Hi,<div><br></div><div>we (Ryan&me) just uploaded our work on buffered MPI writing of XTC trajectories. It can be found in the branch CollectiveIO.</div><div><br></div><div>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.</div>
<div><br></div><div>We have tested it in serial, with PME, with threads, with multi and it seems to work in all cases. </div><div><br></div><div>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%.</div>
<div><br></div><div>Feedback on the code change is very welcome. If you want to look at the diff, I suggest to use:</div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 12.7315px; border-collapse: collapse; ">git difftool afd66e48c4e608 #this is the origin/master from when we uploaded the branch</span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Please let us know what you would like us to change before we merge this into master.</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Thanks</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Ryan & Roland</span></font></div><div><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>
865-241-1537, ORNL PO BOX 2008 MS6309<br>
</div>