simtk.org

Posted: **Thu Nov 09, 2017 3:19 pm**

Hi everyone,

I seem to be having some difficulty with installing on Ubuntu as well. The package downloads fine, but upon running issues a few warnings then an abort trap on a line that reads

Code: Select all

case "$SV_BATCH_MODE" in

Output follows. I also tried building from source on ubuntu. It compiles, but then fails when run similarly in the start-up script.

Is there anything you would suggest trying please?

Thank you,
Alex

Code: Select all

argc 1


 *** simvascularApp: initializeLibraryPaths! *** 


Warning:  SV_PLUGIN_PATH doesn't exist!

Adding to plugin search path (/usr/local/sv/simvascular/2017-08-14/Bin/plugins)
Adding to plugin search path (/usr/local/sv/simvascular/2017-08-14/Bin/lib/plugins)
Adding to plugin search path (/usr/local/sv/simvascular/2017-08-14/Bin/plugins)
Adding to plugin search path (/usr/local/sv/simvascular/2017-08-14/Bin/bin/plugins)
Adding to plugin search path (/usr/local/sv/simvascular/2017-08-14/Bin/lib/plugins)
!Thu Nov  9 12:50:22 2017 
0.111! WARNING: The plugin liborg_mitk_gui_qt_registration.so was not found in /usr/local/sv/simvascular/2017-08-14/sv_externals/lib/plugins
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
Thu Nov 9 12:50:23 2017 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate, /usr/local/sv/ext/build/gnu-4.8/x64/mitk-2016.03/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
[0.604] Logfile: /home/alex/.local/share/SimVascular/SimVascularApplication_1918439754/data/9/mitk-0.log
[0.787] OpenCASCADE module loaded.
/usr/local/sv/simvascular/2017-08-14/simvascular: line 90: 25148 Aborted                 (core dumped) $SV_HOME/Bin/simvascular $*

Posted: **Fri Nov 10, 2017 9:27 am**

Hi again Alex,

Sounds like SimVascular doesn't want to make it easy on you

What version of ubuntu is this?

Is the output that you posted where it is crashing? I don't see where it is crashing on the SV_BATCH_MODE line.

Also, how are you starting SimVascular from the downloaded package? Have you tried both clicking the icon and running from command line?

Thanks!

SimVascular Development Team

Posted: **Fri Nov 10, 2017 11:28 am**

Hi Adam,

Ubuntu version is 14.04.5. It is a Marsden lab machine that I have not used for anything besides trying to install SimVascular when my mac was complaining, so I'm not sure of its overall status.

The SV_BATCH_MODE is what is on line 90 in the script simvascualar, which it seemed to suggest from the second to last line of the terminal output:

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/usr/local/sv/simvascular/2017-08-14/simvascular: line 90: 25148 Aborted                 (core dumped)

Both clicking and command line with the prebuilt give the line 90 message.

I will not worry about this for now with the mac one working (unless you think it is cause for concern) and possibly do a fresh ubuntu install or something.

Thank you,
Alex

Posted: **Sun Nov 12, 2017 5:29 pm**

Hello Alex,

I just tried installing the SimVascular binary release on a clean release of Ubutu 14.04.5 in a virtual machine. It installs and runs without any problems, so your computer must have some other software installed that is causing the problem.

The software should install in /usr/local/sv, so you could check this directory to see if there is extraneous files installed as this could be one potential source of problems. You could try:

% rm -Rf /usr/local/sv
% rm -Rf ~/.local/share/SimVascular

Make sure both directories are completely uninstalled and then try again. Also check /usr/local/bin to see if there are any pointers to old installations of SV since this is a Marsden lab machine.

Nathan
SimVascular Developer Team

simtk.org

Errors on ubuntu install

Errors on ubuntu install

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Re: Errors on ubuntu install

Re: Errors on ubuntu install