Help regarding MITK - AIAA
ivanwilliammd opened this issue · 5 comments
ivanwilliammd commented
Hello, I'm currently having problem installing MITK 2018.04.2 http://www.mitk.org/download/releases/MITK-2018.04.2/Nvidia/Linux/
May I ask what is the prerequisite for AIAA Client and how to install it?
I already install nvidia-docker2, and have NGC account what is the next step?
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-root'
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
Sel Jul 30 18:53:23 2019 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate, /home/kislinsk/MITK-superbuild/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
[Tue Jul 30 18:53:23 2019
0.404] Logfile: /home/ivanwilliam/.local/share/DKFZ/MITK Workbench_737102135/data/9/mitk-0.log
[0.517] [BlueBerry] LOG: Warning: Detected recursive attempt by part org.mitk.views.datamanager to create itself (this is probably, but not necessarily, a bug)
!1.071! 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.
[0730/185324.247955:WARNING:stack_trace_posix.cc(699)] Failed to open file: /tmp/.glnL7i5O (deleted)
Error: No such file or directory
[0730/185324.247981:WARNING:stack_trace_posix.cc(699)] Failed to open file: /home/ivanwilliam/.glvnd5jOSUp (deleted)
Error: No such file or directory
[12376:12376:0730/185324.315885:ERROR:zygote_host_impl_linux.cc(90)] Running as root without --no-sandbox is not supported. See https://crbug.com/638180.
Received signal 11 SEGV_MAPERR 000000000008
#0 0x7feadede3d2f <unknown>
#1 0x7feadd80cb9d <unknown>
#2 0x7feadede423e <unknown>
#3 0x7feb25583f20 <unknown>
#4 0x7feb25f78404 QReadWriteLock::lockForRead()
#5 0x7feb1ea587e6 QSqlDatabase::contains()
#6 0x7feb25307856 ctkPluginStorageSQL::getConnection()
#7 0x7feb25307d11 ctkPluginStorageSQL::close()
#8 0x7feb25308060 ctkPluginStorageSQL::~ctkPluginStorageSQL()
#9 0x7feb252cd5e6 ctkPluginFrameworkContext::uninit()
#10 0x7feb252cc630 ctkPluginFrameworkFactory::~ctkPluginFrameworkFactory()
#11 0x7feb252e2ac4 QScopedPointer<>::~QScopedPointer()
#12 0x7feb25588615 __cxa_finalize
#13 0x7feb252b0ee3 <unknown>
r8: 0000000002a8434c r9: 00007feb268c7120 r10: 00000000029f0998 r11: 000000000000004e
r12: 00000000028a1080 r13: 0000000002321d90 r14: 0000000001e6ac70 r15: 00007fff6cc5df90
di: 0000000000000008 si: 0000000000000002 bp: 0000000000000000 bx: 0000000000000008
dx: 0000000000000001 ax: 0000000000000000 cx: 00007feb268c67a0 sp: 00007fff6cc5de30
ip: 00007feb25f78404 efl: 0000000000010246 cgf: 002b000000000033 erf: 0000000000000006
trp: 000000000000000e msk: 0000000000001000 cr2: 0000000000000008
[end of stack trace]
Calling _exit(1). Core file will not be generated.
System information:
OS: Ubuntu 18.04 LTS,
Hardware: Palit RTX 2080 8GB, 32GB RAM DDR4, Intel i7-8700,
NVIDIA driver:418.67
CUDA: 10.1
Tue Jul 30 18:56:02 2019
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 418.67 Driver Version: 418.67 CUDA Version: 10.1 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 GeForce RTX 2080 Off | 00000000:01:00.0 On | N/A |
| 30% 39C P8 21W / 225W | 251MiB / 7949MiB | 6% Default |
+-------------------------------+----------------------+----------------------+
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2019 NVIDIA Corporation
Built on Wed_Apr_24_19:10:27_PDT_2019
Cuda compilation tools, release 10.1, V10.1.168
Best regards,
Ivan WH
SachidanandAlle commented
I see the problem is related to OpenGL and dependencies. @kislinsk can you please help
And meanwhile @ivanwilliammd you can try using Windows/Mac version of MITK and configure AIAA server IP and verify NVIDIA actions
For AIAA Client, you can build it from source, or you can download binaries from https://github.com/NVIDIA/ai-assisted-annotation-client/releases and install
It installs library and few tools to get hands on experience for NVIDIA APIs defined (like segmentation, dextr3d, models etc...) and for C++, I guess there should not be any dependency requirement. If you are looking to build from source, then you can follow: https://docs.nvidia.com/clara/aiaa/sdk-api/docs/build.html
kislinsk commented
@ivanwilliammd also wrote into our bug tracker. I recommended to run the Workbench as non-root user as the line of interest seems to be [12376:12376:0730/185324.315885:ERROR:zygote_host_impl_linux.cc(90)] Running as root without --no-sandbox is not supported. See https://crbug.com/638180.
