Update mov run #994

lee1043 · 2023-11-02T23:22:35Z

No description provided.

…update_mov_run

lee1043 · 2023-11-28T21:47:24Z

@acordonez would you be able to help verifying this PR won't break the MoV demo?

acordonez · 2023-11-28T23:50:22Z

@lee1043 I'm getting a segmentation fault when I run the first example. This looks like the issue I saw with my changes in the variability_across_timescales driver, where importing shapely after importing cdat libraries causes a segmentation fault. I can get the driver to run normally if I put an "import shapely" statement at the top of variability_modes_driver.py, but the pre-commit hooks don't like that. If you have a better fix I can also use that in variability_across_timescales.

Here's the full text:

Fatal Python error: Segmentation fault

Current thread 0x00007f66ad834740 (most recent call first):
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/shapely/predicates.py", line 69 in has_z
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/shapely/decorators.py", line 77 in wrapped
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/shapely/geometry/base.py", line 607 in has_z
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/shapely/geometry/base.py", line 206 in coords
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/shapely/geometry/linestring.py", line 119 in xy
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/patch.py", line 54 in geos_to_path
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 1542 in _boundary
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 583 in __clear
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 596 in clear
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/matplotlib/axes/_base.py", line 683 in __init__
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 416 in __init__
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/matplotlib/figure.py", line 768 in add_subplot
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/matplotlib/pyplot.py", line 1122 in axes
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/pcmdi_metrics/variability_mode/lib/plot_map.py", line 203 in plot_map_cartopy
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/pcmdi_metrics/variability_mode/lib/plot_map.py", line 104 in plot_map
  File "/home/ordonez4/miniconda3/envs/pmp_dev/bin/variability_modes_driver.py", line 446 in <module>

Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, cdtime._cdtime, lazy_object_proxy.cext, cdms2.Cdunif, regrid2._regrid, regrid2._scrip, cdms2._bindex, yaml._yaml, cytoolz.utils, cytoolz.itertoolz, cytoolz.functoolz, cytoolz.dicttoolz, cytoolz.recipes, psutil._psutil_linux, psutil._psutil_posix, markupsafe._speedups, tornado.speedups, msgpack._cmsgpack, lz4._version, lz4.block._block, genutil.array_indexing, genutil.udunits_wrap, _brotli, shapely.lib, shapely._geos, shapely._geometry_helpers, pyarrow.lib, pyarrow._hdfsio, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, pyarrow._compute, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.indexing, pandas._libs.index, pandas._libs.internals, pandas._libs.join, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, cftime._cftime, scipy._lib._ccallback_c, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy._lib._uarray._uarray, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.fftpack.convolve, lxml._elementpath, lxml.etree, numpy.linalg.lapack_lite, lz4.frame._frame, pyproj._compat, pyproj._datadir, pyproj._network, pyproj._geod, pyproj.list, pyproj._crs, pyproj.database, pyproj._transformer, pyproj._sync, cartopy.trace, fiona._err, fiona._env, fiona.crs, fiona._geometry, fiona.schema, fiona.ogrext, matplotlib._c_internal_utils, PIL._imaging, matplotlib._path, kiwisolver._cext, matplotlib._image (total: 145)

lee1043 · 2023-11-29T00:41:52Z

put an "import shapely" statement at the top of variability_modes_driver.py

@acordonez it is interesting to know this would prevent the error. What about if "import shapely" is added at the top of lib/plot_map.py? Could you please check if this would work? I am studying pre-commit settings to see if there is any way to make it an exception.

lee1043 · 2023-11-29T00:45:22Z

@acordonez I guess this might be related to the version of shapely, which we couldn't update to the latest because of the limit in the Python version that is tied with the CDAT...

acordonez · 2023-11-29T00:46:55Z

put an "import shapely" statement at the top of variability_modes_driver.py

@acordonez it is interesting to know this would prevent the error. What about if "import shapely" is added at the top of lib/plot_map.py? Could you please check if this would work? I am studying pre-commit settings to see if there is any way to make it an exception.

@lee1043 When I saw this problem before, shapely has to be called before any cdat packages in the entire run. So if the driver script imports cdat before shapely, even if shapely is called in another script, it causes the segmentation fault.

acordonez · 2023-11-29T00:48:28Z

@acordonez I guess this might be related to the version of shapely, which we couldn't update to the latest because of the limit in the Python version that is tied with the CDAT...

@lee1043 I tried a few different versions of shapely, even old ones, with variability_across_timescales and couldn't find one that would work. It might be something to do with underlying C packages that get called by both shapely and cdat, but I didn't investigate the underlying cause that deeply.

…t can consider it as an exception

lee1043 · 2023-11-29T01:04:52Z

@acordonez thank you for the comments, very helpful! I revised the driver script to import shapely at the top and added # noqa tag (indicating "NO-QA", NO Quality Assurance) and adjusted pre-commit setting in .pre-commit-config.yaml to allow pre-commit skipping checks for lines with the tag. Could you please check if this address the segmentation fault issue?

acordonez · 2023-11-29T16:26:24Z

@lee1043 The segmentation fault is gone!

