OpenMP problems on Apple M1 hardware #610

d3e5560 · 2022-11-21T03:56:47Z

No description provided.

d3e5560 · 2022-11-21T04:13:34Z

Compiling NEPR of a macintosh Powerbook Pro Apple M1 Max chipset, OS=Ventura 13.0.1.
The error is encountered when compiling the code, following these instructions (https://neper.info/doc/introduction.html#installing-neper) exactly.

There appears to be some problem with accessing the libraries for OpenMP appropriately in the new instances installed by XCode. The offending bit of code is when attempting to access <omp.h>.

I have tried many work-arounds, each of them failing to resolve the problem. I am hoping that the code authors are routinely compiling on a macintosh (they appear quite mac savvy), and perhaps have some resolution for this compilation failure. Any help that can be provided would be most appreciated.

Full "make" output appears below.

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In file included from /Users/woodbd/codes/neper/src/neut/neut_odf/neut_odf1.cpp:5:
/Users/woodbd/codes/neper/src/neut/neut_odf/neut_odf_.h:5:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
In file included from /Users/woodbd/codes/neper/src/neut/neut_odf/neut_odf2.cpp:5:
/Users/woodbd/codes/neper/src/neut/neut_odf/neut_odf_.h:5:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
In file included from /Users/woodbd/codes/neper/src/neut/neut_odf/neut_odf3.cpp:5:
/Users/woodbd/codes/neper/src/neut/neut_odf/neut_odf_.h:5:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
/Users/woodbd/codes/neper/src/neut/neut_mesh/neut_mesh_fprintf/neut_mesh_fprintf_bcs/neut_mesh_fprintf_bcs1.c:19:7: warning: variable 'bcqty' set but not used [-Wunused-but-set-variable]
int bcqty = 0;
^
1 warning generated.
In file included from /Users/woodbd/codes/neper/src/neut/neut_seedset/neut_seedset2.cpp:6:
In file included from /Users/woodbd/codes/neper/src/neut/neut_structs/neut_nfcloud_struct.hpp:3:
/Users/woodbd/codes/neper/src/contrib/nanoflann/nanoflann.hpp:1477:36: warning: definition of implicit copy constructor for 'KDTreeSingleIndexDynamicAdaptor_<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]
KDTreeSingleIndexDynamicAdaptor_ operator=( const KDTreeSingleIndexDynamicAdaptor_& rhs ) {
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.0.sdk/usr/include/c++/v1/_memory/allocator.h:154:28: note: in implicit copy constructor for 'nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>' first required here
::new ((void)__p) _Up(_VSTD::forward<_Args>(_args)...);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.0.sdk/usr/include/c++/v1/memory/allocator_traits.h:290:13: note: in instantiation of function template specialization 'std::allocator<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>>::construct<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>, const nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3> &>' requested here
__a.construct(__p, _VSTD::forward<Args>(args)...);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.0.sdk/usr/include/c++/v1/vector:1085:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>>>::construct<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>, const nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3> &, void>' requested here
__alloc_traits::construct(this->__alloc(), _VSTD::__to_address(__pos), _x);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.0.sdk/usr/include/c++/v1/vector:1178:9: note: in instantiation of member function 'std::vector<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>>::__construct_at_end' requested here
construct_at_end(n, x);
^
/Users/woodbd/codes/neper/src/contrib/nanoflann/nanoflann.hpp:1755:30: note: in instantiation of member function 'std::vector<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>>::vector' requested here
std::vector<my_kd_tree_t> index(treeCount, my_kd_tree_t(dim /dim/, dataset, treeIndex, index_params));
^
