[gmx-users] MPI

[Justin A. Lemkul]

Florian Dommert wrote:
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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.
> 

Good point, but it should also be noted that the warning shows up regardless of 
the version.  I use version 1.4.2, and I'm still cautioned against using version 
< 1.4.1 despite this fact.

-Justin

> /Flo
> 
>> 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
> 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
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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