VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Wed Sep 21 2016 - 09:14:48 CDT

Indeed, adding the flag -lrt to the general definition of the cuda_libs
in the configure file solves this issue and the cvs code compiles ...

However, I find that the new VMD starts significantly slower than the
1.9.2 version compiled exactly on the same machine with exactly the same
libs.

Anybody else experiencing this ?

Best
Vlad

On 09/21/2016 03:26 PM, Vlad Cojocaru wrote:
> 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