HPC Systems

This page collects instructions for building and running Cardinal on a number of High-Performance Computing (HPC) systems. Because default modules and settings change on HPC systems with time, the instructions below may become deprecated, but we try to keep this information up-to-date. Note that the absence of a particular HPC system from this list does not imply that Cardinal will not build/run on that system - only that documentation has not yet been created.

In addition to these provided module and environment settings, you must follow the build instructions on the Getting Started page.

note

NekRS can sometimes fail to correctly pre-compile its kernels on these HPC systems. We recommend precompiling NekRS (with the nrspre script) if you run into issues. See the NekRS documentation for more information.

Bebop

Bebop is an HPC system at Argonne National Laboratory (ANL) with an Intel Broadwell partition (36 cores/node) and an Intel Knights Landing partition (64 cores/node).

note

Note that if you want to build Cardinal via a job script, you will also need to module load numactl/2.0.12-355ef36 because make can find libnuma-dev on the login nodes, but you need to explicitly load it for compute nodes.

Listing 1: Sample ~/.bashrc for Bebop

module purge
module load gcc/9.2.0-pkmzczt
module load openmpi/4.1.1-ckyrlu7
module load cmake/3.20.3-vedypwm
module load python/intel-parallel-studio-cluster.2019.5-zqvneip/3.6.9

export CC=mpicc
export CXX=mpicxx
export FC=mpif90

# Revise for your Cardinal repository location
DIRECTORY_WHERE_YOU_HAVE_CARDINAL=$HOME

# This is needed because your home directory on Bebop is actually a symlink
HOME_DIRECTORY_SYM_LINK=$(realpath -P $DIRECTORY_WHERE_YOU_HAVE_CARDINAL)
export NEKRS_HOME=$HOME_DIRECTORY_SYM_LINK/cardinal/install

# Revise for your cross sections location
export OPENMC_CROSS_SECTIONS=$HOME_DIRECTORY_SYM_LINK/cross_sections/endfb-vii.1-hdf5/cross_sections.xml

Listing 2: Sample job script for Bebop with the startup project code

#!/bin/bash

# Usage:
# 1. Copy to the directory where you have your files
# 2. Update any needed environment variables and input file names in this script
# 3. sbatch job_bebop

#SBATCH --job-name=cardinal
#SBATCH --account=startup
#SBATCH --partition=bdwall
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=36
#SBATCH --output=run.out
#SBATCH --error=run.error
#SBATCH --time=00:10:00

module purge
module load cmake/3.20.3-vedypwm
module load gcc/9.2.0-pkmzczt
module load openmpi/4.1.1-ckyrlu7
module load python/intel-parallel-studio-cluster.2019.5-zqvneip/3.6.9

# Revise for your repository and cross section data locations
DIRECTORY_WHERE_YOU_HAVE_CARDINAL=$HOME
HOME_DIRECTORY_SYM_LINK=$(realpath -P $DIRECTORY_WHERE_YOU_HAVE_CARDINAL)
export NEKRS_HOME=$HOME_DIRECTORY_SYM_LINK/cardinal/install

export CARDINAL_DIR=$HOME_DIRECTORY_SYM_LINK/cardinal

# The name of the input file you want to run
input_file=openmc.i

# Run a Cardinal case
srun -n 36 $CARDINAL_DIR/cardinal-opt -i $input_file > logfile

Frontier

Frontier is an HPC system at Oak Ridge National Laboratory (ORNL) with 9408 AMD compute nodes, each with 4 AMD MI250X, each with 2 Graphics Compute Dies (GCDs), which you can think of as representing 8 GPUs per node. Remember that in order to build Cardinal with GPU support, set the appropriate variable in the Makefile to true (1):


OCCA_CUDA_ENABLED=0
OCCA_HIP_ENABLED=1
OCCA_OPENCL_ENABLED=0

When building the PETSc, libMesh, and Wasp dependencies from the scripts, you'll also need to pass some additional settings to libMesh.


./contrib/moose/scripts/update_and_rebuild_petsc.sh
./contrib/moose/scripts/update_and_rebuild_libmesh.sh --enable-xdr-required --with-xdr-include=/usr/include
./contrib/moose/scripts/update_and_rebuild_wasp.sh

Listing 3: Sample ~/.bashrc for Frontier

if [ $LMOD_SYSTEM_NAME = frontier ]; then
    module purge
    module load PrgEnv-gnu craype-accel-amd-gfx90a cray-mpich rocm cray-python/3.9.13.1 cmake/3.21.3
    module unload cray-libsci

    # Revise for your Cardinal repository location
    DIRECTORY_WHERE_YOU_HAVE_CARDINAL=$HOME/frontier
    cd $DIRECTORY_WHERE_YOU_HAVE_CARDINAL

    HOME_DIRECTORY_SYM_LINK=$(realpath -P $DIRECTORY_WHERE_YOU_HAVE_CARDINAL)
    export NEKRS_HOME=$HOME_DIRECTORY_SYM_LINK/cardinal/install

    export OPENMC_CROSS_SECTIONS=/lustre/orion/fus166/proj-shared/novak/cross_sections/endfb-vii.1-hdf5/cross_sections.xml
fi

Listing 4: Sample job script for Frontier

#/bin/bash

# Usage:
# 1. Copy to the directory where you have your files
# 2. Update any needed environment variables and input files names in this script
# 3. ./job_frontier [casename] <nodes> <hh:mm>
#    where [casename] is the NekRS case (used for precompiling). If not using
#                     NekRS, omit this field.
#          <nodes>    is the number of nodes you want to use
#          <hh::mm>   is the maximum wall time you want

