[PyMOL] RE: vmd-l: VMD crash on athlon64 with licorice representation

[Warren D. <wa...@de...>]

Sabuj & others,

I just posted a special linux/nvidia test build at http://delsci.com/beta
that eliminates the crash on my 64 bit Opteron system, and (reportedly) on
at least one 32-bit system.  For those who have been experiencing issue with
the nVidia drivers, I would appreciate knowing whether or not it eliminates
the PyMOL crash on your system as well.

As I was discussing with John a few days back, the evidence is now virtually
overwhelming that the latest generation nVidia drivers are broken with
certain (but not all) hardware configurations.  Though the crash can be
eliminated by flushing the OpenGL pipeline almost continuously when drawing
problematic geometries (as the above build does), this workaround will have
a significant negative impact on performance, and is thus not acceptable as
a long-term solution.  

Given that the problem isn't going away all by itself, we may need to
assemble a simple demonstration test case (with source code) that we can
file as a clear & convincing bug report to nVidia in order to ultimately get
this issue resolved.  

What is the situation on Windows exactly?  Are PyMOL and VMD still broken
there as well?  I just assembled an WinXP/nVidia-based 32 bit system that
was supposed to reproduce this crash, but haven't yet been able to do so
with the latest drivers...

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                     
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213           
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834     
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...      
 

> -----Original Message-----
> From: own...@ks... 
> [mailto:own...@ks...] On Behalf Of Sabuj Pattanayek
> Sent: Thursday, May 12, 2005 4:09 PM
> To: vm...@ks...
> Subject: Re: vmd-l: VMD crash on athlon64 with licorice representation
> 
> Hi,
> 
> Yes, I get the same licorice crash when running vmd 1.8.3 
> with "setenv VMDSIMPLEGRAPHICS 1". I sent a the error report 
> to lin...@nv... some time ago, but without the 
> generated system information from nvidia-bug-report.sh. I 
> never received a reply. I'll resend this time with the system 
> information.
> 
> I also tried getting a backtrace from vmd when it crashes but 
> I could not. It may have something to do with the fact that 
> vmd uses SIGABRT instead of SIGSEGV or maybe it's compiled 
> with too many optimizations and no -g flag?
> 
> I was able to get a backtrace from pymol however and I'm sure 
> the problem is very similar to vmd's. It looks like the 
> function glXChannelRectSyncSGIX () from 
> /usr/lib/opengl/nvidia/lib/libGL.so.1 is trying to allocate 
> some bogus memory addresses/pointers which is causing the 
> program to crash in mallopt () from /lib/libc.so.6 . Here's 
> the backtrace, sorry if its really long:
> 
>  OpenGL-based graphics engine:
>   GL_VENDOR: NVIDIA Corporation
>   GL_RENDERER: Quadro4 750 XGL/AGP/SSE/3DNOW!
>   GL_VERSION: 1.5.3 NVIDIA 71.74
>  Hardware stereo capability detected.
> [New Thread -1297941584 (LWP 16400)]
>  Adapting to Quadro hardware...
