xESMF: Kernel dies running tutorial example

I am running the tutorial at https://xesmf.readthedocs.io/en/latest/Curvilinear_grid.html and the kernel dies. I updated all packages and still have issues. Does anybody have any idea where the incompatibility is coming from? here is the environment I am running in:

name: pangeo
channels:
  - conda-forge
  - defaults
dependencies:
  - asn1crypto=0.24.0=py36_3
  - bleach=2.1.3=py_0
  - bokeh=0.13.0=py36_0
  - bottleneck=1.2.1=py36h7eb728f_1
  - cffi=1.11.5=py36h5e8e0c9_1
  - cftime=1.0.1=py36h7eb728f_0
  - chardet=3.0.4=py36_3
  - click=6.7=py_1
  - cloudpickle=0.5.2=py_0
  - cryptography=2.3.1=py36hdffb7b8_0
  - cryptography-vectors=2.3.1=py36_0
  - curl=7.59.0=0
  - cycler=0.10.0=py36_0
  - cytoolz=0.9.0.1=py36_0
  - dask=0.17.1=py_2
  - dask-core=0.17.1=py_0
  - dask-jobqueue=0.1.1=py_0
  - decorator=4.2.1=py36_0
  - distributed=1.21.3=py36_0
  - docrep=0.2.3=py36_0
  - entrypoints=0.2.3=py36_1
  - esmf=7.1.0r=1
  - esmpy=7.1.0r=py36_1
  - expat=2.2.5=0
  - fontconfig=2.13.1=h65d0f4c_0
  - freetype=2.9.1=h6debe1e_4
  - geos=3.6.2=hfc679d8_3
  - gettext=0.19.8.1=0
  - gmp=6.1.2=0
  - h5netcdf=0.6.2=py_0
  - h5py=2.8.0=py36h470a237_0
  - hdf4=4.2.13=0
  - hdf5=1.10.1=2
  - heapdict=1.0.0=py36_0
  - html5lib=1.0.1=py_0
  - icu=58.2=0
  - idna=2.7=py36_2
  - ipykernel=4.8.2=py36_0
  - ipython=6.2.1=py36_1
  - ipython_genutils=0.2.0=py36_0
  - jedi=0.11.1=py36_0
  - jinja2=2.10=py36_0
  - jpeg=9c=h470a237_1
  - jsonschema=2.6.0=py36_1
  - jupyter_client=5.2.3=py36_0
  - jupyter_core=4.4.0=py_0
  - jupyterlab=0.31.12=py36_1
  - jupyterlab_launcher=0.10.5=py36_0
  - kiwisolver=1.0.1=py36_1
  - krb5=1.14.2=0
  - libedit=3.1.20170329=0
  - libffi=3.2.1=3
  - libiconv=1.15=0
  - libnetcdf=4.5.0=3
  - libpng=1.6.34=0
  - libsodium=1.0.15=1
  - libssh2=1.8.0=2
  - libtiff=4.0.9=he6b73bb_1
  - libuuid=2.32.1=h470a237_2
  - libxcb=1.13=0
  - libxml2=2.9.8=0
  - libxslt=1.1.32=h88dbc4e_2
  - locket=0.2.0=py36_1
  - lxml=4.2.4=py36hc9114bc_0
  - markupsafe=1.0=py36_0
  - mistune=0.8.3=py_0
  - mpi=1.0=mpich
  - mpi4py=3.0.0=py36_0
  - mpich=3.2.1=0
  - msgpack-python=0.5.5=py36_0
  - nbconvert=5.3.1=py_1
  - nbformat=4.4.0=py36_0
  - nbserverproxy=0.8.3=py36_0
  - ncurses=5.9=10
  - netcdf-fortran=4.4.4=7
  - netcdf4=1.4.0=py36_0
  - notebook=5.4.1=py36_0
  - olefile=0.45.1=py_1
  - openblas=0.2.20=8
  - owslib=0.16.0=py_1
  - packaging=17.1=py_0
  - pandas=0.23.4=py36hf8a1672_0
  - pandoc=2.1.3=0
  - pandocfilters=1.4.1=py36_0
  - parso=0.1.1=py_0
  - partd=0.3.8=py36_0
  - pexpect=4.4.0=py36_0
  - pickleshare=0.7.4=py36_0
  - pillow=5.2.0=py36hc736899_1
  - pip=9.0.2=py36_0
  - proj4=4.9.3=h470a237_8
  - prompt_toolkit=1.0.15=py36_0
  - psutil=5.4.3=py36_0
  - ptyprocess=0.5.2=py36_0
  - pycparser=2.18=py_1
  - pyepsg=0.3.2=py_1
  - pygments=2.2.0=py36_0
  - pyopenssl=18.0.0=py36_0
  - pyparsing=2.2.0=py36_0
  - pyproj=1.9.5.1=py36h508ed2a_3
  - pyshp=1.2.12=py_0
  - pysocks=1.6.8=py36_2
  - python-dateutil=2.7.0=py_0
  - pytz=2018.3=py_0
  - pyyaml=3.12=py36_1
  - pyzmq=17.0.0=py36_3
  - readline=7.0=0
  - requests=2.19.1=py36_1
  - send2trash=1.5.0=py_0
  - setuptools=39.0.1=py36_0
  - shapely=1.6.4=py36h164cb2d_1
  - simplegeneric=0.8.1=py36_0
  - six=1.11.0=py36_1
  - sortedcontainers=1.5.9=py36_0
  - tblib=1.3.2=py36_0
  - terminado=0.8.1=py36_0
  - testpath=0.3.1=py36_0
  - tk=8.6.8=ha92aebf_0
  - toolz=0.9.0=py_0
  - tornado=5.0.1=py36_1
  - traitlets=4.3.2=py36_0
  - urllib3=1.23=py36_1
  - wcwidth=0.1.7=py36_0
  - webencodings=0.5=py36_0
  - wheel=0.30.0=py36_2
  - xarray=0.10.8=py36_0
  - xorg-libxau=1.0.8=3
  - xorg-libxdmcp=1.1.2=3
  - xz=5.2.4=h470a237_1
  - yaml=0.1.7=0
  - zeromq=4.2.3=2
  - zict=0.1.3=py_0
  - zlib=1.2.11=0
  - blas=1.0=mkl
  - ca-certificates=2018.03.07=0
  - cartopy=0.16.0=py36hf32a85a_0
  - certifi=2018.8.24=py36_1
  - dbus=1.13.2=h714fa37_1
  - glib=2.56.1=h000015b_0
  - gst-plugins-base=1.14.0=hbbd80ab_1
  - gstreamer=1.14.0=hb453b48_1
  - intel-openmp=2018.0.0=hc7b2577_8
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-ng=7.2.0=hdf63c60_3
  - libgfortran=3.0.0=1
  - libgfortran-ng=7.2.0=hdf63c60_3
  - libopenblas=0.2.20=h9ac9557_7
  - libstdcxx-ng=7.2.0=hdf63c60_3
  - matplotlib=2.2.3=py36hb69df0a_0
  - mkl=2019.0=117
  - mkl_fft=1.0.4=py36h4414c95_1
  - mkl_random=1.0.1=py36h4414c95_1
  - numpy=1.15.0=py36h1b885b7_0
  - numpy-base=1.15.0=py36h3dfced4_0
  - openssl=1.0.2p=h14c3975_0
  - pcre=8.42=h439df22_0
  - pyqt=5.9.2=py36h22d08a2_0
  - python=3.6.3=h1284df2_4
  - qt=5.9.6=h52aff34_0
  - scikit-learn=0.19.1=py36h7aa7ec6_0
  - scipy=1.1.0=py36hc49cb51_0
  - sip=4.19.8=py36hf484d3e_0
  - sqlite=3.24.0=h84994c4_0
prefix: /glade/u/home/gloege/miniconda3/envs/pangeo

