VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 11 2013 - 01:10:51 CST

Norman,
  Yeas, the QuadBuffered modes require support from the underlying
video driver, and that's where the conflict with the X11 composite
extension crops up. Many of the other stereo modes in VMD are implemented`
through creative use of the OpenGL stencil buffer, and they don't require
stereo support from the underlying OpenGL driver. Those stereo
modes should still work even when QuadBuffer is unavailable.

Cheers,
  John

On Wed, Dec 11, 2013 at 08:06:44AM +0100, Norman Geist wrote:
> So only for Quadbuffered, Row Interleaved works fine.
>
> Norman Geist.
>
> > -----Ursprüngliche Nachricht-----
> > Von: John Stone [mailto:johns_at_ks.uiuc.edu]
> > Gesendet: Dienstag, 10. Dezember 2013 17:28
> > An: Robert Wohlhueter
> > Cc: Norman Geist; Josh Vermaas
> > Betreff: Re: AW: AW: vmd-l: vmd-1.9.1 broken after upgrade to Ubuntu
> > 13.10
> >
> > Bob,
> > I forgot to comment on your X11 warnings. I have VMD print very
> > noticable warnings about the X11 composite extension because the
> > composite extension has (over the years) been responsible for a wide
> > range of OpenGL bugs caused by interference with the proper behavior
> > of the OpenGL drivers. Even now, today, the composite extension is
> > incompatible with stereoscopic display, so if you had a Quadro card
> > and wanted to use VMD in stereo with a 3-D display, you would
> > absolutely have to to disable the composite extension in your
> > X11 configuration.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Dec 10, 2013 at 11:19:15AM -0500, Robert Wohlhueter wrote:
> > > Norm, Josh, John,
> > >
> > > Thanks all for your advice and info. I downloaded vmd-1.9.2a35,
> > which
> > > runs fine: that is, the cuda error of 1.9.1 is eliminated (the
> > > what-me-worry X11 warnings remain.)
> > >
> > > I will benchmark a "Quicksurf" generation (comparing 1.9.1 to
> > 1.9.2a35)
> > > later, but for now I'm satisfied that everything seems to be
> > working.
> > >
> > > Bob W.
> > >
> > > On 12/10/13 1:57 AM, Norman Geist wrote:
> > >
> > > The CUDA accelerated feature in VMD that I'm currently missing
> > most of
> > > the time is "Quicksurf" as very fast surface visualization, fast
> > enough
> > > to even play a trajectory with changing surface, no chance with
> > surf or
> > > msms. Some other features are ion placement, radial pair
> > distribution
> > > and sure some more. But if you didn't notice, you might be ok
> > with the
> > > current situation.
> > >
> > >
> > >
> > > Best wishes
> > >
> > >
> > >
> > > Norman Geist.
> > >
> > >
> > >
> > > Von: Robert Wohlhueter [mailto:bobwohlhueter_at_earthlink.net]
> > > Gesendet: Montag, 9. Dezember 2013 16:08
> > > An: Norman Geist
> > > Betreff: Re: AW: vmd-l: vmd-1.9.1 broken after upgrade to Ubuntu
> > 13.10
> > >
> > >
> > >
> > > Norm,
> > >
> > > Thanks. Yeah, I figured I could safely ignore the X11 warning.
> > The
> > > cuda issue is trickier: with my new software (cuda 5.5) and
> > hardware
> > > (660Ti) installation, an NVIDIA test suite of cuda sample
> > programs runs
> > > fine, and, better yet, the cuda version of NAMD2 blazes. So I
> > conclude
> > > that VMD-1.9.1 is working, just not in cuda mode. But I'm not
> > sure
> > > which parts of VMD actually utilize cuda, and how -- that is my
> > > satisfaction with VMD is probably satisfaction with an
> > effectively
> > > non-cuda version.
> > >
> > > But since I'm too dumb to notice the difference, I'll be
> > patient, and
> > > pleasantly surprised with 1.9.2.
> > >
> > > Thanks for your pointers.
> > >
> > > Bob W.
> > >
> > > On 12/9/13 2:25 AM, Norman Geist wrote:
> > >
> > > CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
> > >
> > >
> > >
> > > As far as I understand, the current VMD 1.9.1 CUDA code is
> > incompatible with the latest CUDA runtime and driver from Nvidia. So
> > the message is seen everywhere since a 600 series card. The message
> > tells that the syntax of the used commands has changed and the "old"
> > code isn't working anymore. This is expected to be fixed with 1.9.2.
> > >
> > >
> > >
> > > Regarding the "composite", you would notice if it would be a problem
> > for you. For instance due transparent windows.
> > >
> > >
> > >
> > > Norman Geist.