# additional variables you may want to change
: ${PROJ_ID:="FUS166"}
: ${CARDINAL_I:=openmc.i}
: ${CARDINAL_DIR:=/ccs/home/novak/frontier/cardinal}
: ${QUEUE:="batch"}
: ${NEKRS_HOME:="$CARDINAL_DIR/install"}
: ${OCCA_CACHE_DIR:="$PWD/.cache/occa"}
: ${CARDINAL_BIN:="$CARDINAL_DIR/cardinal-opt"}
: ${OPENMC_CROSS_SECTIONS:=/lustre/orion/fus166/proj-shared/novak/cross_sections/endfb-vii.1-hdf5/cross_sections.xml}
: ${NEKRS_CACHE_BCAST:=1}
: ${NEKRS_SKIP_BUILD_ONLY:=1}

# =============================================================================
# Adapted from nrsqsub_frontier
# =============================================================================

if [ -z "$PROJ_ID" ]; then
  echo "ERROR: PROJ_ID is empty"
  exit 1
fi

if [ -z "$QUEUE" ]; then
  echo "ERROR: QUEUE is empty"
  exit 1
fi

if [ $# -lt 2 ] || [ $# -gt 3 ]; then
  echo "usage: [PROJ_ID] [QUEUE] $0 [casename] <number of compute nodes> <hh:mm>"
  exit 0
fi

NVME_HOME="/mnt/bb/$USER/"

bin=$CARDINAL_BIN
bin_nekrs=${NEKRS_HOME}/bin/nekrs
case=$1
nodes=$2
time=$3
gpu_per_node=8
cores_per_numa=7

# special rules for OpenMC-only cases
if [ $# -eq 2 ]; then
  nodes=$1
  time=$2
fi

let nn=$nodes*$gpu_per_node
let ntasks=nn
backend=HIP

if [ ! -f $bin ]; then
  echo "Cannot find" $bin
  exit 1
fi

if [ $# -ne 2 ]; then
  if [ ! -f $case.par ]; then
    echo "Cannot find" $case.par
    exit 1
  fi

  if [ ! -f $case.udf ]; then
    echo "Cannot find" $case.udf
    exit 1
  fi

  if [ ! -f $case.re2 ]; then
    echo "Cannot find" $case.re2
    exit 1
  fi
fi

striping_unit=16777216
max_striping_factor=400
let striping_factor=$nodes/2
if [ $striping_factor -gt $max_striping_factor ]; then
  striping_factor=$max_striping_factor
fi
if [ $striping_factor -lt 1 ]; then
  striping_factor=1
fi

MPICH_MPIIO_HINTS="*:cray_cb_write_lock_mode=2:cray_cb_nodes_multiplier=4:striping_unit=${striping_unit}:striping_factor=${striping_factor}:romio_cb_write=enable:romio_ds_write=disable:romio_no_indep_rw=true"

# sbatch
SFILE=s.bin
echo "#!/bin/bash" > $SFILE
echo "#SBATCH -A $PROJ_ID" >>$SFILE
echo "#SBATCH -J cardinal_$case" >>$SFILE
echo "#SBATCH -o %x-%j.out" >>$SFILE
echo "#SBATCH -t $time:00" >>$SFILE
echo "#SBATCH -N $nodes" >>$SFILE
echo "#SBATCH -p $QUEUE" >>$SFILE
echo "#SBATCH -C nvme" >>$SFILE
echo "#SBATCH --exclusive" >>$SFILE
echo "#SBATCH --ntasks-per-node=$gpu_per_node" >>$SFILE
echo "#SBATCH --gpus-per-task=1" >>$SFILE
echo "#SBATCH --gpu-bind=closest" >>$SFILE
echo "#SBATCH --cpus-per-task=$cores_per_numa" >>$SFILE

echo "module load PrgEnv-gnu" >> $SFILE
echo "module load craype-accel-amd-gfx90a" >> $SFILE
echo "module load cray-mpich" >> $SFILE
echo "module load rocm" >> $SFILE
echo "module unload cray-libsci" >> $SFILE
echo "module list" >> $SFILE

echo "rocm-smi" >>$SFILE
echo "rocm-smi --showpids" >>$SFILE

echo "squeue -u \$USER" >>$SFILE

echo "export MPICH_GPU_SUPPORT_ENABLED=1" >>$SFILE

## These must be set before compiling so the executable picks up GTL
echo "export PE_MPICH_GTL_DIR_amd_gfx90a=\"-L${CRAY_MPICH_ROOTDIR}/gtl/lib\"" >> $SFILE
echo "export PE_MPICH_GTL_LIBS_amd_gfx90a=\"-lmpi_gtl_hsa\"" >> $SFILE

#echo "export PMI_MMAP_SYNC_WAIT_TIME=1800" >> $SFILE # avoid timeout by MPI init for large job

echo "ulimit -s unlimited " >>$SFILE
echo "export NEKRS_HOME=$NEKRS_HOME" >>$SFILE
echo "export NEKRS_GPU_MPI=1 " >>$SFILE

echo "export NVME_HOME=$NVME_HOME" >>$SFILE

echo "export MPICH_MPIIO_HINTS=$MPICH_MPIIO_HINTS" >>$SFILE
echo "export MPICH_MPIIO_STATS=1" >>$SFILE

echo "export MPICH_OFI_NIC_POLICY=NUMA" >>$SFILE
echo "export NEKRS_CACHE_BCAST=$NEKRS_CACHE_BCAST" >> $SFILE