/Users/woodbd/codes/neper/src/contrib/nanoflann/nanoflann.hpp:1785:4: note: in instantiation of member function 'nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>::init' requested here
init();
^
/Users/woodbd/codes/neper/src/neut/neut_seedset/neut_seedset2.cpp:161:21: note: in instantiation of member function 'nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>::KDTreeSingleIndexDynamicAdaptor' requested here
(*pnf_tree) = new NFTREE (3, *pnf_cloud);
^
In file included from /Users/woodbd/codes/neper/src/neut/neut_mesh/neut_mesh_geom/neut_mesh_geom1.cpp:5:
In file included from /Users/woodbd/codes/neper/src/neut/neut_mesh/neut_mesh_geom/neut_mesh_geom.h:12:
In file included from /Users/woodbd/codes/neper/src/neut/neut_structs/neut_nfcloud_struct.hpp:3:
/Users/woodbd/codes/neper/src/contrib/nanoflann/nanoflann.hpp:1477:36: warning: definition of implicit copy constructor for 'KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]
KDTreeSingleIndexDynamicAdaptor operator=( const KDTreeSingleIndexDynamicAdaptor& rhs ) {
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.0.sdk/usr/include/c++/v1/_memory/allocator.h:154:28: note: in implicit copy constructor for 'nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>' first required here
::new ((void*)__p) _Up(_VSTD::forward<_Args>(_args)...);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.0.sdk/usr/include/c++/v1/memory/allocator_traits.h:290:13: note: in instantiation of function template specialization 'std::allocator<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>>::construct<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>, const nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3> &>' requested here
__a.construct(__p, _VSTD::forward<Args>(args)...);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.0.sdk/usr/include/c++/v1/vector:1085:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>>>::construct<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>, const nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3> &, void>' requested here
__alloc_traits::construct(this->__alloc(), _VSTD::__to_address(__pos), _x);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX13.0.sdk/usr/include/c++/v1/vector:1178:9: note: in instantiation of member function 'std::vector<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>>::construct_at_end' requested here
construct_at_end(n, x);
^
/Users/woodbd/codes/neper/src/contrib/nanoflann/nanoflann.hpp:1755:30: note: in instantiation of member function 'std::vector<nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>>::vector' requested here
std::vector<my_kd_tree_t> index(treeCount, my_kd_tree_t(dim /dim/, dataset, treeIndex, index_params));
^
/Users/woodbd/codes/neper/src/contrib/nanoflann/nanoflann.hpp:1785:4: note: in instantiation of member function 'nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>::init' requested here
init();
^
/Users/woodbd/codes/neper/src/neut/neut_mesh/neut_mesh_geom/neut_mesh_geom1.cpp:1221:17: note: in instantiation of member function 'nanoflann::KDTreeSingleIndexDynamicAdaptor<nanoflann::L2_Simple_Adaptor<double, NFCLOUD>, NFCLOUD, 3>::KDTreeSingleIndexDynamicAdaptor' requested here
nf_tree = new NFTREE (3, nf_cloud);
^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
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[ 94%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_png/nev_print_png_mesh/nev_print_png_mesh_3d/nev_print_png_mesh_3d1.c.o
[ 94%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_smoothing/nem_smoothing2.c.o
[ 94%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_png/nev_print_png_csys/nev_print_png_csys1.c.o
[ 94%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_pf/nev_print_pf2.c.o
[ 94%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh3.c.o
[ 94%] Building C object neper_m/CMakeFiles/neper_m.dir/nem/nem_tess/nem_tess1.c.o
[ 94%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_povray/nev_povray1.c.o
