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Published 20 hours ago • verified publisher icon isciences

Installation error on HPC system related to GCC

Open nelerey opened this issue 3 years ago • 7 comments

I'm encountering problems installing exactextract on my university's linux cluster.

After loading modules of the dependencies listed, the list of loaded modules is the following:

  1) geos/3.8.1   2) proj/6.0.0   3) gdal/3.1.0   4) gmp/6.1.2   5) mpfr/4.0.2   6) mpc/1.1.0   7) cmake/3.16.0-rc4   8) gcc/9.2.0

Even though the loaded GCC version appears to be 9.2.0, I get the following output and error when attempting to install exactextract following the precise instructions in the README:

$  cmake -DCMAKE_BUILD_TYPE=Release ..
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /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: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at CMakeLists.txt:16 (message):
  gcc 5.0+ is required to build exactextract

-- Configuring incomplete, errors occurred!
See also "<my_folder>/exactextract/cmake-build-release/CMakeFiles/CMakeOutput.log".

It says “The C compiler identification is GNU 4.8.5” and “gcc 5.0+ is required to build exactextract”, which doesn’t seem to match the loaded version 9.2.0 compiler…

CMakeOutput.log file content:

Click to expand log file content 
The system is: Linux - 3.10.0-1062.1.2.el7.x86_64 - x86_64
Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
Compiler: /usr/bin/cc 
Build flags: 
Id flags:  

The output was:
0


Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"

The C compiler identification is GNU, found in "/gpfs/home/<my_folder>/exactextract/cmake-build-release/CMakeFiles/3.16.5/CompilerIdC/a.out"

Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded.
Compiler: /usr/bin/c++ 
Build flags: 
Id flags:  

The output was:
0


Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"

The CXX compiler identification is GNU, found in "/gpfs/home/<my_folder>/exactextract/cmake-build-release/CMakeFiles/3.16.5/CompilerIdCXX/a.out"

Determining if the C compiler works passed with the following output:
Change Dir: /gpfs/home/<my_folder>/exactextract/cmake-build-release/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake cmTC_cf159/fast && /usr/bin/gmake -f CMakeFiles/cmTC_cf159.dir/build.make CMakeFiles/cmTC_cf159.dir/build
gmake[1]: Entering directory `/gpfs/home/<my_folder>/exactextract/cmake-build-release/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_cf159.dir/testCCompiler.c.o
/usr/bin/cc    -o CMakeFiles/cmTC_cf159.dir/testCCompiler.c.o   -c /gpfs/home/<my_folder>/exactextract/cmake-build-release/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTC_cf159
/gpfs/software/ada/cmake/cmake-3.16.5-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_cf159.dir/link.txt --verbose=1
/usr/bin/cc    -L/gpfs/software/ada/geos/3.8.1/lib -L/gpfs/software/ada/gdal/3.1.0/lib -L/gpfs/software/ada/proj/6.0.0/lib  CMakeFiles/cmTC_cf159.dir/testCCompiler.c.o  -o cmTC_cf159 
gmake[1]: Leaving directory `/gpfs/home/<my_folder>/exactextract/cmake-build-release/CMakeFiles/CMakeTmp'



