CMB-Superbuild issueshttps://gitlab.kitware.com/cmb/cmb-superbuild/-/issues2024-03-26T17:50:25-04:00https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/130Superbuild fails when linking tbb to ParaView with lld2024-03-26T17:50:25-04:00Jason LuckhardtSuperbuild fails when linking tbb to ParaView with lldUsing lld-17,
Ubuntu 20.04,
GCC 9.4.0,
Superbuilds TBB.
```
[54/81] Performing build step for 'paraview'
FAILED: superbuild/superbuild/paraview/stamp/paraview-build /opt/project/build/superbuild/superbuild/paraview/stamp/paraview-build ...Using lld-17,
Ubuntu 20.04,
GCC 9.4.0,
Superbuilds TBB.
```
[54/81] Performing build step for 'paraview'
FAILED: superbuild/superbuild/paraview/stamp/paraview-build /opt/project/build/superbuild/superbuild/paraview/stamp/paraview-build cd /opt/project/build/superbuild/superbuild/paraview/build && /opt/project/cmake-3.26.4/bin/cmake -P /opt/project/build/superbuild/superbuild/sb-paraview-build.cmake && /opt/project/cmake-3.26.4/bin/cmake -E touch /opt/project/build/superbuild/superbuild/paraview/stamp/paraview-build [1/13500] Building CXX object VTK/Interaction/Widgets/CMakeFiles/InteractionWidgets-objects.dir/vtkAffineRepresentation.cxx.o
[2/13500] Building CXX object VTK/Interaction/Widgets/CMakeFiles/InteractionWidgets-objects.dir/vtkAngleRepresentation.cxx.o
[3/13500] Linking CXX executable bin/vtkProbeOpenGLVersion-pv5.11
FAILED: bin/vtkProbeOpenGLVersion-pv5.11 : && /usr/bin/c++ -march=core2 -mno-avx512f -fPIC -std=c++11 -g -Wl,-lc -Wl,-lc VTK/Rendering/OpenGL2/CMakeFiles/vtkProbeOpenGLVersion.dir/vtkProbeOpenGLVersion.cxx.o -o bin/vtkProbeOpenGLVersion-pv5.11 -Wl,-rpath,"\$ORIGIN/../lib:/opt/project/projectsdk/lib:" lib/libvtkImaging-pv5.11.so.5.11 /opt/project/projectsdk/lib/libpng.so /opt/project/projectsdk/lib/libz.so /opt/project/projectsdk/lib/libz.so lib/libvtkIO-pv5.11.so.5.11 lib/libvtkDICOMParser-pv5.11.so.5.11 lib/libvtkmetaio-pv5.11.so.5.11 lib/libvtktiff-pv5.11.so.5.11 lib/libvtkjpeg-pv5.11.so.5.11 lib/libvtkRenderingHyperTreeGrid-pv5.11.so.5.11 lib/libvtkRenderingUI-pv5.11.so.5.11 lib/libvtkFilters-pv5.11.so.5.11 lib/libvtkverdict-pv5.11.so.5.11 lib/libvtkfmt-pv5.11.so.5.11 lib/libvtkRendering-pv5.11.so.5.11 /usr/lib/x86_64-linux-gnu/libX11.so lib/libvtkCommon-pv5.11.so.5.11 lib/libvtkpugixml-pv5.11.so.5.11 lib/libvtkloguru-pv5.11.so.5.11 -lpthread /opt/project/projectsdk/lib/libtbb.so.12.5 lib/libvtkkissfft-pv5.11.so.5.11 /usr/lib/x86_64-linux-gnu/libXcursor.so /usr/lib/x86_64-linux-gnu/libXrender.so /usr/lib/x86_64-linux-gnu/libXfixes.so /usr/lib/x86_64-linux-gnu/libX11.so lib/libvtkOpenGL-pv5.11.so.5.11 lib/libvtkglew-pv5.11.so.5.11 /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libOpenGL.so lib/libvtksys-pv5.11.so.5.11 -ldl -Wl,-rpath-link,/opt/project/build/superbuild/superbuild/paraview/build/lib:/opt/project/projectsdk/lib && : /usr/bin/ld: lib/libvtkCommon-pv5.11.so.5.11: undefined reference to `tbb::detail::r1::execute(tbb::detail::d1::task_arena_base&, tbb::detail::d1::delegate_base&)' /usr/bin/ld: lib/libvtkCommon-pv5.11.so.5.11: undefined reference to `tbb::detail::r1::cancel_group_execution(tbb::detail::d1::task_group_context&)' /usr/bin/ld: lib/libvtkRendering-pv5.11.so.5.11: undefined reference to `tbb::detail::r1::deallocate_memory(void*)' /usr/bin/ld: lib/libvtkRendering-pv5.11.so.5.11: undefined reference to `tbb::detail::r1::cache_aligned_allocate(unsigned long)' /usr/bin/ld: lib/libvtkRendering-pv5.11.so.5.11: undefined reference to `tbb::detail::r1::cache_aligned_deallocate(void*)' /usr/bin/ld: lib/libvtkRendering-pv5.11.so.5.11: undefined reference to `tbb::detail::r1::allocate_memory(unsigned long)' /usr/bin/ld: lib/libvtkRendering-pv5.11.so.5.11: undefined reference to `tbb::detail::r1::execute_and_wait(tbb::detail::d1::task&, tbb::detail::d1::task_group_context&, tbb::detail::d1::wait_context&, tbb::detail::d1::task_group_context&)' /usr/bin/ld: lib/libvtkCommon-pv5.11.so.5.11: undefined reference to `tbb::detail::r1::terminate(tbb::detail::d1::task_arena_base&)'
```https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/120Linux CI runners require LD_LIBRARY_PATH due to Qt2024-01-03T23:12:53-05:00David ThompsonLinux CI runners require LD_LIBRARY_PATH due to QtThe aeva/session (and presumably other repos, hence an issue on cmb-superbuild) require the linux CI runner to have [the LD_LIBRARY_PATH set like so](https://gitlab.kitware.com/aeva/session/-/merge_requests/82/diffs#eb70bee14b9c013767235...The aeva/session (and presumably other repos, hence an issue on cmb-superbuild) require the linux CI runner to have [the LD_LIBRARY_PATH set like so](https://gitlab.kitware.com/aeva/session/-/merge_requests/82/diffs#eb70bee14b9c013767235e58e66b5583fe843077_11_11). This is because the build attempts to run qhelpgenerator and other qt programs that link to the superbuild's libbz2.so which appears to lack an rpath.Ben BoeckelBen Boeckelhttps://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/129pybind11 update for python 3.112023-08-30T11:23:06-04:00Aron Helserpybind11 update for python 3.11Pybind11 was updated in the common superbuild from version 2.9.x to 2.10.x in order to support Python 3.11.
This update caused MacOS x86 test errors, namely:
```
The following tests FAILED:
146 - testImportPythonOperation (SEGFAULT)
...Pybind11 was updated in the common superbuild from version 2.9.x to 2.10.x in order to support Python 3.11.
This update caused MacOS x86 test errors, namely:
```
The following tests FAILED:
146 - testImportPythonOperation (SEGFAULT)
159 - TestManagersAccess (SEGFAULT)
```
This will need to be resolved before updating pybind11 for CMB.https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/110OCCT only uses system fontconfig2023-05-18T14:04:31-04:00Ben BoeckelOCCT only uses system fontconfigThe `occt` package doesn't support custom `fontconfig` package, so it always uses the system copy. We should add `find_package(Fontconfig)` and use it instead of just assuming it is around.
See https://dev.opencascade.org/index.php?q=no...The `occt` package doesn't support custom `fontconfig` package, so it always uses the system copy. We should add `find_package(Fontconfig)` and use it instead of just assuming it is around.
See https://dev.opencascade.org/index.php?q=node/1295 for upstream collaboration here.
