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
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Received on Tue May 24 2011 - 13:30:04 PDT
