[gmx-developers] repeatability of runs?

[Hardy, Adam]

I'm having a similar problem lately. I've been plotting cumulative averages and after a restart (using the full precision binary files) I saw a significant increase in average pressure (>20 bar in a system at ~360 bar). I've made some changes to the virial code which excludes some frozen atoms from the calculation so I had thought it was perhaps an error on my part causing this. I'm also seeing divergence on a similar scale doing multiple simulations from the same .tpr file. 

I've done similar stuff before last year on different systems without frozen atoms and not seen this problem, particularly after restarts, I did not see this pressure jump. I'm doing a bit more work today to try and establish whether it's my changes causing this or something else.

I haven't used the -reprod command, should this have such a large effect?

Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS, UK

________________________________________
From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of Shirts, Michael R. (mrs5pt) [mrs5pt at eservices.virginia.edu]
Sent: 16 February 2015 03:31
To: gmx-developers at gromacs.org
Subject: [gmx-developers] repeatability of runs?

Hi, all-

Is anyone else having issues with repeatability of runs?  When I start
from the same tpr using one thread (to avoid load rebalancing) on the same
machine, I find that it diverges after the first step.  It appears to be
an issue with the virial.  Any thoughts?  It seems like the code should be
binary repeatable at this level.  Makes it hard to debug a problem!

Best,
~~~~~~~~~~~~
Michael Shirts
Associate Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434) 243-1821

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