[gmx-users] GROMACS 4.5.1 and MPI

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 23 18:46:11 CEST 2010

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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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