[gmx-developers] GDB Debugging - GROMACS(v-3.3.3) Application with OpenMPI(v-1.2.5/v-1.2.6)

Florian Dommert dommert at fias.uni-frankfurt.de
Fri Apr 18 13:30:31 CEST 2008

Mark Abraham wrote:

> Daniel Larsson wrote:
>> On Apr 17, 2008, at 19:36, Mukesh K Srivastava wrote:
>>> Hi.
>>> Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3)
>>> application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had
>>> properly configured OpenMPI with debug option and also configured
>>> Gromacs alongwith FFTW succesfully. I can perform p2bdbx_mpi,
>>> editconf_mpi, genbox_mpi, grompp_mpi compilation and finally
>>> mdrun_mpi without any error or warning messages. But while executing
>>> mdrun_mpi w.r.t mprun, I get libmpi.so.0 not found.
>> This is probably not really any help but just to clarify, as far as I
>> know, only mdrun can be run in parallel.
> True. The online instructions for installation indicate that you need
> to do "make mdrun" and "make install-mdrun" only when compiling an MPI
> version.
> Mark
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I am not a user of OpenMPI, but it seems the MPI library path is not in
your LD_LIBRARY_PATH. In my opinion you should not be able to run an MPI
application with your setup.

Since I don't know what kind of shell you are using, I cannot give
precise help. But for the BASH you would have to add a line in the
~/.bashrc like:

export LD_LIBRARY_PATH=/home/user/local/mpi/lib:$LD_LIBRARY_PATH


Florian Dommert

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47522
Fax:   +49(0)69 / 798 - 47611

EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert

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