> sh: line 1: egrep: command not found
> 
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread -1220909360 (LWP 16367)]
> 0xb7d70708 in mallopt () from /lib/libc.so.6
> (gdb) bt
> #0  0xb7d70708 in mallopt () from /lib/libc.so.6
> #1  0xb7d6f549 in free () from /lib/libc.so.6
> #2  0xb7f1a10a in glXChannelRectSyncSGIX () from
> /usr/lib/opengl/nvidia/lib/libGL.so.1
> #3  0xb21b75a8 in ?? ()
> #4  0xb7abbe85 in _nv000845gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #5  0xb21b75a8 in ?? ()
> #6  0xb3bf2040 in ?? ()
> #7  0x00000000 in ?? ()
> #8  0x00009cef in ?? ()
> #9  0x08549590 in ?? ()
> #10 0x00000020 in ?? ()
> #11 0xb3bf2040 in ?? ()
> #12 0xb21b5550 in ?? ()
> #13 0x00009cef in ?? ()
> #14 0x08549590 in ?? ()
> #15 0x00000000 in ?? ()
> #16 0x00000000 in ?? ()
> #17 0x00000000 in ?? ()
> #18 0x00001ea8 in ?? ()
> #19 0xb3c4560c in ?? ()
> #20 0xb3c45654 in ?? ()
> #21 0x08667278 in ?? ()
> #22 0x00000000 in ?? ()
> #23 0x00000000 in ?? ()
> #24 0x00000000 in ?? ()
> #25 0x00000000 in ?? ()
> #26 0x00000003 in ?? ()
> #27 0xb3c43570 in ?? ()
> #28 0xb3c43570 in ?? ()
> #29 0xb7abcb0b in _nv000845gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #30 0xb3bf2040 in ?? ()
> #31 0xb3bf2040 in ?? ()
> #32 0xb7ab24ca in _nv000845gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #33 0xb3bf2040 in ?? ()
> #34 0xb3bf2040 in ?? ()
> #35 0xb21b746c in ?? ()
> #36 0xb21b746c in ?? ()
> #37 0x00000000 in ?? ()
> #38 0xb21b53d8 in ?? ()
> #39 0xb3bf2040 in ?? ()
> #40 0xb19eee68 in ?? ()
> #41 0x00000000 in ?? ()
> #42 0x00009cef in ?? ()
> #43 0x08549590 in ?? ()
> #44 0xb7f897db in ?? ()
> #45 0x0818a92d in RepWireBondRender ()
> #46 0xb19eee98 in ?? ()
> #47 0xb19eee8c in ?? ()
> #48 0xb2160a80 in ?? ()
> #49 0x00000007 in ?? ()
> #50 0x0888c748 in ?? ()
> #51 0x00000000 in ?? ()
> #52 0xb76e1307 in _nv000814gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #53 0xb3bf8f24 in ?? ()
> #54 0xb3bf2040 in ?? ()
> #55 0xb3bf8ed4 in ?? ()
> #56 0xb3bf2040 in ?? ()
> #57 0xb7964591 in _nv000851gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #58 0x080d528b in ObjectUseColor ()
> #59 0xb2cf037f in ?? ()
> #60 0x08112fab in CoordSetRender ()
> #61 0xb2160a80 in ?? ()
> #62 0x00000000 in ?? ()
> #63 0x00000000 in ?? ()
> #64 0x08549590 in ?? ()
> #65 0x0886b930 in ?? ()
> #66 0x00000000 in ?? ()
> #67 0x00000000 in ?? ()
> #68 0xbff9b468 in ?? ()
> #69 0xbff9b4c4 in ?? ()
> #70 0x00000007 in ?? ()
> #71 0x0814725c in ObjectMoleculeRender ()
> #72 0x0888c748 in ?? ()
> #73 0x00000000 in ?? ()
> #74 0x00000000 in ?? ()
> #75 0x00000000 in ?? ()
> #76 0x0886b930 in ?? ()
> #77 0x08893df0 in ?? ()
> #78 0xbff9b1ec in ?? ()
> #79 0xbff9b49c in ?? ()
> #80 0x08893df0 in ?? ()
> #81 0x0867bf60 in ?? ()
> #82 0x080fd178 in SceneRenderAll ()
> #83 0x0886b930 in ?? ()
> #84 0x00000000 in ?? ()
> #85 0x00000000 in ?? ()
> #86 0x00000000 in ?? ()
> ---Type <return> to continue, or q <return> to quit---
> #87 0x00000000 in ?? ()
> #88 0xbff9b49c in ?? ()
> #89 0xbff9b4c4 in ?? ()
> #90 0xbff9b48c in ?? ()
> #91 0x00000000 in ?? ()
> #92 0x086da0c8 in ?? ()
