Public bug reported: In Ubuntu 12.10, the UCSF Chimera molecular graphics program, http://www.cgl.ucsf.edu/chimera/, crashes when the SideView tool is brought up. This was not a problem with Ubuntu 12.04. I have reproduced the bug with Intel Integrated graphics, and have a bug report from a user that it happens with the AMD proprietary driver. So it is probably not the "new and improved" Intel driver (the usual suspect), but something more basic, like compiz/unity or whatever Ubuntu is using now.
To reproduce the bug, download and install UCSF Chimera from http://www.cgl.ucsf.edu/chimera/. Then, using the menus, use File / Fetch by ID ... to get the 1yti data set from the PDB (Protein DataBank), and then bring the SideView with Favorites / SideView. On my "Intel Corporation 82G33/G31 Express Integrated Graphics Controller (rev 02)" system, if the SideView is displayed before fetching the data, then it works. That suggests that it is a bug with sharing OpenGL data with a context that already has data in it. Here is the backtrace from gdb: Program terminated with signal 6, Aborted. #0 0xb7732424 in __kernel_vsyscall () (gdb) where 20 #0 0xb7732424 in __kernel_vsyscall () #1 0xb74611df in ?? () #2 0xb75d9000 in ?? () Backtrace stopped: previous frame inner to this frame (corrupt stack?) ProblemType: Bug DistroRelease: Ubuntu 12.10 Package: xorg 1:7.7+1ubuntu4 ProcVersionSignature: Ubuntu 3.5.0-18.29-generic 3.5.7 Uname: Linux 3.5.0-18-generic i686 .tmp.unity.support.test.0: ApportVersion: 2.6.1-0ubuntu6 Architecture: i386 CompizPlugins: [core,bailer,detection,composite,opengl,decor,regex,resize,gnomecompat,compiztoolbox,move,grid,animation,mousepoll,workarounds,wall,place,fade,vpswitch,snap,imgpng,scale,session,expo,ezoom,unitymtgrabhandles,unityshell] CompositorRunning: compiz Date: Wed Nov 14 16:53:02 2012 DistUpgraded: 2012-11-14 15:16:36,826 DEBUG enabling apt cron job DistroCodename: quantal DistroVariant: ubuntu ExtraDebuggingInterest: Yes GraphicsCard: Intel Corporation 82G33/G31 Express Integrated Graphics Controller [8086:29c2] (rev 02) (prog-if 00 [VGA controller]) Subsystem: Hewlett-Packard Company Device [103c:2a73] InstallationDate: Installed on 2010-10-18 (758 days ago) InstallationMedia: Ubuntu 10.10 "Maverick Meerkat" - Release i386 (20101007) MachineType: Hewlett-Packard HP Compaq dx2400 Microtower MarkForUpload: True ProcEnviron: TERM=xterm PATH=(custom, no user) XDG_RUNTIME_DIR=<set> LANG=en_US.UTF-8 SHELL=/bin/bash ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.5.0-18-generic root=UUID=9823d8c7-5498-469e-8bf2-7b8340e9c590 ro quiet splash vt.handoff=7 SourcePackage: xorg Symptom: display UpgradeStatus: Upgraded to quantal on 2012-11-14 (0 days ago) dmi.bios.date: 04/21/2008 dmi.bios.vendor: American Megatrends Inc. dmi.bios.version: 5.23 dmi.board.name: 2A73h dmi.board.vendor: PEGATRON CORPORATION dmi.board.version: 1.01 dmi.chassis.asset.tag: MXL8220VQN dmi.chassis.type: 3 dmi.chassis.vendor: Hewlett-Packard dmi.chassis.version: Chassis Version dmi.modalias: dmi:bvnAmericanMegatrendsInc.:bvr5.23:bd04/21/2008:svnHewlett-Packard:pnHPCompaqdx2400Microtower:pvr:rvnPEGATRONCORPORATION:rn2A73h:rvr1.01:cvnHewlett-Packard:ct3:cvrChassisVersion: dmi.product.name: HP Compaq dx2400 Microtower dmi.sys.vendor: Hewlett-Packard version.compiz: compiz 1:0.9.8.4+bzr3407-0ubuntu1 version.libdrm2: libdrm2 2.4.39-0ubuntu1 version.libgl1-mesa-dri: libgl1-mesa-dri 9.0-0ubuntu1 version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A version.libgl1-mesa-glx: libgl1-mesa-glx 9.0-0ubuntu1 version.xserver-xorg-core: xserver-xorg-core 2:1.13.0-0ubuntu6 version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.7.3-0ubuntu2 version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:6.99.99~git20120913.8637f772-0ubuntu1 version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.20.9-0ubuntu2 version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:1.0.2-0ubuntu3 ** Affects: xorg (Ubuntu) Importance: Undecided Status: New ** Tags: apport-bug compiz-0.9 i386 quantal running-unity ubuntu -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to xorg in Ubuntu. https://bugs.launchpad.net/bugs/1078983 Title: Sharing OpenGL contexts causes crash Status in “xorg” package in Ubuntu: New Bug description: In Ubuntu 12.10, the UCSF Chimera molecular graphics program, http://www.cgl.ucsf.edu/chimera/, crashes when the SideView tool is brought up. This was not a problem with Ubuntu 12.04. I have reproduced the bug with Intel Integrated graphics, and have a bug report from a user that it happens with the AMD proprietary driver. So it is probably not the "new and improved" Intel driver (the usual suspect), but something more basic, like compiz/unity or whatever Ubuntu is using now. To reproduce the bug, download and install UCSF Chimera from http://www.cgl.ucsf.edu/chimera/. Then, using the menus, use File / Fetch by ID ... to get the 1yti data set from the PDB (Protein DataBank), and then bring the SideView with Favorites / SideView. On my "Intel Corporation 82G33/G31 Express Integrated Graphics Controller (rev 02)" system, if the SideView is displayed before fetching the data, then it works. That suggests that it is a bug with sharing OpenGL data with a context that already has data in it. Here is the backtrace from gdb: Program terminated with signal 6, Aborted. #0 0xb7732424 in __kernel_vsyscall () (gdb) where 20 #0 0xb7732424 in __kernel_vsyscall () #1 0xb74611df in ?? () #2 0xb75d9000 in ?? () Backtrace stopped: previous frame inner to this frame (corrupt stack?) ProblemType: Bug DistroRelease: Ubuntu 12.10 Package: xorg 1:7.7+1ubuntu4 ProcVersionSignature: Ubuntu 3.5.0-18.29-generic 3.5.7 Uname: Linux 3.5.0-18-generic i686 .tmp.unity.support.test.0: ApportVersion: 2.6.1-0ubuntu6 Architecture: i386 CompizPlugins: [core,bailer,detection,composite,opengl,decor,regex,resize,gnomecompat,compiztoolbox,move,grid,animation,mousepoll,workarounds,wall,place,fade,vpswitch,snap,imgpng,scale,session,expo,ezoom,unitymtgrabhandles,unityshell] CompositorRunning: compiz Date: Wed Nov 14 16:53:02 2012 DistUpgraded: 2012-11-14 15:16:36,826 DEBUG enabling apt cron job DistroCodename: quantal DistroVariant: ubuntu ExtraDebuggingInterest: Yes GraphicsCard: Intel Corporation 82G33/G31 Express Integrated Graphics Controller [8086:29c2] (rev 02) (prog-if 00 [VGA controller]) Subsystem: Hewlett-Packard Company Device [103c:2a73] InstallationDate: Installed on 2010-10-18 (758 days ago) InstallationMedia: Ubuntu 10.10 "Maverick Meerkat" - Release i386 (20101007) MachineType: Hewlett-Packard HP Compaq dx2400 Microtower MarkForUpload: True ProcEnviron: TERM=xterm PATH=(custom, no user) XDG_RUNTIME_DIR=<set> LANG=en_US.UTF-8 SHELL=/bin/bash ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.5.0-18-generic root=UUID=9823d8c7-5498-469e-8bf2-7b8340e9c590 ro quiet splash vt.handoff=7 SourcePackage: xorg Symptom: display UpgradeStatus: Upgraded to quantal on 2012-11-14 (0 days ago) dmi.bios.date: 04/21/2008 dmi.bios.vendor: American Megatrends Inc. dmi.bios.version: 5.23 dmi.board.name: 2A73h dmi.board.vendor: PEGATRON CORPORATION dmi.board.version: 1.01 dmi.chassis.asset.tag: MXL8220VQN dmi.chassis.type: 3 dmi.chassis.vendor: Hewlett-Packard dmi.chassis.version: Chassis Version dmi.modalias: dmi:bvnAmericanMegatrendsInc.:bvr5.23:bd04/21/2008:svnHewlett-Packard:pnHPCompaqdx2400Microtower:pvr:rvnPEGATRONCORPORATION:rn2A73h:rvr1.01:cvnHewlett-Packard:ct3:cvrChassisVersion: dmi.product.name: HP Compaq dx2400 Microtower dmi.sys.vendor: Hewlett-Packard version.compiz: compiz 1:0.9.8.4+bzr3407-0ubuntu1 version.libdrm2: libdrm2 2.4.39-0ubuntu1 version.libgl1-mesa-dri: libgl1-mesa-dri 9.0-0ubuntu1 version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A version.libgl1-mesa-glx: libgl1-mesa-glx 9.0-0ubuntu1 version.xserver-xorg-core: xserver-xorg-core 2:1.13.0-0ubuntu6 version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.7.3-0ubuntu2 version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:6.99.99~git20120913.8637f772-0ubuntu1 version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.20.9-0ubuntu2 version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:1.0.2-0ubuntu3 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/1078983/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : desktop-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp
