Getting an account

New users have to ask Byron

Password-less ssh

Environment

Pleiades uses csh and not bash, add the following to your ~/.cshrc:

#ISSM
setenv ISSM_DIR /home1/mmorligh/issm/trunk/
source $ISSM_DIR/etc/environment.csh

#Packages
module load pkgsrc
module load comp-intel/2016.2.181
module load mpi-sgi/mpt

And replace ISSM_DIR with your actual trunk. Log out and log back in to apply this change.

Installing ISSM on Pleiades

Pleiades will only be used to run the code, you will use your local machine for pre and post processing, you will never use Pleiades' matlab. You can check out ISSM and install the following packages:

• cmake
• PETSc (use the pleiades 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

For documentation of pleiades, see here: ​http://www.nas.nasa.gov/hecc/support/kb/

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

./configure \
 --prefix=$ISSM_DIR \
 --with-wrappers=no \
 --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
 --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
 --with-mpi-include=" " \
 --with-mpi-libflags=" -lmpi" \
 --with-mkl-libflags="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm " \
 --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
 --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \
 --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
 --with-cxxoptflags="-O3 -axAVX" \
 --with-fortran-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/ -lifcore -lifport" \
 --with-vendor="intel-pleiades" \
 --enable-development

Installing ISSM on Pleiades with Dakota

For Dakota to run, you you will still need to make autotools, cmake PETSc, and m1qn3.

In addition, will need to build the external package:

• boost, install-1.55-pleiades.sh
• dakota, install-6.2-pleiades.sh

Finally, add the following to your configuration script:

 --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
 --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \

pfe_settings.m

You have to add a file in $ISSM_DIR/src/m entitled pfe_settings.m with your personal settings:

cluster.login='mmorligh';
cluster.queue='devel';
cluster.codepath='/u/mmorligh/issm/trunk/bin';
cluster.executionpath='/u/mmorligh/issm/trunk/execution/';
cluster.grouplist='s1690';

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=pfe()

Make sure your module list includes pkgsrc, comp-intel/2016.2.181, and mpi-sgi/mpt .

Running jobs on Pleiades

On Pleiades, the more nodes and the longer the requested time, the more you will have to wait in the queue. So choose your settings wisely:

md.cluster=pfe('numnodes',8,'time',30,'processor','wes','queue','devel');
md.cluster.time=10;

to have a maximum job time of 10 minutes and 8 westmere nodes. If the run lasts longer than 10 minutes, it will be killed and you will not be able to retrieve your results.

Now if you want to check the status of your job and the queue you are using, use this command:

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.

If you want to load results from the cluster manually (for example if you have an error due to an internet interruption), you find in the informations Matlab gave you /home/srebuffi/trunk-jpl/execution//SOMETHING/JOBNAME.lock , you copy the SOMETHING and you type in Matlab:

md=loadresultsfromcluster(md,'SOMETHING');