Up until two days ago I had a working sci-chemistry/pymol-2.5.0-r3. However, both yesterday and today I upgraded my system (emerge --update --newuse --newrepo --ask -vt --deep --complete-graph=y --changed-deps=y @world) and a whole lot of packages were updated or rebuilt. To my surprise, one or some of them must have broken pymol because now, whener I try to load a PDB, it exits with a segfault message: ===== $ pymol PyMOL(TM) Molecular Graphics System, Version 2.5.0. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help <command-name>" for information on a specific command. Hit ESC anytime to toggle between text and graphics. There was an error intializing GLEW. Basic graphics, including shaders and volumes may be unavailable. GLEW-Error: Unknown error OpenGL graphics engine: GL_VENDOR: AMD GL_RENDERER: AMD Radeon RX 470 Graphics (polaris10, LLVM 16.0.6, DRM 3.49, 6.1.31-gentoo) GL_VERSION: 4.6 (Compatibility Profile) Mesa 23.1.3 Detected 16 CPU cores. Enabled multithreaded rendering. PyMOL>import sys, os PyMOL>pymol_git = os.path.abspath(os.path.join(os.path.expanduser('/home/ramiro/docking/'), 'Pymol-script-repo')) PyMOL>os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules') PyMOL>sys.path.append(pymol_git) PyMOL>sys.path.append(os.environ['PYMOL_GIT_MOD']) PyMOL>home_dir = os.path.abspath(os.path.join(os.path.expanduser('/home/ramiro/docking/'), 'pymol')) PyMOL>if not os.path.exists(home_dir): os.makedirs(home_dir) PyMOL>os.chdir(home_dir) PyMOL>set use_shaders, 1 Setting: use_shaders set to on. PyMOL>set fetch_path, /home/ramiro/Dropbox/docking/PDBs/pymol_fetch/ Setting: fetch_path set to /home/ramiro/Dropbox/docking/PDBs/pymol_fetch/. PyMOL>set internal_gui_width, 400 Setting: internal_gui_width set to 400. PyMOL>set ray_opaque_background, off Setting: ray_opaque_background set to 0. Not a JPEG file: starts with 0x89 0x50 Not a JPEG file: starts with 0x89 0x50 Not a JPEG file: starts with 0x89 0x50 Not a JPEG file: starts with 0x89 0x50 Not a JPEG file: starts with 0x89 0x50 kf.coreaddons: "Could not load plugin from /usr/lib64/qt5/plugins/openofficeorgthumbnail.so: Failed to extract plugin meta data from '/usr/lib64/qt5/plugins/openofficeorgthumbnail.so'" HEADER MEMBRANE PROTEIN / HYDROLASE 05-OCT-07 2RH1 TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF HUMAN B2-ADRENERGIC G PROTEIN- TITLE 2 COUPLED RECEPTOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-ADRENERGIC RECEPTOR/T4-LYSOZYME CHIMERA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-2 ADRENERGIC RECEPTOR, BETA-2 ADRENOCEPTOR, BETA-2 COMPND 5 ADRENORECEPTOR / LYSIS PROTEIN, MURAMIDASE, ENDOLYSIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. CmdLoad: "" loaded as "2rh1". Violación de segmento (`core' generado)
remerging pymol does not solve the issue, which happens in my two boxes.
Sorry, I forgot to include the warning showed after emerging it: ===== >>> Completed (1 of 1) sci-chemistry/pymol-2.5.0-r3::gentoo * Messages for package sci-chemistry/pymol-2.5.0-r3: * Non-PEP517 builds are deprecated for ebuilds using plain distutils. * Please migrate to DISTUTILS_USE_PEP517=setuptools. * Please see Python Guide for more details: * https://projects.gentoo.org/python/guide/distutils.html * Python extension modules (*.so) found installed. Please set: * DISTUTILS_EXT=1 * in the ebuild. * python_foreach_impl has been called directly while using distutils-r1. * Please redefine python_*() phase functions to meet your expectations * instead. * GNU info directory index is up-to-date.
