# CMB 3D modeling

**URL:** <https://discourse.kitware.com/t/cmb-3d-modeling/1254>\
**Category:** Computational Model Builder (CMB)\
**Created:** [March 18, 2024, 8:24pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254 "2024-03-18T20:24:02Z")\
**Posts on this page:** 20\
**Page:** 2

<div class="post-metadata">

**Author:** ![Tomas\_Ribeiro](https://discourse.kitware.com/letter_avatar_proxy/v4/letter/t/b2d939/32.png) [@Tomas\_Ribeiro](https://discourse.kitware.com/u/Tomas_Ribeiro)\
**Post date:** [April 11, 2024, 2:41am UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/21 "2024-04-11T02:41:58Z")

</div>

Hi @johnt and @aron.helser. Thank you so much for the time spent helping me try to build the super build. I ran the command successfully:

```auto
cmake -GNinja -DUSE_SYSTEM_qt5=ON -DQt5_DIR=../../Qt5.15/5.15.2/gcc_64/lib/cmake/Qt5

```

I assume we have to run this command inside the source directory, since it is the only one which contains the CMakeLists.txt file.

Is there any other step that I need to take before I can build the CMB SuperBuild?

I apologize for replying so late,  
Best,  
Tomas

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 11, 2024, 1:17pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/22 "2024-04-11T13:17:01Z")

</div>

Hi Tomas.

1. No, you should **run cmake in the build directory** NOT the source directory. CMake will generate all of the build files for the compiler & linker. Pass in the path to the source directory as the final argument.

2. After you run cmake in the build directory, then run ninja in the same directory. That should start a long process of building all of the dependency libraries first, then the cmb project, which builds modelbuilder.

So the steps should be:

```auto
> cd <build-directory>
> rm -rf . # clear out everything already there
> cmake -GNinja -DUSE_SYSTEM_qt5=ON -DQt5_DIR=../../Qt5.15/5.15.2/gcc_64/lib/cmake/Qt5 <path-to-source-directory>
> ninja

```

On my linux machine, the build (ninja) takes nearly an hour, so be patient. If there is an error somewhere, we’ll want to look at the messages dumped to the terminal.

---

<div class="post-metadata">

**Author:** ![Tomas\_Ribeiro](https://discourse.kitware.com/letter_avatar_proxy/v4/letter/t/b2d939/32.png) [@Tomas\_Ribeiro](https://discourse.kitware.com/u/Tomas_Ribeiro)\
**Post date:** [April 11, 2024, 5:04pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/23 "2024-04-11T17:04:54Z")

</div>

HI @johnt. Following your steps, the command:

```auto
rm -rf .

```

Was not working, however, this one did:

```auto
rm -rf ./*

```

Continuing the process, everything went correctly, except the last step, which gives me this error:

```auto
ninja: error: loading 'build.ninja': No such file or directory

```

Sorry about all the trouble,  
Tomas

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 11, 2024, 5:42pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/24 "2024-04-11T17:42:39Z")

</div>

Ah, yes, I should have written `rm -rf *` to clear the build directory.

And I’m presuming you did this **before** running cmake 🙂

Running cmake should generate the `build.ninja` file among lots of other files. If that is not the case, please post the terminal messages from the cmake command.

---

<div class="post-metadata">

**Author:** ![Tomas\_Ribeiro](https://discourse.kitware.com/letter_avatar_proxy/v4/letter/t/b2d939/32.png) [@Tomas\_Ribeiro](https://discourse.kitware.com/u/Tomas_Ribeiro)\
**Post date:** [April 11, 2024, 5:45pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/25 "2024-04-11T17:45:11Z")

</div>

I ran the cmake command:

```auto
cmake -GNinja -DUSE_SYSTEM_qt5=ON -DQt5_DIR=../../Qt5.15/5.15.2/gcc_64/lib/cmake/Qt5 ../cmb-superbuild/

```

Before running ninja. I tried doing it again, but it´s giving me the same error.

@johnt I noticed this message after running the cmake command (Build files have been written to: /home/tomas/test-cmb/cmb-superbuild). Is this supposed to happen? I assume the files should be written to the build directory, and not the source directory.

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 11, 2024, 6:22pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/26 "2024-04-11T18:22:29Z")

</div>

Sorry, ignore my message about directories.

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 11, 2024, 7:15pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/27 "2024-04-11T19:15:39Z")

</div>

Can you post the directory contents after running cmake? that is, run

`> ls -al`

I would also be interested in confirming the output from the cmake command.

