Gromacs

GROMACS 4.6

    The Gromacs 4.6 release will mainly be a performance improvement release with a limited set of few new features.

    As the major transition to 5.0 has been started in the master branch , the 4.6 code will have to be based on the 4.x codebase. Therefor, we made an exception and have branched release-4-6 off from the release-4-5-patches branch (instead of master).

    How to get it
    git clone git://git.gromacs.org/gromacs.git
    cd gromacs
    git checkout --track -b release-4-6 origin/release-4-6
    
    Major features (almost) ready to be merged into the 4.6 branch:
    • Improved PME parallelization and more SSE optimization for PME spread/gather+solve.
    • New GPU non-bonded kernels which work with almost all features of GROMACS.
    • New, always energy conserving SSE kernels. The new kernels are optional and slower than the old ones for water, faster for non-water.

     

    Features currently not supported by the new GPU and SSE kernels:
    • Free-energy calculations
    • Implicit solvent (but this will still be supported on the GPU through OpenMM)
    • User interaction tables
    • Switch and shift interactions (but those are not important, as there is an exact cut-off)
    • Test particle insertion
    New features considered for inclusion:
    • Automatic history tracking of all GROMACS commands and output files.
    • Inclusion of the AdressMacs adaptive resolution simulation technique.
    • Multiple lambda functionality for free energy calculations.
    • Efficient DPD and SD integrators.

    But please keep in mind that the core developers are (as always) very short on time, so new features will only be included when they are thoroughly checked, well coded and work with all possible setups, especially in parallel. Features that won't make it into 4.6 will go into 5.0.

     

    Changes to the configuration/build system:
    • Switch to CMake; automake will be deprecated.
    • Support for MPI+OpenMP parallelization.
    • CTest + CDash for automated tests

     

    Some reminders for 4.6 that are not showstoppers or redmine issues

    Stuff that just maybe might sneak in

    • bluegene kernels
    • bundle DSSP code (license seems OK, would stop gmx-users spam, would stop them changing the API on us again)
    Testing
    • Run tests with 2D/3D decomposition.
    • Run test with PP-PME load balancing.
    • Run tests with -nb gpu_cpu mode. (?)
    Page last modified 18:58, 19 Dec 2012 by lindahl