search

caporaso-lab / sourcetracker2

SourceTracker2
BSD 3-Clause "New" or "Revised" License
60 stars 45 forks source link

Warning/Error with ipython hanging, solved by installing directly from github #141

Open nickp60 opened 2 years ago

nickp60 commented 2 years ago

Hi Sourcetracker2 team. Would it be possible to make a new release, and update the version of Sourcetracker2 available on pip? It appears that there have been some changes that break the version installable via pip ( 2.0.1 ). Potentially related to https://github.com/ipython/ipyparallel/issues/303

I installed the software as described in the readme, and ran the following

$ sourcetracker2 gibbs -i genus.txt -m map.txt -o example1/ --jobs 8
/Users/nwaters/miniconda3/envs/st2/lib/python3.5/site-packages/ipyparallel/util.py:214: RuntimeWarning: IPython could not determine IPs for LSKI3305: [Errno 8] nodename nor servname provided, or not known
  RuntimeWarning)

... which hangs indefinitely, no cpu load that I could see in each of the spawned ipyparallel jobs.

Here is my conda env:

# packages in environment at /Users/me/miniconda3/envs/st2:
#
# Name                    Version                   Build  Channel
appnope                   0.1.0                    py35_0    conda-forge
asn1crypto                1.4.0              pyh9f0ad1d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.1                      py_0    conda-forge
biom-format               2.1.6                    pypi_0    pypi
blas                      1.1                    openblas    conda-forge
brotlipy                  0.7.0            py35h470a237_0    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
cachecontrol              0.12.6                     py_0    conda-forge
certifi                   2018.8.24             py35_1001    conda-forge
cffi                      1.11.5           py35h5e8e0c9_1    conda-forge
chardet                   3.0.4                    py35_3    conda-forge
click                     7.1.2              pyh9f0ad1d_0    conda-forge
cryptography              2.3.1            py35hdffb7b8_0    conda-forge
cryptography-vectors      2.3.1                    py35_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
decorator                 5.1.0              pyhd8ed1ab_0    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
future                    0.16.0                   py35_2    conda-forge
h5py                      2.8.0            py35h7eb728f_2    conda-forge
hdf5                      1.10.2               hc401514_3    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
ipykernel                 5.5.6                    pypi_0    pypi
ipyparallel               6.3.0                    pypi_0    pypi
ipython                   7.0.1            py35h24bf2e0_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.12.1                   py35_0    conda-forge
jupyter-client            6.1.12                   pypi_0    pypi
jupyter-core              4.6.3                    pypi_0    pypi
kiwisolver                1.0.1            py35h2d50403_2    conda-forge
libcxx                    12.0.1               habf9029_0    conda-forge
libffi                    3.2.1             hb1e8313_1007    conda-forge
libgfortran               3.0.1                         0    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
libzlib                   1.2.11            h9173be1_1013    conda-forge
lockfile                  0.12.2                     py_1    conda-forge
matplotlib                3.0.0            py35h54f8f79_0  
msgpack-python            0.5.6            py35h2d50403_3    conda-forge
natsort                   7.1.1              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h2e338ed_4    conda-forge
nose                      1.3.7                    py35_2    conda-forge
numpy                     1.15.2          py35_blas_openblashd3ea46f_0  [blas_openblas]  conda-forge
openblas                  0.2.20                        8    conda-forge
openssl                   1.0.2u               h0b31af3_0    conda-forge
pandas                    0.23.4           py35hf8a1672_0    conda-forge
parso                     0.7.1              pyh9f0ad1d_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       20.3.4             pyhd8ed1ab_0    conda-forge
prompt-toolkit            2.0.10                   pypi_0    pypi
prompt_toolkit            3.0.20               hd8ed1ab_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 18.0.0                   py35_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pysocks                   1.6.8                    py35_2    conda-forge
python                    3.5.5                h5001a0f_2    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
pyzmq                     20.0.0                   pypi_0    pypi
readline                  7.0               hcfe32e1_1001    conda-forge
requests                  2.25.1             pyhd3deb0d_0    conda-forge
scikit-bio                0.5.1                    py35_0    biocore
scipy                     1.1.0           py35_blas_openblash7943236_201  [blas_openblas]  conda-forge
seaborn                   0.9.0                      py_0    conda-forge
setuptools                40.4.3                   py35_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sourcetracker             2.0.1                    pypi_0    pypi
sqlite                    3.28.0               h9721f7c_0    conda-forge
statsmodels               0.9.0                    py35_0    conda-forge
tk                        8.6.11               h5dbffcc_1    conda-forge
tornado                   5.1.1            py35h470a237_0    conda-forge
traitlets                 4.3.2                    py35_0    conda-forge
urllib3                   1.26.7             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zlib                      1.2.11            h9173be1_1013    conda-forge

When installing from git (pip uninstall sourcetracker && pip install git+https://github.com/biota/sourcetracker2.git) the same command works, presumably due to the switch from to python's multiprocessing library. Hope that helps someone out there.