---

<div class="post-metadata">

**Author:** ![Tomas\_Ribeiro](https://discourse.kitware.com/letter_avatar_proxy/v4/letter/t/b2d939/32.png) [@Tomas\_Ribeiro](https://discourse.kitware.com/u/Tomas_Ribeiro)\
**Post date:** [April 11, 2024, 7:21pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/28 "2024-04-11T19:21:57Z")

</div>

Hi @johnt, after running the command, I get this:

```auto
total 8
drwxr-xr-x 2 tomas tomas 4096 Apr 11 12:57 .
drwxr-xr-x 4 tomas tomas 4096 Apr 4 14:36 ..

```

And the output from the cmake command is:

```auto
CMake Warning at superbuild/CMakeLists.txt:72 (message):
  Forcing CMAKE_POSITION_INDEPENDENT_CODE to be ON as required by
  BUILD_SHARED_LIBS.

-- found package: ace3p
-- found package: aeva
-- found package: cmb2d
-- found package: mb-docker
-- found package: modelbuilder
-- found package: truchas
-- found package: windtunnel
-- Default package: <none>
-- Determined source version for cmb: 23.01.100
-- Determined source version for smtk: 24.01.101
-- Determined source version for paraview: 5.11.0
-- Determined source version for vtk: 9.0.0
-- Enabling cxx11 for: eigen, nlohmannjson, pegtl, pybind11, smtk, smtkresourcemanagerstate
-- Enabling boost for: cmb, paraview, smtk, smtkresourcemanagerstate
-- Enabling eigen for: moab, smtk
-- Enabling zlib for: freetype, hdf5, libarchive, netcdf, paraview, png, python3
-- Enabling szip for: hdf5
-- Enabling hdf5 for: moab, netcdf, smtk
-- Enabling netcdf for: moab, paraview, smtk
-- Enabling moab for: cmb, smtk
-- Enabling nlohmannjson for: cmb, smtk
-- Enabling bzip2 for: libarchive, python3
-- Enabling png for: freetype, paraview, python3
-- Enabling ffi for: python3
-- Enabling sqlite for: python3
-- Enabling python3 for: cmb, pybind11, pythonsetuptools
-- Enabling freetype for: paraview
-- Enabling qt5 as requested.
-- Enabling paraview for: cmb, smtkresourcemanagerstate
-- Enabling pythonsetuptools for: pybind11
-- Enabling pybind11 for: cmb
-- Enabling libxml2 for: libarchive
-- Enabling libarchive for: smtk, smtkresourcemanagerstate
-- Enabling pegtl for: smtk
-- Enabling smtk as requested.
-- Enabling smtkresourcemanagerstate as requested.
-- Enabling cmb as requested.
-- Building projects: cxx11, boost, eigen, zlib, szip, hdf5, netcdf, moab, nlohmannjson, bzip2, png, ffi, sqlite, python3, freetype, qt5, paraview, pythonsetuptools, pybind11, libxml2, libarchive, pegtl, smtk, smtkresourcemanagerstate, cmb
-- Configuring done
-- Generating done
-- Build files have been written to: /home/tomas/test-cmb/cmb-superbuild

```

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 11, 2024, 7:29pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/29 "2024-04-11T19:29:56Z")

</div>

So cmake says it is writing files:

> [@Tomas\_Ribeiro](#):
>
> `-- Build files have been written to: /home/tomas/test-cmb/cmb-superbuild`

but when you go to that directory it’s empty? Maybe there is something about WSL, but this is very strange.

Maybe we need to do some sanity checks to confirm that cmake generates files on WSL. Let me look at the cmake docs and see if we can run a simple experiment.

---

<div class="post-metadata">

**Author:** ![gustafson](https://discourse.kitware.com/user_avatar/discourse.kitware.com/gustafson/32/916_2.png) [@gustafson](https://discourse.kitware.com/u/gustafson)\
**Post date:** [April 11, 2024, 7:30pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/30 "2024-04-11T19:30:19Z")

