NameError: name 'OpenMode' is not defined

[nombac]

After upgrading SurfaceTopography beyond version 1.13.13, I started encountering the following error.

Python 3.12.6 (main, Sep  7 2024, 05:43:35) [Clang 15.0.0 (clang-1500.3.9.4)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import SurfaceTopography as st
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/SurfaceTopography/__init__.py", line 54, in <module>
    import SurfaceTopography.Uniform.common  # noqa: F401
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/SurfaceTopography/Uniform/common.py", line 33, in <module>
    from ..FFTTricks import make_fft
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/SurfaceTopography/FFTTricks.py", line 25, in <module>
    import muFFT
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/muFFT/__init__.py", line 53, in <module>
    from muGrid import Communicator
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/muGrid/__init__.py", line 54, in <module>
    def FileIONetCDF(file_name, open_mode=OpenMode.Read, communicator=None):
                                          ^^^^^^^^
NameError: name 'OpenMode' is not defined
>>> 

% python3 -m pip list 
Package            Version
------------------ -----------
build              1.0.3
certifi            2024.8.30
charset-normalizer 3.3.2
contourpy          1.3.0
cycler             0.12.1
defusedxml         0.7.1
DiscoverVersion    0.2.4
et-xmlfile         1.1.0
fonttools          4.53.1
h5py               3.11.0
idna               3.10
igor2              0.5.8
installer          0.7.0
kiwisolver         1.4.7
Mako               1.3.5
Markdown           3.6
MarkupSafe         2.1.5
matplotlib         3.9.2
muFFT              0.92.0
muGrid             0.92.4
NuMPI              0.6.1
numpy              2.1.1
numpyencoder       0.3.0
openpyxl           3.1.5
packaging          24.1
pandas             2.2.2
pillow             10.4.0
pip                24.1.2
pyparsing          3.1.4
pyproject_hooks    1.1.0
python-dateutil    2.9.0.post0
pytz               2024.2
PyYAML             6.0.2
requests           2.32.3
scipy              1.14.1
setuptools         74.1.2
six                1.16.0
SurfaceTopography  1.16.2
tifffile           2024.8.30
tiffile            2018.10.18
tzdata             2024.1
urllib3            2.2.3
wheel              0.44.0
xmltodict          0.13.0

[pastewka]

This is a problem with a downstream package. The problem is fixed by the update has not yet been released. I will do this today.

[nombac]

On a different Mac, I encountered the following errors. Does this indicate that SurfaceTopography requires mpi4py? After installing mpi4py via pip, the errors disappeared.

Python 3.12.6 (main, Sep  7 2024, 05:43:35) [Clang 15.0.0 (clang-1500.3.9.4)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import SurfaceTopography
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/SurfaceTopography/__init__.py", line 54, in <module>
    import SurfaceTopography.Uniform.common  # noqa: F401
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/SurfaceTopography/Uniform/common.py", line 33, in <module>
    from ..FFTTricks import make_fft
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/SurfaceTopography/FFTTricks.py", line 25, in <module>
    import muFFT
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/muFFT/__init__.py", line 53, in <module>
    from muGrid import Communicator
  File "/Users/shirose/Library/Python/3.12/lib/python/site-packages/muGrid/__init__.py", line 46, in <module>
    raise RuntimeError("MPI support is enabled for muGrid but mpi4py is not available.")
RuntimeError: MPI support is enabled for muGrid but mpi4py is not available.

