Fail to launch SimVascular for linux

Provides a system for patient-specific cardiovascular modeling and simulation.
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Amirtaha Taebi
Posts: 35
Joined: Fri Oct 12, 2018 3:54 pm

Re: Fail to launch SimVascular for linux

Post by Amirtaha Taebi » Thu Mar 28, 2019 7:59 pm

Hi David,

Thanks! I installed the MPI and gfortran as well.

I am sorry. It seems that I did not well explain the case in my previous message. The GUI pops-up when I run simvascular in the command line. I can open a project that I had previously built in my windows machine. I am able to see information about my model (such as caps and faces), mesh, and simulation settings, but I can't see the 3D model and rotate it in the Display window (I can't also see the meshes that I had created before).

Here are the details that appear in my terminal after I run simvascular with MPI and gfortran installed. It seems that I still get some errors from OpenGL (I'm not sure tho).

Code: Select all

mirtatae@petmrrecon:/usr/local$ simvascular
No plugins installed for current SimVascular installed version.
!Thu Mar 28 19:24:13 2019
0.359! WARNING: In load_impl at /usr/local/sv/ext/2019.02/release/gl2/src/mitk-2018.04.0/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.55: cannot open shared object file: No such file or directory
!0.359! WARNING: In AutoLoadModulesFromPath at /usr/local/sv/ext/2019.02/release/gl2/src/mitk-2018.04.0/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /usr/local/sv/simvascular/2019-03-17/svExternals/lib/MitkCore/libMitkCESTIO.so failed.
!0.366! WARNING: In load_impl at /usr/local/sv/ext/2019.02/release/gl2/src/mitk-2018.04.0/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.55: cannot open shared object file: No such file or directory
!0.366! WARNING: In AutoLoadModulesFromPath at /usr/local/sv/ext/2019.02/release/gl2/src/mitk-2018.04.0/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /usr/local/sv/simvascular/2019-03-17/svExternals/lib/MitkCore/libMitkMultilabelIO.so failed.
!0.433! WARNING: In load_impl at /usr/local/sv/ext/2019.02/release/gl2/src/mitk-2018.04.0/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.55: cannot open shared object file: No such file or directory
!0.433! WARNING: In AutoLoadModulesFromPath at /usr/local/sv/ext/2019.02/release/gl2/src/mitk-2018.04.0/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /usr/local/sv/simvascular/2019-03-17/svExternals/lib/MitkCore/libMitkDICOMReaderServices.so failed.
!0.435! WARNING: In load_impl at /usr/local/sv/ext/2019.02/release/gl2/src/mitk-2018.04.0/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.55: cannot open shared object file: No such file or directory
!0.435! WARNING: In AutoLoadModulesFromPath at /usr/local/sv/ext/2019.02/release/gl2/src/mitk-2018.04.0/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /usr/local/sv/simvascular/2019-03-17/svExternals/lib/MitkCore/libMitkDicomRTIO.so failed.
Note: Not using the provisioning file. To use a provisioning file, provide --use-pro flag

Reading custom plugins SV_CUSTOM_PLUGINS environment variable...


Reading plugin paths SV_PLUGIN_PATH environment variable...

   Adding to plugin search path (/usr/local/sv/simvascular/2019-03-17/lib/plugins)
   Adding to plugin search path (/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins)

Checking all plugin paths...

