GROMACS

Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_21e99/fast && /usr/bin/make -f CMakeFiles/cmTC_21e99.dir/build.make CMakeFiles/cmTC_21e99.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building C object CMakeFiles/cmTC_21e99.dir/src.c.o

/usr/bin/cc   -DCMAKE_HAVE_LIBC_PTHREAD   -o CMakeFiles/cmTC_21e99.dir/src.c.o   -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c

Linking C executable cmTC_21e99

/home/stefano/cmake-3.15.3/bin/cmake -E cmake_link_script CMakeFiles/cmTC_21e99.dir/link.txt --verbose=1

/usr/bin/cc  -DCMAKE_HAVE_LIBC_PTHREAD    CMakeFiles/cmTC_21e99.dir/src.c.o  -o cmTC_21e99 

CMakeFiles/cmTC_21e99.dir/src.c.o: In function `main':

src.c:(.text+0x3e): undefined reference to `pthread_create'

src.c:(.text+0x4a): undefined reference to `pthread_detach'

src.c:(.text+0x5b): undefined reference to `pthread_join'

src.c:(.text+0x6f): undefined reference to `pthread_atfork'

collect2: error: ld returned 1 exit status

CMakeFiles/cmTC_21e99.dir/build.make:86: recipe for target 'cmTC_21e99' failed

make[1]: *** [cmTC_21e99] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_21e99/fast' failed

make: *** [cmTC_21e99/fast] Error 2

Source file was:

#include <pthread.h>

void* test_func(void* data)

{

  return data;

}

int main(void)

{

  pthread_t thread;

  pthread_create(&thread, NULL, test_func, NULL);

  pthread_detach(thread);

  pthread_join(thread, NULL);

  pthread_atfork(NULL, NULL, NULL);

  pthread_exit(NULL);

  return 0;

}

Determining if the function pthread_create exists in the pthreads failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_ac83d/fast && /usr/bin/make -f CMakeFiles/cmTC_ac83d.dir/build.make CMakeFiles/cmTC_ac83d.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building C object CMakeFiles/cmTC_ac83d.dir/CheckFunctionExists.c.o

/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_ac83d.dir/CheckFunctionExists.c.o   -c /home/stefano/cmake-3.15.3/share/cmake-3.15/Modules/CheckFunctionExists.c

Linking C executable cmTC_ac83d

/home/stefano/cmake-3.15.3/bin/cmake -E cmake_link_script CMakeFiles/cmTC_ac83d.dir/link.txt --verbose=1

/usr/bin/cc  -DCHECK_FUNCTION_EXISTS=pthread_create    CMakeFiles/cmTC_ac83d.dir/CheckFunctionExists.c.o  -o cmTC_ac83d -lpthreads 

/usr/bin/ld: cannot find -lpthreads

collect2: error: ld returned 1 exit status

CMakeFiles/cmTC_ac83d.dir/build.make:86: recipe for target 'cmTC_ac83d' failed

make[1]: *** [cmTC_ac83d] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_ac83d/fast' failed

make: *** [cmTC_ac83d/fast] Error 2

Determining if files io.h exist failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_1b084/fast && /usr/bin/make -f CMakeFiles/cmTC_1b084.dir/build.make CMakeFiles/cmTC_1b084.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building C object CMakeFiles/cmTC_1b084.dir/HAVE_IO_H.c.o

/usr/bin/cc    -o CMakeFiles/cmTC_1b084.dir/HAVE_IO_H.c.o   -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CheckIncludeFiles/HAVE_IO_H.c

/home/stefano/gromacs-2019.2/build/CMakeFiles/CheckIncludeFiles/HAVE_IO_H.c:2:10: fatal error: io.h: No such file or directory

 #include <io.h>

          ^~~~~~

compilation terminated.

CMakeFiles/cmTC_1b084.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_1b084.dir/HAVE_IO_H.c.o' failed

make[1]: *** [CMakeFiles/cmTC_1b084.dir/HAVE_IO_H.c.o] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_1b084/fast' failed

make: *** [cmTC_1b084/fast] Error 2

Source:

/* */

#include <io.h>

int main(void){return 0;}

Determining if the _fileno exist failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_963c7/fast && /usr/bin/make -f CMakeFiles/cmTC_963c7.dir/build.make CMakeFiles/cmTC_963c7.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building CXX object CMakeFiles/cmTC_963c7.dir/CheckSymbolExists.cxx.o

/usr/bin/c++    -std=c++11      -o CMakeFiles/cmTC_963c7.dir/CheckSymbolExists.cxx.o -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: error: ‘_fileno’ was not declared in this scope

   return ((int*)(&_fileno))[argc];

                   ^~~~~~~

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: note: suggested alternative: ‘fileno’

   return ((int*)(&_fileno))[argc];

