Getting an account

First, you need to send an email to Mathieu and request an account.

ssh configuration

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

Host ronne ronne.ics.uci.edu
   HostName ronne.ics.uci.edu
   User YOURRONNEUSERNAME

and replace YOURRONNEUSERNAME by your ronne username.

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

ssh ronne

Password-less ssh

Once you have the account, you can setup a public key authentification in order to avoid having to input your password for each run. You need to have a SSH public/private key pair. If you do not, you can create a SSH public/private key pair by typing the following command and following the prompts (no passphrase necessary):

$your_localhost% ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter file in which to save the key (/Users/username/.ssh/id_rsa):RETURN
Enter passphrase (empty for no passphrase):RETURN
Enter same passphrase again:RETURN
Your identification has been saved in /Users/username/.ssh/id_rsa.
Your public key has been saved in /Users/username/.ssh/id_rsa.pub.

Two files were created: your private key /Users/username/.ssh/id_rsa, and the public key /Users/username/.ssh/id_rsa.pub. The private key is read-only and only for you, it is used to decrypt all correspondence encrypted with the public key. The contents of the public key need to be copied to ~/.ssh/authorized_keys on your ronne account:

$your_localhost%scp ~/.ssh/id_rsa.pub username@your_remosthost:~

Now on ronne, copy the content of id_rsa.pub:

$your_remosthost%cat ~/id_rsa.pub >> ~/.ssh/authorized_keys
$your_remosthost%rm ~/id_rsa.pub

Environment

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

export ISSM_DIR=PATHTOTRUNK
source $ISSM_DIR/etc/environment.sh
#MATLAB alias
export LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6" #Bug with MATLAB, issmversion gets a bunch of undefined symbols
alias ma='matlab -nodesktop -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath;"'

In order to source ~/.bashrc on startup, create ~/.bash_profile, and add the following lines:

if [ -f ~/.bashrc ]; then
  . ~/.bashrc
fi

Log out and log back in to apply this change.

Installing ISSM on Ronne

You can follow the instructions on the website ​http://issm.jpl.nasa.gov/download/unix/. Choose Petsc v3.12 or later. You should not need Python.

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

./configure \
    --prefix=$ISSM_DIR \
    --without-kml \
    --with-matlab-dir="/usr/local/matlab/" \
    --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
    --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
    --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
    --with-mpi-include=$ISSM_DIR/externalpackages/petsc/install/include  \
    --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort"\
    --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
    --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
    --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
    --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    --with-numthreads=32 \
    --enable-development \
    --enable-debugging

Python and Openssh

In order to install gdal, you need to install the python from the externalpackages. Once that is done, unset the PYTHON-related variables in etc/environment.sh, because this python installation causes future issues with other packages, e.g. PETSC.

Installing ISSM with CoDiPack (AD)

You will need to install the following additional packages:

• codipack
• medipack
• gsl

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

./configure \
   --prefix=$ISSM_DIR\
   --without-kriging \
   --without-kml \
   --without-Gia \
   --without-Love \
   --without-Sealevelchange \
   --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \
   --with-matlab-dir="/usr/local/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=$ISSM_DIR/externalpackages/petsc/install \
   --with-mumps-dir=$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=$ISSM_DIR/externalpackages/triangle/install \
   --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \
   --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
   --with-codipack-dir="$ISSM_DIR/externalpackages/codipack/install" \
   --with-medipack-dir="$ISSM_DIR/externalpackages/medipack/install" \
   --with-numthreads=20  \
   --enable-tape-alloc \
   --enable-development \
   --enable-debugging