[gmx-users] Help with a failing test - gromacs 2019.4 - Test 42

[Raymond Arter]

Hi,

When performing a "make check" on Gromacs 2019.4, I'm getting test 42
failing.
It gives the error:

        Mdrun cannot use the requested (or automatic) number of ranks,
retrying with 8

And the mdrun.out and md.log of swap_x reports:

        The number of ranks you selected (14) contains a large prime factor
7.

I've included the necessary parts of the logs below. Any help would be
appreciated
since I haven't come across this error before.

Regards,

T.


CentOS Linux release 7.6.1810 (Core)
CPU: Intel Xeon Gold 6132
Tesla V100
Cuda: 10.1
Driver: 418.40.04

Output of "make check"

42/46 Test #42: regressiontests/complex .............***Failed  145.88 sec

GROMACS:      gmx mdrun, version 2019.4
Executable:   /gromacs/2019.4/gromacs-2019.4/build/bin/gmx
Data prefix:  /gromacs/2019.4/gromacs-2019.4 (source tree)
Working dir:
 /gromacs/2019.4/gromacs-2019.4/build/tests/regressiontests-2019.4
Command line:
  gmx mdrun -h

Thanx for Using GROMACS - Have a Nice Day

Mdrun cannot use the requested (or automatic) number of ranks, retrying
with 8.

Abnormal return value for ' gmx mdrun    -nb cpu   -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
Re-running orientation-restraints using CPU-based PME
Re-running pull_geometry_angle using CPU-based PME
Re-running pull_geometry_angle-axis using CPU-based PME
Re-running pull_geometry_dihedral using CPU-based PME

Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was
-1
FAILED. Check mdrun.out, md.log file(s) in swap_x for swap_x

Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was
-1
FAILED. Check mdrun.out, md.log file(s) in swap_y for swap_y

Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was
-1
FAILED. Check mdrun.out, md.log file(s) in swap_z for swap_z
3 out of 55 complex tests FAILED

>From the following directory:
/gromacs/2019.4/gromacs-2019.4/build/tests/regressiontests-2019.4/complex/swap_x
and I get the same errors for swap_y and swap_z

== mdrun.out ==

GROMACS:      gmx mdrun, version 2019.4
Executable:   /gromacs/2019.4/gromacs-2019.4/build/bin/gmx
Data prefix:  /gromacs/2019.4/gromacs-2019.4 (source tree)
Working dir:
 /gromacs/2019.4/gromacs-2019.4/build/tests/regressiontests-2019.4/complex/swap_x
Command line:
  gmx mdrun -notunepme

Reading file topol.tpr, VERSION 2019.4 (single precision)
Changing nstlist from 10 to 50, rlist from 1.011 to 1.137

-------------------------------------------------------
Program:     gmx mdrun, version 2019.4
Source file: src/gromacs/domdec/domdec_setup.cpp (line 764)
MPI rank:    0 (out of 14)

Fatal error:
The number of ranks you selected (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
-------------------------------------------------------

== md.out ==

Changing nstlist from 10 to 50, rlist from 1.011 to 1.137

Initializing Domain Decomposition on 14 ranks
Dynamic load balancing: locked
Minimum cell size due to atom displacement: 0.692 nm
Initial maximum distances in bonded interactions:
    two-body bonded interactions: 0.403 nm, Exclusion, atoms 184 187
  multi-body bonded interactions: 0.403 nm, Ryckaert-Bell., atoms 184 187
Minimum cell size due to bonded interactions: 0.443 nm
Maximum distance for 3 constraints, at 120 deg. angles, all-trans: 0.459 nm
Estimated maximum distance required for P-LINCS: 0.459 nm

-------------------------------------------------------
Program:     gmx mdrun, version 2019.4
Source file: src/gromacs/domdec/domdec_setup.cpp (line 764)
MPI rank:    0 (out of 14)

Fatal error:
The number of ranks you selected (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
-------------------------------------------------------