error - Githubissues

ryrl970311 commented 3 years ago

Describe the bug When I ran pyscenic in anaconda environment, it always report "ImportError: cannot import name 'dumps_msgpack' from 'distributed.protocol.core'". How should I solve this problem?

Steps to reproduce the behavior

Command run when the error occurred:
```
pyscenic grn 
...
```

Error encountered:

Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
ImportError: cannot import name 'dumps_msgpack' from 'distributed.protocol.core'

Expected behavior A clear and concise description of what you expected to happen.

Please complete the following information:

pySCENIC version: 0.11.2
Installation method: Conda, Pip
Run environment: conda basic
OS: Ubuntu
Package versions: [obtain using pip freeze, conda list, or skip this if using Docker/Singularity]:
```
...
```

lxwang326 commented 3 years ago

i have the same problem too

ryrl970311 commented 3 years ago

i have the same problem too

Did you solve this problem?

lxwang326 commented 3 years ago

not yet

jpcartailler commented 3 years ago

Probably incompatibility between dask and distributed packages. To avoid these issues, it's best to run pySCENIC from Docker image.

fouerghi commented 3 years ago

Error has also been occurring for me

SalmonellaIIB commented 3 years ago

I am not sure what is the problem. I tried to run "pyscenic grn" too, and after some minutes I have the same error. However, I think is a problem with a new version of a library because after using my previous pyscenic conda environment it worked. I also tested downgrading specific packages such as dask, distributed, numba, and pyscenic, and it did not worked. Here you have the environment that I am using and where pySCENIC seems to run properly. I hope it helps someone!

name: pyscenic_sallmonella channels:

anaconda
conda-forge
defaults dependencies:
_libgcc_mutex=0.1=conda_forge
_openmp_mutex=4.5=1_gnu
_r-mutex=1.0.1=anacondar_1
adjusttext=0.7.3.1=py_1
binutils_impl_linux-64=2.35.1=h193b22a_2
binutils_linux-64=2.35=h67ddf6f_30
bwidget=1.9.14=ha770c72_0
bzip2=1.0.8=h7f98852_4
c-ares=1.17.1=h7f98852_1
ca-certificates=2021.5.30=ha878542_0
cairo=1.16.0=h6cf1ce9_1008
certifi=2021.5.30=py37h89c1867_0
cffi=1.14.5=py37hc58025e_0
curl=7.77.0=hea6ffbf_0
cycler=0.10.0=py_2
cytoolz=0.11.0=py37h7b6447c_0
font-ttf-dejavu-sans-mono=2.37=hab24e00_0
font-ttf-inconsolata=3.000=h77eed37_0
font-ttf-source-code-pro=2.038=h77eed37_0
font-ttf-ubuntu=0.83=hab24e00_0
fontconfig=2.13.1=hba837de_1005
fonts-conda-ecosystem=1=0
fonts-conda-forge=1=0
freetype=2.10.4=h0708190_1
fribidi=1.0.10=h36c2ea0_0
gcc_impl_linux-64=9.3.0=h70c0ae5_19
gcc_linux-64=9.3.0=hf25ea35_30
gettext=0.19.8.1=h0b5b191_1005
gfortran_impl_linux-64=9.3.0=hc4a2995_19
gfortran_linux-64=9.3.0=hdc58fab_30
graphite2=1.3.13=h58526e2_1001
gsl=2.6=he838d99_2
gxx_impl_linux-64=9.3.0=hd87eabc_19
gxx_linux-64=9.3.0=h3fbe746_30
harfbuzz=2.8.1=h83ec7ef_0
icu=68.1=h58526e2_0
jbig=2.1=h7f98852_2003
jinja2=3.0.1=pyhd8ed1ab_0
jpeg=9d=h36c2ea0_0
kernel-headers_linux-64=2.6.32=h77966d4_13
kiwisolver=1.3.1=py37h2527ec5_1
krb5=1.19.1=hcc1bbae_0
lcms2=2.12=hddcbb42_0
ld_impl_linux-64=2.35.1=hea4e1c9_2
lerc=2.2.1=h9c3ff4c_0
libblas=3.9.0=9_openblas
libcblas=3.9.0=9_openblas
libcurl=7.77.0=h2574ce0_0
libdeflate=1.7=h7f98852_5
libedit=3.1.20191231=he28a2e2_2
libev=4.33=h516909a_1
libffi=3.3=h58526e2_2
libgcc-devel_linux-64=9.3.0=h7864c58_19
libgcc-ng=9.3.0=h2828fa1_19
libgfortran-ng=9.3.0=hff62375_19
libgfortran5=9.3.0=hff62375_19
libglib=2.68.3=h3e27bee_0
libgomp=9.3.0=h2828fa1_19
libiconv=1.16=h516909a_0
liblapack=3.9.0=9_openblas
libnghttp2=1.43.0=h812cca2_0
libopenblas=0.3.15=pthreads_h8fe5266_1
libpng=1.6.37=h21135ba_2
libssh2=1.9.0=ha56f1ee_6
libstdcxx-devel_linux-64=9.3.0=hb016644_19
libstdcxx-ng=9.3.0=h6de172a_19
libtiff=4.3.0=hf544144_1
libuuid=2.32.1=h7f98852_1000
libwebp-base=1.2.0=h7f98852_2
libxcb=1.13=h7f98852_1003
libxml2=2.9.12=h72842e0_0
lz4-c=1.9.3=h9c3ff4c_0
make=4.3=hd18ef5c_1
markupsafe=2.0.1=py37h5e8e339_0
matplotlib-base=3.4.2=py37hdd32ed1_0
multicore-tsne=0.1_d4ff4aab=py37hda21425_1
ncurses=6.2=h58526e2_4
numpy=1.20.3=py37h038b26d_1
olefile=0.46=pyh9f0ad1d_1
openjpeg=2.4.0=hb52868f_1
openssl=1.1.1k=h7f98852_0
pango=1.48.5=hb8ff022_0
pcre=8.45=h9c3ff4c_0
pcre2=10.36=h032f7d1_1
pillow=8.2.0=py37h4600e1f_1
pip=21.1.2=pyhd8ed1ab_0
pixman=0.40.0=h36c2ea0_0
pthread-stubs=0.4=h36c2ea0_1001
pycparser=2.20=pyh9f0ad1d_2
pyparsing=2.4.7=pyh9f0ad1d_0
pyreadr=0.4.2=py37hfd22957_0
python=3.7.10=hffdb5ce_100_cpython
python-dateutil=2.8.1=py_0
python_abi=3.7=1_cp37m
pytz=2021.1=pyhd8ed1ab_0
r-base=4.1.0=h9e01966_1
readline=8.1=h46c0cb4_0
rpy2=3.4.5=py37r41h6f94858_0
sed=4.8=he412f7d_0
setuptools=49.6.0=py37h89c1867_3
simplegeneric=0.8.1=py_1
