VMD-L Mailing List

From: Jack Bulat (jack.bulat_at_gmail.com)
Date: Wed May 29 2013 - 13:29:58 CDT

Hi John,

Recently, I've upgraded to Ubuntu 12.04 from 10.04 and now have upgraded NVIDIA drivers (3xx). I noticed that the VMD version 1.9.1 was running very slowly, and narrowed it down to the anti-aliasing problem that's been discussed (since MSAA(16) was displayed upon startup). After successfully installing 32-bit VMD1.9.2a26 just yesterday, I note an improvement; but performance is still sluggish enough to be noticeable. Here's what is displayed upon startup:

Info) VMD for LINUX, version 1.9.2a26 (May 9, 2013)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 16 CPUs detected.
Info) Free system memory: 6240MB (78%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 2 available CUDA accelerators:
Info) [0] Tesla C1060 30 SM_1.3 @ 1.30 GHz, 4.0GB RAM, OIO, ZCP
Info) [1] Quadro NVS 290 2 SM_1.1 @ 0.92 GHz, 255MB RAM, KTO, OIO, ZCP
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: Quadro NVS 290/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFG)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd1.9.2a26/plugins/LINUX/molfile

As you can see, MSAA(4) is shown, which is in line with the correction mentioned earlier in this thread. That said, I figure I could drop MSAA to 2 and get an improvement? However, there's no longer an environmental variable MAXAASAMPLES that's in place by default, and me setting it within VMD has no effect. Could you let me know if the name of the variable has been changed? Or if there's something else I ought to do in order to improve performance?

Thanks,
Jack Bulat
Grad Student, UC Berkeley

On Apr 15, 2013, at 7:51 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Bogdan,
> I'm happy we got this solved. To be honest, I was a little surprised
> that the new NVIDIA drivers changed the antialiasing behavior so radically,
> but I'm glad I've got the new code in place and it's working for you.
> Hopefully this particular kind of problem won't crop up again.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Apr 15, 2013 at 12:51:10PM +0200, Bogdan Costescu wrote:
>> Hi John!
>>
>> I have tested version 1.9.2 alpha 23 and everything works as it should
>> with the 3xx series driver from NVidia. By default, with my setup, VMD
>> chooses 4 samples-per-pixel, which is the same value it chose with the 2xx
>> series. I could change that with the VMDMAXAASAMPLES environmental
>> variable to 2, 8 or 16 and see how the start-up message and display speed
>> changes. All is well now :)
>>
>> Thanks a lot for finding and implementing this solution!
>> Bogdan
>>
>> On Thu, Mar 21, 2013 at 4:43 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>> Bogdan,
>> Sorry for the slow reply, I'm out of town at a conference and I
>> haven't
>> been email accessible for a few days. There was a bug in my code
>> (somehow
>> a half-finished change got into CVS rather than the right one) which
>> I will fix when I return home. The next build should work correctly.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>> On Mon, Mar 18, 2013 at 01:19:09PM +0100, Bogdan Costescu wrote:
>>> Hi John!
>>>
>>> The 1.9.2a20 version seems to have cured the performance issue, but
>>> not with the default setting. I have to set VMDMAXAASAMPLES to 4 to
>>> get about to about the same speed as the 2xx drivers.
>>>
>>> The VMD startup text doesn't change, still reporting:
>>>
>>> Info) [0] GeForce 9400 GT 4 SM_1.1 @ 1.38 GHz, 511MB RAM, KTO,
>> OIO, ZCP
>>> Info) OpenGL renderer: GeForce 9400 GT/PCIe/SSE2
>>> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVFG)
>>> Info) Full GLSL rendering mode is available.
>>> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture
>> (4)
>>>
>>> i.e. the MSAA(16) is still present. When I set VMDMAXAASAMPLES, I see
>>> printed 5 times:
>>>
>>> Info) User-requested OpenGL AA sample depth: 4
>>>
>>> but all that follows is again the same (including MSAA(16)). I don't
>>> know if this is only cosmetic...
>>>
>>> But... the above results hold for driver 310.32; if using 313.09, I
>>> get the slow speed independent of the VMDMAXAASAMPLES setting - but
>>> this being a beta version might not mean much.
>>>
>>> Let me know if you'd like me to test some more.
>>>
>>> Cheers,
>>> Bogdan
>>>
>>> On Fri, Mar 15, 2013 at 3:25 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>>> Bogdan,
>>>> I posted a new test build of VMD, give it a try and let me know
>>>> if it cures the performance issue you'd observed previously.
>>>>
>>>> Cheers,
>>>> John Stone
>>>> vmd_at_ks.uiuc.edu
>>
>> --
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/