Dear Amber users,
When I run some QM/MM/MD calculation on 16 procesors (parallel, 2 nodes, 8
ppn) I notice that the calculations lasts forever and stuck (still running)
at the first picosecond (after 6 hours still at the same step) but when I
use only 1 processor it moves faster, any idea? below my input:
###These lines are for Moab
#MSUB -l nodes=2:ppn=8
#MSUB -l partition=ALL
#MSUB -l walltime=100:00:00
#MSUB -m be
#MSUB -V
#MSUB -o
/export/home/msoliman/scratch/Amber/glycosidase_work/pmf/AM1/one_coordinate/
amber.our
#MSUB -e
/export/home/msoliman/scratch/Amber/glycosidase_work/pmf/AM1/one_coordinate/
amber.err
#MSUB -d
/export/home/msoliman/scratch/Amber/glycosidase_work/pmf/AM1/one_coordinate/
#MSUB -mb
##### Running commands
####nproc=`wc $PBS_NODEFILE | awk '{print $1}'`
exe=/export/home/msoliman/bin/amber10/bin/sander.MPI
nproc=`cat $PBS_NODEFILE | wc -l`
mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i equil.qmmm.in -o
equil.qmmm.out -p com_solvated.top -c com_solvated_opt.qmmm.rst -r
com_solvated_equil.qmmm.rst -ref com_solvated_opt.qmmm.rst
Thanks
Mahmoud
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Received on Tue Apr 19 2011 - 00:30:02 PDT