echo "if [ \$NEKRS_CACHE_BCAST -eq 1 ]; then" >> $SFILE
echo "  export NEKRS_LOCAL_TMP_DIR=\$NVME_HOME" >> $SFILE
echo "fi" >> $SFILE
echo "" >> $SFILE
echo "date" >>$SFILE
echo "" >> $SFILE

bin_nvme=$NVME_HOME"cardinal-bin"
bin_nvme_nekrs=$NVME_HOME"nekrs-bin"
bin_nvme_libs=$bin_nvme"_libs"
bin_nvme_libs_nekrs=$bin_nvme_nekrs"_libs"
echo "sbcast -fp --send-libs $bin $bin_nvme" >> $SFILE
echo "sbcast -fp --send-libs $bin_nekrs $bin_nvme_nekrs" >> $SFILE
echo "if [ ! \"\$?\" == \"0\" ]; then"  >> $SFILE
echo "    echo \"SBCAST failed!\"" >> $SFILE
echo "    exit 1" >> $SFILE
echo "fi" >> $SFILE

echo "export LD_LIBRARY_PATH=$bin_nvme_libs_nekrs:$bin_nvme_libs:${LD_LIBRARY_PATH}" >> $SFILE
echo "export LD_PRELOAD=$bin_nvme_libs/libnekrs.so:$bin_nvme_libs/libocca.so:$bin_nvme_libs/libnekrs-hypre-device.so:$bin_nvme_libs/libnekrs-hypre.so" >> $SFILE

echo "ls -ltra $NVME_HOME" >> $SFILE
echo "ls -ltra $bin_nvme_libs" >> $SFILE
echo "ldd $bin_nvme" >> $SFILE

if [ $NEKRS_SKIP_BUILD_ONLY -eq 0 ]; then
echo "# precompilation" >>$SFILE
echo "srun -N 1 -n 1 $bin_nvme -i $CARDINAL_I --nekrs-setup $case --nekrs-backend $backend --nekrs-device-id 0 --nekrs-build-only $ntasks" >>$SFILE
fi
echo "" >> $SFILE

echo "# actual run" >>$SFILE
echo "srun -N $nodes -n $ntasks $bin_nvme -i $CARDINAL_I --nekrs-setup $case --nekrs-backend $backend --nekrs-device-id 0" >>$SFILE

sbatch $SFILE

Nek5k

Nek5k is a cluster at ANL with 40 nodes, each with 40 cores. We use conda to set up a proper environment on Nek5k for running Cardinal. To use this environment, you will need to follow these steps the first time you use Nek5k:

The first time you log in, run from the command line:


module load openmpi/4.0.1/gcc/8.3.1 cmake openmpi/4.0.1/gcc/8.3.1-hdf5-1.10.6 anaconda3/anaconda3
conda init

Log out, then log back in
Add the following to your ~/.bashrc:


module load openmpi/4.0.1/gcc/8.3.1 cmake openmpi/4.0.1/gcc/8.3.1-hdf5-1.10.6 anaconda3/anaconda3
conda activate

Log out, then log back in

After following these steps, you should not require any further actions to run Cardinal on Nek5k. Your ~/.bashrc should look something like below. The content within the conda initialize section is added automatically by conda when you perform the steps above.

Listing 5: Sample ~/.bashrc for Nek5k

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

module load openmpi/4.0.1/gcc/8.3.1 cmake openmpi/4.0.1/gcc/8.3.1-hdf5-1.10.6 anaconda3/anaconda3

conda activate

# Update for your Cardinal repository location
export NEKRS_HOME=$HOME/cardinal/install

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/shared/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/shared/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/shared/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/shared/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

# need to point to a newer CMake version
export PATH=/shared/cmake-3.24.2/bin:$PATH

Listing 6: Sample job script for Nek5k

#!/bin/bash

# Usage:
# 1. Copy to the directory where you have your files
# 2. Update any needed environment variables and input file names in this script
# 3. qsub job_nek5k

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
#SBATCH --time=00:20:00
#SBATCH --output=pincell.log
#SBATCH -p compute

# Revise for your repository and cross section data locations
export OPENMC_CROSS_SECTIONS=$HOME/cross_sections/endfb71_hdf5/cross_sections.xml
export CARDINAL_DIR=$HOME/cardinal
export NEKRS_HOME=$CARDINAL_DIR/install

# The name of the input file you want to run
input_file=nek_master.i

# Run a Cardinal case
mpirun -np 40 $CARDINAL_DIR/cardinal-opt -i $input_file > logfile

Pinchot

Pinchot is a small Ubuntu server at the University of Illinois hosted in Dr. Novak's lab. While not an HPC system per se, we include these instructions on this page to facilitate development among the Cardinal team. There is no job queue on Pinchot.

Listing 7: Sample ~/.bashrc for Pinchot

module load openmpi/ubuntu/5.0.0
module load hdf5/ubuntu/1.14.3

# change to your Cardinal location (either the shared location in /shared/data,
# or to a location in your home directory
CARDINAL_DIR=$(realpath -P /shared/data/cardinal)
#CARDINAL_DIR=$(realpath -P /home/ajnovak2/cardinal)
export NEKRS_HOME=$CARDINAL_DIR/install

export LIBMESH_JOBS=80
export MOOSE_JOBS=80
export HDF5_ROOT=/software/HDF5-1.14.3-ubuntu22

# revise for your cross section location
export OPENMC_CROSS_SECTIONS=/shared/data/endfb-vii.1-hdf5/cross_sections.xml

export ENABLE_DAGMC=true
export PATH=${PATH}:${NEKRS_HOME}/bin:${CARDINAL_DIR}
export MOOSE_DIR=$CARDINAL_DIR/contrib/moose
export PYTHONPATH=$MOOSE_DIR/python:${PYTHONPATH}

Sawtooth

Sawtooth is an HPC system at Idaho National Laboratory (INL) with 99,792 cores (48 cores per node). The max number of cores a job can run is 80,000, resulting in a max number of nodes of 1666. Every job should use ncpus=48 to maximize the power of each node requested. The below script requests 1 node (select=1). In order to maximizie performance on the node, always use ncpus = mpiprocs * ompthreads = 48, and make sure that --n-threads in the job launch equals the same value as ompthreads.

