9.2 issue during compilation on macOSX
Alberto Salvadori
Hi,
I just installed release 9.2, with great pleasure on my mac. Not working yet.
Here is the error I receive, my OSX is 10.15.4 (19E287) and Xcode 11.5 (11E608c)
Developer Tools:
Version: 11.5 (11E608c)
Location: /Applications/Xcode.app
Applications:
Xcode: 11.5 (16139)
Instruments: 11.5 (64535.75)
SDKs:
iOS:
13.5: (17F65)
iOS Simulator:
13.5: (17F65)
macOS:
10.15.4: (19E258)
19.0:
tvOS:
13.4: (17L255)
tvOS Simulator:
13.4: (17L255)
watchOS:
6.2: (17T255)
watchOS Simulator:
6.2: (17T255)
It seems that a library is sought for in a non existing directory:
bash-3.2$ ls /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff
ls: /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff: No such file or directory
Let me know if I can be of further help.
Thanks!
Alberto
This is a shell with modules and PATHs set to work with Deal.II.
All external libraries and deal.II itself are located in
/Applications/deal.II.app/Contents/Resources/spack/
If you want to set up your daily Terminal to work with deal.II, add
these lines to your ~/.profile file (the first line turns off this message):
export DEAL_II_CONF_SILENT=ON
# DEAL_II_USE_LMOD=ON # if you want to use lmod instead of tcl module
# DEAL_II_ENABLE_VIEW=ON # if you want to set CMAKE_PREFIX_PATH to a view of
. /Applications/deal.II.app/Contents/MacOS/dealii.conf
deal.II and all its dependencies were installed using spack, and are available
through the spack and module or lmod commands, e.g.:
module load dealii
The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.
bash-3.2$
bash-3.2$
bash-3.2$ cd /Users/albertosalvadori/Codes/dealii-9.2/examples/step-17
bash-3.2$ cmake -G 'Unix Makefiles'
CMake Warning:
No source or binary directory provided. Both will be assumed to be the
same as the current working directory, but note that this warning will
become a fatal error in future CMake releases.
-- The C compiler identification is AppleClang 11.0.3.11030032
-- The CXX compiler identification is AppleClang 11.0.3.11030032
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc - works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/openmpi-3.1.6-5strmdmhwolf2dlkebtvhizrmgnsnlce/bin/mpic++
-- Check for working CXX compiler: /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/openmpi-3.1.6-5strmdmhwolf2dlkebtvhizrmgnsnlce/bin/mpic++ - works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Autopilot invoked
###
#
# Project step-17 set up with deal.II-9.2.0 found at
# /Applications/deal.II.app/Contents/Resources/Libraries
#
# CMAKE_BUILD_TYPE: Debug
#
# You can now run
# $ make - to compile and link the program
# $ make run - to (compile, link and) run the program
#
# $ make sign - to sign the executable with the supplied OSX developer key
#
# $ make debug - to switch the build type to 'Debug'
# $ make release - to switch the build type to 'Release'
#
# $ make edit_cache - to change (cached) configuration variables
# and rerun the configure and generate phases of CMake
#
# $ make strip_comments - to strip the source files in this
# directory off their comments; this is irreversible
# $ make clean - to remove the generated executable as well as
# all intermediate compilation files
# $ make runclean - to remove all output generated by the program
# $ make distclean - to clean the directory from _all_ generated
# files (includes clean, runclean and the removal
# of the generated build system)
# $ make info - to view this message again
#
# Have a nice day!
#
###
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/albertosalvadori/Codes/dealii-9.2/examples/step-17
bash-3.2$ make release
Scanning dependencies of target release
[100%] Switching CMAKE_BUILD_TYPE to Release
-- Autopilot invoked
-- Run $ make info to print a detailed help message
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/albertosalvadori/Codes/dealii-9.2/examples/step-17
***
*** Switched to Release mode. Now recompile with: $ make
***
[100%] Built target release
bash-3.2$ make
Scanning dependencies of target step-17
[ 50%] Building CXX object CMakeFiles/step-17.dir/step-17.cc.o
[100%] Linking CXX executable step-17
ld: warning: directory not found for option '-L/Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff'
[100%] Built target step-17
bash-3.2$ ./step-17
dyld: malformed mach-o: load commands size (33840) > 32768
Abort trap: 6
bash-3.2$
Alberto Salvadori
Scanning dependencies of target step-17
[ 50%] Building CXX object CMakeFiles/step-17.dir/step-17.cc.o
[100%] Linking CXX executable step-17
ld: warning: directory not found for option '-L/Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff'
[100%] Built target step-17
It worked, in the sense that :
bash-3.2$ make release
Scanning dependencies of target release
[100%] Switching CMAKE_BUILD_TYPE to Release
-- Autopilot invoked
-- Run $ make info to print a detailed help message
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/albertosalvadori/Codes/dealii-9.2/examples/step-17
***
*** Switched to Release mode. Now recompile with: $ make
***
[100%] Built target release
bash-3.2$ make
Scanning dependencies of target step-17
[ 50%] Building CXX object CMakeFiles/step-17.dir/step-17.cc.o
[100%] Linking CXX executable step-17
[100%] Built target step-17
Nonetheless, the code still does not run neither in debug nor in release mode, providing the following output:
bash-3.2$ ./step-17
dyld: malformed mach-o: load commands size (33840) > 32768
Abort trap: 6
Any help appreciated.
Thanks
Alberto