[gmx-users] MPI and dual-core laptop
gmx3 at hotmail.com
Tue Sep 28 10:36:54 CEST 2010
You don't need MPI within one machine.
Gromacs 4.5 has a built in thread-mpi library that gets built automatically.
> Date: Tue, 28 Sep 2010 10:22:30 +0200
> From: dommert at icp.uni-stuttgart.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] MPI and dual-core laptop
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> On 09/27/2010 08:42 PM, simon sham wrote:
> > Hi,
> > I wanted to test the GROMACS MPI version in my dual-processors laptop. I
> > have installed openmpi 1.4.2 version. However, when I tried to configure
> > GROMACS 4.5.1 with --enable-mpi option, I got the following
> > configuration problem:
> > "checking whether the MPI cc command works... configure: error: Cannot
> > compile and link MPI code with mpicc"
> > mpicc is in my /usr/local/bin directory.
> > Questions:
> > 1. Can I run GROMACS 4.5.1 in a dual-processor laptop?
> > 2. If yes, how should I configure the software?
> > Thanks in advance for your insight.
> > Best,
> > Simon Sham
> it seems the mpicc compiler does not find the necessary libraries to
> link or doesn't even find the compiler. Check if mpicc is in your path.
> To include the missing libraries in the GROMACS configuration use the
> LDFLAGS and CPPFLAGS variables to set the corresponding pathes.
> CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure ...
> If you have to add further include and library directories you have to
> add a further -I/... and/or -L/... and put the whole expression after
> the = into quotes, e.g CPPFLAGS="-I/usr/local/lib
> - -I/home/user/local/fftw3/include" and so on.
> However if you use Gromacs 4.5 I would use and get common with the CMake
> system, which really works fine and also a GUI is available that allows
> you to easy set your variables options.
> - --
> Florian Dommert
> Institute for Computational Physics
> University Stuttgart
> Pfaffenwaldring 27
> 70569 Stuttgart
> Phone: +49(0)711/685-6-3613
> Fax: +49-(0)711/685-6-3658
> EMail: dommert at icp.uni-stuttgart.de
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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