[gmx-developers] Python interface for Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 9 09:44:08 CEST 2010

On 2010-09-09 09.35, Mark Abraham wrote:
>  > People in the Lindahl group are working on parallellizing
>  > analysis tools because they are quickly becoming the bottleneck.
>  > We run simulations of large systems on hundreds of processors,
>  > and due to checkpointing this can be done largely unattended.
> If so, then an important issue to address is using MPI2 parallel IO
> properly. At the moment, for DD, mdrun collects vectors for I/O on the
> master and writes them out in serial. Proper use of parallel I/O might
> be worth the investment in restructuring the output. Maintaining the DD
> processor-local file view suited for I/O of the local atoms is probably
> not any more complex than the existing contortions that are gone through
> to gather global vectors. Likewise, a parallel analysis tool will often
> wish to be doing its I/O in parallel.
> We would probably wish to write our own data representation conversion
> functions to hook into MPI_File_set_view so that we can read/write our
> standard XDR formats in parallel. (Unless, of course, the existing
> "external32" representation can be made to do the job.)
> Mark
We have just submitted a paper on a new, more flexible, trajectory 
format with rudimentary support for parallel I/O. This will provide a 
good basis for further work.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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