VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Wed Sep 21 2016 - 10:17:28 CDT

Thanks a lot John for the explanations,

The startup (and actually also quit) slow times comparing to 1.9.2
version are quite noticeable on my machine (VMD compiled on local SATA
hard drive and running on the same computer (so, no particularly slow
file system involved).

Nevertheless, if its just startup and quit, it does not really matter.
.. I just thought of reporting this in case there is some hidden issue ...

Best
Vlad

On 09/21/2016 04:53 PM, John Stone wrote:
> Hi Vlad,
> The new version of VMD includes a couple of large Tk GUI components that
> take a non-trivial amount of parse time at startup, and this is likely what
> you're noticing. I find it is particularly noticable on machines with slow
> filesystem access.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Sep 21, 2016 at 04:14:48PM +0200, Vlad Cojocaru wrote:
>> 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 

-- 
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