Here you go. #!/bin/bash #$ -S /bin/bash #$ -cwd #$ -N smp1 #$ -l h_vmem=1G /root/usr/local/gromacs/bin/gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eq
Just a word of caution: Looking at the path to the Gromacs installation folder, it resides under "root". In most computing clusters, the /root partition is local to each compute node. That is, the contents of one node's root folder cannot be seen by another compute node. A workaround for this problem would be compile your software in a common folder that is seen and accessible by all nodes. Best regards, Gowtham -- Gowtham, PhD Director of Research Computing, IT Adj. Asst. Professor, ECE and Physics Michigan Technological University P: (906) 487-4096 F: (906) 487-2787 https://it.mtu.edu https://hpc.mtu.edu On Thu, Aug 10, 2017 at 8:38 AM, Subashini K <[email protected]> wrote: > Thank you for the reply. > > How do we do it? > > It is located in /root/usr/local/gromacs/bin/gmx > > What would the correct command then? > > Can you please let me know? > > Thanks, > Subashini.K > > > > On Thu, Aug 10, 2017 at 5:45 PM, Chris Dagdigian <[email protected]> wrote: > >> >> Simply put the system can't find your gromacs binary that is what the >> "gmx: command not found" means. >> >> Just edit your submit script to pass the full path to gmx and you should >> be fine >> >> -Chris >> >> >> Subashini K <mailto:[email protected]> >>> August 10, 2017 at 7:59 AM >>> >>> Hi sun grid engine users, >>> >>> I am new to scripting. >>> >>> I want to run GROMACS MD simulations in sun grid engine through qsub >>> command. >>> >>> #!/bin/bash >>> #$ -S /bin/bash >>> #$ -cwd >>> #$ -N smp1 >>> #$ -l h_vmem=1G >>> gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eq >>> >>> >>> The above contents were in submit.sh file. >>> >>> When I gave, qsub submit.sh, >>> >>> I got the following error >>> >>> /opt/gridengine/default/spool/compute-0-31/job_scripts/4423509: line 8: >>> gmx: command not found >>> >>> >>> What am I supposed to do? I intend to do single processor serial job. >>> >>> How to rectify it? >>> >>> >>> Thanks, >>> Subashini.K >>> _______________________________________________ >>> users mailing list >>> [email protected] >>> https://gridengine.org/mailman/listinfo/users >>> >> >> > > _______________________________________________ > users mailing list > [email protected] > https://gridengine.org/mailman/listinfo/users > >
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