VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue Oct 04 2016 - 08:53:03 CDT

No, sorry .. please ignore my last email ... there is no difference in
animation speed between 1.9.2 and 1.9.3b ... I overlooked something ...

I apologize for the spam !
Vlad

On 10/04/2016 03:33 PM, Vlad Cojocaru wrote:
> 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