[gmx-users] Gromacs Installation troubles

Nicholas Geraedts ngeraedts at gmail.com
Tue Nov 18 11:13:05 CET 2008

Mark - I've followed the instructions on the wiki. The last step says to
email the mailing list, as I have done. I'm not sure about your comment for
not needing a complete make if we're looking for MPI. There are situations
where the program will be used in single-processor mode, as well as MPI. I'm
not too concerned with the time it takes to compile all of this (it's only
about 8 minutes for the whole lot).

Jussi - I'm trying to compile the packages myself since the pre-made RPM's
don't seem to install the libraries needed. Furthermore, the LAM RPM would
constantly complain about not being able to find gcc-g77 - a package found
in CentOS4 but not CentOS5 (it's now referred to as compat-gcc-34-g77 - the
names don't agree so rpm complains). Also, installing LAM from yum fails to
put the required binaries where they belong! There's no lamboot, mpmirun,
lamhalt, etc to be found anywhere in the path. I've found that it's often
much less of a headache if you can find the source and start from scratch
(this is the FreeBSD child in me talking).

My main problem so far is that the library for GSL is installed in the wrong
location and that mdrun_mpi doesn't seem to have been compiled. If the
source is provided, it should be possible to compile it into a functional


On Tue, Nov 18, 2008 at 12:39 AM, Antoine Migeon <
Antoine.Migeon at u-bourgogne.fr> wrote:

>  Hello,
> I have many problem for install Gromacs in Centos 5.2, without MPI for the
> moment.
> I tried you solution, but the package contain only binary prefixed by "g_",
> and the test set doesn't find grompp.
> (after source /usr/bin/GMXRC)
> What the problem ?
> Antoine Migeon
> Université de Bourgogne
> Centre de Ressources Informatiques - Centre de Calcul
> tel : 03 80 39 52 70
> Site du CCUB : http://u-bourgogne.fr/cri-ccub
> Jussi Lehtola a écrit :
> On Mon, 2008-11-17 at 16:59 -0800, Nicholas Geraedts wrote:
>  I'm trying to get Gromacs installed on our systems, but I've been
> running into one error after another. We are running CentOS5 x86-64
> with all the latest updates.
> I've got the following packages downloaded
> lam-7.1.4
> fftw-3.2
> gsl-1.11
> gromacs-4.0
>  Ugh. Why do you want to compile these yourself? Use the distribution
> packages, that way you always can tell what is installed on your system
> and upgrading is easy.
> 1. Enable the Fedora EPEL repositoryhttp://fedoraproject.org/wiki/EPEL/FAQ#howtouse
> 2. Currently Gromacs is only available in EPEL Testing, but will be
> pushed to EPEL Stable. Install Gromacs with
> # yum --enablerepo=epel-testing -y install gromacs gromacs-mpi
> This way you get single and double precision binaries with and without
> MPI support, and all the needed dependencies.
> 3. If you don't want Gromacs to be automatically updated with yum, put
> the line
> exclude = gromacs*
> in /etc/yum.conf. When you want to update Gromacs to the newest version
> available, remove the line and run
> # yum -y update
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