[gmx-users] mpirun error

[Sun Iba]

Thank you very much Andrew

On Wed, Oct 19, 2016 at 10:31 AM, Andrew Guy <andrew.guy at burnet.edu.au>
wrote:

> Hi Sun,
>
> In GROMACS 5.1, all the commands are under the gmx binary. You need to run
> something like:
>
> >> source /your/installation/prefix/here/bin/GMXRC
> >> mpirun -np $NPROCS gmx mdrun_mpi -s md.tpr -c npt.gro -o md_0_1.trr
>
> Go and have a look at some tutorials which use GROMACS 5 or higher, and
> read the manual and documentation. A "No such file or directory" error
> means exactly that - there is no such binary in the gromacs 5.1 directory
> structure.
>
> Andrew
>
> On Wed, Oct 19, 2016 at 3:27 PM, Sun Iba <sun.iba2 at gmail.com> wrote:
>
> > Dear Gromacs users and experts
> > I am trying to run a test job of 1 ns remotely on supercomputer
> clusters. I
> > have prepared .tpr file in my system (v 5.1.1) and submitted the script
> > file on remote server. following is my script file:
> >
> > #######################################################################
> >
> > #!/bin/bash
> > #PBS -l nodes=2:ppn=16
> > #PBS -l walltime=01:00:00
> > #PBS -q TESTq
> > #PBS -e Myerr_$PBS_JOBID
> > #PBS -o myout_$PBS_JOBID
> > #PBS -m abe
> > #PBS -M simranjeetsinghn at gmail.com,8725828727
> > #PBS -r n
> > #PBS -V
> > #PBS -A A_B-PR
> >
> >
> > echo PBS JOB id is $PBS_JOBID
> > echo PBS_NODEFILE is $PBS_NODEFILE
> > echo PBS_QUEUE is $PBS_QUEUE
> > NPROCS=`wc -l < $PBS_NODEFILE`
> > NODES=`cat $PBS_NODEFILE | uniq |wc -l`
> > echo NPROCS is $NPROCS
> > echo $PBS_NODEFILE
> >
> >
> >
> > cd /home/external/sggswu/ssingh/test2/
> >
> > source /opt/app/GROMACS/gromacs-5.1.2/env.sh
> >
> > mpirun -np $NPROCS /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi_d -s
> > md.tpr
> > -c npt.gro -o md_0_1.trr
> >
> > ############################################################
> > ###############
> >
> > AFter execution, the job is terminbated with following error. Please help
> > me resolve it:
> >
> > [proxy:0:0 at ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0 at ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0 at ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0 at ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0 at ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0 at ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > --
> > 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.
>