[gmx-developers] Collective IO
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
Ryan & Roland
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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