Getting an account

You automatically have access to the machine if you are part of Dartmouth's Thayer School of Engineering.

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 authentification

Environment

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

export ISSM_DIR=PATHTOTRUNK
source $ISSM_DIR/etc/environment.sh
alias ma='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 has both Intel and GNU compilers. Installation should be done with the Intel compilers. You can follow the instructions on the website ​http://issm.jpl.nasa.gov/download/unix/. Choose Petsc v3.15 or later. You should not need Python.

Petsc uses GNU compilers by default, so you need to specify to use the Intel compilers. Make sure this is specified in the installation file:

# Configure
cd ${PETSC_DIR}
./config/configure.py \
   --with-cc=icc --with-cxx=icpc --with-fc=ifort \
   --prefix="${PREFIX}" \
   --PETSC_DIR="${PETSC_DIR}" \
   --with-debugging=0 \
   --with-valgrind=0 \
   --with-x=0 \
   --with-ssl=0 \
   --with-pic=1 \
   --download-fblaslapack=1 \
   --download-mpich=1 \
   --download-metis=1 \
   --download-parmetis=1 \
   --download-scalapack=1 \
   --download-mumps=1 \
   --download-zlib=1 \
   --download-hdf5=1

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

#!/bin/bash
./configure \
   CC=icc CXX=icpc F90=ifort FC=ifort \
   --prefix=${ISSM_DIR} \
   --with-numthreads=2 \
   --with-matlab-dir="/thayerfs/apps/matlab/" \
   --with-mpi-include="${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="${ISSM_DIR}/externalpackages/petsc/install" \
   --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
   --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
   --enable-debugging \
   --enable-development