[gmx-users] GROMACS with Torque: Job stuck

[Souparno Adhikary]

I checked the server and scheduler logs. They are as follows:

server log:

08/25/2017 13:49:31.230;256;PBS_Server.25216;Job;11.headnode;enqueuing into batc
h, state 1 hop 1
08/25/2017 13:49:31.230;08;PBS_Server.25216;Job;perform_commit_work;job_id:
11.headnode
08/25/2017 13:49:31.230;02;PBS_Server.25216;node;close_conn;Closing
connection 8 and calling its accompanying function on close
08/25/2017 13:49:31.360;08;PBS_Server.25134;Job;11.headnode;Job
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
08/25/2017 13:49:31.374;13;PBS_Server.25134;Job;11.headnode;Not
sending email: User does not want mail of this type.
08/25/2017 13:50:59.137;02;PBS_Server.25119;Svr;PBS_Server;Torque
Server Version = 6.1.1.1, loglevel = 0

Scheduler log:

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:


Job: 11.headnode

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
exec_host=headnode3/0-1+headnode2/0-1 Resource_List.nodes=2:ppn=2
                          Resource_List.walltime=120:00:00
Resource_List.nodect=2 Resource_List.neednodes=2:ppn=2

@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
GROMACS.


Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.

On Fri, Aug 25, 2017 at 7:56 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> 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?
>
> Mark
>
> On Fri, Aug 25, 2017 at 3:25 PM Souparno Adhikary <souparnoa91 at gmail.com>
> wrote:
>
> > 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.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>