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Starting second MITK instance fails under GNU/Linux
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Description

Steps to reproduce:

  • Start first instance from CLI: ./MitkWorkbench.sh
  • Start secondary instance from CLI: ./MitkWorkbench.sh --BlueBerry.newInstance

Observed behavior:

  • Second instance crashes during start-up.

Expected behavior:

  • Functional second instance.

During start-up the following is logged to CLI, perhaps this may help uncover the cause:

/MitkWorkbench.sh --BlueBerry.newInstance                                                                                     
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
!Thu Oct 10 12:17:36 2019 
0.109! WARNING: Forcing new application instance. The application data will be written to a temporary directory.
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
do okt. 10 12:17:37 2019 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
[0.726] Logfile: /tmp/MITK Workbench-sIOvsD/data/9/mitk-0.log
[0.865] [BlueBerry] LOG: Warning: Detected recursive attempt by part org.mitk.views.datamanager to create itself (this is probably, but not necessarily, a bug)
!1.297! WARNING: An OpenGL Core Profile was requested, but it is not supported on the current platform. Falling back to a non-Core profile. Note that this might cause rendering issues.
[1010/121737.603857:WARNING:stack_trace_posix.cc(699)] Failed to open file: /home/fvdnabee/#7875212 (deleted)
  Error: No such file or directory
LaunchProcess: failed to execvp:
/home/fvdnabee/Downloads/scratch/MITK-v2018.04.2-linux-x86_64/bin/QtWebEngineProcess
[2589209:2589209:1010/121737.674786:FATAL:zygote_host_impl_linux.cc(199)] Check failed: ReceiveFixedMessage(fds[0], kZygoteBootMessage, sizeof(kZygoteBootMessage), &boot_pid). 
#0 0x7fd176111d2f <unknown>
#1 0x7fd17612d24c <unknown>
#2 0x7fd1756c3243 <unknown>
#3 0x7fd1756c2225 <unknown>
#4 0x7fd17572713d <unknown>
#5 0x7fd17527bc76 <unknown>
#6 0x7fd175281136 <unknown>
#7 0x7fd174bcee58 <unknown>
#8 0x7fd174bd036c <unknown>
#9 0x7fd174bbdc11 <unknown>
#10 0x7fd174bbde17 QtWebEngineCore::WebContentsAdapter::WebContentsAdapter()
#11 0x7fd16d7844b0 QWebEnginePagePrivate::QWebEnginePagePrivate()
#12 0x7fd16d7850c4 QWebEnginePage::QWebEnginePage()
#13 0x7fd16d9b2899 <unknown>
#14 0x7fd194edbd3d <unknown>
#15 0x7fd194ede57d <unknown>
#16 0x7fd19503afdb berry::WorkbenchPartReference::GetPart()
#17 0x7fd194eda568 <unknown>
#18 0x7fd195012012 berry::WorkbenchPage::BusyOpenEditorBatched()
#19 0x7fd1950128ee berry::WorkbenchPage::BusyOpenEditor()
#20 0x7fd195012bd0 berry::WorkbenchPage::OpenEditor()
#21 0x7fd195012d24 berry::WorkbenchPage::OpenEditor()
#22 0x7fd194ffd2dd berry::WorkbenchPage::OpenEditor()
#23 0x7fd194ea0b80 <unknown>
#24 0x7fd194ea1cef <unknown>
#25 0x7fd194e662af berry::WorkbenchWindowAdvisor::OpenIntro()
#26 0x7fd19504f90a berry::WorkbenchWindow::Open()
#27 0x7fd19502512f berry::Workbench::BusyOpenWorkbenchWindow()
#28 0x7fd195025364 berry::Workbench::OpenFirstTimeWindow()
#29 0x7fd194e65ced berry::WorkbenchAdvisor::OpenWindows()
#30 0x7fd195023fcf berry::Workbench::Init()
#31 0x7fd19502411c berry::Workbench::RunUI()
#32 0x7fd1950289a5 berry::Workbench::CreateAndRunWorkbench()
#33 0x7fd16d9ade30 <unknown>
#34 0x7fd194805470 <unknown>
#35 0x7fd1a93246c8 ctkDefaultApplicationLauncher::start()
#36 0x7fd1a93500ae ctkPluginFrameworkLauncher::run()
#37 0x7fd1a9352623 ctkPluginFrameworkLauncher::run()
#38 0x7fd1aa129bdf mitk::BaseApplication::main()
#39 0x7fd1a90c52ff Poco::Util::Application::run()
#40 0x000000401199 <unknown>
#41 0x7fd1a95dc153 __libc_start_main
#42 0x000000401259 <unknown>

