xESMF
xESMF copied to clipboard
Published
20 hours ago •
JiaweiZhuang
JiaweiZhuang
ImportError: The ESMF shared library did not load properly.
The error
Traceback (most recent call last):
File "/soge-home/users/chri4118/.conda/envs/crp/lib/python3.7/site-packages/ESMF/interface/loadESMF.py", line 118, in <module>
mode=ct.RTLD_GLOBAL)
File "/soge-home/users/chri4118/.conda/envs/crp/lib/python3.7/ctypes/__init__.py", line 356, in __init__
self._handle = _dlopen(self._name, mode)
OSError: /soge-home/users/chri4118/.conda/envs/crp/lib/./libmpicxx.so.12: undefined symbol: MPIR_Keyval_set_proxy
----> 3 import xesmf as xe
4 import numpy as np
5
~/.conda/envs/crp/lib/python3.7/site-packages/xesmf/__init__.py in <module>
1 from . import util
2 from . import data
----> 3 from . frontend import Regridder
~/.conda/envs/crp/lib/python3.7/site-packages/xesmf/frontend.py in <module>
7 import os
8
----> 9 from . backend import (esmf_grid, add_corner,
10 esmf_regrid_build, esmf_regrid_finalize)
11
~/.conda/envs/crp/lib/python3.7/site-packages/xesmf/backend.py in <module>
17
18 import numpy as np
---> 19 import ESMF
20 import warnings
21 import os
~/.conda/envs/crp/lib/python3.7/site-packages/ESMF/__init__.py in <module>
68 #### IMPORT LIBRARIES #########################################################
69
---> 70 from ESMF.api.esmpymanager import *
71 from ESMF.api.grid import *
72 from ESMF.api.mesh import *
~/.conda/envs/crp/lib/python3.7/site-packages/ESMF/api/esmpymanager.py in <module>
9 from ESMF.api.constants import *
10 from ESMF.util.exceptions import *
---> 11 from ESMF.interface.cbindings import *
12 from ESMF.util.decorators import initialize
13
~/.conda/envs/crp/lib/python3.7/site-packages/ESMF/interface/cbindings.py in <module>
11 import ESMF.api.constants as constants
12 from ESMF.util.decorators import deprecated, netcdf
---> 13 from ESMF.interface.loadESMF import _ESMF
14
15 def copy_struct(src):
~/.conda/envs/crp/lib/python3.7/site-packages/ESMF/interface/loadESMF.py in <module>
119 except:
120 traceback.print_exc(file=sys.stdout)
--> 121 raise ImportError('The ESMF shared library did not load properly.')
ImportError: The ESMF shared library did not load properly.
my environment
Conda list:
conda (crp) chri4118@linux1:/soge-home/projects/crop_yield/ml_drought$ conda list
# packages in environment at /soge-home/users/chri4118/.conda/envs/crp:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
affine 2.2.2 py_0 conda-forge
argparse 1.4.0 <pip>
asn1crypto 0.24.0 <pip>
asn1crypto 0.24.0 py37_0
atomicwrites 1.3.0 py_0 conda-forge
atomicwrites 1.3.0 <pip>
attrs 19.1.0 py_0 conda-forge
aws-sam-translator 1.11.0 <pip>
aws-xray-sdk 2.4.2 <pip>
backcall 0.1.0 py37_0
basemap 1.2.0 py37h673bf1a_1001 conda-forge
basemap-data-hires 1.2.0 0 conda-forge
bcrypt 3.1.6 <pip>
beautifulsoup4 4.7.1 <pip>
blas 1.0 mkl
bleach 3.1.0 py37_0
bokeh 1.0.4 py37_0
boltons 19.1.0 py_0 conda-forge
boltons 19.1.0 <pip>
boost-cpp 1.68.0 h11c811c_1000 conda-forge
boto 2.49.0 <pip>
