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
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Received on Tue May 24 2011 - 20:00:03 PDT
