Sorry for the two responses but I forgot to mention that when i used PBS
with the perl script all my output files went to my home (top level)
directory. So check there for error files.
Hope this helps,
Oliver
On 1 October 2010 12:50, Oliver Grant <olivercgrant.gmail.com> wrote:
> "amber10//exe" ...the double slash in your path looks odd.
>
>
> On 1 October 2010 12:46, Giorgos Lamprinidis <lamprinidis.pharm.uoa.gr>wrote:
>
>> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Oct 01 2010 - 05:00:08 PDT