</div>

Hi @johnt,

I’m working with @Tomas_Ribeiro. Many thanks for trying to help. FYI we’ve tried on several machines (and on both ubuntu and gentoo).

```console
git clone https://gitlab.kitware.com/cmb/cmb-superbuild.git                                                                                                                                                                          
cd cmb-superbuild/                                                                                                                                                                                                                   
git checkout v23.01.0                                                                                                                                                                                                                
git submodule update --init                                                                                                                                                                                                          
                                                                                                                                                                                                                                     
cd ..                                                                                                                                                                                                                                
mkdir build                                                                                                                                                                                                                          
cd build                                                                                                                                                                                                                             
                                                                                                                                                                                                                                     
cmake -GNinja -Wno-dev \                                                                                                                                                                                                             
    -DBUILD_TESTING=0 \                                                                                                                                                                                                              
    -DDEVELOPER_MODE_cmb=1 \                                                                                                                                                                                                         
    -DDEVELOPER_MODE_smtk=1 \                                                                                                                                                                                                        
    -DENABLE_DOCUMENTATION=0 \                                                                                                                                                                                                       
    -DUSE_SYSTEM_boost=1 \                                                                                                                                                                                                           
    -DUSE_SYSTEM_bzip2=1 \                                                                                                                                                                                                           
    -DUSE_SYSTEM_freetype=1 \                                                                                                                                                                                                        
    -DUSE_SYSTEM_hdf5=0 \                                                                                                                                                                                                            
    -DUSE_SYSTEM_libxml2=1 \                                                                                                                                                                                                         
    -DUSE_SYSTEM_netcdf=0 \                                                                                                                                                                                                          
    -DUSE_SYSTEM_pkgconf=1 \                                                                                                                                                                                                         
    -DUSE_SYSTEM_png=1 \                                                                                                                                                                                                             
    -DUSE_SYSTEM_python3=0 \                                                                                                                                                                                                         
    -DUSE_SYSTEM_qt5=1 \                                                                                                                                                                                                             
    -DENABLE_qt5=0 \                                                                                                                                                                                                                 
    -DUSE_SYSTEM_sqlite=0 \                                                                                                                                                                                                          
    -DUSE_SYSTEM_zlib=1 \                                                                                                                                                                                                            
    -DENABLE_pythonsetuptoolsscm=1 \                                                                                                                                                                                                 
    -DCMAKE_INSTALL_PREFIX=/home/pete/local \                                                                                                                                                                                        
    -DENABLE_vtk=1 \                                                                                                                                                                                                                 
    ../cmb-superbuild/                                                                                                                                                                                                               

