Undefined symbols for architecture x86_64 when building software package - clang

Question

Currently trying to build the software package, Neper. I have navigated many errors, but am currently stuck when it comes to this one.
In Terminal (mac), when I build using the make command, I get the following output:
[ 2%] Built target muparser
[ 7%] Built target ut
[ 13%] Built target orilib
[ 42%] Built target neut
[ 53%] Built target neper_v
[ 69%] Built target neper_m
[100%] Built target neper_t
[100%] Linking CXX executable neper
Undefined symbols for architecture x86_64:
"___kmpc_critical", referenced from:
_.omp_outlined. in libneper_m.a(nem_meshing_2D1.c.o)
_.omp_outlined. in libneper_m.a(nem_meshing_3D1.c.o)
_nem_meshing_2D_face in libneper_m.a(nem_meshing_2D2.c.o)
_nem_mesh_2d_gmsh in libneper_m.a(nem_mesh_gmsh1.c.o)
_nem_meshing_2D_face_algo in libneper_m.a(nem_meshing_2D3.c.o)
net_polycomp_cells_updatecell(POLY, SEEDSET, nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD, double>, NFCLOUD, 3, unsigned long>**, int*, int, POLY**, TDYN*) in libneper_t.a(net_polycomp3.cpp.o)
net_polycomp_poly(POLY, SEEDSET, nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD, double>, NFCLOUD, 3, unsigned long>**, int*, int, POLY*, TDYN*) in libneper_t.a(net_polycomp_poly1.cpp.o)
...
"___kmpc_dispatch_init_4", referenced from:
_.omp_outlined. in libneper_t.a(net_utils1.c.o)
_.omp_outlined. in libneper_m.a(nem_meshing_2D1.c.o)
_.omp_outlined..4 in libneper_m.a(nem_meshing_2D1.c.o)
_.omp_outlined. in libneper_m.a(nem_meshing_3D1.c.o)
_.omp_outlined. in libneper_t.a(net_polycomp2.cpp.o)
_.omp_outlined..2 in libneper_t.a(net_polycomp2.cpp.o)
_.omp_outlined..3 in libneper_t.a(net_polycomp2.cpp.o)
...
"___kmpc_dispatch_init_4u", referenced from:
_.omp_outlined..1 in libneper_t.a(net_ori_uniform4.cpp.o)
"___kmpc_dispatch_next_4", referenced from:
_.omp_outlined. in libneper_t.a(net_utils1.c.o)
_.omp_outlined. in libneper_m.a(nem_meshing_2D1.c.o)
_.omp_outlined..4 in libneper_m.a(nem_meshing_2D1.c.o)
_.omp_outlined. in libneper_m.a(nem_meshing_3D1.c.o)
_.omp_outlined. in libneper_t.a(net_polycomp2.cpp.o)
_.omp_outlined..2 in libneper_t.a(net_polycomp2.cpp.o)
_.omp_outlined..3 in libneper_t.a(net_polycomp2.cpp.o)
...
"___kmpc_dispatch_next_4u", referenced from:
_.omp_outlined..1 in libneper_t.a(net_ori_uniform4.cpp.o)
"___kmpc_end_critical", referenced from:
_.omp_outlined. in libneper_m.a(nem_meshing_2D1.c.o)
_.omp_outlined. in libneper_m.a(nem_meshing_3D1.c.o)
_nem_meshing_2D_face in libneper_m.a(nem_meshing_2D2.c.o)
_nem_mesh_2d_gmsh in libneper_m.a(nem_mesh_gmsh1.c.o)
_nem_meshing_2D_face_algo in libneper_m.a(nem_meshing_2D3.c.o)
net_polycomp_cells_updatecell(POLY, SEEDSET, nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD, double>, NFCLOUD, 3, unsigned long>**, int*, int, POLY**, TDYN*) in libneper_t.a(net_polycomp3.cpp.o)
net_polycomp_poly(POLY, SEEDSET, nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD, double>, NFCLOUD, 3, unsigned long>**, int*, int, POLY*, TDYN*) in libneper_t.a(net_polycomp_poly1.cpp.o)
...
"___kmpc_for_static_fini", referenced from:
_.omp_outlined. in libneut.a(neut_tesr_op1.c.o)
_.omp_outlined. in libneper_v.a(nev_data_utils1.c.o)
_.omp_outlined..51 in libneper_v.a(nev_data_utils1.c.o)
_.omp_outlined. in libneper_v.a(nev_print_tesr1.c.o)
_.omp_outlined..2 in libneper_v.a(nev_print_tesr1.c.o)
