*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
--------------------------------------------------------------------------
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
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 23894 on
node r01n19 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
*I'm using Amber 11 with gnu compilers and mpif90. Regards,*
--
--
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
Received on Tue May 24 2011 - 12:30:03 PDT
