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Bug #1917

Bug in calculation of Distance Restraints energy by gmx energy

Added by Vojtech Kuban over 3 years ago. Updated almost 2 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
analysis tools
Target version:
Affected version - extra info:
And some older versions too.
Affected version:
Difficulty:
uncategorized
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Description

Hi there,

I have noticed different values of DistRest energy given by gmx energy (on multiple machines). So I tested it on notebook and found that it depends on numbers of MPI, openMP (even with single MPI). More testing with only 2 dist. rest. showed me that some of dist rest were counted for multiple times. Similar problem has a D.R. viol. calculation.

I am using Gromacs 5.1.1., however I tested it with versions 5.0.5 (GPU, MPI) and 4.6.1 and observed different dist. rest. energies. OS Fedora, Debian.

Hope, it will help!

testingExample-DistRest-bug.zip (2.14 MB) testingExample-DistRest-bug.zip Vojtech Kuban, 03/10/2016 01:22 PM

Related issues

Related to GROMACS - Bug #1316: distance restraints with multiple pairs segv with OpenMPClosed08/07/2013

History

#1 Updated by Mark Abraham over 3 years ago

Thanks for the report. The implementation of some kinds of distance restraints needs work. I'll look into it soon.

#2 Updated by Mark Abraham over 3 years ago

  • Related to Bug #1316: distance restraints with multiple pairs segv with OpenMP added

#3 Updated by Mark Abraham over 3 years ago

  • Status changed from New to Accepted

The measurement of total distance restraint violation does not work reliably with multiple OpenMP threads, because there is a race condition on fcd.disres.sumviol, where each thread writes from ta_disres.

#5 Updated by Mark Abraham almost 2 years ago

  • Target version set to 2018

#6 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Accepted to Resolved

Yes, this now works. For MPI runs we exit and explain that we cannot output pair info with MPI, and with OpenMP I get the same result no matter the number of threads used.

#7 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Resolved to Closed

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