[gmx-users] mpirun error

Sun Iba sun.iba2 at gmail.com
Wed Oct 19 06:27:43 CEST 2016


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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