[gmx-users] Gromacs Installation troubles

[Nicholas Geraedts]

Jussi - I tried installing the packages from the EPEL repo. I removed the
old LAM installation so there's no remnants of it, but now I can't find
mpirun anywhere. It's not listed in the path, nor can I find it in any of
the "usual" installation locations. Any thoughts? gromacs and gromacs-mpi
installed and I can find them using their g_* names.

Mark - forcing the old LAM installation is what caused the start of these
problems. My simulation would complain about not being able to find a
library - one that was supposed to be compiled with the f77 compiler.

Cheers,
-Nick

On Tue, Nov 18, 2008 at 8:34 AM, Jussi Lehtola <jussi.lehtola at helsinki.fi>wrote:

> On Wed, 2008-11-19 at 01:46 +1100, Mark Abraham wrote:
> > > 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).
> >
> > So that's why you can force RPM to do things when you do happen to know
> > better that it does.
>
> Forcing RPM to do things it shouldn't do is not a very bright idea. Also
> never trust RPMs you found somewhere on the internet, often they do very
> stupid and unsafe things.
>
> RPMs in e.g. Fedora are quite safe, since they adhere to a strict
> package policy, which is controlled.
>
> Anyway, when there are already built, guaranteedly safe RPMs for your
> distribution, please use them.
>
> Besides, LAM has been obsolete for some years now, you should use
> OpenMPI instead, which implements e.g. full MPI2. And you can find LAM
> also already in the distribution, you just have to install the lam-devel
> package to be able to compile against it.
>
> > >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).
>
> Not really, since that way
>
> a) you have no idea what software has been installed and where
> b) upgrading software is a pain in the ass
>
> If you use the distribution packages you don't have to worry about
> anything.
>
> Compile software yourself *only if* you want to use some proprietary
> compiler (e.g. Intel), or you want to use some switches in the
> compilation the RPMs haven't been compiled with. And even if you do
> compile stuff yourself, it's often easier to take the SRPMs and edit the
> spec file to make it use the compiler & options you want it to instead
> of manually compiling & installing the software from the source tar
> files.
> --
> ------------------------------------------------------
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.lehtola at helsinki.fi, p. 191 50623
> ------------------------------------------------------
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.lehtola at helsinki.fi
> ------------------------------------------------------
>
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