[gmx-users] restart issues with Gromacs

Nash, Anthony a.nash at ucl.ac.uk
Sun Nov 15 22:30:07 CET 2015

Hi all,

Running Grimaces 5.0.4 with PLUMED 2.2 on a cluster, number of ranks (MPI
processes) is 24. The simulation successfully ran for the maximum cluster
wall time (48 hours).

I attempt to restart the simulations using the following command (with a
sun microsystem grid engine submission script):

gerun mdrun_mpi_d -deffnm neu_mut_meta_K -cpi neu_mut_meta_K.cpt -noappend

However, whilst the queue is telling me that the job is running, the
*.part0002.log file seems stuck at:

When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1
The minimum size for domain decomposition cells is 1.025 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.43 Y 0.56
The maximum allowed distance for charge groups involved in interactions is:
                 non-bonded interactions           1.025 nm
            two-body bonded interactions  (-rdd)   1.025 nm
          multi-body bonded interactions  (-rdd)   1.025 nm
  atoms separated by up to 5 constraints  (-rcon)  1.025 nm

The cluster error file and output file (not gromacs file) contains no
warnings or errors. The gromacs log file contains no warnings or errors.

I have seen this behaviour quite a number of times, going back to early
versions of gromacs 4 around late 2010 (I think). I got into the habit of
a) copying backing up the .cpt files, and b) always using -noappend option
to preserve the .trr file. Has there ever been an explanation as to why
this is happening?

Many thanks

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