On Fri, Feb 8, 2013 at 3:37 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_parallel_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
>
These must be on the same line. If they are on separate lines (and you do
not end the first line with a \ to escape the newline), then it will first
execute <nothing> with 84 cores and then execute sander.MPI with just 1
(the default).
If they _are_ both on the same line, then the only time I've ever seen this
happen before is when the MPI from which mpirun comes from is different
than the MPI used to compile Amber.
> 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 ) !
Based on the error message you got, the problem is not with sander.MPI, but
either how you called sander.MPI or the mismatching MPIs I mentioned above.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Feb 08 2013 - 13:00:04 PST