Detecting C compiler ABI info compiled with the following output:
Change Dir: /gpfs/home/<my_folder>/exactextract/cmake-build-release/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake cmTC_e8a21/fast && /usr/bin/gmake -f CMakeFiles/cmTC_e8a21.dir/build.make CMakeFiles/cmTC_e8a21.dir/build
gmake[1]: Entering directory `/gpfs/home/<my_folder>/exactextract/cmake-build-release/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_e8a21.dir/CMakeCCompilerABI.c.o
/usr/bin/cc   -v -o CMakeFiles/cmTC_e8a21.dir/CMakeCCompilerABI.c.o   -c /gpfs/software/ada/cmake/cmake-3.16.5-Linux-x86_64/share/cmake-3.16/Modules/CMakeCCompilerABI.c
Using built-in specs.
COLLECT_GCC=/usr/bin/cc
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) 
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_e8a21.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64'
 /usr/libexec/gcc/x86_64-redhat-linux/4.8.5/cc1 -quiet -v /gpfs/software/ada/cmake/cmake-3.16.5-Linux-x86_64/share/cmake-3.16/Modules/CMakeCCompilerABI.c -quiet -dumpbase CMakeCCompilerABI.c -mtune=generic -march=x86-64 -auxbase-strip CMakeFiles/cmTC_e8a21.dir/CMakeCCompilerABI.c.o -version -o /tmp/ccMKpexp.s
GNU C (GCC) version 4.8.5 20150623 (Red Hat 4.8.5-36) (x86_64-redhat-linux)
	compiled by GNU C version 4.8.5 20150623 (Red Hat 4.8.5-36), GMP version 6.0.0, MPFR version 3.1.1, MPC version 1.0.1
warning: GMP header version 6.0.0 differs from library version 6.1.2.
warning: MPC header version 1.0.1 differs from library version 1.1.0.
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring nonexistent directory "/usr/lib/gcc/x86_64-redhat-linux/4.8.5/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../x86_64-redhat-linux/include"
ignoring duplicate directory "/gpfs/software/ada/proj/6.0.0/include"
  as it is a non-system directory that duplicates a system directory
#include "..." search starts here:
#include <...> search starts here:
 /gpfs/software/ada/mpc/1.1.0/include
 /gpfs/software/ada/mpfr/4.0.2/include
 /gpfs/software/ada/gmp/6.1.2/include
 /gpfs/software/ada/proj/6.0.0/include
 /usr/lib/gcc/x86_64-redhat-linux/4.8.5/include
 /usr/local/include
 /usr/include
End of search list.
GNU C (GCC) version 4.8.5 20150623 (Red Hat 4.8.5-36) (x86_64-redhat-linux)
	compiled by GNU C version 4.8.5 20150623 (Red Hat 4.8.5-36), GMP version 6.0.0, MPFR version 3.1.1, MPC version 1.0.1
warning: GMP header version 6.0.0 differs from library version 6.1.2.
warning: MPC header version 1.0.1 differs from library version 1.1.0.
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c0b461ba69dba093bfc939a7fa8b7724
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_e8a21.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64'
 as -v --64 -o CMakeFiles/cmTC_e8a21.dir/CMakeCCompilerABI.c.o /tmp/ccMKpexp.s
GNU assembler version 2.27 (x86_64-redhat-linux) using BFD version version 2.27-34.base.el7
COMPILER_PATH=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/
LIBRARY_PATH=/gpfs/software/ada/compilers/gcc/9.2.0/lib64/../lib64/:/gpfs/software/ada/compilers/gcc/9.2.0/lib/../lib64/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/gpfs/software/ada/mpc/1.1.0/lib/:/gpfs/software/ada/mpfr/4.0.2/lib/:/gpfs/software/ada/gmp/6.1.2/lib/:/gpfs/software/ada/compilers/gcc/9.2.0/lib64/:/gpfs/software/ada/compilers/gcc/9.2.0/lib/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_e8a21.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64'
Linking C executable cmTC_e8a21
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Using built-in specs.
COLLECT_GCC=/usr/bin/cc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) 
COMPILER_PATH=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/
LIBRARY_PATH=/gpfs/software/ada/compilers/gcc/9.2.0/lib64/../lib64/:/gpfs/software/ada/compilers/gcc/9.2.0/lib/../lib64/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/gpfs/software/ada/mpc/1.1.0/lib/:/gpfs/software/ada/mpfr/4.0.2/lib/:/gpfs/software/ada/gmp/6.1.2/lib/:/gpfs/software/ada/compilers/gcc/9.2.0/lib64/:/gpfs/software/ada/compilers/gcc/9.2.0/lib/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-L/gpfs/software/ada/geos/3.8.1/lib' '-L/gpfs/software/ada/gdal/3.1.0/lib' '-L/gpfs/software/ada/proj/6.0.0/lib' '-v' '-o' 'cmTC_e8a21' '-mtune=generic' '-march=x86-64'
 /usr/libexec/gcc/x86_64-redhat-linux/4.8.5/collect2 --build-id --no-add-needed --eh-frame-hdr --hash-style=gnu -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTC_e8a21 /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtbegin.o -L/gpfs/software/ada/geos/3.8.1/lib -L/gpfs/software/ada/gdal/3.1.0/lib -L/gpfs/software/ada/proj/6.0.0/lib -L/gpfs/software/ada/compilers/gcc/9.2.0/lib64/../lib64 -L/gpfs/software/ada/compilers/gcc/9.2.0/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/gpfs/software/ada/mpc/1.1.0/lib -L/gpfs/software/ada/mpfr/4.0.2/lib -L/gpfs/software/ada/gmp/6.1.2/lib -L/gpfs/software/ada/compilers/gcc/9.2.0/lib64 -L/gpfs/software/ada/compilers/gcc/9.2.0/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. CMakeFiles/cmTC_e8a21.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crtn.o
gmake[1]: Leaving directory `/gpfs/home/<my_folder>/exactextract/cmake-build-release/CMakeFiles/CMakeTmp'



