Thanks @ivana. Chemistry is an issue in this example cause it was not included in the test Let me ping @batm developper of this example. The chemistry needs to be included in the nightly test.
Hello,
Thanks @ngoc . I agree, chemistry needs to be included in the test, and I’ll update the example with alternative chemistry modules.
The “zsh: bus error” has been noticed on the student’s MacOS but hasn’t occurred on my Linux system (openSUSE Tumbleweed on AMD Ryzen Threadripper 3970X Processor) with both Geant4 versions 11.1 and 11.2.
As expected, Geant4-DNA with chemistry requires significant memory and CPU time. When using the command, the chemical reactions started printing on the terminal after ~3 min, and the full simulation finished in 2 h 50 min, running on 2 parallel cores.
I’ve already sent my video recording of the simulation illustration to the student by email.
Hello! I try to run another example “pdb4dna”
This is what I do…
/usr/local/bin ~/g4test/chem3-build
~/g4test/chem3-build
sarahabdelaziz@Sarahs-MacBook-Pro chem3-build % cd ..
sarahabdelaziz@Sarahs-MacBook-Pro g4test % ls
chem3 chem3-build neuron neuron-build
sarahabdelaziz@Sarahs-MacBook-Pro g4test % cp -r /usr/local/share/Geant4/examples/extended/medical/dna/pdb4dna .
sarahabdelaziz@Sarahs-MacBook-Pro g4test % ls
chem3 chem3-build neuron neuron-build pdb4dna
sarahabdelaziz@Sarahs-MacBook-Pro g4test % ls pdb4dna
1ZBB.pdb History gui.mac init_vis.mac pdb4dna.out vis.mac
CMakeLists.txt README include pdb4dna.cc runInGUI.mac
GNUmakefile analysis.C init.mac pdb4dna.in src
sarahabdelaziz@Sarahs-MacBook-Pro g4test % mkdir pdb4dna-build
sarahabdelaziz@Sarahs-MacBook-Pro g4test % ls
chem3 chem3-build neuron neuron-build pdb4dna pdb4dna-build
sarahabdelaziz@Sarahs-MacBook-Pro g4test % cd pdb4dna-build
sarahabdelaziz@Sarahs-MacBook-Pro pdb4dna-build % ccmake ../pdb4dna
In ccmake,
CMAKE_BUILD_TYPE
CMAKE_INSTALL_PREFIX /usr/local
CMAKE_OSX_ARCHITECTURES
CMAKE_OSX_DEPLOYMENT_TARGET 14.6
CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.
I press c to configure
Page 1 of 1
EXPAT_LIBRARY_RELEASE */Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.
Geant4_DIR */usr/local/lib/cmake/Geant4
PTL_DIR */usr/local/lib/cmake/Geant4/PTL
Qt53DCore_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DCore
Qt53DExtras_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DExtras
Qt53DInput_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DInput
Qt53DLogic_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DLogic
Qt53DRender_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DRender
Qt5Core_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Core
Qt5Gamepad_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Gamepad
Qt5Gui_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Gui
Qt5Network_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Network
Qt5OpenGL_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5OpenGL
Qt5Widgets_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Widgets
Qt5_DIR */opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5
WITH_GEANT4_UIVIS *ON
X11_xcb_xkb_INCLUDE_PATH */opt/homebrew/include
CMAKE_BUILD_TYPE
CMAKE_INSTALL_PREFIX /usr/local
CMAKE_OSX_ARCHITECTURES
CMAKE_OSX_DEPLOYMENT_TARGET 14.6
CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.
Then
sarahabdelaziz@Sarahs-MacBook-Pro pdb4dna-build % cmake ../pdb4dna
-- Configuring done (0.3s)
CMake Error in CMakeLists.txt:
Imported target "Geant4::G4Tree" includes non-existent path
"/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
* The path was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and references files it does not
provide.
CMake Error in CMakeLists.txt:
Imported target "Geant4::G4Tree" includes non-existent path
"/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
* The path was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and references files it does not
provide.
-- Generating done (0.9s)
CMake Generate step failed. Build files cannot be regenerated correctly.
Could you help me to know, what is this problem, please?
This is almost certainly the result of an upgrade to the MacOS system, and the Geant4PackageCache.cmake file that Geant4 installs. See this post: Rebuilding Geant4 10.7.2 - #2 by bmorgan for instructions on how to remove that file, just adapt it to the path to your Geant4 installation.
Thanks. I am sorry, I try to understand but I do not know what should I do? Could you help me?
I update Mac to Sequoia 15 and now it is up to date. Also, update Xcode with predictive code completion model.
Should I change anything in ccmake?
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CMAKE_BUILD_TYPE
CMAKE_INSTALL_PREFIX /usr/local
CMAKE_OSX_ARCHITECTURES
CMAKE_OSX_DEPLOYMENT_TARGET
CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.
EXPAT_LIBRARY_RELEASE /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.
