/src/m/dev']);
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devpath;
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end
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* in ISSM, install the following external packages (so in trunk-jpl/externalpackages) in this order:
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- autotools
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- mpich (version 3.2 macosx64)
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- cmake
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- petsc (version 3.9 macosx64)
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- m1qn3
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- triangle
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between each package installed you should source the environment
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source $ISSM_DIR/etc/environment.sh
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* Reconfigure ISSM:
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cd $ISSM_DIR
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autoreconf -ivf
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* Create a configure.sh file in $ISSM_DIR with the following lines (adjust the paths if need be):
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#!/bin/bash
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./configure \
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--prefix=$ISSM_DIR \
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--with-matlab-dir="/Applications/MATLAB_R2018b.app/" \
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--with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
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--with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \
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--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \
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--with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
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--with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
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--with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \
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--with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \
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--with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
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--with-ocean="yes" \
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--with-numthreads=4 \
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--enable-development \
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--enable-debugging
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* Configure ISSM in $ISSM_DIR:
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./configure.sh
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* Compile ISSM in $ISSM_DIR:
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make -j8
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make install
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# =========
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# Installation instructions on macOS High Sierra 10.13.6
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# Install Xcode from Mac App Store then
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xcode-select --install
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# Install gfrotran 5.2
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# https://gcc.gnu.org/wiki/GFortranBinaries
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# http://coudert.name/software/gfortran-5.2-Yosemite.dmg
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# Install cmake-3.4.0
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# https://cmake.org/download/
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# https://cmake.org/files/v3.4/cmake-3.4.0-Darwin-x86_64.dmg
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cd /usr/local/bin
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sudo ln -sf /Applications/Utilities/CMake.app/Contents/bin/cmake .
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# In .bashrc add:
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# export ISSM_DIR='/PUT_FULL_ISSM_PATHNAME_HERE/trunk-jpl'
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# source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR
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svn up
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source $ISSM_DIR/etc/environment.sh
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cd externalpackages
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mkdir matlab
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cd matlab
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ln -sf /Applications/MATLAB_R2016b.app install
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# add 10.13 lines similar to 10.10 lines in
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# /Applications/MATLAB_R2015b.app/bin/maci64/mexopts/*.xml
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# http://issm.jpl.nasa.gov/documentation/faq/matlab/
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cp /Applications/MATLAB_R2016b.app/bin/.matlab7rc.sh ~
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# under mac|maci|maci64)
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# change: # LDPATH_PREFIX='$MATLAB/sys/opengl/lib/$ARCH'
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# to: LDPATH_PREFIX='/usr/local/gfortran/lib'
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# In ~/matlab/startup.m add:
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# % ISSM paths
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# ISSM_DIR=getenv('ISSM_DIR');
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# if length(ISSM_DIR)>0
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# addpath([ISSM_DIR '/bin/']);
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# addpath([ISSM_DIR '/lib/'],[ISSM_DIR '/scripts']);
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# addpath([ISSM_DIR '/src/m/dev']);
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# devpath;
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# end
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cd ../autotools/
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./install.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../mpich
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install-3.2-macosx64.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../petsc
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install-3.9-macosx64.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../triangle
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install-macosx64.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../m1qn3
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install.sh
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source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR
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autoreconf -ivf
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../config-macosx64-nodakota.sh
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make -j 8 install
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# =========
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# Installation instructions on Mac OS X El Capitan 10.11.1
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# Install gfrotran 5.2
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# https://gcc.gnu.org/wiki/GFortranBinaries
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# http://coudert.name/software/gfortran-5.2-Yosemite.dmg
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# Install cmake-3.4.0
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# https://cmake.org/download/
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# https://cmake.org/files/v3.4/cmake-3.4.0-Darwin-x86_64.dmg
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cd /usr/local/bin
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sudo ln -sf /Applications/Utilities/CMake.app/Contents/bin/cmake .
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# In .bashrc add:
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# export ISSM_DIR='/PUT_FULL_ISSM_PATHNAME_HERE/trunk-jpl'
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# source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR
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svn up
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source $ISSM_DIR/etc/environment.sh
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cd externalpackages/matlab
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ln -sf /Applications/MATLAB_R2015b.app install
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# replace 10.10 with 10.11 in
