[gmx-users] problem: gromacs run on gpu

[leila karami]

Dear Gromacs users,

I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using
command:

gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on

All things are ok.

When I use this command in a script to do md simulation by queuing system:

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#!/bin/bash
#$ -S /bin/bash
#$ -q gpu.q
#$ -cwd
#$ -N cell_1
#$ -e error_1.dat
#$ -o output_1.dat
echo "Job started at date"
gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on
echo "Job Ended at date"
-----------------------------------------------------------------------------------------------------

I encountered with following error:

Program:     gmx mdrun, VERSION 5.1.3
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -pin
    Invalid value: on

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Halting program gmx mdrun
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

-------------------------------------------------------------------------------------------------------

How to resolve this error?
Any help will be highly appreciated