Chemistry benchmarks

Input files and batch scripts for benchmarking strong scalability of selected chemistry software on CSC's supercomputers (Puhti, Mahti, Roihu, LUMI).

Setup inspired by https://github.com/mvsjober/ml-benchmarks.

Usage

Select a benchmark and Slurm settings of your choice in accordance with the system you're running on. For example, the GROMACS ADH benchmark could be run on Puhti using 40 cores with one thread per MPI rank as follows:

module purge
module load gcc/11.3.0 openmpi/4.1.4 gromacs/2023.2
sbatch slurm/puhti-mpi40-omp1.sh gromacs.sh benchmarks/adh.tpr

Important

Remember to load all required environment modules before running sbatch.

Systems overview

System	Partition	Nodes	CPU compute	Cores per node	GPU compute	GPUs per node
Puhti	CPU	682	Intel Xeon Gold 6230	2 x 20 cores	n/a	n/a
	GPU	80	Intel Xeon Gold 6230	2 x 20 cores	Nvidia V100	4
Mahti	CPU	1404	AMD EPYC Rome 7H12	2 x 64 cores	n/a	n/a
	GPU	24	AMD EPYC Rome 7H12	2 x 64 cores	Nvidia A100	4
Roihu	CPU	486	AMD EPYC Turin 9965	2 x 192 cores	n/a	n/a
	GPU	132	Nvidia Grace	4 x 72 cores	Nvidia H100	4
LUMI	CPU	2048	AMD EPYC Milan 7763	2 x 64 cores	n/a	n/a
	GPU	2978	AMD EPYC Trento 7A53	1 x 64 cores	AMD MI250X	81

Available benchmarks

See benchmarks.

GROMACS

From J. Chem. Phys. 153, 134110 (2020); doi: 10.1063/5.0018516

• adh.tpr: Alcohol dehydrogenase solvated in TIP3P water in a truncated dodecahedron box and using the AMBER99sb-ildn force field. 95561 atoms, 2 fs time-step, 0.9 nm cut-offs, 0.1125 nm PME grid spacing, h-bond constraints, NVT ensemble.
• stmv.tpr: Satellite Tobacco Mosaic Virus solvated in TIP3P using cubic box and the CHARMM27 force field. 1066628 atoms, 2 fs time-step, 1.2 nm cut-offs, h-bond constraints, 0.15 nm PME grid spacing, NVT ensemble.

CP2K

From https://github.com/cp2k/cp2k/tree/master/benchmarks

• cp2k-qs.sh: 256 water molecules (768 atoms, 2048 electrons) in a 19.7 cubic angstrom cell. BOMD is run for 10 steps using Quickstep DFT and a 280 Ry cut-off at the LDA/TZV2P level of theory. The initial electron density is guessed based on atomic orbitals and the OT method is applied for SCF.
• cp2k-hyb.sh: 64 water molecules (192 atoms, 512 electrons) in a 12.4 cubic angstrom cell. BOMD is run for 10 steps using Quickstep DFT and a 400 Ry cut-off at the PBE0/TZVP level of theory. The initial electron density is guessed based on atomic orbitals and the OT method is applied for SCF.
• cp2k-ls-scf.sh: Quickstep density matrix linear scaling DFT calculation of 6144 atoms in a 39 cubic angstrom box (2048 water molecules in total). An LDA functional is used with a DZVP MOLOPT basis set and a 300 Ry cut-off.
• cp2k-diag.sh: Quickstep DFT calculation of hexagonal boron nitride adsorbed on Rh(111) (914 atoms, 6536 electrons). The PBE-D3 functional is used with a DZVP MOLOPT basis set and a 500 Ry cut-off. Standard diagonalization with Fermi-Dirac smearing (300 K) and the ELPA library is applied for SCF.

Amber

From https://ambermd.org/GPUPerformance.php

• amber-cellulose.sh: Cellulose nanofibril in TIP3P water in a cubic box. 408609 atoms, 4 fs time-step, 0.9 nm cut-offs, NPT ensemble. Single GPU benchmark.

LAMMPS

• in.lj: Atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 neighbors per atom), NVE integration. System size is scaled by a factor of 4 along each spatial coordinate, resulting in a system of 2048000 atoms.

NAMD

TBA

Quantum ESPRESSO

TBA

Footnotes

1. Strictly speaking, each LUMI GPU node has 4 GPUs. However, each MI250X GPU is composed of two graphics compute dies (GCDs), which from a software (and Slurm) perspective act as separate GPU devices. ↩