DD error can't be avoided with the suggested manual decomposition option - Redmine #3336
$ $gmx mdrun $optsn -nsteps 10000 -resetstep 8000 -ntmpi 14 -npme 0 -dd 7 2 1
:-) GROMACS - gmx mdrun, 2020.1-dev-20200115-0fdb424-dirty (-:
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GROMACS: gmx mdrun, version 2020.1-dev-20200115-0fdb424-dirty
Executable: /nethome/pszilard-projects/gromacs/gromacs-20/build_AVX512_256_gcc8_cuda10.1/bin/gmx
Data prefix: /nethome/pszilard/projects/gromacs/gromacs-20 (source tree)
Working dir: /nethome/pszilard-projects/gromacs/bench/LUMI-bench/aqp_ensemble/test_dev-purley01
Command line:
gmx mdrun -v -noconfout -pin on -nsteps 10000 -resetstep 8000 -ntmpi 14 -npme 0 -dd 7 2 1
Back Off! I just backed up md.log to ./#md.log.2#
Reading file topol.tpr, VERSION 2020.1-dev-20200120-4cebec1 (single precision)
Overriding nsteps with value passed on the command line: 10000 steps, 25 ps
Changing nstlist from 40 to 100, rlist from 1.2 to 1.287
-------------------------------------------------------
Program: gmx mdrun, version 2020.1-dev-20200115-0fdb424-dirty
Source file: src/gromacs/domdec/domdec_setucpp (line 784)
MPI rank: 8 (out of 14)
Fatal error:
The number of ranks selected for particle-particle work (14) contains a large
prime factor 7. In most cases this will lead to bad performance. Choose a
number with smaller prime factors or set the decomposition (option -dd)
manually.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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Program: gmx mdrun, version 2020.1-dev-20200115-0fdb424-dirty
Source file: src/gromacs/domdec/domdec_setucpp (line 784)
(from redmine: issue id 3336, created on 2020-01-22 by pszilard, closed on 2020-02-24)
- Changesets:
- Revision b4bf4c08 by Berk Hess on 2020-01-23T15:09:35Z:
Fix DD rank count prime check
The domain decomposition would refuse to run with large prime factors
in the MPI rank count even when the grid was specified by the user.
Fixes #3336
Change-Id: I92f20ce18f314db68890650e76741b0ee70c05df