"Certificate for xcslc1 has no `subjectAltName`" error is preventing building of ancillaries

[jokea]

Hi,

I have some suites that I'm just getting back to; I haven't run them since exvmsrose was retired and so I'm trying to get them going again. When I try to build the ancillaries on my suite u-bc310, the suite fails with the following error

/usr/lib64/python2.6/site-packages/requests/packages/urllib3/connection.py:337: SubjectAltNameWarning: Certificate for xcslc1 has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/shazow/urllib3/issues/497 for details.)
  SubjectAltNameWarning
/home/d04/jokea/cylc-run/u-bc310/share/fcm_make_ants/lib/python2.7/site-packages/iris/fileformats/grib/__init__.py:59: IrisDeprecation: The module iris.fileformats.grib is deprecated since v1.10. Please install the package 'iris_grib' package instead.
  "The module iris.fileformats.grib is deprecated since v1.10. "
Traceback (most recent call last):
  File "/home/d04/jokea/cylc-run/u-bc310/share/fcm_make_ants/bin/ancil_landseamask.py", line 23, in <module>
    import ants
  File "/home/d04/jokea/cylc-run/u-bc310/share/fcm_make_ants/lib/python2.7/site-packages/ants/__init__.py", line 5, in <module>
    import analysis
  File "/home/d04/jokea/cylc-run/u-bc310/share/fcm_make_ants/lib/python2.7/site-packages/ants/analysis/__init__.py", line 40, in <module>
    import _merge
  File "/home/d04/jokea/cylc-run/u-bc310/share/fcm_make_ants/lib/python2.7/site-packages/ants/analysis/_merge.py", line 16, in <module>
    from shapely.vectorized import contains
  File "/home/d04/jokea/cylc-run/u-bc310/share/fcm_make_ants/lib/python2.7/site-packages/shapely/vectorized/__init__.py", line 3, in <module>
    from ._vectorized import (contains, touches)
ImportError: /home/d04/jokea/cylc-run/u-bc310/share/fcm_make_ants/lib/python2.7/site-packages/shapely/vectorized/_vectorized.so: undefined symbol: GEOSPreparedTouches_r
[FAIL] ${ANTS_PYTHON_PATH}/bin/python -s ${ANTS_PYTHON_PATH}/bin/ancil_landseamask.py ${source} --target-grid ${target_grid} \
[FAIL] -o ${output} --ants-config ${ANTS_CONFIG} <<'__STDIN__'
[FAIL] 
[FAIL] '__STDIN__' # return-code=1
2019-06-10T15:30:24Z CRITICAL - failed/EXIT
/usr/lib64/python2.6/site-packages/requests/packages/urllib3/connection.py:337: SubjectAltNameWarning: Certificate for xcslc1 has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/shazow/urllib3/issues/497 for details.)
  SubjectAltNameWarning

Based on the other tickets, this error (albeit likely related to the exvmsrose/xcslc1 switch) seems a bit generic, so I'm not sure where to start diagnosing the issue. A grep search through the suite reveals no mention of exvmsrose anywhere (which was the issue in one of the other tickets)

Any ideas?

Thanks,
John

[dcase]

You are running a python binary /home/d04/jokea/cylc-run/u-bc310/share/fcm_make_ants/bin/python which should be able to import all the modules that you need, but when you get to the line import ants it sees that something hasn't been set up correctly.

This is a Python issue, rather than exvmsrose. I'm not sure what the best way to solve this is, as you'd hope that when you pulled the code to your suite, it was all set up perfectly. Perhaps check the repository and see if there's a later version???

I hope that this is a useful start,
Dave

[simon]

Hi,

A strange one this. For some reason python isn't finding one of the shared libraries required for ants. As a workaround, try pre-pending the "command default" in ants_mask and ants_vegfrac in rose edit with LD_PRELOAD=/home/d03/hadsw/miniconda2/envs/ants_v0.8.0/lib/libgeos_c.so.1.10.2 so they that look like LD_PRELOAD=/home/d03/hadsw/miniconda2/envs/ants_v0.8.0/lib/libgeos_c.so.1.10.2 ${ANTS_PYTHON_PATH}/bin/python ...