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 $NPROCS gmx mdrun_mpi -s md.tpr -c npt.gro -o md_0_1.trr Go and have a look at some tutorials which use GROMACS 5 or higher, and read the manual and documentation. A "No such file or directory" error means exactly that - there is no such binary in the gromacs 5.1 directory structure. Andrew On Wed, Oct 19, 2016 at 3:27 PM, Sun Iba <sun.i...@gmail.com> wrote: > Dear Gromacs users and experts > I am trying to run a test job of 1 ns remotely on supercomputer clusters. I > have prepared .tpr file in my system (v 5.1.1) and submitted the script > file on remote server. following is my script file: > > ####################################################################### > > #!/bin/bash > #PBS -l nodes=2:ppn=16 > #PBS -l walltime=01:00:00 > #PBS -q TESTq > #PBS -e Myerr_$PBS_JOBID > #PBS -o myout_$PBS_JOBID > #PBS -m abe > #PBS -M simranjeetsin...@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...@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...@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...@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...@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...@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...@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) > -- > 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. > -- 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.