pip packages

Package              Version
-------------------- -----------
asn1crypto           0.24.0
bleach               2.1.3
bokeh                0.13.0
Bottleneck           1.2.1
Cartopy              0.16.0
certifi              2018.8.24
cffi                 1.11.5
cftime               1.0.1
chardet              3.0.4
click                6.7
cloudpickle          0.5.2
cryptography         2.3.1
cryptography-vectors 2.3.1
cycler               0.10.0
Cython               0.28.3
cytoolz              0.9.0.1
dask                 0.17.1
dask-jobqueue        0.1.1
decorator            4.2.1
distributed          1.21.3
docrep               0.2.3
entrypoints          0.2.3
ESMPy                7.1.0.dev0
h5netcdf             0.6.2
h5py                 2.8.0
heapdict             1.0.0
html5lib             1.0.1
idna                 2.7
ipykernel            4.8.2
ipython              6.2.1
ipython-genutils     0.2.0
jedi                 0.11.1
Jinja2               2.10
jsonschema           2.6.0
jupyter-client       5.2.3
jupyter-core         4.4.0
jupyterlab           0.31.12
jupyterlab-launcher  0.10.5
kiwisolver           1.0.1
locket               0.2.0
lxml                 4.2.4
MarkupSafe           1.0
matplotlib           2.2.3
mistune              0.8.3
mkl-fft              1.0.4
mkl-random           1.0.1
mpi4py               3.0.0
msgpack-python       0.5.5
nbconvert            5.3.1
nbformat             4.4.0
nbserverproxy        0.8.3
netCDF4              1.4.0
notebook             5.4.1
numpy                1.15.0
olefile              0.45.1
OWSLib               0.16.0
packaging            17.1
pandas               0.23.4
pandocfilters        1.4.1
parso                0.1.1
partd                0.3.8
pexpect              4.4.0
pickleshare          0.7.4
Pillow               5.2.0
pip                  18.0
prompt-toolkit       1.0.15
psutil               5.4.3
ptyprocess           0.5.2
pycparser            2.18
pyepsg               0.3.2
Pygments             2.2.0
pyOpenSSL            18.0.0
pyparsing            2.2.0
pyproj               1.9.5.1
pyshp                1.2.12
PySocks              1.6.8
python-dateutil      2.7.0
pytz                 2018.3
PyYAML               3.12
pyzmq                17.0.0
requests             2.19.1
scikit-learn         0.19.1
scipy                1.1.0
Send2Trash           1.5.0
setuptools           39.0.1
Shapely              1.6.4.post1
simplegeneric        0.8.1
six                  1.11.0
sortedcontainers     1.5.9
tblib                1.3.2
terminado            0.8.1
testpath             0.3.1
toolz                0.9.0
tornado              5.0.1
traitlets            4.3.2
urllib3              1.23
wcwidth              0.1.7
webencodings         0.5
wheel                0.30.0
xarray               0.10.8
xesmf                0.1.1
zict                 0.1.3

About this issue

  • Original URL
  • State: open
  • Created 6 years ago
  • Comments: 22 (9 by maintainers)

Commits related to this issue

Most upvoted comments

@lgloege update, this works:


conda create -n test_esmpy python=3.7
source activate test_esmpy
conda install esmpy 
conda install xesmf
git clone https://github.com/JiaweiZhuang/xESMF.git xESMF
cd xESMF/
py.test -v xesmf