Getting an account

more to come...

ssh configuration

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

Host aurora aurora.jpl.nasa.gov
   HostName aurora.jpl.nasa.gov
  User YOURUSERNAME
  HostKeyAlias aurora.jpl.nasa.gov
  HostbasedAuthentication no

and replace YOURUSERNAME by your JPL username.

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

ssh aurora

Password-less ssh

Once you have the account, you can setup a public key authentication 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 aurora or halo account:

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

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

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

Environment

On aurora, add the following lines to ~/.bash_login:

export ISSM_DIR=PATHTOTRUNK
source $ISSM_DIR/etc/environment.sh
source /usr/share/Modules/init/bash
module load intel/cluster-toolkit-2013.5.192
module load apps/matlab-2016b

export PATH="$PATH:~/bin:$ISSM_DIR/scripts"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/intel/impi/4.1.3/intel64/lib/"

Log out and log back in to apply this change.

Installing ISSM on aurora

aurora can be used to run the code or with MATLAB locally. You can check out ISSM and install the following packages:

• autotools
• PETSc (use the aurora script and follow the instructions, you will need to submit a job and compile PETSc manually, do not make test, it will not work on the cluster)
• m1qn3

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

./configure \
   --prefix=$ISSM_DIR \
   --with-matlab-dir=$MATLAB_DIR \
   --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
   --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
   --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
   --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
   --with-mpi-include="/opt/intel/impi/4.1.3/intel64/include/" \
   --with-mpi-libflags="-L/opt/intel/impi/4.1.3/intel64/lib/ -lmpi -lmpiif" \
   --with-petsc-arch=$ISSM_ARCH \
   --with-mkl-libflags="-L/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \
   --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
   --with-fortran-lib="-L/opt/intel/composer_xe_2013.5.192/compiler/lib/intel64/ -lifcore -lifport" \
   --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
   --with-cxxoptflags="-O3" \
   --with-vendor=intel-aurora \
   --enable-development \
   --enable-debugging

aurora_settings.m

To launch from your local computer, you have to add a file in $ISSM_DIR/src/m entitled aurora_settings.m with your personal settings on your local issm install:

cluster.login='schlegel';
cluster.codepath='/home/schlegel/issm/trunk/bin';
cluster.executionpath='/home/schlegel/issm/trunk/execution';

Use your username for the login and enter your code path and execution path. These settings will be picked up automatically by matlab when you do md.cluster=aurora()

Note that the `executionpath' creates temporary binary files that can be removed once the job is complete. For this reason, you can set the path to be somewhere on the /aurora_nobackup/issm or /halo_nobackup/issm filesystem, which is unlimited temporary storage on these systems.

Running jobs on aurora

On aurora, you can use up to 256 cpus. The more nodes and the longer the requested time, the more you will have to wait in the queue. So choose your settings wisely: ​https://hpcs.jpl.nasa.gov/Users/HPC_resources.html

If you are running from your local machine:

md.cluster=aurora();

This will default to 1 node, 24 cpus.

To change the number of cpus use:

cluster.cpuspernode=3;

Before you run your job, make sure to open a port first and enter the port number in md.cluster. Here is a handy alias:

alias auroratunnel='ssh -L 1070:localhost:22 aurora'

That will open port number 1070 that you can then use in ISSM so that you don't need to enter your password.

Or, if you are launching from MATLAB on aurora/halo:

md.cluster=localaurora();

To submit a job on aurora, do:

qsub job.queue

Now if you want to check the status of your job and the queue you are using, type in the bash with the aurora/halo session:

qstat -u USERNAME

You can delete your job manually by typing:

qdel JOBID

where JOBID is the ID of your job (indicated in the Matlab session). Matlab indicates too the directory of your job where you can find the files JOBNAME.outlog and JOBNAME.errlog. The outlog file contains the informations that would appear if you were running your job on your local machine and the errlog file contains the error information in case the job encounters an error.