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Bug #2902

2019.1 equilibration issue? (Intel 2018u3)

Added by Stefan Becuwe 7 months ago. Updated 6 months ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
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Description

Hello

While testing our GROMACS installation, I used an input file from one of our users. It works well on GROMACS 2018.3, but not on GROMACS 2019.1.
In both cases, I used the same compiler (Intel 2018u3), same configuration settings to compile GROMACS, same hardware and same parameters to mdrun.
In attachment, I add input files (0519-2018.tpr is for 2018.1, 0519.tpr is for 2019.1) and logfiles from the 2019.1 run.
Should I change something to the configuration settings to get it working? Thanks!

FYI: The same input file does work on the user's workstation (single node) using GCC 7.3 and NVIDIA's v10 toolbox.

Kind regards
Stefan

0519-2018.tpr.gz (1.92 MB) 0519-2018.tpr.gz Stefan Becuwe, 03/22/2019 02:08 PM
0519.tpr.gz (1.92 MB) 0519.tpr.gz Stefan Becuwe, 03/22/2019 02:09 PM
0519.e170821 (4.13 KB) 0519.e170821 Stefan Becuwe, 03/22/2019 02:09 PM
0519.log (20 KB) 0519.log Stefan Becuwe, 03/22/2019 02:09 PM
0519.e180906 (4.36 KB) 0519.e180906 Stefan Becuwe, 04/18/2019 02:06 PM
0519.log (20 KB) 0519.log Stefan Becuwe, 04/18/2019 02:06 PM
0519-gromacs-2018_3.log (37.2 KB) 0519-gromacs-2018_3.log Stefan Becuwe, 04/29/2019 01:31 PM
0519-updategroups-1node.log (32.1 KB) 0519-updategroups-1node.log Stefan Becuwe, 04/30/2019 08:16 AM
0519-updategroups-4nodes.e184543 (6.26 KB) 0519-updategroups-4nodes.e184543 Stefan Becuwe, 04/30/2019 08:16 AM
0519-updategroups-4nodes.log (20.9 KB) 0519-updategroups-4nodes.log Stefan Becuwe, 04/30/2019 08:16 AM

History

#1 Updated by Erik Lindahl 7 months ago

Hi Stefan,

Can you try to run "make check" (ideally with all the regressiontests enabled too)? That might be able to help us diagnose right away whether it's a compiler issue.

Cheers,

Erik

#2 Updated by Stefan Becuwe 7 months ago

Hello Erik

I already ran "make check" (with regression tests) for issue #2876, but it seemed the few errors reported were not serious.

Kind regards
Stefan

#3 Updated by Stefan Becuwe 6 months ago

Hello Erik

Just an update: it's exactly the same problem with GROMACS 2019.2, compiled as described above with Intel 2018u3.
Do you have any suggestions to get this computation working in GROMACS 2019.x? Thanks!

Kind regards
Stefan

#4 Updated by Berk Hess 6 months ago

Could you also add a log file for a working simulation with 2018 with an as similar as possible hardware setup?

#5 Updated by Stefan Becuwe 6 months ago

Hello Berk

Just added 0519-gromacs-2018_3.log
Thanks for looking at it!

Kind regards
Stefan

#6 Updated by Berk Hess 6 months ago

Thanks.

Could you run 2019 with then environment variable GMX_NO_UPDATEGROUPS set? The issue could be triggered (but not directly) caused by the update groups feature.

#7 Updated by Stefan Becuwe 6 months ago

Hello Berk

I add the logfiles from the runs with GMX_NO_UPDATEGROUPS on 1 node and 4 nodes (the same number of nodes as the successful GROMACS 2018 run).
The run on 1 node finishes, the run on 4 nodes crashes.

Kind regards
Stefan

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