<div dir="ltr">If your branch is fairly up to date, then I would suspect this might be another/known issue with affinities and Sander's update to threadMPI in 972ab1f9a0. There's supposed to be a partial fix <a href="https://gerrit.gromacs.org/2433">https://gerrit.gromacs.org/2433</a> that still seems to have some issues. NFI what is relevant.<div>
<br></div><div>Mark</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sat, Jun 15, 2013 at 8:25 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I have a weird issue using domain decomposition (warning: in a non-standard branch).<br>
<br>
On one machine it stops after:<br>
Initializing Domain Decomposition on 8 nodes<br>
Dynamic load balancing: auto<br>
Will sort the charge groups at every domain (re)decomposition<br>
Initial maximum inter charge-group distances:<br>
two-body bonded interactions: 67.844 nm, WAXS Debye, atoms 7183 7652<br>
multi-body bonded interactions: 0.425 nm, Proper Dih., atoms 2633 2641<br>
Minimum cell size due to bonded interactions: 74.628 nm<br>
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm<br>
Estimated maximum distance required for P-LINCS: 0.819 nm<br>
ERROR: The initial cell size (8.951949) is smaller than the cell size limit (74.628166)<br>
<br>
------------------------------<u></u>-------------------------<br>
Program mdrun, VERSION 5.0-dev-20130613-766db7a-<u></u>unknown<br>
Source code file: /home/spoel/GG/waxs/gromacs/<u></u>src/gromacs/mdlib/domdec.c, line: 6641<br>
<br>
<br>
on the other machine running the same binary it does not stop. There is a difference between the machines though, since one of them is old it gives this warning:<br>
Using 8 MPI threads<br>
<br>
WARNING: Oversubscribing the available 0 logical CPU cores with 8 thread-MPI threads.<br>
This will cause considerable performance loss!<br>
<br>
<br>
Since the check al the way above is dependent on a clause<br>
if (nc[XX] > 0)<br>
it could be that the information on the number of threads is only effectuated in the domain decomposition AFTER the check for cell sizes.<br>
<br>
In other words I suspect that the handling of number of threads (I pass -nt 8) does not work completely as expected (which probably would hold in the master branch too then).<br>
<br>
I could try to make a test case against the master branch...<span class="HOEnZb"><font color="#888888"><br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
-- <br>
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</font></span></blockquote></div><br></div>