Listing 8: Sample ~/.bashrc for Sawtooth

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

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

module purge
module load use.moose
module load moose-tools
module load openmpi/4.1.6-gcc-12.3.0-panw
module load cmake/3.27.7-gcc-12.3.0-5cfk

# Revise for your repository location
export NEKRS_HOME=$HOME/cardinal/install
export OPENMC_CROSS_SECTIONS=$HOME/cross_sections/endfb-vii.1-hdf5/cross_sections.xml

Listing 9: Sample job script with the moose project code

#!/bin/bash

# Launch your job by entering the following into the terminal:
# qsub job_sawtooth

#PBS -l select=1:ncpus=48:mpiprocs=24:ompthreads=2
#PBS -l walltime=5:00
#PBS -m ae
#PBS -N cardinal
#PBS -j oe
#PBS -P moose
#PBS -V

module purge
module load use.moose
module load moose-tools
module load openmpi/4.1.5_ucx1.14.1
module load cmake/3.27.7-gcc-12.3.0-5cfk

# Revise for your repository location
export CARDINAL_DIR=$HOME/cardinal
export OMP_PROC_BIND=true

# Run an OpenMC case
cd $CARDINAL_DIR/test/tests/neutronics/feedback/lattice
rm logfile
mpirun $CARDINAL_DIR/cardinal-opt -i openmc_master.i --n-threads=2 > logfile

# Run a NekRS case
cd $CARDINAL_DIR/test/tests/cht/sfr_pincell
rm logfile
mpirun $CARDINAL_DIR/cardinal-opt -i nek_master.i > logfile

Summit

Summit is an HPC system at ORNL with approximately 4,600 compute nodes, each of which has two IBM POWER9 processors and six NVIDIA Tesla V100 GPUs. Remember that in order to build Cardinal with GPU support, set the appropriate variable in the Makefile to true (1):


OCCA_CUDA_ENABLED=1
OCCA_HIP_ENABLED=0
OCCA_OPENCL_ENABLED=0

Listing 10: Sample ~/.bashrc for Summit

module purge
module load DefApps-2023
module unload xl/16.1.1-10 lsf-tools/2.0 xalt/1.2.1 hsi/5.0.2.p5
module load gcc/9.1.0
module load python/3.7.0-anaconda3-5.3.0
module load hdf5/1.10.7
module load cmake/3.27.7
module load eigen/3.3.9
module load nsight-compute/2021.2.1
module load nsight-systems/2021.3.1.54
module load cuda/11.0.3

# Revise for your Cardinal repository location
DIRECTORY_WHERE_YOU_HAVE_CARDINAL=$MEMBERWORK/nfi128/summit
cd $DIRECTORY_WHERE_YOU_HAVE_CARDINAL

# This is needed because your home directory on Summit is actually a symlink
HOME_DIRECTORY_SYM_LINK=$(realpath -P $DIRECTORY_WHERE_YOU_HAVE_CARDINAL)
export NEKRS_HOME=$HOME_DIRECTORY_SYM_LINK/cardinal/install
export OCCA_DIR=$NEKRS_HOME

export HDF5_ROOT=/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/gcc-9.1.0/hdf5-1.10.7-yxvwkhm4nhgezbl2mwzdruwoaiblt6q2
export HDF5_INCLUDE_DIR=$HDF5_ROOT/include
export HDF5_LIBDIR=$HDF5_ROOT/lib

export OPENMC_CROSS_SECTIONS=$HOME_DIRECTORY_SYM_LINK/cross_sections/endfb-vii.1-hdf5/cross_sections.xml

Listing 11: Sample job script for Summit

#/bin/bash

# Usage:
# 1. Copy to the directory where you have your files
# 2. Update any needed environment variables and input files names in this script
# 3. ./job_summit [casename] <nodes> <hh:mm>
#    where [casename] is the NekRS case (used for precompiling). If you are not using
#                     NekRS, omit this field.
#          <nodes> is the number of nodes you want to use
#          <hh::mm> is the maximum wall time you want

# additional variables you may want to change
: ${PROJ_ID:=""}
: ${CARDINAL_I:=nek_master.i}
: ${CARDINAL_DIR:=/gpfs/alpine/cfd151/scratch/novak/cardinal}
: ${NEKRS_HOME:="$CARDINAL_DIR/install"}
: ${OCCA_CACHE_DIR:="$PWD/.cache/occa"}
: ${CARDINAL_BIN:="$CARDINAL_DIR/cardinal-opt"}
: ${OPENMC_CROSS_SECTIONS:=/autofs/nccs-svm1_home1/novak/cross_sections/endfb71_hdf5/cross_sections.xml}

# =============================================================================
# Adapted from nrsqsub_summit
# =============================================================================

if [ -z "$PROJ_ID" ]; then
  echo "ERROR: PROJ_ID is empty"
  exit 1
fi

if [ $# -lt 2 ] || [ $# -gt 3 ]; then
  echo "usage: [PROJ_ID] [CPUONLY=1] $0 [casename] <number of compute nodes> <hh:mm>"
  exit 0
fi

