[gmx-users] restart issues with Gromacs
a.nash at ucl.ac.uk
Sun Nov 15 23:19:37 CET 2015
Ok, so it sounds very much like it¹s on the cluster side. I¹ll fire this
across to one of the sys admins and see if they can find out what the
problem is, although I have no idea what and if they will find anything.
>From the looks of it, the reading of the checkpoint file data was fine
(else I expect an MD5 hashkey error IF my memory serves me right).
Dr Anthony Nash
Department of Chemistry
University College London
On 15/11/2015 22:12, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of mark.j.abraham at gmail.com> wrote:
>GROMACS assumes the file systems actually write to disk when you use the
>system call that means that, and works correctly if so. But if the file
>system or its configuration don't actually do that (for "performance" or
>erroneous reasons), then all bets are off. mdrun can't even know if it's
>being lied to, because, well, it's being lied to...
>On Sun, 15 Nov 2015 22:30 Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>> Hi all,
>> Running Grimaces 5.0.4 with PLUMED 2.2 on a cluster, number of ranks
>> processes) is 24. The simulation successfully ran for the maximum
>> 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
>> 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
>> 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
>> 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
>> a) copying backing up the .cpt files, and b) always using -noappend
>> to preserve the .trr file. Has there ever been an explanation as to why
>> this is happening?
>> Many thanks
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