CP2K
CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
Versions
The latest version installed is CP2K 8.2. You can load the module compiled with GCC using
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 cp2k/8.2
You can also choose to use the version compiled with the Intel compiler if you prefer, but it seems less stable, as it sometimes crashes for unknown reasons.
module load StdEnv/2020 intel/2020.1.217 openmpi/4.0.3 cp2k/8.2
Example job
Here we will use the static calculation example from the CP2K website
First, log into one of our clusters and download the needed files with the following commands:
wget https://www.cp2k.org/_media/static_calculation.tgz tar xvfz static_calculation.tgz cd static_calculation/sample_output_no_smearing
Then, in that directory, create the following job submission script, with the account name changed to the one you are using.
#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --ntasks=4 # number of MPI processes
#SBATCH --mem-per-cpu=4G # memory; default unit is megabytes
#SBATCH --time=0-00:15 # time (DD-HH:MM)
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 cp2k/8.2
srun cp2k.popt -o Si_bulk8.out Si_bulk8.inp
To submit this job, execute:
sbatch mpi_job.sh
To see if the job completed, run the command
sq
If your job is no longer listed, that means it has completed.
The output of CP2K will be located in the file Si_bulk8.out. There will also be an output file named slurm-*.out which should be empty if the calculation completed without error.
Threaded/MPI jobs
The installation of CP2K version 8.2 and later includes both the MPI executable cp2k.popt and the OpenMP/MPI executable cp2k.psmp, which may give better performance for some calculations. Our test shows a 10% performance increase for QS/H2O-512.inp benchmark when using 2 threads per MPI process, compared to running MPI-only executable cp2k.popt (both runs used the same number of CPU cores in total).
Below is an example OpenMP/MPI job submission file for the Beluga cluster. To use on other clusters, the number of tasks would have to be adjusted to match the number of cores available on the nodes of that cluster. The performance changes when threads are used is highly problem dependent, and running the cp2k.psmp executable may actually be slower for some cases, so you must benchmark your code and choose the right option for your particular case.
#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --nodes=2
#SBATCH --ntasks=40 # number of MPI processes
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=3G # memory; default unit is megabytes
#SBATCH --time=0-00:59 # time (DD-HH:MM)
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 cp2k/8.2
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun --cpus-per-task=$OMP_NUM_THREADS cp2k.psmp -o H2O-512.out H2O-512.inp