NVME_HOME="/mnt/bb/$USER/"
XL_HOME="/sw/summit/xl/16.1.1-3/xlC/16.1.1"

: ${CPUONLY:=0}
export NEKRS_HOME
export OPENMC_CROSS_SECTIONS
export OCCA_CACHE_DIR
export NEKRS_HYPRE_NUM_THREADS=1
export OGS_MPI_SUPPORT=1
export OCCA_CXX=
export OCCA_CXXFLAGS="-O3 -qarch=pwr9 -qhot -DUSE_OCCA_MEM_BYTE_ALIGN=64"
export OCCA_LDFLAGS="$XL_HOME/lib/libibmc++.a"

#export OCCA_VERBOSE=1
#export OMPI_LD_PRELOAD_POSTPEND=$OLCF_SPECTRUM_MPI_ROOT/lib/libmpitrace.so

#export PAMI_ENABLE_STRIPING=1
#export PAMI_IBV_ADAPTER_AFFINITY=1
#export PAMI_IBV_DEVICE_NAME="mlx5_0:1,mlx5_3:1"
#export PAMI_IBV_DEVICE_NAME_1="mlx5_3:1,mlx5_0:1"

# work-around for barrier issue
export OMPI_MCA_coll_ibm_collselect_mode_barrier=failsafe

bin=$CARDINAL_BIN
case=$1
nodes=$2
time=$3
gpu_per_node=6
cores_per_socket=21

# special rules for OpenMC-only cases
if [ $# -eq 2 ]; then
  nodes=$1
  time=$2
fi

let nn=$nodes*$gpu_per_node
let ntasks=nn
backend=CUDA

if [ $CPUONLY -eq 1 ]; then
  backend=CPU
  let nn=2*$nodes
  let ntasks=$nn*$cores_per_socket
fi

if [ ! -f $bin ]; then
  echo "Cannot find" $bin
  exit 1
fi

if [ $# -ne 2 ]; then
  if [ ! -f $case.par ]; then
    echo "Cannot find" $case.par
    exit 1
  fi

  if [ ! -f $case.udf ]; then
    echo "Cannot find" $case.udf
    exit 1
  fi

  if [ ! -f $case.oudf ]; then
    echo "Cannot find" $case.oudf
    exit 1
  fi

  if [ ! -f $case.re2 ]; then
    echo "Cannot find" $case.re2
    exit 1
  fi
fi

mkdir -p $OCCA_CACHE_DIR 2>/dev/null

if [ $# -eq 3 ]; then
  while true; do
    read -p "Do you want precompile? [Y/N]" yn
    case $yn in
      [Yy]* )
        echo $NEKRS_HOME
        mpirun -pami_noib -np 1 $NEKRS_HOME/bin/nekrs --setup $case --build-only $ntasks --backend $backend;
        if [ $? -ne 0 ]; then
          exit 1
        fi
        break ;;
      * )
        break ;;
    esac
  done
fi

if [ $CPUONLY -eq 1 ]; then
  jsrun="jsrun -X 1 -n$nodes -r1 -a1 -c1 -g0 -b packed:1 -d packed cp -a $OCCA_CACHE_DIR/* $NVME_HOME; export OCCA_CACHE_DIR=$NVME_HOME; jsrun -X 1 -n$nn -a$cores_per_socket -c$cores_per_socket -g0 -b packed:1 -d packed $bin -i $CARDINAL_I"
else
  jsrun="jsrun -X 1 -n$nodes -r1 -a1 -c1 -g0 -b packed:1 -d packed cp -a $OCCA_CACHE_DIR/* $NVME_HOME; export OCCA_CACHE_DIR=$NVME_HOME; jsrun --smpiargs='-gpu' -X 1 -n$nn -r$gpu_per_node -a1 -c2 -g1 -b rs -d packed $bin -i $CARDINAL_I --nekrs-backend $backend --nekrs-device-id 0"
fi

cmd="bsub -nnodes $nodes -alloc_flags NVME -W $time -P $PROJ_ID -J cardinal_$case \"${jsrun}\""
echo $cmd
$cmd

Eddy

Eddy is a cluster at ANL with eleven 32-core nodes, five 40-core nodes, and six 80-core nodes.

Listing 12: Sample ~/.bashrc for Eddy

module purge
module load moose-dev-gcc
module load cmake/3.25.0

export HDF5_ROOT=/opt/moose/seacas
export HDF5_INCLUDE_DIR=$HDF5_ROOT/include
export HDF5_LIBDIR=$HDF5_ROOT/lib

# Revise for your Cardinal repository location
DIRECTORY_WHERE_YOU_HAVE_CARDINAL=$HOME

# This is needed because your home directory on Eddy is actually a symlink
HOME_DIRECTORY_SYM_LINK=$(realpath -P $DIRECTORY_WHERE_YOU_HAVE_CARDINAL)
export NEKRS_HOME=$HOME_DIRECTORY_SYM_LINK/cardinal/install
export OPENMC_CROSS_SECTIONS=$HOME_DIRECTORY_SYM_LINK/cross_sections/endfb-vii.1-hdf5/cross_sections.xml

!listing! scripts/job_eddy language=bash caption=Sample job script for Eddy with the 32-core partition id=e2

(scripts/job_bebop)

#!/bin/bash

# Usage:
# 1. Copy to the directory where you have your files
# 2. Update any needed environment variables and input file names in this script
# 3. sbatch job_bebop

