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Parallelization fails -- TypeError: cannot pickle '_abc._abc_data' object #41

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katrinaCode opened this issue Jan 4, 2023 · 4 comments
Open

Parallelization fails -- TypeError: cannot pickle '_abc._abc_data' object #41

katrinaCode opened this issue Jan 4, 2023 · 4 comments

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@katrinaCode
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katrinaCode commented Jan 4, 2023 •
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Hi pySustain team,

I am running into the following error when setting parallelization = True in ZscoreSustain: "TypeError: cannot pickle '_abc._abc_data' object". This error is picked up ~60 times, always tracing to the pickle.py or the _dill.py files within the pysustain package. This has happened using both Jupyter Notebook and Spyder, however I can run Sustain fine when parallelization is set to False.

Error Traceback: 
File "[pysustain package location]/lib/python3.10/site-packages/spyder_kernels/py3compat.py", line 356, in compat_exec
  exec(code, globals, locals)

File [notebook], line 231, in <module>
  prob_subtype_stage  = sustain_input.run_sustain_algorithm()

File "[pysustain package location]/lib/python3.10/site-packages/pySuStaIn/AbstractSustain.py", line 164, in run_sustain_algorithm
  ml_likelihood_mat_EM        = self._estimate_ml_sustain_model_nplus1_clusters(self.__sustainData, ml_sequence_prev_EM, ml_f_prev_EM) #self.__estimate_ml_sustain_model_nplus1_clusters(self.__data, ml_sequence_prev_EM, ml_f_prev_EM)

File "[pysustain package location]/lib/python3.10/site-packages/pySuStaIn/AbstractSustain.py", line 615, in _estimate_ml_sustain_model_nplus1_clusters
  ml_likelihood_mat               = self._find_ml(sustainData)

File "[pysustain package location]/lib/python3.10/site-packages/pySuStaIn/AbstractSustain.py", line 704, in _find_ml
  pool_output_list                    = self.pool.map(partial_iter, seed_sequences.spawn(self.N_startpoints))

File "[pysustain package location]/lib/python3.10/site-packages/pathos/multiprocessing.py", line 135, in map
  return _pool.map(star(f), zip(*args)) # chunksize

File "[pysustain package location]/lib/python3.10/site-packages/multiprocess/pool.py", line 367, in map
  return self._map_async(func, iterable, mapstar, chunksize).get()

File "[pysustain package location]/lib/python3.10/site-packages/multiprocess/pool.py", line 774, in get
  raise self._value

File "[pysustain package location]/lib/python3.10/site-packages/multiprocess/pool.py", line 540, in _handle_tasks
  put(task)

File "[pysustain package location]/lib/python3.10/site-packages/multiprocess/connection.py", line 214, in send
  self._send_bytes(_ForkingPickler.dumps(obj))

File "[pysustain package location]/lib/python3.10/site-packages/multiprocess/reduction.py", line 54, in dumps
  cls(buf, protocol, *args, **kwds).dump(obj)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 394, in dump
  StockPickler.dump(self, obj)

File "[pysustain package location]/lib/python3.10/pickle.py", line 487, in dump
  self.save(obj)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/pickle.py", line 902, in save_tuple
  save(element)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/pickle.py", line 887, in save_tuple
  save(element)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/pickle.py", line 887, in save_tuple
  save(element)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 1824, in save_function
  _save_with_postproc(pickler, (_create_function, (

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 1089, in _save_with_postproc
  pickler.save_reduce(*reduction)

File "[pysustain package location]/lib/python3.10/pickle.py", line 692, in save_reduce
  save(args)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/pickle.py", line 887, in save_tuple
  save(element)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 603, in save
  self.save_reduce(obj=obj, *rv)

File "[pysustain package location]/lib/python3.10/pickle.py", line 692, in save_reduce
  save(args)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/pickle.py", line 887, in save_tuple
  save(element)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 1427, in save_instancemethod0
  pickler.save_reduce(MethodType, (obj.__func__, obj.__self__), obj=obj)

