In /var/crash there is only one relevant crash file and I tried ubuntu-bug YOURFILE.crash but nothing happens, the command just hangs forever. I've tried "https://errors.ubuntu.com/user/ID where ID is the content of file /var/lib/whoopsie/whoopsie-id" but it just says "Sorry, you are not a member of a group that is allowed to see the data from error reports. Please fill out this form to request access." but that form wanted me to give my personal info which I'm not comfortable with.
Below there are outputs of running the affected apps from a terminal window. ------------------------------------------------------------------------- anna@anna:~$ vmd rlwrap: Command not found. /home/anna/Programy/vmd/vmd_LINUXAMD64: /lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /home/anna/Programy/vmd/vmd_LINUXAMD64) Info) VMD for LINUXAMD64, version 1.9.4a38 (October 17, 2019) Info) http://www.ks.uiuc.edu/Research/vmd/ Info) Email questions and bug reports to v...@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, 8 CPUs detected. Info) CPU features: SSE2 AVX AVX2 FMA Info) Free system memory: 11GB (68%) Info) No CUDA accelerator devices available. Warning) Detected X11 'Composite' extension: if incorrect display occurs Warning) try disabling this X server option. Most OpenGL drivers Warning) disable stereoscopic display when 'Composite' is enabled. Info) OpenGL renderer: Mesa Intel(R) UHD Graphics 620 (WHL GT2) Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS) Info) Full GLSL rendering mode is available. Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8) Info) Dynamically loaded 3 plugins in directory: Info) /home/anna/Programy/vmd/plugins/LINUXAMD64/molfile Aborted (core dumped) ------------------------------------------------------------------------- anna@anna:~/Programy/Biovia/Discovery-Studio/bin$ ./DiscoveryStudio2020 # Parse application name from $0 unless it's already set for us if [ -z "$ACCELRYS_APPNAME" ] ; then ACCELRYS_APPNAME=`basename $0` fi # Path to the installation abspath="$(cd "${0%/*}" 2>/dev/null; echo "$PWD"/"${0##*/}")" libfolder=`dirname "$abspath"` ACCELRYS_ROOT="$libfolder/.." # Source the global resource configuration file GLOBALRC=$ACCELRYS_ROOT/etc/shrc if [ -f "$GLOBALRC" ] ; then . $GLOBALRC fi # Bourne Shell Resource Configuration file for the DS client and server # applications if [ -z "$ACCELRYS_ROOT" ] ; then echo "ACCELRYS_ROOT is not set" exit 1 fi # Detect the platform name if [ -z "$ACCELRYS_PLATFORM" ] ; then case `uname` in IRIX64) ACCELRYS_PLATFORM=irix;; IRIX*) ACCELRYS_PLATFORM=irix;; AIX) ACCELRYS_PLATFORM=aix;; OSF1) ACCELRYS_PLATFORM=tru64;; SunOS) ACCELRYS_PLATFORM=solaris;; Linux) ACCELRYS_PLATFORM=linux;; CYGWIN*)ACCELRYS_PLATFORM=win32;; *) ACCELRYS_PLATFORM=unknown;; esac # special case for Itanium if [ `uname -m` = "ia64" ] ; then ACCELRYS_PLATFORM=linux_ia64 fi fi export ACCELRYS_PLATFORM # Set up the executable and library paths PATH=$ACCELRYS_ROOT/bin:$ACCELRYS_ROOT/lib:$PATH LD_LIBRARY_PATH=$ACCELRYS_ROOT/lib:$ACCELRYS_ROOT/lib64 export ACCELRYS_ROOT export PATH export LD_LIBRARY_PATH # -- Begin License check # Set up the License Pack environment # IMPORTANT - Any changes to this section should also be made in # the apps/accelrys/ds/data/shrc file until these two files # can be replaced by a single file, if possible lp_location=$ACCELRYS_ROOT/share/license/data/lp_location if [ -r "$lp_location" ] ; then lp_dir=`cat "$lp_location"` if [ -d "$lp_dir" ]; then lp_varfile=$lp_dir/etc/lp_echovars if [ -r "$lp_varfile" ] ; then eval `"$lp_varfile" -l sh` else echo "Required file $lp_varfile can not be read." fi else echo "License Pack location ($lp_dir) is not a valid location." echo "Run $ACCELRYS_ROOT/bin/config_lp_location <location of LicensePack>" echo "to reconfigure." fi else echo "Required file '$lp_location' can not be read." fi # -- End License check if [ "$ACCELRYS_PLATFORM" != "irix" -a "$ACCELRYS_PLATFORM" != "aix" ] ; then # Avoids difficult-to-debug crashes for several apps ulimit -s 10240 fi # Source the application resource configuration file APPRC=$ACCELRYS_ROOT/share/$ACCELRYS_APPNAME/shrc if [ -f "$APPRC" ] ; then . $APPRC fi # Default value for how we exec the application if [ -z "$ACCELRYS_EXEC" ] ; then ACCELRYS_EXEC=exec fi # The binary executable for the application ACCELRYS_BIN=$ACCELRYS_ROOT/lib/${ACCELRYS_APPNAME}-bin if [ ! -f "$ACCELRYS_BIN" ] ; then echo "ERROR: Application binary '$ACCELRYS_BIN' does not exist" 2>&1 exit 1 fi # Print out the environment if debug mode is on if [ "$ACCELRYS_DEBUG" -ne 0 ] ; then ACCELRYS_QUIET=0 env fi GJS_DEBUG_TOPICS=JS ERROR;JS LOG LESSOPEN=| /usr/bin/lesspipe %s CONDA_PROMPT_MODIFIER=(base) MSI_LICENSE_FILE=/home/anna/Programy/Biovia/LicensePack/Licenses USER=anna SSH_AGENT_PID=35121 XDG_SESSION_TYPE=x11 SHLVL=1 LD_LIBRARY_PATH=/home/anna/Programy/Biovia/LicensePack/linux/lib:/home/anna/Programy/Biovia/Discovery-Studio/bin/../lib:/home/anna/Programy/Biovia/Discovery-Studio/bin/../lib64 HOME=/home/anna CONDA_SHLVL=1 OLDPWD=/home/anna/Programy/Biovia/Discovery-Studio/Discovery-Studio ACCELRYS_PLATFORM=linux DESKTOP_SESSION=ubuntu BIOVIA_LICENSE_PLATFORM=linux GNOME_SHELL_SESSION_MODE=ubuntu GTK_MODULES=gail:atk-bridge MANAGERPID=34936 DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus COLORTERM=truecolor BIOVIA_LIC_PACK_DIR=/home/anna/Programy/Biovia/LicensePack IM_CONFIG_PHASE=1 LOGNAME=anna JOURNAL_STREAM=9:767533 _=./DiscoveryStudio2020 PKG_CONFIG_PATH=/usr/local/lib/pkgconfig XDG_SESSION_CLASS=user USERNAME=anna TERM=xterm-256color GNOME_DESKTOP_SESSION_ID=this-is-deprecated AMBERHOME=/home/anna/Programy/tangram BABEL_LIBDIR=/usr/lib/openbabel/ WINDOWPATH=3 PATH=/home/anna/Programy/Biovia/LicensePack/linux/bin:/home/anna/Programy/Biovia/Discovery-Studio/bin/../bin:/home/anna/Programy/Biovia/Discovery-Studio/bin/../lib:/home/anna/Programy/tangram/bin:/home/anna/Programy/tangram/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/anna/Programy/BIOVIA/Discovery-Studio:/home/anna/Programy/vmd/bin:/home/anna/Programy/molden/bin:/home/anna/.local/bin:/home/anna/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin SESSION_MANAGER=local/anna:@/tmp/.ICE-unix/35166,unix/anna:/tmp/.ICE-unix/35166 VMDBABELBIN=/usr/bin/obabel INVOCATION_ID=52749891b6aa4173a510adcdebaf01a1 XDG_MENU_PREFIX=gnome- GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/465dc0e0_3d8d_4560_bef9_90414c973fae XDG_RUNTIME_DIR=/run/user/1000 DISPLAY=:1 LANG=pl_PL.UTF-8 XDG_CURRENT_DESKTOP=ubuntu:GNOME XMODIFIERS=@im=ibus XDG_SESSION_DESKTOP=ubuntu XAUTHORITY=/run/user/1000/gdm/Xauthority LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36: GNOME_TERMINAL_SERVICE=:1.402 SSH_AUTH_SOCK=/tmp/ssh-8M0Y14J1z5du/agent.35053 CONDA_PYTHON_EXE=/home/anna/Programy/tangram/bin/python SHELL=/bin/bash QT_ACCESSIBILITY=1 GDMSESSION=ubuntu LESSCLOSE=/usr/bin/lesspipe %s %s CONDA_DEFAULT_ENV=base ACCELRYS_ROOT=/home/anna/Programy/Biovia/Discovery-Studio/bin/.. GPG_AGENT_INFO=/run/user/1000/gnupg/S.gpg-agent:0:1 GJS_DEBUG_OUTPUT=stderr NCIPLOT_HOME=/home/anna/Programy/tangram/etc/nciplot QT_IM_MODULE=ibus PWD=/home/anna/Programy/Biovia/Discovery-Studio/bin XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg CONDA_EXE=/home/anna/Programy/tangram/bin/conda XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop CONDA_PREFIX=/home/anna/Programy/tangram VTE_VERSION=6003 # no early binding unset LD_BIND_NOW # Exec the application with the original command-line args if [ "$ACCELRYS_QUIET" -ne 0 ] ; then $ACCELRYS_EXEC $ACCELRYS_BIN $ACCELRYS_OPTIONS "$@" > /dev/null 2>&1 else $ACCELRYS_EXEC $ACCELRYS_BIN $ACCELRYS_OPTIONS "$@" fi Aborted (core dumped) ------------------------------------------------------------------------- anna@anna:~$ pymol PyMOL(TM) Molecular Graphics System, Version 2.4.0. 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. No module named '_tkinter' Unable to initialize plugin 'energyPlot' (pmg_tk.startup.energyPlot). No module named '_tkinter' Unable to initialize plugin 'apbs_tools' (pmg_tk.startup.apbs_tools). Detected OpenGL version 4.6. Shaders available. Geometry shaders not available Detected GLSL version 4.60. OpenGL graphics engine: GL_VENDOR: Intel GL_RENDERER: Mesa Intel(R) UHD Graphics 620 (WHL GT2) GL_VERSION: 4.6 (Compatibility Profile) Mesa 20.3.0 Naruszenie ochrony pamięci (zrzut pamięci) ------------------------------------------------------------------------- anna@anna:~/Programy/molden/bin$ ./gmolden Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: Naruszenie ochrony pamięci (zrzut pamięci) ------------------------------------------------------------------------- anna@anna:~$ avogadro2 Locale: "pl_PL" translation success "/usr/share/qt5/translations" translation success Extension plugins dynamically found... 22 Checking for "commands" scripts in "/home/anna/.local/share/OpenChemistry/Avogadro/commands" Checking for "commands" scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/commands" Checking for "commands" scripts in "/usr/local/share/OpenChemistry/Avogadro/commands" Checking for "commands" scripts in "/usr/share/OpenChemistry/Avogadro/commands" Checking for "commands" scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/commands" Checking for "commands" scripts in "/usr/bin/../lib/x86_64-linux-gnu/avogadro2/scripts/commands" OBProcess::executeObabel: Running "obabel" "-L formats read" OBProcess::executeObabel: Running "obabel" "-L formats write" OBProcess::executeObabel: Running "obabel" "-L forcefields" OBProcess::executeObabel: Running "obabel" "-V" "obabel" found: "obabel: Open Babel 3.0.0 -- Mar 11 2020 -- 11:52:36" "Navigator" added "Editor" added "Selection" added "Manipulator" added "BondCentric" added "MeasureTool" added "PlayerTool" added Naruszenie ochrony pamięci (zrzut pamięci) ------------------------------------------------------------------------- In /var/crash there is only one relevant crash file and I tried ubuntu-bug YOURFILE.crash but nothing happens, the command just hangs forever. I've tried "https://errors.ubuntu.com/user/ID where ID is the content of file /var/lib/whoopsie/whoopsie-id" but it just says "Sorry, you are not a member of a group that is allowed to see the data from error reports. Please fill out this form to request access." -- You received this bug