[gmx-users] Newest version of Gromacs 4.5 installation

Mark Abraham mark.abraham at anu.edu.au
Thu Sep 2 03:42:18 CEST 2010

----- Original Message -----
From: Moeed <lecielll at googlemail.com>
Date: Thursday, September 2, 2010 6:44
Subject: [gmx-users] Newest version of Gromacs 4.5 installation
To: gmx-users at gromacs.org

> Hi,
> We are installing the newest version of Gromacs - 4.5 on our cluster (running CentOS) for parallel purposes. We are also using Openmpi version 1.4. However upon installing Gromacs using the command:
> ./configure --enable-mpi
> we ran into this problem below:
> * Seems you are compiling with MPI support. You can install the MPI-
>   enabled programs with suffixed names to have both MPI and non-MPI
>   versions. This is useful e.g. on supercomputers where you usually
>    cannot run MPI-linked programs on the login node.
>   Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double).
>   You only need MPI for mdrun, so if you already have non-MPI stuff
>   installed you can issue make mdrun; make install-mdrun.
>   There are known problems with some MPI implementations:
>              OpenMPI version < 1.4.1
>              MVAPICH2 version <= 1.4.1
> * On most platforms you can save 10X space with dynamic libraries, although
>    the binaries might be less portable. Why not try --enable-shared ?
> Does this imply that we must update our current Openmpi version from 1.4 to 1.41 in order for Gromacs to be installed?

No, it's only a warning. Feel free to ignore it, but if you get mystifying problems, upgrading MPI is your first port of call.

> Also, what are the pros and cons of using '--enable-shared'?

 Smaller installation footprint. Perhaps smaller code execution memory footprint. Potentially more work to do making sure the execution environment has access to the shared libraries as well as the executable. Mess if you mis-manage having multiple versions installed at the same time. More hassle in heterogenous computing environments.


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