Building error using cmake: cannot find -lpthreads

Question

I have c++ project that was smoothly running on a given machine, and now I am trying to compile it on another one with the same operating system (Xubuntu 14.04).

I've installed all the dependencies and I'am using cmake to build the project, although it stops with the following error:

Determining if the function pthread_create exists in the pthreads failed with the following output: ... /usr/bin/ld: cannot find -lpthreads

The cmakelists.txt lines that include the compiler flags are as follows:

set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -lpthread -DNDEBUG -DEIGEN_MPL2_ONLY")
set(CMAKE_C_FLAGS_DEBUG "-g -O0 -Wall -lpthread -DEIGEN_MPL2_ONLY")
set(CMAKE_CXX_FLAGS "${CMAKE_C_FLAGS} -O3 -lpthread -I/usr/include/freetype2 -DNDEBUG -DEIGEN_MPL2_ONLY")
set(CMAKE_CXX_FLAGS_DEBUG "-g -O0 -Wall -lpthread -I/usr/include/freetype2 -DEIGEN_MPL2_ONLY")

I have done some research and have already tried the following:

-used -pthread/-threads/-thread/-lpthreads instead of -lpthread, which does not solve the issue and makes the build stop without finding the following package: find_package (Threads)

• changed the order of -lpthread in the cmakelists line above, which gives the same error
• used different versions o gcc/g++: tried 4.4, 4.6 and 4.8, without any change
• created a symbolic link to libpthread.so in /usr/lib/, without any change

I would appreciate some help, since I am already short on ideas on what to try next.

Edit 1

The library is where it should:

$ find /lib -name "*pthread*"
/lib/x86_64-linux-gnu/libpthread-2.19.so
/lib/x86_64-linux-gnu/libpthread.so.0

The pthread_create is also found:

$ nm /lib/x86_64-linux-gnu/libpthread.so.0 | grep "pthread_create"
0000000000008430 t __pthread_create_2_1
00000000000081430 T pthread_create@@GLIBC_2.2.5

I have also verified that both libpthread-stubs0 and libc6-dev are present.

Edit 2

This is part of the FindThreads.cmake file content, located in /usr/share/cmake-2.8/Modules/:

if(CMAKE_HAVE_SPROC_H AND NOT CMAKE_THREAD_PREFER_PTHREAD)
  # We have sproc
  set(CMAKE_USE_SPROC_INIT 1)
else()
  # Do we have pthreads?
  CHECK_INCLUDE_FILES("pthread.h" CMAKE_HAVE_PTHREAD_H)
  if(CMAKE_HAVE_PTHREAD_H)

    #
    # We have pthread.h
    # Let's check for the library now.
    #
    set(CMAKE_HAVE_THREADS_LIBRARY)
    if(NOT THREADS_HAVE_PTHREAD_ARG)
      # Check if pthread functions are in normal C library
      CHECK_SYMBOL_EXISTS(pthread_create pthread.h CMAKE_HAVE_LIBC_CREATE)
      if(CMAKE_HAVE_LIBC_CREATE)
        set(CMAKE_THREAD_LIBS_INIT "")
        set(CMAKE_HAVE_THREADS_LIBRARY 1)
        set(Threads_FOUND TRUE)
      endif()

      if(NOT CMAKE_HAVE_THREADS_LIBRARY)
        # Do we have -lpthreads
        CHECK_LIBRARY_EXISTS(pthreads pthread_create "" CMAKE_HAVE_PTHREADS_CREATE)
        if(CMAKE_HAVE_PTHREADS_CREATE)
          set(CMAKE_THREAD_LIBS_INIT "-lpthreads")
          set(CMAKE_HAVE_THREADS_LIBRARY 1)
          set(Threads_FOUND TRUE)
        endif()