  plugin (org_commontk_configadmin)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_commontk_configadmin.so]
  plugin (org_commontk_eventadmin)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_commontk_eventadmin.so]
  plugin (org_blueberry_core_runtime)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_blueberry_core_runtime.so]
  plugin (org_blueberry_core_expressions)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_blueberry_core_expressions.so]
  plugin (org_blueberry_core_commands)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_blueberry_core_commands.so]
  plugin (org_blueberry_ui_qt)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_blueberry_ui_qt.so]
  plugin (org_blueberry_ui_qt_help)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_blueberry_ui_qt_help.so]
  plugin (org_blueberry_ui_qt_log)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_blueberry_ui_qt_log.so]
  plugin (org_mitk_core_services)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_core_services.so]
  plugin (org_mitk_gui_common)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_common.so]
  plugin (org_mitk_planarfigure)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_planarfigure.so]
  plugin (org_mitk_core_ext)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_core_ext.so]
  plugin (org_mitk_gui_qt_application)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_application.so]
  plugin (org_mitk_gui_qt_ext)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_ext.so]
  plugin (org_mitk_gui_qt_extapplication)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_extapplication.so]
  plugin (org_mitk_gui_qt_common)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_common.so]
  plugin (org_mitk_gui_qt_stdmultiwidgeteditor)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_stdmultiwidgeteditor.so]
  plugin (org_mitk_gui_qt_common_legacy)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_common_legacy.so]
  plugin (org_mitk_gui_qt_datamanager)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_datamanager.so]
  plugin (org_mitk_gui_qt_properties)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_properties.so]
  plugin (org_mitk_gui_qt_basicimageprocessing)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_basicimageprocessing.so]
  plugin (org_mitk_gui_qt_dicom)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_dicom.so]
  plugin (org_mitk_gui_qt_geometrytools)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_geometrytools.so]
  plugin (org_mitk_gui_qt_imagenavigator)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_imagenavigator.so]
  plugin (org_mitk_gui_qt_measurementtoolbox)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_measurementtoolbox.so]
  plugin (org_mitk_gui_qt_python)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_python.so]
  plugin (org_mitk_gui_qt_segmentation)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_segmentation.so]
  plugin (org_mitk_gui_qt_volumevisualization)
    resolves to [/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_volumevisualization.so]
  plugin (org_sv_gui_qt_application)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_application.so]
  plugin (org_sv_projectdatanodes)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_projectdatanodes.so]
  plugin (org_sv_gui_qt_datamanager)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_datamanager.so]
  plugin (org_sv_gui_qt_projectmanager)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_projectmanager.so]
  plugin (org_sv_gui_qt_pathplanning)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_pathplanning.so]
  plugin (org_sv_gui_qt_modeling)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_modeling.so]
  plugin (org_sv_gui_qt_segmentation)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_segmentation.so]
  plugin (org_sv_gui_qt_meshing)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_meshing.so]
  plugin (org_sv_gui_qt_simulation)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_simulation.so]
  plugin (org_sv_gui_qt_imageprocessing)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_imageprocessing.so]
  plugin (org_sv_gui_qt_svfsi)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_svfsi.so]
  plugin (org_sv_pythondatanodes)
    resolves to [/usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_pythondatanodes.so]

