[gmx-developers] Python interface for Gromacs

Mark Abraham mark.abraham at anu.edu.au
Thu Sep 9 09:35:50 CEST 2010

> 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.) 


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