Cc: @ryan.krattiger1https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/122Install license files2022-05-17T05:27:01-04:00Ben BoeckelInstall license filesThe superbuild now supports tracking license files of built projects. Use it to inject licenses into the various packages.
Cc: @ryan.krattiger1 @dcthomp @mwestphalThe superbuild now supports tracking license files of built projects. Use it to inject licenses into the various packages.
Cc: @ryan.krattiger1 @dcthomp @mwestphalhttps://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/121On Linux Paraview option CMAKE_INSTALL_RPATH_USE_LINK_PATH set twice2022-02-07T22:06:32-05:00chart3388On Linux Paraview option CMAKE_INSTALL_RPATH_USE_LINK_PATH set twiceWhen compiling on linux the option ```-DCMAKE_INSTALL_RPATH_USE_LINK_PATH``` is set twice in the configure options for ParaView. It is set once to FALSE on [projects/paraview.cmake#L9](projects/paraview.cmake#L9) and then it is also set...When compiling on linux the option ```-DCMAKE_INSTALL_RPATH_USE_LINK_PATH``` is set twice in the configure options for ParaView. It is set once to FALSE on [projects/paraview.cmake#L9](projects/paraview.cmake#L9) and then it is also set to TRUE on [projects/paraview.cmake#L143](projects/paraview.cmake#L143)
You end up with both arguments in the sb-paraview-configure.cmake.https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/117Package logic enforces opencasecasesession to be enabled for cmb2021-07-14T14:39:06-04:00chart3388Package logic enforces opencasecasesession to be enabled for cmbThe package logic in ```packages/modelbuilder/modelbuilder.configure.cmake``` enforces opencascadesession always to be enabled even if I have explicitly passed to CMake to not enable it. There are reasons I want to build CMB but not wit...The package logic in ```packages/modelbuilder/modelbuilder.configure.cmake``` enforces opencascadesession always to be enabled even if I have explicitly passed to CMake to not enable it. There are reasons I want to build CMB but not with opencascadesession but I'm not able to enforce this with this option. Worse yet in the CMakeCache it shows it as off but it is still being enabled.
FYI: @ben.boeckelhttps://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/112python3 on macos does not support ssl2021-06-14T18:26:48-04:00John Tourtellottpython3 on macos does not support sslThis is blocking the SLAC project. It's probably a feature request.
Using the superbuild python3, we cannot connect to https sites in order to submit simulation jobs to NERSC and (someday) AWS. The easiest way to see this is to trying i...This is blocking the SLAC project. It's probably a feature request.
Using the superbuild python3, we cannot connect to https sites in order to submit simulation jobs to NERSC and (someday) AWS. The easiest way to see this is to trying importing the python ssl module into pvpython, e.g.
```
tortuga2:full-superbuild john$ ./install/bin/pvpython
Python 3.8.8 (default, May 15 2021, 20:32:00)
[Clang 10.0.1 (clang-1001.0.46.4)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import ssl
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/john/projects/slac/build/full-superbuild/install/lib/python3.8/ssl.py", line 98, in <module>
import _ssl # if we can't import it, let the error propagate
ModuleNotFoundError: No module named '_ssl'
>>>
```
With nothing to lose, I added `_ssl` to the modules list in the common-superbuild `superbuild_install_superbuild_python3()` but that made no difference.Ryan Krattigerryan.krattiger@kitware.comRyan Krattigerryan.krattiger@kitware.comhttps://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/107Modelbuilder manual tests Mon 08-Feb-20212021-02-11T17:45:56-05:00John TourtellottModelbuilder manual tests Mon 08-Feb-2021Please run ace3p tests of latest modelbuilder packages
* Files are in this folder: https://data.kitware.com/#collection/58fa68228d777f16d01e03e5/folder/6020ccfc2fa25629b94d0aae
