greedy
greedy copied to clipboard
pyushkevich
newest VTK cannot be found
When compiling greedy, it asked for VTK binary directory. Following similar issue here, I installed VTK but now is giving this error:
From the VTK git repo I could not find IOCore or IOGeometry or the others. Could you suggest how to resolve this? Thank you!
Ubuntu system.
GREEDY Version: 1.3.0-alpha Released Sep 28, 2022
GIT Info:
Branch : master
SHA : ee6a9efa12fea5fe9a746babc7c53b54ab49a1c2
Date : 2022-09-28 07:52:39 -0400
CMake Error at CMakeLists.txt:66 (FIND_PACKAGE):
Found package configuration file:
/home/ubuntu/code/vtk/build/vtk-config.cmake
but it set VTK_FOUND to FALSE so package "VTK" is considered to be NOT
FOUND. Reason given by package:
Could not find the VTK package with the following required components:
IOCore, IOGeometry, IOLegacy, IOPLY.
Thank you - I am using the newest one from git clone --recursive https://gitlab.kitware.com/vtk/vtk.git
Please try v9.1.0. You can always find the required vtk version from this line in the CMakeLists.txt https://github.com/pyushkevich/greedy/blob/ee6a9efa12fea5fe9a746babc7c53b54ab49a1c2/CMakeLists.txt#L66
We haven't tested with the latest vtk branch.
The most recent version was 9.2.0. I installed v9.1.0 now but getting the same error... :/
I just tried to replicate on the mac and it was the same error. Any suggestions would be appreciated!
I would try following steps:
- Delete everything from the binary folder and reconfigure the project using cmake
- Make sure the VTK_DIR in your CMakeCache.txt file in your greedy binary folder is pointing to the vtk v9.1.0 binary folder
Thank you.
- I did delete everything (including ITK and VTK and greedy) and reconfigured all from cmake but it throws the same error (both mac and linux)
- I did confirm that CMakeCache.tct is pointing to the 9.1.0 version.
Also. where are IOCore, IOLegacy etc located in VTK? From quick search on vtk source, I was not able to pinpoint where they are.
Can you share the CMakeCache.txt in your greedy binary folder?
You can find the module enable info in the CMakeCache.txt file in the vtk binary folder. VTK group the modules in folders. For example, the IOCore module is located at /{vtkbinaryfolder}/IO/Core
It's also a way to find related module name for specific filter. If the filter located at Filter/General/..., then the module to include is FilterGeneral
Here is the CMakeCache.txt from the greedy binary - thanks so much!
It looks OK. Can you also attach the CMakeCache.txt from you VTK build directory?
I don't see any issues in these files.
Has vtk been successfully built? Can you check the lib directory under vtk binary folder, to see if the library binaries have been generated there.
What were the cmake command (or configurations) you were using to configure vtk and greedy?
Are you still getting the "not found" error message when configuring greedy or is there anything else generated?
for both VTK and greedy i am using ccmake, and for the configuration for greedy I only changed CMAKE_BUILD_TYPE=Release (as instructed from the website).
For vtk, these are some of the build configurations I have (no error with this config, but when turning on VTK_GROUP_ENABLE_Rendering it throws error telling it cannot find OpenGL..)
BUILD_SHARED_LIBS ON
CMAKE_BUILD_TYPE Release
CMAKE_INSTALL_PREFIX /usr/local
OPENGL_GLES2_INCLUDE_DIR OPENGL_GLES2_INCLUDE_DIR-NOTFOUND
OPENGL_GLES3_INCLUDE_DIR OPENGL_GLES3_INCLUDE_DIR-NOTFOUND
VTK_BUILD_DOCUMENTATION OFF
VTK_BUILD_EXAMPLES OFF
VTK_BUILD_SCALED_SOA_ARRAYS OFF
VTK_BUILD_TESTING OFF
VTK_EXTRA_COMPILER_WARNINGS OFF
VTK_GLEXT_FILE /home/ubuntu/code/vtk-v9.1.0/Utilities/ParseOGLExt/h
VTK_GLXEXT_FILE /home/ubuntu/code/vtk-v9.1.0/Utilities/ParseOGLExt/h
VTK_GROUP_ENABLE_Imaging DEFAULT
VTK_GROUP_ENABLE_MPI DONT_WANT
VTK_GROUP_ENABLE_Qt DEFAULT
VTK_GROUP_ENABLE_Rendering DONT_WANT
VTK_GROUP_ENABLE_StandAlone DONT_WANT
VTK_GROUP_ENABLE_Views DEFAULT
VTK_GROUP_ENABLE_Web DEFAULT
VTK_PYTHON_VERSION 3
VTK_SMP_IMPLEMENTATION_TYPE Sequential
VTK_USE_CUDA OFF
VTK_USE_LARGE_DATA OFF
VTK_USE_MEMKIND OFF
VTK_USE_MPI OFF
VTK_WGLEXT_FILE /home/ubuntu/code/vtk-v9.1.0/Utilities/ParseOGLExt/h
VTK_WRAP_JAVA OFF
VTK_WRAP_PYTHON OFF
Yes I think the library binaries have been generated for VTK...