!0.695! WARNING: Failed to install plugin  QUrl("file:///usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_dicom.so") : ctkPluginException: Failed to install plugin
        at 0x7f61d63636b6: ctkBackTrace::ctkBackTrace(unsigned long) + 0xa6 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61d637fe57: ctkException::ctkException(QString const&, ctkException const&) + 0x47 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61d638064d: ctkRuntimeException::ctkRuntimeException(QString const&, ctkException const&) + 0x1d in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61ec2091f4: ctkPluginException::ctkPluginException(QString const&, ctkPluginException::Type const&, ctkException const&) + 0x24 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec244c5c: ??? + 0xec244c5c in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec206ab2: ctkPluginContext::installPlugin(QUrl const&, QIODevice*) + 0x32 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec2237fb: ??? + 0xec2237fb in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec221e41: ctkPluginFrameworkLauncher::startup(QRunnable*) + 0x251 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec222379: ctkPluginFrameworkLauncher::run(QRunnable*, QVariant const&) + 0x49 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ebdacd0f: 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 /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libMitkAppUtil.so
        at 0x7f61e9d2a29f: Poco::Util::Application::run() + 0x2f in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libPocoUtil.so.31
        at 0x7f61f8eba312: sv4guiMain(int, char**, bool, bool) + 0x10a2 in /usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_application.so
        at 0x40368c: ??? + 0x40368c in /usr/local/sv/simvascular/2019-03-17/bin/simvascular
        at 0x7f61eea7309b: __libc_start_main + 0xeb in /lib/x86_64-linux-gnu/libc.so.6
        at 0x403c59: ??? + 0x403c59 in /usr/local/sv/simvascular/2019-03-17/bin/simvascular
Caused by: ctkPluginException: The plugin "/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_dicom.so" could not be loaded: Cannot load library /usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_dicom.so: (libMitkDicomRTIO.so: cannot open shared object file: No such file or directory)
        at 0x7f61d63636b6: ctkBackTrace::ctkBackTrace(unsigned long) + 0xa6 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61d637fd8e: ctkException::ctkException(QString const&) + 0x3e in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61d63805fd: ctkRuntimeException::ctkRuntimeException(QString const&) + 0x1d in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61ec209191: ctkPluginException::ctkPluginException(QString const&, ctkPluginException::Type const&) + 0x21 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec24e11b: ??? + 0xec24e11b in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec24fdf1: ??? + 0xec24fdf1 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec25002f: ??? + 0xec25002f in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec2445b8: ??? + 0xec2445b8 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        ... 10 more
!0.704! WARNING: Failed to install plugin  QUrl("file:///usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_segmentation.so") : ctkPluginException: Failed to install plugin
        at 0x7f61d63636b6: ctkBackTrace::ctkBackTrace(unsigned long) + 0xa6 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61d637fe57: ctkException::ctkException(QString const&, ctkException const&) + 0x47 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61d638064d: ctkRuntimeException::ctkRuntimeException(QString const&, ctkException const&) + 0x1d in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61ec2091f4: ctkPluginException::ctkPluginException(QString const&, ctkPluginException::Type const&, ctkException const&) + 0x24 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec244c5c: ??? + 0xec244c5c in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec206ab2: ctkPluginContext::installPlugin(QUrl const&, QIODevice*) + 0x32 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec2237fb: ??? + 0xec2237fb in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec221e41: ctkPluginFrameworkLauncher::startup(QRunnable*) + 0x251 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec222379: ctkPluginFrameworkLauncher::run(QRunnable*, QVariant const&) + 0x49 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ebdacd0f: 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 /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libMitkAppUtil.so
        at 0x7f61e9d2a29f: Poco::Util::Application::run() + 0x2f in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libPocoUtil.so.31
        at 0x7f61f8eba312: sv4guiMain(int, char**, bool, bool) + 0x10a2 in /usr/local/sv/simvascular/2019-03-17/lib/plugins/liborg_sv_gui_qt_application.so
        at 0x40368c: ??? + 0x40368c in /usr/local/sv/simvascular/2019-03-17/bin/simvascular
        at 0x7f61eea7309b: __libc_start_main + 0xeb in /lib/x86_64-linux-gnu/libc.so.6
        at 0x403c59: ??? + 0x403c59 in /usr/local/sv/simvascular/2019-03-17/bin/simvascular
Caused by: ctkPluginException: The plugin "/usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_segmentation.so" could not be loaded: Cannot load library /usr/local/sv/simvascular/2019-03-17/svExternals/lib/plugins/liborg_mitk_gui_qt_segmentation.so: (libicuuc.so.55: cannot open shared object file: No such file or directory)
        at 0x7f61d63636b6: ctkBackTrace::ctkBackTrace(unsigned long) + 0xa6 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61d637fd8e: ctkException::ctkException(QString const&) + 0x3e in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61d63805fd: ctkRuntimeException::ctkRuntimeException(QString const&) + 0x1d in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKCore.so.0.1
        at 0x7f61ec209191: ctkPluginException::ctkPluginException(QString const&, ctkPluginException::Type const&) + 0x21 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec24e11b: ??? + 0xec24e11b in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec24fdf1: ??? + 0xec24fdf1 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec25002f: ??? + 0xec25002f in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        at 0x7f61ec2445b8: ??? + 0xec2445b8 in /usr/local/sv/simvascular/2019-03-17/svExternals/lib/libCTKPluginFramework.so.0.1
        ... 10 more
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
Thu Mar 28 19:24:15 2019 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate, /usr/local/sv/ext/2019.02/release/gl2/build/gnu/5.4/x64/mitk-2018.04.0/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
