[gmx-users] Linker error during GMX make

[Clemens Grimm]

Dear Szilárd,

I finally downloaded the package again and repeated cmake/make. For  
whatever reason, it finally linked flawlessly. Thanks for your help!

Best,
Clemens

Zitat von Szilárd Páll <pall.szilard at gmail.com>:

> 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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--------------------------------------------------
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
-------------------------------------------------