[gmx-users] Gromacs on Pathscale/Infiniband?

[pim schravendijk]

On 7/13/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
>
>
> From: Susan Chacko <susanc at helix.nih.gov>
> Subject: [gmx-users] Gromacs on Pathscale/Infiniband?
>
> Hi all,
>
> We have a bunch of Opterons connected with Infiniband. I'm trying to
> get Gromacs compiled for these nodes. I successfully built FFTW
> 3.1.2, but my Gromacs 3.3.1 config goes about halfway and then fails
> with
>
> checking size of int... configure: error: cannot compute sizeof
> (int), 77
>
> These are the flags I'm using:
> ./configure --with-fft=fftw3 --enable-float --prefix=/usr/local/src/
> gromacs/gromacs-ib --enable-mpi
>
> Any suggestions? Has anyone else successfully built/run Gromacs with
> Pathscale/IB?
>
> All help much appreciated,
> Susan.
>
>
I recently installed with mpich in an infiniband opteron cluster (don't know
too many details, it just worked).

However, if you look at that error string in
http://www.gromacs.org/external/search.html you will find a range of the
same errors, all from 2006, mostly mpi related, and all unsolved. You can
read however that you will find more info in the config.log, for example the
top post in that list has this error in the config.log:

./conftest: error while loading shared libraries: liblamf77mpi.so.0:
cannot open shared object file: No such file or directory

It looks like it can't find the libraries (in that case f77 mpi libs) that
it's looking for :) Maybe they can be installed, or maybe just
--disable-fortran (or something like that, don't know the exact one) would
solve that particular case.

So check config.log and post what you find there.

Make sure you get the problem solved, because the combination of gromacs and
infiniband-connected opterons is pretty fast :)

-- 
greetings, Pim
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