I'm getting another error in section 3.2.1 (and seeing a similar error in 3.3.1):

%%bash
variability_modes_driver.py -p basic_mov_param_sst.py --case_id "PDO" --msyear 1900 --meyear 2005

mip: cmip5
exp: historical
fq: mo
realm: atm
EofScaling: False
RmDomainMean: True
LandMask: True
nc_out_obs, plot_obs: True True
nc_out_model, plot_model: True True
CMEC:False
mode: PDO
seasons: ['monthly']
models: ['ACCESS1-0']
number of models: 1
realization:  r1i1p1
parallel: False
demo_output/PDO
demo_output/PDO
demo_output/PDO
Estimate landmask

Traceback (most recent call last):
  File "/home/ordonez4/miniconda3/envs/pmp_dev/bin/variability_modes_driver.py", line 444, in <module>
    plot_map(
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/pcmdi_metrics/variability_mode/lib/plot_map.py", line 103, in plot_map
    plot_map_cartopy(
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/pcmdi_metrics/variability_mode/lib/plot_map.py", line 204, in plot_map_cartopy
    im = ax.contourf(
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 315, in wrapper
    return func(self, *args, **kwargs)
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 359, in wrapper
    return func(self, *args, **kwargs)
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 1659, in contourf
    bboxes = [col.get_datalim(self.transData)
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 1659, in <listcomp>
    bboxes = [col.get_datalim(self.transData)
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/matplotlib/collections.py", line 266, in get_datalim
    paths = [transform.transform_path_non_affine(p) for p in paths]
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/matplotlib/collections.py", line 266, in <listcomp>
    paths = [transform.transform_path_non_affine(p) for p in paths]
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/matplotlib/transforms.py", line 2439, in transform_path_non_affine
    return self._a.transform_path_non_affine(path)
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 182, in transform_path_non_affine
    geoms = cpatch.path_to_geos(src_path,
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/cartopy/mpl/patch.py", line 180, in path_to_geos
    collection[-1][0].contains(geom.exterior)):
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/shapely/geometry/base.py", line 658, in contains
    return _maybe_unpack(shapely.contains(self, other))
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/shapely/decorators.py", line 77, in wrapped
    return func(*args, **kwargs)
  File "/home/ordonez4/miniconda3/envs/pmp_dev/lib/python3.10/site-packages/shapely/predicates.py", line 540, in contains
    return lib.contains(a, b, **kwargs)
shapely.errors.GEOSException: TopologyException: side location conflict at 257.5 68.5. This can occur if the input geometry is invalid.
[WARNING] yaksa: 10 leaked handle pool objects

…n to prevent error from shapely

lee1043 · 2023-11-30T01:47:03Z

@acordonez thank you for checking this. I think the error was caused by combinations of multiple factors -- cdms variable with cartopy, 1e20 being used for fill value that was not appreciated by xarray. I add workarounds and confirmed that demo notebook is working without any issue. Could you please double check if this is true on your end as well?

acordonez · 2023-11-30T16:44:12Z

@lee1043 The notebook ran perfectly this time

acordonez · 2023-11-30T16:44:45Z

@lee1043 Should I merge this?

lee1043 · 2023-11-30T16:46:52Z

@acordonez Excellent, thank you for double checking!

lee1043 · 2023-11-30T16:47:25Z

@lee1043 Should I merge this?

@acordonez let me clean up a few more things and will merge it.

lee1043 and others added 9 commits October 8, 2023 15:25

update

14eacbe

update

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Merge branch 'main' into update_mov_run

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update

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Merge branch 'update_mov_run' of github.com:PCMDI/pcmdi_metrics into …

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…update_mov_run

update;

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pre-commit check

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keep shapely version to 2.0.1 because of python version limit for cdat

75c54e1

Merge branch 'main' into update_mov_run

edb61e2

lee1043 self-assigned this Nov 23, 2023

lee1043 marked this pull request as ready for review November 28, 2023 21:46

lee1043 requested a review from acordonez November 28, 2023 21:46

lee1043 added the minor label Nov 28, 2023

lee1043 added this to the v3.1.2 milestone Nov 28, 2023

add import shapely at the top and adjust isort setting thus pre-commi…

ec4bb3d

…t can consider it as an exception

lee1043 added 6 commits November 29, 2023 16:56

use xarray data array to plot map with cartopy, and adjust 1e20 as na…

327d169

…n to prevent error from shapely

pre-commit test: style fix

cef14df

clean up

b36a5f0

clean up and bug fix

9bdba9d

clean up

8f7a10d

clean up

77acd3d

lee1043 added the graphic label Nov 30, 2023

acordonez approved these changes Nov 30, 2023

View reviewed changes

lee1043 and others added 2 commits November 30, 2023 14:19

clean up

1baba96

Merge branch 'main' into update_mov_run

f1d711a

lee1043 merged commit a90ed96 into main Nov 30, 2023
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lee1043 deleted the update_mov_run branch November 30, 2023 23:27

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Update mov run #994

Update mov run #994

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Update mov run #994

Update mov run #994

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