Smithsonian / Smithsonian/layup
Conda installing assit and rebound on a fresh env causes issues
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- Dominant language
- Python
- Stars
- 10
- Forks
- 2
- Avg merge
- 1d 43m
- Merged PRs (30d)
- 58
Description
Conda installing assist and rebound causes OS errors in Layup when ran. Most likely a version issue.
Layup works if assist and rebound are only installed with pip install -e '.[dev]'
Below is the error message that occurs if assist and rebound are conda-installed:
Traceback (most recent call last):
File "/users/40294714/.conda/envs/layup/bin/layup", line 6, in <module>
sys.exit(main())
^^^^^^
File "/mnt/scratch2/users/40294714/layup/src/layup_cmdline/main.py", line 101, in main
code = verb_main()
^^^^^^^^^^^
File "/mnt/scratch2/users/40294714/layup/src/layup_cmdline/comet.py", line 106, in main
return execute(args)
^^^^^^^^^^^^^
File "/mnt/scratch2/users/40294714/layup/src/layup_cmdline/comet.py", line 110, in execute
from layup.comet import comet_cli
File "/mnt/scratch2/users/40294714/layup/src/layup/comet.py", line 7, in <module>
import rebound, assist
File "/users/40294714/.conda/envs/layup/lib/python3.11/site-packages/assist/__init__.py", line 13, in <module>
clibassist = cdll.LoadLibrary(pymodulespath + '/../libassist' + suffix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/users/40294714/.conda/envs/layup/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
return self._dlltype(name)
^^^^^^^^^^^^^^^^^^^
File "/users/40294714/.conda/envs/layup/lib/python3.11/ctypes/__init__.py", line 376, in __init__
self._handle = _dlopen(self._name, mode)
^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: /users/40294714/.conda/envs/layup/lib/python3.11/site-packages/assist/../libassist.cpython-311-x86_64-linux-gnu.so: undefined symbol: reb_simulation_create_from_simulationarchive_with_messages
- I have described the situation in which the bug arose, including what code was executed, information about my environment, and any applicable data others will need to reproduce the problem.
- I have included available evidence of the unexpected behavior (including error messages, screenshots, and/or plots) as well as a description of what I expected instead.
- If I have a solution in mind, I have provided an explanation and/or pseudocode and/or task list.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the fresh Conda environment and compare it with the working pip install -e '.[dev]' setup. Read src/layup/comet.py and the traceback's assist/__init__.py loading path, then inspect the installed assist and rebound versions and their native-library compatibility. Done means Conda-installed dependencies let Layup start without the undefined-symbol OSError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- devops
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100