ssh into a node and try "which gmx"
Either it will be found in your path, or it won't. Or "ls /usr/local/gromacs/bin/gmx" and see if exists. Best to include the full path to the things you need every time. Using "which" makes things a little easier i.e. GMX=`which gmx` and then use $GMX in your script. Or GROMACSPATH="/usr/local/gromacs" and GROMACSBIN="/usr/local/gromacs/bin" and use those vars as needed. Ian On Fri, Aug 11, 2017 at 8:22 AM, Subashini K <subashinik2...@gmail.com> wrote: > Hi, > > > Can anyone cross check it? If so, how? > > Or, should we ask the system administrator? > > Thanks, > Subashini.K > > On Fri, Aug 11, 2017 at 4:37 PM, Gowtham <g...@mtu.edu> wrote: > >> >> Is the folder, /usr/local/gromacs, shared across all nodes in your >> cluster? >> >> >> On Fri, Aug 11, 2017 at 1:59 AM Subashini K <subashinik2...@gmail.com> >> wrote: >> >>> Hi, >>> >>> (1) GROMACS is installed in /usr/local/gromacs/bin/ >>> >>> Not in root as I mentioned earlier. >>> >>> (2) When I gave >>> >>> >>> #!/bin/bash >>> #$ -S /bin/bash >>> #$ -cwd >>> #$ -N smp1 >>> #$ -l h_vmem=1G >>> usr/local/gromacs/bin/gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eq >>> >>> I got the same error again. >>> >>> But, when I run it directly my login node, gmx mdrun -ntmpi 1 -ntomp 8 >>> -v -deffnm eq the command works fine. >>> >>> >>> I realize, the problem lies in my scripiting. How to fix it? Is there >>> any special method to set the path in the above submit.sh file? >>> >>> Executable: /usr/local/gromacs/bin/gmx >>> Library dir: /usr/local/gromacs/share/gromacs/top >>> >>> >>> Can anyone help me? >>> >>> Thanks, >>> Subashini.K >>> >>> >>> -- >> >> Gowtham, PhD >> Director of Research Computing, IT >> Adj. Asst. Professor, ECE and Physics >> Michigan Technological University >> >> (906) 487-4096 >> http://it.mtu.edu >> http://hpc.mtu.edu >> > > > _______________________________________________ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users > > -- Ian Kaufman Research Systems Administrator UC San Diego, Jacobs School of Engineering ikaufman AT ucsd DOT edu
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