[gmx-users] GROMACS with Torque: Job stuck
souparnoa91 at gmail.com
Fri Aug 25 18:01:21 CEST 2017
I checked the server and scheduler logs. They are as follows:
08/25/2017 13:49:31.230;256;PBS_Server.25216;Job;11.headnode;enqueuing into batc
h, state 1 hop 1
connection 8 and calling its accompanying function on close
Modified at request of root at headnode
08/25/2017 13:49:31.361;08;PBS_Server.25134;Job;11.headnode;Job Run at
request of root at headnode
sending email: User does not want mail of this type.
Server Version = 22.214.171.124, loglevel = 0
08/25/2017 13:49:31.373;64; pbs_sched.25166;Job;11.headnode;Job Run
The tracejob command is giving me the following output:
08/25/2017 13:49:31.230 S enqueuing into batch, state 1 hop 1
08/25/2017 13:49:31.360 S Job Modified at request of root at headnode
08/25/2017 13:49:31.373 L Job Run
08/25/2017 13:49:31.361 S Job Run at request of root at headnode
08/25/2017 13:49:31.374 S Not sending email: User does not want
mail of this type.
08/25/2017 13:49:31 A queue=batch
08/25/2017 13:49:31 A user=souparno group=souparno jobname=asyn
queue=batch ctime=1503649171 qtime=1503649171 etime=1503649171
start=1503649171 owner=souparno at headnode
@Mark, we are using mpich2-1.4.1p1 at every node. And the GROMACS
version is 5.1.4. Even, at every node, mpi and GROMACS are installed
in the same location i. e. /usr/local/
I tried running simple "echo" jobs and they are running successfully.
That's why it seems to me that it might be a problem with integrating
Department of Microbiology,
University of Calcutta.
On Fri, Aug 25, 2017 at 7:56 PM, Mark Abraham <mark.j.abraham at gmail.com>
> Sounds like an issue with some infrastructure being mismatched (e.g.
> different MPI at compile and run time). Does it work when you run a
> different MPI-used program, compiled and run using the same approach?
> On Fri, Aug 25, 2017 at 3:25 PM Souparno Adhikary <souparnoa91 at gmail.com>
> > Hi,
> > This is related to running GROMACS through mpirun and Torque. After I
> > installed Torque in our lab cluster, I went on to test GROMACS using a
> > simple run. I wrote a Torque script as follows:
> > #!/bin/sh
> > #PBS -N asyn
> > #PBS -q batch
> > #PBS -l nodes=4:ppn=4
> > #PBS -l walltime=120:00:00
> > cd $PBS_O_WORKDIR
> > cat $PBS_NODEFILE>nodes
> > mpirun -np 16 gmx_mpi mdrun -deffnm asyn_10ns
> > After I submit this file using qsub command, the job is properly
> > showing using pbsnodes command in other mom units.
> > But, the job stays as R in 00:00:00 in the list. I presume, this might
> > be an error from my part in setting up GROMACS with Torque. I compiled
> > GROMACS with -DGMX_MPI=ON
> > The nodes file is not written and the job stays stuck.
> > Can anyone familiar with job scheduling help me in this regard???
> > Souparno Adhikary,
> > CHPC Lab,
> > Department of Microbiology,
> > University of Calcutta.
> > --
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