Hi Jason,
I followed your suggestion and use the following script:
#!/bin/bash
#PBS -l mem=1gb
#PBS -l walltime=01:10:00
#PBS -N m8_npt
echo "Num Procs is `cat $PBS_NODEFILE | wc -l`"
source /usr/local/modules/init/bash
module load amber/x86_64/gnu/12_mpi
module load mvapich2/1.8
cd $PBS_O_WORKDIR
mpirun -f NODEFILE -np 8 pmemd.MPI -O -i eq_1_heat.in -p com_solvated_m8.top -c min_solventonly_5.rst -r eq_1_heat.rst -x eq_1_heat.mdcrd -o eq_1_heat.out -ref min_solventonly_5.rst
I use this NODEFILE:
node001
node002
node003
node004
node005
node006
node007
node008
Strangely enough, i didn't get any output, although when i view the running jobs under my account the job is still running....I also noticed this behavior before when i was using the (#PBS -l nodes=8) in the script before..
Also, i removed the -f NODEFILE keyword from the command line and typed the command you sent me, the output contained this line:
Num Procs is 1
I also got this logfile:
Static FFT Slab Distribution:
FFT slabs assigned to 8 tasks
Maximum of 12 xy slabs per task
Maximum of 12 zx slabs per task
Count of FFT xy slabs assigned to each task:
12 12 12 12 12 12 12 12
Count of FFT xz slabs assigned to each task:
12 12 11 11 11 11 11 11
Could you please comment...I feel as if one processor is doing 8 jobs....Is it true....???
Regards
Marawan
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Received on Fri Sep 21 2012 - 00:00:02 PDT
