Can't import fiona because `libgdal.29.dylib` can't be found #1131

ischmidt20 · 2022-01-20T04:32:27Z

ischmidt20
Jan 20, 2022

Expected behavior and actual behavior.

import fiona should import the fiona module.

Instead, I see the following:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/homebrew/lib/python3.9/site-packages/fiona/__init__.py", line 86, in <module>
    from fiona.collection import BytesCollection, Collection
  File "/opt/homebrew/lib/python3.9/site-packages/fiona/collection.py", line 11, in <module>
    from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: dlopen(/opt/homebrew/lib/python3.9/site-packages/fiona/ogrext.cpython-39-darwin.so, 0x0002): Library not loaded: /opt/homebrew/opt/gdal/lib/libgdal.29.dylib
  Referenced from: /opt/homebrew/lib/python3.9/site-packages/fiona/ogrext.cpython-39-darwin.so
  Reason: tried: '/opt/homebrew/opt/gdal/lib/libgdal.29.dylib' (no such file), '/usr/local/lib/libgdal.29.dylib' (no such file), '/usr/lib/libgdal.29.dylib' (no such file), '/opt/homebrew/Cellar/gdal/3.4.1_1/lib/libgdal.29.dylib' (no such file), '/usr/local/lib/libgdal.29.dylib' (no such file), '/usr/lib/libgdal.29.dylib' (no such file)

Operating system

M1 Mac running macOS Monterey 12.1

Fiona and GDAL version and provenance

Fiona version 1.8.20 installed via pip

GDAL version 3.4.1_1 installed with brew

I "fixed" the issue simply by running the following command:

cp /opt/homebrew/Cellar/gdal/3.4.1_1/lib/libgdal.30.dylib /opt/homebrew/Cellar/gdal/3.4.1_1/lib/libgdal.29.dylib

But I thought I would report a bug because I couldn't find any information on this issue, and the "solution" is not obvious.

Answered by sgillies

Aug 4, 2022

Update: I've got a hypothesis at #1131 (reply in thread). Please read it before you rename your library.

To be clear: the project does not endorse renaming the shared library file. It's likely to trip you up again in the future.

I've converted this to a discussion and hope that someone who knows homebrew inside and out can explain how to get homebrew libgdal into good working order.

View full answer

sgillies · 2022-01-20T15:53:23Z

sgillies
Jan 20, 2022
Maintainer

@ischmidt20 I'm sorry you're having a hard time. The line ImportError: dlopen(/opt/homebrew/lib/python3.9/site-packages/fiona/ogrext.cpython-39-darwin.so, 0x0002): Library not loaded: /opt/homebrew/opt/gdal/lib/libgdal.29.dylib suggests to me that your fiona installation was built based on an older version of GDAL that no longer exists on your computer. Instead of copying the shared library, I recommend reinstalling the fiona package.

0 replies

krober10nd · 2022-01-30T01:48:23Z

krober10nd
Jan 30, 2022

I faced the same issue. I had to rebuild from source. Reinstalling via pip did not avoid the error.

0 replies

nicolegoebel · 2022-06-07T17:57:05Z

nicolegoebel
Jun 7, 2022

renaming libgdal.30.dylib to libgdal.29.dylab worked for me (but my files were in /usr/local/opt/gdal/lib/

0 replies

sgillies · 2022-06-07T20:48:45Z

sgillies
Jun 7, 2022
Maintainer

@nicolegoebel renaming the libraries will almost certainly break something. I can't recommend anything other than what @krober10nd has done. Install GDAL using homebrew, make sure that gdal-config is on your executable path, and then pip install --no-binary=fiona fiona.

0 replies

nicolegoebel · 2022-06-08T00:39:43Z

nicolegoebel
Jun 8, 2022

Okay thanks!!

…

On Tue, Jun 7, 2022 at 1:48 PM Sean Gillies ***@***.***> wrote: @nicolegoebel <https://github.com/nicolegoebel> renaming the libraries will almost certainly break something. I can't recommend anything other than what @krober10nd <https://github.com/krober10nd> has done. Install GDAL using homebrew, make sure that gdal-config is on your executable path, and then pip install --no-binary=fiona fiona. — Reply to this email directly, view it on GitHub <#1054 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AANPPCSZYALVSVMHW7EFBODVN6YTTANCNFSM5MLWPVUA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Nicole Goebel Data Scientist ACLIMA INC Direct (415) 735-5389 | Email ***@***.*** 10 Lombard St. Suite 400 | San Francisco, CA 94111 Hello, we're Aclima <http://www.aclima.io/>. This email and any attachments may contain private, confidential and privileged material for the sole use of the intended recipient. If you are not the intended recipient, please immediately delete this email and any attachments.

0 replies

nicolegoebel · 2022-06-08T01:06:36Z

nicolegoebel
Jun 8, 2022

Actually this did not work for me and now I am back to where I started. Except that there is no longer a libgdal.XX.dylib file. Can you make any recommendations to fix this?? THanks!

0 replies

ischmidt20 · 2022-06-08T02:04:22Z

ischmidt20
Jun 8, 2022
Author

I also want to chime in and say that reinstalling gdal and fiona with various combinations of arguments never fixed this. The only thing that worked was simply renaming the file as described above, which I'll admit was a very surprising solution.

0 replies

rickemery · 2022-08-04T16:58:33Z

rickemery
Aug 4, 2022

I am having having this issue as well, but I have libgdal.31.dylib and am missing libgdal.30.dylib. No reinstalling has worked for me. I had to rename the files as mentioned above.

0 replies

sgillies · 2022-08-04T18:49:57Z

sgillies
Aug 4, 2022
Maintainer

Update: I've got a hypothesis at #1131 (reply in thread). Please read it before you rename your library.

To be clear: the project does not endorse renaming the shared library file. It's likely to trip you up again in the future.

I've converted this to a discussion and hope that someone who knows homebrew inside and out can explain how to get homebrew libgdal into good working order.

0 replies

jameshalgren · 2023-01-27T23:21:12Z

jameshalgren
Jan 27, 2023

The same issue cropped up with fiona 1.18 and libgdal.32 on macOS with brew installed gdal at version 3.6.2. The same correction -- copying (I just created a symlink...) the file to create the path to the sought-for but missing earlier version.

(pyenv310) % pip install --force fiona
Collecting fiona
  Using cached Fiona-1.8.22-cp310-cp310-macosx_12_0_arm64.whl
  ...
  Attempting uninstall: fiona
    Found existing installation: Fiona 1.8.22
    Uninstalling Fiona-1.8.22:
      Successfully uninstalled Fiona-1.8.22
(pyenv310) % python test_script_importing_fiona.py
Traceback (most recent call last):
  ...
ImportError: dlopen(/Users/user/pyenv310/lib/python3.10/site-packages/fiona/ogrext.cpython-310-darwin.so, 0x0002): Library not loaded: '/opt/homebrew/opt/gdal/lib/libgdal.31.dylib'
  Referenced from: '/Users/user/pyenv310/lib/python3.10/site-packages/fiona/ogrext.cpython-310-darwin.so'
  Reason: tried: '/opt/homebrew/opt/gdal/lib/libgdal.31.dylib' (no such file), '/usr/local/lib/libgdal.31.dylib' (no such file), '/usr/lib/libgdal.31.dylib' (no such file), '/opt/homebrew/Cellar/gdal/3.6.2_2/lib/libgdal.31.dylib' (no such file), '/usr/local/lib/libgdal.31.dylib' (no such file), '/usr/lib/libgdal.31.dylib' (no such file)
(pyenv310) % ls /opt/homebrew/Cellar/gdal/3.6.2_2/lib/libgdal.*
/opt/homebrew/Cellar/gdal/3.6.2_2/lib/libgdal.32.3.6.2.dylib
(pyenv310) % ln -s /opt/homebrew/Cellar/gdal/3.6.2_2/lib/libgdal.32.3.6.2.dylib /opt/homebrew/Cellar/gdal/3.6.2_2/lib/libgdal.31.dylib
(pyenv310) % python test_script_importing_fiona.py
running script ...

5 replies

seanrichardson95 Jan 30, 2023

Ran into this too. I just renamed my file to .31. and things seem to be working (for now)

sgillies Jan 30, 2023
Maintainer

@ischmidt20 @seanrichardson95 I think with the 1.9.0 release done I was able to free up some brain cells to think harder about this. I have a hypothesis.

There are no macosx arm wheels for 1.8.22 on PyPI. Thus Using cached Fiona-1.8.22-cp310-cp310-macosx_12_0_arm64.whl tells me that this wheel was built from source and saved the last time you ran pip install fiona on your computer. It links libgdal.31.dylib and I believe that is because your homebrew GDAL version then was 3.5.

My hypothesis continues: since, you've upgraded to 3.6.2. libgdal.31.dylib is gone (replaced by libgdal.32.dylib), but that wheel still needs it. And since pip can't tell that your cached wheel is incompatible with GDAL 3.6, it doesn't know that you need to pass over the cached wheel and make a completely new one.

Can you try something for me please? Remove your symlinks or restore the .dylib file to its true name. Then run and test the following.

pip install --force-reinstall --no-cache-dir fiona

This will ignore cached wheels. I'm eager to hear what happens.

Afterwards, you might want to remove all the old cached wheels.

pip cache remove Fiona*

seanrichardson95 Jan 31, 2023

Sorry @sgillies , I just finally got server at my work to actually run on my local environment so I'm not going to do anything to possibly mess that up. If this was for a personal project I'd give it a try tho!

sgillies Jan 31, 2023
Maintainer

@seanrichardson95 I understand. Keep my comment in mind in case you ever upgrade homebrew on your server again.

ischmidt20 Feb 1, 2023
Author

@sgillies So I uninstalled and reinstalled gdal to ensure a clean installation with the latest version. Then I reinstalled fiona with pip via your command above. I opened a new python session and was able to import fiona with no errors! I still have to play around to make sure everything works as expected, but I think your solution may have done the trick. Thanks!

marianhlavac · 2023-02-21T21:55:19Z

marianhlavac
Feb 21, 2023

Same issue here, running commands as suggested in #1131 (reply in thread) did not help.

2 replies

jameshalgren Mar 8, 2023

This issue cropped up again and required the same fix. You can see comparing the brew path below with my previous comment that I've updated gdal somewhere along the way (there was a reason for that but I don't recall exactly). When I returned to work on the fiona-related branch, the error had returned.

Unfortunately, this didn't seem to fix it:

pip install --force-reinstall --no-cache-dir fiona

Maybe I missed a step?

This fixed it, like before.

(pyenv310) % ln -s /opt/homebrew/Cellar/gdal/3.6.2_3/lib/libgdal.32.3.6.2.dylib /opt/homebrew/Cellar/gdal/3.6.2_3/lib/libgdal.31.dylib

sgillies Mar 14, 2023
Maintainer

I'm beginning to suspect that nothing short of a fiona homebrew formula will work. If you're using homebrew GDAL and homebrew Python, might as well get Fiona the same route.

A reminder: renaming your shared library files is a terrible hack.

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Can't import fiona because `libgdal.29.dylib` can't be found #1131

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Can't import fiona because libgdal.29.dylib can't be found #1131

Expected behavior and actual behavior.

Operating system

Fiona and GDAL version and provenance

Replies: 11 comments · 7 replies

sgillies Jan 20, 2022 Maintainer

sgillies Jun 7, 2022 Maintainer

ischmidt20 Jun 8, 2022 Author

sgillies Aug 4, 2022 Maintainer

sgillies Jan 30, 2023 Maintainer

sgillies Jan 31, 2023 Maintainer

ischmidt20 Feb 1, 2023 Author

sgillies Mar 14, 2023 Maintainer

Can't import fiona because `libgdal.29.dylib` can't be found #1131

Replies: 11 comments 7 replies

sgillies
Jan 20, 2022
Maintainer

sgillies
Jun 7, 2022
Maintainer

ischmidt20
Jun 8, 2022
Author

sgillies
Aug 4, 2022
Maintainer

sgillies Jan 30, 2023
Maintainer

sgillies Jan 31, 2023
Maintainer

ischmidt20 Feb 1, 2023
Author

sgillies Mar 14, 2023
Maintainer