VMD-L Mailing List

From: Pietro Amodeo (pamodeo_at_icb.cnr.it)
Date: Mon Nov 19 2012 - 12:58:26 CST

John,

yes, the dedicated memory is only 128MB, but with NVidia 295.XX drivers
VMD worked fluently.

I turned off the X11 composite extension, but no influence on FPS rate
was observed.

Just two additional (and probably useless or confusing) observations:

1) the FPS rate is ~14 FPS when no molecule at all (only axes, no VMD
logo) is displayed, ~12 FPS with a ~330-residue protein and ~10 FPS when
the same protein in solvated in a water box;

2) there is some other parameter determining the status of the PC that
can adversely affect vmd performances. Probably, resuming after suspend
mode determines such condition, since, even after a fresh restart of X
server, vmd performances dropped to the horrible 3 FPS observed with
304.xx and 310.10-beta drivers. However they returned to the values
shown in 1) soon after reboot (even starting and exiting vmd several
times). In any case this behaviour is only observed (and we can't
univocally assign it to suspend mode since before it entered the suspend
mode the laptop worked for a full day with different programs) with
310.19, since 304.xx and 310.10-beta performed badly even after a fresh
reboot.

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
>> >>--