[ 94%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_utils/nem_utils.c.o
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[ 94%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_partition/nem_partition3.c.o
[ 94%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_writemesh/nem_writemesh2.c.o
[ 95%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_png/nev_print_png_mesh/nev_print_png_mesh_1d/nev_print_png_mesh_1d1.c.o
[ 95%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_transport/nem_transport2.c.o
[ 96%] Building C object neper_m/CMakeFiles/neper_m.dir/nem/nem_tess/nem_tess3.c.o
[ 97%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_meshing/nem_meshing_3d/nem_meshing_3d2.c.o
[ 97%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_order/nem_order2.c.o
[ 97%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_transform/nem_transform2.c.o
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[ 99%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_pf/nev_print_pf_ptsprint_density/nev_print_pf_ptsprint_density1.c.o
[ 99%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_meshing/nem_meshing_pinching/nem_meshing_pinching3.c.o
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[ 99%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_png/nev_print_png_mesh/nev_print_png_mesh1.c.o
[ 99%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_show/nev_show_point/nev_show_point1.c.o
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[100%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_png/nev_print_png_mesh/nev_print_png_mesh_3d/nev_print_png_mesh_3d2.c.o
[100%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_partition/nem_partition2.c.o
[100%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_png/nev_print_png_mesh/nev_print_png_mesh_nodes/nev_print_png_mesh_nodes1.c.o
[100%] Building C object neper_m/CMakeFiles/neper_m.dir/nem_meshing_para/nem_meshing_para_cl/nem_meshing_para_cl1.c.o
In file included from /Users/woodbd/codes/neper/src/neper_m/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh2.c:5:
/Users/woodbd/codes/neper/src/neper_m/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh.h:14:9: fatal error: 'omp.h' file not found
#include<omp.h>
^~~~~~~
In file included from /Users/woodbd/codes/neper/src/neper_m/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh1.c:5:
/Users/woodbd/codes/neper/src/neper_m/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh.h:14:9: fatal error: 'omp.h' file not found
#include<omp.h>
^~~~~~~
In file included from /Users/woodbd/codes/neper/src/neper_m/nem/nem_mesh_gmsh/nem_mesh_gmsh2.c:5:
/Users/woodbd/codes/neper/src/neper_m/nem/nem_mesh_gmsh/nem_mesh_gmsh.h:14:9: fatal error: 'omp.h' file not found
#include<omp.h>
^~~~~~~
In file included from /Users/woodbd/codes/neper/src/neper_m/nem/nem_mesh_gmsh/nem_mesh_gmsh1.c:5:
/Users/woodbd/codes/neper/src/neper_m/nem/nem_mesh_gmsh/nem_mesh_gmsh.h:14:9: fatal error: 'omp.h' file not found
#include<omp.h>
^~~~~~~
In file included from /Users/woodbd/codes/neper/src/neper_m/nem/nem_mesh_gmsh/nem_mesh_gmsh3.c:5:
/Users/woodbd/codes/neper/src/neper_m/nem/nem_mesh_gmsh/nem_mesh_gmsh.h:14:9: fatal error: 'omp.h' file not found
#include<omp.h>
^~~~~~~
In file included from /Users/woodbd/codes/neper/src/neper_m/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh3.c:5:
/Users/woodbd/codes/neper/src/neper_m/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh.h:14:9: fatal error: 'omp.h' file not found
#include<omp.h>
^~~~~~~
/Users/woodbd/codes/neper/src/neper_s/nes_pproc/nes_pproc_entity/nes_pproc_entity_builtin/nes_pproc_entity_builtin2.c:8:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
/Users/woodbd/codes/neper/src/neper_s/nes_pproc/nes_pproc_entity/nes_pproc_entity_builtin/nes_pproc_entity_builtin1.c:8:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
/Users/woodbd/codes/neper/src/neper_s/nes_pproc/nes_pproc_entity/nes_pproc_entity2.c:8:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