six=1.16.0=pyh6c4a22f_0
sqlite=3.35.5=h74cdb3f_0
sysroot_linux-64=2.12=h77966d4_13
tk=8.6.10=h21135ba_1
tktable=2.10=hb7b940f_3
toolz=0.11.1=py_0
tornado=6.1=py37h5e8e339_1
tzlocal=2.1=pyh9f0ad1d_0
wheel=0.36.2=pyhd3deb0d_0
xorg-kbproto=1.0.7=h7f98852_1002
xorg-libice=1.0.10=h7f98852_0
xorg-libsm=1.2.3=hd9c2040_1000
xorg-libx11=1.7.2=h7f98852_0
xorg-libxau=1.0.9=h7f98852_0
xorg-libxdmcp=1.1.3=h7f98852_0
xorg-libxext=1.3.4=h7f98852_1
xorg-libxrender=0.9.10=h7f98852_1003
xorg-libxt=1.2.1=h7f98852_2
xorg-renderproto=0.11.1=h7f98852_1002
xorg-xextproto=7.3.0=h7f98852_1002
xorg-xproto=7.0.31=h7f98852_1007
xz=5.2.5=h516909a_1
zlib=1.2.11=h516909a_1010
zstd=1.5.0=ha95c52a_0
pip:
- aiohttp==3.7.4.post0
- anndata==0.7.6
- arboreto==0.1.6
- argon2-cffi==20.1.0
- async-generator==1.10
- async-timeout==3.0.1
- attrs==21.2.0
- backcall==0.2.0
- bleach==3.3.0
- bokeh==2.3.2
- boltons==21.0.0
- cached-property==1.5.2
- chardet==4.0.0
- click==8.0.1
- cloudpickle==1.6.0
- cmake==3.20.2
- ctxcore==0.1.1
- dask==2.30.0
- decorator==4.4.2
- defusedxml==0.7.1
- dill==0.3.3
- distributed==2.30.0
- dunamai==1.5.5
- entrypoints==0.3
- frozendict==2.0.2
- fsspec==2021.5.0
- get-version==3.0
- h5py==3.2.1
- heapdict==1.0.1
- idna==2.10
- importlib-metadata==4.5.0
- interlap==0.2.7
- ipykernel==5.5.5
- ipython==7.24.1
- ipython-genutils==0.2.0
- ipywidgets==7.6.3
- jedi==0.18.0
- joblib==1.0.1
- jsonschema==3.2.0
- jupyter==1.0.0
- jupyter-client==6.1.12
- jupyter-console==6.4.0
- jupyter-core==4.7.1
- jupyterlab-pygments==0.1.2
- jupyterlab-widgets==1.0.0
- legacy-api-wrap==1.2
- llvmlite==0.36.0
- locket==0.2.1
- loompy==3.0.6
- louvain==0.7.0
- matplotlib-inline==0.1.2
- mistune==0.8.4
- msgpack==1.0.2
- multidict==5.1.0
- multiprocessing-on-dill==3.5.0a4
- natsort==7.1.1
- nbclient==0.5.3
- nbconvert==6.0.7
- nbformat==5.1.3
- nest-asyncio==1.5.1
- networkx==2.5.1
- notebook==6.4.0
- numba==0.53.1
- numexpr==2.7.3
- numpy-groupies==0.9.13
- packaging==20.9
- pandas==1.2.4
- pandocfilters==1.4.3
- parso==0.8.2
- partd==1.2.0
- patsy==0.5.1
- pexpect==4.8.0
- pickleshare==0.7.5
- prometheus-client==0.11.0
- prompt-toolkit==3.0.18
- psutil==5.8.0
- ptyprocess==0.7.0
- pyarrow==0.16.0
- pygments==2.9.0
- pynndescent==0.5.2
- pyrsistent==0.17.3
- pyscenic==0.11.1
- python-igraph==0.9.4
- pyyaml==5.4.1
- pyzmq==22.1.0
- qtconsole==5.1.0
- qtpy==1.9.0
- requests==2.25.1
- scanpy==1.7.2
- scikit-learn==0.24.2
- scipy==1.6.3
- seaborn==0.11.1
- send2trash==1.5.0
- sinfo==0.3.4
- sortedcontainers==2.4.0
- statsmodels==0.12.2
- stdlib-list==0.8.0
- tables==3.6.1
- tblib==1.7.0
- terminado==0.10.0
- testpath==0.5.0
- texttable==1.6.3
- threadpoolctl==2.1.0
- tqdm==4.61.0
- traitlets==5.0.5
- typing-extensions==3.10.0.0
- umap-learn==0.5.1
- urllib3==1.26.5
- wcwidth==0.2.5
- webencodings==0.5.1
- widgetsnbextension==3.5.1
- xlrd==1.2.0
- yarl==1.6.3
- zict==2.0.0
- zipp==3.4.1

aertslab / pySCENIC

error #305