Dear All,
I'm trying to run parallel Amber 11 on a cluster with PBS. I've checked the
parallel installation and it's quite fine (the log file attached).
However, the performance is always between 0.1 and 0.5 ns/day, no matter the
number of processors I choose. Is there something missing in my script?
Here are the changes I made on my configure (for the parallel version):
mpicc --> icc -lmpi
mpif90 --> ifort -lmpi
This generated the correct config.h needed for the fortran compiler.
However, the problem persists with gnu installing, so I guess it has nothing
to do with the installation, but it's pretty much a submission problem. Here
is an example of my job:
#!/bin/bash
#
#################################################
# THIS JOB IS TO EQUILIBRATE THE SYSTEM AT 300K #
# TO BE USED IN FUTURE SIMULATIONS. IT STARTS #
# FROM THE EQUILIBRATION ON CHACOBO, WHERE 1ns #
# WAS PERFORMED AFTER THE DNA WAS RELEASED. #
#################################################
#
#PBS -S /bin/sh
#
# Nome do job
#PBS -N prod_slow
#
#Erro na saida padrao
#PBS -j oe
#
# Chamada do ambiente paralelo e numero de slots
#PBS -l select=64:ncpus=1
#PBS -l walltime=200:00:00
#
cd $PBS_O_WORKDIR
export sander=/home/u/bbr/bin/amber11/bin/pmemd.MPI
l=heat20
f=prod01
mpiexec -n 64 $sander -O -i $PWD/$f.in -o $PWD/$f.out -inf $PWD/$f.inf \
-c $PWD/1D20_wat_tip3pf.$l -ref $PWD/1D20_wat_tip3pf.$l -r
$PWD/1D20_wat_tip3pf.$f \
-p $PWD/1D20_wat_tip3pf.top -x $PWD/1D20_wat_tip3pf$f.x -e
$PWD/1D20_wat_tip3pf$f.ene
Details of the cluster: Novell SUSE Linux Enterprise Server 11-SP1, 32
processor units. Each one with 64 GB of RAM and 2 processors dodecacore AMD
Opteron 6176 SE 2.3 GHz, ending up with 768 nucleus.
It should give a better performance on 64 nodes, for a 10bp dna with +-
4.000 water molecules.
Any suggestion would be very grateful,
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Mon Aug 29 2011 - 13:30:02 PDT
