Justin A. Lemkul
jalemkul at vt.edu
Sat Sep 25 19:21:24 CEST 2010
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:
> 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.
>> simon sham wrote:
>>> This is the same email that I'd sent yesterday but has not got posted?
>>> 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.
>>> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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