Compilation error: Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed

[morien]

System: CentOS 8
uname -a
Linux xxx.xxx.xxx 4.18.0-147.5.1.el8_1.x86_64 #1 SMP Wed Feb 5 02:00:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

I've got boost 1.66 (plus devel) and cmake 3.20.2, so I have my dependencies satisfied, but I'm unable to compile, seeing this in my CMakeError.log:

Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /data/metagenomics_apps/taxator-tk/core/bin/CMakeFiles/CMakeTmp

Run Build Command(s):/bin/gmake -f Makefile cmTC_8f709/fast && /bin/gmake  -f CMakeFiles/cmTC_8f709.dir/build.make CMakeFiles/cmTC_8f709.dir/build
gmake[1]: Entering directory '/data/metagenomics_apps/taxator-tk/core/bin/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_8f709.dir/src.c.o
/bin/cc -DCMAKE_HAVE_LIBC_PTHREAD   -o CMakeFiles/cmTC_8f709.dir/src.c.o -c /data/metagenomics_apps/taxator-tk/core/bin/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_8f709
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_8f709.dir/link.txt --verbose=1
/bin/cc -rdynamic CMakeFiles/cmTC_8f709.dir/src.c.o -o cmTC_8f709 
CMakeFiles/cmTC_8f709.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'
collect2: error: ld returned 1 exit status
gmake[1]: *** [CMakeFiles/cmTC_8f709.dir/build.make:99: cmTC_8f709] Error 1
gmake[1]: Leaving directory '/data/metagenomics_apps/taxator-tk/core/bin/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:127: cmTC_8f709/fast] Error 2


Source file was:
#include <pthread.h>

static 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: /data/metagenomics_apps/taxator-tk/core/bin/CMakeFiles/CMakeTmp

Run Build Command(s):/bin/gmake -f Makefile cmTC_4c3a1/fast && /bin/gmake  -f CMakeFiles/cmTC_4c3a1.dir/build.make CMakeFiles/cmTC_4c3a1.dir/build
gmake[1]: Entering directory '/data/metagenomics_apps/taxator-tk/core/bin/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_4c3a1.dir/CheckFunctionExists.c.o
/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_4c3a1.dir/CheckFunctionExists.c.o -c /usr/share/cmake/Modules/CheckFunctionExists.c
Linking C executable cmTC_4c3a1
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_4c3a1.dir/link.txt --verbose=1
/bin/cc  -DCHECK_FUNCTION_EXISTS=pthread_create -rdynamic CMakeFiles/cmTC_4c3a1.dir/CheckFunctionExists.c.o -o cmTC_4c3a1  -lpthreads 
/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
gmake[1]: *** [CMakeFiles/cmTC_4c3a1.dir/build.make:99: cmTC_4c3a1] Error 1
gmake[1]: Leaving directory '/data/metagenomics_apps/taxator-tk/core/bin/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:127: cmTC_4c3a1/fast] Error 2

[fungs]

Hey, thanks for reporting this issue! That is a strange error and seems to have nothing to do with taxator-tk itself, but the cmake build system. I currently don't have the time to test myself, so I'm guessing by the error message:

The library to link to for using POSIX threads (pthreads) is not available in the search path. taxator-tk uses multiple CPU cores with threads. Can you look for the library using

find /usr/lib /lib -name libpthread.so

? For me (Ubuntu/Debian) this yields

> find /usr/lib /lib -name libpthread.so
/usr/lib/x86_64-linux-gnu/libpthread.so

> dpkg -S /usr/lib/x86_64-linux-gnu/libpthread.so
libc6-dev:amd64: /usr/lib/x86_64-linux-gnu/libpthread.so

So the latter package contains the libary. However, it should be installed on every modern Linux system, so I suspect that the cmake check simply does not work correctly for some reason.

[fungs]

Does the binary package which you can download in the releases section on GitHub work for you?

[morien]

Thanks for responding, I appreciate it.

Find produces this, so the pthreads library is installed:

> find /usr/lib /lib -name libpthread.so
/usr/lib/libpthread.so

I don't know if there's a dpkg equivalent in CentOS that will reproduce the output you have for the second command, but glibc-devel-2.28-189.el8.x86_64 is the equivalent package for libc6-dev, and it is installed.

I'm messing around with the binary (thanks, I didn't realize it was available, I usually compile from source if the conda install fails for a bioinformatic tool like this). I can get the help menu, but I don't seem to have a custom blastdb that's got a taxdump file, even though I have taxonIDs in all my custom blastdbs. So, I'll have to make one that lastal will accept as input before I test out the taxator binary otherwise I'll have to test with the entire NCBI NT, which seems excessive. I'll try this by the end of the week and report back.

[fungs]

The format or repacks is pretty simple and well documented. You will find some for download here:

https://nextcloud.bifo.helmholtz-hzi.de/s/kgtfteoQ9LfzQZx (it currently has a certificate error but otherwise works)

and an example on how to build one in this blog post

https://scienceblog.fungs.de/posts/taxator-tk-marine-refpack/

Regarding the error, I will give it a try in a CentOS environment once I've got some time. Could be, that this is an issue with the build system CMake itself.