[gmx-users] Parallel do_dssp analysis over mpi?
erikm at xray.bmc.uu.se
Mon Nov 8 22:33:40 CET 2010
Justin A. Lemkul skrev 2010-11-08 21.05:
> Erik Marklund wrote:
>> You can use the -b and -e flags to analyze parts of your trajectory
>> and patch the results together afterwards.
> But does that really save time? Patching .xpm files is not entirely
> straightforward. Might end up taking a lot more time :)
Nevertheless, if the 48 h runtime is a problem, then splitting the
analysis into shorter chunks is the way to go here. Note however that an
MPI-powered do_dssp would not make the results come any faster than what
I suggested, but it would be much more convenient since one wouldn't
have to patch together the xpm oneself. I think there's a
frame-decomposition framework for the analysis tools under production,
but I suspect it's far from ready.
>> Justin A. Lemkul skrev 2010-11-08 20.51:
>>> Ali Naqvi wrote:
>>>> Dear All,
>>>> I have a trajectory of 100ns and have been trying to analyze it
>>>> using dssp program. I guess this question also goes for other
>>>> analysis programs like g_rama, g_rdf and what not.
>>>> Since the trajectory is big, it takes hours to analyze with
>>>> do_dssp.. infact 48 hours. I have been able to analyse only one set
>>>> of 100ns and have 7 more trajectories. Is it possible to get it
>>>> running in parallel to expedite the analysis? If so, which flags
>>>> need to be appended?
>>> The only Gromacs program that is MPI-aware is mdrun. Unless modify
>>> the source code, then none of the other commands will run in parallel.
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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