[gmx-users] MPI and dual-core laptop

[Berk Hess]

Hi,

You don't need MPI within one machine.
Gromacs 4.5 has a built in thread-mpi library that gets built automatically.

Berk

> 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
> 
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> 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
> > 
> > 
> 
> Hi,
> 
>  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.
> 
> /Flo
> 
> 
> - -- 
> Florian Dommert
> Dipl.-Phys.
> 
> 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
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.10 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> 
> iEYEARECAAYFAkyhpcYACgkQLpNNBb9GiPm1AgCfWcXsF7zs+fGV2gGFiGgG1H4o
> tC0AoJRxehKCtgYNSq8qa5fqbEagde8a
> =YCG5
> -----END PGP SIGNATURE-----
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100928/9777b38e/attachment.html>