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CMakeError.log

Stefano Guglielmo, 09/20/2019 05:38 PM

 
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Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
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Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp
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Run Build Command(s):/usr/bin/make cmTC_9e1bd/fast && /usr/bin/make -f CMakeFiles/cmTC_9e1bd.dir/build.make CMakeFiles/cmTC_9e1bd.dir/build
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make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'
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Building C object CMakeFiles/cmTC_9e1bd.dir/src.c.o
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/usr/bin/cc   -DCMAKE_HAVE_LIBC_PTHREAD   -o CMakeFiles/cmTC_9e1bd.dir/src.c.o   -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c
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Linking C executable cmTC_9e1bd
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/home/stefano/cmake-3.15.3/bin/cmake -E cmake_link_script CMakeFiles/cmTC_9e1bd.dir/link.txt --verbose=1
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/usr/bin/cc  -DCMAKE_HAVE_LIBC_PTHREAD    CMakeFiles/cmTC_9e1bd.dir/src.c.o  -o cmTC_9e1bd 
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CMakeFiles/cmTC_9e1bd.dir/src.c.o: In function `main':
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src.c:(.text+0x3e): undefined reference to `pthread_create'
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src.c:(.text+0x4a): undefined reference to `pthread_detach'
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src.c:(.text+0x5b): undefined reference to `pthread_join'
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src.c:(.text+0x6f): undefined reference to `pthread_atfork'
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collect2: error: ld returned 1 exit status
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CMakeFiles/cmTC_9e1bd.dir/build.make:86: recipe for target 'cmTC_9e1bd' failed
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void* test_func(void* data)
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int main(void)
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{
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  pthread_create(&thread, NULL, test_func, NULL);
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  pthread_exit(NULL);
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}
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Determining if the function pthread_create exists in the pthreads failed with the following output:
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Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp
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Run Build Command(s):/usr/bin/make cmTC_6b6aa/fast && /usr/bin/make -f CMakeFiles/cmTC_6b6aa.dir/build.make CMakeFiles/cmTC_6b6aa.dir/build
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make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'
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Building C object CMakeFiles/cmTC_6b6aa.dir/CheckFunctionExists.c.o
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/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_6b6aa.dir/CheckFunctionExists.c.o   -c /home/stefano/cmake-3.15.3/share/cmake-3.15/Modules/CheckFunctionExists.c
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Linking C executable cmTC_6b6aa
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/home/stefano/cmake-3.15.3/bin/cmake -E cmake_link_script CMakeFiles/cmTC_6b6aa.dir/link.txt --verbose=1
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/usr/bin/cc  -DCHECK_FUNCTION_EXISTS=pthread_create    CMakeFiles/cmTC_6b6aa.dir/CheckFunctionExists.c.o  -o cmTC_6b6aa -lpthreads 
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/usr/bin/ld: cannot find -lpthreads
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collect2: error: ld returned 1 exit status
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CMakeFiles/cmTC_6b6aa.dir/build.make:86: recipe for target 'cmTC_6b6aa' failed
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Determining if files io.h exist failed with the following output:
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Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp
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Run Build Command(s):/usr/bin/make cmTC_f3043/fast && /usr/bin/make -f CMakeFiles/cmTC_f3043.dir/build.make CMakeFiles/cmTC_f3043.dir/build
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make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'
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Building C object CMakeFiles/cmTC_f3043.dir/HAVE_IO_H.c.o
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/usr/bin/cc    -o CMakeFiles/cmTC_f3043.dir/HAVE_IO_H.c.o   -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CheckIncludeFiles/HAVE_IO_H.c
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/home/stefano/gromacs-2019.2/build/CMakeFiles/CheckIncludeFiles/HAVE_IO_H.c:2:10: fatal error: io.h: No such file or directory
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 #include <io.h>
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          ^~~~~~
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compilation terminated.
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CMakeFiles/cmTC_f3043.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_f3043.dir/HAVE_IO_H.c.o' failed
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make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'
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Building CXX object CMakeFiles/cmTC_0280b.dir/CheckSymbolExists.cxx.o
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/usr/bin/c++    -std=c++11      -o CMakeFiles/cmTC_0280b.dir/CheckSymbolExists.cxx.o -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
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/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
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/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: error: ‘_fileno’ was not declared in this scope
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                   ^~~~~~~
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/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: note: suggested alternative: ‘fileno’
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CMakeFiles/cmTC_0280b.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_0280b.dir/CheckSymbolExists.cxx.o' failed
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File /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
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/* */
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int main(int argc, char** argv)
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#ifndef _fileno
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make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'
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Building CXX object CMakeFiles/cmTC_5e049.dir/CheckSymbolExists.cxx.o
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/usr/bin/c++    -std=c++11      -o CMakeFiles/cmTC_5e049.dir/CheckSymbolExists.cxx.o -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
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/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:2:10: fatal error: io.h: No such file or directory
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 #include <io.h>
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          ^~~~~~
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compilation terminated.
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CMakeFiles/cmTC_5e049.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_5e049.dir/CheckSymbolExists.cxx.o' failed
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File /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
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#ifndef _commit
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Building CXX object CMakeFiles/cmTC_5e2e4.dir/CheckSymbolExists.cxx.o
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/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
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Performing C SOURCE FILE Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED failed with the following output:
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/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c:3:18: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘f’
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