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  collapse include dir [/usr/lib/gcc/x86_64-redhat-linux/4.8.5/include] ==> [/usr/lib/gcc/x86_64-redhat-linux/4.8.5/include]
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nelerey avatar Mar 18 '21 15:03 nelerey

It sounds like you have multiple versions of GCC installed and gcc is pointing to version 4.8.5. If the newer version is installed as, say, gcc-9, you could do cmake -DMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++-9 ..

dbaston avatar Mar 18 '21 16:03 dbaston

Thank you for your reply! I loaded the modules in a different order, which apparently made gcc point to the correct version, and now seem to have managed to successfully build the build files and run "make".

However, in the very last step, "sudo make install" fails with the following error:

make: *** No rule to make target `install'.  Stop.

Interestingly this is the exact same error I get on my local machine (macOS catalina).

nelerey avatar Mar 18 '21 21:03 nelerey

Can you post an updated log? It sounds like cmake didn't find GDAL.

dbaston avatar Mar 18 '21 22:03 dbaston

You are right, I get warnings about gdal in both instances. Apologies for not noticing sooner, it didn't stop the compilation so I glanced over it (not used to compiling programs).

On HPC, it did not find GDAL >=2, although GDAL 3.1.0 seems to be loaded. Locally, I was using a conda environment that has gdal 3.0.4 and geos 3.8.1 in it.

HPC log file:

The system is: Linux - 3.10.0-1062.1.2.el7.x86_64 - x86_64 Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded. Compiler: /gpfs/software/ada/compilers/gcc/9.2.0/bin/gcc Build flags: Id flags:

The output was: 0

Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"

The C compiler identification is GNU, found in "/gpfs/home/remoteusename/phd_code/exactextract/cmake-build-release/CMakeFiles/3.16.0-rc4/CompilerIdC/a.out"

Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded. Compiler: /gpfs/software/ada/compilers/gcc/9.2.0/bin/c++ Build flags: Id flags:

The output was: 0

Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"

The CXX compiler identification is GNU, found in "/gpfs/home/remoteusename/phd_code/exactextract/cmake-build-release/CMakeFiles/3.16.0-rc4/CompilerIdCXX/a.out"

Determining if the C compiler works passed with the following output: Change Dir: /gpfs/home/remoteusename/phd_code/exactextract/cmake-build-release/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake cmTC_b6ddd/fast && /usr/bin/gmake -f CMakeFiles/cmTC_b6ddd.dir/build.make CMakeFiles/cmTC_b6ddd.dir/build gmake[1]: Entering directory /gpfs/home/remoteusename/phd_code/exactextract/cmake-build-release/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_b6ddd.dir/testCCompiler.c.o /gpfs/software/ada/compilers/gcc/9.2.0/bin/gcc -o CMakeFiles/cmTC_b6ddd.dir/testCCompiler.c.o -c /gpfs/home/remoteusename/phd_code/exactextract/cmake-build-release/CMakeFiles/CMakeTmp/testCCompiler.c Linking C executable cmTC_b6ddd /gpfs/software/ada/cmake/cmake-3.16.0-rc4-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_b6ddd.dir/link.txt --verbose=1 /gpfs/software/ada/compilers/gcc/9.2.0/bin/gcc -L/gpfs/software/ada/gdal/3.1.0/lib -L/gpfs/software/ada/proj/6.0.0/lib -L/gpfs/software/ada/geos/3.8.1/lib CMakeFiles/cmTC_b6ddd.dir/testCCompiler.c.o -o cmTC_b6ddd gmake[1]: Leaving directory /gpfs/home/remoteusename/phd_code/exactextract/cmake-build-release/CMakeFiles/CMakeTmp'

