VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Dec 10 2013 - 00:57:37 CST

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.
 

-----Ursprüngliche 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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