Compilation/linking issue

[Rodriguez]

Hello,

We've been trying to compile smina, and there seems to be a problem in the linking process.

After compilation, when linking, it fails with an error that indicates that pthreads.h wasn't found.

The CMakeFiles/CMakeError.log file in the build/ directory shows the following error:

/cm/shared/apps/gcc/6.3.0/bin/cc  -DCMAKE_HAVE_LIBC_PTHREAD CMakeFiles/cmTC_d7504.dir/src.c.o -o cmTC_d7504 
CMakeFiles/cmTC_d7504.dir/src.c.o: In function `main':
src.c:(.text+0x2d): undefined reference to `pthread_create'
src.c:(.text+0x39): undefined reference to `pthread_detach'
src.c:(.text+0x45): undefined reference to `pthread_cancel'
src.c:(.text+0x56): undefined reference to `pthread_join'
src.c:(.text+0x6a): undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
gmake[1]: *** [cmTC_d7504] Error 1
gmake[1]: Leaving directory `/root/smina/smina-code/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_d7504/fast] Error 2

The cmake command being used is as follows:

# cmake -DCMAKE_INSTALL_PREFIX=/cm/shared/apps/smina/c849cb -DBOOST_ROOT=/cm/shared/apps/boost/gcc/4.9.3/1.60.0 -DCMAKE_MODULE_PATH=/cm/shared/apps/eigen/3.3.7/cmake -DOPENBABEL_DIR=/cm/shared/apps/openbabel/3.1.1 -DCMAKE_THREAD_PREFER_PTHREAD=ON ..

Any assistance with this issue is appreciated.
Thank you.

[David Koes]

Try adding target_link_libraries(smina Threads::Threads) to the end of CMakeLists.txt

[Rodriguez]

We've tried adding the line, but the error persists.

Here's the full CMakeError.log output:

Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /root/smina/smina-code/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake cmTC_f9bc3/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_f9bc3.dir/build.make CMakeFiles/cmTC_f9bc3.dir/build
gmake[1]: Entering directory `/root/smina/smina-code/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_f9bc3.dir/src.c.o
/cm/shared/apps/gcc/6.3.0/bin/cc   -DCMAKE_HAVE_LIBC_PTHREAD -o CMakeFiles/cmTC_f9bc3.dir/src.c.o -c /root/smina/smina-code/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_f9bc3
/cm/shared/apps/cmake/3.18.1/bin/cmake -E cmake_link_script CMakeFiles/cmTC_f9bc3.dir/link.txt --verbose=1
/cm/shared/apps/gcc/6.3.0/bin/cc  -DCMAKE_HAVE_LIBC_PTHREAD CMakeFiles/cmTC_f9bc3.dir/src.c.o -o cmTC_f9bc3
CMakeFiles/cmTC_f9bc3.dir/src.c.o: In function `main':
src.c:(.text+0x2d): undefined reference to `pthread_create'
src.c:(.text+0x39): undefined reference to `pthread_detach'
src.c:(.text+0x45): undefined reference to `pthread_cancel'
src.c:(.text+0x56): undefined reference to `pthread_join'
src.c:(.text+0x6a): undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
gmake[1]: *** [cmTC_f9bc3] Error 1
gmake[1]: Leaving directory `/root/smina/smina-code/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_f9bc3/fast] Error 2


Source file was:
#include 

void* test_func(void* data)
{
  return data;
}

int main(void)
{
  pthread_t thread;
  pthread_create(&thread, NULL, test_func, NULL);
  pthread_detach(thread);
  pthread_cancel(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: /root/smina/smina-code/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake cmTC_d1cc0/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_d1cc0.dir/build.make CMakeFiles/cmTC_d1cc0.dir/build
gmake[1]: Entering directory `/root/smina/smina-code/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_d1cc0.dir/CheckFunctionExists.c.o
/cm/shared/apps/gcc/6.3.0/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_d1cc0.dir/CheckFunctionExists.c.o -c /cm/shared/apps/cmake/3.18.1/share/cmake-3.18/Modules/CheckFunctionExists.c
Linking C executable cmTC_d1cc0
/cm/shared/apps/cmake/3.18.1/bin/cmake -E cmake_link_script CMakeFiles/cmTC_d1cc0.dir/link.txt --verbose=1
/cm/shared/apps/gcc/6.3.0/bin/cc  -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTC_d1cc0.dir/CheckFunctionExists.c.o -o cmTC_d1cc0  -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
gmake[1]: *** [cmTC_d1cc0] Error 1
gmake[1]: Leaving directory `/root/smina/smina-code/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_d1cc0/fast] Error 2

[David Koes]

You need to figure out how to communicate to your version of cmake that -lpthread is needed at link time. What I sent works for cmake 3.12.4 running on ubuntu 20.04. You may want to try upgrading your cmake.

[Rodriguez]

We've upgraded cmake to 3.18.1 and the issue persists. We've managed to compile it on Ubuntu as a test, but not on our working environment on CentOS.

Any other ideas to link pthreads with cmake?

Thank you.

[David Koes]

Try adding target_link_libraries(smina pthread)

[Rodriguez]

We tried adding the line, but the problem persists.

As a test, using the code that CMake uses to verify the presence of “pthreads”:

#include 

void* test_func(void* data)
{
  return data;
}

int main(void)
{
  pthread_t thread;
  pthread_create(&thread, NULL, test_func, NULL);
  pthread_detach(thread);
  pthread_cancel(thread);
  pthread_join(thread, NULL);
  pthread_atfork(NULL, NULL, NULL);
  pthread_exit(NULL);

  return 0;
}

and attempting to compile it, if it’s compiled with “-lpthreads”, as is generated by the smina CMake it outputs an error:

# gcc -o obj.o src.c -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status

But it succeeds if "-lpthread” is used instead:

# gcc -o obj.o src.c -lpthread
# ls
obj.o  src.c

Perhaps the problem is that CMake is generating the library’s name incorrectly?

[David Koes]

What is the link line that is causing the error (run make -DVERBOSE=1)? Could your pthread library possibly be in a non-standard location?

[Rodriguez]

The solution was compiling a new version of Boost. It seems to be working well now.

Thank you for your quick responses and support.