Detecting C compiler ABI info compiled with the following output: Change Dir: /gpfs/home/remoteusename/phd_code/exactextract/cmake-build-release/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake cmTC_bcd44/fast && /usr/bin/gmake -f CMakeFiles/cmTC_bcd44.dir/build.make CMakeFiles/cmTC_bcd44.dir/build gmake[1]: Entering directory /gpfs/home/remoteusename/phd_code/exactextract/cmake-build-release/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_bcd44.dir/CMakeCCompilerABI.c.o /gpfs/software/ada/compilers/gcc/9.2.0/bin/gcc -v -o CMakeFiles/cmTC_bcd44.dir/CMakeCCompilerABI.c.o -c /gpfs/software/ada/cmake/cmake-3.16.0-rc4-Linux-x86_64/share/cmake-3.16/Modules/CMakeCCompilerABI.c Using built-in specs. 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-Wno-implicit-int-float-conversion -Wno-c99-designator -Wno-final-dtor-non-final-class -Wno-extra-semi-stmt -Wno-misleading-indentation -Wno-quoted-include-in-framework-header -Wno-implicit-fallthrough -Wno-enum-enum-conversion -Wno-enum-float-conversion -fdebug-compilation-dir /Users/localusername/packages/exactextract/cmake-build-release/CMakeFiles/CMakeTmp -ferror-limit 19 -fmessage-length 0 -stack-protector 1 -fstack-check -mdarwin-stkchk-strong-link -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fgnuc-version=4.2.1 -fobjc-runtime=macosx-10.15.0 -fmax-type-align=16 -fdiagnostics-show-option -o CMakeFiles/cmTC_86443.dir/CMakeCCompilerABI.c.o -x c /Applications/CMake.app/Contents/share/cmake-3.20/Modules/CMakeCCompilerABI.c] ignore line: [clang -cc1 version 12.0.0 (clang-1200.0.32.29) default target x86_64-apple-darwin19.6.0] ignore line: [ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/local/include"] ignore line: [ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/Library/Frameworks"] ignore line: [#include "..." search starts here:] ignore line: [#include <...> search starts here:] ignore line: [ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include] ignore line: [ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include] ignore line: [ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include] ignore line: [ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/System/Library/Frameworks (framework directory)] ignore line: [End of search list.] ignore line: [Linking C executable cmTC_86443] ignore 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[/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk] ==> ignore arg [-o] ==> ignore arg [cmTC_86443] ==> ignore arg [-search_paths_first] ==> ignore arg [-headerpad_max_install_names] ==> ignore arg [-v] ==> ignore arg [CMakeFiles/cmTC_86443.dir/CMakeCCompilerABI.c.o] ==> ignore arg [-lSystem] ==> lib [System] arg [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/lib/darwin/libclang_rt.osx.a] ==> lib [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/lib/darwin/libclang_rt.osx.a] Library search paths: [;/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/lib] Framework search paths: [;/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/System/Library/Frameworks/] remove lib [System] remove lib [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/lib/darwin/libclang_rt.osx.a] collapse library dir [/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/lib] ==> [/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/lib] collapse framework dir [/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/System/Library/Frameworks/] ==> [/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/System/Library/Frameworks] implicit libs: [] implicit dirs: [/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/lib] implicit fwks: [/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/System/Library/Frameworks]