this is what im seeing under the vtk-build/lib:
./lib/cmake:
vtk-9.1
./lib/vtk:
hierarchy
ubuntu@ip-172-31-71-153:~/code/vtk_build$ ls ./lib/*/*
./lib/cmake/vtk-9.1:
FindCGNS.cmake Findutf8cpp.cmake
FindEXPAT.cmake VTK-targets.cmake
FindEigen3.cmake VTK-vtk-module-find-packages.cmake
FindExprTk.cmake VTK-vtk-module-properties.cmake
FindFFMPEG.cmake patches
FindFontConfig.cmake vtk-config-version.cmake
FindFreetype.cmake vtk-config.cmake
FindGL2PS.cmake vtk-find-package-helpers.cmake
FindGLEW.cmake vtk-prefix.cmake
FindJOGL.cmake vtk-use-file-compat.cmake
FindJsonCpp.cmake vtk-use-file-deprecated.cmake
FindLZ4.cmake vtk-use-file-error.cmake
FindLZMA.cmake vtkCMakeBackports.cmake
FindLibHaru.cmake vtkDetectLibraryType.cmake
FindLibPROJ.cmake vtkEncodeString.cmake
FindLibXml2.cmake vtkHashSource.cmake
FindMySQL.cmake vtkModule.cmake
FindNetCDF.cmake vtkModuleGraphviz.cmake
FindODBC.cmake vtkModuleJson.cmake
FindOGG.cmake vtkModuleTesting.cmake
FindOSMesa.cmake vtkModuleWrapJava.cmake
FindOpenSlide.cmake vtkModuleWrapPython.cmake
FindOpenVR.cmake vtkObjectFactory.cmake
FindPEGTL.cmake vtkObjectFactory.cxx.in
FindSDL2.cmake vtkObjectFactory.h.in
FindTBB.cmake vtkTestingDriver.cmake
FindTHEORA.cmake vtkTestingRenderingDriver.cmake
Finddouble-conversion.cmake vtkTopologicalSort.cmake
Findmpi4py.cmake
./lib/vtk/hierarchy:
VTK
For linux shared library binaries, you need to look for .so files. It looks like they are missing from the build folder. Those .cmake files are not binaries. Is there any lib64 folder that contains those files?
The lib or lib64 folder should look like this:
cmake libvtkImagingColor-9.1.so.1 libvtkIOVeraOut-9.1.so
libvtkcgns-9.1.so libvtkImagingColor-9.1.so.9.1.0 libvtkIOVeraOut-9.1.so.1
libvtkcgns-9.1.so.1 libvtkImagingCore-9.1.so libvtkIOVeraOut-9.1.so.9.1.0
libvtkcgns-9.1.so.9.1.0 libvtkImagingCore-9.1.so.1 libvtkIOVideo-9.1.so
libvtkChartsCore-9.1.so libvtkImagingCore-9.1.so.9.1.0 libvtkIOVideo-9.1.so.1
libvtkChartsCore-9.1.so.1 libvtkImagingFourier-9.1.so libvtkIOVideo-9.1.so.9.1.0
libvtkChartsCore-9.1.so.9.1.0 libvtkImagingFourier-9.1.so.1 libvtkIOXML-9.1.so
...
CMake build projects via two-step process, first is configuration. After configuration shown "Configuration Done, Generating Done", a make or cmake --build . command need to be executed to actually compile the project.
Have you executed the actual building step after configuring the project using ccmake?