1 error generated.
1 error generated.
1 error generated.
make[2]: *** [neper_s/CMakeFiles/neper_s.dir/nes_pproc/nes_pproc_entity/nes_pproc_entity_builtin/nes_pproc_entity_builtin2.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [neper_s/CMakeFiles/neper_s.dir/nes_pproc/nes_pproc_entity/nes_pproc_entity2.c.o] Error 1
make[2]: *** [neper_m/CMakeFiles/neper_m.dir/nem/nem_mesh_gmsh/nem_mesh_gmsh2.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [neper_s/CMakeFiles/neper_s.dir/nes_pproc/nes_pproc_entity/nes_pproc_entity_builtin/nes_pproc_entity_builtin1.c.o] Error 1
/Users/woodbd/codes/neper/src/neper_v/nev_show/nev_show_point/nev_show_point1.c:31:7: warning: variable 'varqty' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if (status)
^~~~~~
/Users/woodbd/codes/neper/src/neper_v/nev_show/nev_show_point/nev_show_point1.c:56:27: note: uninitialized use occurs here
ut_free_2d_char (&vars, varqty);
^~~~~~
/Users/woodbd/codes/neper/src/neper_v/nev_show/nev_show_point/nev_show_point1.c:31:3: note: remove the 'if' if its condition is always true
if (status)
^~~~~~~~~~~
/Users/woodbd/codes/neper/src/neper_v/nev_show/nev_show_point/nev_show_point1.c:10:19: note: initialize the variable 'varqty' to silence this warning
int i, j, varqty, status;
^
= 0
1 error generated.
1 error generated.
make[2]: *** [neper_m/CMakeFiles/neper_m.dir/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh1.c.o] Error 1
make[2]: *** [neper_m/CMakeFiles/neper_m.dir/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh2.c.o] Error 1
1 warning generated.
/Users/woodbd/codes/neper/src/neper_v/nev_print/nev_print_pf/nev_print_pf2.c:263:12: warning: variable 'y' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
else if (!strcmp (Print.space, "ipf"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/woodbd/codes/neper/src/neper_v/nev_print/nev_print_pf/nev_print_pf2.c:272:81: note: uninitialized use occurs here
fprintf (file, "label("%s", scale(scale)*(%.3f, %.3f), NE);\n", legp, xmin, y);
^
/Users/woodbd/codes/neper/src/neper_v/nev_print/nev_print_pf/nev_print_pf2.c:263:8: note: remove the 'if' if its condition is always false
else if (!strcmp (Print.space, "ipf"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/woodbd/codes/neper/src/neper_v/nev_print/nev_print_pf/nev_print_pf2.c:248:21: note: initial/Users/woodbd/codes/neper/src/neper_s/nes_pproc/nes_pproc_entity/nes_pproc_entity_builtin/nes_pproc_entity_builtin3.c:8:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
ize the variable 'y' to silence this warning
double xmin = 0, y, xshift;
^
= 0.0
1 error generated.
1 error generated.
1 error generated.
1 error generated.
make[2]: *** [neper_m/CMakeFiles/neper_m.dir/nem_meshing/nem_meshing_2d/nem_meshing_2d_face_mesh_gmsh/nem_meshing_2d_face_mesh_gmsh3.c.o] Error 1
make[2]: make[2]: *** [neper_m/CMakeFiles/neper_m.dir/nem/nem_mesh_gmsh/nem_mesh_gmsh3.c.o] Error 1
*** [neper_s/CMakeFiles/neper_s.dir/nes_pproc/nes_pproc_entity/nes_pproc_entity_builtin/nes_pproc_entity_builtin3.c.o] Error 1
make[2]: *** [neper_m/CMakeFiles/neper_m.dir/nem/nem_mesh_gmsh/nem_mesh_gmsh1.c.o] Error 1
make[1]: *** [neper_s/CMakeFiles/neper_s.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
1 warning generated.
make[1]: *** [neper_m/CMakeFiles/neper_m.dir/all] Error 2
[100%] Linking CXX static library libneper_v.a
[100%] Built target neper_v
make: *** [all] Error 2

d3e5560 changed the title ls OpenMP problems on Apple M1 hardware Nov 21, 2022

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OpenMP problems on Apple M1 hardware #610

OpenMP problems on Apple M1 hardware #610

d3e5560 commented Nov 21, 2022 •

edited by rquey

d3e5560 commented Nov 21, 2022

OpenMP problems on Apple M1 hardware #610

OpenMP problems on Apple M1 hardware #610

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d3e5560 commented Nov 21, 2022 • edited by rquey

d3e5560 commented Nov 21, 2022

d3e5560 commented Nov 21, 2022 •

edited by rquey