Geant4_DIR /usr/local/lib/cmake/Geant4
PTL_DIR /usr/local/lib/cmake/Geant4/PTL
Qt53DCore_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DCore
Qt53DExtras_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DExtras
Qt53DInput_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DInput
Qt53DLogic_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DLogic
Qt53DRender_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt53DRender
Qt5Core_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Core
Qt5Gamepad_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Gamepad
Qt5Gui_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Gui
Qt5Network_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Network
Qt5OpenGL_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5OpenGL
Qt5Widgets_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5Widgets
Qt5_DIR /opt/homebrew/Cellar/qt@5/5.15.13_1/lib/cmake/Qt5
WITH_GEANT4_UIVIS ON
X11_xcb_xkb_INCLUDE_PATH /opt/homebrew/include
Did you see the link to the other forum posting that Ben included in his reply?
Were you able to try the suggestion there, and then reconfigure your build as you did your first time?
Yes, but I do not know where should I find this file?
Did you see the path quoted in the message? Did you notice the “-install” suffix that was part of the directory path mentioned? Do you know where you specified your Geant4 installation directory?
Given:
The file should probably be at /usr/local/lib/cmake/Geant4/Geant4PackageCache.cmake
Do you mean that I should replace
Geant4_DIR / usr/ local/ lib/ cmake / Geant4
With
Geant4_DIR / usr/ local/ lib/ cmake / Geant4/ Geant4PackageCache.cmake
I write it down by myself during configure ccmake ?
.
No. All you need to do is:
- Remove the /usr/local/lib/cmake/Geant4/Geant4PackageCache.cmake file
- Rerun CMake for your build of pdb4dna
Thanks.
sarahabdelaziz@Sarahs-MacBook-Pro ~ % cd /usr/local/lib/cmake/Geant4/
sarahabdelaziz@Sarahs-MacBook-Pro Geant4 % ls
G4EXPATShim.cmake Geant4Config.cmake Modules
G4FreetypeShim.cmake Geant4ConfigVersion.cmake PTL
G4HDF5Shim.cmake Geant4LibraryDepends-release.cmake UseGeant4.cmake
G4MotifShim.cmake Geant4LibraryDepends.cmake
G4X11Shim.cmake Geant4PackageCache.cmake
sarahabdelaziz@Sarahs-MacBook-Pro Geant4 % rm Geant4PackageCache.cmake
override rw-r--r-- root/wheel for Geant4PackageCache.cmake? y
rm: Geant4PackageCache.cmake: Permission denied
sarahabdelaziz@Sarahs-MacBook-Pro Geant4 % sudo rm Geant4PackageCache.cmake
Password:
sarahabdelaziz@Sarahs-MacBook-Pro Geant4 % ls
G4EXPATShim.cmake G4X11Shim.cmake Geant4LibraryDepends.cmake
G4FreetypeShim.cmake Geant4Config.cmake Modules
G4HDF5Shim.cmake Geant4ConfigVersion.cmake PTL
G4MotifShim.cmake Geant4LibraryDepends-release.cmake UseGeant4.cmake
Then for ccmake
The C compiler identification is AppleClang 16.0.0.16000026
The CXX compiler identification is AppleClang 16.0.0.16000026
Detecting C compiler ABI info
Detecting C compiler ABI info - done
Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -
skipped
Detecting C compile features
Detecting C compile features - done
Detecting CXX compiler ABI info
Detecting CXX compiler ABI info - done
Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -
skipped
Detecting CXX compile features
Detecting CXX compile features - done
Found EXPAT:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.0.sdk/usr/lib/libexpat.tbd
(found suitable version "2.6.1", minimum required is "2.5.0")
Performing Test CMAKE_HAVE_LIBC_PTHREAD
Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
Found Threads: TRUE
CMake Error at /opt/homebrew/Cellar/cmake/3.30.3/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package):
By not providing "FindQt5Core.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "Qt5Core", but
CMake did not find one.
Could not find a package configuration file provided by "Qt5Core" with any
of the following names:
Qt5CoreConfig.cmake
qt5core-config.cmake
Add the installation prefix of "Qt5Core" to CMAKE_PREFIX_PATH or set
"Qt5Core_DIR" to a directory containing one of the above files. If
"Qt5Core" provides a separate development package or SDK, be sure it has
been installed.
Call Stack (most recent call first):
/usr/local/lib/cmake/Geant4/Geant4Config.cmake:394 (find_dependency)
CMakeLists.txt:14 (find_package)
Configuring incomplete, errors occurred!
Page 1 of 1
CMAKE_BUILD_TYPE *
CMAKE_INSTALL_PREFIX */usr/local
CMAKE_OSX_ARCHITECTURES *
CMAKE_OSX_DEPLOYMENT_TARGET *
CMAKE_OSX_SYSROOT */Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.
Geant4_DIR */usr/local/lib/cmake/Geant4
PTL_DIR */usr/local/lib/cmake/Geant4/PTL
Qt5Core_DIR *Qt5Core_DIR-NOTFOUND
WITH_GEANT4_UIVIS *ON
What should I do, please?
Ah, apologies, I’d missed that you’d configured with Qt5 and through homebrew. This is an unfortunate corner case of the Geant4PackageCache.cmake, though one it’s intended to assist with. There are two ways to solve this:
-
From the build directory where you ran
ccmake, runcmake -DCMAKE_PREFIX_PATH=$(brew --prefix qt@5) . -
Reinstall Geant4 itself to create the new
Geant4PackageCache.cmakefile for the upgraded system. Of course, that’s quite a big job, so I’d recommend the first option.
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