Getting an account

New users have to ask the PIs (Eric Larour or Mathieu Morlighem) to request a NASA account for them if they don't have one already:

• go to ​https://www.nas.nasa.gov/hecc/portal/accounts select option 3 ("I want to request a NASA identity for one of my new users")
• provide the information requested

Then, a NAS account has to be created by the new user:

• go to ​https://www.nas.nasa.gov/hecc/portal/accounts select option 2 ("I want to request and account for myself")
• provide the information requested using either GID = s5692 for Eric's group or GID = s1507 for Mathieu's group
• the PI will receive an email to approve the request
• All users must complete NASA-mandatory Basic IT Security Training (This year's training is called "FY2016 CYBERSECURITY AND SENSITIVE UNCLASSIFIED INFORMATION AWARENESS TRAINING").

Password-less ssh

Follow the steps outlined here ​http://www.nas.nasa.gov/hecc/support/kb/Setting-Up-SSH-Passthrough_232.html

Environment

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

#init lib paths
setenv LD_LIBRARY_PATH $HOME
setenv DYLD_LIBRARY_PATH $HOME

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

#Packages
module load pkgsrc/2020Q4
module load comp-intel/2016.2.181
module load mpi-hpe/mpt

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

Installing ISSM on Pleiades

Do NOT install mpich. We have to use the one provided by NAS. 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:

• PETSc (use the pleiades script install-3.13-pleiades.sh)
• m1qn3

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

You will need to run the following commands before configuring ISSM:

cd $ISSM_DIR
autoreconf -ivf

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

#!/bin/csh

./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-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
 --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 PETSc and m1qn3, but you will need to make sure you are using the intel mpi and that the externalpackages are built with the mpi compilers.

In your ~/.cshrc, add the following lines:

#Set compilers
setenv CC mpicc
setenv CXX mpicxx
setenv F77 mpif77

And change your loaded packages to (note the removal of the pkgsrc):

#Packages
module load comp-intel/2018.3.222
module load mpi-intel/2018.3.222

Then log out and log back in, and reinstall the following packages:

• PETSc (use the pleiades script install-3.14-pleiades.sh)
• m1qn3

In addition, will need to build the external package:

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

Finally, you will need to use the following configuration script:

#!/bin/csh

./configure \
 --prefix=$ISSM_DIR \
 --enable-standalone-libraries \
 --with-wrappers=no \
 --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
 --with-metis-dir=$PETSC_ROOT \
 --with-petsc-dir=$PETSC_ROOT \
 --with-scalapack-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
 --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
 --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
 --with-mpi-include=" " \
 --with-mpi-libflags=" -lmpi" \
 --with-mkl-libflags="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \
 --with-mumps-dir=$PETSC_ROOT \
 --with-fortran-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin/ -lifcore -lifport -lgfortran" \
 --with-cxxoptflags="-O3 " \
 --with-vendor="intel-pleiades-mpi" \
 --enable-development

Remember, you will need to run the following commands before configuring ISSM:

cd $ISSM_DIR
autoreconf -ivf

Note, if you would like the capabilities of pkgsrc/2020Q4, including updated svn, make sure that you build dakota without that package loaded. Once you have ISSM compiled and installed with dakota, feel free to add back in to your ~/.cshrc:

#Packages
module load pkgsrc/2020Q4

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='s5692';

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()

Without dakota, make sure your module list includes scicon/app-tools, comp-intel/2016.2.181, and mpi-hpe/mpt. With dakota, make sure your module list includes scicon/app-tools, comp-intel/2018.3.222, and mpi-intel/2018.3.222. You can specify your own list of modules by adding to pfe_settings.m, for example:

cluster.modules = {'comp-intel/2018.3.222' 'mpi-intel/2018.3.222' 'scicon/app-tools'};

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','bro','queue','devel');
md.cluster.time=10;

to have a maximum job time of 10 minutes and 8 broadwell 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,'runtimename','SOMETHING');