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, add the following lines to ~/.bashrc:

#Module loading                                                                                           
module load Automake/1.15-intel-2016a
module load libtool/2.4.6-intel-2016a
module load CMake/3.5.2-intel-2016a
module load intel/2016a
module load ParMETIS/4.0.3-intel-2016a
module load MUMPS/5.1.1-intel-2016a-parmetis
module load PETSc/3.7.2-intel-2016a-Python-2.7.11
module load FFTW/3.3.4-intel-2016a
module load OpenSSL/1.0.1s-intel-2016a
#ISSM                                                                                                     
export ISSM_DIR=PATHTOISSM

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

Installing ISSM on Vilje

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:

run ./scripts/automakererun.sh

Use the following configuration script:

#!/bin/sh
./configure \
    --prefix=$ISSM_DIR \
    --without-kriging \
    --with-wrappers=no \
    --with-petsc-dir="/global/hds/software/cpu/eb3/PETSc/3.7.2-intel-2016a-Python-2.7.11" \
    --with-mpi-include="/global/hds/software/cpu/eb3/impi/5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25/include64" \
    --with-mpi-libflags="-L/global/hds/software/cpu/eb3/impi/5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25/lib64 -lmpich -lmpichf90 -lmpichcxx -lmpl" \
    --with-metis-dir="/global/hds/software/cpu/eb3/ParMETIS/4.0.3-intel-2016a/include" \
    --with-mumps-dir="/global/hds/software/cpu/eb3/MUMPS/5.1.1-intel-2016a-parmetis" \
    --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
    --with-hypre-dir="/global/hds/software/cpu/eb3/Hypre/2.11.1-intel-2016a" \
    --with-mkl-libflags="-L/global/hds/software/cpu/eb3/imkl/11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25/mkl/lib/intel64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lmkl_scalapack_lp64 -L/global/hds/software/cpu/eb3/FFTW/3.3.4-intel-2016a/lib/ -lfftw3_mpi -L/global/hds/software/cpu/eb3/SuiteSparse/4.5.3-intel-2016a-ParMETIS-4.0.3/lib -lklu -lamd -lamd -lbtf -lsuitesparseconfig -lumfpack -lcholmod -L/global/hds/software/cpu/eb3/ifort/2016.1.150-GCC-4.9.3-2.25/lib/intel64 -lifcore -lifport -L/global/hds/software/cpu/eb3/OpenSSL/1.0.1s-intel-2016a/lib -lssl -L/global/hds/software/cpu/eb3/SCOTCH/6.0.4-intel-2016a/lib -lesmumps -lptesmumps  -lptscotch  -lptscotcherr  -lptscotcherrexit -lscotch -lscotcherr -lscotcherrexit -lscotch_group" \
    --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
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.