VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Wed Sep 21 2016 - 08:26:17 CDT

Thanks Axel,

The glibc version is 2.19 and is the same as the one CUDA was installed
against ....

But I could not find "-lrt" in the linking options ... In the VMD
configure file in only appears at arch = SUMMIT or SOLARIS under
"cuda_libs" ... I will try to add it to the general $cuda_libs and see
if it works

Best
Vlad

On 09/21/2016 03:10 PM, Axel Kohlmeyer wrote:
> On Wed, Sep 21, 2016 at 8:42 AM, Vlad Cojocaru
> <vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:
>> Dear all,
>>
>> I am trying to compile VMD (CVS today) on a LINUXAMD64 arch with openSUSE
>> 42.1 (gcc 4.8.5), cuda 7.5.18 but I get the following error:
>>
>>
>> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:
>> /apps/nvidia/cuda/7.5.18/lib64/libcudart_static.a(libcudart_static.a.o):
>> undefined reference to symbol 'shm_unlink@@GLIBC_2.2.5'
>> /lib64/librt.so.1: error adding symbols: DSO missing from command line
>> collect2: error: ld returned 1 exit status
>> Makefile:608: recipe for target 'vmd_LINUXAMD64' failed
>> make: *** [vmd_LINUXAMD64] Error 1
>>
>>
>> Did anybody experience this and knows a way to resolve the issue?
> this most likely means, that you either didn't link with -lrt
> correctly or that your glibc version is too old compared with the one
> used to compile the CUDA toolkit.
>
> axel.
>
>> Thanks a lot
>>
>> Best wishes
>> Vlad
>>
>> --
>> Dr. Vlad Cojocaru
>> Computational Structural Biology Laboratory
>> Department of Cell and Developmental Biology
>> Max Planck Institute for Molecular Biomedicine
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>
>
> 

-- 
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru