RosettaCommons / RosettaCommons/RFdiffusion

Cannot install RFDiffusion on VM with X86-64, pytorch_cuda-12.8.1, RTX 5090 GPU

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Description

Hello everyone,
I use vm to install RFDiffusion with spec:
X86-64, RTX 5090 GPU
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2025 NVIDIA Corporation
Built on Fri_Feb_21_20:23:50_PST_2025
Cuda compilation tools, release 12.8, V12.8.93
Build cuda_12.8.r12.8/compiler.35583870_0

It gave errors when running Conda Install SE3-Transformer code:
conda env create -f env/SE3nv.yml
conda activate SE3nv
cd env/SE3Transformer
pip install --no-cache-dir -r requirements.txt
python setup.py install
cd ../.. # change into the root directory of the repository
pip install -e . # install the rfdiffusion module from the root of the repository

The output errors are as follows. I'd like to learn any suggestions or advice! Thank you very much!
/workspace/RFdiffusion/rfdiffusion/inference/model_runners.py", line 722, in sample_step
msa_prev, pair_prev, px0, state_prev, alpha, logits, plddt = self.model(msa_masked,
File "/venv/SE3nv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1051, in _call_impl
return forward_call(*input, **kwargs)
File "/workspace/RFdiffusion/rfdiffusion/RoseTTAFoldModel.py", line 103, in forward
msa, pair, R, T, alpha_s, state = self.simulator(seq, msa_latent, msa_full, pair, xyz[:,:,:3],
File "/venv/SE3nv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1051, in _call_impl
return forward_call(*input, **kwargs)
File "/workspace/RFdiffusion/rfdiffusion/Track_module.py", line 420, in forward
msa_full, pair, R_in, T_in, state, alpha = self.extra_block[i_m](msa_full,
File "/venv/SE3nv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1051, in _call_impl
return forward_call(*input, **kwargs)
File "/workspace/RFdiffusion/rfdiffusion/Track_module.py", line 332, in forward
R, T, state, alpha = self.str2str(msa, pair, R_in, T_in, xyz, state, idx, motif_mask=motif_mask, cyclic_reses=cyclic_reses, top_k=0)
File "/venv/SE3nv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1051, in _call_impl
return forward_call(*input, **kwargs)
File "/venv/SE3nv/lib/python3.9/site-packages/torch/cuda/amp/autocast_mode.py", line 141, in decorate_autocast
return func(args, **kwargs)
File "/workspace/RFdiffusion/rfdiffusion/Track_module.py", line 266, in forward
shift = self.se3(G, node.reshape(B
L, -1, 1), l1_feats, edge_feats)
File "/venv/SE3nv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1051, in _call_impl
return forward_call(*input, **kwargs)
File "/workspace/RFdiffusion/rfdiffusion/SE3_network.py", line 83, in forward
return self.se3(G, node_features, edge_features)
File "/venv/SE3nv/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1051, in _call_impl
return forward_call(*input, **kwargs)
File "/venv/SE3nv/lib/python3.9/site-packages/se3_transformer/model/transformer.py", line 140, in forward
basis = basis or get_basis(graph.edata['rel_pos'], max_degree=self.max_degree, compute_gradients=False,
File "/venv/SE3nv/lib/python3.9/site-packages/se3_transformer/model/basis.py", line 166, in get_basis
with nvtx_range('spherical harmonics'):
File "/venv/SE3nv/lib/python3.9/contextlib.py", line 119, in enter
return next(self.gen)
File "/venv/SE3nv/lib/python3.9/site-packages/torch/cuda/nvtx.py", line 59, in range
range_push(msg.format(*args, **kwargs))
File "/venv/SE3nv/lib/python3.9/site-packages/torch/cuda/nvtx.py", line 28, in range_push 2755: /wor" 20:40 17-Oct-25
return _nvtx.rangePushA(msg)
File "/venv/SE3nv/lib/python3.9/site-packages/torch/cuda/nvtx.py", line 9, in _fail
raise RuntimeError("NVTX functions not installed. Are you sure you have a CUDA build?")
RuntimeError: NVTX functions not installed. Are you sure you have a CUDA build?

Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.

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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 with env/SE3nv.yml and env/SE3Transformer/requirements.txt, then reproduce the installation and run described in the issue. Trace the failure from rfdiffusion/Track_module.py through rfdiffusion/SE3_network.py to se3_transformer/model/basis.py; done means the documented environment installs and the reported run no longer fails at the NVTX call.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, pytorch
Domain
devops, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
28/100

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