[0.750] Logfile: /home/mirtatae/.local/share/SimVascular/SimVascularApplication_525109161/data/9/mitk-0.log
[0.783] OpenCASCADE module loaded.
activator.start
[0.899] [BlueBerry] LOG: Warning: Detected recursive attempt by part org.sv.views.datamanager to create itself (this is probably, but not necessarily, a bug)
#1.017# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 469
vtkShaderProgram (0x259db00): Shader object was not initialized, cannot attach it.
#1.116# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 469
vtkShaderProgram (0x2886240): Shader object was not initialized, cannot attach it.
#1.209# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 469
vtkShaderProgram (0x2abffd0): Shader object was not initialized, cannot attach it.
#1.303# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 469
vtkShaderProgram (0x2e30870): Shader object was not initialized, cannot attach it.
[1.442] **** Activating legacy standalone functionality
[1.442] setting active flag
#1.524# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2e30870): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#1.524# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2e30870):
#1.609# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2abffd0): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#1.610# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2abffd0):
#1.693# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2886240): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#1.693# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2886240):
#1.776# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x259db00): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#1.776# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x259db00):
!1.945! WARNING: QObject::connect: No such signal QWebEngineView::linkClicked(const QUrl& )
[1.991] [BlueBerry] BlueBerry Workbench ready
!1.991! WARNING: QXcbConnection: XCB error: 145 (Unknown), sequence: 171, resource id: 0, major code: 139 (Unknown), minor code: 20
#2.039# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2e30870): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.039# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2e30870):
#2.090# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2abffd0): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.090# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2abffd0):
#2.127# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2886240): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.127# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2886240):
#2.166# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x259db00): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.166# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x259db00):
#2.212# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2e30870): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.212# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2e30870):
#2.251# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2abffd0): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.251# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2abffd0):
#2.286# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2886240): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.286# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2886240):
#2.323# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x259db00): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.323# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x259db00):
#2.363# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2e30870): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.363# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2e30870):
#2.401# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2abffd0): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.401# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2abffd0):
#2.435# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x2886240): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.435# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x2886240):
#2.472# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 430
vtkShaderProgram (0x259db00): 1: #version 140
2: #ifdef GL_ES
3: #if __VERSION__ == 300
4: #define attribute in
5: #define varying out
6: #endif // 300
7: #else // GL_ES
8: #define highp
9: #define mediump
10: #define lowp
11: #if __VERSION__ == 150
12: #define attribute in
13: #define varying out
14: #endif
15: #endif // GL_ES
16:
17:
18: /*=========================================================================
19:
20:   Program:   Visualization Toolkit
21:   Module:    vtkPolyData2DVS.glsl
22:
23:   Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
24:   All rights reserved.
25:   See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
26:
27:      This software is distributed WITHOUT ANY WARRANTY; without even
28:      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
29:      PURPOSE.  See the above copyright notice for more information.
30:
31: =========================================================================*/
32:
33: // all variables that represent positions or directions have a suffix
34: // indicating the coordinate system they are in. The possible values are
35: // MC - Model Coordinates
36: // WC - WC world coordinates
37: // VC - View Coordinates
38: // DC - Display Coordinates
39:
40: attribute vec4 vertexWC;
41:
42: // material property values
43: //VTK::Color::Dec
44:
45: // Texture coordinates
46: //VTK::TCoord::Dec
47:
48: // Apple Bug
49: //VTK::PrimID::Dec
50:
51: uniform mat4 WCVCMatrix;  // World to view matrix
52:
53: void main()
54: {
55:   // Apple Bug
56:   //VTK::PrimID::Impl
57:
58:   gl_Position = WCVCMatrix*vertexWC;
59:   //VTK::TCoord::Impl
60:   //VTK::Color::Impl
61: }
62:
#2.472# [VtkError] ERROR: ERROR: In /usr/local/sv/ext/2019.02/release/gl2/src/vtk-8.1.1/Rendering/OpenGL2/vtkShaderProgram.cxx, line 431
vtkShaderProgram (0x259db00):
#3.051# ERROR: Uncaught TypeError: Cannot read property 'appendChild' of null
And here is the Details after I click "Create Data Files for Simulation"
/usr/local/sv/svsolver/2019-02-07/bin/svpre: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
Also, I tried this. I created the "Files for Simulation" in my windows machine and copied/pasted them in the simulation directory in my Linux machine. Then I ran the simulation. It took a second. The popup window says "Job steady: Finished". But there is no folder with the detailed solution in my simulation folder. Here are the details in the popup window:
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------

