ssh configuration

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

Host gscc login.gscc.umt.edu
   HostName login.gscc.umt.edu
   User USERNAME                
   HostKeyAlias login.gscc.umt.edu
   HostbasedAuthentication no

and replace USERNAME by your gscc username.

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

ssh gscc

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 already have one, you can skip their creation described below. 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 gscc account:

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

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

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

Install

Install Anaconda

We will install ISSM within an Anaconda environment on GSCC. The Anaconda environment will act as an isolated compile environment. To install Anaconda3 run

wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-x86_64.sh
chmod 755 Anaconda3-2020.11-Linux-x86_64.sh
./Anaconda3-2020.11-Linux-x86_64.sh

Answer no at the final prompt. Activate Anaconda by typing.

source ~/anaconda3/bin/activate

Setup Anaconda3 environment

Now we'll set up an Anaconda environment called issm. Create a file on GSCC called environment.yml. Copy the following contents:

name: issm
channels:
  - conda-forge
dependencies:
  - python=3.7
  - gcc_linux-64
  - gxx_linux-64
  - fortran-compiler
  - petsc=3.12
  - numpy
  - scipy
  - matplotlib
  - cmake
  - libtool
  - lapack
  - netcdf4
  - mpi
  - libtool
  - automake
  - pip

With Anacodna activated, run the following to create and activate the environment.

conda env create -f environment.yml
conda activate issm

Install ISSM

Copy ISSM files on your home directory on GSCC, add the following lines to your ~/.bashrc on GSCC:

module unload rocks-openmpi
export ISSM_DIR=/home/jd231341e/trunk-jpl/
export CONDA_DIR=/home/jd231341e/anaconda3/envs/test/
source $ISSM_DIR/etc/environment.sh
source ~/anaconda3/bin/activate
conda activate issm

This will automatically activate the Anaconda environment when you login and disable the default MPI in favor of Anaconda's installed MPI version. Most of the dependencies can be installed through Conda but m1qn3 needs to be installed manually

source $ISSM_DIR/etc/environment.sh 
cd $ISSM_DIR/externalpackages/m1qn3
./install.sh

Now we can configure and install ISSM via:

cd $ISSM_DIR 
source $ISSM_DIR/etc/environment.sh
autoreconf -ivf
./configure \
    --prefix="$ISSM_DIR" \
    --disable-static \
    --enable-development \
    --with-numthreads=8 \
    --with-python-version=3.7 \
    --with-python-dir="$CONDA_DIR" \
    --with-python-numpy-dir="$CONDA_DIR/lib/python3.7/site-packages/numpy/core/include/numpy" \
    --with-fortran-lib="-L$CONDA_DIR/lib/gcc/x86_64-conda-linux-gnu/7.5.0/ -lgfortran" \
    --with-mpi-include="$CONDA_DIR/lib/include" \
    --with-mpi-libflags="-L$CONDA_DIR/lib" \
    --with-metis-dir="$CONDA_DIR/lib" \
    --with-scalapack-dir="$CONDA_DIR/lib" \
    --with-mumps-dir="$CONDA_DIR/lib" \
    --with-petsc-dir="$CONDA_DIR" \
    --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install"
make --jobs=8
make install

Example Run on GSCC

If you have ISSM installed on your own machine with the Matlab interface and the GSCC cluster file, you can launch runs using the gscc cluster. For example:

md.cluster=gscc();
md.cluster.np = 2;
md.cluster.time = 60*60*10;
md=solve(md,'Transient');
md=loadresultsfromcluster(md,'LAUNCHSTRING','JOBNAME');

` To troubleshoot, note that logfiles for submitted runs will appear in trunk-jpl/execution/ on GSCC. The input file, and queue file for SLURM will appear here.