* Scripts are at this url: https://johnkit.github.io/ace3p-...Please run ace3p tests of latest modelbuilder packages
* Files are in this folder: https://data.kitware.com/#collection/58fa68228d777f16d01e03e5/folder/6020ccfc2fa25629b94d0aae
* Scripts are at this url: https://johnkit.github.io/ace3p-production/test-pages/
* Download and run Windows
* Then try linux - known issue that ubuntu keypad not working
* Run omega3p, t3p, and track3p testsJae FishJae Fishhttps://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/108Problem with Modelbuilder/macOS packages accessing filesystem2021-02-08T16:16:42-05:00John TourtellottProblem with Modelbuilder/macOS packages accessing filesystemThe symptoms aren't completely characterized, but the primary problem is that the file dialog in the macOS modelbuilder nightly packages does not display most/all of the file system. Using the latest nightly build (08-Feb-2021) (folder h...The symptoms aren't completely characterized, but the primary problem is that the file dialog in the macOS modelbuilder nightly packages does not display most/all of the file system. Using the latest nightly build (08-Feb-2021) (folder https://data.kitware.com/#collection/58fa68228d777f16d01e03e5/folder/6020ccfc2fa25629b94d0aae) the following actions/observations were made:
* Downloaded onto macbook pro running Big Sur (11.1)
* Using, e.g., the File => Open menu brings up a pqFileDialog. In most cases the right-hand part of the dialog is blank.
* Sometimes when clicking the "Desktop" item in the left hand side, a macOS popup appears asking if the user want to grant access to that folder. Selecting the option to permit access does not change the right-hand display - it remains blank.
* The new-file icon works, that is, it creates new folders, however they do not appear in the file dialog (the display remains blank)
* We also downloaded PV 5.9 onto the same machine and did NOT observe these symptoms with that executable.
* We noted that PV 5.9 uses Qt 5.15.1 and the nightly modelbuilder uses Qt 5.15.0https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/84Create RGG package bundle2019-12-17T13:15:50-05:00Ben BoeckelCreate RGG package bundleAdd a mode to the superbuild to make an RGG-centric package. Also add CI for it.
Cc: @bob.obaraAdd a mode to the superbuild to make an RGG-centric package. Also add CI for it.
Cc: @bob.obarahttps://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/80Add sphinx/doxygen as a superbuild project2019-01-02T14:14:10-05:00Haocheng LIUAdd sphinx/doxygen as a superbuild projectPackaging CMB needs superbuild python which prevents it from using
sphinx installed via pip. In order to package cmb with documentation
sphinx/doxygen need to be added as a superbuild project. For now we just disable the doc in cmb night...Packaging CMB needs superbuild python which prevents it from using
sphinx installed via pip. In order to package cmb with documentation
sphinx/doxygen need to be added as a superbuild project. For now we just disable the doc in cmb nightly linux package.https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/75Failed to build gdal using gcc 5.2.12017-11-03T10:01:04-04:00Jean-Christophe Fillion-RobinFailed to build gdal using gcc 5.2.1Building with
```
cd /tmp && \
git clone git@gitlab.kitware.com:cmb/cmb-superbuild.git && \
pushd cmb-superbuild && \
git submodule init ...Building with
```
cd /tmp && \
git clone git@gitlab.kitware.com:cmb/cmb-superbuild.git && \
pushd cmb-superbuild && \
git submodule init && \
git submodule update --recursive && \
popd && \
mkdir cmb-superbuild-build && \
cd cmb-superbuild-build
cmake \
-DUSE_SYSTEM_qt5:BOOL=1 \
-DUSE_SYSTEM_python:BOOL=1 \
-DQt5_DIR:PATH=/home/jcfr/Software/Qt5.9.1/5.9.1/gcc_64/lib/cmake/Qt5 \
-DENABLE_cmbusersguide:BOOL=0 \
-DENABLE_opencv:BOOL=0 \
-DENABLE_smtk:BOOL=0 \
-DENABLE_smtkusersguide:BOOL=0 \
-DBUILD_TESTING:BOOL=0 \
../cmb-superbuild
make -j5
[...]
