Getting an account

First, you need to get an account from NOTUR, the webpage for you request is : ​https://www.metacenter.no/user/application/form/notur/.

ssh configuration

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

Host fram fram.sigma2.no
    HostName fram.sigma2.no
    User YOURFRAMUSERNAME

and replace YOURFRAMUSERNAME by your stallo username.

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

ssh fram

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 stallo account:

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

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

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

remember to have correct rights for the .ssh and the authorized_keys (else key wont work) chmod 700 ~/.ssh chmod 600 ~/.ssh/authorized_keys

Environment

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

#ISSM                                                                                                     
export ISSM_DIR=/cluster/work/users/USERNAME/ISSMDIRNAME

Log out and log back in or source you .bashrc to apply this change.

Installing ISSM on fram

Now, checkout the source code using instructions at ​https://issm.jpl.nasa.gov/download/.

If it is the first time you are installing issm on fram you will need to run libtoolize (make sure to run it on /cluster not your home directory):

libtoolize

The only package from external packages that you may require (if you need to run some inversion) is m1qn3. Install it from external packages

cd externalpackages/m1qn3
./install.sh

Once this is done in ISSM_DIR do:

./scripts/automakererun.sh

Use the following configuration script:

#!/bin/sh
#fram configuration script
                                                                                                          
module restore system
module load libtool/2.4.6-GCCcore-6.3.0
module load Automake/1.15.1-GCCcore-6.3.0/
module load CMake/3.9.1
module load PETSc/3.8.0-intel-2017a-Python-2.7.13
module load ParMETIS/4.0.3-intel-2017a

./configure \
    --prefix=$ISSM_DIR \
    --without-kriging \
    --with-wrappers=no \
    --with-petsc-dir="/cluster/software/PETSc/3.8.0-intel-2017a-Python-2.7.13/" \
    --with-mpi-include="/cluster/software/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/include64" \
    --with-mpi-libflags="-L/cluster/software/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/lib64 -lm\
pich -lmpichf90 -lmpichcxx -lmpl" \
    --with-metis-dir="/cluster/software/ParMETIS/4.0.3-intel-2017a/include/" \
    --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
    --enable-development

You can then make your configuration file executable (if it is not already) execute it and install ISSM:

chmod +x configure.sh
./configure.sh
make install

fram_settings.py

def fram_settings(md):                                                                                                                     
    md.login='YOURNOTURLOGIN'
    md.queue='normal'
    md.codepath='YOURCODEPATH'#should be in /cluster/work/users/USERNAME/ISSMNAME
    md.executionpath='YOUREXECPATH'#should be in /cluster/work/users/USERNAME/execution
    md.accountname='nn4659k'#this is for ice2ice
    md.numnodes=1
    md.numprocess=16
    return md

fram_settings.m

The use of the Python version of the code is encouraged at Uib but you are welcome to clone the python settings.