On Thu, Nov 17, 2016, Thakur, Abhishek wrote:
>
> I am using cshell My script is
>
> #!/bin/csh -f
> set amber = $AMBERHOME/bin/MMPBSA.py.MPI
> mpirun -np 16 $amber -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.out -sp PRMT7_WT.prmtop -cp complex.prmtop -rp receptor.prmtop -lp peptide.prmtop -y *.crd
OK: you may have to source $AMBERHOME/amber.csh *inside* the above
script. You are setting variables in your bashrc file, but it is possible
that not all of them are being transferred to the C-shell instance that you
are starting.
As has alredy been noted, please try running a serial job first, to help see
if the problem is related to MPI or just to shell variables.
> #test -f /nethome/axt651/apps/amber14/amber.csh && source /nethome/axt651/apps/amber14/amber.csh
If you leave the "#" as the first character, the above line will be ignored.
If you remove the "#" character, it will fail, since this is in your bashrc
file, and is using bash to (try to) execute a C-shell script.
I would recommend that you avoid all use of the C-shell, especially since you
seem to be somewhat unfamiliar with issues involved in using different shells.
Stick with bash.
....dac
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Received on Fri Nov 18 2016 - 06:30:03 PST
