VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 09 2013 - 09:19:01 CST

Hi,
  You'll need to use one of the test versions of VMD 1.9.2 since you have
upgraded your GPU hardware to a Kepler-based GPU chip (GeForce GTX 660 Ti).
The VMD 1.9.1 release pre-dates Kepler and didn't have the right compilation
flags to support Kepler, so to cure this problem, just grab one of the
recent test builds of VMD 1.9.2 here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

We will soon begin releasing the first beta releases of VMD 1.9.2,
and a few weeks after that will be the official release. We run the
test versions regularly here in our lab, so there's no reason to fear
running one of these builds of VMD to address your problem in the
short-term.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Dec 08, 2013 at 01:00:24PM -0500, Robert Wohlhueter wrote:
> 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 

-- 
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/