> #93 0xb773e8c2 in _nv000812gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #94 0x08549590 in ?? ()
> #95 0xbff9b49c in ?? ()
> #96 0xbff9b4c4 in ?? ()
> #97 0x00000000 in ?? ()
> #98 0x00000000 in ?? ()
> #99 0x00000000 in ?? ()
> #100 0x00000000 in ?? ()
> #101 0x086a6fec in ?? ()
> #102 0xb2c7b008 in ?? ()
> #103 0x00000000 in ?? ()
> #104 0x000001f0 in ?? ()
> #105 0x0000035c in ?? ()
> #106 0x00000000 in ?? ()
> #107 0x00000000 in ?? ()
> #108 0xb7a7b9f5 in _nv000845gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #109 0x08667278 in ?? ()
> #110 0x00000000 in ?? ()
> #111 0x00000000 in ?? ()
> #112 0x0000035c in ?? ()
> #113 0x00000195 in ?? ()
> #114 0x00000000 in ?? ()
> #115 0x08667278 in ?? ()
> #116 0x08675d00 in ?? ()
> #117 0x00000000 in ?? ()
> #118 0x00000003 in ?? ()
> #119 0x0869b690 in ?? ()
> #120 0x08668ad0 in ?? ()
> #121 0x000001f0 in ?? ()
> #122 0x0000035c in ?? ()
> #123 0x08667278 in ?? ()
> #124 0xb3b55c84 in ?? ()
> #125 0x08668acc in ?? ()
> #126 0x00000002 in ?? ()
> #127 0x0869d408 in ?? ()
> #128 0x08668b4c in ?? ()
> #129 0x00000000 in ?? ()
> #130 0xb78962b8 in _nv000840gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #131 0x003f5c84 in ?? ()
> #132 0x08634f38 in ?? ()
> #133 0x0866bb00 in ?? ()
> #134 0x08667278 in ?? ()
> #135 0x08675d00 in ?? ()
> #136 0xb78968d4 in _nv000840gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #137 0xb7a61519 in _nv000851gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #138 0x00000000 in ?? ()
> #139 0x08667278 in ?? ()
> #140 0xb7a626f6 in _nv000851gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #141 0x08667278 in ?? ()
> #142 0x0866bb00 in ?? ()
> #143 0x085e66c8 in ?? ()
> #144 0x00000000 in ?? ()
> #145 0x086a8bf8 in ?? ()
> #146 0x086a8bf8 in ?? ()
> #147 0x00000280 in ?? ()
> #148 0x000001e0 in ?? ()
> #149 0x08660c7f in ?? ()
> #150 0xb789691d in _nv000840gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #151 0x00000000 in ?? ()
> #152 0xbff9b3ec in ?? ()
> #153 0xbff9b4c4 in ?? ()
> #154 0x3f2ccccc in ?? ()
> #155 0x3e800000 in ?? ()
> #156 0xbff9b48c in ?? ()
> #157 0x00000402 in ?? ()
> #158 0x00000001 in ?? ()
> #159 0x00000001 in ?? ()
> #160 0x43d59aca in ?? ()
> #161 0x41a00000 in ?? ()
> #162 0x08675d00 in ?? ()
> #163 0xbff9b3ec in ?? ()
> #164 0x08675cd0 in ?? ()
> #165 0x00000000 in ?? ()
> #166 0x00000000 in ?? ()
> #167 0x00000000 in ?? ()
> #168 0xf21a0000 in ?? ()
> #169 0x402145a4 in ?? ()
> #170 0x3faaaaab in ?? ()
> #171 0x08667278 in ?? ()
> #172 0xb7f1a33f in glXChannelRectSyncSGIX () from
> /usr/lib/opengl/nvidia/lib/libGL.so.1
> #173 0x086da0c8 in ?? ()
> ---Type <return> to continue, or q <return> to quit---
> #174 0x08675d00 in ?? ()
> #175 0xbff9b3ec in ?? ()
> #176 0x08675cd0 in ?? ()
> #177 0x08667278 in ?? ()
> #178 0xb7f0bf6b in ?? () from /usr/lib/opengl/nvidia/lib/libGL.so.1
> #179 0x08634f38 in ?? ()
> #180 0x08675d00 in ?? ()
> #181 0x00000001 in ?? ()
> #182 0xb7f334e4 in _nv000658gl () from 
> /usr/lib/opengl/nvidia/lib/libGL.so.1
> #183 0x08675d00 in ?? ()
> #184 0xbff9b3ec in ?? ()
