[gmx-users] MPI and dual-core laptop

Florian Dommert dommert at icp.uni-stuttgart.de
Tue Sep 28 10:22:30 CEST 2010

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


 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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