```

This attempt to build fails on vtk:

```auto
FAILED: VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkSEPReader.cxx.o 
/usr/bin/c++ -DIOImage_EXPORT -Dkiss_fft_scalar=double -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/IO/Image -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Common/Core -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/Core -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Common/ExecutionModel -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/ExecutionModel -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Common/DataModel -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/DataModel -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Common/Math -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/Math -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/kissfft/vtkkissfft -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/kissfft/vtkkissfft -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Common/Transforms -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/Transforms -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Imaging/Core -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Imaging/Core -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Common/Misc -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/Misc -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Common/System -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/System -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Utilities/DICOMParser -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Utilities/DICOMParser -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/jpeg/vtkjpeg -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/jpeg/vtkjpeg -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Utilities/MetaIO/vtkmetaio -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Utilities/MetaIO/vtkmetaio -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/pugixml/vtkpugixml -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/pugixml/vtkpugixml -I/home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/tiff/vtktiff/libtiff -I/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/tiff/vtktiff/libtiff -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Utilities/KWIML -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Utilities/KWIML -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Utilities/KWSys -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Utilities/KWSys -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/kissfft -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/kissfft -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/jpeg -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/jpeg -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/Utilities/MetaIO -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Utilities/MetaIO -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/png -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/png -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/pugixml -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/pugixml -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/tiff -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/tiff -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/build/VTK/ThirdParty/zlib -isystem /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/ThirdParty/zlib -march=core2 -mno-avx512f -fPIC -std=c++11 -O3 -DNDEBUG -std=c++11 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkSEPReader.cxx.o -MF VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkSEPReader.cxx.o.d -o VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkSEPReader.cxx.o -c /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.cxx
In file included from /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.cxx:16:
/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.h:34:6: warning: elaborated-type-specifier for a scoped enum must not use the ‘class’ keyword
   34 | enum class EndiannessType : std::uint8_t
      | ~~~~^~~~~
      | -----
/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.h:34:12: error: use of enum ‘EndiannessType’ without previous declaration
   34 | enum class EndiannessType : std::uint8_t
      | ^ ~~~~~~~~~~~~~
/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.h:34:27: error: expected unqualified-id before ‘:’ token
   34 | enum class EndiannessType : std::uint8_t
      | ^
/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.h:106:19: error: ‘int32_t’ is not a member of ‘std’; did you mean ‘int32_t’?
  106 | std::array<std::int32_t, 6> ComputeExtent() const;
      | ^ ~~~~~~
In file included from /usr/include/sys/types.h:155,
                 from /usr/include/stdlib.h:514,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/cstdlib:79,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/ext/string_conversions.h:43,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/bits/basic_string.h:4109,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/string:54,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/bits/locale_classes.h:40,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/bits/ios_base.h:41,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/ios:44,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/istream:40,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/fstream:40,
                 from /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/Core/vtkIOStream.h:29,
                 from /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/Core/vtkSystemIncludes.h:39,
                 from /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/Core/vtkIndent.h:28,
                 from /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/Core/vtkObjectBase.h:53,
                 from /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/Core/vtkObject.h:45,
                 from /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/Common/ExecutionModel/vtkExtentTranslator.h:29,
                 from /home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.h:24:
/usr/include/bits/stdint-intn.h:26:19: note: ‘int32_t’ declared here
   26 | typedef __int32_t int32_t;
      | ^ ~~~~~~
/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.h:106:19: error: ‘int32_t’ is not a member of ‘std’; did you mean ‘int32_t’?
  106 | std::array<std::int32_t, 6> ComputeExtent() const;
      | ^ ~~~~~~
/usr/include/bits/stdint-intn.h:26:19: note: ‘int32_t’ declared here
   26 | typedef __int32_t int32_t;
      | ^ ~~~~~~
/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.h:106:29: error: template argument 1 is invalid

SNIPPED

      | ^ ~~~~~~~~~
/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.cxx:536:34: error: ‘DataFormatType’ has not been declared
  536 | else if (this->DataFormat == DataFormatType::XDR_DOUBLE)
      | ^ ~~~~~~~~~~~~~
/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.cxx: In member function ‘void vtkSEPReader::ReadDataPiece(FILE*, char*&, vtkIdType, vtkIdType)’:
/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.cxx:556:76: error: ‘class vtkSEPReader’ has no member named ‘DataFormat’
  556 | std::size_t len = details::DataFormatSize[static_cast<std::size_t>(this->DataFormat)];
      | ^ ~~~~~~~~~
[2713/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkNIFTIImageReader.cxx.o
[2714/20955] Generating the wrap hierarchy for VTK::IOImage
[2715/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkPNGWriter.cxx.o
[2716/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkVolumeReader.cxx.o
[2717/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkSLCReader.cxx.o
[2718/20955] Building C object VTK/ThirdParty/jpeg/vtkjpeg/CMakeFiles/jpeg.dir/jchuff.c.o
[2719/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkMedicalImageProperties.cxx.o
[2720/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkTGAReader.cxx.o
[2721/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkTIFFWriter.cxx.o
[2722/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkVolume16Reader.cxx.o
[2723/20955] Building CXX object VTK/Imaging/Hybrid/CMakeFiles/ImagingHybrid.dir/vtkBooleanTexture.cxx.o
[2724/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkOMETIFFReader.cxx.o
[2725/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkPNGReader.cxx.o
[2726/20955] Building CXX object VTK/Imaging/Hybrid/CMakeFiles/ImagingHybrid.dir/vtkCheckerboardSplatter.cxx.o
[2727/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkNrrdReader.cxx.o
[2728/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkTIFFReader.cxx.o
[2729/20955] Building CXX object VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkImageReader.cxx.o
ninja: build stopped: subcommand failed.
CMake Error at /home/pete/software/kitware-stuff/build/superbuild/sb-paraview-build.cmake:47 (message):
  Failed with exit code 1

ninja: build stopped: subcommand failed.

```

It seems a problem with vtk (maybe and gcc13?) rather than CMB. Any thoughts on that? I’ve truncated the error due to character limits. I can send more it its useful.

Many thanks,  
Pete

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 11, 2024, 8:53pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/31 "2024-04-11T20:53:51Z")

</div>

Thanks for the report Pete. We haven’t seen this error before. It might be related to gcc13. I talked to our VTK folks and they would like see if you can generate the preprocessor output. To do that, we are asking you to:

1. cd to `<build-directory>/superbuild/paraview/build`

2. Rerun that very long compile command (that begins `/usr/bin/c++ `) with one substitution:

- Near the end of the command, remove the part that sets the output: `-o VTK/IO/Image/CMakeFiles/IOImage-objects.dir/vtkSEPReader.cxx.o`
- Replace that text with `-o preproc.txt -E`

3. That should generate a `preproc.txt` in the build directory. Please post the file here.

I hope my instructions are clear.

