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Subject: [OMPI users] Running MPI jobs from external Hard Disk
From: Chaudhari, Mangesh I (mchaudha_at_[hidden])
Date: 2011-07-05 15:44:52


hi all,

I m trying to run a job from external hard disk and its giving me errors my output log is as follows

Currently Loaded Modulefiles:
  1) modules 4) mpich/mpich-mx-1.2.7..7-gcc.64
  2) tools/torque-maui 5) tools/amber10-mx
  3) tools/mx
Host: node10
Date: Tue Jul 5 15:17:32 EDT 2011
Dir: /home/mic
This job has allocated 8 nodes
mnode10 mnode10 mnode10 mnode10 mnode10 mnode10 mnode10 mnode10
[0] MPI Abort by user Aborting program !

  Unit 5 Error on OPEN: inp0
mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 10.11.1.10, killing all.
mpiexec: Warning: tasks 0-7 died with signal 15 (Terminated).
mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 10.11.1.10, killing all.

  Unit 5 Error on OPEN: inp1
[0] MPI Abort by user Aborting program !
mpiexec: Warning: tasks 0-7 died with signal 15 (Terminated).
mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 10.11.1.10, killing all.
[0] MPI Abort by user Aborting program !

  Unit 5 Error on OPEN: inp2
mpiexec: Warning: tasks 0-7 died with signal 15 (Terminated).

  Unit 5 Error on OPEN: inp3
[0] MPI Abort by user Aborting program !
mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 10.11.1.10, killing all.
mpiexec: Warning: tasks 0-7 died with signal 15 (Terminated).

-----------------------------------------------

my script file is as follows :

### Number of nodes and processors per node.
#PBS -l nodes=1:ppn=8
#PBS -j oe
#PBS -N GAFF_R60

#AMBERHOME="/usr/local/amber10-mx"

#Set up environment modules
. /usr/local/Modules/3.2.6/init/bash
module purge
module initclear
module load tools/amber10-mx
module initadd tools/amber10-mx

#module output
module list

#Job output header
PBS_O_WORKDIR=`pwd`
cd $PBS_O_WORKDIR
PBS_O_HOME=/home/bk3
echo Host: $HOSTNAME
echo Date: $(date)
echo Dir: $PWD

#calculate number of CPUs
NPROCS=`wc -l < $PBS_NODEFILE`
echo This job has allocated $NPROCS nodes
echo `cat $PBS_NODEFILE`

#set DO_PARALLEL
export DO_PARALLEL="mpiexec"
#export DO_PARALLEL_1="mpirun -np 1 -machinefile $PBS_NODEFILE"

#run amber10 sander.MPI

$DO_PARALLEL pmemd -O -i inp0 -p prmtop -c inpcrd -o mdout0 -r restrt0 -e mden0 -inf mdinfo0
$DO_PARALLEL pmemd -O -i inp1 -p prmtop -c restrt0 -o mdout1 -x mdcrd1 -r restrt1 -e mden1 -inf mdinfo1
#
$DO_PARALLEL pmemd -O -i inp2 -p prmtop -c restrt1 -o mdout2 -x mdcrd2 -r restrt2 -e mden2 -inf mdinfo2
#
$DO_PARALLEL pmemd -O -i inp3 -p prmtop -c restrt2 -o mdout3 -x mdcrd3 -r restrt3 -e mden3 -inf mdinfo3 -v mdvel3

------------------------------------------------

I dont know much about MPIs so donot know where exactly the problem is ...

Thanks in advance ... !!!