how to fix import pygimli error libcholmod.so.3 on Mybinder

[stefanazzz]

Problem description

When trying to run from my Github repository using MyBinder,
import pygimli gives the following error:

"libcholmod.so.3: cannot open shared object file: No such file or directory (...)"

This can be fixed by adding python=3.8 to the yml environment file (see file below)

Your environment

from environment.yml file on github:

channels:
  - conda-forge
  - gimli
  - defaults
dependencies:
  - python=3.8          <-- add this line to make "import pygimli" work correctly
  - pygimli>=1.1.0

Notes

I suppose that 1.1.0 is compatible only with 3.8 not more recent versions. Note that pygimli >=1.5.0 shows the same problem when compiled with the current (May 2024) default mybinder python 3.11.x. I tried a few combinations but so far only 1.1.0 and 3.8 seem to work on mybinder.

[halbmy]

Can you try using pip install pygimli instead?

[stefanazzz]

Yes Thomas, I will try that too and let you know

…

On Mon, 20 May 2024 at 22:12, Thomas Günther ***@***.***> wrote: Can you try using pip install pygimli instead? — Reply to this email directly, view it on GitHub <#722 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKX4DUTOFK64XKTP6QXQMITZDJRKNAVCNFSM6AAAAABH745DUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRRGIYTKMJXGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ruboerner]

Is #721 (comment) probably related?

[stefanazzz]

yes, using pip in the environment.yml file also works (rather than downgrading to python 3.8): channels: - conda-forge - gimli - defaults dependencies: - pip: - pygimli

…

On Mon, May 20, 2024 at 10:12 PM Thomas Günther ***@***.***> wrote: Can you try using pip install pygimli instead? — Reply to this email directly, view it on GitHub <#722 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKX4DUTOFK64XKTP6QXQMITZDJRKNAVCNFSM6AAAAABH745DUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRRGIYTKMJXGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[stefanazzz]

to reply to Ralph-Uwe, possibly related, but I would not know how to implement the symbolic links on github/mybinder

…

On Thu, May 23, 2024 at 7:42 AM Ralph-Uwe Börner ***@***.***> wrote: Is #721 (comment) <#721 (comment)> probably related? — Reply to this email directly, view it on GitHub <#722 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKX4DUUJ7TLDDIYSZ2R6CQ3ZDWFTTAVCNFSM6AAAAABH745DUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRWGM2DMNBYGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[prisae]

Just to mention it here too: The same happens on Github Actions: While conda install -c gimli pygimli does work, loading pygimli results in

ImportError: libcholmod.so.3: cannot open shared object file: No such file or directory

[prisae]

I just got hit by this even on my local machine (Ubuntu 22.04.4) with Python 3.11.

[carsten-forty2]

For win and linux and py310, py311 you can try pip install pygimli which may help.
However, the pgcore package which comes with the pip installation is not compatible with the current master and dev branch. If you want to use git sources with the pgcore from pip, you need to switch to the wheel branch which should not far away from dev and will be rebased to the new dev after some more tests.

[prisae]

Cool, thanks, that works for now!

[prisae]

This was marked as completed, but I keep running into this issue also with pyGIMLi 1.5.2, when using conda. When using pip, pyGIMLi installs a s..tload of stuff, basically re-building my entire environment, and subsequently fails of dependency issues.

Nothing urgent, but I think something still to keep an eye on...?

[halbmy]

You're completely right, we should leave this issue open until it is solved properly and not only a hack mixing conda and pip. As the dependency is with pgcore and not pyGIMLi, we will solve it only with pyGIMLi v1.6, i.e. a core update.

[prisae]

This time this suggestion made it possible (thanks @halbmy):

conda create -n pg -c gimli -c conda-forge "pygimli>=1.5.0" python=3.10 suitesparse=5

(the suitesparse=5-bit).