Building libmesh on HPC - undefined reference to std:file_system #29121

TheGreatCid · 2024-11-22T21:30:28Z

TheGreatCid
Nov 22, 2024

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Hi all,

I am building libmesh on an HPC. I running into issues with the update_and_rebuild_libmesh.sh script. The configuration phase finishes successfully but I run into issues with the build portion of the script.

I posted what outputs on error into the log box below.

I'm not sure what is causing this. Some type of linking issue?

Let me know what else I can provide to help solve this issue.

(Optional) code in question / simulation log / errors

/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
ld: skipping incompatible /usr/lib/libdl.so when searching for -ldl
ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
make[1]: *** [Makefile:14509: output_libmesh_version-opt] Error 1
make[1]: *** Waiting for unfinished jobs....
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
make[1]: *** [Makefile:14329: fparser_parse-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
make[1]: *** [Makefile:14455: meshnorm-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
make[1]: *** [Makefile:14419: meshdiff-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
make[1]: *** [Makefile:14365: matrixconvert-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
make[1]: *** [Makefile:14491: meshtool-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
make[1]: *** [Makefile:14383: meshavg-opt] Error 1
ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
make[1]: *** [Makefile:14563: splitter-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
ld: skipping incompatible /usr/lib/libc.so when searching for -lc
make[1]: *** [Makefile:14545: solution_components-opt] Error 1
make[1]: *** [Makefile:14293: compare-opt] Error 1
make[1]: *** [Makefile:14275: calculator-opt] Error 1
make[1]: *** [Makefile:14527: projection-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
make[1]: *** [Makefile:14437: meshid-opt] Error 1
make[1]: *** [Makefile:14401: meshbcid-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
ld: skipping incompatible /usr/lib/libdl.so when searching for -ldl
ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
make[1]: *** [Makefile:14347: getpot_parse-opt] Error 1
make[1]: *** [Makefile:14473: meshplot-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
make[1]: *** [Makefile:14311: embedding-opt] Error 1
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_find_extension() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_root_directory() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::has_filename() const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen/libsrc/core//libngcore.so: undefined reference to `std::filesystem::temp_directory_path[abi:cxx11]()'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::status(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::compare(std::filesystem::__cxx11::path const&) const'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::create_directories(std::filesystem::__cxx11::path const&)'
/ascldap/users/detorre/raccoon/moose/libmesh/build/contrib/netgen/build/netgen//libnglib.so: undefined reference to `std::filesystem::__cxx11::path::replace_extension(std::filesystem::__cxx11::path const&)'
make[1]: *** [Makefile:14251: amr-opt] Error 1
make[1]: Leaving directory '/home/detorre/raccoon/moose/libmesh/build'
make: *** [Makefile:34013: all-recursive] Error 1

Encountering Errors? Please include diagnostic output

##################################################################################################
Influential Environment Variables

CC=mpicc
CONDA_CHANNEL=https://conda.software.inl.gov/public
CONDA_EXE=/home/detorre/miniforge/bin/conda
CONDA_PYTHON_EXE=/home/detorre/miniforge/bin/python
CONDA_SHLVL=0
CURL_CA_BUNDLE=
CXX=mpicxx
F77=mpif77
F90=mpif90
F95=ifort
FC=mpif90
http_proxy=http://proxy.sandia.gov:80
https_proxy=http://proxy.sandia.gov:80
HTTPS_PROXY=http://proxy.sandia.gov:80
LD_LIBRARY_PATH=/opt/toss/openmpi/4.1/intel/lib:/usr/lib64/nvidia:/projects/global/toss4/compilers/intel/intel_2021/oneapi/compiler/2021.3.0/linux/lib:/projects/global/toss4/compilers/intel/intel_2021/oneapi/compiler/2021.3.0/linux/lib/x64:/projects/global/toss4/compilers/intel/intel_2021/oneapi/compiler/2021.3.0/linux/compiler/lib/intel64_lin
MODULESHOME=/usr/share/lmod/lmod
MOOSE_JOBS=25
PATH=/ascldap/users/detorre/bin:/home/detorre/miniforge/condabin:/opt/toss/openmpi/4.1/intel/bin:/projects/global/toss4/compilers/intel/intel_2021/oneapi/compiler/2021.3.0/linux/bin/intel64:/projects/global/toss4/compilers/intel/intel_2021/oneapi/compiler/2021.3.0/linux/bin:/usr/lpp/mmfs/bin:/opt/ibm/MCStore/bin:/opt/ibm/MCStore/scripts:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
REQUESTS_CA_BUNDLE=/etc/ssl/certs/snl-plus-zscaler.crt
SSL_CERT_FILE=/etc/ssl/certs/snl-plus-zscaler.crt

