Skylab HPC users guide

This guide contains system-specific information as well as tips and tricks for running skylab on supported HPC systems.

General Tips for HPC Systems

Many HPC systems do not allow you to run MPI jobs from the login nodes. So, after building JEDI, you’ll have to run the tests either in batch mode through a job submission program such as slurm via the sbatch command, or by accessing a compute node interactively through a command like salloc. An advantage of submitting a job ‘to the queue’ through the slurm scheduler is that you can then logout of the system, or continue to use your terminal after sumbitting your script while the tests run. The test results will be written into a slurm-<jobNumber> file which will appear in which ever directory from which you submitted the job.

An alternative to using the batch script is to request an interactive session and run the ctests there. After logging into the interactive session, reload the modules (Using spack-stack modules to build and run JEDI), go to the bundle build directory and run the tests:

<reload the modules>
cd <path-to-bundle-build-directory>
ctest 2>&1 |tee ctest.log

SBATCH

Here is a sample slurm batch script for running ctest. Note that you will need to add appropriate #SBATCH directives for specifying a computing account, quality of service, job partition, and so on.

HPCs using SBATCH: Orion, Discover, Hera, and S4

#!/usr/bin/bash
#SBATCH --job-name=<name>
#SBATCH --nodes=1
#SBATCH --account <account>
#SBATCH --partition <partition>
#SBATCH --qos <qos>
#SBATCH --time=0:10:00
#SBATCH --mail-user=<email-address>

source /etc/bashrc

# Insert the module purge and load statements in here

module list
ulimit -s unlimited
ulimit -v unlimited

export SLURM_EXPORT_ENV=ALL
export HDF5_USE_FILE_LOCKING=FALSE

cd <path-to-bundle-build-directory>
ctest -E get_

exit 0

Note that the options specified with #SBATCH includes the number of nodes but not the number of tasks needed. This is most appropriate for running ctest because some tests require a different number of MPI tasks than others. However, if you run an application individually, you should specify #SBATCH --ntasks <number> instead of #SBATCH --nodes=<number>, as shown in the following example. The slurm job scheduler will properly determine how many nodes your job requires. Specifying --ntasks instead of --nodes in the #SBATCH header commands will mandate that your computing allocation will only be charged for what you use. This is preferable for more computationally intensive jobs.

#!/usr/bin/bash
#SBATCH --job-name=<name>
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=1
#SBATCH --time=0:10:00
#SBATCH --mail-user=<email-address>

source /etc/bashrc

# Insert the module purge and load statements in here

ulimit -s unlimited
ulimit -v unlimited

export SLURM_EXPORT_ENV=ALL
export HDF5_USE_FILE_LOCKING=FALSE

# make sure the number of tasks it requires matches the SBATCH --ntasks specification above
cd <path-to-bundle-build-directory>
# Note that --ntasks=4 below is not needed in this case - srun will use what's in the SBATCH line above
srun --ntasks=4 --cpu_bind=core --distribution=block:block test_ufo_radiosonde_opr testinput/radiosonde.yaml

exit 0

Note

JEDI applications (like most NWP applications) require a decent amount of memory, in which case asking for just a fraction of a node may fail with out of memory errors. This can be avoided by asking for an entire node (or, for larger jobs, more nodes) and running with fewer MPI tasks than each node provides by using #SBATCH --nodes=1 and srun --ntasks=4, for example.

Submit and monitor your jobs with these commands

sbatch <batch-script>
squeue -u <your-user-name>

You can delete jobs with the scancel command.

PBS

PBS is another way to run batch scripts for completing ctests.

HPCs that use PBS: Derecho, Casper, and Narwhal

The following is a sample batch script to run the remaining unit tests. Note that some ctests require up to 24 MPI tasks.

#!/bin/bash
#PBS -N ctest-ufo-gnu
#PBS -A <account-number>
#PBS -l walltime=00:20:00
#PBS -l select=1:ncpus=24:mpiprocs=24
#PBS -q regular
#PBS -j oe
#PBS -k eod
#PBS -m abe
#PBS -M <your-email>

# Insert the appropriate module purge and load commands here

# cd to your build directory.  Make sure that these binaries were built
# with the same module that is loaded above

cd <build-directory>

# now run ctest
ctest -E get_

System Specific Information

Casper

The Casper cluster is a heterogeneous system of specialized data analysis and visualization resources, large-memory, multi-GPU nodes, and high-throughput computing nodes.

