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 stallo stallo.uit.no
    HostName stallo.uit.no
    User YOURSTALLOUSERNAME

and replace YOURSTALLOUSERNAME by your stallo username.

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

ssh stallo

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 Stallo, copy the content of id_rsa.pub:

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

Environment

On Stallo, we were ask not to load modules in .bashrc if possible. This is fine, just use the load command that are on top of the configure.sh while installing and while running the loads are taken care of by the queue file. You still need an ISSM path in your .bashrc as follows:

#ISSM                                                                                                     
export ISSM_DIR=PATHTOISSM

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

Installing ISSM on Stallo

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 stallo you will need to run libtoolize:

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. Notur support made a great job at having a properly installed PETSc here so we have a clean configure file,:

#!/bin/sh
#Stallo configuration script
#this uses system stuff, you need to load the following:
module purge
module load CMake/3.8.0-GCCcore-6.3.0
module load Automake/1.15.1-GCCcore-6.3.0
module load libtool/2.4.6
#module load OpenSSL/1.1.0e-intel-2017a
module load PETSc/3.7.5-intel-2017a-downloaded-deps

./configure \
    --prefix=$ISSM_DIR \
    --without-kriging \
    --with-wrappers=no \
    --with-petsc-dir="/global/hds/software/cpu/eb3/PETSc/3.7.5-intel-2017a-downloaded-deps" \
    --with-mpi-include="/global/hds/software/cpu/eb3/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/include64" \
    --with-mpi-libflags="-L/global/hds/software/cpu/eb3/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/lib64 -lmpich -lmpichf90 -lmpichcxx -lmpl" \
    --with-metis-dir="/global/hds/software/cpu/eb3/PETSc/3.7.5-intel-2017a-downloaded-deps" \
    --with-mumps-dir="/global/hds/software/cpu/eb3/PETSc/3.7.5-intel-2017a-downloaded-deps" \
    --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
    --with-hypre-dir="/global/hds/software/cpu/eb3/PETSc/3.7.5-intel-2017a-downloaded-deps" \
    --with-mkl-libflags="-L/global/hds/software/cpu/eb3/imkl/2017.1.132-iimpi-2017a/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core  -lmkl_scalapack_lp64 -lpthread" \
    --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

stallo_settings.py

def stallo_settings(md):                                                                                                                     
    md.login='YOURNOTURLOGIN'
    md.queue='normal'
    md.codepath='YOURCODEPATH'#home is fne
    md.executionpath='YOUREXECPATH'#should be in /global/work/username to avoid flooding your home
    md.accountname='nn4659k'#this is for ice2ice
    md.numnodes=1
    md.numprocess=16
    return md

stallo_settings.m

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