> > >
> > >
> > >
> > > -----Urspru:ngliche Nachricht-----
> > >
> > > Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> > >
> > > Auftrag von Robert Wohlhueter
> > >
> > > Gesendet: Sonntag, 8. Dezember 2013 19:00
> > >
> > > An: John Stone; Josh Vermaas; vmd-l_at_ks.uiuc.edu
> > >
> > > Betreff: Re: vmd-l: vmd-1.9.1 broken after upgrade to Ubuntu 13.10
> > >
> > >
> > >
> > > Sorry, for my long silence on this issue. Basically, vmd is
> > working:
> > >
> > > A
> > >
> > > rather complete hardware and software overhaul (upgraded to GTX
> > 660Ti,
> > >
> > > and NVIDIA's cuda 5.5 -- too many changes to really know what did
> > the
> > >
> > > trick), gets vmd-1.9.1 up and working again (under Ubuntu 13.10 on
> > >
> > > AMD64.)
> > >
> > >
> > >
> > > Frankly, I had to scuttle the distribution start-up script entirely,
> > >
> > > not
> > >
> > > just the "rlwrap" parts; just "manually" set a couple relevant
> > envvars,
> > >
> > > then call the binary (vmd-LINUXAMD64) directly, with a customized
> > >
> > > .vmdrc.
> > >
> > >
> > >
> > > But there is still a nagging cuda problem, which, I'm embrassed to
> > say,
> > >
> > > I do not know grasp the consequences of (in many ways vmd works
> > fine.
> > >
> > > The relevant output on starting vmd is:
> > >
> > >
> > >
> > > Info) -------------------------------------------------------------
> > >
> > > Info) Multithreading available, 4 CPUs detected.
> > >
> > > Info) Free system memory: 6651MB (83%)
> > >
> > > Info) Creating CUDA device pool and initializing hardware...
> > >
> > > CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
> > >
> > > Info) Detected 1 available CUDA accelerator:
> > >
> > > Info) [0] GeForce GTX 660 Ti 7 SM_3.0 @ 0.98 GHz, 2.0GB RAM, KTO,
> > OIO,
> > >
> > > ZCP
> > >
> > > Warning) Detected X11 'Composite' extension: if incorrect display
> > >
> > > occurs
> > >
> > > Warning) try disabling this optional X server feature.
> > >
> > >
> > >
> > > The causes and consequences are totally opaque to me. Also, I have
> > no
> > >
> > > idea of how to disable the "composite" X-server feature, though I
> > also
> > >
> > > see no obviously deleterious consequences of it.
> > >
> > >
> > >
> > > Any words of wisdom on these issues?
> > >
> > >
> > >
> > > Thanks,
> > >
> > > Bob W.
> > >
> > >
> > >
> > > On 11/26/13 8:08 PM, John Stone wrote:
> > >
> > > Robert, Josh,
> > >
> > > Regarding rlwrap, if it causes you trouble, feel free to disable
> > >
> > > it...
> > >
> > > VMD doesn't care about rlwrap. This is something that we added to
> > >
> > > the
> > >
> > > VMD startup script to please users that prefer command interfaces
> > >
> > > with
> > >
> > > up/down arrow command histories and similar features as one might
> > >
> > > have
> > >
> > > popular command shells and various GNU tools on Linux. VMD itself
> > >
> > > doesn't
> > >
> > > know anything about rlwrap and will run just fine without it.
> > >
> > >
> > >
> > > Cheers,
> > >
> > > John Stone
> > >
> > > vmd_at_ks.uiuc.edu
> > >
> > >
> > >
> > > On Tue, Nov 26, 2013 at 06:42:09PM -0600, Josh Vermaas wrote:
> > >
> > > Hi Robert,
> > >
> > >
> > >
> > > Based on when the segfault is occurring, and the general list of
> > >
> > > things
> > >
> > > that break on an upgrade, it might just be a version mismatch
> > >
> > > caused by
> > >
> > > conflicting versions of the nvidia driver package. This happens
> > >
> > > to me when
> > >
> > > nvidia-current gets upgraded, as it will pick up the new driver,
> > >
> > > but won't
> > >
> > > get rid of the old ones. One thing I would check is the result
> > >
> > > of ldd
> > >
> > > vmd_LINUXAMD64 in /usr/local/lib. On my system, which uses
> > >
> > > version 319.37,
> > >
> > > this is what a fraction of it looks like:
> > >
> > > libGL.so.1 => /usr/lib/nvidia-current/libGL.so.1
> > >
> > > (0x00002b4635b53000)
> > >
> > > libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1
> > >
> > > (0x00002b4635e82000)
> > >
> > > libcudart.so.4 => not found
> > >
> > > libnvidia-tls.so.319.37 =>
> > >
> > > /usr/lib/nvidia-current/tls/libnvidia-tls.so.319.37
> > >
> > > (0x00002b4637a31000)
> > >
> > > libnvidia-glcore.so.319.37 =>
> > >
> > > /usr/lib/nvidia-current/libnvidia-glcore.so.319.37
> > >
> > > (0x00002b4637c34000)
> > >
> > > Libcudart isn't actually needed unless you need one of the
> > >
> > > commands that
> > >
> > > uses GPU acceleration, but the other 4 had better resolve, and
> > >
> > > should all
> > >
> > > resolve to libraries corresponding to the right version (in my
> > >
> > > case
> > >
> > > 319.37). Manually removing old installed versions of the nvidia
> > >
> > > drivers is
> > >
> > > how I tend to fix these problems when they come up.