notification because you are a member of Ubuntu Touch seeded packages, which is subscribed to mesa in Ubuntu. https://bugs.launchpad.net/bugs/1908273 Title: Software stopped working Status in mesa package in Ubuntu: Incomplete Bug description: After update to Ubuntu 20.04.1 LTS some of my software stopped working, all of it is visualization software: VMD, Discovery Studio, PyMOL, Gmolden, Avogadro. ProblemType: Bug DistroRelease: Ubuntu 20.04 Package: xorg 1:7.7+19ubuntu14 ProcVersionSignature: Ubuntu 5.4.0-54.60-generic 5.4.65 Uname: Linux 5.4.0-54-generic x86_64 ApportVersion: 2.20.11-0ubuntu27.13 Architecture: amd64 BootLog: Error: [Errno 13] Brak dostępu: '/var/log/boot.log' CasperMD5CheckResult: skip CompositorRunning: None CurrentDesktop: ubuntu:GNOME Date: Tue Dec 15 14:41:52 2020 DistUpgraded: 2020-11-21 20:16:19,197 ERROR got error from PostInstallScript ./xorg_fix_proprietary.py (g-exec-error-quark: Wykonanie procesu potomnego „./xorg_fix_proprietary.py” (Nie ma takiego pliku ani katalogu) się nie powiodło (8)) DistroCodename: focal DistroVariant: ubuntu ExtraDebuggingInterest: Yes, if not too technical GraphicsCard: Intel Corporation UHD Graphics 620 (Whiskey Lake) [8086:3ea0] (rev 02) (prog-if 00 [VGA controller]) Subsystem: Hewlett-Packard Company UHD Graphics 620 (Whiskey Lake) [103c:8537] InstallationDate: Installed on 2020-05-20 (208 days ago) InstallationMedia: Ubuntu 19.10 "Eoan Ermine" - Release amd64 (20191017) Lsusb: Bus 002 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub Bus 001 Device 003: ID 138a:00ab Validity Sensors, Inc. Bus 001 Device 002: ID 0408:5373 Quanta Computer, Inc. HP HD Camera Bus 001 Device 004: ID 8087:0aaa Intel Corp. Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub MachineType: HP HP ProBook 440 G6 ProcEnviron: TERM=xterm-256color PATH=(custom, no user) XDG_RUNTIME_DIR=<set> LANG=pl_PL.UTF-8 SHELL=/bin/bash ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-5.4.0-54-generic root=UUID=d81f0b8d-3e0f-4039-a46f-5c1c780cac2c ro quiet splash vt.handoff=7 SourcePackage: xorg UpgradeStatus: Upgraded to focal on 2020-11-21 (23 days ago) dmi.bios.date: 04/27/2020 dmi.bios.vendor: HP dmi.bios.version: R71 Ver. 01.11.01 dmi.board.name: 8537 dmi.board.vendor: HP dmi.board.version: KBC Version 51.2A.00 dmi.chassis.asset.tag: 5CD0097RK4 dmi.chassis.type: 10 dmi.chassis.vendor: HP dmi.modalias: dmi:bvnHP:bvrR71Ver.01.11.01:bd04/27/2020:svnHP:pnHPProBook440G6:pvr:rvnHP:rn8537:rvrKBCVersion51.2A.00:cvnHP:ct10:cvr: dmi.product.family: 103C_5336AN HP ProBook dmi.product.name: HP ProBook 440 G6 dmi.product.sku: 5PQ09EA#AKD dmi.sys.vendor: HP version.compiz: compiz N/A version.libdrm2: libdrm2 2.4.101-2 version.libgl1-mesa-dri: libgl1-mesa-dri 20.0.8-0ubuntu1~20.04.1 version.libgl1-mesa-glx: libgl1-mesa-glx 20.0.8-0ubuntu1~20.04.1 version.xserver-xorg-core: xserver-xorg-core 2:1.20.8-2ubuntu2.6 version.xserver-xorg-input-evdev: xserver-xorg-input-evdev N/A version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:19.1.0-1 version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.99.917+git20200226-1 version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:1.0.16-1 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/mesa/+bug/1908273/+subscriptions -- Mailing list: https://launchpad.net/~touch-packages Post to : touch-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~touch-packages More help : https://help.launchpad.net/ListHelp