#SBATCH --job-name=cardinal
#SBATCH --account=startup
#SBATCH --partition=bdwall
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=36
#SBATCH --output=run.out
#SBATCH --error=run.error
#SBATCH --time=00:10:00

module purge
module load cmake/3.20.3-vedypwm
module load gcc/9.2.0-pkmzczt
module load openmpi/4.1.1-ckyrlu7
module load python/intel-parallel-studio-cluster.2019.5-zqvneip/3.6.9

# Revise for your repository and cross section data locations
DIRECTORY_WHERE_YOU_HAVE_CARDINAL=$HOME
HOME_DIRECTORY_SYM_LINK=$(realpath -P $DIRECTORY_WHERE_YOU_HAVE_CARDINAL)
export NEKRS_HOME=$HOME_DIRECTORY_SYM_LINK/cardinal/install

export CARDINAL_DIR=$HOME_DIRECTORY_SYM_LINK/cardinal

# The name of the input file you want to run
input_file=openmc.i

# Run a Cardinal case
srun -n 36 $CARDINAL_DIR/cardinal-opt -i $input_file > logfile

(scripts/job_frontier)

#/bin/bash

# Usage:
# 1. Copy to the directory where you have your files
# 2. Update any needed environment variables and input files names in this script
# 3. ./job_frontier [casename] <nodes> <hh:mm>
#    where [casename] is the NekRS case (used for precompiling). If not using
#                     NekRS, omit this field.
#          <nodes>    is the number of nodes you want to use
#          <hh::mm>   is the maximum wall time you want

# additional variables you may want to change
: ${PROJ_ID:="FUS166"}
: ${CARDINAL_I:=openmc.i}
: ${CARDINAL_DIR:=/ccs/home/novak/frontier/cardinal}
: ${QUEUE:="batch"}
: ${NEKRS_HOME:="$CARDINAL_DIR/install"}
: ${OCCA_CACHE_DIR:="$PWD/.cache/occa"}
: ${CARDINAL_BIN:="$CARDINAL_DIR/cardinal-opt"}
: ${OPENMC_CROSS_SECTIONS:=/lustre/orion/fus166/proj-shared/novak/cross_sections/endfb-vii.1-hdf5/cross_sections.xml}
: ${NEKRS_CACHE_BCAST:=1}
: ${NEKRS_SKIP_BUILD_ONLY:=1}

# =============================================================================
# Adapted from nrsqsub_frontier
# =============================================================================

if [ -z "$PROJ_ID" ]; then
  echo "ERROR: PROJ_ID is empty"
  exit 1
fi

if [ -z "$QUEUE" ]; then
  echo "ERROR: QUEUE is empty"
  exit 1
fi

if [ $# -lt 2 ] || [ $# -gt 3 ]; then
  echo "usage: [PROJ_ID] [QUEUE] $0 [casename] <number of compute nodes> <hh:mm>"
  exit 0
fi

NVME_HOME="/mnt/bb/$USER/"

bin=$CARDINAL_BIN
bin_nekrs=${NEKRS_HOME}/bin/nekrs
case=$1
nodes=$2
time=$3
gpu_per_node=8
cores_per_numa=7

# special rules for OpenMC-only cases
if [ $# -eq 2 ]; then
  nodes=$1
  time=$2
fi

let nn=$nodes*$gpu_per_node
let ntasks=nn
backend=HIP

if [ ! -f $bin ]; then
  echo "Cannot find" $bin
  exit 1
fi

if [ $# -ne 2 ]; then
  if [ ! -f $case.par ]; then
    echo "Cannot find" $case.par
    exit 1
  fi

  if [ ! -f $case.udf ]; then
    echo "Cannot find" $case.udf
    exit 1
  fi

  if [ ! -f $case.re2 ]; then
    echo "Cannot find" $case.re2
    exit 1
  fi
fi

striping_unit=16777216
max_striping_factor=400
let striping_factor=$nodes/2
if [ $striping_factor -gt $max_striping_factor ]; then
  striping_factor=$max_striping_factor
fi
if [ $striping_factor -lt 1 ]; then
  striping_factor=1
fi

MPICH_MPIIO_HINTS="*:cray_cb_write_lock_mode=2:cray_cb_nodes_multiplier=4:striping_unit=${striping_unit}:striping_factor=${striping_factor}:romio_cb_write=enable:romio_ds_write=disable:romio_no_indep_rw=true"

# sbatch
SFILE=s.bin
echo "#!/bin/bash" > $SFILE
echo "#SBATCH -A $PROJ_ID" >>$SFILE
echo "#SBATCH -J cardinal_$case" >>$SFILE
echo "#SBATCH -o %x-%j.out" >>$SFILE
echo "#SBATCH -t $time:00" >>$SFILE
echo "#SBATCH -N $nodes" >>$SFILE
echo "#SBATCH -p $QUEUE" >>$SFILE
echo "#SBATCH -C nvme" >>$SFILE
echo "#SBATCH --exclusive" >>$SFILE
echo "#SBATCH --ntasks-per-node=$gpu_per_node" >>$SFILE
echo "#SBATCH --gpus-per-task=1" >>$SFILE
echo "#SBATCH --gpu-bind=closest" >>$SFILE
echo "#SBATCH --cpus-per-task=$cores_per_numa" >>$SFILE

echo "module load PrgEnv-gnu" >> $SFILE
echo "module load craype-accel-amd-gfx90a" >> $SFILE
echo "module load cray-mpich" >> $SFILE
echo "module load rocm" >> $SFILE
echo "module unload cray-libsci" >> $SFILE
echo "module list" >> $SFILE

echo "rocm-smi" >>$SFILE
echo "rocm-smi --showpids" >>$SFILE

echo "squeue -u \$USER" >>$SFILE

echo "export MPICH_GPU_SUPPORT_ENABLED=1" >>$SFILE

## These must be set before compiling so the executable picks up GTL
echo "export PE_MPICH_GTL_DIR_amd_gfx90a=\"-L${CRAY_MPICH_ROOTDIR}/gtl/lib\"" >> $SFILE
echo "export PE_MPICH_GTL_LIBS_amd_gfx90a=\"-lmpi_gtl_hsa\"" >> $SFILE

