Table of Contents

CP2K

Versatile ab initio and classical molecular dynamics. CP2k is suited for large parallel quantum chemistry calculations, in particular for AIMD.

Available

  • Puhti: 6.1
  • Mahti: 7.1

License

CP2k is freely available under the GPL license.

Usage

Check which versions are recommended:

module avail cp2k

You can find all installed versions with:

module spider cp2k

With each new project make sure that your job can efficiently utilize all the cores you request in the batch script.

Example batch script for Puhti using MPI-only parallelization

#!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --ntasks-per-node=40
#SBATCH --nodes=2
#SBATCH --mem-per-cpu=2GB
#SBATCH --partition=large
#SBATCH --account=<project>

module load cp2k

srun cp2k.popt H2O-32.inp > H2O-32.out

Example batch script for Mahti using mixed MPI-OpenMP parallelization

#!/bin/bash
#SBATCH --time=00:05:00
#SBATCH --ntasks-per-node=32  # 2 - 128
#SBATCH --cpus-per-task=4     # 128 / ntasks-per-node
#SBATCH --nodes=2
#SBATCH --partition=test
#SBATCH --account=<project>

module purge
module load cp2k/7.1-elpa

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
export OMP_PLACES=cores

srun cp2k.psmp H2O-32.inp > H2O-32.out

Performance notes

Mahti:

The following table shows average time [s] for one MD step for H2O-64 benchmark in Mahti. The column headers show how many omp-threads were used per mpi-task.

Nodes d1 d2 d4 d8
1 1.048 1.03 0.97 1.088
2 0.772 0.678 0.578 0.786
4 0.72 0.494 0.504 0.534
  • For 64 water molecules, the best performance is obtained with 2 full nodes, 32 mpi-tasks, and 4 OMP-threads per task (like the Mahti example) For this system the performance does not scale beyond 2 nodes.
  • Mixed parallization is efficient: choose tasks and threads so that they add up to 128 (physical) cores available per node (or upto 40 on Puhti)
  • Test for optimal run parameters for your model system and method
  • A version linked with ELPA (like the one above) is significantly faster with (metallic) systems that require large matrix diagonalizations for SCF
  • There are additional versions available at /appl/soft/chem/cp2k/7.1_extra, please see corresponding README.txt, but the one above is the fastest found so far

References

CP2K prints out a list of relevant publications towards the end of the log file. Choose and cite the ones relevant to the methods you've used.

More Information

Last edited Mon Aug 17 2020