---

<div class="post-metadata">

**Author:** ![dcthomp](https://discourse.kitware.com/user_avatar/discourse.kitware.com/dcthomp/32/10_2.png) [@dcthomp](https://discourse.kitware.com/u/dcthomp)\
**Post date:** [April 12, 2024, 2:21pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/32 "2024-04-12T14:21:43Z")

</div>

@gustafson I believe I have [seen this error before](https://stackoverflow.com/questions/20459120/elaborated-type-specifier-for-a-scoped-enum-must-not-use-the-class-keyword). Try adding

```cpp
#include <cstddef>

```

to the top of `/home/pete/software/kitware-stuff/build/superbuild/paraview/src/VTK/IO/Image/vtkSEPReader.h` with the other includes. If that fixes things, it has already been fixed in a newer version of VTK and ParaView than CMB uses by default. gcc13 is indeed more strict about defining things only in one system header and not unnecessarily including others.

---

<div class="post-metadata">

**Author:** ![gustafson](https://discourse.kitware.com/user_avatar/discourse.kitware.com/gustafson/32/916_2.png) [@gustafson](https://discourse.kitware.com/u/gustafson)\
**Post date:** [April 13, 2024, 3:46pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/33 "2024-04-13T15:46:20Z")

</div>

Hi David,

Thanks for this tip. I feel like we’ve made progress. I was able to get vtk to build, but it took some work. I had to explore several tagged versions before I found one that seemed buildable based on the error messages I found. (This was tag v9.2.5). Based on that tag, I applied the following patch:

```auto
diff --git a/IO/Image/vtkSEPReader.h b/IO/Image/vtkSEPReader.h
index a7d8aad151..73f8200969 100644
--- a/IO/Image/vtkSEPReader.h
+++ b/IO/Image/vtkSEPReader.h
@@ -27,6 +27,8 @@
 
 #include <array> // for std::array
 #include <string> // for std::string
+#include <cstddef> // Added by Pete
+#include <cstdint> // Added by Pete
 
 namespace details
 {
diff --git a/IO/PIO/PIOData.h b/IO/PIO/PIOData.h
index 8eddfb5b92..c6ccdd8e8b 100644
--- a/IO/PIO/PIOData.h
+++ b/IO/PIO/PIOData.h
@@ -12,6 +12,8 @@
 #include <string.h>
 #include <string>
 #include <valarray>
+#include <cstddef> // Added by Pete
+#include <cstdint> // Added by Pete
 
 VTK_ABI_NAMESPACE_BEGIN
 struct Cstring_less
diff --git a/Rendering/Matplotlib/vtkMatplotlibMathTextUtilities.h b/Rendering/Matplotlib/vtkMatplotlibMathTextUtilities.h
index cbccd727dd..c227336c3f 100644
--- a/Rendering/Matplotlib/vtkMatplotlibMathTextUtilities.h
+++ b/Rendering/Matplotlib/vtkMatplotlibMathTextUtilities.h
@@ -50,6 +50,8 @@
 #include "vtkRenderingMatplotlibModule.h" // For export macro
 
 #include <vector> // for std::vector
+#include <cstddef> // Added by Pete
+#include <cstdint> // Added by Pete
 
 struct _object;
 typedef struct _object PyObject;
diff --git a/ThirdParty/libproj/vtklibproj/src/proj_json_streaming_writer.hpp b/ThirdParty/libproj/vtklibproj/src/proj_json_streaming_writer.hpp
index 6267684218..ae1f391f5f 100644
--- a/ThirdParty/libproj/vtklibproj/src/proj_json_streaming_writer.hpp
+++ b/ThirdParty/libproj/vtklibproj/src/proj_json_streaming_writer.hpp
@@ -33,6 +33,8 @@
 
 #include <vector>
 #include <string>
+#include <cstddef> // Added by Pete
+#include <cstdint> // Added by Pete
 
 #define CPL_DLL
 
diff --git a/ThirdParty/vtkm/vtkvtkm/vtk-m b/ThirdParty/vtkm/vtkvtkm/vtk-m
index 618c40a91b..cfd6d3fbe5 160000
--- a/ThirdParty/vtkm/vtkvtkm/vtk-m
+++ b/ThirdParty/vtkm/vtkvtkm/vtk-m
@@ -1 +1 @@
-Subproject commit 618c40a91b9085e279e0103e97c8dfd1114665b3
+Subproject commit cfd6d3fbe534343d217c2dce47a46763692db0ec

```

After that, vtk built to the end, and the superbuild claimed to be finished.

Unfortunately, CMB modelbuilder itself is not built. Here is a log, with ‘Up-to-date’ messages suppressed.

```auto
pete@pilot ~/software/kitware-stuff/build $ grep -v 'Up-to-date' log.txt 
[1/16] Performing update step (git update) for 'paraview'
[2/16] Skipping patch step (no custom command) for 'paraview'
[3/16] Performing update step (git update) for 'cmbworkflows'
HEAD is now at 69561d6 Merge branch 'migrate-ace3p-truchas' into 'master'
[4/16] Skipping patch step (no custom command) for 'cmbworkflows'
[5/16] No configure step for 'cmbworkflows'
[6/16] No build step for 'cmbworkflows'
[7/16] Performing install step for 'cmbworkflows'
[8/16] Completed 'cmbworkflows'
[9/16] Performing configure step for 'paraview'
Not searching for unused variables given on the command line.
-- Using 'QtHelp' without 'QtWebEngine' will ignore embedded javascript and *.js files for documentation
-- VTK version: 9.2.5-1970-g6fc11578d8
CMake Warning (dev) at /usr/share/cmake/Modules/CMakeDependentOption.cmake:89 (message):
  Policy CMP0127 is not set: cmake_dependent_option() supports full Condition
  Syntax. Run "cmake --help-policy CMP0127" for policy details. Use the
  cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
  VTK/Common/Core/CMakeLists.txt:47 (cmake_dependent_option)
This warning is for project developers. Use -Wno-dev to suppress it.

-- Unable to determine HDF5 C flags from HDF5 wrapper.
-- Unable to determine HDF5 C version_var from HDF5 wrapper.
CMake Deprecation Warning at ThirdParty/QtTesting/vtkqttesting/CMakeLists.txt:2 (CMAKE_MINIMUM_REQUIRED):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- Enabled modules: VTK(162), ParaView(49 + 8)
-- Configuring done (4.7s)
-- Generating done (2.7s)
-- Build files have been written to: /home/pete/software/kitware-stuff/build/superbuild/paraview/build
[10/16] Performing build step for 'paraview'
[1/6] Generating Fortran dyndep file Clients/Catalyst/CMakeFiles/Catalyst-objects.dir/Fortran.dd
[2/6] Generating Fortran dyndep file Clients/PythonCatalyst/CMakeFiles/PythonCatalyst-objects.dir/Fortran.dd
[3/6] Automatic MOC and UIC for target paraview
[4/5] Building CXX object Clients/ParaView/CMakeFiles/paraview.dir/ParaViewMainWindow.cxx.o
[5/5] Linking CXX executable bin/paraview
[11/16] Performing install step for 'paraview'
[0/1] Install the project...
-- Install configuration: "Release"
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/vtk/VTK-vtk-module-properties.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/vtk/vtk-prefix.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/vtk/VTK-vtk-module-find-packages.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/ParaView-vtk-module-properties.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/ParaViewClients-vtk-module-properties.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/SLACTools-vtk-module-properties.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/SLACTools-vtk-module-find-packages.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/ParaViewPlugins-paraview-plugin-properties.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/vtk/vtkmodules-vtk-python-module-properties.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/paraview.modules-vtk-python-module-properties.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/bin/paraview
-- Set non-toolchain portion of runtime path of "/home/pete/software/kitware-stuff/build/install/bin/paraview" to "$ORIGIN/../lib"
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/paraview-prefix.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/ParaView-vtk-module-find-packages.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/ParaView-client-xml.cmake
[12/16] Completed 'paraview'
[13/16] No configure step for 'vtk'
[14/16] No build step for 'vtk'
[15/16] No install step for 'vtk'
[16/16] Completed 'vtk'

```

Suspecting I might not have configured correctly, I found that indeed CMB should be enabled:

```auto
pete@pilot ~/software/kitware-stuff/build $ grep -i enable CMakeCache.txt |grep -i cmb
ENABLE_cmb:BOOL=ON
ENABLE_cmbusersguide:BOOL=OFF
ENABLE_cmbworkflows:BOOL=1

```

FWIW Enabling ENABLE\_cmbusersguide didn’t make a difference.

