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CDAT / cdat

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cdat - install from channel - many test failures -- Library not loaded: @rpath/libnetcdf.11.dylib( both linux and macOS) #2212

Closed muryanto1 closed 6 years ago

muryanto1 commented 6 years ago

``macos_cdat_latest_channel_py3 - https://circleci.com/gh/CDAT/cdat/5189

install: conda create -n cdat_latest_channel_py3 -c cdat/label/v80 -c conda-forge -c cdat python=3.6 cdat

source activate cdat_latest_channel_py3; conda install -c conda-forge -c cdat -c pcmdi/label/nightly -c pcmdi nose coverage image-compare pcmdi_metrics cia easydev nbsphinx mesalib; source deactivate"

macos_cdat_latest_channel_py2 - https://circleci.com/gh/CDAT/cdat/5184

Lots of test failures due to: b'ERROR: Failure: ImportError (dlopen(/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/cdtime.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libnetcdf.11.dylib' b' Referenced from: /Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/cdtime.cpython-36m-darwin.so' b' Reason: image not found)' b'----------------------------------------------------------------------' b'Traceback (most recent call last):' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/nose/failure.py", line 39, in runTest' b' raise self.exc_val.with_traceback(self.tb)' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/nose/loader.py", line 417, in loadTestsFromName' b' addr.filename, addr.module)' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/nose/importer.py", line 47, in importFromPath' b' return self.importFromDir(dir_path, fqname)' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/nose/importer.py", line 94, in importFromDir' b' mod = load_module(part_fqname, fh, filename, desc)' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/imp.py", line 235, in load_module' b' return load_source(name, filename, file)' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/imp.py", line 172, in load_source' b' module = _load(spec)' b' File "", line 684, in _load' b' File "", line 665, in _load_unlocked' b' File "", line 678, in exec_module' b' File "", line 219, in _call_with_frames_removed' b' File "/Users/distiller/project/workdir/genutil/tests/test_genutil_udunits2_additions.py", line 1, in ' b' import genutil' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/genutil/init.py", line 5, in ' b' from .grower import grower # noqa' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/genutil/grower.py", line 3, in ' b' import cdms2 as cdms' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/cdms2/init.py", line 20, in ' b' from .cdmsobj import CdArray, CdChar, CdByte, CdDouble, CdFloat, CdFromObject, CdInt, CdLong, CdScalar, CdShort, CdString # noqa' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/cdms2/cdmsobj.py", line 5, in ' b' from . import cdmsNode' b' File "/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/cdms2/cdmsNode.py", line 10, in ' b' import cdtime' b'ImportError: dlopen(/Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/cdtime.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libnetcdf.11.dylib' b' Referenced from: /Users/distiller/project/workdir/miniconda/envs/cdat_latest_channel_py3/lib/python3.6/site-packages/cdtime.cpython-36m-darwin.so' b' Reason: image not found'

dnadeau4 commented 6 years ago

I moved the cdtime label from v80 to v80netcdf11. That was moved from conda-forge by @doutriaux1 but not sure it it is needed anymore.

doutriaux1 commented 6 years ago

@dnadeau4 it it works again like that then fine, I can't remember exactly why I had to do a v80 label, but it was around the time you were upgrading the compilers. It might be fixed now and unncessary then. @muryanto1 does this fix the issue?

muryanto1 commented 6 years ago

I verified that from our nightly run, Denis' changes fix the issue, not seeing "Library not loaded: @rpath/libnetcdf.11.dylib'" anymore.

doutriaux1 commented 6 years ago

@muryanto1 the install from yaml still works?

doutriaux1 commented 6 years ago

@muryanto1 this is why I add cdtime in a special v80 channel. I'll try to fix the yamls...