File "[pysustain package location]/lib/python3.10/pickle.py", line 692, in save_reduce
  save(args)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/pickle.py", line 887, in save_tuple
  save(element)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 1824, in save_function
  _save_with_postproc(pickler, (_create_function, (

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 1084, in _save_with_postproc
  pickler._batch_setitems(iter(source.items()))

File "[pysustain package location]/lib/python3.10/pickle.py", line 998, in _batch_setitems
  save(v)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 1698, in save_type
  _save_with_postproc(pickler, (_create_type, (

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 1070, in _save_with_postproc
  pickler.save_reduce(*reduction, obj=obj)

File "[pysustain package location]/lib/python3.10/pickle.py", line 692, in save_reduce
  save(args)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/pickle.py", line 902, in save_tuple
  save(element)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 560, in save
  f(self, obj)  # Call unbound method with explicit self

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 1186, in save_module_dict
  StockPickler.save_dict(pickler, obj)

File "[pysustain package location]/lib/python3.10/pickle.py", line 972, in save_dict
  self._batch_setitems(obj.items())

File "[pysustain package location]/lib/python3.10/pickle.py", line 998, in _batch_setitems
  save(v)

File "[pysustain package location]/lib/python3.10/site-packages/dill/_dill.py", line 388, in save
  StockPickler.save(self, obj, save_persistent_id)

File "[pysustain package location]/lib/python3.10/pickle.py", line 578, in save
  rv = reduce(self.proto)

TypeError: cannot pickle '_abc._abc_data' object
System and package info:
  • MacBook Pro 2021
  • Python 3.10.6

