Getting gfortran compiler error when running example

[OrbitalMechanic]

Attempting to run an example for fortranmagic on a Mac Pro (2019) running Mac OSX ver. 13.3.1 (a) Ventura. I'm running

[Clang 14.0.6 ] :: Anaconda, Inc. on darwin

When running the example hosted on https://github.com/mgaitan/fortran_magic:

In[2]: %load_ext fortranmagic

In[3]: %%fortran

       subroutine f1(x, y, z)
            real, intent(in) :: x,y
            real, intent(out) :: z
            z = sin(x+y)
       end subroutine f1

The message I get is

   /Users/user/opt/anaconda3/bin/python -m numpy.f2py --noarch --fcompiler=gnu95 --compiler=unix --f90flags="-d" -m _fortran_magic_553c13c268582acb90e6b36e15d4b416 -c /Users/user/.cache/ipython/fortran/_fortran_magic_553c13c268582acb90e6b36e15d4b416.f90
running build
running config_cc
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
INFO: build_src
INFO: building extension "_fortran_magic_553c13c268582acb90e6b36e15d4b416" sources
INFO: f2py options: []
INFO: f2py:> /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/_fortran_magic_553c13c268582acb90e6b36e15d4b416module.c
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9
Reading fortran codes...
    Reading file '/Users/user/.cache/ipython/fortran/_fortran_magic_553c13c268582acb90e6b36e15d4b416.f90' (format:free)
Post-processing...
    Block: _fortran_magic_553c13c268582acb90e6b36e15d4b416
            Block: f1
Post-processing (stage 2)...
Building modules...
    Building module "_fortran_magic_553c13c268582acb90e6b36e15d4b416"...
    Generating possibly empty wrappers"
    Maybe empty "_fortran_magic_553c13c268582acb90e6b36e15d4b416-f2pywrappers.f"
        Constructing wrapper function "f1"...
          z = f1(x,y)
    Wrote C/API module "_fortran_magic_553c13c268582acb90e6b36e15d4b416" to file "/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/_fortran_magic_553c13c268582acb90e6b36e15d4b416module.c"
INFO:   adding '/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/fortranobject.c' to sources.
INFO:   adding '/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9' to include_dirs.
copying /Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c -> /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9
copying /Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.h -> /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9
INFO:   adding '/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/_fortran_magic_553c13c268582acb90e6b36e15d4b416-f2pywrappers.f' to sources.
INFO: build_src: building npy-pkg config files
running build_ext
INFO: customize UnixCCompiler
INFO: customize UnixCCompiler using build_ext
INFO: customize Gnu95FCompiler
INFO: Found executable /usr/local/bin/gfortran
INFO: customize Gnu95FCompiler using build_ext
INFO: building '_fortran_magic_553c13c268582acb90e6b36e15d4b416' extension
INFO: compiling C sources
INFO: C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/user/opt/anaconda3/include -arch x86_64 -I/Users/user/opt/anaconda3/include -fPIC -O2 -isystem /Users/user/opt/anaconda3/include -arch x86_64 -ftrapping-math

creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/var
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/var/folders
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/var/folders/2r
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9
INFO: compile options: '-DNPY_DISABLE_OPTIMIZATION=1 -I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9 -I/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/user/opt/anaconda3/include/python3.9 -c'
INFO: clang: /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/_fortran_magic_553c13c268582acb90e6b36e15d4b416module.c
INFO: clang: /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/fortranobject.c
INFO: compiling Fortran sources
INFO: Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/local/bin/gfortran -d -arch x86_64 -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -d -arch x86_64 -fPIC -O3 -funroll-loops
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/Users
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/Users/user
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/Users/user/.cache
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/Users/user/.cache/ipython
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/Users/user/.cache/ipython/fortran
INFO: compile options: '-I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9 -I/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/user/opt/anaconda3/include/python3.9 -c'
INFO: gfortran:f90: /Users/user/.cache/ipython/fortran/_fortran_magic_553c13c268582acb90e6b36e15d4b416.f90