boto3 1.9.153 <pip>
botocore 1.12.153 <pip>
Bottleneck 1.2.1 <pip>
bottleneck 1.2.1 py37h3010b51_1001 conda-forge
bs4 0.0.1 <pip>
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2018.11.29 ha4d7672_0 conda-forge
cachetools 3.0.0 <pip>
cairo 1.14.12 h8948797_3
cartopy 0.17.0 py37hbb7e04d_1
cdsapi 0.1.4 <pip>
certifi 2019.6.16 py37_0 conda-forge
cffi 1.12.3 py37h8022711_0 conda-forge
cfgrib 0.9.7 py_0 conda-forge
cfn-lint 0.21.3 <pip>
cftime 1.0.3.4 <pip>
cftime 1.0.3.4 py37hdd07704_0
chardet 3.0.4 py37_1
chardet 3.0.4 <pip>
click 7.0 py_0 conda-forge
click-plugins 1.0.4 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
climate-indices 1.0.4 <pip>
cloudpickle 0.6.1 py37_0
colorcet 1.0.0 py37_0
cryptography 2.3.1 py37hc365091_0
cryptography 2.4.2 <pip>
cudatoolkit 10.0.130 0
curl 7.64.1 hf8cf82a_0 conda-forge
cycler 0.10.0 py37_0
Cython 0.29.3 <pip>
cytoolz 0.9.0.1 py37h14c3975_1
dask 1.2.2 py_2 conda-forge
dask-core 1.2.2 py_0 conda-forge
datashader 0.6.8 py_0 pyviz
datashape 0.5.4 py37_1
dbus 1.13.2 h714fa37_1
decorator 4.3.0 py37_0
descartes 1.1.0 py_2 conda-forge
dill 0.2.9 <pip>
distributed 1.28.1 py37_0 conda-forge
docker 4.0.1 <pip>
docutils 0.14 <pip>
earthengine-api 0.1.164 <pip>
eccodes 2.12.3 h1ba12e4_2 conda-forge
ecdsa 0.13.2 <pip>
entrypoints 0.3 py37_0
esmf 7.1.0r hdfb41a0_1003 conda-forge
esmpy 7.1.0r py37h24bf2e0_2 conda-forge
expat 2.2.5 he0dffb1_0
ffmpeg 3.1.3 0 menpo
fiona 1.8.4 py37h1c6dbfb_1002 conda-forge
fire 0.1.3 py_1 conda-forge
flake8 3.7.7 py37_0 conda-forge
fontconfig 2.13.1 h2176d3f_1000 conda-forge
freetype 2.9.1 h8a8886c_1
freexl 1.0.5 h14c3975_0
future 0.17.1 <pip>
gdal 2.4.0 py37heb36068_1001 conda-forge
geojson 2.4.1 py_0 conda-forge
geopandas 0.4.0 py_1 conda-forge
geoplot 0.2.4 py_0 conda-forge
geos 3.7.1 he6710b0_0
geotiff 1.4.3 h1105359_1000 conda-forge
gettext 0.19.8.1 hd7bead4_3
giflib 5.1.4 h14c3975_1
glib 2.56.2 had28632_1001 conda-forge
gmp 6.1.2 h6c8ec71_1
google-api-python-client 1.7.7 <pip>
google-auth 1.6.2 <pip>
google-auth-httplib2 0.0.3 <pip>
gst-plugins-base 1.12.5 h3865690_1000 conda-forge
gstreamer 1.12.5 h0cc0488_1000 conda-forge
hdf4 4.2.13 h9a582f1_1002 conda-forge
hdf5 1.10.5 nompi_h3c11f04_1100 conda-forge
heapdict 1.0.0 py37_2
holoviews 1.11.2 <pip>
holoviews 1.11.0 pyh39e3cac_0 pyviz
httplib2 0.12.0 <pip>
icu 58.2 h9c2bf20_1
idna 2.8 <pip>
idna 2.8 py37_0
imageio 2.4.1 py37_0
inspect2 0.1 <pip>
intel-openmp 2019.1 144
ipdb 0.11 py_2 conda-forge
ipykernel 5.1.0 py37h39e3cac_0
ipython 7.2.0 py37h39e3cac_0
ipython_genutils 0.2.0 py37_0
ipywidgets 7.4.2 py37_0
jasper 1.900.1 h07fcdf6_1006 conda-forge
jedi 0.13.2 py37_0
Jinja2 2.10.1 <pip>
jinja2 2.10 py37_0
Jinja2 2.10 <pip>
jmespath 0.9.4 <pip>
joblib 0.13.1 <pip>
jpeg 9c h14c3975_1001 conda-forge
json-c 0.13.1 h1bed415_0
jsondiff 1.1.2 <pip>
jsonpatch 1.23 <pip>
jsonpickle 1.2 <pip>
jsonpointer 2.0 <pip>
jsonschema 2.6.0 py37_0
jupyter 1.0.0 py37_7
jupyter_client 5.2.4 py37_0
jupyter_console 6.0.0 py37_0
jupyter_core 4.4.0 py37_0
kealib 1.4.10 he7154bc_1002 conda-forge
kiwisolver 1.0.1 py37hf484d3e_0
krb5 1.16.3 h05b26f9_1001 conda-forge
libaec 1.0.4 hf484d3e_0 conda-forge
libboost 1.67.0 h46d08c1_4
libcurl 7.64.1 hda55be3_0 conda-forge
libcxx 7.0.0 h6bb024c_1002 conda-forge
libdap4 3.19.1 hd48c02d_1000 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.1.0 hdf63c60_0
libgdal 2.4.0 h982c1cc_1001 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0
libiconv 1.15 h63c8f33_5
libkml 1.3.0 h590aaf7_4
libnetcdf 4.6.2 h056eaf5_1002 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libpq 10.6 h13b8bad_1000 conda-forge
libsodium 1.0.16 h1bed415_0
libspatialindex 1.8.5 hf484d3e_1003 conda-forge
libspatialite 4.3.0a hb08deb6_19
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 8.2.0 hdf63c60_1
libtiff 4.0.10 h2733197_1001
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h1bed415_1
libxml2 2.9.8 h26e45fe_1
libxslt 1.1.33 h7d1a2b0_0
linecache2 1.0.0 <pip>
llvm-meta 7.0.0 0 conda-forge
llvmlite 0.27.0 py37hd408876_0
lmoments3 1.0.4 <pip>
locket 0.2.0 py37_1
lxml 4.3.0 py37hefd8a0e_0
MarkupSafe 1.1.0 <pip>
markupsafe 1.1.0 py37h7b6447c_0
matplotlib 3.0.2 py37h8a2030e_1001 conda-forge
matplotlib-base 3.0.2 py37h167e16e_1001 conda-forge
mccabe 0.6.1 py_1 conda-forge
mistune 0.8.4 py37h7b6447c_0
mkl 2019.1 144
mkl_fft 1.0.11 py37h14c3975_0 conda-forge
mkl_random 1.0.2 py37h637b7d7_2 conda-forge
mock 3.0.5 <pip>
more-itertools 7.0.0 <pip>
more-itertools 4.3.0 py37_1000 conda-forge
moto 1.3.8 <pip>
mpi 1.0 mpich conda-forge
mpich 3.2.1 h1c2f66e_1008 conda-forge
mpl-animation 0.1 <pip>
msgpack-python 0.6.1 py37hfd86e86_1
multipledispatch 0.6.0 py37_0
multiprocess 0.70.7 <pip>
munch 2.3.2 py_0 conda-forge
nbconvert 5.3.1 py37_0
nbformat 4.4.0 py37_0
nco 1.0.0 <pip>
ncurses 6.1 hf484d3e_1002 conda-forge
netcdf-fortran 4.4.5 hea25ff8_1000 conda-forge
netcdf4 1.4.2 py37h808af73_0 anaconda
networkx 2.2 py37_1
ninja 1.9.0 py37hfd86e86_0
notebook 5.7.4 py37_0
numba 0.42.0 py37h962f231_0
numpy 1.16.2 py37h7e9f1db_0
numpy-base 1.16.2 py37hde5b4d6_0
olefile 0.46 py37_0
openjpeg 2.3.0 h05c96fa_1
openssl 1.1.1b h14c3975_1 conda-forge
osmnx 0.8.2 <pip>
owslib 0.17.0 py37_0
packaging 18.0 py37_0
pandas 0.24.2 py37hb3f55d8_0 conda-forge
pandoc 2.2.3.2 0
pandocfilters 1.4.2 py37_1
param 1.8.2 <pip>
param 1.8.2 py_0 pyviz
paramiko 2.4.2 <pip>
parso 0.3.1 py37_0
partd 0.3.9 py37_0
pathos 0.2.3 <pip>
patsy 0.5.1 py_0 conda-forge
pcre 8.41 hc27e229_1
pexpect 4.6.0 py37_0
pickleshare 0.7.5 py37_0
pillow 5.4.1 py37h34e0f95_0
pint 0.9 py37_2 conda-forge
pip 19.1.1 py37_0 conda-forge
pixman 0.34.0 hceecf20_3
pluggy 0.11.0 py_0 conda-forge
poppler 0.67.0 h2fc8fa2_1002 conda-forge
poppler-data 0.4.9 0
postgresql 10.6 h66cca7a_1000 conda-forge
pox 0.2.5 <pip>
ppft 1.6.4.9 <pip>
proj4 5.2.0 he6710b0_1
prometheus_client 0.5.0 py37_0
prompt_toolkit 2.0.7 py37_0
psutil 5.4.8 py37h7b6447c_0
psycopg2 2.7.6.1 py37hb7f436b_1000 conda-forge
ptyprocess 0.6.0 py37_0
py 1.8.0 py_0 conda-forge
pyasn1 0.4.5 <pip>
pyasn1-modules 0.2.3 <pip>
