[gmx-developers] Collective IO

Roland Schulz roland at utk.edu
Fri Oct 1 00:11:46 CEST 2010


we (Ryan&me) just uploaded our work on buffered MPI writing of XTC
trajectories. It can be found in the branch CollectiveIO.

We buffer a number of frames and use MPI IO to write those frames from a
number of nodes (see previous mails for details). The XTC trajectory is
written at least at every checkpoint guaranteeing that no frames are lost if
a simulation crashes.

We have tested it in serial, with PME, with threads, with multi and it seems
to work in all cases.

For 3 million atoms on 8192 writing every 1000 steps the performance is
increased from 21ns/day to 34ns/day and the time spent in comm.
energies decreases from 47% to 7%.

Feedback on the code change is very welcome. If you want to look at the
diff, I suggest to use:
git difftool afd66e48c4e608    #this is the origin/master from when we
uploaded the branch

Please let us know what you would like us to change before we merge this
into master.

Ryan & Roland

ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20100930/4185f3b4/attachment.html>

More information about the gromacs.org_gmx-developers mailing list