geod_lineinit undefined

[JoesephPaulSmith]

Description

Installed cartopy for python 3.6.8 in a virtual environment via pip under Linux. Going on to import cartopy under a Python prompt, I get an ImportError, indicating that geod_lineinit is an undefined symbol. Below is the traceback, with the path to the folder with the virtual environment abbreviated as "./"

Code to reproduce

import cartopy

Traceback

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "./venv/lib/python3.6/site-packages/cartopy/__init__.py", line 96, in <module>
    import cartopy.crs
  File "./venv/lib/python3.6/site-packages/cartopy/crs.py", line 39, in <module>
    import cartopy.trace
ImportError: ./venv/lib/python3.6/site-packages/cartopy/trace.cpython-36m-x86_64-linux-gnu.so: undefined symbol: geod_lineinit

Full environment definition

Operating system

Linux

Cartopy version

0.18.0

conda list

NA

pip list

Package           Version
----------------- -----------
backcall          0.1.0
beautifulsoup4    4.9.1
bokeh             2.0.2
Cartopy           0.18.0
certifi           2020.4.5.2
cftime            1.1.3
chardet           3.0.4
click             7.1.2
cloudpickle       1.4.1
contextvars       2.4
cycler            0.10.0
Cython            0.29.19
dask              2.18.0
dask-jobqueue     0.7.1
decorator         4.4.2
distributed       2.18.0
docopt            0.6.2
fsspec            0.7.4
HeapDict          1.0.1
idna              2.9
immutables        0.14
ipykernel         5.3.0
ipython           7.15.0
ipython-genutils  0.2.0
jedi              0.17.0
Jinja2            2.11.2
jupyter-client    6.1.3
jupyter-core      4.6.3
kiwisolver        1.2.0
locket            0.2.0
MarkupSafe        1.1.1
matplotlib        3.2.1
msgpack           1.0.0
netCDF4           1.5.3
numpy             1.18.5
OWSLib            0.20.0
packaging         20.4
pandas            1.0.4
parso             0.7.0
partd             1.1.0
pexpect           4.8.0
pickleshare       0.7.5
Pillow            7.1.2
pip               20.1.1
prompt-toolkit    3.0.5
psutil            5.7.0
ptyprocess        0.6.0
Pydap             3.2.2
Pygments          2.6.1
pykdtree          1.3.1
pyparsing         2.4.7
pyproj            2.6.1.post1
pyshp             2.1.0
python-dateutil   2.8.1
pytz              2020.1
PyYAML            5.3.1
pyzmq             19.0.1
requests          2.23.0
scipy             1.4.1
setuptools        47.1.1
Shapely           1.7.0
six               1.15.0
sortedcontainers  2.2.2
soupsieve         2.0.1
tblib             1.6.0
toolz             0.10.0
tornado           6.0.4
traitlets         4.3.3
typing-extensions 3.7.4.2
urllib3           1.25.9
wcwidth           0.2.4
WebOb             1.8.6
wheel             0.34.2
zict              2.0.0

[greglucas]

Do you have system level GEOS and PROJ installed? If so, which versions of those? I think this may be a GEOS library interfacing issue.

[JoesephPaulSmith]

Yes: GEOS 3.8.1 and PROJ 6.1.1

[QuLogic]

What's the output of ldd ./venv/lib/python3.6/site-packages/cartopy/trace.cpython-36m-x86_64-linux-gnu.so?

[JoesephPaulSmith]

Here you go:

ldd ./venv/lib/python3.6/site-packages/cartopy/trace.cpython-36m-x86_64-linux-gnu.so
        linux-vdso.so.1 =>  (0x00002aaaaaaab000)
        libproj.so.0 => /lib64/libproj.so.0 (0x00002aaaaacee000)
        libgeos_c.so.1 => /cm/shared/apps/geos/3.8.1/lib/libgeos_c.so.1 (0x00002aaaaaf41000)
        libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00002aaaab179000)
        libstdc++.so.6 => /cm/local/apps/gcc/6.1.0/lib64/libstdc++.so.6 (0x00002aaaab69e000)
        libm.so.6 => /lib64/libm.so.6 (0x00002aaaaba20000)
        libgcc_s.so.1 => /cm/local/apps/gcc/6.1.0/lib64/libgcc_s.so.1 (0x00002aaaabd22000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aaaabf39000)
        libc.so.6 => /lib64/libc.so.6 (0x00002aaaac156000)
        libgeos.so.3.8.1 => /cm/shared/apps/geos/3.8.1/lib/libgeos.so.3.8.1 (0x00002aaaac519000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaac8b7000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00002aaaacabc000)
        /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)

[QuLogic]

And is /lib64/libproj.so.0 the correct and expected location? I see geos is in some other non-standard location.

[QuLogic]

And is /lib64/libproj.so.0 the correct and expected location? I see geos is in some other non-standard location.

[JoesephPaulSmith]

Yes, it's a shared HPC environment, so things may be located differently

[umlvcheng]

Hi, did you fix the issue at end? I face the same issues

[greglucas]

We have just released v0.22 which should help with the compatibility between packages and installation much easier. Please open a new issue if you are still having problems.