VMD-L Mailing List

From: Pietro Amodeo (pamodeo_at_icb.cnr.it)
Date: Mon Nov 19 2012 - 14:03:38 CST

John,

anther update to the strange behaviour of the 8400M GS laptop:

1) I can confirm that with 310.19 drivers suspend mode (that never was
a problem with 295.xx and older drivers, since this PC has been
suspended for tenths of times between reboots with no performance issues
with vmd or other programs) causes severe degradation (4-5 FPS for no
molecule) in vmd performances that can't be cured just with a X restart,
but requires a PC reboot;

2) if the vmd graphic window is (even slightly) resized, performances
are terribly affected, since with the solvated 330-residue protein of
our previous tests, FPS can either increase from ~12-15 to 20-30 (see 3)
or drop to 4-5, when, using any representation, the windows is partly
obscured by the system menubar. On the contrary, it's not very affected
(if any) by overlap with other (I tried terminal) windows;

3) for a given optimal windows size FPS for the 330-residue protein +
water/ion varies from 4-5 (all-licorice) to 20 (protein new
cartoons-water lines) or 30 (simple representation like all-lines or
protein new cartoons-water/ions invisible).

I hope these symptoms may be more suggestive to you than they are to
me...

Cheers,
Pietro

On Mon, 19 Nov 2012 11:25:48 -0600, John Stone wrote:
> Pietro,
> One thing I notice is that your GPU only as 128MB of memory.
> This is a small enough amount of memory that it could present a
> challenge if you've got a few things soaking up GPU RAM.
> Have you tried turning off the X11 composite / compiz extension?
> The compositing window manager eats GPU memory, so that might
> alleviate some of the performance issue you're seeing.
> I would try that first thing. If that doesn't work, I could try
> giving you a VMD that uses a shallower bit-depth framebuffer and
> see if that has any impact.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Nov 19, 2012 at 05:25:33PM +0100, Pietro Amodeo wrote:
>> 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
>> >>--