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'ld: symbol(s) not found for architecture x86_64' Problem with compiling the intro_to_forpy.F90 example on MacOS #44

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sankalpjena opened this issue Jun 14, 2022 · 6 comments
Open

'ld: symbol(s) not found for architecture x86_64' Problem with compiling the intro_to_forpy.F90 example on MacOS #44

sankalpjena opened this issue Jun 14, 2022 · 6 comments

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@sankalpjena
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I'm using the following gfortran:
GNU Fortran (Homebrew GCC 11.3.0_1) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

My python version is 3.9.12 and package manager is conda.

Upon compiling the program with: gfortran intro_to_forpy.F90 forpy_mod.o -fno-lto python3-config --ldflags
I get the following error:

$ gfortran intro_to_forpy.F90 forpy_mod.o -fno-lto `python3-config --ldflags`
Undefined symbols for architecture x86_64:
  "_PyBool_FromLong", referenced from:
      ___forpy_mod_MOD_forpy_initialize_bool in forpy_mod.o
  "_PyBuffer_FillContiguousStrides", referenced from:
      ___forpy_mod_MOD_ndarray_create_nocopy_helper in forpy_mod.o
  "_PyBuffer_IsContiguous", referenced from:
      ___forpy_mod_MOD_get_data_helper in forpy_mod.o
  "_PyBuffer_Release", referenced from:
      ___forpy_mod_MOD_get_data_helper in forpy_mod.o
  "_PyBytes_AsString", referenced from:
      ___forpy_mod_MOD_unbox_value_char_1d in forpy_mod.o
  "_PyBytes_FromStringAndSize", referenced from:
      ___forpy_mod_MOD_box_value_char_1d_as_bytestr in forpy_mod.o
      ___forpy_mod_MOD_box_value_chars_as_bytestr in forpy_mod.o
  "_PyComplex_AsCComplex", referenced from:
      ___forpy_mod_MOD_unbox_value_complex_real64 in forpy_mod.o
      ___forpy_mod_MOD_unbox_value_complex_real32 in forpy_mod.o
  "_PyComplex_FromDoubles", referenced from:
      ___forpy_mod_MOD_box_value_complex_real64 in forpy_mod.o
      ___forpy_mod_MOD_box_value_complex_real32 in forpy_mod.o
      ___forpy_mod_MOD_forpy_initialize_complex in forpy_mod.o
  "_PyDict_Clear", referenced from:
      ___forpy_mod_MOD_dict_clear in forpy_mod.o
  "_PyDict_Copy", referenced from:
      ___forpy_mod_MOD_dict_copy in forpy_mod.o
  "_PyDict_GetItemString", referenced from:
      ___forpy_mod_MOD_print_py in forpy_mod.o
      ___forpy_mod_MOD_forpy_initialize_exceptions in forpy_mod.o
  "_PyDict_Items", referenced from:
      ___forpy_mod_MOD_dict_items in forpy_mod.o
  "_PyDict_Keys", referenced from:
      ___forpy_mod_MOD_dict_keys in forpy_mod.o
  "_PyDict_New", referenced from:
      ___forpy_mod_MOD_dict_create in forpy_mod.o
  "_PyDict_Values", referenced from:
      ___forpy_mod_MOD_dict_values in forpy_mod.o
  "_PyErr_Clear", referenced from:
      ___forpy_mod_MOD_err_clear in forpy_mod.o
      ___forpy_mod_MOD_is_ndarray in forpy_mod.o
      ___forpy_mod_MOD_forpy_initialize_exceptions in forpy_mod.o
  "_PyErr_GivenExceptionMatches", referenced from:
      ___forpy_mod_MOD_exception_matches in forpy_mod.o
  "_PyErr_Occurred", referenced from:
      ___forpy_mod_MOD_have_exception in forpy_mod.o
      ___forpy_mod_MOD_err_print in forpy_mod.o
      ___forpy_mod_MOD_exception_matches in forpy_mod.o
      ___forpy_mod_MOD_unbox_value_complex_real64 in forpy_mod.o
