[gmx-users] mpirun error

[Andrew Guy]

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)
> --
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