> #185 0x08675d00 in ?? ()
> #186 0xbff9b3ec in ?? ()
> #187 0xbff9b3ec in ?? ()
> #188 0x08675d00 in ?? ()
> #189 0xb78a6c21 in _nv000844gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #190 0xb78a6c86 in _nv000844gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #191 0x08667278 in ?? ()
> #192 0xbff9b3ec in ?? ()
> #193 0x08675d00 in ?? ()
> #194 0x08667278 in ?? ()
> #195 0x00004100 in ?? ()
> #196 0x01f9b4a4 in ?? ()
> #197 0x00000000 in ?? ()
> #198 0x00000c00 in ?? ()
> #199 0x00000000 in ?? ()
> #200 0xb786dcf7 in _nv001092gl () from
> /usr/lib/opengl/nvidia/lib/libGLcore.so.1
> #201 0x08667278 in ?? ()
> #202 0xbff9b3ec in ?? ()
> #203 0x08675d00 in ?? ()
> #204 0xb3bf2040 in ?? ()
> #205 0x00000100 in ?? ()
> #206 0x00004100 in ?? ()
> #207 0x3f800000 in ?? ()
> #208 0x0866bb00 in ?? ()
> #209 0x08675d00 in ?? ()
> #210 0x00000000 in ?? ()
> #211 0xb3bf2040 in ?? ()
> #212 0xb6e59a48 in ?? ()
> #213 0x4b7fffff in ?? ()
> #214 0x00000002 in ?? ()
> #215 0x0000001f in ?? ()
> #216 0x00000001 in ?? ()
> #217 0x00000000 in ?? ()
> #218 0x00000002 in ?? ()
> #219 0xb6e59a58 in ?? ()
> #220 0x00000000 in ?? ()
> #221 0x00000000 in ?? ()
> #222 0x01f0035c in ?? ()
> #223 0xf1f00000 in ?? ()
> #224 0x01f01000 in ?? ()
> #225 0x00000058 in ?? ()
> #226 0x00000000 in ?? ()
> #227 0x00000000 in ?? ()
> #228 0x00000000 in ?? ()
> #229 0x3f800000 in ?? ()
> #230 0x01010101 in ?? ()
> #231 0x3f800000 in ?? ()
> #232 0x00000000 in ?? ()
> #233 0x000000ff in ?? ()
> #234 0x00000000 in ?? ()
> #235 0x08675d00 in ?? ()
> #236 0x00000000 in ?? ()
> #237 0x08675d00 in ?? ()
> #238 0x00004100 in ?? ()
> #239 0x00000000 in ?? ()
> #240 0x00000000 in ?? ()
> #241 0x00000000 in ?? ()
> #242 0x3f800000 in ?? ()
> #243 0xb3bf2040 in ?? ()
> #244 0x3f5ed1c4 in ?? ()
> #245 0x00000000 in ?? ()
> #246 0x00000000 in ?? ()
> #247 0xb3bf037f in ?? ()
> #248 0x3f4ccccd in ?? ()
> #249 0x3f4ccccd in ?? ()
> #250 0x3f4ccccd in ?? ()
> #251 0x3f800000 in ?? ()
> #252 0xbe2aaaab in ?? ()
> #253 0x3f955555 in ?? ()
> #254 0x00000000 in ?? ()
> #255 0x3f800000 in ?? ()
> #256 0xbf000000 in ?? ()
> #257 0x3f000000 in ?? ()
> #258 0x00000000 in ?? ()
> #259 0x00000000 in ?? ()
> #260 0x0000035c in ?? ()
> ---Type <return> to continue, or q <return> to quit---
> #261 0x000001f0 in ?? ()
> #262 0x00000000 in ?? ()
> #263 0x00000000 in ?? ()
> #264 0x3f800000 in ?? ()
> #265 0x00000000 in ?? ()
> #266 0x00000000 in ?? ()
> #267 0x00000000 in ?? ()
> #268 0x3f800000 in ?? ()
> #269 0x00000000 in ?? ()
> #270 0x00000000 in ?? ()
> #271 0x00000000 in ?? ()
> #272 0x00000000 in ?? ()
> #273 0x3f800000 in ?? ()
> #274 0x080cc5dc in OrthoDoDraw ()
> #275 0x08549590 in ?? ()
> #276 0x00000000 in ?? ()
> #277 0x00000000 in ?? ()
> #278 0x00000000 in ?? ()
> #279 0x00000000 in ?? ()
> #280 0x08549590 in ?? ()
> #281 0x085ce870 in ?? ()
> #282 0x0000035c in ?? ()
> #283 0xbff9b5b0 in ?? ()
> #284 0x00000000 in ?? ()
> #285 0x00000000 in ?? ()
> #286 0x00000000 in ?? ()
> #287 0xb7f6aed4 in pthread_mutex_lock () from 
> /lib/libpthread.so.0 Previous frame inner to this frame 
> (corrupt stack?)
