[gmx-users] using gromacs with an specific GCC

Szilárd Páll szilard.pall at cbr.su.se
Thu Oct 13 03:26:03 CEST 2011

Hi Nathalia,

Right, gcc 4.1 is quite controversial as these is bug in it which is
though to be causing mdrun crashes. So you better stay away from 4.1
as well as from other old gcc versions. I'd recommend 4.5 or 4.6 as
these have gotten really good, even compared to icc - at least when it
comes to Gromacs performance. I'd especially recommend 4.6 if you're
using Nehalem CPUs (with the -mtune/-march=corei7 flag).

Compiling gcc is rather straightforward and there are plenty of guide online.

When it comes to running binaries, depending on where you install the
new gcc you might have to set the LD_LIBRARY_PATH to contain the
custom gcc installation's lib directory before the standard lib path.
This is of course unless you link statically against standard


On Mon, Oct 10, 2011 at 6:51 PM, Nathalia Garces <natsgarces at gmail.com> wrote:
> Good morning,
> I'm trying to use Scientific Linux 5.5 to run Gromacs 4.5.4. The problem is
> that the default version of gcc in this distribution is 4.1, which is broken
> for Gromacs!!
> I can install a newer version of gcc in compatible mode with gcc 4.1, but
> the last one will still be the default.
> Now, my problem is that I don't know how to specify to Gromacs to use the
> newer version. I've seen that you can specify which gcc to use while you
> configure the program, but I found no information of how to specify which
> compiler to use while running a MD simulation??.. I mean when using mdrun
> command or even while using every command in Gromacs.
> Thank you for four answer
> Nathalia
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