Thank you that was super helpful - I just built the VTK, and now the lib from the vtk shows these:
ls ./lib/
cmake libvtkCommonTransforms-9.1.so.9.1.0
libvtkCommonCore-9.1.so libvtkWrappingTools-9.1.so
libvtkCommonCore-9.1.so.1 libvtkWrappingTools-9.1.so.1
libvtkCommonCore-9.1.so.9.1.0 libvtkWrappingTools-9.1.so.9.1.0
libvtkCommonDataModel-9.1.so libvtkkissfft-9.1.so
libvtkCommonDataModel-9.1.so.1 libvtkkissfft-9.1.so.1
libvtkCommonDataModel-9.1.so.9.1.0 libvtkkissfft-9.1.so.9.1.0
libvtkCommonMath-9.1.so libvtkloguru-9.1.so
libvtkCommonMath-9.1.so.1 libvtkloguru-9.1.so.1
libvtkCommonMath-9.1.so.9.1.0 libvtkloguru-9.1.so.9.1.0
libvtkCommonMisc-9.1.so libvtkpugixml-9.1.so
libvtkCommonMisc-9.1.so.1 libvtkpugixml-9.1.so.1
libvtkCommonMisc-9.1.so.9.1.0 libvtkpugixml-9.1.so.9.1.0
libvtkCommonSystem-9.1.so libvtksys-9.1.so
libvtkCommonSystem-9.1.so.1 libvtksys-9.1.so.1
libvtkCommonSystem-9.1.so.9.1.0 libvtksys-9.1.so.9.1.0
libvtkCommonTransforms-9.1.so vtk
but it seems ccmake for greedy show the exact same error messages.. here is the full error messages..
GREEDY Version: 1.3.0-alpha Released Sep 28, 2022
GIT Info:
Branch : master
SHA : ee6a9efa12fea5fe9a746babc7c53b54ab49a1c2
Date : 2022-09-28 07:52:39 -0400
CMake Error at CMakeLists.txt:66 (FIND_PACKAGE):
Found package configuration file:
/home/ubuntu/code/vtk_build/vtk-config.cmake
but it set VTK_FOUND to FALSE so package "VTK" is considered to be NOT
FOUND. Reason given by package:
Could not find the VTK package with the following required components:
IOCore, IOGeometry, IOLegacy, IOPLY.
Configuring incomplete, errors occurred!
Thanks so much for the help!! 🙏
The IOCore, IOGeometry, IOLegacy, IOPLY modules has not been built according your build configurations.
If you check this file under vtk source directory /vtk/IO/Core/vtk.module you will find which module group you need to turn on to have IOCore module enabled. Similarly for other modules.
So you need to turn on VTK_GROUP_ENABLE_StandAlone in your ccmake configuration to enable these modules. Set it to WANT or YES and build again to see if it works.
More about vtk modules: https://vtk.org/doc/nightly/html/md__builds_gitlab-kitware-sciviz-ci_Documentation_Doxygen_ModuleSystem.html
Thanks so much, this is super helpful!! I turned on the standalone and now VTK has these modules.
And configuration of greedy was successful! However when I tried to run make -j 8, I got this error this time..
...
/home/ubuntu/code/greedy_dir/greedy/src/GreedyAPI.cxx: In instantiation of ‘std::__cxx11::string GreedyApproach<VDim, TReal>::PrintIter(int, int, const MultiComponentMetricReport&) const [with unsigned int VDim = 4; TReal = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/home/ubuntu/code/greedy_dir/greedy/src/GreedyAPI.cxx:3275:16: required from here
/home/ubuntu/code/greedy_dir/greedy/src/GreedyAPI.cxx:1528:12: warning: zero-length gnu_printf format string [-Wformat-zero-length]
CMakeFiles/Makefile2:256: recipe for target 'CMakeFiles/test_accum.dir/all' failed
make[1]: *** [CMakeFiles/test_accum.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 60%] Linking CXX static library libgreedyapi.a
[ 60%] Built target greedyapi
Makefile:165: recipe for target 'all' failed
Could you suggest what might went wrong??? thanks so much!!!
The actual error message was printed before the section you pasted. Can you attach the entire building output including the error message?
Thanks so much Jilei! This is what i am seeing now...
[ 6%] Built target text_to_hex
[ 30%] Built target docs_to_hex
make[2]: *** No rule to make target '/home/ubuntu/code/ITK-build/lib/libitkdouble-conversion-5.2.a', needed by 'test_accum'. Stop.
CMakeFiles/Makefile2:256: recipe for target 'CMakeFiles/test_accum.dir/all' failed
make[1]: *** [CMakeFiles/test_accum.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 56%] Built target greedyapi
Makefile:165: recipe for target 'all' failed
make: *** [all] Error 2
[RESOLVED. ] Thank you! You were totally right and I needed to build ITK ...! thanks so much for the help on installation!!! @jilei-hao