      ___forpy_mod_MOD_unbox_value_complex_real32 in forpy_mod.o
      ___forpy_mod_MOD_unbox_value_real64 in forpy_mod.o
      ___forpy_mod_MOD_unbox_value_real32 in forpy_mod.o
      ...
  "_PyErr_Print", referenced from:
      ___forpy_mod_MOD_err_print in forpy_mod.o
  "_PyErr_SetString", referenced from:
      ___forpy_mod_MOD_raise_exception in forpy_mod.o
  "_PyEval_GetBuiltins", referenced from:
      ___forpy_mod_MOD_print_py in forpy_mod.o
      ___forpy_mod_MOD_forpy_initialize_exceptions in forpy_mod.o
  "_PyFloat_AsDouble", referenced from:
      ___forpy_mod_MOD_unbox_value_real64 in forpy_mod.o
      ___forpy_mod_MOD_unbox_value_real32 in forpy_mod.o
  "_PyFloat_FromDouble", referenced from:
      ___forpy_mod_MOD_box_value_real64 in forpy_mod.o
      ___forpy_mod_MOD_box_value_real32 in forpy_mod.o
      ___forpy_mod_MOD_forpy_initialize_float in forpy_mod.o
  "_PyImport_ImportModule", referenced from:
      ___forpy_mod_MOD_import_py in forpy_mod.o
      ___forpy_mod_MOD_forpy_initialize_numpy in forpy_mod.o
  "_PyList_Append", referenced from:
      ___forpy_mod_MOD_list_append_chars in forpy_mod.o
      ___forpy_mod_MOD_list_append_char_1d in forpy_mod.o
      ___forpy_mod_MOD_list_append_logical in forpy_mod.o
      ___forpy_mod_MOD_list_append_complex_real64 in forpy_mod.o
      ___forpy_mod_MOD_list_append_complex_real32 in forpy_mod.o
      ___forpy_mod_MOD_list_append_real64 in forpy_mod.o
      ___forpy_mod_MOD_list_append_real32 in forpy_mod.o
      ...
  "_PyList_Insert", referenced from:
      ___forpy_mod_MOD_list_insert_int64 in forpy_mod.o
      ___forpy_mod_MOD_list_insert_int32 in forpy_mod.o
  "_PyList_New", referenced from:
      ___forpy_mod_MOD_list_create_empty in forpy_mod.o
  "_PyList_Reverse", referenced from:
      ___forpy_mod_MOD_list_reverse in forpy_mod.o
  "_PyList_Sort", referenced from:
      ___forpy_mod_MOD_list_sort in forpy_mod.o
  "_PyLong_AsLongLongAndOverflow", referenced from:
      ___forpy_mod_MOD_unbox_value_int64 in forpy_mod.o
      ___forpy_mod_MOD_unbox_value_int32 in forpy_mod.o
  "_PyLong_FromLongLong", referenced from:
      ___forpy_mod_MOD_box_value_int64_as_long in forpy_mod.o
      ___forpy_mod_MOD_box_value_int32_as_long in forpy_mod.o
  "_PyMapping_HasKey", referenced from:
      ___forpy_mod_MOD_mapping_contains in forpy_mod.o
  "_PyMemoryView_FromBuffer", referenced from:
      ___forpy_mod_MOD_ndarray_create_nocopy_helper in forpy_mod.o
  "_PyModule_AddObject", referenced from:
      ___forpy_mod_MOD_pythonmodule_add_object in forpy_mod.o
  "_PyModule_Create2", referenced from:
      ___forpy_mod_MOD_pythonmodule_init in forpy_mod.o
  "_PyObject_Call", referenced from:
      ___forpy_mod_MOD_ndarray_create_nocopy_helper in forpy_mod.o
      ___forpy_mod_MOD_call_py_object in forpy_mod.o
  "_PyObject_DelItem", referenced from:
      ___forpy_mod_MOD_mapping_delitem_chars in forpy_mod.o
      ___forpy_mod_MOD_mapping_delitem_int64 in forpy_mod.o
      ___forpy_mod_MOD_mapping_delitem_int32 in forpy_mod.o
      ___forpy_mod_MOD_mapping_delitem_object in forpy_mod.o
  "_PyObject_GetAttr", referenced from:
      ___forpy_mod_MOD_object_getattribute in forpy_mod.o
      ___forpy_mod_MOD_forpy_initialize_numpy in forpy_mod.o
  "_PyObject_GetBuffer", referenced from:
      ___forpy_mod_MOD_get_data_helper in forpy_mod.o
