[gmx-developers] repeatability of runs?

Hardy, Adam ah259 at hw.ac.uk
Mon Feb 16 11:37:51 CET 2015

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!

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

Gromacs Developers mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers or send a mail to gmx-developers-request at gromacs.org.

We invite research leaders and ambitious early career researchers to 
join us in leading and driving research in key inter-disciplinary themes. 
Please see www.hw.ac.uk/researchleaders for further information and how
to apply.

Heriot-Watt University is a Scottish charity
registered under charity number SC000278.

More information about the gromacs.org_gmx-developers mailing list