Packages:
alabaster @ file:///home/ktietz/src/ci/alabaster_1611921544520/work
anyio==3.6.2
applaunchservices @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_96v71vcny2/croots/recipe/applaunchservices_1661854626389/work
appnope==0.1.3
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
arrow @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_bc9ine8jfo/croot/arrow_1666726871970/work
astroid @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_9fsa1cbbec/croots/recipe/astroid_1659023133872/work
asttokens==2.0.8
atomicwrites==1.4.0
attrs==22.1.0
autopep8 @ file:///opt/conda/conda-bld/autopep8_1650463822033/work
awkde @ git+https://github.com/noxtoby/awkde.git@1c31e55fe54c0cad80ab423a9605fc9ddfb2614c
Babel==2.10.3
backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
beautifulsoup4 @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_croot-cdiouih5/beautifulsoup4_1650462164803/work
binaryornot @ file:///tmp/build/80754af9/binaryornot_1617751525010/work
black @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_d0nhgmyc3l/croots/recipe/black_1660237813406/work
bleach==5.0.1
brotlipy==0.7.0
certifi @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_0ek9yztvu3/croot/certifi_1665076692562/work/certifi
cffi @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_62rp5d8fd4/croots/recipe/cffi_1659598655556/work
chardet @ file:///Users/builder/ci_310/chardet_1642531418028/work
charset-normalizer==2.1.1
click @ file:///opt/concourse/worker/volumes/live/2d66025a-4d79-47c4-43be-6220928b6c82/volume/click_1646056610594/work
cloudpickle @ file:///tmp/build/80754af9/cloudpickle_1632508026186/work
colorama @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_b8ecd5af-5e60-48b8-80ac-92164ecb9b9bxkf0tkfp/croots/recipe/colorama_1657009097162/work
contourpy==1.0.5
cookiecutter @ file:///opt/conda/conda-bld/cookiecutter_1649151442564/work
cryptography @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_3evwafgyg8/croot/cryptography_1665612651044/work
cycler==0.11.0
debugpy==1.6.3
decorator @ file:///opt/conda/conda-bld/decorator_1643638310831/work
defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
diff-match-patch @ file:///Users/ktietz/demo/mc3/conda-bld/diff-match-patch_1630511840874/work
dill @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_88dxe9g1aq/croot/dill_1667919544494/work
docutils @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_10cfb287-0327-45ef-a38e-53dffd30cef1nwpvy20e/croots/recipe/docutils_1657175439973/work
entrypoints @ file:///opt/concourse/worker/volumes/live/5eb4850e-dcbc-41ad-5f22-922bac778f70/volume/entrypoints_1649926457041/work
executing==1.1.1
fastjsonschema @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_b5c1gee32t/croots/recipe/python-fastjsonschema_1661368622875/work
flake8 @ file:///opt/conda/conda-bld/flake8_1648129545443/work
fonttools==4.38.0
future==0.18.2
idna @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_00jf0h4zbt/croot/idna_1666125573348/work
imagesize @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_4a6ed1be-fe30-4d6a-91d4-f867600caa0be5_dxzvt/croots/recipe/imagesize_1657179500955/work
importlib-metadata @ file:///opt/concourse/worker/volumes/live/a8740f82-0523-4b08-5bb5-afa0c929f5e0/volume/importlib-metadata_1648562424930/work
inflection==0.5.1
intervaltree @ file:///Users/ktietz/demo/mc3/conda-bld/intervaltree_1630511889664/work
ipykernel==6.16.2
ipython==8.5.0
ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work
isort @ file:///tmp/build/80754af9/isort_1628603791788/work
jedi @ file:///opt/concourse/worker/volumes/live/18b71546-5bde-4add-72d1-7d16b76f0f7a/volume/jedi_1644315243726/work
jellyfish @ file:///opt/concourse/worker/volumes/live/d045b25f-e3af-4008-4edc-a00aeffb8b33/volume/jellyfish_1647962558521/work
Jinja2 @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_6adj7x0ejx/croot/jinja2_1666908137966/work
jinja2-time @ file:///opt/conda/conda-bld/jinja2-time_1649251842261/work
joblib==1.2.0
json5==0.9.10
jsonschema @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_d832da7jx3/croots/recipe/jsonschema_1663375475386/work
jupyter-server==1.21.0
jupyter_client==7.4.4
jupyter_core @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_fc_0us_ta7/croot/jupyter_core_1668084443574/work
jupyterlab==3.5.0
jupyterlab-pygments==0.2.2
jupyterlab_server==2.16.1
jupyterthemes==0.20.0
kde-ebm @ git+https://github.com/ucl-pond/kde_ebm.git@26ee48f7f723a82e4ff740e59b9745aa7def3daa
keyring @ file:///Users/builder/ci_310/keyring_1642616528347/work
kiwisolver==1.4.4
lazy-object-proxy @ file:///Users/builder/ci_310/lazy-object-proxy_1642533824465/work
lesscpy==0.15.1
lxml @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_1902c961-4bd2-4871-a3c5-70b7317a6521kpj7nz2o/croots/recipe/lxml_1657545138937/work
