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
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