RosettaCommons / RosettaCommons/RFdiffusion
FileNotFoundError - sym_rots.npz
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Description
Specifically when trying to use symmetry mode, via the argument:
--config-name=symmetry
I'm getting this both on a k8s cluster as well as just running in Docker:
`Successful diffuser init
[2024-12-21 05:08:50,867][rfdiffusion.inference.symmetry][INFO] - Initializing tetrahedral symmetry order.
Error executing job with overrides: ['inference.output_prefix=/app/outputs/sym', 'inference.symmetry=tetrahedral', 'inference.num_designs=3', 'contigmap.contigs=[120]', 'inference.model_directory_path=/app/models', 'inference.input_pdb=/app/inputs/1qys.pdb']
Traceback (most recent call last):
File "/app/RFdiffusion/scripts/run_inference.py", line 54, in main
sampler = iu.sampler_selector(conf)
File "/usr/local/lib/python3.9/dist-packages/rfdiffusion/inference/utils.py", line 511, in sampler_selector
sampler = model_runners.SelfConditioning(conf)
File "/usr/local/lib/python3.9/dist-packages/rfdiffusion/inference/model_runners.py", line 37, in init
self.initialize(conf)
File "/usr/local/lib/python3.9/dist-packages/rfdiffusion/inference/model_runners.py", line 137, in initialize
self.symmetry = symmetry.SymGen(
File "/usr/local/lib/python3.9/dist-packages/rfdiffusion/inference/symmetry.py", line 78, in init
self._init_from_symrots_file(global_sym)
File "/usr/local/lib/python3.9/dist-packages/rfdiffusion/inference/symmetry.py", line 200, in _init_from_symrots_file
obj = np.load(fn)
File "/usr/local/lib/python3.9/dist-packages/numpy/lib/npyio.py", line 417, in load
fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.9/dist-packages/rfdiffusion/inference/sym_rots.npz'
Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.`
Upon dropping into the container environment, I notice all files from the repo dir
rfdiffusion/inference/
are present within
/usr/local/lib/python3.9/dist-packages/rfdiffusion/inference
EXCEPT for the sym_rots.npz file
I'm not entirely sure why, however when I edit the Dockerfile to manually copy over that file:
RUN cp /app/RFdiffusion/rfdiffusion/inference/sym_rots.npz /usr/local/lib/python3.9/dist-packages/rfdiffusion/inference/
The container runs without errors and generates symmetrical proteins.
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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 inspecting the Dockerfile and how rfdiffusion/inference/sym_rots.npz is included in the installed package at /usr/local/lib/python3.9/dist-packages/rfdiffusion/inference/. Rebuild the image and run symmetry mode with --config-name=symmetry; done means the file is present in the installed package and the reported FileNotFoundError no longer occurs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, python
- Domain
- build-system, devops
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100