/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/usr/local/sv/svsolver/2019-02-07/bin/svsolver: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
Thank you very much.
Your help and time is so much appreciated.
Amirtaha

User avatar
David Parker
Posts: 1736
Joined: Tue Aug 23, 2005 2:43 pm

Re: Fail to launch SimVascular for linux

Post by David Parker » Thu Mar 28, 2019 9:16 pm

Hi Amirtaha,

The svpre and svsolver problems are caused by missing gfortran3 libraries. I instructed you to install the wrong library, sorry! You need to install the gfortran3 library using sudo apt-get install gfortran3.

For the libicuuc.so.55 warning install using sudo apt-get install libicu-dev.

I'm not sure what's going on with the OpenGL error, maybe update your graphics card drivers?

Do this:

1) sudo apt install mesa-utils
2) glxinfo | grep -i opengl

Post the output of 2) please.

Cheers,
Dave

User avatar
Amirtaha Taebi
Posts: 35
Joined: Fri Oct 12, 2018 3:54 pm

Re: Fail to launch SimVascular for linux

Post by Amirtaha Taebi » Fri Mar 29, 2019 11:49 am

Hi David,

Thanks for your help. Here is what I did and what I got.

I tried sudo apt-get install gfortran3 but it couldn't locate it. I installed sudo apt-get install libgfortran3 instead. I had libicu-dev installed already. After this, I gave it a try. Now, it created the files for simulation successfully. But it couldn't run the simulation. I tried with 1, 16, 24, 36, and 40 processors, respectively. It didn't work. Here is a sample of Details in the popup window after I ran the simulation on 16 processors.

Code: Select all

he process ID for myrank (0) is (33820).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33826).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 

The process ID for myrank (0) is (33762).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33772).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33775).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33787).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33791).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33792).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33804).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33806).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33816).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation

 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33830).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33840).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based

The process ID for myrank (0) is (33844).


The number of processes is 1.

 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 DensitySolver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep Default Input File: Not Setup.

: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible Time Integration Rule: Second Order

 Time Step Size: 0.1
 Number of Timesteps Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3

 Print Error Indicators: False
 Number of Force Surfaces: 1
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
: Implicit
 Number of RCR Surfaces:  Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 Density: 1.06
 Viscosity: 0.04 RCR Values From File: True
 Backflow Stabilization Coefficient: 
 Solver Type0.2
 Deformable Wall: False
 Residual Control: : svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES SweepTrue
 Residual Criteria: 0.01
 Minimum Required Iterations: : 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
3
 Step Construction: 0 1 0 1
 Solver Task:  Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
Full Simulation

 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


The process ID for myrank (0) is (33849).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 

The process ID for myrank (0) is (33850).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp 
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 Default Input File: Not Setup.
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0