  "_PyObject_GetItem", referenced from:
      ___forpy_mod_MOD_dict_get_helper2 in forpy_mod.o
      ___forpy_mod_MOD_dict_get_helper in forpy_mod.o
      ___forpy_mod_MOD_mapping_getitem_chars_chars in forpy_mod.o
      ___forpy_mod_MOD_mapping_getitem_chars_char_1d in forpy_mod.o
      ___forpy_mod_MOD_mapping_getitem_chars_logical in forpy_mod.o
      ___forpy_mod_MOD_mapping_getitem_chars_complex_real64 in forpy_mod.o
      ___forpy_mod_MOD_mapping_getitem_chars_complex_real32 in forpy_mod.o
      ...
  "_PyObject_IsInstance", referenced from:
      ___forpy_mod_MOD_is_ndarray in forpy_mod.o
  "_PyObject_IsTrue", referenced from:
      ___forpy_mod_MOD_unbox_value_logical in forpy_mod.o
  "_PyObject_Length", referenced from:
      ___forpy_mod_MOD_unbox_value_char_1d in forpy_mod.o
      ___forpy_mod_MOD_mapping_len_int64 in forpy_mod.o
      ___forpy_mod_MOD_mapping_len_int32 in forpy_mod.o
      ___forpy_mod_MOD_sequence_len_int64 in forpy_mod.o
      ___forpy_mod_MOD_sequence_len_int32 in forpy_mod.o
  "_PyObject_SetAttr", referenced from:
      ___forpy_mod_MOD_object_delattr in forpy_mod.o
      ___forpy_mod_MOD_object_setattr in forpy_mod.o
  "_PyObject_SetItem", referenced from:
      ___forpy_mod_MOD_dict_get_helper in forpy_mod.o
      ___forpy_mod_MOD_mapping_setitem_chars_chars in forpy_mod.o
      ___forpy_mod_MOD_mapping_setitem_chars_char_1d in forpy_mod.o
      ___forpy_mod_MOD_mapping_setitem_chars_logical in forpy_mod.o
      ___forpy_mod_MOD_mapping_setitem_chars_complex_real64 in forpy_mod.o
      ___forpy_mod_MOD_mapping_setitem_chars_complex_real32 in forpy_mod.o
      ___forpy_mod_MOD_mapping_setitem_chars_real64 in forpy_mod.o
      ...
  "_PyObject_Str", referenced from:
      ___forpy_mod_MOD_cast_nonstrict_to_chars in forpy_mod.o
      ___forpy_mod_MOD_str_create_object in forpy_mod.o
  "_PyRun_SimpleString", referenced from:
      ___forpy_mod_MOD_run_string in forpy_mod.o
      ___forpy_mod_MOD_forpy_initialize_sys_argv in forpy_mod.o
  "_PySequence_Concat", referenced from:
      ___forpy_mod_MOD_tuple_add in forpy_mod.o
      ___forpy_mod_MOD_list_add in forpy_mod.o
  "_PySequence_Contains", referenced from:
      ___forpy_mod_MOD_sequence_contains in forpy_mod.o
  "_PySequence_Count", referenced from:
      ___forpy_mod_MOD_sequence_count_int64 in forpy_mod.o
      ___forpy_mod_MOD_sequence_count_int32 in forpy_mod.o
  "_PySequence_DelItem", referenced from:
      ___forpy_mod_MOD_list_delitem_int64 in forpy_mod.o
      ___forpy_mod_MOD_list_delitem_int32 in forpy_mod.o
  "_PySequence_GetItem", referenced from:
      ___forpy_mod_MOD_sequence_getitem_int64_chars in forpy_mod.o
      ___forpy_mod_MOD_sequence_getitem_int64_char_1d in forpy_mod.o
      ___forpy_mod_MOD_sequence_getitem_int64_logical in forpy_mod.o
      ___forpy_mod_MOD_sequence_getitem_int64_complex_real64 in forpy_mod.o
      ___forpy_mod_MOD_sequence_getitem_int64_complex_real32 in forpy_mod.o
      ___forpy_mod_MOD_sequence_getitem_int64_real64 in forpy_mod.o
      ___forpy_mod_MOD_sequence_getitem_int64_real32 in forpy_mod.o
      ...
  "_PySequence_Index", referenced from:
      ___forpy_mod_MOD_sequence_index_int64 in forpy_mod.o
      ___forpy_mod_MOD_sequence_index_int32 in forpy_mod.o
  "_PySequence_List", referenced from:
      ___forpy_mod_MOD_list_create_object in forpy_mod.o
