simon sham wrote:
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.
The error message suggests that perhaps a different version of the MPI
implementation was used to compile the code. Find out from your admin how
Gromacs was built.
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?
No, as a matter of fact, none of the other Gromacs utilities are MPI-aware.
-Justin
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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