I also agree that the OpenGL environment or driver installation may not be in a clean state.
ivanwilliammd commented
Thank you @kislinsk & @SachidanandAlle , I have try run it without root and the error shown below
May I ask, how can I start OpenGL environment & driver installation in a clean state, what version of driver and CUDA needed for this apps?
$ sh MitkWorkbench.sh
!Tue Jul 30 19:26:00 2019
0.384! WARNING: Startup error: ctkPluginDatabaseException: ctkPluginFramework: Insufficient permissions to write to database: /home/ivanwilliam/.local/share/DKFZ/MITK Workbench_737102135/plugins.db
at 0x7f6a6b36f646: ctkBackTrace::ctkBackTrace(unsigned long) + 0xa6 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKCore.so.0.1
at 0x7f6a6b38ba2e: ctkException::ctkException(QString const&) + 0x3e in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKCore.so.0.1
at 0x7f6a6b38c29d: ctkRuntimeException::ctkRuntimeException(QString const&) + 0x1d in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKCore.so.0.1
at 0x7f6a715703c1: ctkPluginDatabaseException::ctkPluginDatabaseException(QString const&, ctkPluginDatabaseException::Type const&) + 0x21 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f6a715b05fa: ??? + 0x715b05fa in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f6a715b2057: ??? + 0x715b2057 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f6a715b78c3: ??? + 0x715b78c3 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f6a71577c1a: ??? + 0x71577c1a in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f6a71572b81: ctkPluginFramework::start(QFlags<ctkPlugin::StartOption> const&) + 0xf1 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f6a71589f6a: ctkPluginFrameworkLauncher::startup(QRunnable*) + 0x21a in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f6a7158a4d9: ctkPluginFrameworkLauncher::run(QRunnable*, QVariant const&) + 0x49 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f6a72d10bdf: mitk::BaseApplication::main(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) + 0x15f in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libMitkAppUtil.so
at 0x7f6a712ff2ff: Poco::Util::Application::run() + 0x2f in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libPocoUtil.so.60
at 0x401199: ??? + 0x401199 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/MitkWorkbench
at 0x7f6a71c31b97: __libc_start_main + 0xe7 in /lib/x86_64-linux-gnu/libc.so.6
at 0x401259: ??? + 0x401259 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/MitkWorkbench
Aborted (core dumped)
Meanwhile adding --Blueberry.clean show this error
$ sh MitkWorkbench.sh --BlueBerry.clean
!Tue Jul 30 19:35:44 2019
0.388! WARNING: Startup error: ctkPluginDatabaseException: ctkPluginFramework: Insufficient permissions to write to database: /home/ivanwilliam/.local/share/DKFZ/MITK Workbench_737102135/plugins.db
at 0x7f1e2a511646: ctkBackTrace::ctkBackTrace(unsigned long) + 0xa6 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKCore.so.0.1
at 0x7f1e2a52da2e: ctkException::ctkException(QString const&) + 0x3e in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKCore.so.0.1
at 0x7f1e2a52e29d: ctkRuntimeException::ctkRuntimeException(QString const&) + 0x1d in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKCore.so.0.1
at 0x7f1e307123c1: ctkPluginDatabaseException::ctkPluginDatabaseException(QString const&, ctkPluginDatabaseException::Type const&) + 0x21 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f1e307525fa: ??? + 0x307525fa in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f1e30754057: ??? + 0x30754057 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f1e307598c3: ??? + 0x307598c3 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f1e30719c1a: ??? + 0x30719c1a in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f1e30714b81: ctkPluginFramework::start(QFlags<ctkPlugin::StartOption> const&) + 0xf1 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f1e3072bf6a: ctkPluginFrameworkLauncher::startup(QRunnable*) + 0x21a in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f1e3072c4d9: ctkPluginFrameworkLauncher::run(QRunnable*, QVariant const&) + 0x49 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libCTKPluginFramework.so.0.1
at 0x7f1e31eb2bdf: mitk::BaseApplication::main(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) + 0x15f in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libMitkAppUtil.so
at 0x7f1e304a12ff: Poco::Util::Application::run() + 0x2f in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/libPocoUtil.so.60
at 0x401199: ??? + 0x401199 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/MitkWorkbench
at 0x7f1e30dd3b97: __libc_start_main + 0xe7 in /lib/x86_64-linux-gnu/libc.so.6
at 0x401259: ??? + 0x401259 in /home/ivanwilliam/MITK-v2018.04.2-linux-x86_64/bin/MitkWorkbench
Aborted (core dumped)
I already try downloading binaries from https://github.com/NVIDIA/ai-assisted-annotation-client/releases and install the sh package using this instruction (https://docs.nvidia.com/clara/sdk-api/docs/quickstart.html) but I can't seem to run it.
Best regards
kislinsk commented
As you tried to start the Workbench as root first, it cannot access its files now that were created as root. Do:
sudo rm -rf /home/ivanwilliam/.local/share/DKFZ
./MitkWorkbench.sh
If you still get an error try to ./MitkWorkbench.sh one more time.
ivanwilliammd commented
Marvelous, that solve my problem. Thanks a lot @kislinsk