pycodestyle 2.5.0 py_0 conda-forge
pycparser 2.19 py37_1 conda-forge
pycparser 2.19 <pip>
pyct 0.4.6 py_0 pyviz
pyct-core 0.4.6 py_0 pyviz
pyepsg 0.4.0 py37_0
pyflakes 2.1.1 py_0 conda-forge
pygments 2.3.1 py37_0
pykdtree 1.3.1 py37hdd07704_2
PyNaCl 1.3.0 <pip>
pyopenssl 18.0.0 py37_0
pyparsing 2.3.1 py37_0
pyproj 1.9.6 py37hc0953d3_1000 conda-forge
pyqt 5.6.0 py37h22d08a2_6
pysal 1.14.4.post2 py37_1001 conda-forge
pysheds 0.2.6 py37h14c3975_0 conda-forge
pyshp 1.2.12 py37_0 anaconda
pysocks 1.6.8 py37_0
pytest 4.4.1 <pip>
pytest 4.5.0 py37_0 conda-forge
pytest-flake8 1.0.4 py37_0 conda-forge
python 3.7.3 h33d41f4_1 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
python-jose 3.0.1 <pip>
pytorch 1.1.0 py3.7_cuda10.0.130_cudnn7.5.1_0 pytorch
pytz 2019.1 py_0 conda-forge
pyviz-comms 0.7.0 <pip>
pyviz_comms 0.7.0 py_0 pyviz
pywavelets 1.0.1 py37hdd07704_0
pyyaml 3.13 py37h14c3975_0
pyzmq 17.1.2 py37he6710b0_2
qt 5.6.2 hf70d934_9 conda-forge
qtconsole 4.4.3 py37_0
rasterio 1.0.13 <pip>
rasterio 1.0.22 py37h5b3f9e8_0 conda-forge
rasterstats 0.13.0 <pip>
readline 8.0 hf8c457e_0 conda-forge
requests 2.21.0 py37_0
responses 0.10.6 <pip>
rsa 4.0 <pip>
rtree 0.8.3 py37_1000 conda-forge
s3transfer 0.2.0 <pip>
salem 0.2.4 <pip>
scikit-image 0.15.0 <pip>
scikit-image 0.14.1 py37he6710b0_0
scikit-learn 0.20.2 py37hd81dba3_0
scipy 1.2.1 py37h7c811a0_0
scipy 1.3.0 <pip>
seaborn 0.9.0 py_0 conda-forge
seaborn 0.9.0 <pip>
send2trash 1.5.0 py37_0
setuptools 41.0.1 py37_0 conda-forge
shap 0.28.5 <pip>
shapely 1.6.4 py37h86c5351_0
simplejson 3.16.0 <pip>
sip 4.18.1 py37hf484d3e_2
six 1.12.0 py37_1000 conda-forge
snuggs 1.4.2 <pip>
snuggs 1.4.3 py_0 conda-forge
sortedcontainers 2.1.0 py37_0
soupsieve 1.9.1 <pip>
sqlalchemy 1.2.16 py37h14c3975_1000 conda-forge
sqlite 3.28.0 hcee41ef_1 conda-forge
statsmodels 0.9.0 py37h3010b51_1000 conda-forge
tblib 1.3.2 py37_0
terminado 0.8.1 py37_1
testpath 0.4.2 py37_0
tk 8.6.9 hed695b0_1002 conda-forge
toolz 0.9.0 py37_0
torchvision 0.2.2 py_3 pytorch
tornado 5.1.1 py37h7b6447c_0
tqdm 4.30.0 <pip>
traceback2 1.4.0 <pip>
traitlets 4.3.2 py37_0
tzcode 2018g h14c3975_1001 conda-forge
unittest2 1.1.0 <pip>
uritemplate 3.0.0 <pip>
urllib3 1.24.1 py37_0
urllib3 1.24.1 <pip>
wcwidth 0.1.7 py37_0
webencodings 0.5.1 py37_1
websocket-client 0.56.0 <pip>
Werkzeug 0.15.4 <pip>
wheel 0.33.4 py37_0 conda-forge
widgetsnbextension 3.4.2 py37_0
wrapt 1.11.1 <pip>
xarray 0.12.2 py_0 conda-forge
xclim 0.9b0 py_0 conda-forge
xerces-c 3.2.2 h780794e_0
xesmf 0.1.1 <pip>
xmltodict 0.12.0 <pip>
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.1.7 had09818_2
zeromq 4.3.1 he6710b0_3
zict 0.1.3 py37_0
zlib 1.2.11 h14c3975_1004 conda-forge
Your env listing shows a mixture of conda-forge and defaults channel packages. See this. The recommendation is to place conda-forge channel before defaults and use the strict setting.
I run into the same problem. Interestingly, the ImportError disappears when I run import ESMF before every other import.