> 
> Maybe that helps in tracking it down,
> Sabuj Pattanayek
> 
> John Stone wrote:
> > Sabuj,
> >   Did you try running VMD using the VMDSIMPLEGRAPHICS 
> environment variable?
> > Can you try that and tell me if that affects how it 
> interacts with the 
> > nVidia drivers you've experienced problems with thus far?
> > I'd like to know if it's related to the use of various OpenGL 
> > extensions or if the new nVidia drivers also fail on plain 
> OpenGL 1.1 calls.
> > Did you ever get a chance to email the bug to lin...@nv...?
> > They provide a bug reporter script that they include with their 
> > drivers that provides the information they need about your Linux 
> > installation to help them fix the problem.  Their bug 
> reporting script 
> > is normally installed in:
> >   /usr/bin/nvidia-bug-report.sh
> > 
> > It creates a nvidia-bug-report.log file they want you to 
> mail to them.
> > 
> > Thanks,
> >   John Stone
> >   vm...@ks...
> > 
> > On Thu, May 12, 2005 at 01:21:48PM -0500, Sabuj Pattanayek wrote:
> > 
> >>Hi,
> >>
> >>Yes, I have found that 1.0.6629 for Quadros is the only 
> version which 
> >>doesn't crash vmd and pymol on x86 (32bit) systems.
> >>
> >>ftp://download.nvidia.com/XFree86/Linux-x86/1.0-6629/NVIDIA-
> Linux-x86-
> >>1.0-6629-pkg1.run
> >>
> >>Hope that helps,
> >>Sabuj Pattanayek
> >>
> >>Karsten Suhre wrote:
> >>
> >>>Hi,
> >>>
> >>>Is the problem you report with the NVIDIA driver only limitted to 
> >>>x86_64 systems?
> >>>
> >>>My AMD Athlon 2400 bi-proc (32 bit SuSE 9.2 Nvidia Quadro vers. 
> >>>1.0-7174) also crashes whenever I switch from Line mode to 
> anything 
> >>>rendered. Does this mean that downgrading of the driver is 
> the only solution?
> >>>
> >>>Thank you very much for your help,
> >>>
> >>>Kind regards,
> >>>
> >>>Karsten.
> >>>
> >>>
> >>>On Thursday 12 May 2005 01:18, Sabuj Pattanayek wrote:
> >>>
> >>>
> >>>>Hi,
> >>>>
> >>>>The latest x86_64 driver for linux used in a native 64bit 
> >>>>environment (kernel & system & vmd64):
> >>>>
> >>>>NVRM version: NVIDIA Linux x86_64 NVIDIA Kernel Module  1.0-7174
> >>>>
> >>>>..seems to work fine and doesn't have the problems that 
> the 7xxx 32 
> >>>>bit drivers have with 32 bit systems and vmd-32bit. In 
> other words I 
> >>>>can recreate that problem if I use vmd32 in the 64bit environment.
