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

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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