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 -- 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-requ...@gromacs.org.