/Users/user/opt/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
In file included from /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/_fortran_magic_553c13c268582acb90e6b36e15d4b416module.c:22:
In file included from /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/fortranobject.h:13:
In file included from /Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.hIn file included from /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/fortranobject.c::2:
12In file included from :
/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9/fortranobject.hIn file included from :/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h13::
1948In file included from :
/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:
/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h::1717::22::  warning: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]"Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

#warning "Using deprecated NumPy API, disable it with " \#warning "Using deprecated NumPy API, disable it with " \

 ^
 ^
1 warning generated.
1 warning generated.
gfortran: error: missing argument to '-d'
error: Command "/usr/local/bin/gfortran -d -arch x86_64 -fPIC -O3 -funroll-loops -I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9 -I/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/user/opt/anaconda3/include/python3.9 -c -c /Users/user/.cache/ipython/fortran/_fortran_magic_553c13c268582acb90e6b36e15d4b416.f90 -o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/Users/user/.cache/ipython/fortran/_fortran_magic_553c13c268582acb90e6b36e15d4b416.o" failed with exit status 1

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[2], line 1
----> 1 get_ipython().run_cell_magic('fortran', '-vvv --fcompiler gnu95 --compiler unix --f90flags "-d" --noarch', '\nsubroutine f1(x, y, z)\n    real, intent(in) :: x,y\n    real, intent(out) :: z\n\n    z = sin(x+y)\n\nend subroutine f1\n')

File ~/opt/anaconda3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2475, in InteractiveShell.run_cell_magic(self, magic_name, line, cell)
   2473 with self.builtin_trap:
   2474     args = (magic_arg_s, cell)
-> 2475     result = fn(*args, **kwargs)
   2477 # The code below prevents the output from being displayed
   2478 # when using magics with decodator @output_can_be_silenced
   2479 # when the last Python token in the expression is a ';'.
   2480 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):

File ~/opt/anaconda3/lib/python3.9/site-packages/fortranmagic.py:368, in FortranMagics.fortran(self, line, cell)
    365 res = self._run_f2py(f2py_args + ['-m', module_name, '-c', f90_file],
    366                      verbosity=args.verbosity)
    367 if res != 0:
--> 368    raise RuntimeError("f2py failed, see output")
    370 self._code_cache[key] = module_name
    371 module = imp.load_dynamic(module_name, module_path)

RuntimeError: f2py failed, see output

Any suggestions?

[Serge3leo]

gfortran: error: missing argument to '-d'
error: Command "/usr/local/bin/gfortran -d -arch x86_64 -fPIC -O3 -funroll-loops -I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/src.macosx-10.9-x86_64-3.9 -I/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/user/opt/anaconda3/include/python3.9 -c -c /Users/user/.cache/ipython/fortran/_fortran_magic_553c13c268582acb90e6b36e15d4b416.f90 -o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpbtg3sti3/Users/user/.cache/ipython/fortran/_fortran_magic_553c13c268582acb90e6b36e15d4b416.o" failed with exit status 1

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[2], line 1
----> 1 get_ipython().run_cell_magic('fortran', '-vvv --fcompiler gnu95 --compiler unix --f90flags "-d" --noarch', '\nsubroutine f1(x, y, z)\n    real, intent(in) :: x,y\n    real, intent(out) :: z\n\n    z = sin(x+y)\n\nend subroutine f1\n')

You have erroneous arguments cell magic %%fortran -vvv --fcompiler gnu95 --compiler unix --f90flags "-d" --noarch.

Under macOS, cell magic %%fortran should work fine without any arguments.

It is recommended to reset the saved configuration by line magic %fortran_config --defaults

[OrbitalMechanic]

Thank you for responding to my post.

I added the line %fortran_config --defaults only to get an error from f2py as shown in the attached screen-snap.

Any suggestions?

[Serge3leo]

Please print detailed output by %%fortran -vvv and details software versions lists. Unfortunately, fortran-magic without the -vvv key does not print build error diagnostics.

Perhaps the errors are related to the fact that numpy, python, etc. are run from the anaconda hierarchy, but GNU fortran from `/usr/local/bin'. Compiler flags, library locations, etc., may be incompatible.