Detecting CXX compiler ABI info compiled with the following output: Change Dir: /Users/localusername/packages/exactextract/cmake-build-release/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_517dd/fast && /Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/cmTC_517dd.dir/build.make CMakeFiles/cmTC_517dd.dir/build Building CXX object CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -mmacosx-version-min=10.15 -v -Wl,-v -MD -MT CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o -MF CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o.d -o CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o -c /Applications/CMake.app/Contents/share/cmake-3.20/Modules/CMakeCXXCompilerABI.cpp Apple clang version 12.0.0 (clang-1200.0.32.29) Target: x86_64-apple-darwin19.6.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin clang: warning: -Wl,-v: 'linker' input unused [-Wunused-command-line-argument] ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include/c++/v1" "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.15.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -Werror=implicit-function-declaration -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -discard-value-names -main-file-name CMakeCXXCompilerABI.cpp -mrelocation-model pic -pic-level 2 -mthread-model posix -mframe-pointer=all -fno-strict-return -masm-verbose -munwind-tables -target-sdk-version=11.1 -target-cpu penryn -dwarf-column-info -debugger-tuning=lldb -target-linker-version 609.8 -v -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0 -dependency-file CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o.d -skip-unused-modulemap-deps -MT CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o -sys-header-deps -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -stdlib=libc++ -internal-isystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1 -internal-isystem /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/local/include -internal-isystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include -internal-externc-isystem /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include -internal-externc-isystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include -Wno-reorder-init-list -Wno-implicit-int-float-conversion -Wno-c99-designator -Wno-final-dtor-non-final-class -Wno-extra-semi-stmt -Wno-misleading-indentation -Wno-quoted-include-in-framework-header -Wno-implicit-fallthrough -Wno-enum-enum-conversion -Wno-enum-float-conversion -fdeprecated-macro -fdebug-compilation-dir /Users/localusername/packages/exactextract/cmake-build-release/CMakeFiles/CMakeTmp -ferror-limit 19 -fmessage-length 0 -stack-protector 1 -fstack-check -mdarwin-stkchk-strong-link -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fgnuc-version=4.2.1 -fobjc-runtime=macosx-10.15.0 -fcxx-exceptions -fexceptions -fmax-type-align=16 -fdiagnostics-show-option -o CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o -x c++ /Applications/CMake.app/Contents/share/cmake-3.20/Modules/CMakeCXXCompilerABI.cpp clang -cc1 version 12.0.0 (clang-1200.0.32.29) default target x86_64-apple-darwin19.6.0 ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/local/include" ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/Library/Frameworks" #include "..." search starts here: #include <...> search starts here: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/System/Library/Frameworks (framework directory) End of search list. Linking CXX executable cmTC_517dd /Applications/CMake.app/Contents/bin/cmake -E cmake_link_script CMakeFiles/cmTC_517dd.dir/link.txt --verbose=1 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -mmacosx-version-min=10.15 -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_517dd Apple clang version 12.0.0 (clang-1200.0.32.29) Target: x86_64-apple-darwin19.6.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld" -demangle -lto_library /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/libLTO.dylib -dynamic -arch x86_64 -platform_version macos 10.15.0 11.1 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -o cmTC_517dd -search_paths_first -headerpad_max_install_names -v CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o -lc++ -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/lib/darwin/libclang_rt.osx.a @(#)PROGRAM:ld PROJECT:ld64-609.8 BUILD 15:07:46 Dec 18 2020 configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em Library search paths: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/lib Framework search paths: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/System/Library/Frameworks/

Parsed CXX implicit include dir info from above output: rv=done found start of include info found start of implicit include info add: [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1] add: [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include] add: [/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include] add: [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include] end of search list found collapse include dir [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1] ==> [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1] collapse include dir [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include] ==> [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include] collapse include dir [/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include] ==> [/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include] collapse include dir [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include] ==> [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include] implicit include dirs: [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1;/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include;/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include;/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include]

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ignore line: [ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include] ignore line: [ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include] ignore line: [ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/System/Library/Frameworks (framework directory)] ignore line: [End of search list.] ignore line: [Linking CXX executable cmTC_517dd] ignore line: [/Applications/CMake.app/Contents/bin/cmake -E cmake_link_script CMakeFiles/cmTC_517dd.dir/link.txt --verbose=1] ignore line: [/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -mmacosx-version-min=10.15 -Wl -search_paths_first -Wl -headerpad_max_install_names -v -Wl -v CMakeFiles/cmTC_517dd.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_517dd ] ignore line: 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nelerey avatar Mar 19 '21 10:03 nelerey

On HPC, it did not find GDAL >=2, although GDAL 3.1.0 seems to be loaded.

It will look for GDAL by running the gdal-config command. It may be that you have GDAL installed but not the development package (gdal-dev, gdal-devel or similar -- depending in your platform)

dbaston avatar Mar 19 '21 11:03 dbaston

Thank you. It appeared to have compiled correctly on my local machine now, but when testing exactextract -h the following error appears:

dyld: Library not loaded: /usr/local/opt/netcdf/lib/libnetcdf.18.dylib
  Referenced from: /usr/local/opt/gdal/lib/libgdal.28.dylib
  Reason: image not found
Abort trap: 6

I tried searching for what could be going on here but didn't find answers online.

nelerey avatar Mar 22 '21 16:03 nelerey

Does GDAL work otherwise; can you run gdalinfo ?

dbaston avatar Mar 24 '21 00:03 dbaston