jubench-gromacs
JUPITER Benchmark Suite: GROMACS Benchmark
Science Score: 62.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: acs.org, zenodo.org -
○Academic email domains
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✓Institutional organization owner
Organization fzj-jsc has institutional domain (www.fz-juelich.de) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.2%) to scientific vocabulary
Repository
JUPITER Benchmark Suite: GROMACS Benchmark
Basic Info
- Host: GitHub
- Owner: FZJ-JSC
- License: mit
- Default Branch: main
- Size: 13.7 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
- Releases: 2
Metadata Files
README.md
JUPITER Benchmark Suite: GROMACS
-10.5281%2Fzenodo.12737073-blue){kind=icon}
This benchmark is part of the JUPITER Benchmark Suite. See the repository of the suite for some general remarks.
This repository contains the GROMACS benchmark. DESCRIPTION.md contains details for compilation, execution, and evaluation.
GROMACS is a versatile package to perform molecular dynamics, i.e., simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins, lipids, and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Quickstart
Compilation
The JUBE script automatically downloads GROMACS from the official website, and the input for the two possible runs from the PRACE Unified European Applications Benchmark Suite. It's just a matter of using the following commands:
```bash module load JUBE jube run jubegromacsbuild.xml
```
This should take about an hour.
Execution
In similar fashion, execute the two sub-benchmarks with the according JUBE scripts:
bash
jube run jube_gromacs_STMV_bench.xml
jube run jube_gromacs_ionchannel_bench.xml
JUBE sample output
ionchannel_run (CPU)
| Nodes | MPI tasks | Threads per Task | Performance [ns/d] | Wall t[s] | MFLOPs | | ------ | --------- | ---------------- | ------------------ | --------- | ------------- | | 64 | 256 | 6 | 354.035 | 15.253 | 136650833.463 |
STMV_run (GPU)
| Nodes | MPI tasks | Threads per Task | GPUs per Node | Performance [ns/d] | Wall t[s] | MFLOPs | Version | Compiler | |-------|-----------|------------------|---------------|--------------------|-----------|-----------------|---------|----------| | 256 | 1024 | 6 | 4 | 72.172 | 23.945 | 43979566371.330 | 2023RC1 | NVHPC |
Owner
- Name: Jülich Supercomputing Centre
- Login: FZJ-JSC
- Kind: organization
- Location: Germany
- Website: https://www.fz-juelich.de/en/ias/jsc
- Twitter: fzj_jsc
- Repositories: 29
- Profile: https://github.com/FZJ-JSC
Jülich Supercomputing Centre provides HPC resources and expertise. Part of Forschungszentrum Jülich.
Citation (CITATION.cff)
cff-version: 1.2.0
title: "JUPITER Benchmark Suite: GROMACS"
message: >-
In addition to citing this benchmark repository, please also cite either the JUPITER Benchmark Suite or the accompanying SC24 paper
authors:
- given-names: Jan H.
family-names: Meinke
affiliation: Forschungszentrum Jülich, Jülich Supercomputing Centre
orcid: 'https://orcid.org/0000-0003-2831-9761'
- given-names: Alexandre
family-names: Strube
affiliation: Forschungszentrum Jülich, Jülich Supercomputing Centre
orcid: 'https://orcid.org/0000-0002-9177-6474'
- given-names: Andreas
family-names: Herten
affiliation: Forschungszentrum Jülich, Jülich Supercomputing Centre
orcid: 'https://orcid.org/0000-0002-7150-2505'
- given-names: Sebastian
family-names: Achilles
affiliation: Forschungszentrum Jülich, Jülich Supercomputing Centre
orcid: 'https://orcid.org/0000-0002-1943-6803'
- given-names: Kaveh
family-names: Haghighi Mood
affiliation: Forschungszentrum Jülich, Jülich Supercomputing Centre
orcid: 'https://orcid.org/0000-0002-8578-4961'
abstract: "The GROMACS benchmark of the JUPITER Benchmark Suite"
identifiers:
- type: doi
value: 10.5281/zenodo.12787776
description: Version-agnostic Zenodo Identifier
repository-code: 'https://github.com/FZJ-JSC/jubench-gromacs/'
license: MIT
date-released: '2024-07-20'
references:
- title: "JUPITER Benchmark Suite"
type: software
doi: 10.5281/zenodo.12737073