From: Robert Wohlhueter (bobwohlhueter_at_earthlink.net)
Date: Sun Dec 08 2013 - 12:00:24 CST

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