CMAKE_HAVE_LIBC_PTHREAD - Failed; Built target lammps make: *** [all] Error 2

LAMMPS LAMMPS Installation
,
1

During the cmake, which I have as:
cmake -D CMAKE_INSTALL_PREFIX=/path/to/lammps-23Jun2022 -D ENABLE_TESTING=yes -D CMAKE_CXX_COMPILER=g++ -D MPI_CXX_COMPILER=mpicxx -D BUILD_MPI=yes -D BUILD_OMP=yes -D PKG_VTK=yes -D PKG_GRANULAR=on -D PKG_EXTRA-FIX=on -D PKG_FIX=on -D CMAKE_BUILD_TYPE=Release -D CMAKE_CXX_FLAGS_RELEASE="-Ofast -DNDEBUG" -D PKG_USER-OMP=yes -D PKG_MOLECULE=yes ../cmake

-- Found Python: /usr/local/bin/python3.7 (found version "3.7.3") found components: Interpreter 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- 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  
-- Looking for a Fortran compiler
-- Looking for a Fortran compiler - /usr/bin/f95
-- Skipping Tests for the LAMMPS Fortran Module: cannot identify Fortran compiler
-- Skipping Tests for the LAMMPS Python Module: must enable BUILD_SHARED_LIBS
-- Found Python: /usr/local/bin/python3.7 (found suitable version "3.7.3", minimum required is "3.5") found components: Interpreter 
-- Could NOT find YAML (missing: YAML_LIBRARY YAML_INCLUDE_DIR) 
-- Downloading https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz

It ends with:

[ 80%] Building CXX object CMakeFiles/lammps.dir/path/to/lammps-23Jun2022/src/VTK/dump_vtk.cpp.o
[ 80%] Linking CXX static library liblammps.a
[ 80%] Built target lammps
make: *** [all] Error 2

cat  ./CMakeFiles/CMakeError.log 
Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /path/to/lammps-23Jun2022/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_46140/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_46140.dir/build.make CMakeFiles/cmTC_46140.dir/build
gmake[1]: Entering directory `/path/to/lammps-23Jun2022/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_46140.dir/src.c.o
/cm/local/apps/gcc/7.2.0/bin/gcc -DCMAKE_HAVE_LIBC_PTHREAD  -fPIE -o CMakeFiles/cmTC_46140.dir/src.c.o -c /path/to/lammps-23Jun2022/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_46140
/path/to/cmake-3.21.2/cmake-3.21.2-linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_46140.dir/link.txt --verbose=1
/cm/local/apps/gcc/7.2.0/bin/gcc CMakeFiles/cmTC_46140.dir/src.c.o -o cmTC_46140 
CMakeFiles/cmTC_46140.dir/src.c.o: In function `main':
src.c:(.text+0x2f): undefined reference to `pthread_create'
src.c:(.text+0x3b): undefined reference to `pthread_detach'
src.c:(.text+0x47): undefined reference to `pthread_cancel'
src.c:(.text+0x58): undefined reference to `pthread_join'
src.c:(.text+0x6c): undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
gmake[1]: *** [cmTC_46140] Error 1
gmake[1]: Leaving directory `/path/to/lammps-23Jun2022/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_46140/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: /path/to/lammps-23Jun2022/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_3a19c/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_3a19c.dir/build.make CMakeFiles/cmTC_3a19c.dir/build
gmake[1]: Entering directory `/path/to/lammps-23Jun2022/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_3a19c.dir/CheckFunctionExists.c.o
/cm/local/apps/gcc/7.2.0/bin/gcc   -DCHECK_FUNCTION_EXISTS=pthread_create -fPIE -o CMakeFiles/cmTC_3a19c.dir/CheckFunctionExists.c.o -c /path/to/cmake-3.21.2/cmake-3.21.2-linux-x86_64/share/cmake-3.21/Modules/CheckFunctionExists.c
Linking C executable cmTC_3a19c
/path/to/cmake-3.21.2/cmake-3.21.2-linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_3a19c.dir/link.txt --verbose=1
/cm/local/apps/gcc/7.2.0/bin/gcc   -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTC_3a19c.dir/CheckFunctionExists.c.o -o cmTC_3a19c  -lpthreads 
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
gmake[1]: *** [cmTC_3a19c] Error 1
gmake[1]: Leaving directory `/path/to/lammps-23Jun2022/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_3a19c/fast] Error 2

Modules & versions loaded:

openmpi/gcc/64/4.0.0 
openblas/0.3.3   
ffmpeg/4.2.1
cmake/3.21.2 
gcc/7.2.0

RHEL 7. Other CMake errors::

