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Bug #1931

mdrun complains that -nt is 1 when it is really 16 (with -dd set)

Added by Chris Neale over 3 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

source in gromacs-5.1.2/src/programs/mdrun/runner.c seems to be throwing an error around line 824 in version 5.1.2 when I use "mdrun -nt 16 -dd 2 2 4" (see below). However, when I use the same code except I call "mdrun -nt 36 -dd 3 3 4" then it works just fine (not shown). It also works just fine when I remove the "-dd 2 2 4" and maintain "-nt 16" (not shown).

Here is some of the output to stderr/stdout:

...
GROMACS: gmx mdrun, VERSION 5.1.2
Executable: /nh/nest/u/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
Data prefix: /nh/nest/u/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial
Command line:
gmx mdrun -nt 16 -notunepme -deffnm MD -dlb yes -npme 0 -cpt 60 -maxh 60 -cpi MD.cpt -dd 2 2 4

Running on 1 node with total 24 cores, 48 logical cores
Hardware detected:
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX_256

Compiled SIMD instructions: AVX_256, GROMACS could use AVX2_256 on this machine, which is better

Reading file MD.tpr, VERSION 5.1.2 (single precision)
Changing nstlist from 10 to 40, rlist from 1.2 to 1.234

-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.2
Source code file: /nh/nest/u/cneale/exe/GROMACS/source/gromacs-5.1.2/src/programs/mdrun/runner.cpp, line: 826

Fatal error:
The -dd or -npme option request a parallel simulation, but the number of threads (option -nt) is 1
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Associated revisions

Revision 44d8bb87 (diff)
Added by Berk Hess over 3 years ago

Correct mdrun tMPI (non-)parallel error message

Fixes #1931

Change-Id: Ifad46c7f62099a2cd80d70ccbe46bf3f2b5751e0

History

#1 Updated by Berk Hess over 3 years ago

  • Status changed from New to Accepted

Please attach the md.log file.

Do the (non) use of the options -npme and -cpi affect the behavior?

#2 Updated by Chris Neale over 3 years ago

Dear Berk:

excluding the -npme and -cpi options does not affect the behaviour. I have provided 4 log files here. Three have various combinations of -npme and -cpi (used or not) and the fourth excludes the -dd option (the last run being the only one without the error message and the only one that actually ran).

https://www.dropbox.com/sh/a0uyjgzwkbbrbke/AABdD_FGasY1m-9OLb7BPDxVa?dl=1

Thank you,
Chris.

#3 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1931.
Uploader: Berk Hess ()
Change-Id: Ifad46c7f62099a2cd80d70ccbe46bf3f2b5751e0
Gerrit URL: https://gerrit.gromacs.org/5757

#4 Updated by Berk Hess over 3 years ago

  • Status changed from Accepted to Fix uploaded
  • Assignee set to Berk Hess
  • Target version set to 5.1.3

The error message incorrectly complains about the -nt option. You need to set the -ntmpi option.

#5 Updated by Berk Hess over 3 years ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Erik Lindahl over 3 years ago

  • Status changed from Resolved to Closed

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