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 eq


for 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
users@gridengine.org
https://gridengine.org/mailman/listinfo/users

--
Dr. Alexander Hasselhuhn
Rahel-Straus-Str. 4
76137 Karlsruhe
Tel. +49 176 64066387

Attachment: smime.p7s
Description: S/MIME Cryptographic Signature

_______________________________________________
users mailing list
users@gridengine.org
https://gridengine.org/mailman/listinfo/users

Reply via email to