CP2K

What is 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. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, …), and classical force fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Quantum Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method. CP2K is written in Fortran 2003 and can be run efficiently in parallel using a combination of multi-threading, MPI, and CUDA. It is freely available under the GPL license.

On this page you will find the launching and submission syntax for CP2K code on ENEA-GRID . This is not a tutorial about using CP2K code; for that purpose you may find documentation and tutorial on the official web site www.cp2k.org/.

ENEA-GRID/CRESCO utilization rules.

JOB SUBMISSION SCRIPT on CRESCO6

To submit on CRESCO6 use the script named cp2k . To know the installed versions simply type from a terminal:

<user@cresco6x001 ~> cp2k --version

For help on how to use the script type from a terminal:

<user@cresco6x001 ~> cp2k-help

To submit a job on CRESCO6 with LSF commands, the general syntax is:

<user@cresco6x001 ~> export OMP_NUM_THREADS=nthreads
<user@cresco6x001 ~> bsub -n N -q queue bsub_options -o lsf_file.out -e file.err cp2k version mode input.inp output.out

Where:

version CP2K version (e.g. 6.1.0)
mode sopt, popt, psmp

Examples:

  • To submit a job on CRESCO6 using the 6.1.0 version with only MPI parallelism and using 96 cores (i.e. 2 nodes):

bsub -n 96 -q cresco6_48h24 -o lsf_file.out -e file.err cp2k 6.1.0 popt input.inp output.out

  • To submit the same job using 96 cores (i.e. 2nodes) on CRESCO6 using the 6.1.0 version but with hybrid MPI+OpenMP parallelism with 4 OpenMP threads (i.e. 24 MPI processes and 4 OpenMP threads, 24*4=96 total processes), you need to set and export the OMP_NUM_THREADS variable and remember that CRESCO6 has 48 cores per node (so ptile=48):

export OMP_NUM_THREADS=4
bsub -n 96 -q cresco6_48h24 -R "span[ptile=48]" -o lsf_file.out -e file.err cp2k 6.1.0 psmp input.inp output.out

  • To submit a job on CRESCO6 using the intel compiler and the serial version:

bsub -n 1 -q cresco6_h4 -o lsf_file.out -e file.err cp2k 6.1.0 sopt input.inp output.out

JOB SUBMISSION SCRIPT on XCRESCO

XCRESCO is a cluster (58 nodes + 2 login nodes) with 32 IBM powerpc cpus per node (with hyperthreading enabled) and 4 NVIDIA Volta V100 GPUs per node. In this cluster only CP2K with cuda support is installed. Jobs are submitted by means of SLURM with the sbatch command.

Example of a script to submit a job in hybrid mode with omp package (32 tasks, 2 threads per task and 4 gpus (for a total of 2 nodes occupied)):

#!/bin/ksh
#SBATCH --job-name=job_64_cores
#SBATCH --output=%x.%j.out         # Note: %x == job-name and %j == job_id
#SBATCH --error=%x.%j.err          #
#SBATCH –nodes=2                   # number of requested nodes
#SBATCH --ntasks-per-node=16       # number of mpi processes per single node
#SBATCH --cpus-per-task=2          # number of cores per single mpi process (i.e. number of threads for every mpi process)
#SBATCH --gpus-per-node=4          # number of requested gpus per node (from 1 to 4 in xcresco)
#SBATCH --time=00:30:00            # max duration of a job format: <hh:mm:ss>, up to 24 h
#SBATCH --exclusive                # exclusive use of requested nodes
module purge
module load profile/phys
module load cp2k/2024.1
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
mpirun cp2k.psmp -i file.inp -o file.out

Submit the previous script (named, e.g. submit.sh) with the command:

<user@xcrescox001> sbatch submit.sh