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GROMACS on Hybrid CPU-GPU and CPU-MIC Clusters: Preliminary Porting Experiences, Results and Next Steps

Sadaf Alam, Ugo Varetto
Swiss National Supercomputing Centre, Lugano, Switzerland
PRACE, 2014

@article{alam2014gromacs,

   title={GROMACS on Hybrid CPU-GPU and CPU-MIC Clusters: Preliminary Porting Experiences, Results and Next Steps},

   author={Alam, Sadaf and Varetto, Ugo},

   year={2014}

}

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This report introduces hybrid implementation of the Gromacs application, and provides instructions on building and executing on PRACE prototype platforms with Graphical Processing Units (GPU) and Many Intergrated Cores (MIC) accelerator technologies. GROMACS currently employs message-passing MPI parallelism, multi-threading using OpenMP and contains kernels for non-bonded interactions that are accelerated using the CUDA programming language. As a result, the execution model is multi-faceted where end users can tune the application execution according to the underlying platforms. We present results that have been collected on the PRACE prototype systems as well as on other GPU and MIC accelerated platforms with similar configurations. We also report on the preliminary porting effort that involves a fully portable implementation of GROMACS using OpenCL programming language instead of CUDA, which is only available on NVIDIA GPU devices.
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