Because of space limitations on your home directory, it’s a good idea to locate your build directory on the glade filesystems:

cd /glade/work/<username>
mkdir jedi/build; cd jedi/build

Warning

Please do not use too many threads to speed up the compilation, Casper system administrator might terminate your login node.

The system configuration on Casper will not allow you to run mpi jobs from the login node. If you try to run ctest from here, the mpi tests will fail. To run the jedi unit tests you will have to either submit a batch job or request an interactive session.

To request an interactive session on Casper run execcasper. Invoking it without an argument will start an interactive shell on the first available HTC node. The default wall-clock time is 6 hours. To use another type of node, include a select statement specifying the resources you need. The execcasper command accepts all PBS flags and resource specifications as detailed by man qsub.

Casper uses PBS and an example job submission script is given here.

Casper documentation:

Derecho

Derecho is a 19.87-petaflops, high-performance computer built for NCAR and hosted at the NCAR-Wyoming Supercomputing Center.

Because of space limitations on your home directory, it’s a good idea to build your code on the glade filesystems (work or scratch):

Warning

Please do not use too many threads to speed up the compilation, Derecho system administrator might terminate your login node.

The system configuration on Derecho will not allow you to run mpi jobs from the login node. If you try to run ctest from here, the mpi tests will fail. To run the jedi unit tests you will have to either submit a batch job or request an interactive session.

To request an interactive session on Derecho run qsub -I.

Derecho uses PBS and an example job submission script is given here.

Derecho documentation:

Discover

Discover is 90,000 core supercomputing cluster capable of delivering 3.5 petaflops of high-performance computing for Earth system applications from weather to seasonal to climate predictions.

The “scratch” directory on Discover is in the ~/NOBACKUP file system (see the NCCS user guide). So, build JEDI and set up your JEDI_ROOT to a directory here.

Build jedi on the login-node (with 4 or fewer processes i.e. -j4 or less), and use the special commands for running ecbuild on intel/GNU.

Intel build

For Intel, when using ecbuild, use:

ecbuild -DMPIEXEC_EXECUTABLE="/usr/local/intel/oneapi/2021/mpi/2021.5.0/bin/mpirun" -DMPIEXEC_NUMPROC_FLAG="-np"

Run the get_ ctests also on the login-node, but run the rest of the tests interactively on a compute node using the salloc command as described in the documentation below or using SBATCH. It will take about an hour and a half to run the tests, so be sure to request at least 90 minutes for the interactive job. FYI, it will likely take a while for the request for the interactive session to be granted.

GNU build

For GNU, when using ecbuild, use:

ecbuild -DMPIEXEC_EXECUTABLE="/usr/bin/srun" -DMPIEXEC_NUMPROC_FLAG="-n"

Then run all ctests directly from the login node.

Discover is a heterogeneous system with different CPU architectures and operating systems on the login and compute nodes. The default login node is of the newest Intel Cascade Lake generation, and we recommend requesting the same node type when running interactive jobs or batch jobs, which is accomplished by the argument --constraint="cas". If older node types are used (Skylake, Haswell), users may see warnings like “no version information available” for certain libraries in the default location /usr/lib64.

To request an interactive compute node on discover, run the following:

salloc --constraint="cas" --nodes=1 --ntasks-per-node=24 --time=2:00:00

Discover uses SBATCH and an example job submission script is given here.

Discover documentation:

ecflow and Discover login-nodes

When you log on to Discover, you will be placed onto a different login-node each time (eg, discover11, discover12, etc). You can’t choose which login-node you get, and you cannot easily ssh between login-nodes.

This means you will have to take a few extra steps to get your experiments to show up in the ecflow GUI properly, and you can address this in one of several ways (in all cases you will still have to manually set your ECF_PORT environment variable):

  1. (Recommended) Leave your activate.sh script with the default of re-setting your ECF_HOST for each new session and have an ecflow server configured on each login-node. So, when you log into a new session, you either use the server you have previously configured on that node or configure a new server if you haven’t already configured one on that node. In this case, you will still have to have the same ECF_PORT for each of the separate servers you have on different nodes (which you had to set manually as noted in the documentation). For best results, shutdown the ecflow server (ecflow_stop.sh -p $ECF_PORT) before ending each session and logging out.

    Note

    With this approach, you will have several servers appear in your ecflow GUI. Jobs will run through the server running on the node you submitted the job from. Also, to help you keep track of the servers, name the server with the name of the login-node on which it is running.

