[gmx-users] MPI

Florian Dommert dommert at icp.uni-stuttgart.de
Sat Sep 25 19:19:42 CEST 2010

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On 09/24/2010 09:18 PM, Justin A. Lemkul wrote:
> Guess my reply never hit the list, either, but it's in the archive:
> http://lists.gromacs.org/pipermail/gmx-users/2010-September/054259.html
> -Justin

Besides Justins answer perhaps you should consider using a newer version
of OpenMPI as you should receive a warning, when compiling with OpenMPI
< 1.4.1.


> simon sham wrote:
>> Hi,
>> This is the same email that I'd sent yesterday but has not got posted?
>> Hi,
>> I have some questions about installation of GROMACS with MPI.
>> Our system administrator has installed the 4.5.1 version in our
>> system. When I tested the software with
>> "openmpi/openmpi-1.3.3-gcc/bin/mpirun" with mdrun_mpi, I got all sorts
>> of error message such as
>> "opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol
>> `ompi_mpi_byte' has different size in shared object, consider
>> re-linking", and many others.
>> My questions:
>> 1. When I prepare my system for simulations, do I have to consistently
>> use *_mpi functions in gromacs_4.5.1_mpi directory?
>> 2. Are there any details that I need to pay attention when I configure
>> the software with openmpi?
>> Thanks for your help in advance.
>> Best,
>> Simon Sham

- -- 
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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