  "_PySequence_SetItem", referenced from:
      ___forpy_mod_MOD_mutablesequence_setitem_int64_chars in forpy_mod.o
      ___forpy_mod_MOD_mutablesequence_setitem_int64_char_1d in forpy_mod.o
      ___forpy_mod_MOD_mutablesequence_setitem_int64_logical in forpy_mod.o
      ___forpy_mod_MOD_mutablesequence_setitem_int64_complex_real64 in forpy_mod.o
      ___forpy_mod_MOD_mutablesequence_setitem_int64_complex_real32 in forpy_mod.o
      ___forpy_mod_MOD_mutablesequence_setitem_int64_real64 in forpy_mod.o
      ___forpy_mod_MOD_mutablesequence_setitem_int64_real32 in forpy_mod.o
      ...
  "_PySequence_Tuple", referenced from:
      ___forpy_mod_MOD_tuple_create_object in forpy_mod.o
  "_PySys_GetObject", referenced from:
      ___forpy_mod_MOD_get_sys_path in forpy_mod.o
  "_PyTuple_New", referenced from:
      ___forpy_mod_MOD_ndarray_create_nocopy_helper in forpy_mod.o
      ___forpy_mod_MOD_tuple_create_int64 in forpy_mod.o
      ___forpy_mod_MOD_tuple_create_int32 in forpy_mod.o
  "_PyTuple_SetItem", referenced from:
      ___forpy_mod_MOD_ndarray_create_nocopy_helper in forpy_mod.o
      ___forpy_mod_MOD_tuple_setitem_int64_object in forpy_mod.o
      ___forpy_mod_MOD_tuple_setitem_int32_object in forpy_mod.o
      ___forpy_mod_MOD_tuple_setitem_int64_chars in forpy_mod.o
      ___forpy_mod_MOD_tuple_setitem_int64_char_1d in forpy_mod.o
      ___forpy_mod_MOD_tuple_setitem_int64_logical in forpy_mod.o
      ___forpy_mod_MOD_tuple_setitem_int64_complex_real64 in forpy_mod.o
      ...
  "_PyType_IsSubtype", referenced from:
      ___forpy_mod_MOD_is_unicode in forpy_mod.o
      ___forpy_mod_MOD_is_bool in forpy_mod.o
      ___forpy_mod_MOD_is_complex in forpy_mod.o
      ___forpy_mod_MOD_is_float in forpy_mod.o
  "_PyUnicode_AsUTF8AndSize", referenced from:
      ___forpy_mod_MOD_unbox_value_char_1d in forpy_mod.o
  "_PyUnicode_DecodeUTF8", referenced from:
      ___forpy_mod_MOD_box_value_char_1d_as_unicodestr in forpy_mod.o
      ___forpy_mod_MOD_box_value_chars_as_unicodestr in forpy_mod.o
      ___forpy_mod_MOD_forpy_initialize_unicode in forpy_mod.o
  "_Py_DecRef", referenced from:
      ___forpy_mod_MOD_cast_nonstrict_to_chars in forpy_mod.o
      ___forpy_mod_MOD_ndarray_create_nocopy_helper in forpy_mod.o
      ___forpy_mod_MOD_dict_get_chars_chars in forpy_mod.o
      ___forpy_mod_MOD_dict_get_chars_char_1d in forpy_mod.o
      ___forpy_mod_MOD_dict_get_chars_logical in forpy_mod.o
      ___forpy_mod_MOD_dict_get_chars_complex_real64 in forpy_mod.o
      ___forpy_mod_MOD_dict_get_chars_complex_real32 in forpy_mod.o
      ...
  "_Py_Finalize", referenced from:
      ___forpy_mod_MOD_forpy_finalize in forpy_mod.o
  "_Py_IncRef", referenced from:
      ___forpy_mod_MOD_unsafe_cast_from_c_ptr in forpy_mod.o
      ___forpy_mod_MOD_pythonmodule_add_object in forpy_mod.o
      ___forpy_mod_MOD_assign_py_nonetype in forpy_mod.o
      ___forpy_mod_MOD_assign_py_module_py in forpy_mod.o
      ___forpy_mod_MOD_assign_py_type_py in forpy_mod.o
      ___forpy_mod_MOD_assign_py_ndarray in forpy_mod.o
      ___forpy_mod_MOD_assign_py_dict in forpy_mod.o
      ...
  "_Py_Initialize", referenced from:
      ___forpy_mod_MOD_forpy_initialize in forpy_mod.o
  "_Py_IsInitialized", referenced from:
      ___forpy_mod_MOD_forpy_initialize in forpy_mod.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status

