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GROMACS with CUDA-aware MPI direct GPU communication support

Alan Gray; Gaurav Garg


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  <identifier identifierType="DOI">10.5281/zenodo.3890247</identifier>
  <creators>
    <creator>
      <creatorName>Alan Gray</creatorName>
    </creator>
    <creator>
      <creatorName>Gaurav Garg</creatorName>
    </creator>
  </creators>
  <titles>
    <title>GROMACS with CUDA-aware MPI direct GPU communication support</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>GROMACS</subject>
    <subject>molecular dynamics</subject>
    <subject>CUDA-aware MPI</subject>
    <subject>heterogeneous acceleration</subject>
    <subject>GPU</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-05-07</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3890247</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo" resourceTypeGeneral="Software">10.5281/zenodo.3773801</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3890246</relatedIdentifier>
  </relatedIdentifiers>
  <version>2021-GPUcomm-JCP</version>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/LGPL-2.1">GNU Library General Public License v2.1 or later</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;This source code contains the GROMACS version used for the following manuscript:&lt;br&gt;
P&amp;aacute;ll, S., Zhmurov, A., Bauer, P., Abraham, M., Lundborg, M., Gray, A., Hess, B, &amp;amp; Lindahl, E.. (2020). Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. The Journal of Chemical Physics, 2020&lt;/p&gt;

&lt;p&gt;The source code is based on the GROMACS 2021-dev code-base version 5a6ece397e36365b2b377ec4b7dbf57265b648c3&lt;br&gt;
the code modifications add CUDA-aware MPI support for halo-exchange and PME-PP communication&lt;br&gt;
as well as resolve a number of related issues and limitations. Original git hash of the code is&lt;br&gt;
b60021d95ebd1025ff6e235cbb381585d73533d3.&lt;/p&gt;</description>
  </descriptions>
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