154383
doi
10.1002/anie.201510054
oai:zenodo.org:154383
user-eu
user-bioexcel
Szilárd Páll
Martin Fechner
Ansgar Esztermann
Bert L. de Groot
Helmut Grubmüller
Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan
Carsten Kutzner
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
<p>The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well-exploited with a combination of single instruction multiple data, multithreading, and message passing interface (MPI)-based single program multiple data/multiple program multiple data parallelism while graphics processing units (GPUs) can be used as accelerators to compute interactions off-loaded from the CPU. Here, we evaluate which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled and benchmarked compute nodes with various CPU/GPU combinations to identify optimal compositions in terms of raw trajectory production rate, performance-to-price ratio, energy efficiency, and several other criteria. Although hardware prices are naturally subject to trends and fluctuations, general tendencies are clearly visible. Adding any type of GPU significantly boosts a node's simulation performance. For inexpensive consumer-class GPUs this improvement equally reflects in the performance-to-price ratio. Although memory issues in consumer-class GPUs could pass unnoticed as these cards do not support error checking and correction memory, unreliable GPUs can be sorted out with memory checking tools. Apart from the obvious determinants for cost-efficiency like hardware expenses and raw performance, the energy consumption of a node is a major cost factor. Over the typical hardware lifetime until replacement of a few years, the costs for electrical power and cooling can become larger than the costs of the hardware itself. Taking that into account, nodes with a well-balanced ratio of CPU and consumer-class GPU resources produce the maximum amount of GROMACS trajectory over their lifetime.</p>
Zenodo
2016-04-28
info:eu-repo/semantics/article
646427
user-eu
user-bioexcel
award_title=Centre of Excellence for Biomolecular Research; award_number=675728; award_identifiers_scheme=url; award_identifiers_identifier=https://cordis.europa.eu/projects/675728; funder_id=00k4n6c32; funder_name=European Commission;
1579542081.120091
5349635
md5:561b2a32256c32a73ae75747e0ed2edd
https://zenodo.org/records/154383/files/Gapsys_et_al-2016-Angewandte_Chemie_International_Edition.pdf
9295883
md5:2f1ea9c8937026c3598b3085abb3bccc
https://zenodo.org/records/154383/files/anie201510054-sup-0001-misc_information.pdf
public
Journal of Computational Chemistry
36
26
1990–2008
2016-04-28