Could you please help?

Thanking you

Best regards
Sankalp Jena
@sankalpjena sankalpjena changed the title Problem with compiling the intro_to_forpy.F90 example on MacOS ld: symbol(s) not found for architecture x86_64 Problem with compiling the intro_to_forpy.F90 example on MacOS Jun 15, 2022
@sankalpjena sankalpjena changed the title ld: symbol(s) not found for architecture x86_64 Problem with compiling the intro_to_forpy.F90 example on MacOS 'ld: symbol(s) not found for architecture x86_64' Problem with compiling the intro_to_forpy.F90 example on MacOS Jun 15, 2022
@ylikx
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ylikx commented Jun 16, 2022

Ok, that means that it could not link with libpython. Try python3-config --ldflags --embed. The embed option was added in newer versions of Python and is probably necessary for successfully linking.

@sankalpjena
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Ok, that means that it could not link with libpython. Try python3-config --ldflags --embed. The embed option was added in newer versions of Python and is probably necessary for successfully linking.

I tried this and I'm getting the error that library wasn't found:

% gfortran intro_to_forpy.F90 forpy_mod.o -fno-lto `python3-config --ldflags --embed`
ld: library not found for -lpython3.9
collect2: error: ld returned 1 exit status

I tried export LD_LIBRARY_PATH=/usr/local/Caskroom/miniconda/base/envs/data_sc_env/lib:$LD_LIBRARY_PATH as well, but it didn't work

@ylikx
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ylikx commented Jun 17, 2022

Did you activate the conda environment with conda activate?
What is the output of python3-config --ldflags --embed on your system?

@sankalpjena
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python3-config --ldflags --embed

Yes, I have activated my conda environment:

(data_sc_env) sankalp@jenambp collisionV1 % gfortran intro_to_forpy.F90 forpy_mod.o -fno-lto `python3-config --ldflags --embed`
ld: library not found for -lpython3.9
collect2: error: ld returned 1 exit status

The output:

(data_sc_env) sankalp@jenambp collisionV1 % python3-config --ldflags --embed
-L/usr/local/Caskroom/miniconda/base/envs/data_sc_env/lib/python3.9/config-3.9-darwin -lpython3.9 -ldl -framework CoreFoundation

@ylikx
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ylikx commented Jun 19, 2022

Apparently there is no shared library libpython3.9 in the directory specified by the python3-config output (/usr/local/Caskroom/miniconda/base/envs/data_sc_env/lib/python3.9/config-3.9-darwin). Check if there is a shared library named something like libpython3.9.dylib. If not, maybe you can find it in some other directory and adjust the path accordingly.

I do not have a macOS machine available, therefore I cannot test the setup with macOS + anaconda myself. It could also be that Python is built without shared library support.

@wakeupthemonkey
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I get this error: The 'sklearn' PyPI package is deprecated, use 'scikit-learn'

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@ylikx @sankalpjena @wakeupthemonkey