[gmx-users] MPI and dual-core laptop

Carsten Kutzner ckutzne at gwdg.de
Tue Sep 28 09:34:46 CEST 2010


if you only want to use the two processors of you laptop you
can simple leave away the --enable-mpi flag. Then it will
work in parallel using threads. Use mdrun -nt 2 -s ...
to specify two threads.

If you anyhow want to compile with MPI, take a look
at the config.log file (search for 'Cannot compile and link MPI code')
to check the actual cause of your problem,
probably some library was not found.


On Sep 27, 2010, at 8:42 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
> -- 
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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