Received signal 6
#0 0x7fd176111d2f <unknown>
#1 0x7fd174b3ab9d <unknown>
#2 0x7fd17611223e <unknown>
#3 0x7fd1a95f0fb0 <unknown>
#4 0x7fd1a95f0f25 __GI_raise
#5 0x7fd1a95da897 __GI_abort
#6 0x7fd1761107a9 <unknown>
#7 0x7fd17612d39f <unknown>
#8 0x7fd1756c3243 <unknown>
#9 0x7fd1756c2225 <unknown>
#10 0x7fd17572713d <unknown>
#11 0x7fd17527bc76 <unknown>
#12 0x7fd175281136 <unknown>
#13 0x7fd174bcee58 <unknown>
#14 0x7fd174bd036c <unknown>
#15 0x7fd174bbdc11 <unknown>
#16 0x7fd174bbde17 QtWebEngineCore::WebContentsAdapter::WebContentsAdapter()
#17 0x7fd16d7844b0 QWebEnginePagePrivate::QWebEnginePagePrivate()
#18 0x7fd16d7850c4 QWebEnginePage::QWebEnginePage()
#19 0x7fd16d9b2899 <unknown>
#20 0x7fd194edbd3d <unknown>
#21 0x7fd194ede57d <unknown>
#22 0x7fd19503afdb berry::WorkbenchPartReference::GetPart()
#23 0x7fd194eda568 <unknown>
#24 0x7fd195012012 berry::WorkbenchPage::BusyOpenEditorBatched()
#25 0x7fd1950128ee berry::WorkbenchPage::BusyOpenEditor()
#26 0x7fd195012bd0 berry::WorkbenchPage::OpenEditor()
#27 0x7fd195012d24 berry::WorkbenchPage::OpenEditor()
#28 0x7fd194ffd2dd berry::WorkbenchPage::OpenEditor()
#29 0x7fd194ea0b80 <unknown>
#30 0x7fd194ea1cef <unknown>
#31 0x7fd194e662af berry::WorkbenchWindowAdvisor::OpenIntro()
#32 0x7fd19504f90a berry::WorkbenchWindow::Open()
#33 0x7fd19502512f berry::Workbench::BusyOpenWorkbenchWindow()
#34 0x7fd195025364 berry::Workbench::OpenFirstTimeWindow()
#35 0x7fd194e65ced berry::WorkbenchAdvisor::OpenWindows()
#36 0x7fd195023fcf berry::Workbench::Init()
#37 0x7fd19502411c berry::Workbench::RunUI()
#38 0x7fd1950289a5 berry::Workbench::CreateAndRunWorkbench()
#39 0x7fd16d9ade30 <unknown>
#40 0x7fd194805470 <unknown>
#41 0x7fd1a93246c8 ctkDefaultApplicationLauncher::start()
#42 0x7fd1a93500ae ctkPluginFrameworkLauncher::run()
#43 0x7fd1a9352623 ctkPluginFrameworkLauncher::run()
#44 0x7fd1aa129bdf mitk::BaseApplication::main()
#45 0x7fd1a90c52ff Poco::Util::Application::run()
#46 0x000000401199 <unknown>
#47 0x7fd1a95dc153 __libc_start_main
#48 0x000000401259 <unknown>
  r8: 0000000000000000  r9: 00007ffe25101fa0 r10: 0000000000000008 r11: 0000000000000246
 r12: 00007fd1a997f3c0 r13: 00007ffe25102450 r14: 00000000000000b0 r15: 00007fd1a997e700
  di: 0000000000000002  si: 00007ffe25101fa0  bp: 00007ffe251021f0  bx: 00007fd19dd857c0
  dx: 0000000000000000  ax: 0000000000000000  cx: 00007fd1a95f0f25  sp: 00007ffe25101fa0
  ip: 00007fd1a95f0f25 efl: 0000000000000246 cgf: 002b000000000033 erf: 0000000000000000
 trp: 0000000000000000 msk: 0000000000001000 cr2: 0000000000000000
[end of stack trace]
Calling _exit(1). Core file will not be generated.

