I have followed the installation for macOS page but still could not load properly. I read a lot of similar posts and have uninstalled/installed many times. Any help is much appreciated
Machine: M1 MacBook Air
OS: macOS 11.2.3
Python: 3.8 via Conda, all related packages up to date with PyMC3 3.10 requirements
Issues:
when importing theano:
You can find the C code in this temporary file: /var/folders/_c/frfzc_f54tbgbycvmnlj9v_w0000gn/T/theano_compilation_error_j2azim5s
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
75 if version != actual_version:
---> 76 raise ImportError(
77 "Version check of the existing lazylinker compiled file."
ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.211, but found None. Extra debug information: force_compile=False, _need_reload=True
During handling of the above exception, another exception occurred:
ImportError Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
98 if version != actual_version:
---> 99 raise ImportError(
100 "Version check of the existing lazylinker compiled file."
ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.211, but found None. Extra debug information: force_compile=False, _need_reload=True
During handling of the above exception, another exception occurred:
Exception Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/vm.py in <module>
696 )
--> 697 from . import lazylinker_c
698
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
138 args = cmodule.GCC_compiler.compile_args()
--> 139 cmodule.GCC_compiler.compile_str(dirname, code, location=loc, preargs=args)
140 # Save version into the __init__.py file.
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/cmodule.py in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols)
2555 # difficult to read.
-> 2556 raise Exception(
2557 "Compilation failed (return status=%s): %s"
Exception: Compilation failed (return status=1): In file included from /Users/hgu/.theano/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.8.5-64/lazylinker_ext/mod.cpp:1:. In file included from /Users/hgu/opt/anaconda3/include/python3.8/Python.h:25:. /Users/hgu/opt/anaconda3/bin/../include/c++/v1/stdio.h:107:15: fatal error: 'stdio.h' file not found. #include_next <stdio.h>. ^~~~~~~~~. 1 error generated..
During handling of the above exception, another exception occurred:
AttributeError Traceback (most recent call last)
<ipython-input-4-e2d3ee711e72> in <module>
----> 1 import theano
~/opt/anaconda3/lib/python3.8/site-packages/theano/__init__.py in <module>
76 __api_version__ = 1
77
---> 78 from theano import scalar, tensor
79 from theano.compile import (
80 In,
~/opt/anaconda3/lib/python3.8/site-packages/theano/scalar/__init__.py in <module>
----> 1 from .basic import *
2 from .basic_scipy import *
~/opt/anaconda3/lib/python3.8/site-packages/theano/scalar/basic.py in <module>
22
23 import theano
---> 24 from theano import config, gof, printing
25 from theano.gof import Apply, Constant, FunctionGraph, Op, Type, Variable, utils
26 from theano.gradient import DisconnectedType, grad_undefined
~/opt/anaconda3/lib/python3.8/site-packages/theano/printing.py in <module>
17 import theano
18 from theano import config, gof
---> 19 from theano.compile import Function, SharedVariable, debugmode
20 from theano.gof import Apply, Op
21
~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/__init__.py in <module>
----> 1 from theano.compile.debugmode import DebugMode
2 from theano.compile.function.pfunc import Param, pfunc, rebuild_collect_shared
3 from theano.compile.function.types import (
4 AliasedMemoryError,
5 Function,
~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/debugmode.py in <module>
25 std_fgraph,
26 )
---> 27 from theano.compile.mode import Mode, register_mode
28 from theano.compile.ops import OutputGuard, _output_guard
29 from theano.gof import graph, link, ops_with_inner_function, utils
~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/mode.py in <module>
8
9 import theano
---> 10 import theano.gof.vm
11 from theano import config, gof
12 from theano.compile.function.types import Supervisor
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/vm.py in <module>
705 except ImportError:
706 pass
--> 707 except (OSError, theano.gof.cmodule.MissingGXX) as e:
708 # OSError happens when g++ is not installed. In that case, we
709 # already changed the default linker to something else then CVM.
AttributeError: partially initialized module 'theano' has no attribute 'gof' (most likely due to a circular import)
when importing Pymc3
You can find the C code in this temporary file: /var/folders/_c/frfzc_f54tbgbycvmnlj9v_w0000gn/T/theano_compilation_error_nlrt8_5r
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
75 if version != actual_version:
---> 76 raise ImportError(
77 "Version check of the existing lazylinker compiled file."
ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.211, but found None. Extra debug information: force_compile=False, _need_reload=True
During handling of the above exception, another exception occurred:
ImportError Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
98 if version != actual_version:
---> 99 raise ImportError(
100 "Version check of the existing lazylinker compiled file."
ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.211, but found None. Extra debug information: force_compile=False, _need_reload=True
During handling of the above exception, another exception occurred:
Exception Traceback (most recent call last)
<ipython-input-1-0668865beb19> in <module>
1 import numpy as np
----> 2 import pymc3 as pm
3 from scipy.interpolate import griddata, interp2d
4 import theano.tensor as tt
5 from matplotlib import pyplot as plt
~/opt/anaconda3/lib/python3.8/site-packages/pymc3/__init__.py in <module>
37
38
---> 39 __set_compiler_flags()
40
41 from . import gp, ode, sampling
~/opt/anaconda3/lib/python3.8/site-packages/pymc3/__init__.py in __set_compiler_flags()
31 def __set_compiler_flags():
32 # Workarounds for Theano compiler problems on various platforms
---> 33 import theano
34
35 current = theano.config.gcc.cxxflags
~/opt/anaconda3/lib/python3.8/site-packages/theano/__init__.py in <module>
76 __api_version__ = 1
77
---> 78 from theano import scalar, tensor
79 from theano.compile import (
80 In,
~/opt/anaconda3/lib/python3.8/site-packages/theano/scalar/__init__.py in <module>
----> 1 from .basic import *
2 from .basic_scipy import *
~/opt/anaconda3/lib/python3.8/site-packages/theano/scalar/basic.py in <module>
22
23 import theano
---> 24 from theano import config, gof, printing
25 from theano.gof import Apply, Constant, FunctionGraph, Op, Type, Variable, utils
26 from theano.gradient import DisconnectedType, grad_undefined
~/opt/anaconda3/lib/python3.8/site-packages/theano/printing.py in <module>
17 import theano
18 from theano import config, gof
---> 19 from theano.compile import Function, SharedVariable, debugmode
20 from theano.gof import Apply, Op
21
~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/__init__.py in <module>
----> 1 from theano.compile.debugmode import DebugMode
2 from theano.compile.function.pfunc import Param, pfunc, rebuild_collect_shared
3 from theano.compile.function.types import (
4 AliasedMemoryError,
5 Function,
~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/debugmode.py in <module>
25 std_fgraph,
26 )
---> 27 from theano.compile.mode import Mode, register_mode
28 from theano.compile.ops import OutputGuard, _output_guard
29 from theano.gof import graph, link, ops_with_inner_function, utils
~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/mode.py in <module>
8
9 import theano
---> 10 import theano.gof.vm
11 from theano import config, gof
12 from theano.compile.function.types import Supervisor
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/vm.py in <module>
695 "lazylinker will not be imported if theano.config.cxx is not set."
696 )
--> 697 from . import lazylinker_c
698
699 class CVM(lazylinker_c.CLazyLinker, VM):
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
137
138 args = cmodule.GCC_compiler.compile_args()
--> 139 cmodule.GCC_compiler.compile_str(dirname, code, location=loc, preargs=args)
140 # Save version into the __init__.py file.
141 init_py = os.path.join(loc, "__init__.py")
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/cmodule.py in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols)
2554 # prints the exception, having '\n' in the text makes it more
2555 # difficult to read.
-> 2556 raise Exception(
2557 "Compilation failed (return status=%s): %s"
2558 % (status, compile_stderr.replace("\n", ". "))
Exception: Compilation failed (return status=1): In file included from /Users/hgu/.theano/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.8.5-64/lazylinker_ext/mod.cpp:1:. In file included from /Users/hgu/opt/anaconda3/include/python3.8/Python.h:25:. /Users/hgu/opt/anaconda3/bin/../include/c++/v1/stdio.h:107:15: fatal error: 'stdio.h' file not found. #include_next <stdio.h>. ^~~~~~~~~. 1 error generated..