thirdPartyLibs Compilation Error: conduit and scotch libraries

[rafaelmarch3]

I'm facing an error when trying to compile the thirdPartyLibs. Most of the libraries compile without issues, but for conduit and scotch libraries, the following errors appear:

conduit

[ 82%] Linking CXX executable conduit_relay_io_ls
[ 83%] Linking CXX executable conduit_relay_node_viewer
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::check_if_conduit_leaf_is_compatible_with_hdf5_obj(conduit::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)':
conduit_relay_io_hdf5.cpp:(.text+0x1b4f): undefined reference to `H5Oget_info'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::check_if_conduit_object_is_compatible_with_hdf5_tree(conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)':
conduit_relay_io_hdf5.cpp:(.text+0x2b11): undefined reference to `H5Oget_info'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::check_if_conduit_list_is_compatible_with_hdf5_tree(conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)':
conduit_relay_io_hdf5.cpp:(.text+0x30f1): undefined reference to `H5Oget_info'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::write_conduit_empty_to_hdf5_group(long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
conduit_relay_io_hdf5.cpp:(.text+0x5e56): undefined reference to `H5Oget_info_by_name'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::write_conduit_leaf_to_hdf5_group(conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, conduit::Node const&)':
conduit_relay_io_hdf5.cpp:(.text+0xc6d5): undefined reference to `H5Oget_info_by_name'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::write_conduit_node_children_to_hdf5_group(conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, conduit::Node const&) [clone .localalias.355]':
conduit_relay_io_hdf5.cpp:(.text+0xd7b8): undefined reference to `H5Oget_info_by_name'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::read_hdf5_group_into_conduit_node(long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, conduit::Node const&, conduit::Node&)':
conduit_relay_io_hdf5.cpp:(.text+0xf184): undefined reference to `H5Oget_info'
conduit_relay_io_hdf5.cpp:(.text+0xf283): undefined reference to `H5Literate'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::h5l_iterate_traverse_op_func(long, char const*, H5L_info_t const*, void*)':
conduit_relay_io_hdf5.cpp:(.text+0xf811): undefined reference to `H5Oget_info_by_name'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::read_hdf5_tree_into_conduit_node(long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, conduit::Node const&, conduit::Node&)':
conduit_relay_io_hdf5.cpp:(.text+0x106bb): undefined reference to `H5Oget_info'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::hdf5_group_list_child_names(long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
conduit_relay_io_hdf5.cpp:(.text+0x1259a): undefined reference to `H5Oget_info_by_name'
collect2: error: ld returned 1 exit status
make[6]: *** [libs/relay/CMakeFiles/conduit_relay_node_viewer.dir/build.make:101: libs/relay/conduit_relay_node_viewer] Error 1
make[5]: *** [CMakeFiles/Makefile2:555: libs/relay/CMakeFiles/conduit_relay_node_viewer.dir/all] Error 2
make[5]: *** Waiting for unfinished jobs....
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::check_if_conduit_leaf_is_compatible_with_hdf5_obj(conduit::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)':
conduit_relay_io_hdf5.cpp:(.text+0x1b4f): undefined reference to `H5Oget_info'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::check_if_conduit_object_is_compatible_with_hdf5_tree(conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)':
conduit_relay_io_hdf5.cpp:(.text+0x2b11): undefined reference to `H5Oget_info'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::check_if_conduit_list_is_compatible_with_hdf5_tree(conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)':
conduit_relay_io_hdf5.cpp:(.text+0x30f1): undefined reference to `H5Oget_info'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::write_conduit_empty_to_hdf5_group(long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
conduit_relay_io_hdf5.cpp:(.text+0x5e56): undefined reference to `H5Oget_info_by_name'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::write_conduit_leaf_to_hdf5_group(conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, conduit::Node const&)':
conduit_relay_io_hdf5.cpp:(.text+0xc6d5): undefined reference to `H5Oget_info_by_name'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::write_conduit_node_children_to_hdf5_group(conduit::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long, conduit::Node const&) [clone .localalias.355]':
conduit_relay_io_hdf5.cpp:(.text+0xd7b8): undefined reference to `H5Oget_info_by_name'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::read_hdf5_group_into_conduit_node(long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, conduit::Node const&, conduit::Node&)':
conduit_relay_io_hdf5.cpp:(.text+0xf184): undefined reference to `H5Oget_info'
conduit_relay_io_hdf5.cpp:(.text+0xf283): undefined reference to `H5Literate'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::h5l_iterate_traverse_op_func(long, char const*, H5L_info_t const*, void*)':
conduit_relay_io_hdf5.cpp:(.text+0xf811): undefined reference to `H5Oget_info_by_name'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::read_hdf5_tree_into_conduit_node(long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, conduit::Node const&, conduit::Node&)':
conduit_relay_io_hdf5.cpp:(.text+0x106bb): undefined reference to `H5Oget_info'
../../lib/libconduit_relay.a(conduit_relay_io_hdf5.cpp.o): In function `conduit::relay::io::hdf5_group_list_child_names(long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
conduit_relay_io_hdf5.cpp:(.text+0x1259a): undefined reference to `H5Oget_info_by_name'
collect2: error: ld returned 1 exit status
make[6]: *** [libs/relay/CMakeFiles/conduit_relay_io_ls.dir/build.make:101: libs/relay/conduit_relay_io_ls] Error 1
make[5]: *** [CMakeFiles/Makefile2:583: libs/relay/CMakeFiles/conduit_relay_io_ls.dir/all] Error 2
make[4]: *** [Makefile:136: all] Error 2
make[3]: *** [CMakeFiles/conduit.dir/build.make:86: conduit/src/conduit-stamp/conduit-build] Error 2
make[2]: *** [CMakeFiles/Makefile2:343: CMakeFiles/conduit.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:350: CMakeFiles/conduit.dir/rule] Error 2
make: *** [Makefile:199: conduit] Error 2

