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hydroframe / subsettools

Subsetting tools and utilities for ParFlow hydrological modeling
https://hydroframesubsettools.readthedocs.io/en/latest/
MIT License
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Example notebooks don't work, at least on a 2023 Macbook pro #96

Open westb2 opened 1 month ago

westb2 commented 1 month ago

When running the example notebooks I get the following error

Cell code that gives error has the code: mask_solid_paths = st.write_mask_solid(mask=mask, grid=grid, write_dir=static_write_dir)

Error is


CalledProcessError                        Traceback (most recent call last)
File /opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:340, in write_mask_solid(mask, grid, write_dir)
    [339](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:339) try:
--> [340](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:340)     subprocess.run(
    [341](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:341)         [
    [342](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:342)             script_path,
    [343](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:343)             "--mask",
    [344](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:344)             mask_path,
    [345](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:345)             "--pfsol",
    [346](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:346)             solid_path,
    [347](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:347)             "--vtk",
    [348](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:348)             mask_vtk_path,
    [349](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:349)             "--z-bottom",
    [350](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:350)             str(CONUS_Z_BOTTOM),
    [351](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:351)             "--z-top",
    [352](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:352)             str(z_top),
    [353](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:353)         ],
    [354](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:354)         check=True,
    [355](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:355)         capture_output=True,
    [356](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:356)     )
    [357](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:357) except subprocess.CalledProcessError as e:

File /opt/homebrew/anaconda3/envs/test-env/lib/python3.11/subprocess.py:571, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    [570](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/subprocess.py:570)     if check and retcode:
--> [571](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/subprocess.py:571)         raise CalledProcessError(retcode, process.args,
    [572](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/subprocess.py:572)                                  output=stdout, stderr=stderr)
    [573](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/subprocess.py:573) return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '['/Users/ben/parflow_installation/parflow/bin/pfmask-to-pfsol', '--mask', '/Users/ben/subsettools_tutorial/inputs/conus1_upper_verde_conus1_2005WY/static/mask.pfb', '--pfsol', '/Users/ben/subsettools_tutorial/inputs/conus1_upper_verde_conus1_2005WY/static/solidfile.pfsol', '--vtk', '/Users/ben/subsettools_tutorial/inputs/conus1_upper_verde_conus1_2005WY/static/mask_vtk.vtk', '--z-bottom', '0', '--z-top', '500']' died with <Signals.SIGABRT: 6>.

During handling of the above exception, another exception occurred:

CalledProcessError                        Traceback (most recent call last)
    [... skipping hidden 1 frame]

Cell In[35], [line 1](vscode-notebook-cell:?execution_count=35&line=1)
----> [1](vscode-notebook-cell:?execution_count=35&line=1) mask_solid_paths = st.write_mask_solid(mask=mask, grid=grid, write_dir=static_write_dir)

File /opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:358, in write_mask_solid(mask, grid, write_dir)
    [357](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:357) except subprocess.CalledProcessError as e:
--> [358](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:358)     raise subprocess.CalledProcessError("pfmask-to-pfsol error:", e.stderr)
    [360](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/site-packages/subsettools/domain.py:360) print(f"Wrote solidfile and mask_vtk with total z of {z_top} meters")

<class 'str'>: (<class 'TypeError'>, TypeError("'<' not supported between instances of 'str' and 'int'"))
...
    [141](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/subprocess.py:141)         try:
    [142](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/subprocess.py:142)             return "Command '%s' died with %r." % (
    [143](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/test-env/lib/python3.11/subprocess.py:143)                     self.cmd, signal.Signals(-self.returncode))

TypeError: '<' not supported between instances of 'str' and 'int'```
westb2 commented 1 month ago

As an update, the actual exception that pf-mask-to-pfsol is throwing is:

b"dyld[2241]: Library not loaded: @rpath/libpftools.dylib\n Referenced from: <9D55BCC4-B866-3AD1-8CC5-7C9A5E78E6F3> [/Users/ben/parflow_installation/parflow/bin/pfmask-to-pfsol](https://file+.vscode-resource.vscode-cdn.net/Users/ben/parflow_installation/parflow/bin/pfmask-to-pfsol)\n Reason: tried: '/usr/local/lib/libpftools.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libpftools.dylib' (no such file), '/usr/local/lib/libpftools.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libpftools.dylib' (no such file), '/usr/local/lib/libpftools.dylib' (no such file), '/usr/lib/libpftools.dylib' (no such file, not in dyld cache)\n"

This exception was being masked because there was a python error being thrown when trying to handle it.

I was able to fix this by creating a symbolic link within /usr/local/lib to the location my libpftools got installed to. For me this looked like

sudo ln -s ~/parflow_installation/parflow/bin/libpftools.dylib /usr/local/lib/libpftools.dylib

I don't imagine this is the best long term solution. During my parflow install I was careful to set all the required environment variables. Perhaps I missed a step, or perhaps something about the build needs to be updated to support dylib cache linking on newer macs.