On Fri, Oct 1, 2010 at 7:50 AM, Oliver Grant <olivercgrant.gmail.com> wrote:
> "amber10//exe" ...the double slash in your path looks odd.
>
It's odd, but it's a result of the fact that you have
AMBERHOME=/path/to/amber10/
and sander referenced by $AMBERHOME/exe/sander. Putting the 2 together:
/path/to/amber10//exe/sander. I have yet to encounter a system where this
was a problem.
>
> 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
> > >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> 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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AMBER mailing list
AMBER.ambermd.org
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Received on Fri Oct 01 2010 - 05:30:07 PDT
