VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue Oct 04 2016 - 08:33:31 CDT

Hi John, HI all,

Just a short note to this earlier post (see below) .. The trajectory
animation is also affected by the slow down of 1.9.3 beta version ....
It is extremely slow to animate a trajectory comparing to 1.9.2.

Best wishes
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