Incompatibility between MacOSX 26.4 Tahoe and Dealii DMG?

[Joshua Siktar]

Hello! 

I have been using the Dealii installation through the .dmg file on my MacOSX (MacBook Pro, Apple M1 chip, OSX 26.4 Tahoe, and DealII version 9.7.1). Everything was working fine until I updated my OS from 26.3 Tahoe to 26.4, at which point I could not even run the example codes. For instance, if I cd into the step-1 folder, run cmake ., and then make, I get the errors:

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX26.4.sdk/usr/include/c++/v1/cstdio:107:5: error: 

      <cstdio> tried including <stdio.h> but didn't find libc++'s <stdio.h>

      header. This usually means that your header search paths are not

      configured properly. The header search paths should contain the C++

      Standard Library headers before any C Standard Library, and you are

      probably using compiler flags that make that not be the case.

  107 | #   error <cstdio> tried including <stdio.h> but didn't find libc++'s <s...

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX26.4.sdk/usr/include/c++/v1/cmath:571:15: error: 

      expected unqualified-id

  571 |   return std::isinf(__lcpp_x);

I've tried completely deleting and reinstalling the DMG, uninstalling and reinstalling the Xcode tools, and also using the Candi installation instead (which produces essentially the same error during the "make" step of the Dealii installation. Does this mean it is necessary for me to reinstall Dealii by source instead of using the DMG file?

[Luca Heltai]

Hi Joshua,

I’m currently recreating the package for 26.4, but it will take me some time.

A quick fix for you could be the following:

Remove every occurence of

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

from

/Applications/deal.II.app/Contents/Resources/Libraries/lib/cmake/deal.II/deal.IITargets.cmake


i.e.,

cp /Applications/deal.II.app/Contents/Resources/Libraries/lib/cmake/deal.II/deal.IITargets.cmake \
/Applications/deal.II.app/Contents/Resources/Libraries/lib/cmake/deal.II/deal.IITargets.cmake.bak

sed -i '' 's|/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include;||g' \
/Applications/deal.II.app/Contents/Resources/Libraries/lib/cmake/deal.II/deal.IITargets.cmake

Then delete your example build directory contents and try reconfiguring.

The issue may be in the fact that you have XCode installed instead of just the command line tools.

L.

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[Joshua Siktar]

Hello!

I tried your suggestion, and it brought me to a linking error: 

Undefined symbols for architecture arm64: Teuchos::ActiveRCPNodesSetup::ActiveRCPNodesSetup() , referenced from: __GLOBAL__sub_I_step_1.cc in step-1.cc.o Teuchos::ActiveRCPNodesSetup::~ActiveRCPNodesSetup() , referenced from: __GLOBAL__sub_I_step_1.cc in step-1.cc.o ld: symbol(s) not found for architecture arm64 clang++: error: linker command failed with exit code 1 (use -v to see invocation)

However, I was able to get past this error by adding these three commands at the end of the CMakeLists :

target_link_libraries(${TARGET} "/Applications/deal.II.app/Contents/Resources/Libraries/lib/libteuchoscomm.dylib")

target_link_libraries(${TARGET} "/Applications/deal.II.app/Contents/Resources/Libraries/lib/libteuchosparameterlist.dylib")

target_link_libraries(${TARGET} "/Applications/deal.II.app/Contents/Resources/Libraries/lib/libteuchoscore.dylib")

So, I think as long as I don't delete the DMG app again, I am set. Thank you so much!

I am also curious, are these types of issues like the first one I faced typical with the DMG app after a Mac system update, or is this (to your knowledge) specific to the 26.4 release? 

[Luca Heltai]

Good! I’m happy you managed to make it work.

This is an issue that was already raised in the mailing list, due to a mix between command line tools coming from stand-alone installer or via XCode installer.

They have different paths, and the path selection breaks at each software update, so it is difficult to make “one-solution-fits-all”.

I never install the full XCode, but sometimes this breaks it for users that do have XCode. The path

> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

is an example that sometimes (but not always!) is not present when command line tools come from XCode.

I think I will have to do some manual cleanup of the next package (I already do it for several other small issues) but this one showed up after the first Tahoe update.

L.

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