#echo "export PMI_MMAP_SYNC_WAIT_TIME=1800" >> $SFILE # avoid timeout by MPI init for large job

echo "ulimit -s unlimited " >>$SFILE
echo "export NEKRS_HOME=$NEKRS_HOME" >>$SFILE
echo "export NEKRS_GPU_MPI=1 " >>$SFILE

echo "export NVME_HOME=$NVME_HOME" >>$SFILE

echo "export MPICH_MPIIO_HINTS=$MPICH_MPIIO_HINTS" >>$SFILE
echo "export MPICH_MPIIO_STATS=1" >>$SFILE

echo "export MPICH_OFI_NIC_POLICY=NUMA" >>$SFILE
echo "export NEKRS_CACHE_BCAST=$NEKRS_CACHE_BCAST" >> $SFILE

echo "if [ \$NEKRS_CACHE_BCAST -eq 1 ]; then" >> $SFILE
echo "  export NEKRS_LOCAL_TMP_DIR=\$NVME_HOME" >> $SFILE
echo "fi" >> $SFILE
echo "" >> $SFILE
echo "date" >>$SFILE
echo "" >> $SFILE

bin_nvme=$NVME_HOME"cardinal-bin"
bin_nvme_nekrs=$NVME_HOME"nekrs-bin"
bin_nvme_libs=$bin_nvme"_libs"
bin_nvme_libs_nekrs=$bin_nvme_nekrs"_libs"
echo "sbcast -fp --send-libs $bin $bin_nvme" >> $SFILE
echo "sbcast -fp --send-libs $bin_nekrs $bin_nvme_nekrs" >> $SFILE
echo "if [ ! \"\$?\" == \"0\" ]; then"  >> $SFILE
echo "    echo \"SBCAST failed!\"" >> $SFILE
echo "    exit 1" >> $SFILE
echo "fi" >> $SFILE

echo "export LD_LIBRARY_PATH=$bin_nvme_libs_nekrs:$bin_nvme_libs:${LD_LIBRARY_PATH}" >> $SFILE
echo "export LD_PRELOAD=$bin_nvme_libs/libnekrs.so:$bin_nvme_libs/libocca.so:$bin_nvme_libs/libnekrs-hypre-device.so:$bin_nvme_libs/libnekrs-hypre.so" >> $SFILE

echo "ls -ltra $NVME_HOME" >> $SFILE
echo "ls -ltra $bin_nvme_libs" >> $SFILE
echo "ldd $bin_nvme" >> $SFILE

if [ $NEKRS_SKIP_BUILD_ONLY -eq 0 ]; then
echo "# precompilation" >>$SFILE
echo "srun -N 1 -n 1 $bin_nvme -i $CARDINAL_I --nekrs-setup $case --nekrs-backend $backend --nekrs-device-id 0 --nekrs-build-only $ntasks" >>$SFILE
fi
echo "" >> $SFILE

echo "# actual run" >>$SFILE
echo "srun -N $nodes -n $ntasks $bin_nvme -i $CARDINAL_I --nekrs-setup $case --nekrs-backend $backend --nekrs-device-id 0" >>$SFILE

sbatch $SFILE

(scripts/job_nek5k)

#!/bin/bash

# Usage:
# 1. Copy to the directory where you have your files
# 2. Update any needed environment variables and input file names in this script
# 3. qsub job_nek5k

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
#SBATCH --time=00:20:00
#SBATCH --output=pincell.log
#SBATCH -p compute

# Revise for your repository and cross section data locations
export OPENMC_CROSS_SECTIONS=$HOME/cross_sections/endfb71_hdf5/cross_sections.xml
export CARDINAL_DIR=$HOME/cardinal
export NEKRS_HOME=$CARDINAL_DIR/install

# The name of the input file you want to run
input_file=nek_master.i

# Run a Cardinal case
mpirun -np 40 $CARDINAL_DIR/cardinal-opt -i $input_file > logfile

(scripts/job_sawtooth)

#!/bin/bash

# Launch your job by entering the following into the terminal:
# qsub job_sawtooth

#PBS -l select=1:ncpus=48:mpiprocs=24:ompthreads=2
#PBS -l walltime=5:00
#PBS -m ae
#PBS -N cardinal
#PBS -j oe
#PBS -P moose
#PBS -V

module purge
module load use.moose
module load moose-tools
module load openmpi/4.1.5_ucx1.14.1
module load cmake/3.27.7-gcc-12.3.0-5cfk

# Revise for your repository location
export CARDINAL_DIR=$HOME/cardinal
export OMP_PROC_BIND=true

# Run an OpenMC case
cd $CARDINAL_DIR/test/tests/neutronics/feedback/lattice
rm logfile
mpirun $CARDINAL_DIR/cardinal-opt -i openmc_master.i --n-threads=2 > logfile

# Run a NekRS case
cd $CARDINAL_DIR/test/tests/cht/sfr_pincell
rm logfile
mpirun $CARDINAL_DIR/cardinal-opt -i nek_master.i > logfile

(scripts/job_summit)

