Gromacs

GPU acceleration

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    Version as of 05:33, 19 Oct 2019

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    Gromacs version 4.6 and later include a brand-new native GPU acceleration developed in Stockholm under the framework of a grant from the European Research Council (#209825), with heroic efforts in particular by Szilard Pall. This replaces all previous trial GPU code, and comes with a number of important features:

     

    • The new GPU code is fast, and we mean it. Rather than speaking about relative speed, or speedup for a few special cases, this code is typically much faster (3-5x) even when compared to Gromacs running on all cores of a typical desktop. If you put two GPUs in a high-end cluster node, this too will result in a significant acceleration.
    • We have designed a new architecture where we use both CPUs and GPUs for the calculation.
      • This means we support a much wider range of settings with GPUs - pretty much any interactions based on reaction-field or PME work.
      • It also means we can use multiple GPUs efficiently, and the GPU acceleration works in combination with Gromacs' domain decomposition and load balancing code too, for arbitrary triclinic cells.
      • By using the CPU for part of the calculation, we retain full support for virtual interaction sites and other speedup techniques - you can use GPUs with very long timesteps and maintain accuracy (we're not simply making the hydrogens heavy, but properly removing selected internal degrees of freedom).
    • GPU acceleration is now a core part of Gromacs - as long as you have the Cuda development libraries installed it will be enabled automatically during Gromacs configuration.

     

    Page last modified 08:09, 4 Nov 2013 by lindahl