                   ^~~~~~~

                   fileno

CMakeFiles/cmTC_963c7.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_963c7.dir/CheckSymbolExists.cxx.o' failed

make[1]: *** [CMakeFiles/cmTC_963c7.dir/CheckSymbolExists.cxx.o] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_963c7/fast' failed

make: *** [cmTC_963c7/fast] Error 2

File /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:

/* */

#include <stdio.h>

int main(int argc, char** argv)

{

  (void)argv;

#ifndef _fileno

  return ((int*)(&_fileno))[argc];

#else

  (void)argc;

  return 0;

#endif

}

Determining if the _commit exist failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_e6c4f/fast && /usr/bin/make -f CMakeFiles/cmTC_e6c4f.dir/build.make CMakeFiles/cmTC_e6c4f.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building CXX object CMakeFiles/cmTC_e6c4f.dir/CheckSymbolExists.cxx.o

/usr/bin/c++    -std=c++11      -o CMakeFiles/cmTC_e6c4f.dir/CheckSymbolExists.cxx.o -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:2:10: fatal error: io.h: No such file or directory

 #include <io.h>

          ^~~~~~

compilation terminated.

CMakeFiles/cmTC_e6c4f.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_e6c4f.dir/CheckSymbolExists.cxx.o' failed

make[1]: *** [CMakeFiles/cmTC_e6c4f.dir/CheckSymbolExists.cxx.o] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_e6c4f/fast' failed

make: *** [cmTC_e6c4f/fast] Error 2

File /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:

/* */

#include <io.h>

int main(int argc, char** argv)

{

  (void)argv;

#ifndef _commit

  return ((int*)(&_commit))[argc];

#else

  (void)argc;

  return 0;

#endif

}

Determining if the memalign exist failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_0db52/fast && /usr/bin/make -f CMakeFiles/cmTC_0db52.dir/build.make CMakeFiles/cmTC_0db52.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building CXX object CMakeFiles/cmTC_0db52.dir/CheckSymbolExists.cxx.o

/usr/bin/c++    -std=c++11      -o CMakeFiles/cmTC_0db52.dir/CheckSymbolExists.cxx.o -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: error: ‘memalign’ was not declared in this scope

   return ((int*)(&memalign))[argc];

                   ^~~~~~~~

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: note: suggested alternative: ‘main’

   return ((int*)(&memalign))[argc];

                   ^~~~~~~~

                   main

CMakeFiles/cmTC_0db52.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_0db52.dir/CheckSymbolExists.cxx.o' failed

make[1]: *** [CMakeFiles/cmTC_0db52.dir/CheckSymbolExists.cxx.o] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_0db52/fast' failed

make: *** [cmTC_0db52/fast] Error 2

File /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:

/* */

#include <stdlib.h>

int main(int argc, char** argv)

{

  (void)argv;

#ifndef memalign

  return ((int*)(&memalign))[argc];

#else

  (void)argc;

  return 0;

#endif

}

Performing C SOURCE FILE Test _callconv___vectorcall failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_4259c/fast && /usr/bin/make -f CMakeFiles/cmTC_4259c.dir/build.make CMakeFiles/cmTC_4259c.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building C object CMakeFiles/cmTC_4259c.dir/src.c.o

/usr/bin/cc   -D_callconv___vectorcall   -o CMakeFiles/cmTC_4259c.dir/src.c.o   -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c:3:18: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘f’

 int __vectorcall f(int i) {return i;} int main(void) {return f(0);}

                  ^

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c: In function ‘main’:

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c:3:62: warning: implicit declaration of function ‘f’ [-Wimplicit-function-declaration]

 int __vectorcall f(int i) {return i;} int main(void) {return f(0);}

                                                              ^

CMakeFiles/cmTC_4259c.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_4259c.dir/src.c.o' failed

make[1]: *** [CMakeFiles/cmTC_4259c.dir/src.c.o] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_4259c/fast' failed

make: *** [cmTC_4259c/fast] Error 2

Source file was:

#pragma GCC diagnostic error "-Wignored-attributes"

int __vectorcall f(int i) {return i;} int main(void) {return f(0);}

Performing C SOURCE FILE Test _callconv___regcall failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_c81e1/fast && /usr/bin/make -f CMakeFiles/cmTC_c81e1.dir/build.make CMakeFiles/cmTC_c81e1.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building C object CMakeFiles/cmTC_c81e1.dir/src.c.o

/usr/bin/cc   -D_callconv___regcall   -o CMakeFiles/cmTC_c81e1.dir/src.c.o   -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c:3:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘f’

 int __regcall f(int i) {return i;} int main(void) {return f(0);}

               ^

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c: In function ‘main’:

