Hello,
What is the error reported in sanmin_com.1.out? mm_pbsa.pl creates these
input and output files, so it can just create them in the current working
directory and not use any PATH prefix. I don't think this is your error.
Check sanmin_com.1.out for the relevant error message. Also, you may
consider checking out MMPBSA.py at
ambermd.org/tutorials/advanced/tutorial3/py_script. It has an MPI option
(though there are prerequisites installations to do before it can be used).
To use sander.MPI in the mm_pbsa.pl script, you'll have to find out where
sander is called (grep will certainly help here), and substitute in
something like "mpirun -np # sander.MPI" or something. Note that this may
struggle with some MPI implementations... Also, this will have no
(positive) effect on PB calculations, and it won't parallelize the actual
Hessian diagonalization for nmode. The version of mm_pbsa.pl included with
amber11 spawns new compute threads to complete tasks, and MMPBSA.py has an
MPI version that can be used to split the calculation up across several
frames.
Hope this helps,
Jason
On Fri, Oct 1, 2010 at 4:58 AM, Giorgos Lamprinidis <
lamprinidis.pharm.uoa.gr> wrote:
> Dear amber users,
>
> I am using AMBER 10.
> I am trying to run mmpbsa.pl script on a cluster machine using MPI.
> When i run my PBS file i get the following error:
> /users/health/emikros/amber10//exe/sander -O -i sanmin_com.in -o
> sanmin_com.1.out -c /users/health/emikros/NMODE/snapshot_com.crd.1 -p
> /users/health/emikros/NMODE/era_ago_gen_com.prmtop -r sanmin_com.1.restrt
> not running properly
>
> As you can see i need to give the EXACT path for all files when runing
> sander. The prmtop and crd files have the correct path because i defined
> them on binding_energy.mmpbsa script.
> So, how can i define the exact path for all input and output files?
> Also how can i define to use sander.MPI instead of sander?
>
>
> Thanks for your time,
> Dr. George Lamprinidis
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Oct 01 2010 - 04:00:04 PDT
