Gromacs

Versions 4.6.x

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    Release notes for 4.6

    New features
    • Native, hybrid CPU+GPU acceleration with Nvidia GPUs using CUDA, through the new Verlet non-bonded scheme.
    • New Verlet non-bonded scheme which, by default, uses exact cut-off's and a buffered pair-list.
    • New x86 SIMD non-bonded kernels for the usual cut-off scheme, called group scheme and the new verlet scheme, use x86 SIMD intrinsics (no more assembly code):
      • SSE2
      • SSE4.1
      • AVX-128-FMA (for AMD Bulldozer/Piledriver)
      • AVX-256 (for Intel Sandy/Ivy Bridge)
    • Hybrid MPI+OpenMP, or OpenMP-only, parallelization with the Verlet scheme or for PME only nodes.
    • Automated OpenMP thread count choice to use all available cores.
    • Automated locking of processes or threads to cores.
    • Automated load-balancing between non-bonded force and PME mesh tasks between GPU and CPU or between PP and PME processes, by shifting work from the mesh to the non-bonded calculation.
    • New, advanced free energy sampling techniques.
    Bugfixes

    No critical bugfixes. All important fixes are also present in 4.5.6 and documented there.

    Changes that might affect your results

    None for simulations set up with the traditional group cut-off scheme.

    When switching from the group scheme to the Verlet scheme, simulations can get more accurate due to the exact cut-off treatment and buffering (this will, of course, depend on the original cut-off settings used). See the section Cut-off schemes for details.

    4.6-beta2 (2012-12-06)

    Bugfixes and improvements
    • re-enabled AdResS feature (only generic kernels for now);
    • improved OpenMP parallelization performance of non-bonded force calculation with Verlet scheme;
    • fixed segv in Verlet pair-search with trilinic domain-decomposition;
    • fixed incorrect virial with virtual sites and OpenMP;
    • fixed labelling of g_hbond plots;
    • fixed compilation issue with cmake 2.8.10 and GPU acceleration;
    • fixed issues with multi-sim runs and GPU-acceleration.

    4.6-beta1 (2012-11-30)

    First beta, yay! See the release notes above.

    Page last modified 11:19, 7 Dec 2012 by hess