#/bin/bash

# Usage:
# 1. Copy to the directory where you have your files
# 2. Update any needed environment variables and input files names in this script
# 3. ./job_summit [casename] <nodes> <hh:mm>
#    where [casename] is the NekRS case (used for precompiling). If you are not using
#                     NekRS, omit this field.
#          <nodes> is the number of nodes you want to use
#          <hh::mm> is the maximum wall time you want

# additional variables you may want to change
: ${PROJ_ID:=""}
: ${CARDINAL_I:=nek_master.i}
: ${CARDINAL_DIR:=/gpfs/alpine/cfd151/scratch/novak/cardinal}
: ${NEKRS_HOME:="$CARDINAL_DIR/install"}
: ${OCCA_CACHE_DIR:="$PWD/.cache/occa"}
: ${CARDINAL_BIN:="$CARDINAL_DIR/cardinal-opt"}
: ${OPENMC_CROSS_SECTIONS:=/autofs/nccs-svm1_home1/novak/cross_sections/endfb71_hdf5/cross_sections.xml}

# =============================================================================
# Adapted from nrsqsub_summit
# =============================================================================

if [ -z "$PROJ_ID" ]; then
  echo "ERROR: PROJ_ID is empty"
  exit 1
fi

if [ $# -lt 2 ] || [ $# -gt 3 ]; then
  echo "usage: [PROJ_ID] [CPUONLY=1] $0 [casename] <number of compute nodes> <hh:mm>"
  exit 0
fi

NVME_HOME="/mnt/bb/$USER/"
XL_HOME="/sw/summit/xl/16.1.1-3/xlC/16.1.1"

: ${CPUONLY:=0}
export NEKRS_HOME
export OPENMC_CROSS_SECTIONS
export OCCA_CACHE_DIR
export NEKRS_HYPRE_NUM_THREADS=1
export OGS_MPI_SUPPORT=1
export OCCA_CXX=
export OCCA_CXXFLAGS="-O3 -qarch=pwr9 -qhot -DUSE_OCCA_MEM_BYTE_ALIGN=64"
export OCCA_LDFLAGS="$XL_HOME/lib/libibmc++.a"

#export OCCA_VERBOSE=1
#export OMPI_LD_PRELOAD_POSTPEND=$OLCF_SPECTRUM_MPI_ROOT/lib/libmpitrace.so

#export PAMI_ENABLE_STRIPING=1
#export PAMI_IBV_ADAPTER_AFFINITY=1
#export PAMI_IBV_DEVICE_NAME="mlx5_0:1,mlx5_3:1"
#export PAMI_IBV_DEVICE_NAME_1="mlx5_3:1,mlx5_0:1"

# work-around for barrier issue
export OMPI_MCA_coll_ibm_collselect_mode_barrier=failsafe

bin=$CARDINAL_BIN
case=$1
nodes=$2
time=$3
gpu_per_node=6
cores_per_socket=21

# special rules for OpenMC-only cases
if [ $# -eq 2 ]; then
  nodes=$1
  time=$2
fi

let nn=$nodes*$gpu_per_node
let ntasks=nn
backend=CUDA

if [ $CPUONLY -eq 1 ]; then
  backend=CPU
  let nn=2*$nodes
  let ntasks=$nn*$cores_per_socket
fi

if [ ! -f $bin ]; then
  echo "Cannot find" $bin
  exit 1
fi

if [ $# -ne 2 ]; then
  if [ ! -f $case.par ]; then
    echo "Cannot find" $case.par
    exit 1
  fi

  if [ ! -f $case.udf ]; then
    echo "Cannot find" $case.udf
    exit 1
  fi

  if [ ! -f $case.oudf ]; then
    echo "Cannot find" $case.oudf
    exit 1
  fi

  if [ ! -f $case.re2 ]; then
    echo "Cannot find" $case.re2
    exit 1
  fi
fi

mkdir -p $OCCA_CACHE_DIR 2>/dev/null

if [ $# -eq 3 ]; then
  while true; do
    read -p "Do you want precompile? [Y/N]" yn
    case $yn in
      [Yy]* )
        echo $NEKRS_HOME
        mpirun -pami_noib -np 1 $NEKRS_HOME/bin/nekrs --setup $case --build-only $ntasks --backend $backend;
        if [ $? -ne 0 ]; then
          exit 1
        fi
        break ;;
      * )
        break ;;
    esac
  done
fi

if [ $CPUONLY -eq 1 ]; then
  jsrun="jsrun -X 1 -n$nodes -r1 -a1 -c1 -g0 -b packed:1 -d packed cp -a $OCCA_CACHE_DIR/* $NVME_HOME; export OCCA_CACHE_DIR=$NVME_HOME; jsrun -X 1 -n$nn -a$cores_per_socket -c$cores_per_socket -g0 -b packed:1 -d packed $bin -i $CARDINAL_I"
else
  jsrun="jsrun -X 1 -n$nodes -r1 -a1 -c1 -g0 -b packed:1 -d packed cp -a $OCCA_CACHE_DIR/* $NVME_HOME; export OCCA_CACHE_DIR=$NVME_HOME; jsrun --smpiargs='-gpu' -X 1 -n$nn -r$gpu_per_node -a1 -c2 -g1 -b rs -d packed $bin -i $CARDINAL_I --nekrs-backend $backend --nekrs-device-id 0"
fi

cmd="bsub -nnodes $nodes -alloc_flags NVME -W $time -P $PROJ_ID -J cardinal_$case \"${jsrun}\""
echo $cmd
$cmd

Bebop
Frontier
Nek 5 k
Pinchot
Sawtooth
Summit
Eddy