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CP2K

Description

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 Gaussian and Plane Waves (GPW) and the all-electron GPW (GAPW) approaches.

Available Versions

The following versions of CP2K are currently available:

  • Runtime dependencies:
    • None, required libraries and dependencies are loaded automatically with the CP2K/2022.1-foss-2022a module.

You can load the CP2K module with the following command: 

module load CP2K/2022.1-foss-2022a

  • Runtime dependencies:
    • None, required libraries and dependencies are loaded automatically with the CP2K/2023.1-foss-2022a module.

You can load the CP2K module with the following command: 

module load CP2K/2023.1-foss-2022a

  • Runtime dependencies:
    • None, required libraries and dependencies are loaded automatically with the CP2K/2023.1-foss-2022b module.

You can load the CP2K module with the following command: 

module load CP2K/2023.1-foss-2022b

User guide

For more information about the CP2K tutorials and documentation, refer to the CP2K HOWTOs.

Benchmarks

CP2K's grid-based calculation as well as DBCSR's block sparse matrix multiplication (Cannon algorithm) prefer a square number for the total rank-count (2D communication pattern).

It can be more efficient to leave CPU cores unused in order to achieve this square number property rather than using all cores with a "non-preferred" total rank-count. Counter-intuitively, even an unbalanced rank-count per node (i.e. different rank-counts per socket) can be an advantage. Pinning MPI processes and placing threads requires extra care to be taken on a per-node basis to load a dual-socket system in a balanced fashion or to set up space between ranks for the OpenMP threads.

In order to better understand how CP2K utilises the available hardware on Devana and how to get good performance we can examine the effect on benchmark performance of the choice of the number of MPI ranks per node and OpenMP threads.

The following command has been used to run the benchmarks: 

    mpiexec -np $mpi_rank --map-by slot:PE=$omp_thread -x OMP_PLACES=cores -x OMP_PROC_BIND=SPREAD -x OMP_NUM_THREADS=$omp_thread cp2k.psmp -i ${benchmark}.inp > ${benchmark}.out
where mpi_rank and omp_thread are the number of MPI ranks and OMP threads, respectively, and benchmark is the name of the benchmark.

Working directory

Single-node benchmarks have been run on local /work/ storage native to each compute node, which is generally faster than the shared storage hosting the /home/ and /scratch/ directories.

Benchmarks have been made on the following systems:

Ab-initio molecular dynamics of liquid water using the Born-Oppenheimer approach, using Quickstep DFT. Production quality settings for the basis sets (TZV2P) and the planewave cutoff (280 Ry) are chosen, and the Local Density Approximation (LDA) is used for the calculation of the Exchange-Correlation energy. The configurations were generated by classical equilibration, and the initial guess of the electronic density is made based on Atomic Orbitals. The single-node system contains 64 water molecules (192 atoms, 640 electrons) in a 12.4 ų cell and the cross-node system contains 256 water molecules (768 atoms, 2560 electrons) in a 19.7 ų cell. Both MDs are run for 10 steps.

Single node Performance Cross-node Performance
CP2K_single_node_perf CP2K_cross_node_perf
Note

The system was changed for the cross-node benchmarks because the system selected for the single-node calculations is relatively small.

This is a short molecular dynamics run of 1000 time steps in a NPT ensemble at 300K. It consists of 28000 atoms - a 10³ supercell with 28 atoms of iron silicate (Fe2SiO4, also known as Fayalite) per unit cell. The simulation employs a classical potential (Morse with a hard-core repulsive term and 5.5 Å cutoff) with long-range electrostatics using Smoothed Particle Mesh Ewald (SPME) summation. While CP2K does support classical potentials via the Frontiers In Simulation Technology (FIST) module, this is not a typical calculation for CP2K but is included to give an impression of the performance difference between machines for the MM part of a QM/MM calculation.

Single node Performance Cross-node Performance
CP2K_single_node_perf CP2K_cross_node_perf
Note

"Performance drop from single node performance table on left and cross-node performance measured for one node is caused by different disks used during calculations, i.e., single node performance was calculated using local /work/ disk, while cross-node performance was calculated on shared /scratch/ storage."

This is a single-point energy calculation using linear-scaling DFT. It consists of 6144 atoms in a 39 Å3 box (2048 water molecules in total). An LDA functional is used with a DZVP MOLOPT basis set and a 300 Ry cut-off. For large systems the linear-scaling approach for solving Self-Consistent-Field equations will be much cheaper computationally than using standard DFT and allows scaling up to 1 million atoms for simple systems. The linear scaling cost results from the fact that the algorithm is based on an iteration on the density matrix. The cubically-scaling orthogonalisation step of standard Quickstep DFT using OT is avoided and the key operation is sparse matrix-matrix multiplications, which have a number of non-zero entries that scale linearly with system size. These are implemented efficiently in the DBCSR library.

Single node Performance Cross-node Performance
CP2K_single_node_perf CP2K_cross_node_perf

Because of the above-mentioned complexity, a script for planning MPI/OpenMP-hybrid execution, CP2K_plan.sh, is made available to users in /storage-apps/scripts/. For a system with 64 cores per node (two sockets, disabled hyperthreading), setting up the "system metric" looks like: 

    ./CP2K_plan.sh <num-nodes> <ncores-per-node> <nthreads-per-core> <nsockets-per-node>
    ./CP2K_plan.sh 1 64 1 2
    ./CP2K_plan.sh 2 128 1 2

Example run script

You can copy and modify this script as cp2k_run.sh and submit the job to a compute node with the command sbatch cp2k_run.sh.

#!/bin/bash
#SBATCH -J "CP2K"       # name of job in SLURM
#SBATCH --account=<your project>    # project number
#SBATCH --partition=medium  # selected partition (short, medium, long)
#SBATCH --nodes=1       # number of nodes
#SBATCH --ntasks=64     # number of mpi ranks, needs to be tested for the best performance
#SBATCH --cpus-per-task=8   # number of cpus per mpi rank, needs to be tested for the best performance
#SBATCH --time=12:00:00     # time limit for a job
#SBATCH -o stdout.%J.out    # standard output
#SBATCH -e stderr.%J.out    # error output


# Modules
module load CP2K/2022.1-foss-2022a

# Single launcher: srun (SLURM) is used to launch the MPI job.
srun -n ${SLURM_NTASKS} cp2k.popt -i example.inp > outputfile.out

GPU accelerated CP2K

Note

Section under construction

Created by: Marek Štekláč, Marek Štekláč