search

Unidata / netcdf-cxx4

Official GitHub repository for netCDF-C++ libraries and utilities.
Other
124 stars 49 forks source link

Issue building with clang on macOS 11.3 #109

Closed mathomp4 closed 3 years ago

mathomp4 commented 3 years ago

All,

I seem to be having an issue compiling netcdf-cxx4 and it seems to be due to my upgrading my (work) laptop from Catalina to Big Sur. Before the upgrade, netcdf-cxx4 was happy with clang but now it's not.

To wit, my OS is macOS 11.3, the compiler is clang++ (or, rather, mpic++ as I built HDF5 for parallel) from XCode 12.5:

❯ mpic++ --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-1205.0.22.9)
Target: x86_64-apple-darwin20.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

and the issue is that when I try and build the library I get errors. I'm putting the output below, but note that this is built inside a set of libraries I maintain for a climate model, so the GNU make that's called that eventually calls the make in netcdf-cxx4 is not pretty, but it works. To wit:

...
Installing netcdf-cxx4 
make[2]: Entering directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.2.1/src/netcdf-cxx4/build'
Making install in cxx4
make[3]: Entering directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.2.1/src/netcdf-cxx4/build/cxx4'
depbase=`echo ncAtt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I../../cxx4 -I..   -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/netcdf  -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/    -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/zlib    -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/szlib    -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/jpeg    -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/hdf5    -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/hdf    -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/netcdf    -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/udunits2    -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/gsl    -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/antlr2    -fPIC -MT ncAtt.lo -MD -MP -MF $depbase.Tpo -c -o ncAtt.lo ../../cxx4/ncAtt.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  mpic++ -DHAVE_CONFIG_H -I. -I../../cxx4 -I.. -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/netcdf -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/ -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/zlib -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/szlib -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/jpeg -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/hdf5 -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/hdf -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/netcdf -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/udunits2 -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/gsl -I/Users/mathomp4/installed/MPI/nag-7.0_7045/openmpi-4.1.1/Baselibs/6.2.1/Darwin/include/antlr2 -fPIC -MT ncAtt.lo -MD -MP -MF .deps/ncAtt.Tpo -c ../../cxx4/ncAtt.cpp -o ncAtt.o
In file included from ../../cxx4/ncAtt.cpp:1:
In file included from ../../cxx4/ncAtt.h:1:
In file included from ../../cxx4/ncType.h:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:639:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/initializer_list:46:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:37:
../version:1:1: error: expected external declaration
-n 4.3.1
^
../version:1:2: error: unknown type name 'n'
-n 4.3.1
 ^
../version:1:4: error: expected unqualified-id
-n 4.3.1
   ^
In file included from ../../cxx4/ncAtt.cpp:1:
In file included from ../../cxx4/ncAtt.h:1:
In file included from ../../cxx4/ncType.h:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:639:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/initializer_list:46:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:49:9: error: no member named 'ptrdiff_t' in the global namespace
using ::ptrdiff_t;
      ~~^
In file included from ../../cxx4/ncAtt.cpp:1:
In file included from ../../cxx4/ncAtt.h:1:
In file included from ../../cxx4/ncType.h:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:640:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:418:
../version:1:1: error: expected external declaration
-n 4.3.1
^
../version:1:2: error: unknown type name 'n'
-n 4.3.1
 ^
../version:1:4: error: expected unqualified-id
-n 4.3.1
   ^
In file included from ../../cxx4/ncAtt.cpp:1:
In file included from ../../cxx4/ncAtt.h:1:
In file included from ../../cxx4/ncType.h:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:642:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/utility:205:
../version:1:1: error: expected external declaration
-n 4.3.1
^
../version:1:2: error: unknown type name 'n'
-n 4.3.1
 ^
../version:1:4: error: expected unqualified-id
-n 4.3.1
   ^
In file included from ../../cxx4/ncAtt.cpp:1:
In file included from ../../cxx4/ncAtt.h:1:
In file included from ../../cxx4/ncType.h:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:668:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/typeinfo:60:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:83:
../version:1:1: error: expected external declaration
-n 4.3.1
^
../version:1:2: error: unknown type name 'n'
-n 4.3.1
 ^
../version:1:4: error: expected unqualified-id
-n 4.3.1
   ^
In file included from ../../cxx4/ncAtt.cpp:1:
In file included from ../../cxx4/ncAtt.h:1:
In file included from ../../cxx4/ncType.h:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:671:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/new:93:
../version:1:1: error: expected external declaration
-n 4.3.1
^
../version:1:2: error: unknown type name 'n'
-n 4.3.1
 ^
../version:1:4: error: expected unqualified-id
-n 4.3.1
   ^
In file included from ../../cxx4/ncAtt.cpp:1:
In file included from ../../cxx4/ncAtt.h:1:
In file included from ../../cxx4/ncType.h:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:673:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:121:
../version:1:1: error: expected external declaration
-n 4.3.1
^
../version:1:2: error: unknown type name 'n'
-n 4.3.1
 ^
../version:1:4: error: expected unqualified-id
-n 4.3.1
   ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[3]: *** [Makefile:852: ncAtt.lo] Error 1
make[3]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.2.1/src/netcdf-cxx4/build/cxx4'
make[2]: *** [Makefile:543: install-recursive] Error 1
make[2]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.2.1/src/netcdf-cxx4/build'
make[1]: *** [GNUmakefile:887: netcdf-cxx4.install] Error 2
make[1]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.2.1/src'
make: *** [GNUmakefile:393: install] Error 2
aerorahul commented 3 years ago

@mathomp4 See #111 for a possible solution. I should have checked with you.

mathomp4 commented 3 years ago

@mathomp4 See #111 for a possible solution. I should have checked with you.

@aerorahul Ooh. Thanks! You were better than my current "workaround": Don't build netcdf-cxx4 if macOS. 😄 (I have the luxury that I only build the C++ interface because it's essentially free, but not required by GEOS. Yet.)

WardF commented 3 years ago

Thanks, and now that this is on my radar I'll get it merged in before other things bubble back to the top. We'll be minting fresh Fortran and C++ releases shortly, so now is a good time.