HI,
The speed also depends on the size, i.e. the number atoms in your system.
How many atoms are there in your system?
Secondly, it also depends on what the interconnect device that is used to connect the various compute nodes.
For InfiniBand switches have low latency time whereas the normal Ethernet switches have large latency time.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Garima Singh <garimabioinfo.gmail.com>
Sent: 04 July 2017 12:23:42
To: amber.ambermd.org
Subject: [AMBER] Amber md in HPC
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 - 01:00:02 PDT
