On Wed, May 25, 2011 at 8:18 AM, Bruno Rodrigues <bbrodrigues.gmail.com>wrote:
> The cluster administrator claimed that my ./restart.sh should be a BINARY
> file because mpirun only accepts binaries.
>
> I guess it's not the case as it recognizes the commands inside. Do you have
> any clue about the input files for mpirun? I read the man from mpirun and
> it
> just mentions EXECUTABLE, not binary...
>
Depends on the implementation. Your admin would probably know best.
>
> On Tue, May 24, 2011 at 11:48 PM, Bruno Rodrigues <bbrodrigues.gmail.com
> >wrote:
>
> > It says
> >
> > [bbr.newton ~/1D20_wat_salt7]$ ls -ld
> > drwxr-x--- 2 bbr PROJ3801 4096 May 24 23:23 .
> >
> > does it mean I can't read anything from here?
> >
> >
> > On Tue, May 24, 2011 at 5:11 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> >> On Tue, May 24, 2011 at 3:21 PM, Bruno Rodrigues <bbrodrigues.gmail.com
> >> >wrote:
> >>
> >> > *Dear all,
> >> >
> >> > I'm getting an error on trying to run sander in parallel on a Sun Fire
> >> > Cluster. The interactive command is
> >> >
> >> > *qrsh -pe mpich 2 -cwd 'mpirun -n 2 ./restart.sh'
> >> > *
> >> >
> >> > and I get the error below:
> >> >
> >> > *At line 116 of file master_setup.f90
> >> > Fortran runtime error: Cannot write to file opened for READ
> >> >
> >>
> >> Do you have reading permissions for this directory?
> >>
> >>
> >> >
> >>
> --------------------------------------------------------------------------
> >> > mpirun has exited due to process rank 0 with PID 16119 on
> >> > node r01n16 exiting without calling "finalize". This may
> >> > have caused other processes in the application to be
> >> > terminated by signals sent by mpirun (as reported here).
> >> >
> >> >
> >> > *
> >> > This is the restart file:
> >> >
> >> > *#!/bin/sh
> >> >
> >> > #export sander=$AMBERHOME/exe/sander
> >> > #For optimal parallel performance use pmemd instead of sander
> >> > export sander=/home/u/bbr/bin/amber11/bin/pmemd.MPI
> >> >
> >> > l=md8
> >> > f=md9
> >> > $sander -O -i $PWD/$f.in -c $PWD/1D20_wat_salt7.$l -ref
> >> > $PWD/1D20_wat_salt7.$l \
> >> > -r $PWD/1D20_wat_salt7.$f -o $PWD/$f.out -inf $PWD/$f.inf \
> >> > -p $PWD/1D20_wat_salt7.top -x $PWD/1D20_wat_salt7$f.x -e
> >> > $PWD/1D20_wat_salt7$f.ene
> >> >
> >> > *When I switch from pmemd.MPI to sander.MPI, I get an even worse
> error:
> >> >
> >> >
> >> > *MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> >> > with errorcode 1.
> >> >
> >> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> >> > You may or may not see output from other processes, depending on
> >> > exactly when Open MPI kills them.
> >> >
> >>
> --------------------------------------------------------------------------
> >> >
> >> > Unit 6 Error on OPEN:
> >> > /home/u/bbr/1D20_wat_salt7/md9.out
> >> >
> >>
> >> It looks like you don't have write permissions for the directory
> >> /home/u/bbr/1D20_wat_salt7/. What does the command
> >>
> >> ls -ld /home/u/bbr/1D20_wat_salt7
> >>
> >> return?
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > --
> > Bruno Barbosa Rodrigues
> > PhD Student - Physics Department
> > Universidade Federal de Minas Gerais - UFMG
> > Belo Horizonte - Brazil
> >
>
>
>
> --
> --
> Bruno Barbosa Rodrigues
> PhD Student - Physics Department
> Universidade Federal de Minas Gerais - UFMG
> Belo Horizonte - Brazil
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 25 2011 - 06:30:02 PDT