  2. You can start one ecflow server (with the ecflow_start.sh -p $ECF_PORT command) on whichever login-node you are on when submitting your first experiment. For this approach, you will need to manually adjust your activate.sh script to set your ECF_HOST to match the login-node on which you started the server (i.e. the node you are currently on). For example:

    export ECF_HOST=discover13

    Note

    With this approach, you will only have one server appear in your ecflow GUI. Having your ECF_HOST hardcoded will have jobs run through the server on your original login-node, even if you submit the job from another node. This approach is not recommended since it can cause tricky-to-debug issues with environment matching, and will cause you to have to restart your ecflow server and change your activate.sh script every time the discover login-nodes get shut down (e.g., for maintenance).

  3. You can setup an SSH key pair and follow the directions at https://www.nccs.nasa.gov/nccs-users/instructional/logging-in to allow you to SSH between login-nodes.

Hera

Hera is an HPC system located in NOAA’s NESCC facility in Fairmont, WV.

It is recommended that you specify srun as your mpi process manager when building, like so:

ecbuild -DMPIEXEC_EXECUTABLE=`which srun` -DMPIEXEC_NUMPROC_FLAG="-n" <path-to-bundle>
make -j4

To run tests with slurm and srun, you also need to have the following environment variables defined.

export SLURM_ACCOUNT=<account you can run slurm jobs under>
export SALLOC_ACCOUNT=$SLURM_ACCOUNT
export SBATCH_ACCOUNT=$SLURM_ACCOUNT

Hera documentation:

  • Heradoc (only available with NOAA SSO)

Hercules

Hercules is an HPC system located at Mississippi State University for the purpose of furthering NOAA’s scientific research and collaboration.

It shares a file system and log-in credentials with Orion, so see that section (below) for more information.

Hercules documentation:

Narwhal

Narwhal is an HPE Cray EX system located at the Navy DSRC. It has 2,176 standard compute nodes (AMD 7H12 Rome, 128 cores, 238 GB) and 12 large-memory nodes (995 GB). It has 590 TB of memory and is rated at 12.8 peak PFLOPS.

Because of space limitations on your home directory, it’s a good idea to build your code on Narwhal $WORKDIR: /p/work1/$USER.

For Intel and GNU, configure with:

ecbuild -DMPIEXEC_EXECUTABLE=/opt/cray/pe/pals/1.2.2/bin/aprun -DMPIEXEC_NUMPROC_FLAG="-n" <path-to-bundle-source-directory>

Request a full (compute) node in interactive mode on Narwhal run:

qsub -A <project_number> -q HIE -l select=1:ncpus=124:mpiprocs=124 -l walltime=06:00:00 -I

Narwhal uses PBS and an example job submission script is shown here.

Narwhal documentation:

Orion

Orion is an HPC system located at Mississippi State University for the purpose of furthering NOAA’s scientific research and collaboration.

When running ecbuild use the following to direct CMake to use srun for CTest MPI jobs.

ecbuild -DMPIEXEC_EXECUTABLE=$(which srun) -DMPIEXEC_NUMPROC_FLAG="-n"

We do not recommend running the ctests on login nodes because of the computational requirements of these tests. Instead you can submit ctests as a batch job or use an interactive node. To request an interactive session on Orion, you can run the following. Make sure you use the correct account number. This command requests for one node with 24 MPI tasks.

salloc -N1 -n 24 -A <account> --qos=batch --partition=orion --time=480 -I

Orion uses SBATCH and an example job submission script is shown here.

Orion documentation:

S4

S4 is the Satellite Simulations and Data Assimilation Studies supercomputer located at the University of Wisconsin-Madison’s Space Science and Engineering Center.

S4 uses the slurm task manager for parallel mpi jobs and users are advised to use srun instead of mpirun or mpiexec.

Once logged into S4, you must then log into s4-submit to load the spack-stack modules to build and run JEDI.

ssh -Y s4-submit.ssec.wisc.edu

When running ecbuild use the following to direct CMake to use srun for CTest MPI jobs.

ecbuild -DMPIEXEC_EXECUTABLE=$(which srun) -DMPIEXEC_NUMPROC_FLAG="-n"

To request an interactive session on S4, run:

salloc --nodes=1 --time=30 -I
# Required for Intel so that serial jobs of MPI-enabled executables
# run without having to call them through mpiexec/mpirun
unset "${!SLURM@}"

S4 uses SBATCH and an example job submission script is here.

S4 documentation: