AMBER: SANDER and PMEMD with openmpi

From: Ross Walker <>
Date: Fri, 30 May 2008 15:18:04 -0700

Hi All,

It seems a number of people are interested in building both sander and pmemd
using openmpi and so I thought I would post a description of how I did this
on my machine so others can benefit:

>ifort -V
Intel(R) Fortran Compiler for applications running on Intel(R) 64, Version
10.1 Build 20070913 Package ID: l_fc_p_10.1.008
>icc -V
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.

>gcc -v
gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)

>cat /etc/redhat-release
Red Hat Enterprise Linux AS release 4 (Nahant Update 6)

>uname -a
Linux ......... 2.6.9-67.0.4.ELsmp #1 SMP Fri Jan 18 05:00:00 EST 2008
x86_64 x86_64 x86_64 GNU/Linux

>cat /proc/cpuinfo
cpu family : 15
model : 6
model name : Intel(R) Pentium(R) D CPU 3.20GHz

>echo $MKL_HOME

>tar xvzf openmpi-1.2.6.tar.gz
>cd openmpi-1.2.6
>export CC=gcc
>export CXX=g++
>export F77=ifort
>export FC=ifort

>./configure --prefix=/usr/local/mpi/openmpi-1.2.6_ifort10.1.008
>make install

>export MPI_HOME=/usr/local/mpi/openmpi-1.2.6_ifort10.1.008
>export PATH=$MPI_HOME/bin:$PATH

>which mpirun

>mpif90 -show
ifort -g -I/usr/local/mpi/mpich2-1.0.3_ifort9.1.039/include
-L/usr/local/mpi/mpich2-1.0.3_ifort9.1.039/lib -lmpichf90 -lmpichf90 -lmpich
-lpthread -lrt

>cd ~/
>tar xvjf Amber10.tar.bz2
>export AMBERHOME=~/amber10/

>cd $AMBERHOME/src/
>./configure_amber -openmpi -nobintraj ifort
>make parallel

>cd $AMBERHOME/src/pmemd/
> ./configure linux_em64t ifort lam pubfft nobintraj

edit config.h
Line 17:
Change MPI_LIBS = -L$(MPI_LIBDIR) -llamf77mpi -lmpi -llam -ldl -lpthread

Line 23:
Change F90 = ifort
to F90 = mpif90

Line 35:
Change LOAD = ifort
to LOAD = mpif90

>make install

>export DO_PARALLEL='mpirun -np 2'

>cd $AMBERHOME/test/
>make test.parallel
>make test.parallel.QMMM

(Check TEST_FAILURES.diff - all tests passed file did not exist)

>make clean
>make test.PMEMD

(Check TEST_FAILURES.diff - all tests passed file did not exist)


All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Jun 01 2008 - 06:08:06 PDT
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