Can you get a backtrace please? See https://wiki.gentoo.org/wiki/Debugging#Per-package.
(In reply to Sam James from comment #3) > Can you get a backtrace please? See > https://wiki.gentoo.org/wiki/Debugging#Per-package. I'm trying but I don't know how to start gdb properly on pymol. Right now I get this: ===== $ which pymol /usr/bin/pymol $ ls -la /usr/bin/pymol lrwxrwxrwx 1 root root 31 jul 19 08:01 /usr/bin/pymol -> ../lib/python-exec/python-exec2 $ gdb --args /usr/bin/pymol GNU gdb (Gentoo 13.2 vanilla) 13.2 Copyright (C) 2023 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-pc-linux-gnu". Type "show configuration" for configuration details. For bug reporting instructions, please see: <https://bugs.gentoo.org/>. Find the GDB manual and other documentation resources online at: <http://www.gnu.org/software/gdb/documentation/>. For help, type "help". Type "apropos word" to search for commands related to "word"... "/usr/bin/pymol": not in executable format: file format not recognized (gdb) quit $ gdb --args /usr/bin/pymol /usr/lib/python-exec/python-exec2 GNU gdb (Gentoo 13.2 vanilla) 13.2 Copyright (C) 2023 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-pc-linux-gnu". Type "show configuration" for configuration details. For bug reporting instructions, please see: <https://bugs.gentoo.org/>. Find the GDB manual and other documentation resources online at: <http://www.gnu.org/software/gdb/documentation/>. For help, type "help". Type "apropos word" to search for commands related to "word"... "/usr/bin/pymol": not in executable format: file format not recognized (gdb)
Try: gdb --args /usr/bin/python-exec pymol
(In reply to Sam James from comment #5) > Try: gdb --args /usr/bin/python-exec pymol gdb --args /usr/bin/python-exec2c pymol
Thanks. The result: ===== $ gdb --args /usr/bin/python-exec2c pymol GNU gdb (Gentoo 13.2 vanilla) 13.2 Copyright (C) 2023 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-pc-linux-gnu". Type "show configuration" for configuration details. For bug reporting instructions, please see: <https://bugs.gentoo.org/>. Find the GDB manual and other documentation resources online at: <http://www.gnu.org/software/gdb/documentation/>. For help, type "help". Type "apropos word" to search for commands related to "word"... Reading symbols from /usr/bin/python-exec2c... (No debugging symbols found in /usr/bin/python-exec2c) (gdb) run Starting program: /usr/bin/python-exec2c pymol [Thread debugging using libthread_db enabled] Using host libthread_db library "/usr/lib64/libthread_db.so.1". process 46680 is executing new program: /usr/bin/python3.11 [Thread debugging using libthread_db enabled] Using host libthread_db library "/usr/lib64/libthread_db.so.1". [New Thread 0x7fffef45f6c0 (LWP 46683)] [New Thread 0x7fffecd606c0 (LWP 46684)] [New Thread 0x7fffe7fff6c0 (LWP 46685)] [New Thread 0x7fffe65ff6c0 (LWP 46686)] [New Thread 0x7fffe5dfe6c0 (LWP 46687)] [New Thread 0x7fffe55fd6c0 (LWP 46688)] [New Thread 0x7fffe4dfc6c0 (LWP 46689)] [New Thread 0x7fffc3fff6c0 (LWP 46690)] [New Thread 0x7fffc37fe6c0 (LWP 46691)] [New Thread 0x7fffc2ffd6c0 (LWP 46692)] [New Thread 0x7fffc27fc6c0 (LWP 46693)] [Thread 0x7fffc27fc6c0 (LWP 46693) exited] [Thread 0x7fffc2ffd6c0 (LWP 46692) exited] [Thread 0x7fffc37fe6c0 (LWP 46691) exited] [Thread 0x7fffc3fff6c0 (LWP 46690) exited] [New Thread 0x7fffc3fff6c0 (LWP 46694)] [New Thread 0x7fffc37fe6c0 (LWP 46695)] [New Thread 0x7fffc2ffd6c0 (LWP 46696)] [New Thread 0x7fffc27fc6c0 (LWP 46697)] PyMOL(TM) Molecular Graphics System, Version 2.5.0. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help <command-name>" for information on a specific command. Hit ESC anytime to toggle between text and graphics. There was an error intializing GLEW. Basic graphics, including shaders and volumes may be unavailable. GLEW-Error: Unknown error OpenGL graphics engine: GL_VENDOR: AMD GL_RENDERER: AMD Radeon RX 470 Graphics (polaris10, LLVM 16.0.6, DRM 3.49, 6.1.31-gentoo) GL_VERSION: 4.6 (Compatibility Profile) Mesa 23.1.3 Detected 16 CPU cores. Enabled multithreaded rendering. [New Thread 0x7fffb0d0b6c0 (LWP 46712)] PyMOL>import sys, os PyMOL>pymol_git = os.path.abspath(os.path.join(os.path.expanduser('/home/ramiro/docking/'), 'Pymol-script-repo')) PyMOL>os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules') PyMOL>sys.path.append(pymol_git) PyMOL>sys.path.append(os.environ['PYMOL_GIT_MOD']) PyMOL>home_dir = os.path.abspath(os.path.join(os.path.expanduser('/home/ramiro/docking/'), 'pymol')) PyMOL>if not os.path.exists(home_dir): os.makedirs(home_dir) PyMOL>os.chdir(home_dir) PyMOL>set use_shaders, 1 Setting: use_shaders set to on. PyMOL>set fetch_path, /home/ramiro/Dropbox/docking/PDBs/pymol_fetch/ Setting: fetch_path set to /home/ramiro/Dropbox/docking/PDBs/pymol_fetch/. PyMOL>set internal_gui_width, 400 Setting: internal_gui_width set to 400. PyMOL>set ray_opaque_background, off Setting: ray_opaque_background set to 0. [Thread 0x7fffb0d0b6c0 (LWP 46712) exited] [New Thread 0x7fffb0d0b6c0 (LWP 46761)] [New Thread 0x7fffa75056c0 (LWP 46762)] [New Thread 0x7fff9ed046c0 (LWP 46763)] [New Thread 0x7fffa6d046c0 (LWP 46764)] [New Thread 0x7fffa65036c0 (LWP 46765)] [New Thread 0x7fffa5d026c0 (LWP 46766)] [New Thread 0x7fffa55016c0 (LWP 46767)] [New Thread 0x7fffa4d006c0 (LWP 46768)] [New Thread 0x7fff9ffff6c0 (LWP 46769)] [New Thread 0x7fff9f7fe6c0 (LWP 46770)] [New Thread 0x7fff9e5036c0 (LWP 46771)] [New Thread 0x7fff9dd026c0 (LWP 46772)] [New Thread 0x7fff9d5016c0 (LWP 46773)] [New Thread 0x7fff9cd006c0 (LWP 46774)] [Detaching after fork from child process 46775] [New Thread 0x7fff6ffff6c0 (LWP 46777)] kf.service.services: The desktop entry file "/usr/share/applications/org.freedesktop.Xwayland.desktop" has Type= "Application" but no Exec line kf.service.sycoca: Invalid Service : "/usr/share/applications/org.freedesktop.Xwayland.desktop" [New Thread 0x7fff6f7fe6c0 (LWP 46778)] [New Thread 0x7fff6effd6c0 (LWP 46779)] [Detaching after fork from child process 46785] [Detaching after fork from child process 46786] [New Thread 0x7fff6cb5a6c0 (LWP 46787)] [New Thread 0x7fff53fff6c0 (LWP 46788)] [New Thread 0x7fff537fe6c0 (LWP 46789)] [New Thread 0x7fff52ffd6c0 (LWP 46790)] [Detaching after fork from child process 46791] Not a JPEG file: starts with 0x89 0x50 Not a JPEG file: starts with 0x89 0x50 Not a JPEG file: starts with 0x89 0x50 kf.coreaddons: "Could not load plugin from /usr/lib64/qt5/plugins/openofficeorgthumbnail.so: Failed to extract plugin