[  6%] Building C object _deps/libyaml-build/CMakeFiles/yaml.dir/src/dumper.c.o
/path/to/lammps-23Jun2022/build/_deps/libyaml-src/src/api.c: In function ‘yaml_get_version_string’:
/path/to/lammps-23Jun2022/build/_deps/libyaml-src/src/api.c:11:12: error: ‘YAML_VERSION_STRING’ undeclared (first use in this function); did you mean ‘YAML_PARSE_END_STATE’?
     return YAML_VERSION_STRING;
            ^~~~~~~~~~~~~~~~~~~
            YAML_PARSE_END_STATE
/path/to/lammps-23Jun2022/build/_deps/libyaml-src/src/api.c:11:12: note: each undeclared identifier is reported only once for each function it appears in
/path/to/lammps-23Jun2022/build/_deps/libyaml-src/src/api.c: In function ‘yaml_get_version’:
/path/to/lammps-23Jun2022/build/_deps/libyaml-src/src/api.c:21:14: error: ‘YAML_VERSION_MAJOR’ undeclared (first use in this function); did you mean ‘YAML_PARSER_ERROR’?
     *major = YAML_VERSION_MAJOR;
              ^~~~~~~~~~~~~~~~~~
              YAML_PARSER_ERROR
/path/to/lammps-23Jun2022/build/_deps/libyaml-src/src/api.c:22:14: error: ‘YAML_VERSION_MINOR’ undeclared (first use in this function); did you mean ‘YAML_VERSION_MAJOR’?
     *minor = YAML_VERSION_MINOR;
              ^~~~~~~~~~~~~~~~~~
              YAML_VERSION_MAJOR
/path/to/lammps-23Jun2022/build/_deps/libyaml-src/src/api.c:23:14: error: ‘YAML_VERSION_PATCH’ undeclared (first use in this function); did you mean ‘YAML_VERSION_MAJOR’?
     *patch = YAML_VERSION_PATCH;
              ^~~~~~~~~~~~~~~~~~
              YAML_VERSION_MAJOR
make[2]: *** [_deps/libyaml-build/CMakeFiles/yaml.dir/src/api.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[  6%] Building CXX object CMakeFiles/lammps.dir/moto/home/rk3199/lammps-23Jun2022/src/angle.cpp.o
make[1]: *** [_deps/libyaml-build/CMakeFiles/yaml.dir/all] Error 2

-- Found Python: /usr/local/bin/python3.7 (found version "3.7.3") found components: Interpreter 
-- Could NOT find ClangFormat (missing: ClangFormat_EXECUTABLE) (Required is at least version "8.0")
-- Could NOT find ClangFormat (missing: ClangFormat_EXECUTABLE) (Required is at least version "8.0")
-- The following tools and libraries have been found and configured:

And why does it end with:

CMake Warning:
  Manually-specified variables were not used by the project:

    PKG_FIX
    PKG_USER-OMP

What am I doing wrong?

2

There is not enough information here.

You can avoid the YAML failure by disabling the unit testing.

I see that you are requesting packages “FIX” and “USER-OMP” that do not exist.
We regularly and automatically build on RHEL, but with the default compilers.

3

This is not an error. There are multiple ways to enable threads and CMake found one, but it was not the first it was looking for.

4

Well lo and behold I removed -D ENABLE_TESTING=yes, PKG_FIX=on & -D PKG_USER-OMP=yes and it completed. I take it I’d have to follow these instructions for OpenMP.

Thanks for your help.

Rob

5

The proper link is this one: 3.7. Packages with extra build options — LAMMPS documentation

Also, you may want to have a look at: 3.6. Include packages in build — LAMMPS documentation

6

I see that mentions GPU, if I enable the GPU package and this runs on a node without a GPU is there a way to toggle on/off whether a GPU would be needed? In other words, if I enable GPU and it’s used on a non-GPU compute node will it error out?

7

Yes and no. The executable may include the GPU package (or KOKKOS with GPU support), but that will not automatically use the GPU. You need to request using GPU or KOKKOS enabled styles (either explicitly or with the -sf or -suffix flag or suffix command. If you do that on a node without a GPU you get an error.

8

So I get this error:

/host_config.h:139:2: error: #error -- unsupported GNU version! gcc versions later than 9 are not supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
  139 | #error -- unsupported GNU version! gcc versions later than 9 are not supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
      |  ^~~~~
CMake Error at cuda_compile_fatbin_1_generated_lal_atom.cu.fatbin.Release.cmake:212 (message):
  Error generating
  /path/to/lammps-15Sep2022/build/cuda_compile_fatbin_1_generated_lal_atom.cu.fatbin

So I added CUDA_NVCC_FLAGS:STRING=allow-unsupported-compiler to CMakeCache.txt and now get this:

[  4%] Building NVCC fatbin file cuda_compile_fatbin_1_generated_lal_born.cu.fatbin
nvcc fatal   : A single input file is required for a non-link phase when an outputfile is specified

CMake Error at cuda_compile_fatbin_1_generated_lal_atom.cu.fatbin.Release.cmake:212 (message):
  Error generating