_.omp_outlined..3 in libneper_v.a(nev_print_tesr1.c.o)
_.omp_outlined..4 in libneper_v.a(nev_print_tesr1.c.o)
...
"___kmpc_for_static_init_4", referenced from:
_.omp_outlined. in libneut.a(neut_tesr_op1.c.o)
_.omp_outlined. in libneper_v.a(nev_data_utils1.c.o)
_.omp_outlined..51 in libneper_v.a(nev_data_utils1.c.o)
_.omp_outlined. in libneper_v.a(nev_print_tesr1.c.o)
_.omp_outlined..2 in libneper_v.a(nev_print_tesr1.c.o)
_.omp_outlined..3 in libneper_v.a(nev_print_tesr1.c.o)
_.omp_outlined..4 in libneper_v.a(nev_print_tesr1.c.o)
...
"___kmpc_for_static_init_4u", referenced from:
_.omp_outlined. in libneper_t.a(net_ori_uniform3.cpp.o)
_.omp_outlined..1 in libneper_t.a(net_ori_uniform3.cpp.o)
_.omp_outlined..2 in libneper_t.a(net_ori_uniform3.cpp.o)
_.omp_outlined. in libneper_t.a(net_ori_uniform4.cpp.o)
_.omp_outlined..3 in libneper_t.a(net_ori_uniform4.cpp.o)
_.omp_outlined..4 in libneper_t.a(net_ori_uniform4.cpp.o)
"___kmpc_fork_call", referenced from:
_main in neper.c.o
_neper_head in neper.c.o
_net_tess_tesr in libneper_t.a(net_utils1.c.o)
_neut_tesr_rotate in libneut.a(neut_tesr_op1.c.o)
_nem_meshing_2D in libneper_m.a(nem_meshing_2D1.c.o)
_nem_meshing_3D in libneper_m.a(nem_meshing_3D1.c.o)
_nev_data_id_colour in libneper_v.a(nev_data_utils1.c.o)
...
"___kmpc_global_thread_num", referenced from:
_nem_meshing_2D_face in libneper_m.a(nem_meshing_2D2.c.o)
_.omp_outlined. in libneper_t.a(net_polycomp2.cpp.o)
_.omp_outlined..2 in libneper_t.a(net_polycomp2.cpp.o)
_.omp_outlined..3 in libneper_t.a(net_polycomp2.cpp.o)
_.omp_outlined..4 in libneper_t.a(net_polycomp2.cpp.o)
_.omp_outlined..5 in libneper_t.a(net_polycomp2.cpp.o)
_.omp_outlined..6 in libneper_t.a(net_polycomp2.cpp.o)
...
"_omp_get_num_threads", referenced from:
_.omp_outlined. in neper.c.o
"_omp_get_thread_num", referenced from:
_.omp_outlined. in neper.c.o
_nem_mesh_2d_gmsh in libneper_m.a(nem_mesh_gmsh1.c.o)
_nem_mesh_3d_gmsh in libneper_m.a(nem_mesh_gmsh1.c.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [neper] Error 1
make[1]: *** [CMakeFiles/neper.dir/all] Error 2
make: *** [all] Error 2
It seems like it built all the way, but there is some mismatch with these kmpc symbols. From what I've read this seems like an issue on the compiler side (that could be wrong), but I have yet to find any solutions. Any idea on how to fix this error?

Answer 1

This looks similar to this intel question.
I suspect that you need to link with libomp (but that's just a guess)

Answer 2

Check if you have gcc-x, where x is a number. I saw several examples using gcc-8 but that won't work as I had gcc-10.
What I did was go to the terminal, wrote down gcc-, then tab so show the options I had. When using gcc-10 I was able to run openMP without problems
I did brew install gcc and brew install libomp.
cheers

Answer 3

Came across this when doing some search for the same issue. I'm sure you've already had this sorted out but just in case there are other people looking for this. Essentially the gcc comes with mac os is a fake one, it's really apple's clang with the alias "gcc". So the solution is to tell cmake to use the real gcc compilers by running the command:
$ cmake .. -DCMAKE_C_COMPILER=gcc-11 -DCMAKE_CXX_COMPILER=g++-11
I have gcc 11 installed, so you should replace 11 by whatever version you have there. If you don't have a real version of gcc, just do
$ brew install gcc