meta data from '/usr/lib64/qt5/plugins/openofficeorgthumbnail.so'" HEADER MEMBRANE PROTEIN / HYDROLASE 05-OCT-07 2RH1 TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF HUMAN B2-ADRENERGIC G PROTEIN- TITLE 2 COUPLED RECEPTOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-ADRENERGIC RECEPTOR/T4-LYSOZYME CHIMERA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-2 ADRENERGIC RECEPTOR, BETA-2 ADRENOCEPTOR, BETA-2 COMPND 5 ADRENORECEPTOR / LYSIS PROTEIN, MURAMIDASE, ENDOLYSIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. CmdLoad: "" loaded as "2rh1". Thread 1 "pymol" received signal SIGSEGV, Segmentation fault. CShaderPrg::GetAttribLocation (this=this@entry=0x0, name=0x555557a42478 "a_interpolate") at layer0/ShaderPrg.cpp:202 202 if (id && name) { (gdb)
Please type bt in gdb, hit enter, and show the new output
(In reply to Sam James from comment #8) > Please type bt in gdb, hit enter, and show the new output (gdb) bt #0 CShaderPrg::GetAttribLocation (this=this@entry=0x0, name=0x555557a26eb8 "a_interpolate") at layer0/ShaderPrg.cpp:202 #1 0x00007ffff63d096a in CGO_gl_vertex_attribute_1f (I=0x5555562c5950, varg=<optimized out>) at layer1/CGO.cpp:7418 #2 0x00007ffff63dc35d in CGORenderGL (I=0x5555565922a0, color=<optimized out>, set1=0x0, set2=0x0, info=0x7fffffffb3d0, rep=<optimized out>) at layer1/CGO.cpp:7860 #3 0x00007ffff64d0000 in CoordSet::render (this=this@entry=0x555555e8f6a0, info=info@entry=0x7fffffffb3d0) at layer2/CoordSet.cpp:1464 #4 0x00007ffff6512208 in ObjectMolecule::render (this=0x5555578d4660, info=0x7fffffffb3d0) at layer2/ObjectMolecule.cpp:11024 #5 0x00007ffff648dc59 in SceneRenderAllObject (G=0x55555659ef60, I=0x555556c59050, context=0x7fffffffb630, info=0x7fffffffb3d0, normal=0x7fffffffb650, state=0, obj=0x5555578d4660, grid=0x555556c6e504, fat=0, slot_vla=<optimized out>) at layer1/SceneRender.cpp:710 #6 0x00007ffff648e339 in SceneRenderAllObject (fat=0, slot_vla=0x0, grid=0x555556c6e504, obj=0x5555578d4660, state=0, normal=0x7fffffffb650, info=0x7fffffffb3d0, context=0x7fffffffb630, I=0x555556c59050, G=0x55555659ef60) at layer1/SceneRender.cpp:637 #7 SceneRenderAll (G=G@entry=0x55555659ef60, context=context@entry=0x7fffffffb630, normal=normal@entry=0x7fffffffb650, pickmgr=pickmgr@entry=0x0, pass=RenderPass::Opaque, fat=fat@entry=0, width_scale=width_scale@entry=0, grid=0x555556c6e504, dynamic_pass=0, which_objects=SceneRenderWhich::GadgetsLast) at layer1/SceneRender.cpp:845 #8 0x00007ffff648ee44 in DoRendering (G=G@entry=0x55555659ef60, I=I@entry=0x555556c59050, grid=grid@entry=0x555556c6e504, times=times@entry=0, curState=curState@entry=0, normal=normal@entry=0x7fffffffb650, context=0x7fffffffb630, width_scale=width_scale@entry=0, onlySelections=0, excludeSelections=0, offscreen=0) at layer1/SceneRender.cpp:977 #9 0x00007ffff648fd7f in SceneRenderStereoLoop (render_to_texture=0, onlySelections=0, noAA=<optimized out>, fog_active=1, width_scale=0, context=0x7fffffffb630, normal=0x7fffffffb650, curState=0, stereo_double_pump_mono=0, oversize_height=0, oversize_width=0, y=0, x=0, stereo_mode=<optimized out>, must_render_stereo=0, timesArg=<optimized out>, G=0x55555659ef60) at layer1/SceneRender.cpp:1214 #10 SceneRender (G=G@entry=0x55555659ef60, pick=pick@entry=0x0, x=x@entry=0, y=y@entry=0, smp=smp@entry=0x0, oversize_width=oversize_width@entry=0, oversize_height=0, click_side=<optimized out>, force_copy=0) at layer1/SceneRender.cpp:474 #11 0x00007ffff643fa75 in OrthoDoDraw (G=G@entry=0x55555659ef60, render_mode=render_mode@entry=OrthoRenderMode::Main) at layer1/Ortho.cpp:1622 #12 0x00007ffff65cf1ba in ExecutiveDrawNow (G=0x55555659ef60) at layer3/Executive.cpp:11223 #13 0x00007ffff66bf3be in PyMOL_DrawWithoutLock (I=0x555555e27490) at layer5/PyMOL.cpp:2283 #14 0x00007ffff669afbc in Cmd_Draw (self=<optimized out>, args=<optimized out>) at layer4/Cmd.cpp:3584 #15 0x00007ffff7b921f1 in ?? () from /usr/lib64/libpython3.11.so.1.0 #16 0x00007ffff7b4eb1b in _PyObject_MakeTpCall () from /usr/lib64/libpython3.11.so.1.0 #17 0x00007ffff7b004d6 in _PyEval_EvalFrameDefault () from /usr/lib64/libpython3.11.so.1.0 #18 0x00007ffff7c28580 in ?? () from /usr/lib64/libpython3.11.so.1.0 #19 0x00007ffff7b51c1c in ?? () from /usr/lib64/libpython3.11.so.1.0 #20 0x00007ffff201818c in ?? () from /usr/lib/python3.11/site-packages/PyQt5/sip.cpython-311-x86_64-linux-gnu.so #21 0x00007ffff2018267 in ?? () from /usr/lib/python3.11/site-packages/PyQt5/sip.cpython-311-x86_64-linux-gnu.so #22 0x00007ffff0daae14 in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtOpenGL.abi3.so #23 0x00007ffff04c8e15 in QGLWidget::glDraw() () from /usr/lib64/libQt5OpenGL.so.5 #24 0x00007ffff0daa498 in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtOpenGL.abi3.so #25 0x00007ffff04c68dd in QGLWidget::paintEvent(QPaintEvent*) () from /usr/lib64/libQt5OpenGL.so.5 #26 0x00007ffff0dacb7b in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtOpenGL.abi3.so #27 0x00007fffefda7008 in QWidget::event(QEvent*) () from /usr/lib64/libQt5Widgets.so.5 #28 0x00007ffff0dabd6f in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtOpenGL.abi3.so #29 0x00007ffff7b921f1 in ?? () from /usr/lib64/libpython3.11.so.1.0 #30 0x00007ffff7b4eb1b in _PyObject_MakeTpCall () from /usr/lib64/libpython3.11.so.1.0 #31 0x00007ffff7b004d6 in _PyEval_EvalFrameDefault () from /usr/lib64/libpython3.11.so.1.0 #32 0x00007ffff7c28580 in ?? () from /usr/lib64/libpython3.11.so.1.0 #33 0x00007ffff7b51ae2 in ?? () from /usr/lib64/libpython3.11.so.1.0 #34 0x00007ffff201818c in ?? () from /usr/lib/python3.11/site-packages/PyQt5/sip.cpython-311-x86_64-linux-gnu.so #35 0x00007ffff20183c1 in ?? () from /usr/lib/python3.11/site-packages/PyQt5/sip.cpython-311-x86_64-linux-gnu.so #36 0x00007ffff0da7459 in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtOpenGL.abi3.so #37 0x00007ffff0dabbdb in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtOpenGL.abi3.so #38 0x00007fffefd6342e in QApplicationPrivate::notify_helper(QObject*, QEvent*) () from /usr/lib64/libQt5Widgets.so.5 #39 0x00007fffef9aab6e in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtWidgets.abi3.so --Type <RET> for more, q to quit, c to continue without paging--c #40 0x00007ffff1284378 in QCoreApplication::notifyInternal2(QObject*, QEvent*) () from /usr/lib64/libQt5Core.so.5 #41 0x00007fffefd9efa5 in QWidgetPrivate::sendPaintEvent(QRegion const&) () from /usr/lib64/libQt5Widgets.so.5 #42 0x00007fffefd9f8f9 in QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) () from /usr/lib64/libQt5Widgets.so.5 #43 0x00007fffefda05a3 in QWidgetPrivate::paintOnScreen(QRegion const&) () from /usr/lib64/libQt5Widgets.so.5 #44 0x00007fffefdc4103 in ?? () from /usr/lib64/libQt5Widgets.so.5 #45 0x00007fffefd6342e in QApplicationPrivate::notify_helper(QObject*, QEvent*) () from /usr/lib64/libQt5Widgets.so.5 #46 0x00007fffef9aab6e in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtWidgets.abi3.so #47 0x00007ffff1284378 in QCoreApplication::notifyInternal2(QObject*, QEvent*) () from /usr/lib64/libQt5Core.so.5 #48 0x00007ffff1728f21 in QGuiApplicationPrivate::processExposeEvent(QWindowSystemInterfacePrivate::ExposeEvent*) () from /usr/lib64/libQt5Gui.so.5 #49 0x00007ffff17065fb in QWindowSystemInterface::sendWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib64/libQt5Gui.so.5 #50 0x00007ffff1706968 in QWindowSystemInterface::flushWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib64/libQt5Gui.so.5 #51 0x00007ffff12af784 in QObject::event(QEvent*) () from /usr/lib64/libQt5Core.so.5 #52 0x00007fffefd6342e in QApplicationPrivate::notify_helper(QObject*, QEvent*) () from /usr/lib64/libQt5Widgets.so.5 #53 0x00007fffef9aab6e in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtWidgets.abi3.so #54 0x00007ffff1284378 in QCoreApplication::notifyInternal2(QObject*, QEvent*) () from /usr/lib64/libQt5Core.so.5 #55 0x00007ffff12878b3 in QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) () from /usr/lib64/libQt5Core.so.5 #56 0x00007ffff12d64f3 in ?? () from /usr/lib64/libQt5Core.so.5 #57 0x00007ffff571458c in g_main_context_dispatch () from /usr/lib64/libglib-2.0.so.0 #58 0x00007ffff5714838 in ?? () from /usr/lib64/libglib-2.0.so.0 #59 0x00007ffff57148cc in g_main_context_iteration () from /usr/lib64/libglib-2.0.so.0 #60 0x00007ffff12d5ff6 in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib64/libQt5Core.so.5 #61 0x00007ffff1282d9b in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib64/libQt5Core.so.5 #62 0x00007ffff128b076 in QCoreApplication::exec() () from /usr/lib64/libQt5Core.so.5 #63 0x00007fffef9a981d in ?? () from /usr/lib/python3.11/site-packages/PyQt5/QtWidgets.abi3.so #64 0x00007ffff7b921f1 in ?? () from /usr/lib64/libpython3.11.so.1.0 #65 0x00007ffff7b4eb1b in _PyObject_MakeTpCall () from /usr/lib64/libpython3.11.so.1.0 #66 0x00007ffff7b004d6 in _PyEval_EvalFrameDefault () from /usr/lib64/libpython3.11.so.1.0 #67 0x00007ffff7c28580 in ?? () from /usr/lib64/libpython3.11.so.1.0 #68 0x00007ffff7c2863d in PyEval_EvalCode () from /usr/lib64/libpython3.11.so.1.0 #69 0x00007ffff7c6a823 in ?? () from /usr/lib64/libpython3.11.so.1.0 #70 0x00007ffff7c6aa46 in ?? () from /usr/lib64/libpython3.11.so.1.0 #71 0x00007ffff7c6ab20 in ?? () from /usr/lib64/libpython3.11.so.1.0 #72 0x00007ffff7c6d5c9 in _PyRun_SimpleFileObject () from /usr/lib64/libpython3.11.so.1.0 #73 0x00007ffff7c6db70 in _PyRun_AnyFileObject () from /usr/lib64/libpython3.11.so.1.0 #74 0x00007ffff7c8b6b0 in Py_RunMain () from /usr/lib64/libpython3.11.so.1.0 #75 0x00007ffff7c8bc8a in Py_BytesMain () from /usr/lib64/libpython3.11.so.1.0 #76 0x00007ffff784a8ca in ?? () from /usr/lib64/libc.so.6 #77 0x00007ffff784a985 in __libc_start_main () from /usr/lib64/libc.so.6 #78 0x0000555555555081 in _start () (gdb)
