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,

• navigate 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

Current Points of Contact

• Dartmouth Security officer: Sean McNamara, Sean.R.McNamara@… ​https://itc.dartmouth.edu/about/who-we-are/itc-leadership
• UCI IT Security officer: Josh Drummond jdrummon@…
• JPL IT Security officer: Tomas Soderstrom Tomas.J.Soderstrom@…

Setting Up Password-less SSH for NASA NAS HECC

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

Checking Out a Copy of the ISSM Code Repository

Please see the ​ISSM code repository on GitHub for detailed instructions on how to check out a copy of the repository.

Environment

Make sure to clone ISSM in your /nobackup/ directory, where you can save a lot more files than in your home directory.

Add the following to ~/.bashrc,

# Modules
module load mpi-hpe/mpt
module load comp-intel/2020.4.304
module load petsc/3.17.3_intel_mpt_py

# Environment
export MPICXX_CXX=icpx
export MPICC_CC=icx
export MPF90_F90=ifort
export CC="mpicc"
export CXX="mpicxx"
export F77="mpif77"

export COMP_INTEL_ROOT="/nasa/intel/Compiler/2020.4.304/compilers_and_libraries_2020.4.304/linux"

export ISSM_DIR="<ISSM_DIR>"

replacing <ISSM_DIR> with the path to your local copy of the repository. Run source ~/.bashrc to apply these changes to your current environment.

NOTE: If your .bashrc is not loaded when you log in, you will have to add a new file, ~/.bash_login, with the following content,

if [ -f ~/.bashrc ]; then . ~/.bashrc; fi

NOTE: You may need to update the version of the comp-intel module as well as the corresponding value of variable COMP_INTEL_ROOT as recommended/available modules are updated on HECC. Please update this page or ask a project lead to do so when this occurs.

Installing ISSM on Pleiades

​Pleiades cluster documentation

Do NOT install mpich. We have to use the MPI implementation (MPT) provided on HECC. Pleiades will only be used to run solutions, you will use your local machine for pre- and post- processing, you will never use Pleiades' copy of MATLAB.

For an installation of ISSM with basic capabilities, first install the following external packages,

triangle	install-linux.sh
m1qn3		install-linux.sh
semic		install.sh

You will need to run the following before configuring ISSM,

cd $ISSM_DIR
autoreconf -ivf

Use the following configuration script for ISSM (adapt to your needs),

export CFLAGS="-O3"
export CXXFLAGS="-O3 -std=c++11"

./configure \
--prefix="${ISSM_DIR}" \
--enable-development \
--enable-standalone-libraries \
--with-wrappers=no \
--with-graphics-lib="/usr/lib64/libX11.so" \
--with-fortran-lib="-L${COMP_INTEL_ROOT}/compiler/lib/intel64_lin -lifcore -lifport -lgfortran" \
--with-mkl-libflags="-L${COMP_INTEL_ROOT}/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \
--with-mpi-include="/nasa/hpe/mpt/2.30_rhel810/include" \
--with-mpi-libflags="-L/nasa/hpe/mpt/2.30_rhel810/lib -lmpi" \
--with-blas-lapack-lib="-L${COMP_INTEL_ROOT}/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_lapack95_lp64" \
--with-metis-dir="${PETSC_DIR}" \
--with-parmetis-dir="${PETSC_DIR}" \
--with-scalapack-lib="-L${COMP_INTEL_ROOT}/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
--with-mumps-dir="${PETSC_DIR}" \
--with-petsc-dir="${PETSC_DIR}" \
--with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
--with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \

NOTE: As with the version comp-intel module, the version of mpi-hpe/mpt will be updated occasionally. Update the path supplied to --with-mpi-include and --mpi-libflags accordingly.

NOTE: Refer to jenkins/pleiades-basic for external packages and configuration updates that may not yet be listed here.

Installing ISSM on Pleiades with Dakota

For an installation of ISSM with Dakota, first install the following external packages,

gsl			install-pleiades.sh
boost		install-1.7-linux.sh
dakota		install-6.2-pleiades.sh
chaco		install-linux.sh
triangle	install-linux.sh
m1qn3		install-linux.sh
semic		install.sh

Use the following configuration script for ISSM (adapt to your needs),

export CFLAGS="-O3"
export CXXFLAGS="-O3 -std=c++11"

./configure \
--prefix="${ISSM_DIR}" \
--enable-development \
--enable-standalone-libraries \
--with-wrappers=no \
--with-graphics-lib="/usr/lib64/libX11.so" \
--with-fortran-lib="-L${COMP_INTEL_ROOT}/compiler/lib/intel64_lin -lifcore -lifport -lgfortran" \
--with-mkl-libflags="-L${COMP_INTEL_ROOT}/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \
--with-mpi-include="${COMP_INTEL_ROOT}/mpi/intel64/include" \
--with-mpi-libflags="-lmpi" \
--with-blas-lapack-lib="-L${COMP_INTEL_ROOT}/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_lapack95_lp64" \
--with-metis-dir="${PETSC_DIR}" \
--with-parmetis-dir="${PETSC_DIR}" \
--with-mumps-dir="${PETSC_DIR}" \
--with-scalapack-lib="-L${COMP_INTEL_ROOT}/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
--with-petsc-dir="${PETSC_DIR}" \
--with-gsl-dir="${ISSM_DIR}/externalpackages/gsl/install" \
--with-boost-dir="${ISSM_DIR}/externalpackages/boost/install" \
--with-dakota-dir="${ISSM_DIR}/externalpackages/dakota/install" \
--with-chaco-dir="${ISSM_DIR}/externalpackages/chaco/install" \
--with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
--with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \

NOTE: As with the version comp-intel module, the version of mpi-hpe/mpt will be updated occasionally. Update the path supplied to --with-mpi-include and --mpi-libflags accordingly.

