Jason,
Thanks for your detailed response. However there is no sanmin_com1.in or out
file. Here is the full error message from pbs
/users/health/emikros/NMODE: Permission denied.
/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
My working direcory is /users/health/emikros/NMODE and the directory for
sander is /users/health/emikros/amber10//exe/sander
but for some reason the perl script can't write the input file.
I shall also try to run the python version of mmpbsa.....
George
----- Original Message -----
From: "Jason Swails" <jason.swails.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Friday, October 01, 2010 1:37 PM
Subject: Re: [AMBER] runing mmpbsa.pl on cluster
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 01 2010 - 05:00:05 PDT