Subsequently, thinking HDF5 might be the issue, I made sure to enable everything with HDF5 (including removing and recloning, after cmake couldn’t resolve the changes). This again reported the superbuild completing, but didn’t go any further than vtk. Here are the related build flags for cmake.

```auto
pete@pilot ~/software/kitware-stuff/build $ grep -i enable CMakeCache.txt |grep -i -e cmb -e hdf
ENABLE_cmb:BOOL=ON
ENABLE_cmbusersguide:BOOL=OFF
ENABLE_cmbworkflows:BOOL=1
ENABLE_hdf5:BOOL=ON
ENABLE_hdf5cpp:BOOL=ON
//MODIFIED property for variable: ENABLE_hdf5cpp
ENABLE_hdf5cpp-MODIFIED:INTERNAL=ON

```

Am I missing something that would cause modelbuilder to be built? Again, I appreciate your looking at this. We’re anxious to use cmb within Tomas’s thesis. 🙂

Pete

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 15, 2024, 2:17pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/34 "2024-04-15T14:17:58Z")

</div>

I agree with David that these build problems are likely stemming from the newer, more strict, gcc version. We can start working these issue out, but for expediency, I would suggest building with an Ubuntu 22.04 LTS or Centos7 machine. We build paraview and the other dependencies reliably on those machines.

I should have also pointed you to the list of packages that are needed on the build machine. This link has info for Ubuntu 22.04, Ubuntu 18.04, Centos 7, and ArchLinux: [https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md?ref\_type=heads#dependencies](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md?ref_type=heads#dependencies)

---

<div class="post-metadata">

**Author:** ![gustafson](https://discourse.kitware.com/user_avatar/discourse.kitware.com/gustafson/32/916_2.png) [@gustafson](https://discourse.kitware.com/u/gustafson)\
**Post date:** [April 16, 2024, 2:43pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/35 "2024-04-16T14:43:13Z")

</div>

Hi,

I spooled up a fresh virtual machine with **Ubuntu 22.04.4 LTS** which is using gcc11. I was able to build through vtk.

This got to the **same point** that I’m at now with Ubuntu 23.10 and up-to-date gentoo. None are actually building modelbuilder.

```auto
-- Installing: /home/pete/software/kitware-stuff/build/install/lib/cmake/paraview-5.11/ParaView-client-xml.cmake
-- Installing: /home/pete/software/kitware-stuff/build/install/share/licenses/ParaView/Copyright.txt
-- Installing: /home/pete/software/kitware-stuff/build/install/share/licenses/ParaView/License_v1.2.txt
[16/16] Completed 'vtk'
pete@ubuntu2204pilot:~/software/kitware-stuff/build$ ls install/bin/
2to3 idle3 pvdataserver python3.9 vtkWrapClientServer-pv5.11
2to3-3.9 idle3.9 pvpython python3.9-config vtkWrapHierarchy-pv5.11
bsdcat nc-config pvrenderserver python3-config vtkWrapJava-pv5.11
bsdcpio paraview pvserver smTestDriver-pv5.11 vtkWrapPythonInit-pv5.11
bsdtar paraview.conf pybind11-config sqlite3 vtkWrapPython-pv5.11
h5cc paraview-config pydoc3 vtkParseJava-pv5.11
h5hlcc pip3 pydoc3.9 vtkProbeOpenGLVersion-pv5.11
h5minfo pip3.9 python vtkProcessXML-pv5.11
h5mvalidate pvbatch python3 vtkprotoc-pv5.11

```

Could you peak at my cmake config command above to see if there is something I have left out wrt modelbuilder itself?

FWIW I’m documenting my build, so I’ll be able to make a comprehensive post on building in these environments if/when we get through this.

Thanks again,  
Pete

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 16, 2024, 2:57pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/36 "2024-04-16T14:57:11Z")

</div>

That’s great, Pete. We’ve got some VTK work to do here regarding 23.10, but as to building modelbuilder:

I suspect the reason modelbuilder didn’t build is because you set developer mode on for both smtk and cmb. If that was some directions I gave previously, I apologize. You should instead turn both of those off, rerun cmake and rerun ninja.

> [@gustafson](#):
>
> ```auto
> cmake -GNinja -Wno-dev \                                                                                                                                                                                                             
> -DBUILD_TESTING=0 \                                                                                                                                                                                                              
> -DDEVELOPER_MODE_cmb=1 \                                                                                                                                                                                                         
> -DDEVELOPER_MODE_smtk=1 \                                                                                                                                                                                                        
>   
> 
> ```

---

<div class="post-metadata">

**Author:** ![gustafson](https://discourse.kitware.com/user_avatar/discourse.kitware.com/gustafson/32/916_2.png) [@gustafson](https://discourse.kitware.com/u/gustafson)\
**Post date:** [April 16, 2024, 8:37pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/37 "2024-04-16T20:37:36Z")

