VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Dec 11 2013 - 01:06:44 CST

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
> >
> >
> >
> >
> >
> > ---
> >
> > Diese E-Mail ist frei von Viren und Malware, denn der avast!
> Antivirus Schutz ist aktiv.
> >
> > http://www.avast.com
> >
> >
> >
> >
> >
> >
> >
> > ----------------------------------------------------------------
> ------
> >
> > [IMG] Diese E-Mail ist frei von Viren und Malware, denn der
> avast!
> > Antivirus Schutz ist aktiv.
>
> --
> 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/ 

---
Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.
http://www.avast.com