MarkupSafe @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_d4a9444f-bd4c-4043-b47d-cede33979b0fve7bm42r/croots/recipe/markupsafe_1654597878200/work
matplotlib==3.6.0
matplotlib-inline @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_9ddl71oqte/croots/recipe/matplotlib-inline_1662014471815/work
mccabe @ file:///opt/conda/conda-bld/mccabe_1644221741721/work
mistune==2.0.4
multiprocess==0.70.14
mypy-extensions==0.4.3
nbclassic==0.4.5
nbclient==0.7.0
nbconvert==7.2.5
nbformat==5.7.0
nest-asyncio==1.5.6
notebook==6.5.1
notebook_shim==0.2.0
numpy==1.23.4
numpydoc @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_adnyzxppoz/croot/numpydoc_1668085907252/work
p2j==1.3.2
packaging @ file:///tmp/build/80754af9/packaging_1637314298585/work
pandas==1.5.1
pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work
parso @ file:///opt/conda/conda-bld/parso_1641458642106/work
pathos==0.3.0
pathspec @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_e2t1r2kdq7/croots/recipe/pathspec_1659627124303/work
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
Pillow==9.2.0
platformdirs @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_7fs8_2xgrm/croots/recipe/platformdirs_1662711383474/work
pluggy @ file:///opt/concourse/worker/volumes/live/8277900c-164a-49c8-6f2a-f55c3c0154be/volume/pluggy_1648042581708/work
ply==3.11
pox==0.3.2
poyo @ file:///tmp/build/80754af9/poyo_1617751526755/work
ppft==1.7.6.6
prometheus-client==0.15.0
prompt-toolkit==3.0.31
psutil==5.9.3
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
pure-eval==0.2.2
pybind11==2.10.0
pycodestyle @ file:///tmp/build/80754af9/pycodestyle_1636635402688/work
pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work
pydocstyle @ file:///tmp/build/80754af9/pydocstyle_1621600989141/work
pyflakes @ file:///tmp/build/80754af9/pyflakes_1636644436481/work
Pygments==2.13.0
pylint @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_e75_4ydew9/croots/recipe/pylint_1659110352634/work
pyls-spyder==0.4.0
pyobjc-core @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_e7giy3a869/croots/recipe/pyobjc-core_1661848172499/work
pyobjc-framework-Cocoa @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_4c2umern3y/croots/recipe/pyobjc-framework-cocoa_1661850714385/work
pyobjc-framework-CoreServices @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_4717m_ngol/croots/recipe/pyobjc-framework-coreservices_1661853392396/work
pyobjc-framework-FSEvents @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_5atkr691rb/croots/recipe/pyobjc-framework-fsevents_1661852390555/work
pyOpenSSL @ file:///opt/conda/conda-bld/pyopenssl_1643788558760/work
pyparsing @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_3a17y2delq/croots/recipe/pyparsing_1661452538853/work
PyQt5-sip==12.11.0
pyrsistent==0.18.1
PySocks @ file:///Users/builder/ci_310/pysocks_1642536366386/work
pySuStaIn @ git+https://github.com/ucl-pond/pySuStaIn@564f07617a2a11477a18aec0b24d5d80825b0371
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
python-lsp-black @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_14xl6hg757/croots/recipe/python-lsp-black_1661852036282/work
python-lsp-jsonrpc==1.0.0
python-lsp-server @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_6cu9im5n5w/croots/recipe/python-lsp-server_1661813818984/work
python-slugify @ file:///tmp/build/80754af9/python-slugify_1620405669636/work
pytz==2022.5
PyYAML==6.0
pyzmq==24.0.1
QDarkStyle @ file:///tmp/build/80754af9/qdarkstyle_1617386714626/work
qstylizer @ file:///tmp/build/80754af9/qstylizer_1617713584600/work/dist/qstylizer-0.1.10-py2.py3-none-any.whl
QtAwesome @ file:///tmp/build/80754af9/qtawesome_1637160816833/work
qtconsole @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_552cqm7spz/croots/recipe/qtconsole_1662018258355/work
QtPy @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_4e5ppuhz0f/croots/recipe/qtpy_1662014536017/work
requests @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_516b78ce-034d-4395-b9b5-1d78c2847384qtnol99l/croots/recipe/requests_1657734628886/work
rope @ file:///opt/conda/conda-bld/rope_1643788605236/work
Rtree @ file:///Users/builder/ci_310/rtree_1642537064369/work
scikit-learn==1.1.3
scipy==1.9.3
seaborn==0.12.1
Send2Trash==1.8.0
sip @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_88z1zrsfrf/croots/recipe/sip_1659012373083/work
six @ file:///tmp/build/80754af9/six_1644875935023/work
sklearn==0.0
sniffio==1.3.0
snowballstemmer @ file:///tmp/build/80754af9/snowballstemmer_1637937080595/work
sortedcontainers @ file:///tmp/build/80754af9/sortedcontainers_1623949099177/work
soupsieve @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_14fb2zs6e3/croot/soupsieve_1666296397588/work
