Error 'make'ing B1 basic example

edwardrjtaylor · August 6, 2021, 8:24am

Hi I’m new to Geant4 so started with an identical setup on my MAC to that shown in:
(Youtube: “2. How to compile and install Geant4 in MacOS”)

My computer parameters are:
macOS Big Sur 11.5.1

MacOSX11.3.sdk → which I then changed to 10.9 (could try with even earlier versions)

miniconda3

(base) ME@x86_64-apple-darwin13 build % cc --version

Apple clang version 12.0.5 (clang-1205.0.22.11)

Target: x86_64-apple-darwin20.6.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

(base) ME@x86_64-apple-darwin13 build % gcc --version

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1

Apple clang version 12.0.5 (clang-1205.0.22.11)

Target: x86_64-apple-darwin20.6.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

(base) ME@x86_64-apple-darwin13 build % xcode-select -p

/Library/Developer/CommandLineTools

(base) ME@x86_64-apple-darwin13 build % echo $CONDA_BUILD_SYS_ROOT

/opt/MacOSX10.9.sdk

(base) ME@x86_64-apple-darwin13 build % echo $CONDA_BUILD_SYSROOT

/opt/MacOSX10.9.sdk

(base) ME@x86_64-apple-darwin13 build % softwareupdate -i -a

Software Update Tool

Finding available software

No updates are available.

The “ccmake …” command works ok (with the below parameters):

CMAKE_BUILD_TYPE Release
CMAKE_INSTALL_PREFIX /usr/local
CMAKE_OSX_ARCHITECTURES
CMAKE_OSX_DEPLOYMENT_TARGET
CMAKE_OSX_SYSROOT /opt/MacOSX10.9.sdk (note I can use up to 11.3)
Geant4_DIR /usr/local/lib/Geant4-10.7.2
PTL_DIR /usr/local/lib/Geant4-10.7.2/PTL
Qt53DCore_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt53DCore
Qt53DExtras_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt53DExtras
Qt53DInput_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt53DInput
Qt53DLogic_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt53DLogic
Qt53DRender_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt53DRender
Qt5Core_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt5Core
Qt5Gamepad_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt5Gamepad
Qt5Gui_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt5Gui
Qt5Network_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt5Network
Qt5OpenGL_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt5OpenGL
Qt5PrintSupport_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt5PrintSupport
Qt5Widgets_DIR /usr/local/Cellar/qt@5/5.15.2/lib/cmake/Qt5Widgets
WITH_GEANT4_UIVIS ON

The generate command then works ok

Then I try:

(base) ME@x86_64-apple-darwin13 build % make

Consolidate compiler generated dependencies of target exampleB1

[ 12%] Linking CXX executable exampleB1

ld: warning: text-based stub file /Library/Developer/CommandLineTools/SDKs/MacOSX11.1.sdk/System/Library/Frameworks/OpenGL.framework/OpenGL.tbd and library file /Library/Developer/CommandLineTools/SDKs/MacOSX11.1.sdk/System/Library/Frameworks/OpenGL.framework/OpenGL.tbd are out of sync. Falling back to library file for linking.

ld: warning: text-based stub file /Library/Developer/CommandLineTools/SDKs/MacOSX11.1.sdk/usr/lib/libexpat.tbd and library file /Library/Developer/CommandLineTools/SDKs/MacOSX11.1.sdk/usr/lib/libexpat.tbd are out of sync. Falling back to library file for linking.

ld: library not found for -lSystem

clang-10: error: linker command failed with exit code 1 (use -v to see invocation)

make[2]: *** [exampleB1] Error 1

make[1]: *** [CMakeFiles/exampleB1.dir/all] Error 2

make: *** [all] Error 2

I was experiencing the error: (before I changed the SDK I was using from 11.1 to 10.9 and edited cmath to include the full file path of <math.h>)
(base) ME@x86_64-apple-darwin13 build % make

Consolidate compiler generated dependencies of target exampleB1

[ 12%] Building CXX object CMakeFiles/exampleB1.dir/exampleB1.cc.o

In file included from /Users/ME/Documents/PhD/Geant4/geant4.10.07.p02/examples/basic/B1/exampleB1.cc:30:

In file included from /Users/ME/Documents/PhD/Geant4/geant4.10.07.p02/examples/basic/B1/include/B1DetectorConstruction.hh:33:

In file included from /usr/local/include/Geant4/G4VUserDetectorConstruction.hh:37:

In file included from /usr/local/include/Geant4/globals.hh:35:

In file included from /usr/local/include/Geant4/G4ios.hh:35:

In file included from /usr/local/include/Geant4/G4Types.hh:74:

In file included from /Users/ME/miniconda3/bin/…/include/c++/v1/complex:245:

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:317:9: error: no member named ‘signbit’ in the global namespace

using ::signbit;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:318:9: error: no member named ‘fpclassify’ in the global namespace

using ::fpclassify;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:319:9: error: no member named ‘isfinite’ in the global namespace; did you mean ‘finite’?

using ::isfinite;

~~^

/Library/Developer/CommandLineTools/SDKs/MacOSX11.1.sdk/usr/include/math.h:752:12: note: ‘finite’ declared here

extern int finite(double)

^

In file included from /Users/ME/Documents/PhD/Geant4/geant4.10.07.p02/examples/basic/B1/exampleB1.cc:30:

In file included from /Users/ME/Documents/PhD/Geant4/geant4.10.07.p02/examples/basic/B1/include/B1DetectorConstruction.hh:33:

In file included from /usr/local/include/Geant4/G4VUserDetectorConstruction.hh:37:

In file included from /usr/local/include/Geant4/globals.hh:35:

In file included from /usr/local/include/Geant4/G4ios.hh:35:

In file included from /usr/local/include/Geant4/G4Types.hh:74:

In file included from /Users/ME/miniconda3/bin/…/include/c++/v1/complex:245:

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:320:9: error: no member named ‘isinf’ in the global namespace

using ::isinf;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:321:9: error: no member named ‘isnan’ in the global namespace

using ::isnan;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:322:9: error: no member named ‘isnormal’ in the global namespace

using ::isnormal;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:323:9: error: no member named ‘isgreater’ in the global namespace

using ::isgreater;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:324:9: error: no member named ‘isgreaterequal’ in the global namespace

using ::isgreaterequal;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:325:9: error: no member named ‘isless’ in the global namespace

using ::isless;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:326:9: error: no member named ‘islessequal’ in the global namespace

using ::islessequal;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:327:9: error: no member named ‘islessgreater’ in the global namespace

using ::islessgreater;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:328:9: error: no member named ‘isunordered’ in the global namespace

using ::isunordered;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:329:9: error: no member named ‘isunordered’ in the global namespace

using ::isunordered;

~~^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:640:26: error: no template named 'numeric_limits’

bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),

^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:640:60: error: no template named 'numeric_limits’

bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),

^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:641:18: error: no template named 'numeric_limits’

int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>

^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:641:50: error: no template named 'numeric_limits’

int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>

^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:646:17: error: no template named 'numeric_limits’

static_assert(numeric_limits<_FloatT>::radix == 2, “FloatT has incorrect radix”);

^

/Users/ME/miniconda3/bin/…/include/c++/v1/cmath:649:25: error: no template named 'numeric_limits’

return _FloatBigger ? numeric_limits<_IntT>::max() : (numeric_limits<_IntT>::max() >> _Bits << _Bits);

^

fatal error: too many errors emitted, stopping now [-ferror-limit=]

20 errors generated.

make[2]: *** [CMakeFiles/exampleB1.dir/exampleB1.cc.o] Error 1

make[1]: *** [CMakeFiles/exampleB1.dir/all] Error 2

make: *** [all] Error 2

edwardrjtaylor · August 6, 2021, 8:30am

I’m not sure what these errors refer to: I guessed cmath before. I found some links that may make more sense to you than me:

I have tried some the suggestions in:

edwardrjtaylor · August 6, 2021, 8:31am

github.com/ContinuumIO/anaconda-issues

x86_64-apple-darwin13.4.0-clang fails with "unsupported file format" error

opened 03:59PM - 04 Apr 18 UTC

closed 04:24PM - 04 Apr 18 UTC

mcflugen

When I try to compile a program with *x86_64-apple-darwin13.4.0-clang* (4.0.1 bu…ild 10), I get the following error, ``` ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd ld: dynamic main executables must link with libSystem.dylib for architecture x86_64 clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation) ``` I suspect this has something to do with Xcode 9.3 as I only started seeing this problem after upgrading to 9.3. In addition, things are working just fine on another machine with Xcode 9.0. I notice that the above unsupported file format seems to refer to `tapi-tbd-v3`. To reproduce the problem I simply try to compile the following, ```c /* main.c */ int main() { return 0; } ``` with ```bash $ x86_64-apple-darwin13.4.0-clang main.c ``` and I get the above error. If I compile with *clang* (again 4.0.1) it compiles without error.

github.com/bigartm/bigartm

CMAKE fails in anaconda

opened 05:33PM - 26 Apr 18 UTC

closed 03:13AM - 12 Aug 20 UTC

melodywolk

Hi! I'm using Mac OS 10.13.3 I've created a conda environment ``` conda cr…eate -n test python=3.6 clangxx_osx-64 clang_osx-64 ``` When I run the following ``` $ mkdir build && cd build $ cmake .. ``` I have this error message: ``` -- The C compiler identification is Clang 4.0.1 -- The CXX compiler identification is Clang 4.0.1 -- Check for working C compiler: /anaconda/envs/test/bin/x86_64-apple-darwin13.4.0-clang -- Check for working C compiler: /anaconda/envs/test/bin/x86_64-apple-darwin13.4.0-clang -- broken CMake Error at /anaconda/envs/test/share/cmake-3.9/Modules/CMakeTestCCompiler.cmake:51 (message): The C compiler "/anaconda/envs/test/bin/x86_64-apple-darwin13.4.0-clang" is not able to compile a simple test program. ``` Any idea how to solve this? Thank you!

edwardrjtaylor · August 6, 2021, 5:55pm

(base) ME@x86_64-apple-darwin13 build % cd /Library/Developer/CommandLineTools/usr/bin
(base) ME@x86_64-apple-darwin13 bin % ./clang --version
Apple clang version 12.0.5 (clang-1205.0.22.11)
Target: x86_64-apple-darwin20.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin/.

Meanwhile in miniconda3:
(base) ME@x86_64-apple-darwin13 bin % ./clang --version

clang version 10.0.0

Target: x86_64-apple-darwin20.6.0

Thread model: posix

InstalledDir: /Users/ME/miniconda3/bin/.

Don’t know if this makes sense to anyone

allison · August 7, 2021, 10:26am

Hi Edward

Here is my standard reply to users who use YouTube video for installation. If it is not working for you, you should raise an issue on that YouTube thread. The official installation instructions can be found in the User Support section of the Geant4 web page, specifically Installation Guide — Geant4 Installation Guide 10.7 documentation. Please check that your installation procedure conforms with that.

To have video guides like this would be great, and it is good that the author has done this and obviously helped many people. If he - or anyone - wishes to do this on behalf of Geant4, and in collaboration with the Geant4 team so that it is always up to date, it would be very welcome. Meanwhile, we just have the written guide.

John

system · November 5, 2021, 10:27am

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