/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.c:3:59: warning: implicit declaration of function ‘f’ [-Wimplicit-function-declaration]

 int __regcall f(int i) {return i;} int main(void) {return f(0);}

                                                           ^

CMakeFiles/cmTC_c81e1.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_c81e1.dir/src.c.o' failed

make[1]: *** [CMakeFiles/cmTC_c81e1.dir/src.c.o] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_c81e1/fast' failed

make: *** [cmTC_c81e1/fast] Error 2

Source file was:

#pragma GCC diagnostic error "-Wignored-attributes"

int __regcall f(int i) {return i;} int main(void) {return f(0);}

Determining if the function sgemm_ exists failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_e321d/fast && /usr/bin/make -f CMakeFiles/cmTC_e321d.dir/build.make CMakeFiles/cmTC_e321d.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building C object CMakeFiles/cmTC_e321d.dir/CheckFunctionExists.c.o

/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=sgemm_   -o CMakeFiles/cmTC_e321d.dir/CheckFunctionExists.c.o   -c /home/stefano/cmake-3.15.3/share/cmake-3.15/Modules/CheckFunctionExists.c

Linking C executable cmTC_e321d

/home/stefano/cmake-3.15.3/bin/cmake -E cmake_link_script CMakeFiles/cmTC_e321d.dir/link.txt --verbose=1

/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=sgemm_    CMakeFiles/cmTC_e321d.dir/CheckFunctionExists.c.o  -o cmTC_e321d 

CMakeFiles/cmTC_e321d.dir/CheckFunctionExists.c.o: In function `main':

CheckFunctionExists.c:(.text+0x10): undefined reference to `sgemm_'

collect2: error: ld returned 1 exit status

CMakeFiles/cmTC_e321d.dir/build.make:86: recipe for target 'cmTC_e321d' failed

make[1]: *** [cmTC_e321d] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_e321d/fast' failed

make: *** [cmTC_e321d/fast] Error 2

Performing C++ SOURCE FILE Test HAS_NO_MISSING_PROTO failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_92e97/fast && /usr/bin/make -f CMakeFiles/cmTC_92e97.dir/build.make CMakeFiles/cmTC_92e97.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building CXX object CMakeFiles/cmTC_92e97.dir/src.cxx.o

/usr/bin/c++    -std=c++11   -DHAS_NO_MISSING_PROTO -Wno-missing-prototypes   -o CMakeFiles/cmTC_92e97.dir/src.cxx.o -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.cxx

cc1plus: warning: command line option ‘-Wno-missing-prototypes’ is valid for C/ObjC but not for C++

Linking CXX executable cmTC_92e97

/home/stefano/cmake-3.15.3/bin/cmake -E cmake_link_script CMakeFiles/cmTC_92e97.dir/link.txt --verbose=1

/usr/bin/c++      -std=c++11   -DHAS_NO_MISSING_PROTO -Wno-missing-prototypes      CMakeFiles/cmTC_92e97.dir/src.cxx.o  -o cmTC_92e97 

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Source file was:

int main() { return 0;}

Performing C++ SOURCE FILE Test HAS_NO_MSVC_UNUSED failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_d5f79/fast && /usr/bin/make -f CMakeFiles/cmTC_d5f79.dir/build.make CMakeFiles/cmTC_d5f79.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building CXX object CMakeFiles/cmTC_d5f79.dir/src.cxx.o

/usr/bin/c++    -std=c++11   -DHAS_NO_MSVC_UNUSED /wd4101   -o CMakeFiles/cmTC_d5f79.dir/src.cxx.o -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.cxx

c++: error: /wd4101: No such file or directory

CMakeFiles/cmTC_d5f79.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_d5f79.dir/src.cxx.o' failed

make[1]: *** [CMakeFiles/cmTC_d5f79.dir/src.cxx.o] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_d5f79/fast' failed

make: *** [cmTC_d5f79/fast] Error 2

Source file was:

int main() { return 0;}

Performing C++ SOURCE FILE Test HAS_DECL_IN_SOURCE failed with the following output:

Change Dir: /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_a653d/fast && /usr/bin/make -f CMakeFiles/cmTC_a653d.dir/build.make CMakeFiles/cmTC_a653d.dir/build

make[1]: Entering directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Building CXX object CMakeFiles/cmTC_a653d.dir/src.cxx.o

/usr/bin/c++    -std=c++11   -DHAS_DECL_IN_SOURCE -wd1419   -o CMakeFiles/cmTC_a653d.dir/src.cxx.o -c /home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp/src.cxx

c++: error: unrecognized command line option ‘-wd1419’

CMakeFiles/cmTC_a653d.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_a653d.dir/src.cxx.o' failed

make[1]: *** [CMakeFiles/cmTC_a653d.dir/src.cxx.o] Error 1

make[1]: Leaving directory '/home/stefano/gromacs-2019.2/build/CMakeFiles/CMakeTmp'

Makefile:121: recipe for target 'cmTC_a653d/fast' failed

make: *** [cmTC_a653d/fast] Error 2

Source file was:

int main() { return 0;}