NOTE: Refer to jenkins/pleiades-dakota for external packages and configuration updates that may not yet be listed here.

Installing ISSM on Pleiades with Solid Earth Capabilities

For an installation of ISSM with Solid Earth capabilities, first install the following external packages,

zlib		install-1.sh
hdf5		install-1.sh
gsl			install-pleiades.sh
boost		install-1.7-linux.sh
dakota		install-6.2-pleiades.sh
chaco		install-linux.sh
curl		install-7-linux.sh
netcdf		install-4.sh
sqlite		install.sh
proj		install-6.sh
gdal		install-3-linux.sh
gshhg		install.sh
gmt			install-6-pleiades.sh
gmsh		install-4-pleiades.sh
triangle	install-linux.sh
m1qn3		install-linux.sh
semic		install.sh

Use the following configuration script for ISSM (adapt to your needs),

export CFLAGS="-O3"
export CXXFLAGS="-O3 -std=c++11"

--prefix="${ISSM_DIR}" \
--enable-development \
--enable-standalone-libraries \
--with-wrappers=no \
--with-graphics-lib="/usr/lib64/libX11.so" \
--with-fortran-lib="-L${COMP_INTEL_ROOT}/compiler/lib/intel64_lin -lifcore -lifport -lgfortran" \
--with-mkl-libflags="-L${COMP_INTEL_ROOT}/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \
--with-mpi-include="/nasa/hpe/mpt/2.30_rhel810/include" \
--with-mpi-libflags="-L/nasa/hpe/mpt/2.30_rhel810/lib -lmpi" \
--with-blas-lapack-lib="-L${COMP_INTEL_ROOT}/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_lapack95_lp64" \
--with-metis-dir="${PETSC_DIR}" \
--with-parmetis-dir="${PETSC_DIR}" \
--with-scalapack-lib="-L${COMP_INTEL_ROOT}/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
--with-mumps-dir="${PETSC_DIR}" \
--with-hdf5-dir="${ISSM_DIR}/externalpackages/hdf5/install" \
--with-petsc-dir="${PETSC_DIR}" \
--with-gsl-dir="${ISSM_DIR}/externalpackages/gsl/install" \
--with-boost-dir="${ISSM_DIR}/externalpackages/boost/install" \
--with-dakota-dir="${ISSM_DIR}/externalpackages/dakota/install" \
--with-chaco-dir="${ISSM_DIR}/externalpackages/chaco/install" \
--with-proj-dir="${ISSM_DIR}/externalpackages/proj/install" \
--with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
--with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \

NOTE: As with the version comp-intel module, the version of mpi-hpe/mpt will be updated occasionally. Update the path supplied to --with-mpi-include and --mpi-libflags accordingly.

NOTE: Refer to jenkins/pleiades-solid-eartj for external packages and configuration updates that may not yet be listed here.

Installing ISSM on Pleiades with CoDiPack

You will need to build these additional external packages

medipack	install.sh
codipack	install.sh

Your configuration script should look like this,

export CXXFLAGS="-g -Ofast -wd2196"
export CFLAGS="-g -Ofast"

./configure \
--prefix=$ISSM_DIR \
--with-wrappers=no \
--without-Love \
--without-Sealevelchange \
--without-kriging \
--with-mpi-include="${MPI_ROOT}/include" \
--with-mpi-libflags="-L${MPI_ROOT}/lib -lmpi" \
--with-parmetis-dir=${PETSC_DIR} \
--with-metis-dir=${PETSC_DIR} \
--with-mumps-dir=${PETSC_DIR} \
--with-mkl-libflags="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_scalapack_lp64 -lmkl_blacs_sgimpt_lp64 -lmkl_core -lpthread -lm" \
--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
--with-codipack-dir="$ISSM_DIR/externalpackages/codipack/install" \
--with-medipack-dir="$ISSM_DIR/externalpackages/medipack/install" \
--enable-tape-alloc \
--with-fortran-lib="-L${MKLROOT}/../compiler/lib/intel64_lin -lifcore -lifport -lgfortran" \
--enable-development

You will get a lot of warnings while compiling (i.e. warning #2196: routine is both "inline" and "noinline"), which can be ignored.

pfe_settings.m

You have to add a file in $ISSM_DIR/src/m titled pfe_settings.m (on the machine you wish to access Pleiades) with your personal settings:

cluster.login='mmorligh';
cluster.queue='devel';
cluster.codepath='/nobackup/mmorligh/ISSM/bin';
cluster.executionpath='/nobackup/mmorligh/execution/';
cluster.grouplist='s5692';
cluster.port=1099;

use your username for the login and enter your code path and execution path. Be sure to create the final execution directory (mkdir) within the nobackup folder. These settings will be picked up automatically by matlab when you do md.cluster=pfe().

Make sure your module list includes scicon/app-tools, comp-intel/2018.3.222, and /nasa/intel/impi/2021.3/modulefiles/mpi/2021.3.0. You can specify your own list of modules by adding to pfe_settings.m, for example:

cluster.modules = {'mpi-hpe/mpt', 'comp-intel', 'petsc/3.17.3_intel_mpt_py'};

To determine your grouplist, on Pleiades run:

%groups USERNAME

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',1,'time',28,'processor','bro','queue','devel');
md.cluster.time=10;

to have a maximum job time of 10 minutes and 1 broadwell node. If the run lasts longer than 10 minutes, it will be killed and you will not be able to retrieve your results. For more information about the processors, see ​https://www.nas.nasa.gov/hecc/support/kb/pleiades-configuration-details_77.html.

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');