Sphinx @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_5d9f8d69-b80c-4ca1-8876-1698c70b1faeqe461tx8/croots/recipe/sphinx_1657784127805/work
sphinxcontrib-applehelp @ file:///home/ktietz/src/ci/sphinxcontrib-applehelp_1611920841464/work
sphinxcontrib-devhelp @ file:///home/ktietz/src/ci/sphinxcontrib-devhelp_1611920923094/work
sphinxcontrib-htmlhelp @ file:///tmp/build/80754af9/sphinxcontrib-htmlhelp_1623945626792/work
sphinxcontrib-jsmath @ file:///home/ktietz/src/ci/sphinxcontrib-jsmath_1611920942228/work
sphinxcontrib-qthelp @ file:///home/ktietz/src/ci/sphinxcontrib-qthelp_1611921055322/work
sphinxcontrib-serializinghtml @ file:///tmp/build/80754af9/sphinxcontrib-serializinghtml_1624451540180/work
spyder @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_97gv8v17po/croots/recipe/spyder_1663056808858/work
spyder-kernels @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_1c7pyd81si/croots/recipe/spyder-kernels_1662457889999/work
stack-data==0.5.1
tdt==0.5.4
terminado==0.17.0
text-unidecode @ file:///Users/ktietz/demo/mc3/conda-bld/text-unidecode_1629401354553/work
textdistance @ file:///tmp/build/80754af9/textdistance_1612461398012/work
threadpoolctl==3.1.0
three-merge @ file:///tmp/build/80754af9/three-merge_1607553261110/work
tinycss @ file:///tmp/build/80754af9/tinycss_1617713798712/work
tinycss2 @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_56dshjmms6/croot/tinycss2_1668168824483/work
toml @ file:///tmp/build/80754af9/toml_1616166611790/work
tomli @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_90762ba4-f339-47e8-bd29-416854a59b233d27hku_/croots/recipe/tomli_1657175507767/work
tomlkit @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_5fgtm9if1m/croots/recipe/tomlkit_1658946891645/work
tornado @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_1fimz6o0gc/croots/recipe/tornado_1662061695695/work
tqdm==4.64.1
traitlets==5.5.0
typing_extensions @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_ff5_5nqr6l/croots/recipe/typing_extensions_1659638832447/work
ujson @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_cf44fbd5-5db0-48cf-86c4-c8d4e74d1cbbwhgckc99/croots/recipe/ujson_1657544919410/work
Unidecode @ file:///tmp/build/80754af9/unidecode_1614712377438/work
urllib3 @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_7f7kb5tudl/croot/urllib3_1666298941688/work
watchdog @ file:///Users/builder/ci_310/watchdog_1642516765439/work
wcwidth @ file:///Users/ktietz/demo/mc3/conda-bld/wcwidth_1629357192024/work
webencodings==0.5.1
websocket-client==1.4.1
whatthepatch @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_0aabmq0ph3/croots/recipe/whatthepatch_1661795995892/work
wrapt @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_1ade1f68-8354-4db8-830b-ff3072015779vd_2hm7k/croots/recipe/wrapt_1657814407132/work
wurlitzer @ file:///Users/builder/ci_310/wurlitzer_1642539193810/work
yapf @ file:///tmp/build/80754af9/yapf_1615749224965/work
zipp @ file:///private/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_b279673d-f037-44c7-8773-c5a6b6f51037d3wfr9cq/croots/recipe/zipp_1652341773612/work

Thank you for your help!
Katrina
@sea-shunned sea-shunned mentioned this issue Jan 30, 2023
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@sea-shunned
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Hi Katrina,

Many thanks for reporting this to us. I couldn't see the exact dill version in the output that you provided, but locally I've seen that this error occurs with dill==0.3.6 and not with a previous version. Does downgrading via e.g. pip install dill==0.3.5.1 fix this issue for you?

@jadenecke
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dill==0.3.5.1 this did the trick for me, however I was warned by pip and then also adjusted multiprocess==0.70.13 and pathos==0.2.9. It did not throw an error right away with the newer versions, but I also did not let the script finish.

@sea-shunned
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I also got the same, and it hasn't caused any problems (yet).

We are working on a longer term solution, but I am glad this helped in the interm. When the full solution has been integrated, I'll let you know here and close this issue!

Thanks for reporting the problem :)

sea-shunned added a commit that referenced this issue Feb 9, 2023
@sea-shunned
Enforce dill downgrade (temporary fix for #41)
bc38539
@katrinaCode
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Hi all, thank you! Doing the three-package version downgrade as suggested by jadenecke worked and it isn't throwing the error anymore. 🥳

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@sea-shunned @jadenecke @katrinaCode