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: domm...@icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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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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