Using software provided by EESSI

Once the environment is configured to access software provided by EESSI, all a user has to do is loading module, for example:

module load GROMACS/2024.1-foss-2023b

Example job script using EESSI software

We demonstrate the use of EESSI in a job script using GROMACS as an example. Below is a simple job script.

#!/bin/bash
#SBATCH --account=REPLACE_WITH_YOUR_NN****K
#SBATCH --job-name=EESSI_GROMACS
#SBATCH --partition=normal
#SBATCH --mem=16G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=2
#SBATCH --time=5 # short runtime

module load EESSI/2023.06
module load GROMACS/2024.1-foss-2023b

# prepare test data if not yet present
if [ ! -f GROMACS_TestCaseA.tar.gz ]; then
  curl -OL https://repository.prace-ri.eu/ueabs/GROMACS/1.2/GROMACS_TestCaseA.tar.gz
fi
if [ ! -f ion_channel.tpr ]; then
  tar xfz GROMACS_TestCaseA.tar.gz
fi

rm -f ener.edr eessi_logfile.log

# run GROMACS, we use 'time' to measure how long it runs
# note: downscaled to just 1k steps (full run is 10k steps)
time gmx mdrun -ntmpi 2 -ntomp 2 -s ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 1000

Change the account (in line #SBATCH --account=REPLACE...) in the job script above and store it in a file named eessi_gromacs.sh Then, submit it with

sbatch eessi_gromacs.sh

When the job has ended it should have produced a file slurm-JOBID.out where JOBID is the id of the job that was run.

Example job script using locally installed software

We demonstrate the minimal change needed to the run the same software (GROMACS) using the installations provided locally on the HPC systems the following script just comments out the line loading EESSI module (# module load EESSI/2023.06) and load a locally available GROMACS module

#!/bin/bash
#SBATCH --account=REPLACE_WITH_YOUR_NN****K
#SBATCH --job-name=LOCAL_GROMACS
#SBATCH --partition=normal
#SBATCH --mem=16G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=2
#SBATCH --time=5 # short runtime

# module load EESSI/2023.06
module load GROMACS/2023.1-foss-2022a

# prepare test data if not yet present
if [ ! -f GROMACS_TestCaseA.tar.gz ]; then
  curl -OL https://repository.prace-ri.eu/ueabs/GROMACS/1.2/GROMACS_TestCaseA.tar.gz
fi
if [ ! -f ion_channel.tpr ]; then
  tar xfz GROMACS_TestCaseA.tar.gz
fi

rm -f ener.edr eessi_logfile.log

# run GROMACS, we use 'time' to measure how long it runs
# note: downscaled to just 1k steps (full run is 10k steps)
time gmx mdrun -ntmpi 2 -ntomp 2 -s ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 1000

Change the account (in line #SBATCH --account=REPLACE...) in the job script above and store it in a file named local_gromacs.sh Then, submit it with

sbatch local_gromacs.sh

When the job has ended it should have produced a file slurm-JOBID.out where JOBID is the id of the job that was run. For the examples above, the slurm-JOBID.out file contains the following information (among other things):

  • which program was actually run, e.g., GROMACS conveniently reports somthing like

    Executable:   /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/skylake_avx512/software/GROMACS/2024.1-foss-2023b/bin/gmx

    Note, when using EESSI, the exact path will be specific to the compute node the job was running on, because for each machine the version optimised for that CPU architecture is automatically selected.

  • how well GROMACS was run, e.g., it prints Performance information (higher values for ns/day are better, for hours/ns lower values are better),

  • finally, the job statistics at the end show how long the overall job was run (see Elapsed wallclock time) and how well the job used the reserved resources (see Used CPU time and Unused CPU time)

Please, do experiment with the examples above. For example,

  • In a single job script, execute the software twice (line with time gmx ...) to observe different runtimes.

  • Replace GROMACS with another software that is provided by EESSI. All available packages can be listed with

    module avail

Additional information