[gmx-users] problem: gromacs run on gpu

[Alex]

Can you try to open the script in vi, delete the mdrun line and then 
manually retype it?


On 7/12/2017 11:03 PM, leila karami wrote:
> 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:
>
> -----------------------------------------------------------------------------------------------------
> #!/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