[gmx-users] Linker error during GMX make

[Szilárd Páll]

On Mon, Jan 30, 2017 at 1:25 PM, Clemens Grimm
<clemens.grimm at biozentrum.uni-wuerzburg.de> wrote:
>
> Dear All,
>
> I am doing a
>
> cmake . -DGMX_GPU=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/soft
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda DBUILD_SHARED_LIBS=OFF

There's a '-' missing there.

> make
>
> to build gromacs-5.1.4 with openmpi and cuda. After compiling fine, I get
> the following linker error:
>
> /usr/lib/openmpi/lib/libmpi.so: error adding symbols: File in wrong format

My guess is that you are linking against the wrong version of the
library, e.g. 32-bit libmpi.so while compiling the rest in 64-bit.

Quick check: does it link without MPI?

--
Szilárd

> My system is CentOS 7 (centos-release-7-3.1611.el7.centos.x86_64), I have
> installed openmpi from the CentOS repository.
>
> Thanks for your help,
> Clemens
>
>
> --------------------------------------------------
> Dr. Clemens Grimm
> Institut für Biochemie
> Biozentrum der Universität Würzburg
> Am Hubland
> D-97074 Würzburg
> Germany
> e-mail: Clemens.Grimm at biozentrum.uni-wuerzburg.de
> phone : +49 0931 31 84031
> -------------------------------------------------
>
>
> --------------------------------------------------
> Dr. Clemens Grimm
> Institut für Biochemie
> Biozentrum der Universität Würzburg
> Am Hubland
> D-97074 Würzburg
> Germany
> e-mail: Clemens.Grimm at biozentrum.uni-wuerzburg.de
> phone : +49 0931 31 84031
> -------------------------------------------------
>
>
> --------------------------------------------------
> Dr. Clemens Grimm
> Institut für Biochemie
> Biozentrum der Universität Würzburg
> Am Hubland
> D-97074 Würzburg
> Germany
> e-mail: Clemens.Grimm at biozentrum.uni-wuerzburg.de
> phone : +49 0931 31 84031
> -------------------------------------------------
> --
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