##################################################################################################
Compiler(s) (CC CXX FC F77 F90):

CC=/opt/toss/openmpi/4.1/intel/bin/mpicc
CC -show:
icc -I/opt/toss/openmpi/4.1/intel/include -pthread -L/opt/toss/openmpi/4.1/intel/lib -Wl,-rpath -Wl,/opt/toss/openmpi/4.1/intel/lib -Wl,--enable-new-dtags -lmpi
CC version:     icc (ICC) 2021.3.0 20210609

CXX=/opt/toss/openmpi/4.1/intel/bin/mpicxx
CXX -show:
icpc -I/opt/toss/openmpi/4.1/intel/include -pthread -L/opt/toss/openmpi/4.1/intel/lib -Wl,-rpath -Wl,/opt/toss/openmpi/4.1/intel/lib -Wl,--enable-new-dtags -lmpi
CXX version:    icpc (ICC) 2021.3.0 20210609

FC=/opt/toss/openmpi/4.1/intel/bin/mpif90
FC -show:
ifort -I/opt/toss/openmpi/4.1/intel/include -I/opt/toss/openmpi/4.1/intel/lib -L/opt/toss/openmpi/4.1/intel/lib -Wl,-rpath -Wl,/opt/toss/openmpi/4.1/intel/lib -Wl,--enable-new-dtags -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
FC version:     ifort (IFORT) 2021.3.0 20210609

F77=/opt/toss/openmpi/4.1/intel/bin/mpif77
F77 -show:
ifort -I/opt/toss/openmpi/4.1/intel/include -I/opt/toss/openmpi/4.1/intel/lib -L/opt/toss/openmpi/4.1/intel/lib -Wl,-rpath -Wl,/opt/toss/openmpi/4.1/intel/lib -Wl,--enable-new-dtags -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
F77 version:    ifort (IFORT) 2021.3.0 20210609

F90=/opt/toss/openmpi/4.1/intel/bin/mpif90
F90 -show:
ifort -I/opt/toss/openmpi/4.1/intel/include -I/opt/toss/openmpi/4.1/intel/lib -L/opt/toss/openmpi/4.1/intel/lib -Wl,-rpath -Wl,/opt/toss/openmpi/4.1/intel/lib -Wl,--enable-new-dtags -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
F90 version:    ifort (IFORT) 2021.3.0 20210609

OK

##################################################################################################
Python Sanity Checks

Verify `/usr/bin/env python3 --version` (reporting as: Python 3.11.8),
matches versions for: `which python3 && which python`

OK

##################################################################################################
Python Modules (TestHarness, run-ability)

OK

Answered by GiudGiud

Nov 22, 2024

Hello

We do not support intel compilers. Please install again with gcc or clang instead

Guillaume

View full answer

GiudGiud · 2024-11-22T21:35:59Z

GiudGiud
Nov 22, 2024
Collaborator

Hello

We do not support intel compilers. Please install again with gcc or clang instead

Guillaume

1 reply

TheGreatCid Nov 22, 2024
Author

Ah shoot, I didn't realize it grabbed an intel compiler. Thanks

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Building libmesh on HPC - undefined reference to std:file_system #29121

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Building libmesh on HPC - undefined reference to std:file_system #29121

TheGreatCid Nov 22, 2024

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Issue or question about MOOSE

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GiudGiud Nov 22, 2024 Collaborator

TheGreatCid Nov 22, 2024 Author

TheGreatCid
Nov 22, 2024

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Nov 22, 2024
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