VMD-L Mailing List

From: Pietro Amodeo (pamodeo_at_icb.cnr.it)
Date: Mon Nov 19 2012 - 10:25:33 CST

Hi John,

On Sun, 18 Nov 2012 22:25:27 -0600, John Stone wrote:
> Hi,
> Does VMD print any warnings on this machine when it starts?
> (e.g. compiz compositing manager)

this is the VMD start printout:

Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
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, 2 CPUs detected.
Info) Free system memory: 3644MB (92%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce 8400M GS 2 SM_1.1 @ 0.80 GHz, 127MB RAM, KTO,
OIO, ZCP
Warning) Detected X11 'Composite' extension: if incorrect display
occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce 8400M GS/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)
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd-1.9.1/plugins/LINUXAMD64/molfile

It looks the same as before the updates and it differs from that shown
on the GT230M box (apart from obvious differences in memory and device)
only in the GLSL feature that on this latter is GLSL(OVFGS).

> It is quite possible you're hitting a driver bug in the latest
> driver version.

It's quite possible indeed, since after installing the just-released
310.19 stable version of the driver things improved. In fact, now
discontinuities in motion are reduced to a flickering and the FPS
counter shows from 11 to 18 fps with a protein+water system loaded and
different graphic representations.

>
> Can you send the startup messages VMD prints on this machine?
> I'm wondering if your OpenGL installation got damaged during
> the sequence of upgrades you ran.

In general, I manually update NVidia drivers after linux upgrade and
reboot in non-graphic mode. In this way I never experienced problems,
except for badly-bugged drivers.

Please, let me know if you may need any other info.

Thanks,
Pietro

>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Nov 16, 2012 at 08:44:51PM +0100, Pietro Amodeo wrote:
>> Hi,
>>
>> after a kernel upgrade (to 3.6.6-1) on a Fedora 16 laptop (Intel
>> Core
>> Duo, 4GB RAM, NVidia 8400M GS) we had to upgrade NVIDIA driver from
>> 295.59 to 304.64. The result is a terribly slow VMD 1.9.1
>> (practically
>> unusable) displaying <8 fps with no molecule loaded!!!. Things
>> slightly
>> improve with beta driver 310.14 (<=15 fps no mol loaded), but
>> usability
>> is still rather poor (not fluid).
>>
>> Previously, witn NVidia 295.XX drivers, VMD 1.9.1 worked flawlessly
>> on
>> the same laptop. However, with 304.64 or 314.14 all other tested
>> OpenGL
>> programs works correctly and no error message is issued in Xorg.log
>> or
>> when starting VMD.
>>
>> Moreover, VMD 1.9.1 works flawlessly on a Intel i7+NVidia Gt230M
>> laptop
>> with the same FC16+kernel 3.6.6-1 +driver 304.64 combination.
>>
>>
>> Thanks in advance for any hint/help.
>>
>> Pietro
>> On this laptop
>> --