Hi Ross,
Nope. They are on the same line. Do you see them in different lines?. In my
actual script I have written them on the same line.
Thank you
Sajeewa Dewage
On Fri, Feb 8, 2013 at 3:46 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Sajeewa,
>
> This may just be a formatting issue in your email but is your sander.MPI
> on a different line to the mpirun command? If yes then that is your
> problem. Put them on the same line.
>
> All the best
> Ross
>
>
>
> On 2/8/13 12:37 PM, "Sajeewa Pemasinghe" <sajeewasp.gmail.com> wrote:
>
> >Hi all,
> >
> >I have the following script to run TREMD.
> >
> >#!/bin/bash -f
> >#PBS -q egacq
> >#PBS -l nodes=12:ppn=7
> >
> >ulimit -s unlimited
> >
> >export PATH=/wsu/arch/x86_64/mvapich-1.1/bin:/usr/local/amber10/bin:$PATH
> >
> >cd
> >/wsu/home/ej/ej02/ej0271/new_project_5_20_2012/REMD_gb/redtemps/temp_paral
> >lel_with_pmemd/REMD_finally
> >
> >/wsu/arch/x86_64/mvapich-1.1/bin/mpirun -np 84
> >/usr/local/amber10/bin/sander.MPI -ng 42 -groupfile remd.groupfile
> >
> >So I have allocated 84 cpus for 42 groups , so that 2 cpus get allocated
> >per group. But I get the following error message.
> >
> > Error: specified more groups ( 42 ) than the number of processors (1 ) !
> >
> >and the program crashes. As I have already allocated 84 cores for 42
> >groups
> >I don't understand the meaning of the above error.
> >
> >Could anyone help me figure this out?
> >
> >Thank you
> >
> >Sajeewa Dewage
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> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Fri Feb 08 2013 - 13:30:03 PST
