Getting an account

You automatically have access to the Babylon machine if you are part of Dartmouth's Thayer School of Engineering. To request access to Amundsen, please send an email to Helene Seroussi.

ssh configuration

Babylon is actually a cluster of 12 independent servers, so you need to first choose on which one you are going to log in. The status of the cluster usage can be found here : ​https://cluster-usage.thayer.dartmouth.edu/.

You can add the following lines to ~/.ssh/config on your local machine:

Host babylon babylon?.thayer.dartmouth.edu
   Hostname babylon?.thayer.dartmouth.edu
   User USERNAME

and replace USERNAME by your Dartmouth NetID, which is your username.

Once this is done, you can ssh discovery by simply doing:

ssh babylonX 

with X the number of the machine you want to access

Password-less ssh

This machine does not support public key authentication

Environment

On babylon or amundsen, add the following lines to ~/.bashrc:

export ISSM_DIR=PATHTOTRUNK

export FC=gfortran
export F77=gfortran
export F90=gfortran
export CC=gcc
export CXX=g++

source $ISSM_DIR/etc/environment.sh
alias ma='LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6" /thayerfs/apps/matlab/bin/matlab -nodesktop -nosplash -r "addpath $ISSM_DIR/src
/m/dev; devpath;"'

Log out and log back in to apply this change.

Installing ISSM on babylon

Babylon and amundsen have both Intel and GNU compilers. Installation should be done with the GNU compilers. You can follow the instructions on the website ​http://issm.jpl.nasa.gov/download/unix/. Choose PETSc v3.16 or later (install-3.16-linux.sh). You should not need Python.

Use the following configuration script (adapt to your needs):

#!/bin/bash
./configure \
   CC=gcc CXX=g++ F90=gfortran FC=gfortran \
   --prefix=${ISSM_DIR} \
   --with-numthreads=20 \
   --with-matlab-dir="/thayerfs/apps/matlab/" \
   --with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \
   --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpifort -lmpi" \
   --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
   --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
   --with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
   --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
   --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
   --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
   --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
   --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
   --enable-debugging \
   --enable-development

Installing ISSM with CoDiPack (AD)

You will need to install the following *additional* packages:

• codipack
• medipack

Use the following configuration script (adapt to your needs, make sure to NOT include --with-petsc-dir):

./configure \
   CC=gcc CXX=g++ F90=gfortran FC=gfortran CXXFLAGS="-g -O3 -fPIC -std=c++11 -DCODI_ForcedInlines" \
   --prefix=$ISSM_DIR \
   --without-kriging \
   --without-kml \
   --without-Love \
   --without-Sealevelchange \
   --with-matlab-dir="/thayerfs/apps/matlab/" \
   --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include" \
   --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpifort" \
   --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
   --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
   --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
   --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
   --with-codipack-dir="$ISSM_DIR/externalpackages/codipack/install" \
   --with-medipack-dir="$ISSM_DIR/externalpackages/medipack/install" \
   --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \
   --with-numthreads=32 \
   --enable-tape-alloc \
   --enable-development \
   --enable-debugging