From: John Stone (
Date: Thu Jan 12 2017 - 12:32:42 CST

Hi Vlad,
  At present, if you want quad-buffered stereo display (e.g. with the
3D Vision monitors and shutter glasses), the Quadro GPUs are the only
option. That said, I think there's a zero percent chance that any of this
would work with the nouveau drivers. If OpenSUSE force you down the route
of using the nouveau driver during installation, that's somewhat
unfortunately, as I'm sure that any very new GPU model would end up being
problematic, not just the Quadro 4000. In general I don't think that the
nouvaeu drivers would be usable with VMD due to the diversity of advanced
OpenGL features VMD uses. The performance anomalies you described would
certainly be understandable based on my understanding of the maturity of
the nouveau drivers vs. the commercial drivers. There are hundreds
(maybe thousands?) of man-years of performance engineering incorporated in
the commercial NVIDIA drivers that aren't in the nouveau drivers...

The first thing we do installing any new machine is wipe away any trace of
the nouveau drivers immediately replacing them with the NVIDIA drivers.
I suspect things are going to remain this way for quite some time.

The open source drivers like nouveau will probably never manage to
close the performance gap with commercial drivers like NVIDIA's for
OpenGL, as it is a huge API with a constantly evolving set of
functionality and extensions. On the other hand, it is conceivable
that nouveau and similar efforts for other GPUs might be more
competitive for the new Vulkan graphics API (successor to OpenGL),
as Vulkan is a much leaner, focused, and more minimalistic standard
that specifically aims to address the complexity of OpenGL driver
engineering that has gotten completely out-of-hand in the last decade.
The challenge still remains for Vulkan to gain some footing, match some
of the esoteric features of OpenGL that are still missing, and finally
to get widely used in applications. We'll see how it goes...


On Thu, Jan 12, 2017 at 04:02:31PM +0100, Vlad Cojocaru wrote:
> Thanks Hannes, Thanks Giacomo,
> .. for your thoughts/advices .. I think I solved the problem ... I
> think the problem appeared because originally the openSUSE 42.2 could
> not be installed with graphics because of the lack of support for the
> Quadro M4000 by the default nouveau driver. I used a workaround to
> install in text mode and then compile the NVIDIA driver on top of this
> text installation ... With this, actually not only VMD but my entire
> graphics were extremely slow. ...It was just more notable on VMD ...
> What I did now was to switch to text mode, uninstall the NVIDIA driver
> and install it again through the openSUSE 42.2 repositories ... Now, the
> speed appears fine (actually is very fast) ..
> Giacomo, the reason for having Quadro graphics was because I wanted to
> have the 3D vision ... As far as I know on linux this is only possible
> with Quadro cards ... If am wrong here or I am missing something, I'd be
> grateful for an advice on a setup that works with GeForce and stereo
> viewing.
> Thanks again
> Vlad
> On 01/12/2017 03:47 PM, Hannes Loeffler wrote:
> >Hi Vlad,
> >
> >I have a M4000 myself and Dell too (Precision 3620 but would need a
> >closer look for the real specs). But I have only noticeable delays on
> >start-up and and a bit after quit. But I think I had reported this here
> >in a thread of yours.
> >
> >Other than that I have no problems. The vmd version is 1.9.3beta1.
> >Driver version 370.28, compiled myself with CUDA 7.5. I had some
> >strange timeouts when running pmemd, turned out to be the kernel
> >version (currently I have 4.7.8).
> >
> >Have you tried to change any of those and see if that helps? You could
> >also try some other CUDA accelerated software to see if you have
> >problems with that.
> >
> >Cheers,
> >Hannes.
> >
> >
> >On Thu, 12 Jan 2017 14:40:45 +0100
> >Vlad Cojocaru <> wrote:
> >
> >>Dear all,
> >>
> >>I am experiencing a very awkward problem. I have a new Dell high end
> >>workstation (Precision 7810). On this machine VMD (both 1.9.2 and
> >>1.9.3, either compiled from source or downloaded as pre-compiled
> >>binaries is extremely slow. Practically, even loading a simple PDB
> >>(3000 atoms) and drawing as New Cartoon with resolution 50 almost
> >>freezes the VMD window, almost no rotation is possible anymore. This
> >>machine has a Quadro M4000 graphics card (see details below). For a
> >>comparison my older workstations with exactly same OS, same
> >>configurations but with GeForce GTX950 or Quadro K4000 all VMD
> >>executables tested (the same as on the new machine) run with no speed
> >>issues whatsoever.
> >>
> >>Has anyone experienced anything similar ? Are there some simple tests
> >>one can do to pinpoint the potential issue ?
> >>
> >>Best wishes
> >>Vlad
> >>
> >>Some details:
> >>
> >>CPU: Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
> >>RAM: 64 GB
> >>Graphics: NVIDIA Quadro M4000 (driver 375.26, CUDA 8.0.44)
> >>OS:OpenSUSE 42.2 (x86_64)
> >>
> --
> Vlad Cojocaru, Ph.D., Project Group Leader
> 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]

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349