scotch

[ 72%] Linking C executable ../../bin/amk_fft2
[ 72%] Linking C executable ../../bin/amk_grf
[ 72%] Built target amk_fft2
[ 72%] Linking C executable ../../bin/amk_hy
../../lib/libscotch.a(parser_yy.c.o): In function `scotchyyparse':
parser_yy.c:(.text+0xb1b): undefined reference to `scotchyylex'
collect2: error: ld returned 1 exit status
make[6]: *** [src/scotch/CMakeFiles/amk_grf.dir/build.make:102: bin/amk_grf] Error 1
make[5]: *** [CMakeFiles/Makefile2:771: src/scotch/CMakeFiles/amk_grf.dir/all] Error 2
make[5]: *** Waiting for unfinished jobs....
[ 72%] Built target amk_hy
make[4]: *** [Makefile:146: all] Error 2
make[3]: *** [CMakeFiles/scotch.dir/build.make:86: scotch/src/scotch-stamp/scotch-build] Error 2
make[2]: *** [CMakeFiles/Makefile2:604: CMakeFiles/scotch.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:611: CMakeFiles/scotch.dir/rule] Error 2
make: *** [Makefile:329: scotch] Error 2

Any help is appreciated.

Rafael.

[bmhan12]

The conduit error seems to be related to HDF5. Maybe there is an issue with the HDF5 version, or spack variants between HDF5/conduit? Haven't seen this specific error before so cannot say for certain.

The scotch error is related to one of its dependencies, flex.
Try building a different version of flex, or let spack build flex if you are specifying an external flex.

Some posts I found related to the scotch error:
https://stackoverflow.com/questions/34782625/undefined-reference-to-yylex
 
Seifert69/DikuMUD3#70

[rafaelmarch3]

Thanks for your reply. I have flex 2.6.1, which is apparently not compatible with the thirdPartyLibs version of Scotch. I'm trying to compile a different version of flex since I cannot install packages on my corporation's cluster.