You can try creating a minimal environment with fortran compiler by conda env create --name minfm --file minimal-jupyter-enviroment.yml.txt (or mamba env create --name minfm --file minimal-jupyter-enviroment.yml.txt). And then run Jupyter Lab with (cd ~/<test dir> && conda run --name minfm jupyter lab ).

minimal-jupyter-enviroment.yml.txt file see attachment. minimal-jupyter-enviroment.yml.txt

[OrbitalMechanic]

Below is a screen snap where %%fortran -vvv was used. Where can I find the "output" that f2py refers to in the screen snap?

[OrbitalMechanic]

Below are the messages from the run I made with %%fortran -vvv:

Running...
   /Users/user/opt/anaconda3/bin/python -m numpy.f2py -m _fortran_magic_985da1e7b396b6f4badbb368d62bfa08 -c /Users/user/.cache/ipython/fortran/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08.f90
running build
running config_cc
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
INFO: build_src
INFO: building extension "_fortran_magic_985da1e7b396b6f4badbb368d62bfa08" sources
INFO: f2py options: []
INFO: f2py:> /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08module.c
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9
Reading fortran codes...
    Reading file '/Users/user/.cache/ipython/fortran/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08.f90' (format:free)
Post-processing...
    Block: _fortran_magic_985da1e7b396b6f4badbb368d62bfa08
            Block: f1
Applying post-processing hooks...
  character_backward_compatibility_hook
Post-processing (stage 2)...
Building modules...
    Building module "_fortran_magic_985da1e7b396b6f4badbb368d62bfa08"...
    Generating possibly empty wrappers"
    Maybe empty "_fortran_magic_985da1e7b396b6f4badbb368d62bfa08-f2pywrappers.f"
        Constructing wrapper function "f1"...
          z = f1(x,y)
    Wrote C/API module "_fortran_magic_985da1e7b396b6f4badbb368d62bfa08" to file "/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08module.c"
INFO:   adding '/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/fortranobject.c' to sources.
INFO:   adding '/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9' to include_dirs.
copying /Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c -> /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9
copying /Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.h -> /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9
INFO:   adding '/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08-f2pywrappers.f' to sources.
INFO: build_src: building npy-pkg config files
running build_ext
INFO: customize UnixCCompiler
INFO: customize UnixCCompiler using build_ext
INFO: get_default_fcompiler: matching types: '['gnu95', 'nag', 'nagfor', 'absoft', 'ibm', 'intel', 'gnu', 'g95', 'pg']'
INFO: customize Gnu95FCompiler
INFO: Found executable /usr/local/bin/gfortran
INFO: customize Gnu95FCompiler
INFO: customize Gnu95FCompiler using build_ext
INFO: building '_fortran_magic_985da1e7b396b6f4badbb368d62bfa08' extension
INFO: compiling C sources
INFO: C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/user/opt/anaconda3/include -arch x86_64 -I/Users/user/opt/anaconda3/include -fPIC -O2 -isystem /Users/user/opt/anaconda3/include -arch x86_64 -ftrapping-math

creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9
INFO: compile options: '-DNPY_DISABLE_OPTIMIZATION=1 -I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9 -I/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/user/opt/anaconda3/include/python3.9 -c'
INFO: clang: /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08module.c
INFO: clang: /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/fortranobject.c
INFO: compiling Fortran sources
INFO: Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/Users
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/Users/user
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/Users/user/.cache
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/Users/user/.cache/ipython
creating /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/Users/user/.cache/ipython/fortran
INFO: compile options: '-I/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9 -I/Users/user/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/user/opt/anaconda3/include/python3.9 -c'
INFO: gfortran:f90: /Users/user/.cache/ipython/fortran/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08.f90
INFO: gfortran:f77: /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08-f2pywrappers.f
INFO: /usr/local/bin/gfortran -Wall -g -arch x86_64 -Wall -g -undefined dynamic_lookup -bundle /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08module.o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/fortranobject.o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/Users/user/.cache/ipython/fortran/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08.o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08-f2pywrappers.o -L/usr/local/Cellar/gcc/13.1.0/bin/../lib/gcc/current/gcc/x86_64-apple-darwin22/13 -L/usr/local/Cellar/gcc/13.1.0/bin/../lib/gcc/current/gcc/x86_64-apple-darwin22/13/../../.. -L/usr/local/Cellar/gcc/13.1.0/bin/../lib/gcc/current/gcc/x86_64-apple-darwin22/13/../../.. -lgfortran -o ./_fortran_magic_985da1e7b396b6f4badbb368d62bfa08.cpython-39-darwin.so