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# /Applications/MATLAB_R2015b.app/bin/maci64/mexopts/*.xml
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# http://issm.jpl.nasa.gov/documentation/faq/matlab/
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cp /Applications/MATLAB_R2015b.app/bin/.matlab7rc.sh ~
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# under mac|maci|maci64)
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# change: # LDPATH_PREFIX='$MATLAB/sys/opengl/lib/$ARCH'
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# to: LDPATH_PREFIX='/usr/local/gfortran/lib'
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# In ~/matlab/startup.m add:
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# % ISSM paths
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# ISSM_DIR=getenv('ISSM_DIR');
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# if length(ISSM_DIR)>0
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# addpath([ISSM_DIR '/bin/'],[ISSM_DIR '/lib/']);
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# addpath([ISSM_DIR '/scripts'],[ISSM_DIR '/src/m/dev']);
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# devpath;
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# end
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cd ../autotools/
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./install.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../mpich
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install-3.0-macosx64-elcapitan.sh 8
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source $ISSM_DIR/etc/environment.sh
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cd ../petsc
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install-3.6-macosx64.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../triangle
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install-macosx64.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../m1qn3
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install.sh
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source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR
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./scripts/automakererun.sh
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../config-macosx64-nodakota.sh
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make -j 8 install
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#=========
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Installation instructions on skylla
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# In .bashrc add:
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# export ISSM_DIR=$SLR_DIR/components/issm/trunk-jpl
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# source $ISSM_DIR/etc/environment.sh
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# export ISSM_ARCH="linux-gnu-amd64"
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# make sure you are in the bash shell
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bash
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cd $ISSM_DIR
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#svn up -r 17578
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source $ISSM_DIR/etc/environment.sh
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cd externalpackages/matlab
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ln -sf /usr/local/matlab.2010b install
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cd ../autotools/
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./install.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../cmake
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./install.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../mpich
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./install-3.0-linux64.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../petsc
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./install-3.4-linux64.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../tao
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svn up
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./install-2.2.sh
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source $ISSM_DIR/etc/environment.sh
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cd ../triangle
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./install-linux64.sh
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source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR
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./scripts/automakererun.sh
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./configs/config-linux64-skylla.sh
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make -j 8 install
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# In ~/matlab/startup.m add:
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# ISSM_DIR=getenv('ISSM_DIR');
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# addpath([ISSM_DIR '/bin/'],[ISSM_DIR '/lib/'],[ISSM_DIR '/scripts']);
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# Install ISSM: https://issm.jpl.nasa.gov/download/
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# get Xcode
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# install command line xcode
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xcode-select --install
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# get ISSM repo
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cd
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mkdir issm
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cd issm
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git clone [email protected]:ISSMteam/ISSM.git
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# add to ~/.zshrc
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export ISSM_DIR='/Users/dmenemen/issm/ISSM'
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source $ISSM_DIR/etc/environment.sh
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# https://issm.jpl.nasa.gov/download/unix/
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cd $ISSM_DIR/externalpackages/autotools
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install-mac.sh
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source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR/externalpackages/cmake
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install.sh
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source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR/externalpackages/petsc
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install-3.22-mac.sh
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source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR/externalpackages/triangle
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install-mac.sh
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source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR/externalpackages/m1qn3
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install-mac.sh
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source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR
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autoreconf -ivf
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# create configure.sh as per instructions
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# or get from test/MITgcm/documents/config-macOS-arm64.sh
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cd $ISSM_DIR
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cp test/MITgcm/documents/config-macOS-arm64.sh configure.sh
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chmod a+x configure.sh
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./configure.sh
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make
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make install

‎test/MITgcm/documents/config-macOS-arm64.sh‎

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./configure \
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--prefix=${ISSM_DIR} \
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--with-numthreads=2 \
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--with-matlab-dir="/Applications/MATLAB_R2025a.app" \
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--with-fortran-lib="-L/opt/homebrew/Cellar/gcc/15.1.0/lib/gcc/current -lgfortran" \
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--with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \
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--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
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--with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
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--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
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--with-ocean="yes"

‎test/MITgcm/documents/config-macosx64-devel-triton.sh‎

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