> > >
> > >
> > >
> > > In terms of the rlwrap "fun" you've been having, I know this
> > >
> > > seems like a
> > >
> > > stupid thing to do, but unless you need rlwrap for something
> > >
> > > else, the
> > >
> > > stock VMD distribution actually works better without rlwrap
> > >
> > > installed, as
> > >
> > > then the script just complains about a missing rlwrap command
> > >
> > > rather than
> > >
> > > a malformatted command that causes an exit and will load vmd. In
> > >
> > > using
> > >
> > > this approach, it doesn't look like anything obvious is broken.
> > >
> > >
> > >
> > > -Josh Vermaas
> > >
> > >
> > >
> > > On 11/26/13, 4:15 PM, Robert Wohlhueter wrote:
> > >
> > >
> > >
> > > Using Ubuntu 13.10 on an AMD64 computer with NVIDIA GTX275 and
> > >
> > > NVIDIA
> > >
> > > driver 319.32:
> > >
> > > vmd-1.9.1 binary distribution is broken. The same binary on
> > >
> > > same the
> > >
> > > hardware (with NVIDIA 304 driver)
> > >
> > > under Ubuntu 12.10 worked fine.
> > >
> > >
> > >
> > > Using the original installed vmd.csh script, startup seems to
> > >
> > > hang
> > >
> > > because of inability to set
> > >
> > > rlwrap (though in fact the file "vmd_completion.dat" is
> > >
> > > present):
> > >
> > >
> > >
> > >
> > >
> > >
> > #######################################################################
> > >
> > > #####
> > >
> > > bobw_at_winter-linux: ...lib/vmd [56]> /usr/local/bin/vmd
> > >
> > > /usr/local/bin/vmd.wrap
> > >
> > > rlwrap: No match.
> > >
> > >
> > >
> > >
> > #######################################################################
> > >
> > > #####
> > >
> > >
> > >
> > > If I comment out the lines relevant to loading
> > >
> > > vmd_completion.dat, then
> > >
> > > run the script, the "rlwrap"-error is avoided, but I get no
> > >
> > > output at
> > >
> > > all:
> > >
> > >
> > >
> > >
> > >
> > >
> > #######################################################################
> > >
> > > ####
> > >
> > > obw_at_winter-linux: ...lib/vmd [59]> /usr/local/bin/vmd.nowrap
> > >
> > > /usr/local/bin/vmd
> > >
> > > bobw_at_winter-linux: ...lib/vmd [60]>
> > >
> > >
> > >
> > >
> > #######################################################################
> > >
> > > ####
> > >
> > >
> > >
> > > But these are probably minor problems. If I by pass the
> > >
> > > script entirely
> > >
> > > (but with VMDDIR and
> > >
> > > MASTERVMDDIR envvars set manually), I get a little further,
> > >
> > > before
> > >
> > > dumping core:
> > >
> > >
> > >
> > >
> > >
> > >
> > #######################################################################
> > >
> > > #####
> > >
> > > bobw_at_winter-linux: ...vmd/vmd-1.9.1 [60]>./vmd_LINUXAMD64
> > >
> > > ./vmd_LINUXAMD64
> > >
> > > 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, 4 CPUs detected.
> > >
> > > Info) Free system memory: 6482MB (81%)
> > >
> > > Segmentation fault (core dumped)
> > >
> > >
> > >
> > >
> > #######################################################################
> > >
> > > ####
> > >
> > >
> > >
> > > I would guess the problem lies not with Ubuntu 13.10 per se,
> > >
> > > but with
> > >
> > > the
> > >
> > > change in video driver between 12.10 and 13.10. I'm reluctant
> > >
> > > to muck
> > >
> > > around
> > >
> > > with video drivers, in particular to try to revert to NVIDIA
> > >
> > > 304.x,
> > >
> > > since this
> > >
> > > always breaks a lot of programs. Still my hardward/video
> > >
> > > driver must be
> > >
> > > fairly commomplace.
> > >
> > >
> > >
> > > Anyone have clues to what's wrong? I'm grateful for any
> > >
> > > pointers.
> > >
> > >
> > >
> > > Bob Wohlhueter
> > >
> > >
> > >
> > >
> > >
> > > ---
> > >
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> > >
> > >
> > >
> > >
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> > --
> > 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/
>
>
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-- 
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/