Setting up t8code on JUWELS (or other Slurm based systems)

How to set up and run t8code on the JUWELS supercomputer

Setting up t8code on JUWELS is relatively simple. Basically, you can follow the Setup guide.

Required modules

Before compiling t8code you must load an MPI environment, we suggest loading the Intel and newest ParaStationMPI modules, at time of writing this was version 5.5.0-1-mt.

module load Intel
module load ParaStationMPI/5.5.0-1-mt

Make sure that these modules are loaded each time you compile or run code.

Configure and compile

Use your favourite configure options and run make.

If you do not explicitly need to link any blas or lapack code, deactivate linking with the configure flags

--without-blas
--without-lapack

Running an example

JUWELS uses the Slurm batch system. To set up a job you need to write a Slurm job file.

Here is a simple example file to run example/basic/t8_basic on 2 nodes with 48 processes per node:

#!/bin/bash -x
#SBATCH --account=ACCOUNTNAME
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=48
#SBATCH --output=mpi-out_basic_N2.%j
#SBATCH --error=mpi-err_basic_N2.%j
#SBATCH --time=00:10:00

# Make sure to replace ACCOUNTNAME with your JUWELS billing account.
# '--nodes' and '--ntasks-per-node' are the number of compute nodes and MPI ranks per node for this job.
# '--output' and '--error' denote output files for the standard output and error stream, %j denotes the JUWELS jobid.


# UPDATE THESE WHEN YOU UPDATE THE CONFIG ABOVE
NODES=2 # Number of compute nodes. Corresponds to '--nodes=2'.
PPN=48  # Number of MPI ranks per node. Corresponds to '--ntasks-per-node=48'.
NPROCS=$((NODES*PPN))

# The executable to run.
# Edit this path to match your installation.
EXEC=/path/to/your/t8code/tutorials/general/t8_step0_helloworld

# Arguments to pass to the program.
# In this case, no arguments are passed.
ARGS=""

# Logging
echo -------------------
echo Starting new run
echo $EXEC $ARGS
echo -------------------

# Starting the parallel job.
srun -n ${NPROCS} $EXEC $ARGS

Save this in a file named (for example) basic_2Nodes.pbs. You can then submit the job with sbatch:

sbatch basic_2Nodes.pbs