python3: geos_ts_c.cpp:3991: int GEOSCoordSeq_getSize_r(GEOSContextHandle_t, const geos::geom::CoordinateSequence*, unsigned int*): Assertion `0 != cs' failed.

[jpdarela]

Found this error while running ilamb-run. The call of ilamb-setup results in the same libgeos assertion error. The solution was:

1 - uninstall ILAMB, cartopy and shapely using pip
2 - reinstall shapely from source
$ pip3 install shapely --no_binary shapely
3 - reinstall ILAMB from the git repo

I have found this solution while websearching the error. I just did not find the explanation for it.
The same error arises when running the sample datasets.

The messages from my shell:

Searching for model results in /home/jdarela/Desktop/caete/CAETE_BENCHMARK/ILAMB_BENCHMARKS/MODELS/

                                        CAETE-CNP

Parsing config file caete_bcmk.cfg...

                      GrossPrimaryProduction/GBAF Initialized

Running model-confrontation pairs...

                      GrossPrimaryProduction/GBAF CAETE-CNP            Completed  0:00:01

Finishing post-processing which requires collectives...

Geometry must be a Point or LineString
python3: geos_ts_c.cpp:3991: int GEOSCoordSeq_getSize_r(GEOSContextHandle_t, const geos::geom::CoordinateSequence*, unsigned int*): Assertion `0 != cs' failed.
[zabele:16054] *** Process received signal ***
[zabele:16054] Signal: Aborted (6)
[zabele:16054] Signal code:  (-6)
[zabele:16054] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3f040)[0x7f549203f040]
[zabele:16054] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f549203efb7]
[zabele:16054] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f5492040921]
[zabele:16054] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x3048a)[0x7f549203048a]
[zabele:16054] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x30502)[0x7f5492030502]
[zabele:16054] [ 5] /usr/lib/x86_64-linux-gnu/libgeos_c.so.1(GEOSCoordSeq_getSize_r+0x115)[0x7f546d242645]
[zabele:16054] [ 6] /home/jdarela/.local/lib/python3.6/site-packages/cartopy/trace.cpython-36m-x86_64-linux-gnu.so(+0x17346)[0x7f546d4ba346]
[zabele:16054] [ 7] /usr/bin/python3(_PyObject_FastCallKeywords+0x19c)[0x5a9dac]
[zabele:16054] [ 8] /usr/bin/python3[0x50a433]
[zabele:16054] [ 9] /usr/bin/python3(_PyEval_EvalFrameDefault+0x444)[0x50beb4]
[zabele:16054] [10] /usr/bin/python3[0x5095c8]
[zabele:16054] [11] /usr/bin/python3[0x50a2fd]
[zabele:16054] [12] /usr/bin/python3(_PyEval_EvalFrameDefault+0x444)[0x50beb4]
[zabele:16054] [13] /usr/bin/python3[0x507be4]
[zabele:16054] [14] /usr/bin/python3[0x509900]
[zabele:16054] [15] /usr/bin/python3[0x50a2fd]
[zabele:16054] [16] /usr/bin/python3(_PyEval_EvalFrameDefault+0x444)[0x50beb4]
[zabele:16054] [17] /usr/bin/python3[0x507be4]
[zabele:16054] [18] /usr/bin/python3[0x509900]
[zabele:16054] [19] /usr/bin/python3[0x50a2fd]
[zabele:16054] [20] /usr/bin/python3(_PyEval_EvalFrameDefault+0x444)[0x50beb4]
[zabele:16054] [21] /usr/bin/python3[0x507be4]
[zabele:16054] [22] /usr/bin/python3[0x509900]
[zabele:16054] [23] /usr/bin/python3[0x50a2fd]
[zabele:16054] [24] /usr/bin/python3(_PyEval_EvalFrameDefault+0x1226)[0x50cc96]
[zabele:16054] [25] /usr/bin/python3[0x5095c8]
[zabele:16054] [26] /usr/bin/python3[0x50a2fd]
[zabele:16054] [27] /usr/bin/python3(_PyEval_EvalFrameDefault+0x444)[0x50beb4]
[zabele:16054] [28] /usr/bin/python3[0x507be4]
[zabele:16054] [29] /usr/bin/python3[0x509900]
[zabele:16054] *** End of error message ***
Aborted (core dumped)```

[nocollier]

Thanks for this report. I have also experienced strange behavior with the underlying libraries of these packages. Appreciate the fix report so others may find it. I can also recommend using conda, where ILAMB is also available in conda-forge.