Dear Amber user,
I am using fewer nodes this time using below
pbs script. Job run and and still
continue but it only give 7 ns /day which is
very slow.How to get fast result
from HPC. Is it slow because of Sander
module.Can i use PMEMD to get fast calculation using HPC. Iour HPC
#!/bin/csh
#PBS -l walltime=48:00:00
#PBS -N my_job
#PBS -q workq
#PBS -l select=10:ncpus=16:mpiprocs=16
#PBS -l place=scatter:excl
#PBS -V
# Go to the directory from which you submitted the job
cd $PBS_O_WORKDIR
source /usr/share/Modules/init/csh
setenv MPI_DEBUG "all"
setenv MPI_IB_RAILS "2"
setenv MPI_DSM_DISTRIBUTE "1"
setenv MPI_VERBOSE "1"
setenv MPI_BUFS_THRESHOLD "1"
setenv MPI_BUFS_PER_PROC "1024"
source /home/ashoks/amber14/amber14/amber.csh
module load amber14
module load intel-cluster-studio-2013-sp1
cd /home/ashoks/5_garima/pm/pm
mpirun -np 160 sander.MPI -O -i Prod.in -o Prod.out -p cd_cdpm7.prmtop -c
Heat.rst -r prod.rst -x prod.mdcrd -inf p <
http://prod.info>
*Thank You and Best Wishes*
--
*Regards*
Garima Singh
AcSIR-PhD Fellow
Biotechnology Division
C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division)
Central Institute Of Medicinal And Aromatic Plant
CSIR-CIMAP
Lucknow
garimabioinfo.gmail.com
*INDIA* Please don't print this e-mail unless you really need to. Be Green !
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Received on Tue Jul 04 2017 - 00:00:04 PDT
