Hi, you had a typo in your script (the leading slash in the path), you want:
#!/bin/bash #$ -S /bin/bash #$ -cwd #$ -N smp1 #$ -l h_vmem=1G /usr/local/gromacs/bin/gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eqfor these things it might be more convenient to ask a colleague who has a little experience with the linux command line. However, something I would try in your case, which could make your life a little easier (if you also need to send different scripts at some point, and given the computers you want to run your stuff on are set up similar to your interactive machine) is to call bash -l instead of bash, like so
#!/bin/bash -l #$ -S /bin/bash #$ -cwd #$ -N smp1 #$ -l h_vmem=1G gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eq Cheers, Alex Am 11.08.17 um 07:59 schrieb Subashini K:
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 _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
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