VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sun Dec 08 2013 - 15:01:36 CST

Hi Bob,
I don't know what is causing the CUDA error, but I just ignore the X11
warning. I don't know what the composite extension does but it can only
possibly impact what VMD displays on the screen, as X11 is your window
manager. If your molecules look fine (no weird blockiness in the OpenGL
screen), I think you can safely ignore it.
-Josh Vermaas

On 12/08/2013 12:00 PM, 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
>