</div>

I’ve done that, and smtk build is now erroring out on not finding the “units” package.

```auto
cd /home/pete/software/kitware-stuff/build/superbuild/smtk/build && /usr/bin/cmake -P /home/pete/software/kitware-stuff/build/superbuild/sb-smtk-configure.cmake && /usr/bin/cmake -E touch /home/pete/software/kitware-stuff/build/superbuild/smtk/stamp/smtk-configure
Not searching for unused variables given on the command line.
CMake Error at CMakeLists.txt:357 (find_package):
  By not providing "Findunits.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "units", but
  CMake did not find one.

  Could not find a package configuration file provided by "units" with any of
  the following names:

    unitsConfig.cmake
    units-config.cmake

  Add the installation prefix of "units" to CMAKE_PREFIX_PATH or set
  "units_DIR" to a directory containing one of the above files. If "units"
  provides a separate development package or SDK, be sure it has been
  installed.

-- Configuring incomplete, errors occurred!
See also "/home/pete/software/kitware-stuff/build/superbuild/smtk/build/CMakeFiles/CMakeOutput.log".
CMake Error at /home/pete/software/kitware-stuff/build/superbuild/sb-smtk-configure.cmake:47 (message):
  Failed with exit code 1

[23/35] Completed 'vtk'
ninja: build stopped: subcommand failed.

```

Can you confirm that this is the correct source library? The superbuild hasn’t pulled anything.

> **[GitHub - nholthaus/units: a compile-time, header-only, dimensional analysis...](https://github.com/nholthaus/units)**
>
> a compile-time, header-only, dimensional analysis and unit conversion library built on c++14 with no dependencies. - nholthaus/units

Also, is there an ubuntu package for this? I can’t seem to find it if there is. Thanks,

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 17, 2024, 12:42am UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/38 "2024-04-17T00:42:54Z")

</div>

I don’t know what went wrong here.

1. No, `units` is not the github project you indicated. It’s one of the packages that is built by cmb-superbuild. (fyi its repository is at [https://gitlab.kitware.com/units/units](https://gitlab.kitware.com/units/units))

2. When you reran cmake, “units” should have been in the list of packages written to the terminal. On my machine, that list is

```auto
-- Building projects: cxx11, boost, eigen, zlib, szip, bzip2, png, ffi, sqlite, xz, python3, hdf5, netcdf, moab, nlohmannjson, freetype, qt5, paraview, pythonsetuptools, pybind11, libxml2, libarchive, pegtl, units, fmt, smtk, cmb

```

(`units` is fourth from the last) Would you rerun cmake and compare with this list?

3. If the `units` project was configured by cmake, you will find a folder at `<build-directory>/superbuild/units`. And if the build completed, the “missing” `unitsConfig.cmake` file will be at `<build-directory>/install/lib/cmake/units-23.05.0/unitsConfig.cmake`.

---

<div class="post-metadata">

**Author:** ![gustafson](https://discourse.kitware.com/user_avatar/discourse.kitware.com/gustafson/32/916_2.png) [@gustafson](https://discourse.kitware.com/u/gustafson)\
**Post date:** [April 17, 2024, 1:47pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/39 "2024-04-17T13:47:49Z")

</div>

Hmm… no I’m not getting units as a package.

```auto
-- Building projects: cxx11, boost, eigen, zlib, szip, hdf5, netcdf, moab, nlohmannjson, bzip2, png, ffi, sqlite, python3, freetype, qt5, paraview, pythonsetuptools, pybind11, libxml2, libarchive, pegtl, pythonsetuptoolsscm, smtk, cmbworkflows, smtkresourcemanagerstate, cmb, vtk

```

There appears to be some version inconsistency in the superbuild. A challenge I’m sure, with so many dependencies. When I checkout master instead of the v23.01.0, cmake does pickup the units package. I’m trying to build from master now, though I’m hesitant to use that bleeding edge. 🙂

Note your current release branch points to something from 2020 (a version 6). Perhaps that should point to something more recent?

For now, it is building on master branch. I’ll report back.

---

<div class="post-metadata">

**Author:** ![johnt](https://discourse.kitware.com/user_avatar/discourse.kitware.com/johnt/32/147_2.png) [@johnt](https://discourse.kitware.com/u/johnt)\
**Post date:** [April 17, 2024, 2:09pm UTC](https://discourse.kitware.com/t/cmb-3d-modeling/1254/40 "2024-04-17T14:09:33Z")

</div>

Yes, our versioning has not kept up with the development pace.

- So yes, definitely use the cmb-superbuild:master (commit d4d8c364).
- You will also need to run `git submodule update`.
- And be sure to delete the full build tree before rerunning cmake and ninja. Otherwise older project builds will pollute/corrupt things.

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