Bug #1931

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

Added by Chris Neale about 4 years ago. Updated about 4 years ago.

Target version:
Affected version - extra info:
Affected version:


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

Associated revisions

Revision 44d8bb87 (diff)
Added by Berk Hess about 4 years ago

Correct mdrun tMPI (non-)parallel error message

Fixes #1931

Change-Id: Ifad46c7f62099a2cd80d70ccbe46bf3f2b5751e0


#1 Updated by Berk Hess about 4 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 about 4 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).

Thank you,

#3 Updated by Gerrit Code Review Bot about 4 years ago

Gerrit received a related patchset '1' for Issue #1931.
Uploader: Berk Hess ()
Change-Id: Ifad46c7f62099a2cd80d70ccbe46bf3f2b5751e0
Gerrit URL:

#4 Updated by Berk Hess about 4 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 about 4 years ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Erik Lindahl about 4 years ago

  • Status changed from Resolved to Closed

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