Installing in Ubuntu 22.04 potential errors and solutions.

Provides a system for patient-specific cardiovascular modeling and simulation.
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Ignacio Bartol
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Installing in Ubuntu 22.04 potential errors and solutions.

Post by Ignacio Bartol » Mon Aug 19, 2024 7:16 am

Hi all,

As recommended per Dave Parker, I am posting this suggestion originally posted on the project GitHub here.
The latest release is intended to support Ubuntu up to 20.04, and some problems may arise while trying to execute in Ubuntu 22.04. I will reproduce the errors after installation but before execution and after execution below. Specially a warning in execution may cause the SimVascular to not load DICOM files, which is the first step in the pipeline most likely.

Errors after installation before execution
1. Error message `libXss.so.1: cannot open shared object file: No such file or directory.` Solution:

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sudo apt-get install libxss1
2. Error message `libsmime3.so: cannot open shared object file: No such file or directory` Solution:

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sudo apt-get install libnss3
3. Error message `libasound.so.2: cannot open shared object file: No such file or directory` Solution:

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sudo apt-get install libasound2
4. Error message `libasound.so.2: cannot open shared object file: No such file or directory` Solution:

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sudo apt-get install libasound2
After doing that the program executed with some warnings that I am detailing below.

Errors after installation and after execution

The error below was causing SimVascular to not properly load a DICOM file because the MitkDICOM associated plugins were not loading.

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!1.139! WARNING: In load_impl at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.66: cannot open shared object file: No such file or directory                                                
!1.139! WARNING: In AutoLoadModulesFromPath at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /usr/local/sv/simvascular/2023-03-27/svExternals/lib/MitkCore/libMitkDICOMReaderServices.so failed.                                                                                                                   
!1.142! WARNING: In load_impl at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.66: cannot open shared object file: No such file or directory                                               

!1.142! WARNING: In AutoLoadModulesFromPath at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /usr/local/sv/simvascular/2023-03-27/svExternals/lib/MitkCore/libMitkCESTIO.so failed.                                                                                                                                 
!1.269! WARNING: In load_impl at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.66: cannot open shared object file: No such file or directory                                               

!1.269! WARNING: In AutoLoadModulesFromPath at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /usr/local/sv/simvascular/2023-03-27/svExternals/lib/MitkCore/libMitkMultilabelIO.so failed.                                                                                                                           
!1.273! WARNING: In load_impl at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.66: cannot open shared object file: No such file or directory                                               

!1.273! WARNING: In AutoLoadModulesFromPath at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /usr/local/sv/simvascular/2023-03-27/svExternals/lib/MitkCore/libMitkDicomRTIO.so failed.                                                                                                                              
!1.277! WARNING: In load_impl at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.66: cannot open shared object file: No such file or directory                                               

!1.277! WARNING: In AutoLoadModulesFromPath at /usr/local/sv/ext/2019.06/release/gl2/src/mitk-2018.04.2/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /usr/local/sv/simvascular/2023-03-27/svExternals/lib/MitkCore/libMitkDICOMQIIO.so failed.
This solution worked for me:

First open the sources list:

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sudo gedit /etc/apt/sources.list
Then add the Ubuntu 20 packages as a source by copying the following text to that file:

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deb http://security.ubuntu.com/ubuntu focal-security main
Then update and install the desired package:

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sudo apt-get update

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sudo apt-get install libicu66
Another error also raised when trying to run a simulation using the SvSolver `error while loading shared libraries: libvtkIOXML-7.1.so.7.1p: cannot open shared object file: No such file or directory`

What worked for me was installing the following shared library:

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sudo apt-get install libvtk7.1p
Expected behavior
I don't think there will be an easy solution to find missing packages during installation since it's very OS dependent, but I wanted to post this here in case anyone else is running into the same trouble.

Desktop (please complete the following information):
- Linux ta1302000242 5.15.153.1-microsoft-standard-WSL2 # 1 SMP Fri Mar 29 23:14:13 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
- Distributor ID: Ubuntu
Description: Ubuntu 22.04.3 LTS
Release: 22.04
Codename: jammy
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