Parameter Values setup as below:
----------------------------------------------
 Equation of State: Incompressible
 Time Step Size: 0.1 Time Varying Boundary Conditions From File: True

 Number of Timesteps: 100
 Viscous Control BCT File Type: DAT
 Number of BCT Files: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1: 1
 BCT Matching Type: Global Node ID

 Surface ID's for Force Calculation: 1
 BCT Time Scale Factor: 1.0
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow:  Equation of State: Incompressible
0
 Density: 1.06
 Time Step Size: 0.1
 Viscosity: 0.04
 Number of Timesteps: 100
 Solver Type: svLS
 svLS Type: NS Viscous Control: Viscous
 Number of Timesteps between Restarts: 5

 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations:  Print Average Solution: True
 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
Print Error Indicators: False
 Number of Force Surfaces:  Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 1
 Surface ID's for Force Calculation: 1400
 Time Integration Rule
 Force Calculation Method: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow:  Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
0
 Density: 1.06
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling:  Viscosity: 0.04
Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File Solver Type: svLS
: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 100
 Number of Solves per Left-hand-side Formation: 1: 3
 Step Construction: 0 1 0 1
 Solver Task: 
 Tolerance on Momentum Equations: 0.05
 Full Simulation

Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation

 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 
 
 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.
 


Here is the output of 2:
mirtatae@petmrrecon:~$ glxinfo | grep -i opengl
OpenGL vendor string: VMware, Inc.
OpenGL renderer string: llvmpipe (LLVM 7.0, 256 bits)
OpenGL version string: 3.1 Mesa 18.2.8
OpenGL shading language version string: 1.40
OpenGL context flags: (none)
OpenGL extensions:
Thank you very much,
Amirtaha

User avatar
Amirtaha Taebi
Posts: 35
Joined: Fri Oct 12, 2018 3:54 pm

Re: Fail to launch SimVascular for linux

Post by Amirtaha Taebi » Fri Mar 29, 2019 12:40 pm

I also tried running the simulation directly from the command line. It gives me the same output.

Code: Select all

mirtatae@petmrrecon:~/research/Patient5_cm/Simulations/steady$ mpiexec -n 1 /usr/local/sv/svsolver/2019-02-07/svsolver solver.inp

The process ID for myrank (0) is (4127).


The number of processes is 1.

Solver Input Files listed as below:
------------------------------------
 Local Config: solver.inp
 Default Input File: Not Setup.

Parameter Values setup as below:
----------------------------------------------
 Time Varying Boundary Conditions From File: True
 BCT File Type: DAT
 Number of BCT Files: 1
 BCT Matching Type: Global Node ID
 BCT Time Scale Factor: 1.0
 Equation of State: Incompressible
 Time Step Size: 0.1
 Number of Timesteps: 100
 Viscous Control: Viscous
 Number of Timesteps between Restarts: 5
 Print Average Solution: True
 Print Error Indicators: False
 Number of Force Surfaces: 1
 Surface ID's for Force Calculation: 1
 Force Calculation Method: Velocity Based
 Apply Wall Deformation: False
 Number of Surfaces which Output Pressure and Flow: 0
 Density: 1.06
 Viscosity: 0.04
 Solver Type: svLS
 svLS Type: NS
 Number of Krylov Vectors per GMRES Sweep: 100
 Number of Solves per Left-hand-side Formation: 1
 Tolerance on Momentum Equations: 0.05
 Tolerance on Continuity Equations: 0.4
 Tolerance on svLS NS Solver: 0.4
 Maximum Number of Iterations for svLS NS Solver: 1
 Maximum Number of Iterations for svLS Momentum Loop: 2
 Maximum Number of Iterations for svLS Continuity Loop: 400
 Time Integration Rule: Second Order
 Time Integration Rho Infinity: 0.5
 Flow Advection Form: Convective
 Quadrature Rule on Interior: 2
 Quadrature Rule on Boundary: 3
 Number of Elements Per Block: 255
 Number of Coupled Surfaces: 46
 Pressure Coupling: Implicit
 Number of RCR Surfaces: 46
 List of RCR Surfaces: 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
 RCR Values From File: True
 Backflow Stabilization Coefficient: 0.2
 Deformable Wall: False
 Residual Control: True
 Residual Criteria: 0.01
 Minimum Required Iterations: 3
 Step Construction: 0 1 0 1
 Solver Task: Full Simulation


 Fatal: Total Element Block Allocation Exceeded.
 Use more processors for this problem or modify MAXBLK in the code.

