NERSC-Perlmutter¶

Perlmutter is an HPE Cray EX supercomputer located at National Energy Research Scientific Computing Center (NERSC). Perlmutter has both GPU-accelerated nodes and CPU-only nodes.

$ ssh <username>@saul-p1.nersc.gov

Building WEST (GPU)¶

WEST executables can be compiled using the following script (tested on October 22, 2024):

$ cat build_west.sh
#!/bin/bash

module unload darshan
module load PrgEnv-nvidia
module load nvidia/23.9
module load cudatoolkit/12.2
module load craype-accel-nvidia80
module load cray-python/3.11.5

./configure --with-cuda=$CUDA_HOME --with-cuda-runtime=12.2 --with-cuda-cc=80 --with-cuda-mpi=yes

# Manually edit make.inc:

# MPIF90 = ftn
# F90 = ftn
# CC = cc
# LD = ftn
# BLAS_LIBS = # leave blank
# LAPACK_LIBS = # leave blank

make -j 8 pw

cd West

make conf PYT=python3 PYT_LDFLAGS="`python3-config --ldflags --embed`"
make -j 8 all

To use the script do:

$ bash build_west.sh

Running WEST Jobs (GPU)¶

The following is an example executable script run_west.sh to run the wstat.x WEST executable on two GPU nodes of Perlmutter with 4 MPI ranks and 4 GPUs per node. The <project_name> must be replaced with an active project allocation.

Important: The following environment variable is needed to work around a bug in ROMIO, Cray MPICH.

export ROMIO_FSTYPE_FORCE="ufs:"

Important: It is recommended to run the calculation from the Lustre file system ($PSCRATCH instead of /home).

$ cat run_west.sh
#!/bin/bash

#SBATCH --job-name=WEST
#SBATCH --time=00:20:00
#SBATCH --account=<project_name>
#SBATCH --constraint=gpu
#SBATCH --qos=debug
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --gpus-per-node=4
#SBATCH --cpus-per-task=32

module unload darshan
module load PrgEnv-nvidia
module load nvidia/23.9
module load cudatoolkit/12.2
module load craype-accel-nvidia80
module load cray-python/3.11.5

export LD_LIBRARY_PATH=/opt/cray/pe/python/3.11.5/lib:$LD_LIBRARY_PATH
export OMP_NUM_THREADS=1
export SLURM_CPU_BIND=cores
export MPICH_GPU_SUPPORT_ENABLED=1
export ROMIO_FSTYPE_FORCE="ufs:"

srun -n 8 ./wstat.x -i wstat.in &> wstat.out

Job submission is done with the following:

$ sbatch run_west.sh

Building WEST (CPU)¶

WEST executables can be compiled using the following script (tested on October 22, 2024):

$ cat build_west.sh
#!/bin/bash

module unload darshan
module load cpu
module load cray-fftw/3.3.10.6
module load cray-python/3.11.5

export CRAYPE_LINK_TYPE=dynamic
export MPIF90=ftn
export F90=ftn
export CC=cc

./configure --enable-openmp --with-scalapack

# Manually edit make.inc:

# DFLAGS = -D__FFTW3 -D__MPI -D__SCALAPACK
# IFLAGS = -I. -I$(TOPDIR)/include -I$(TOPDIR)/FoX/finclude -I/opt/cray/pe/fftw/3.3.10.6/x86_milan/include
# BLAS_LIBS = # leave blank
# LAPACK_LIBS = # leave blank

make -j 8 pw

cd West

make conf PYT=python3 PYT_LDFLAGS="`python3-config --ldflags --embed`"
make -j 8 all

To use the script do:

$ bash build_west.sh

Running WEST Jobs (CPU)¶

The following is an example executable script run_west.sh to run the wstat.x WEST executable on two CPU nodes of Perlmutter with 128 MPI ranks per node. The <project_name> must be replaced with an active project allocation.

Important: The following environment variable is needed to work around a bug in ROMIO, Cray MPICH.

export ROMIO_FSTYPE_FORCE="ufs:"

Important: It is recommended to run the calculation from the Lustre file system ($PSCRATCH instead of /home).

$ cat run_west.sh
#!/bin/bash

#SBATCH --job-name=WEST
#SBATCH --time=00:20:00
#SBATCH --account=<project_name>
#SBATCH --constraint=cpu
#SBATCH --qos=debug
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=128
#SBATCH --cpus-per-task=2

module unload darshan
module load cpu
module load cray-fftw/3.3.10.6
module load cray-python/3.11.5

export LD_LIBRARY_PATH=/opt/cray/pe/python/3.11.5/lib:$LD_LIBRARY_PATH
export OMP_NUM_THREADS=1
export SLURM_CPU_BIND=cores
export ROMIO_FSTYPE_FORCE="ufs:"

srun -n 256 ./wstat.x -i wstat.in &> wstat.out

Job submission is done with the following:

$ sbatch run_west.sh