more to come

Download ISSM

svn --username XXX --password XXX checkout ​http://issm.ess.uci.edu/svn/issm/issm/trunk-jpl

Environment

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

module load system subversion
module load impi/2019
module load imkl/2019
export ISSM_DIR=PATHTOTRUNK
source $ISSM_DIR/etc/environment.sh

Log out and log back in to apply this change.

Installing ISSM on Sherlock

You need to install the following packages in this exact sequence:

• autotools (install.sh)
• petsc (install-3.9-sherlock.sh)
• m1qn3 (install.sh)

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

./configure \
   --prefix=$ISSM_DIR \
   --with-wrappers=no \
   --with-kml=no \
   --with-bamg=no \
   --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
   --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
   --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
   --with-mpi-include="/share/software/user/restricted/impi/2019//compilers_and_libraries_2019.0.117/linux/mpi/intel64/include" \
   --with-mpi-libflags="-L/data/apps/mpi/openmpi-1.8.3/gcc/4.8.3/lib -lmpicxx -lmpifort -lmpi" \
   --with-mkl-libflags="-L/share/software/user/restricted/imkl/2019/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread" \
   --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
   --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
   --with-numthreads=16 \
   --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/ -lgfortran" \
   --enable-debugging 

sherlock_settings.m

HPC staff ask that no "serious work" should be done on your home directory, you should create an execution directory as /pub/$USERNAME/execution.

You have to add a file in $ISSM_DIR/src/m entitled hpc_settings.m with your personal settings on your local ism install:

cluster.login='mmorligh';
cluster.port=8000;
cluster.queue='pub64';
cluster.codepath='/data/users/mmorligh/trunk-jpl/bin/';
cluster.executionpath='/data/users/mmorligh/trunk-jpl/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=hpc()

Running jobs on Sherlock

On hpc, you can use up to 64 cores per node. 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=sherlock('numnodes',1,'cpuspernode',8);

The list of available queues is 'pub64','free64','free48','free*,pub64' and 'free*'.

to have a job of 8 cores on one node. 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, type in the bash with the hpc 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.

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');