GSL - MSPRIME incompatibility

[raywray]

Also, I noticed a change from yesterday to today. Now, when I'm trying to run a generic slim model, I get this error:

Traceback (most recent call last):
  File "/home/raya/Documents/Projects/CoalMinerExamples/simulation_scripts/python/generate_data_stdpopsim.py", line 2, in <module>
    import stdpopsim
  File "/anaconda3/envs/coalminer_examples_env/lib/python3.12/site-packages/stdpopsim/__init__.py", line 12, in <module>
    from .genetic_maps import *  # NOQA
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/anaconda3/envs/coalminer_examples_env/lib/python3.12/site-packages/stdpopsim/genetic_maps.py", line 6, in <module>
    import msprime
  File "/anaconda3/envs/coalminer_examples_env/lib/python3.12/site-packages/msprime/__init__.py", line 28, in <module>
    from msprime._msprime import (
ImportError: libgsl.so.25: cannot open shared object file: No such file or directory

the only thing I've done with my conda environment is install python==3.12.2 and stdpopsim. I think this is an msprime problem, but I'm not positive. Has anyone else had this issue?

[petrelharp]

There are issues with GSL and msprime installation, and this seems to be one of them. Can you clarify - you've had a fresh conda environment, and just installed stdpopsim in it? What OS are you on?

[raywray]

Yes, fresh conda env with the only installations being stdpopsim. I even just tried it again with another fresh installation. I'm using Mac Sonoma 14.5.

[petrelharp]

Perhaps try explicitly asking conda to install msprime? I've not encountered this problem, but I thought the GSL-related problems came from installing msprime with pip rather than conda.

[raywray]

I tried linking the different libgsl's and that seemed to work