[gmx-users] Issue with regression test.

Raymond Arter raymondarter at gmail.com
Wed Aug 1 12:49:26 CEST 2018

Dear All,

I'm building Gromacs 2018.2 and I've run in to a small issue that I would
like feed back on.

One of the regression tests fails with the following entered in to the log

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...

Abnormal return value for ' gmx mdrun -ntmpi 12      -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 6      -notunepme >mdrun.out
2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in nbnxn_vsite for nbnxn_vsite
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

However, on the advice of a colleague I run the following command in the

    gmx mdrun -ntmpi 4 -notunepme

And got the following result:

Reading file topol.tpr, VERSION 2018.2 (single precision)
Non-default thread affinity set, disabling internal thread affinity
Can not increase nstlist because verlet-buffer-tolerance is not set or used

Using 4 MPI threads
Using 3 OpenMP threads per tMPI thread

On host ****** 4 GPUs auto-selected for this run.
Mapping of GPU IDs to the 4 GPU tasks in the 4 ranks on this node:

Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'Protein'
20 steps,      0.1 ps.

step 20 Turning on dynamic load balancing, because the performance loss due
to load imbalance is 3.3 %.

Writing final coordinates.

Back Off! I just backed up confout.gro to ./#confout.gro.1#

 Dynamic load balancing report:
 DLB was turned on during the run due to measured imbalance.
 Average load imbalance: 13.0%.
 The balanceable part of the MD step is 25%, load imbalance is computed
from this.
 Part of the total run time spent waiting due to load imbalance: 3.3%.
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0
% Y 0 %

NOTE: 6 % of the run time was spent in domain decomposition,
      17 % of the run time was spent in pair search,
      you might want to increase nstlist (this has no effect on accuracy)

               Core t (s)   Wall t (s)        (%)
       Time:        1.932        0.161     1200.0
                 (ns/day)    (hour/ns)
Performance:       56.337        0.426

Is this just a problem with the regression test and the build of Gromacs is
fine, or
is there a problem with the build I have done?

Thanks in advance.


More information about the gromacs.org_gmx-users mailing list