[ 11%] Performing build step for 'gdal'
CMake Error at /tmp/cmb-superbuild-build/superbuild/gdal/stamp/gdal-build-Release.cmake:16 (message):
Command failed: 1
'/home/jcfr/Software/cmake-3.9.0-Linux-x86_64/bin/cmake' '-P' '/tmp/cmb-superbuild-build/superbuild/sb-gdal-build.cmake'
See also
/tmp/cmb-superbuild-build/superbuild/gdal/stamp/gdal-build-*.log
```
leads to the following error:
```
$ cat /tmp/cmb-superbuild-build/superbuild/gdal/stamp/gdal-build-err.log
In file included from /tmp/cmb-superbuild-build/superbuild/gdal/src/gcore/gdal.h:41:0,
from /tmp/cmb-superbuild-build/superbuild/gdal/src/gcore/gdal_priv.h:53,
from /tmp/cmb-superbuild-build/superbuild/gdal/src/gcore/gdalmajorobject.cpp:30:
/tmp/cmb-superbuild-build/superbuild/gdal/src/port/cpl_port.h:382:12: error: ‘constexpr bool std::isnan(double)’ conflicts with a previous declaration
using std::isnan;
^
In file included from /usr/include/features.h:364:0,
from /usr/include/stdio.h:27,
from /tmp/cmb-superbuild-build/superbuild/gdal/src/port/cpl_port.h:143,
from /tmp/cmb-superbuild-build/superbuild/gdal/src/gcore/gdal.h:41,
from /tmp/cmb-superbuild-build/superbuild/gdal/src/gcore/gdal_priv.h:53,
from /tmp/cmb-superbuild-build/superbuild/gdal/src/gcore/gdalmajorobject.cpp:30:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:234:1: note: previous declaration ‘int isnan(double)’
__MATHDECL_1 (int,isnan,, (_Mdouble_ __value)) __attribute__ ((__const__));
^
In file included from /tmp/cmb-superbuild-build/superbuild/gdal/src/port/cpl_minixml.h:33:0,
from /tmp/cmb-superbuild-build/superbuild/gdal/src/ogr/gml2ogrgeometry.cpp:41:
/tmp/cmb-superbuild-build/superbuild/gdal/src/port/cpl_port.h:382:12: error: ‘constexpr bool std::isnan(double)’ conflicts with a previous declaration
using std::isnan;
^
[...]
```https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/68OSX: moab does not install `MOABTargets*cmake` files.2017-09-30T12:17:59-04:00David ThompsonOSX: moab does not install `MOABTargets*cmake` files.The moab superbuild installs `MOABConfig.cmake` to `install/lib/cmake/MOAB` but when SMTK/CMB are pointed to it, things fail (at least on my 2 macos machines) because `MOABTargets-release.cmake` and `MOABTargets.cmake` are missing. They ...The moab superbuild installs `MOABConfig.cmake` to `install/lib/cmake/MOAB` but when SMTK/CMB are pointed to it, things fail (at least on my 2 macos machines) because `MOABTargets-release.cmake` and `MOABTargets.cmake` are missing. They do not appear to be generated.https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/67OSX: vxl build fails with latest homebrew jpeg2017-09-14T15:23:20-04:00David ThompsonOSX: vxl build fails with latest homebrew jpegVXL cannot use jpeg 9b (falling back to 8d succeeds, but breaks other homebrew packages). The error messages look like:
```
/Stage/Build/cmb/common-superbuild/superbuild/vxl/src/core/vil1/file_formats/vil1_jpeg_compressor.cxx:58:5: erro...VXL cannot use jpeg 9b (falling back to 8d succeeds, but breaks other homebrew packages). The error messages look like:
```
/Stage/Build/cmb/common-superbuild/superbuild/vxl/src/core/vil1/file_formats/vil1_jpeg_compressor.cxx:58:5: error: no matching
function for call to 'jpeg_start_compress'
jpeg_start_compress (&jobj, write_all_tables);
^~~~~~~~~~~~~~~~~~~
/usr/local/include/jpeglib.h:1010:14: note: candidate function not viable: no known conversion from 'bool' to 'jpeg_boolean' for 2nd
argument
EXTERN(void) jpeg_start_compress JPP((j_compress_ptr cinfo,
^
```https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/66OSX: Homebrew hdf5 breaks superbuild2017-09-11T14:25:34-04:00David ThompsonOSX: Homebrew hdf5 breaks superbuildIf HDF5 is installed by Homebrew, the netcdf in superbuild will find it and generate link errors (macos 10.11 certainly, others probably).If HDF5 is installed by Homebrew, the netcdf in superbuild will find it and generate link errors (macos 10.11 certainly, others probably).https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/17Associate workflow template file extensions with CMB apps2017-08-10T12:38:47-04:00David ThompsonAssociate workflow template file extensions with CMB appsWe are working towards packaging workflow template-files in the folder that the CMB apps. Users should be able to double-click on a template file to open the corresponding app instead of opening the app and then opening the template.