/Users/user/opt/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/lib/libSystem.tbd' for architecture x86_64
collect2: error: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -g -arch x86_64 -Wall -g -undefined dynamic_lookup -bundle /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08module.o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/fortranobject.o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/Users/user/.cache/ipython/fortran/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08.o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08-f2pywrappers.o -L/usr/local/Cellar/gcc/13.1.0/bin/../lib/gcc/current/gcc/x86_64-apple-darwin22/13 -L/usr/local/Cellar/gcc/13.1.0/bin/../lib/gcc/current/gcc/x86_64-apple-darwin22/13/../../.. -L/usr/local/Cellar/gcc/13.1.0/bin/../lib/gcc/current/gcc/x86_64-apple-darwin22/13/../../.. -lgfortran -o ./_fortran_magic_985da1e7b396b6f4badbb368d62bfa08.cpython-39-darwin.so" failed with exit status 1

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[2], line 1
----> 1 get_ipython().run_cell_magic('fortran', '-vvv', '\nsubroutine f1(x, y, z)\n    real, intent(in) :: x,y\n    real, intent(out) :: z\n\n    z = sin(x+y)\n\nend subroutine f1\n')

File ~/opt/anaconda3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2475, in InteractiveShell.run_cell_magic(self, magic_name, line, cell)
   2473 with self.builtin_trap:
   2474     args = (magic_arg_s, cell)
-> 2475     result = fn(*args, **kwargs)
   2477 # The code below prevents the output from being displayed
   2478 # when using magics with decodator @output_can_be_silenced
   2479 # when the last Python token in the expression is a ';'.
   2480 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):

File ~/opt/anaconda3/lib/python3.9/site-packages/fortranmagic.py:368, in FortranMagics.fortran(self, line, cell)
    365 res = self._run_f2py(f2py_args + ['-m', module_name, '-c', f90_file],
    366                      verbosity=args.verbosity)
    367 if res != 0:
--> 368    raise RuntimeError("f2py failed, see output")
    370 self._code_cache[key] = module_name
    371 module = imp.load_dynamic(module_name, module_path)

RuntimeError: f2py failed, see output

Any further thoughts?

[Serge3leo]

ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/lib/libSystem.tbd' for architecture x86_64
collect2: error: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -g -arch x86_64 -Wall -g -undefined dynamic_lookup -bundle /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08module.o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/fortranobject.o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/Users/user/.cache/ipython/fortran/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08.o /var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/var/folders/2r/4bw6nw0x58z0_ybx632_h14m0000gq/T/tmpj1od4m5k/src.macosx-10.9-x86_64-3.9/_fortran_magic_985da1e7b396b6f4badbb368d62bfa08-f2pywrappers.o -L/usr/local/Cellar/gcc/13.1.0/bin/../lib/gcc/current/gcc/x86_64-apple-darwin22/13 -L/usr/local/Cellar/gcc/13.1.0/bin/../lib/gcc/current/gcc/x86_64-apple-darwin22/13/../../.. -L/usr/local/Cellar/gcc/13.1.0/bin/../lib/gcc/current/gcc/x86_64-apple-darwin22/13/../../.. -lgfortran -o ./_fortran_magic_985da1e7b396b6f4badbb368d62bfa08.cpython-39-darwin.so" failed with exit status 1

I have not encountered such an error, but a Yandex search says that the error is related to gfortran configuration errors. Probably after the macOS update.

Open Terminal for Environments base by anaconda-navigator (or use conda activate base by macOS Terminal.app):

1. Try compile simple fortran "Hello world" program by gfortran;
2. Try create simple python extension module by python -m numpy.f2py -c fib1.f -m fib1;
3. Check simple python extension by python -c 'import fib1, numpy as np; a=np.zeros(8,"d"); fib1.fib(a); print(a)'.

fib1.f.txt

P.S. Of course, it is good practice to create a separate environment for each big project, and use the base environment only for managing environments, installing packages and updates. But since you have a problem in the base environment, you have to use it.