I found the culprit: current stable wayland. I use Plasma (always stable version). It occurred to me to close my wayland session and start up a new one using X11: all of a sudden, the problem is gone and pymol loads any PDB normally, as expected. This also solves a similar issue I was having with Inkscape but hadn't reported it yet: whenever I tried to drag&drop a file from a Dolphin window into a working Inkscape window, the Dolphin window the file was being dragged from would close (Inkscpae window is unaffected). Howver, starting my GUI Plasma session as X11 solves this issue, too, and allows Inkscape to show the pop-up dialog asking how you want to import the file into its window, importing it with no issues afterwards.
Does it help downgrading to x11-base/xwayland-23.1.1 ?
(In reply to Pacho Ramos from comment #11) > Does it help downgrading to x11-base/xwayland-23.1.1 ? Would try. In the meantime, there's this related bug: https://bugs.gentoo.org/910562
(In reply to Pacho Ramos from comment #11) > Does it help downgrading to x11-base/xwayland-23.1.1 ? No, it doesn't. Same issues both with loading files in pymol and drad&drop from Dolphin into Inkscape.
Thanks As a side note: in the backtraces you are posting here and in the other bug, there are many lines as: in ?? () from /usr/lib64/libwayland-client.so.0 The "??" is signaling that the library mentioned in "from" is missing debugging symbols
(In reply to Pacho Ramos from comment #14) > Thanks > > As a side note: in the backtraces you are posting here and in the other bug, > there are many lines as: > in ?? () from /usr/lib64/libwayland-client.so.0 > > The "??" is signaling that the library mentioned in "from" is missing > debugging symbols No, I'm not the reporter of the other bug. I simply commented to confirm it.
Linked bug does not look related.
(In reply to urcindalo from comment #15) > No, I'm not the reporter of the other bug. I simply commented to confirm it. But the backtrace in this bug also misses debug symbols for some libs. Like qtcore, glib (those showing "??" in the line corresponding to them) Which desktop are you using? KDE, gnome or other? Thanks
Is this still happening with qtwayland-5.15.10-r4?
(In reply to Pacho Ramos from comment #18) > Is this still happening with qtwayland-5.15.10-r4? Yes, pymol still segfaults when loading a pdb file in a Plasma wayland session. The problem is solved though when DnD a file into Inkscape, as I commented on a previous message.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dfe0f62750dadf6273bd4146db194c7165181781 commit dfe0f62750dadf6273bd4146db194c7165181781 Author: Alexey Shvetsov <alexxy@gentoo.org> AuthorDate: 2024-05-17 19:20:35 +0000 Commit: Alexey Shvetsov <alexxy@gentoo.org> CommitDate: 2024-05-17 19:20:35 +0000 sci-chemistry/pymol: Update to 3.0.0 and drop old Closes: https://bugs.gentoo.org/862441 Closes: https://bugs.gentoo.org/910511 Closes: https://bugs.gentoo.org/929762 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> sci-chemistry/pymol/Manifest | 2 +- sci-chemistry/pymol/pymol-2.5.0-r3.ebuild | 100 --------------------- .../{pymol-2.5.0-r5.ebuild => pymol-3.0.0.ebuild} | 9 +- 3 files changed, 6 insertions(+), 105 deletions(-)