...We are working towards packaging workflow template-files in the folder that the CMB apps. Users should be able to double-click on a template file to open the corresponding app instead of opening the app and then opening the template.
This involves figuring out how platforms (Mac OS X, Linux, Windows) register file extensions with applications and making it part of the package installation process.Ben BoeckelBen Boeckelhttps://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/62OCE is not building with VS2015 compiler when CGM session is on2017-08-07T12:57:44-04:00Haocheng LIUOCE is not building with VS2015 compiler when CGM session is onError message is as follows:
```
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE\vadefs.h(145): error C2338: va_start argument must not have reference type and must not be parenthesized
C:\Kitware\haocheng\CMB\buildAll\sup...Error message is as follows:
```
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE\vadefs.h(145): error C2338: va_start argument must not have reference type and must not be parenthesized
C:\Kitware\haocheng\CMB\buildAll\superbuild\oce\src\src\OSD\OSD_FileNode.cxx(972): note: see reference to function template instantiation 'void __vcrt_va_start_verify_argument_type<OSD_Error&>(void) throw()' being compiled
ninja: build stopped: subcommand failed.
```
So according to **Coding towards google and Stack overflow**, adding [#define _CRT_NO_VA_START_VALIDATION](https://github.com/libgdx/fbx-conv/issues/95) would fix the problem. But I got no luck.Haocheng LIUHaocheng LIUhttps://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/63passing flag SUPERBUILD_ALLOW_DEBUG:BOOL=ON would fail the build on windows2017-08-07T11:27:28-04:00Haocheng LIUpassing flag SUPERBUILD_ALLOW_DEBUG:BOOL=ON would fail the build on windowsIf we are doing a debug superbuild on Windows, hdf5 would be built in debug mode. Then when building netcdf, it would complains that it cannot find `hdf5.lib` in ${CMB_SUPERBUILD_DIR}/install/lib, which now is `hdf5_D.lib`.
Tested on Ke...If we are doing a debug superbuild on Windows, hdf5 would be built in debug mode. Then when building netcdf, it would complains that it cannot find `hdf5.lib` in ${CMB_SUPERBUILD_DIR}/install/lib, which now is `hdf5_D.lib`.
Tested on Kerbin.
[link](https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2010-March/002879.html)https://gitlab.kitware.com/cmb/cmb-superbuild/-/issues/46Upstream opencv patch2017-07-31T05:28:55-04:00Ben BoeckelUpstream opencv patch- [ ] [opencv-coreimage-videoio-link](https://gitlab.kitware.com/cmb/cmb-superbuild/blob/master/projects/apple/patches/opencv-coreimage-videoio-link.patch)
@jacob-becker- [ ] [opencv-coreimage-videoio-link](https://gitlab.kitware.com/cmb/cmb-superbuild/blob/master/projects/apple/patches/opencv-coreimage-videoio-link.patch)
@jacob-becker