> >>>>Surprisingly the same is true for pymol64 and pymol32.
> >>>>
> >>>>You said you were running XP Pro on the athlon64 machine correct? 
> >>>>You may qualify for upgrading to winxp64 
> >>>>(http://www.microsoft.com/windowsxp/64bit/upgrade/default.mspx). 
> >>>>Then maybe you can try the 64bit nvidia driver? Or switching to 
> >>>>linux64 may be an option.
> >>>>
> >>>>..Sabuj Pattanayek
> >>>>
> >>>>Carlos Simmerling wrote:
> >>>>
> >>>>
> >>>>>Hi John,
> >>>>>I just got this sort of figured out but didn't know how 
> to mail a 
> >>>>>reply to my own post. You're right, it's the nvidia drivers, not 
> >>>>>the athlon64. I had been using 71.84.
> >>>>>
> >>>>>I read another post about issues with the linux driver 
> and quadros 
> >>>>>so I tried both a new leaked driver (76.50) and an old 
> one (67.22).
> >>>>>76.50 did not work but 67.22 does, so I think it might 
> be the same 
> >>>>>quad strips problem you mentioned.
> >>>>>thanks a lot for the quick reply!
> >>>>>Carlos
> >>>>>
> >>>>>=========================================================
> ==========
> >>>>>Carlos L. Simmerling, Ph.D.
> >>>>>Associate Professor           Phone: (631) 632-1336
> >>>>>Center for Structural Biology Fax:   (631) 632-1555
> >>>>>Stony Brook University        Web:   
> http://comp.chem.sunysb.edu/carlos
> >>>>>Stony Brook, NY 11794-5115    E-mail: 
> car...@st...
> >>>>>=========================================================
> ==========
> >>>>>
> >>>>>John Stone wrote:
> >>>>>
> >>>>>
> >>>>>>Hi Carlos,
> >>>>>>What version of the nVidia drivers are you running on that 
> >>>>>>machine?  Do you experience a crash with any other 
> representation?
> >>>>>>I've been hearing of some problems with nVidia drivers recently
> >>>>>
> >>>>>>from around the molecular graphics community (not just 
> VMD), it's
> >>>>>
> >>>>>>possible that you're a victim of this recent phenomina.
> >>>>>>What does VMD print in the text console when it first 
> starts up?  
> >>>>>>If you can send me the startup messages, that would be very 
> >>>>>>helpful.
> >>>>>>
> >>>>>>Thanks,
> >>>>>>John Stone
> >>>>>>vm...@ks...
> >>>>>>
> >>>>>>On Wed, May 11, 2005 at 09:13:25AM -0400, Carlos 
> Simmerling wrote:
> >>>>>>
> >>>>>>
> >>>>>>>Hi all,
> >>>>>>>VMD is working fine on my pentium 4 PC under XP.
> >>>>>>>I just got an Athlon64 PC (with XP) and a quadro FX1100.
> >>>>>>>VMD works ok, but when I add a licorice representation 
> it always 
> >>>>>>>crashed. The same thing works fine on my other (Intel) 
> PCs under 
> >>>>>>>windows.
> >>>>>>>
> >>>>>>>Has anyone else seen this? I couldn't find anything in the 
> >>>>>>>archives, and the amd64 binaries seem to be for unixes only.
> >>>>>>>
> >>>>>>>Any ideas? I can send more info if it would help.
> >>>>>>>Carlos
> >>>>>>>
> >>>>>>>--
> >>>>>>>=======================================================
> ==========
> >>>>>>>==
> >>>>>>>Carlos L. Simmerling, Ph.D.
> >>>>>>>Associate Professor           Phone: (631) 632-1336
> >>>>>>>Center for Structural Biology Fax:   (631) 632-1555
> >>>>>>>Stony Brook University        Web:   
> http://comp.chem.sunysb.edu/carlos
> >>>>>>>Stony Brook, NY 11794-5115    E-mail: 
> car...@st...
> >>>>>>>=======================================================
> ============
> > 
> > 
> 
>