        # Ok, how about -lpthread
        CHECK_LIBRARY_EXISTS(pthread pthread_create "" CMAKE_HAVE_PTHREAD_CREATE)
        if(CMAKE_HAVE_PTHREAD_CREATE)
          set(CMAKE_THREAD_LIBS_INIT "-lpthread")
          set(CMAKE_HAVE_THREADS_LIBRARY 1)
          set(Threads_FOUND TRUE)
        endif()

        if(CMAKE_SYSTEM MATCHES "SunOS.*")
          # On sun also check for -lthread
          CHECK_LIBRARY_EXISTS(thread thr_create "" CMAKE_HAVE_THR_CREATE)
          if(CMAKE_HAVE_THR_CREATE)
            set(CMAKE_THREAD_LIBS_INIT "-lthread")
            set(CMAKE_HAVE_THREADS_LIBRARY 1)
            set(Threads_FOUND TRUE)
          endif()
        endif()
      endif()
    endif()

    if(NOT CMAKE_HAVE_THREADS_LIBRARY)
      # If we did not found -lpthread, -lpthread, or -lthread, look for -pthread
      if("THREADS_HAVE_PTHREAD_ARG" MATCHES "^THREADS_HAVE_PTHREAD_ARG")
        message(STATUS "Check if compiler accepts -pthread")
        try_run(THREADS_PTHREAD_ARG THREADS_HAVE_PTHREAD_ARG
          ${CMAKE_BINARY_DIR}
          ${CMAKE_ROOT}/Modules/CheckForPthreads.c
          CMAKE_FLAGS -DLINK_LIBRARIES:STRING=-pthread
          COMPILE_OUTPUT_VARIABLE OUTPUT)

        if(THREADS_HAVE_PTHREAD_ARG)
          if(THREADS_PTHREAD_ARG STREQUAL "2")
            set(Threads_FOUND TRUE)
            message(STATUS "Check if compiler accepts -pthread - yes")
          else()
            message(STATUS "Check if compiler accepts -pthread - no")
            file(APPEND
              ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log
              "Determining if compiler accepts -pthread returned ${THREADS_PTHREAD_ARG} instead of 2. The compiler had the following output:\n${OUTPUT}\n\n")
          endif()
        else()
          message(STATUS "Check if compiler accepts -pthread - no")
          file(APPEND
            ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log
            "Determining if compiler accepts -pthread failed with the following output:\n${OUTPUT}\n\n")
        endif()

      endif()

      if(THREADS_HAVE_PTHREAD_ARG)
        set(Threads_FOUND TRUE)
        set(CMAKE_THREAD_LIBS_INIT "-pthread")
      endif()

    endif()
  endif()
endif()

Edit 3

Used a minimal Cmakelists.txt as follows:

cmake_minimum_required (VERSION 2.4)
find_package(Threads)

Which produced the following output:

-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found.
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE 

Answer 1

The problem was happening when running cmake. Though, in this case cmake was not the problem the error was silent and the -lpthreads related error/warning was the only thing being written to the cmake error log file, although that was not causing any issue. I've done a minimal version of the cmakelists.txt and started testing it line by line until I found which package was causing it to stop: finally I found it was a version mismatch...

Hint: search for the actual error message

Typically you'd look for the last error message. However, this (often useful) strategy in such cases leads astray.

What you are looking at is the CMakeCache.txt, the CMakeOutput.log or the CMakeError.log. How comes? When some of the macros or tests in the configure phase fails, CMake "helpfully" dumps these files to the output. Unfortunately, these files can be thousands of lines long, and typically contain lots of "*** Error: xyz" entries, for various configure checks. The one for "-lpthreads" just accidentally happened to be the last one in the log...

Solution: go through the log from the top, identify the section with the configure checks, find the last configure check prior to the point, where CMake identifies failure and dumps its logs. You might also try so search for the text "Configuring incomplete, errors occurred!"

Typically you'll either find a very precise actual error message there, or at least you find the name / path of the macro or function called last, and this allows you to pinpoint down what actually went wrong.