I don't see Open MPI in your list of modules - looks to me like you are using MPICH? If so, you should send this to their mailing list.
On Jul 5, 2011, at 1:44 PM, Chaudhari, Mangesh I wrote: > 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 ... !!! > > > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