% python3 -m pip list 
Package            Version     Editable project location
------------------ ----------- ---------------------------------------------------------
certifi            2024.8.30
charset-normalizer 3.3.2
contourpy          1.3.0
cycler             0.12.1
defusedxml         0.7.1
DiscoverVersion    0.2.4
et-xmlfile         1.1.0
fonttools          4.53.1
h5py               3.11.0
idna               3.10
igor2              0.5.8
imageio            2.35.1
kiwisolver         1.4.7
lazy_loader        0.4
Mako               1.3.5
Markdown           3.6
MarkupSafe         2.1.5
matplotlib         3.9.2
mpi4py             4.0.0
muFFT              0.92.1
muGrid             0.92.5
networkx           3.3
NuMPI              0.6.1
numpy              2.1.1
numpyencoder       0.3.0
openpyxl           3.1.5
packaging          24.1
pandas             2.2.2
pillow             10.4.0
pip                24.1.2
pyparsing          3.1.4
python-dateutil    2.9.0.post0
pytz               2024.2
PyYAML             6.0.2
requests           2.32.3
scikit-image       0.24.0
scipy              1.14.1
setuptools         74.1.2
six                1.16.0
SurfaceTopography  1.16.2
tifffile           2024.8.30
tiffile            2018.10.18
tzdata             2024.1
urllib3            2.2.3
xmltodict          0.13.0

[pastewka]

The first issue should be fixed.

Note that both issue will only appear if the code needs to be compiled (and is not installed via a Python "binary wheel"). We currently have binary wheels for Linux Intel and ARM and Mac ARM. If you are on Intel Mac (my suspicion) then the code will need to be compiled and no binary is downloaded.

This means the code will autodetect features/libraries it can find on the system. It looks to me like you have the MPI-libraries installed but no NetCDF. The code compiles with MPI enabled, but is then confused that the Python module mpi4py is missing. The easiest solution to fix this is to just install mpi4py. There is no downside to have the C-part of the code compiled MPI-enabled.

Sorry for the mess. The code is designed to also work on HPC systems, this is why there is a reasonably complicated autodetection of multiple features going on to support various combinations of MPI, NetCDF, and FFT libraries installed on these systems. The binary wheels are serial only and have NetCDF build-in.

[pastewka]

PS: First issues is fixed if you update to muFFT 0.92.1

[nombac]

Thank you for the clarification. Yes, I'm using an Intel Mac. Is it possible to manually enable or disable these libraries (MPI, NetCDF, and FFT)?

…

On Fri, Sep 20, 2024 at 4:57 PM Lars Pastewka ***@***.***> wrote: The first issue should be fixed. Note that both issue will only appear if the code needs to be compiled (and is not installed via a Python "binary wheel"). We currently have binary wheels for Linux Intel and ARM and Mac ARM. If you are on Intel Mac (my suspicion) then the code will compile. This means the code will autodetect features. It looks to me like you have the MPI-libraries installed but no NetCDF. The code compiles with MPI enabled, but is then confused that the Python module mpi4py is missing. The easiest solution to fix this is to just install mpi4py. Sorry for the mess. The code is designed to also work on HPC systems, this is why there is a reasonably complicated autodetection of multiple features going on so support various combinations of MPI, NetCDF, and FFT libraries installed on these systems. The binary wheels are serial only and have NetCDF build-in. — Reply to this email directly, view it on GitHub <#392 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJIYRNRMQGP6KIJH6Z4XCM3ZXPIORAVCNFSM6AAAAABOO23TUWVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANZQGE4DINA> . You are receiving this because you authored the thread.Message ID: <ContactEngineering/SurfaceTopography/repo-discussions/392/comments/10701844 @github.com>

[pastewka]

Sorry, you can't manually disable those. It will detect what is available.

[pastewka]

Hi @nombac - there are now Intel Mac wheels, which should simplify (and solve) installation on your end. Let me know if there are problems.

[nombac]

Thank you very much. I'll try it in the next opportunity.

…

On Fri, Sep 27, 2024 at 7:48 PM Lars Pastewka ***@***.***> wrote: Hi @nombac <https://github.com/nombac> - there are now Intel Mac wheels, which should simplify (and solve) installation on your end. Let me know if there are problems. — Reply to this email directly, view it on GitHub <#392 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJIYRNRHEVV6LJ5PHP4DR3TZYUZWZAVCNFSM6AAAAABOO23TUWVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANZXGQYTSOI> . You are receiving this because you were mentioned.Message ID: <ContactEngineering/SurfaceTopography/repo-discussions/392/comments/10774199 @github.com>