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David Parker
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Re: Fail to launch SimVascular for linux

Post by David Parker » Fri Mar 29, 2019 1:21 pm

Hi Amirtaha,

For the solver failing it looks like MPI is not working correctly: "The number of processes is 1.", this should be 16. I've seen that when I have ParaView installed it messes up my MPI installation. Try setting your mpiexec path in SV Preferences to /usr/bin/mpiexec.hydra.

As for the OpenGL problem, the OpenGL renderer string: llvmpipe you got means that your GPU hardware acceleration is disabled and you are using the CPU for graphics. See https://bugs.launchpad.net/ubuntu/+sour ... ug/1752938. What graphics card are you using?

Cheers,
Dave

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Amirtaha Taebi
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Joined: Fri Oct 12, 2018 3:54 pm

Re: Fail to launch SimVascular for linux

Post by Amirtaha Taebi » Sat Mar 30, 2019 10:13 am

Hi David,

I followed your recipe for the solver and it worked. I'm running a simulation and once its done I will post the result if it worked fine. Thank you very much.

About the OpenGL thing, my installed GPU is nvidia k80. The driver version is 396.44. The GPU is already enable for Tensorflow. I found that k80 is not on the list of OpenGL support. Is there a way to make OpenGL to use k80 or the on-board display unit?
https://developer.nvidia.com/opengl-driver


Thanks,
Amirtaha

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David Parker
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Re: Fail to launch SimVascular for linux

Post by David Parker » Sat Mar 30, 2019 12:37 pm

Hi Amirtaha,

Good that the solver is working! The next SimVascular release will help identify problems with finding solver binaries, MPI implementation, etc.

The Nvidea Tesla K80 is a compute device and does not support graphics. Do you have a graphics card installed? Post what you see in your computer's Settings->Details page and what is output by the command grep -i chipset /var/log/Xorg.0.log. It might be that you have the wrong driver or mesa installed.

Cheers,
Dave

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Amirtaha Taebi
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Re: Fail to launch SimVascular for linux

Post by Amirtaha Taebi » Sat Mar 30, 2019 6:43 pm

Hi David,

I'm using a cluster and I can access it just through command line. Is there a command that I can use instead?

This is the output by the command grep -i chipset /var/log/Xorg.0.log:
[ 31.348] (II) NOUVEAU driver for NVIDIA chipset families :
[ 31.348] (II) VESA: driver for VESA chipsets: vesa

Thanks,
Amirtaha

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David Parker
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Re: Fail to launch SimVascular for linux

Post by David Parker » Mon Apr 01, 2019 8:22 am

Hi Amirtaha,

I am a bit confused here! You need to run SimVascular (not the solver) on a workstation or laptop that has a display and graphics card. It will not run on a cluster I think, unless you are doing some sort of distributed rendering, setting the the X server up to do that.

Cheers,
Dave

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Amirtaha Taebi
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Re: Fail to launch SimVascular for linux

Post by Amirtaha Taebi » Mon Apr 01, 2019 11:29 am

Hi David,

Sorry, I needed to be more careful about the words that I used.

The server is a stand-alone server, not in a cluster. You can think of it as a Ubuntu PC but no direct screen attached to it. It has nvidia K80 GPU although we only use it for deep learning. The server is designed to run computational jobs. So no desktop environment is installed.

Thanks,
Amirtaha

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