# Shapely fails to import in analysis3-25.04: undefined symbol GEOSGeom\_getExtent\_r **URL:** \ **Category:** Infrastructure\ **Tags:** help, conda\ **Created:** [18 May 2025 20:57 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518 "2025-05-18T20:57:25Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![dpath2o](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/dpath2o/32/1093_2.png) [@dpath2o](https://forum.access-hive.org.au/u/dpath2o)\ **Post date:** [18 May 2025 20:57 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/1 "2025-05-18T20:57:25Z")
Hi team, This environment was working yesterday, but today I’m seeing this error in `analysis3-25.04`: > ImportError: shapely/lib.cpython-311-x86\_64-linux-gnu.so: undefined symbol: GEOSGeom\_getExtent\_r Traceback: ```python --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 3 1 import sys, os#, pygmt 2 sys.path.insert(0, '/home/581/da1339/AFIM/src/AFIM/src') ----> 3 from sea_ice_processor import SeaIceProcessor 4 from sea_ice_plotter import SeaIcePlotter 5 from grounded_iceberg_processor import GroundedIcebergProcessor File ~/AFIM/src/AFIM/src/sea_ice_processor.py:5 3 import pandas as pd 4 import numpy as np ----> 5 import xesmf as xe 6 from pathlib import Path 7 from datetime import datetime, timedelta File /g/data/xp65/public/apps/med_conda/envs/analysis3-25.04/lib/python3.11/site-packages/xesmf/ __init__.py:3 1 # flake8: noqa ----> 3 from . import data, util 4 from .frontend import Regridder, SpatialAverager 6 try: File /g/data/xp65/public/apps/med_conda/envs/analysis3-25.04/lib/python3.11/site-packages/xesmf/util.py:5 3 import numpy as np 4 import xarray as xr ----> 5 from shapely.geometry import MultiPolygon, Polygon 7 try: 8 import esmpy as ESMF File /g/data/xp65/public/apps/med_conda/envs/analysis3-25.04/lib/python3.11/site-packages/shapely/ __init__.py:1 ----> 1 from shapely.lib import GEOSException # NOQA 2 from shapely.lib import Geometry # NOQA 3 from shapely.lib import geos_version, geos_version_string # NOQA ImportError: /g/data/xp65/public/apps/med_conda/envs/analysis3-25.04/lib/python3.11/site-packages/shapely/lib.cpython-311-x86_64-linux-gnu.so: undefined symbol: GEOSGeom_getExtent_r ``` This appears to be a mismatch between the `shapely` Python package (which expects GEOS 3.11+) and the GEOS C library on the system. Can someone please check whether the linked `libgeos_c.so` in this environment is out of sync with the installed version of `shapely`? Thanks! ---
**Author:** ![dpath2o](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/dpath2o/32/1093_2.png) [@dpath2o](https://forum.access-hive.org.au/u/dpath2o)\ **Post date:** [18 May 2025 20:59 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/2 "2025-05-18T20:59:51Z")
I believe that solution might be as simple as: ```bash conda install shapely=1.8 ``` or maybe downgrade both ```bash conda install shapely=1.8 geos=3.10 ``` ---
**Author:** ![dpath2o](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/dpath2o/32/1093_2.png) [@dpath2o](https://forum.access-hive.org.au/u/dpath2o)\ **Post date:** [18 May 2025 22:46 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/3 "2025-05-18T22:46:07Z")
Believe the problem is effecting multiple libraries, not just shapely. ```python /g/data/xp65/public/apps/med_conda/envs/analysis3-25.04/lib/python3.11/site-packages/xarray/backends/plugins.py:110: RuntimeWarning: Engine 'rasterio' loading failed: /g/data/xp65/public/apps/med_conda/envs/analysis3-25.04/lib/python3.11/site-packages/rasterio/../../.././libspatialite.so.8: undefined symbol: GEOSMakeValidParams_create_r external_backend_entrypoints = backends_dict_from_pkg(entrypoints_unique) ``` That reported when doing this: ```python P_kmt_mod = "/g/data/gv90/da1339/grounded_icebergs/MyThin_db/kmt_mod_thinned-0p75_v1p50.nc" P_kmt_org = "/g/data/gv90/da1339/grounded_icebergs/MyThin_db/KMT_original_reformatted_with_coordinates.nc" ds_mod = xr.open_dataset(P_kmt_mod) ds_org = xr.open_dataset(P_kmt_org) kmt_mod = ds_mod['kmt'].values kmt_org = ds_org['kmt'].values lat = ds_mod['lat'] lon = ds_mod['lon'] print("MOD KMT LAND CELL COUNT:", np.sum(kmt_mod == 1)) print("ORG KMT LAND CELL COUNT:", np.sum(kmt_org == 1)) print("Total mismatches:", np.sum(kmt_mod != kmt_org)) print("Unique values in KMT MODIFIED:", np.unique(kmt_mod)) print("Unique values in KMT ORIGINAL:", np.unique(kmt_org)) assert kmt_mod.shape == kmt_org.shape == lat.shape == lon.shape mask_diff = (kmt_org == 1) & (kmt_mod != 1) lat_diff = lat.where(mask_diff) lon_diff = lon.where(mask_diff) mask_flat = ~np.isnan(lat_diff) lat_diff = lat_diff.values[mask_flat] lon_diff = lon_diff.values[mask_flat] print(f"🔍 Found {lat_diff.size} grid cells where 1s were removed") ``` That is, after commenting out `import xesmf` ---
**Author:** ![Aidan](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/aidan/32/42_2.png) [@Aidan](https://forum.access-hive.org.au/u/Aidan)\ **Post date:** [19 May 2025 00:12 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/4 "2025-05-19T00:12:32Z")
Thanks for the report @dpath2o. This is in scope for ACCESS-NRI support. I will find someone who can assist you with this. ---
**Author:** ![rbeucher](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/rbeucher/32/11_2.png) [@rbeucher](https://forum.access-hive.org.au/u/rbeucher)\ **Post date:** [19 May 2025 00:39 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/6 "2025-05-19T00:39:57Z")
Hi @dpath2o, The analysis3-25.04 environment is frozen. I have just tried with analysis3-25.05 which has shapely v2.0 and geos 3.12. It looks like it is importing properly. Can you try for me please and let us know? ---
**Author:** ![rbeucher](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/rbeucher/32/11_2.png) [@rbeucher](https://forum.access-hive.org.au/u/rbeucher)\ **Post date:** [19 May 2025 01:09 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/7 "2025-05-19T01:09:49Z")
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**Author:** ![dpath2o](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/dpath2o/32/1093_2.png) [@dpath2o](https://forum.access-hive.org.au/u/dpath2o)\ **Post date:** [19 May 2025 01:32 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/8 "2025-05-19T01:32:37Z")
Thanks @rbeucher . Yes, `import xesmf` is working now for `conda/analysis3` kernel in `/g/data/xp65/public/modules`. Sorry but I don’t have specific options for `analysis3-25.05` when I start my ARE session using `/g/data/xp65/public/modules`. With `hh5`, I did have a range of kernels to choose from. I’m probably not doing something to enable this feature in ARE with `xp65`. Do you have a suggestion? (I realise that this is separate to this thread. So I understand if you can’t answer that here). ---
**Author:** ![rbeucher](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/rbeucher/32/11_2.png) [@rbeucher](https://forum.access-hive.org.au/u/rbeucher)\ **Post date:** [27 May 2025 00:30 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/9 "2025-05-27T00:30:52Z")
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**Author:** ![atteggiani](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/atteggiani/32/212_2.png) [@atteggiani](https://forum.access-hive.org.au/u/atteggiani)\ **Post date:** [15 July 2025 03:25 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/10 "2025-07-15T03:25:30Z")
@dpath2o Since a solution was found for your initial question, I will close this topic. If you still have problems finding kernels, please check if there are already related topics in the forum, otherwise feel free to open a new topic about that. Thank you. ---
**Author:** ![atteggiani](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/atteggiani/32/212_2.png) [@atteggiani](https://forum.access-hive.org.au/u/atteggiani)\ **Post date:** [15 July 2025 03:25 UTC](https://forum.access-hive.org.au/t/shapely-fails-to-import-in-analysis3-25-04-undefined-symbol-geosgeom-getextent-r/4518/11 "2025-07-15T03:25:33Z")