MITK version: 2018.04.2 release
OS: Linux 5.3.4-arch1-1-ARCH with gnome 3.34 (wayland)
OpenGL info (from glxinfo):

Extended renderer info (GLX_MESA_query_renderer):
    Vendor: Intel Open Source Technology Center (0x8086)
    Device: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2)  (0x5917)
    Version: 19.2.0
    Accelerated: yes
    Video memory: 3072MB
    Unified memory: yes
    Preferred profile: core (0x1)
    Max core profile version: 4.5
    Max compat profile version: 3.0
    Max GLES1 profile version: 1.1
    Max GLES[23] profile version: 3.2
OpenGL vendor string: Intel Open Source Technology Center
OpenGL renderer string: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) 
OpenGL core profile version string: 4.5 (Core Profile) Mesa 19.2.0
OpenGL version string: 3.0 Mesa 19.2.0

I'd welcome any suggestions to help diagnose this issue.

Event Timeline

Note: on another computer (running Ubuntu + 1080ti's with nvidia 430.50 drivers), MITK with newInstance also falls backs to a non core profile but the second instance does start successfully.
I'm thinking that maybe my system is missing a library or that it is related to the MESA drivers for intel's UHD?

Firstly, thank you very much for the detailed and complete bug report. It really is a pleasure to have all information without asking for every detail.

Secondly, a side note for myself: strip the debug information from the official release builds. :-)

We will try to reproduce your bug at least on Ubuntu machines and other officially supported operating sytstems but I'm afraid we cannot provide a smooth support for other distributions as it would open the flood gates for all kinds of distro-related specifics that we simply do not have the resources to support even if we wanted to.

Works for me on various Ubuntu machines and Windows.

Thank you for your efforts. I completely understand your decision with regards to Ubuntu as the main Linux platform. When I have time I'll try to start MITK from an Ubuntu live CD on this machine and report my findings here. One remark: if the issue in MITK is due to an issue with an upstream version of MITK dependencies (or system libraries), then we might encounter this issue in future versions of Ubuntu.

One question: what GFX hardware and software was in your linux testing system? Was this testing done in a VM or on 'raw' machine? Perhaps this issue is related to intel UHD and a (newer) version of Mesa or some other OpenGL component? The live CD experiment should help here. Which ubuntu version did you test with (18.04 or newer)?

I tested with Ubuntu 16.04 in VM and also on a Ubuntu 18.04 host. Nvidia graphics.

In the past there were indeed sometimes issues with MITK running on Intel graphics hardware mostly on notebooks but as far as I remember it was always resolved by updating the driver. In case the machine had Intel AND Nvidia, it helped to force MITK to use the Nvidia graphics in the graphics settings of the driver. Reason for the latter issue is usually lacking OpenGL 3.2+ support on older Intel graphics hardware.

You can also test an MITK 2016.11 installer as the requirement of a newer OpenGL version was introduced in MITK 2018.04 with VTK 8.x.

You can also test an MITK 2016.11 installer as the requirement of a newer OpenGL version was introduced in MITK 2018.04 with VTK 8.x.

The reported issue is absent in the 2016.11 release on my Arch system. I'll test 2018.04.2 later under Ubuntu.
Would it be worth trying a development version of MITK on this system? I understand that there aren't nightly releases nor other dev releases for MITK?

That's a strong indicator that your graphics H/W causes trouble with the "modern" OpenGL version that VTK 8.x requires. I'm open for new ideas but I think this is something that is not fixable other than trying newer drivers or more recent H/W. In theory, everything not older than 6-7years should work with OpenGL 3.2, but as it turned out, there's a lot of fake-compatibility in older drivers.

That said, you will most probably have the same issues with a development version of MITK. MITK Diffusion provides nightly installers: ftp://ftp.dkfz-heidelberg.de/outgoing/MitkDiffusion

kislinsk triaged this task as Normal priority.Nov 4 2019, 9:48 AM