installation problem, what is wrong ? #33
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I am having the same issue despite installing it a few times. Were you able to find a resolution? |
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I know more people who has the same issue.
The interesting moment that the earlier downloaded program was installed without this issue.
This appeared after the latest updates.
From: rgogal ***@***.***>
Reply to: uw-ipd/RoseTTAFold2NA ***@***.***>
Date: Tuesday, 6 December 2022 at 20:31
To: uw-ipd/RoseTTAFold2NA ***@***.***>
Cc: Ekaterina Morgunova ***@***.***>, Author ***@***.***>
Subject: Re: [uw-ipd/RoseTTAFold2NA] installation problem, what is wrong ? (Issue #33)
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I am having the same issue despite installing it a few times. Were you able to find a resolution?
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Same here, I was wondering if this is because of the CUDA version? I am using CUDA11.5.119 on Ubuntu 22.04.1 LTS. |
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I got mine running. My CUDA version was 11.3 and it is not compatible with pytorch 1.13 which is installed with the environment file. Pytorch 1.13 is only compatible with CUDA 11.6 and above. I had to downgrade my pytorch version in my environment. Here is the command I used. |
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I had the same error as KatjaM2020 and the solution by rgogal worked for me as well. |
I am using the CUDA 11.6 and NVIDIA-SMI 470.161.03, but the problem is still there. |
Do you have any specific reasons for using the CUDA 11.3 version? I am on 11.6 but the problem still can't be solved. |
I started with 11.6, but that did not work for me. This was with Pytorch 1.13. I then downgraded both and it worked for me. |
I don't have access to change my CUDA version (working on university HPC) so had no choice but to use 11.3. |
I installed all requirements from the file in repository, had the same problem, tried this downgrading of libraries versions, but problem remains. If anyone have ideas what could be wrong, I would be very grateful. Thank you in advance |
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I have the same error when trying to run my script as @KatjaM2020 I am running it on: Any developments on this? |
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What worked for me was uninstalling PyTorch and installing the Preview (Nightly) build acording to my OS and CUDA version. |
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Hello everyone, please see #105 for potential solution. |
ld2NA/RoseTTAFold2NA/example$ ../run_RF2NA.sh t000_ protein.fa R:RNA.fa
Running RoseTTAFold2NA to predict structures
Running on CPU
plddt best
/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/amp/autocast_mode.py:202: UserWarning: User provided device_type of 'cuda', but CUDA is not available. Disabling
warnings.warn('User provided device_type of 'cuda', but CUDA is not available. Disabling')
Traceback (most recent call last):
File "/media/katja/BIGDATA/RoseTTAFold2NA/RoseTTAFold2NA/network/predict.py", line 345, in
pred.predict(inputs=args.inputs, out_prefix=args.prefix, ffdb=ffdb)
File "/media/katja/BIGDATA/RoseTTAFold2NA/RoseTTAFold2NA/network/predict.py", line 225, in predict
self.run_model(Ls, msa_orig, ins_orig, t1d, t2d, xyz_t, xyz_t[:,0], alpha_t, "%s%02d"%(out_prefix, i_trial))
File "/media/katja/BIGDATA/RoseTTAFold2NA/RoseTTAFold2NA/network/predict.py", line 269, in _run_model
logit_s, logit_aa_s, logit_pae, init_crds, alpha_prev, _, pred_lddt_binned, msa_prev, pair_prev, state_prev = self.model(
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1190, in _call_impl
return forward_call(*input, **kwargs)
File "/media/katja/BIGDATA/RoseTTAFold2NA/RoseTTAFold2NA/network/RoseTTAFoldModel.py", line 96, in forward
msa, pair, xyz, alpha_s, xyzallatom, state = self.simulator(
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1190, in _call_impl
return forward_call(*input, **kwargs)
File "/media/katja/BIGDATA/RoseTTAFold2NA/RoseTTAFold2NA/network/Track_module.py", line 430, in forward
msa_full, pair, xyz, state, alpha = self.extra_block[i_m](msa_full, pair,
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1190, in _call_impl
return forward_call(*input, **kwargs)
File "/media/katja/BIGDATA/RoseTTAFold2NA/RoseTTAFold2NA/network/Track_module.py", line 356, in forward
xyz, state, alpha = self.str2str(msa.float(), pair.float(), xyz.detach().float(), state.float(), idx, top_k=top_k)
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1190, in _call_impl
return forward_call(*input, **kwargs)
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/amp/autocast_mode.py", line 14, in decorate_autocast
return func(args, **kwargs)
File "/media/katja/BIGDATA/RoseTTAFold2NA/RoseTTAFold2NA/network/Track_module.py", line 223, in forward
shift = self.se3(G, node.reshape(BL, -1, 1), l1_feats, edge_feats)
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1190, in _call_impl
return forward_call(*input, **kwargs)
File "/media/katja/BIGDATA/RoseTTAFold2NA/RoseTTAFold2NA/network/SE3_network.py", line 83, in forward
return self.se3(G, node_features, edge_features) #, clamp_d=clamp_d)
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1190, in _call_impl
return forward_call(*input, **kwargs)
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/se3_transformer-1.0.0-py3.8.egg/se3_transformer/model/transformer.py", line 163, in forward
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/se3_transformer-1.0.0-py3.8.egg/se3_transformer/model/basis.py", line 166, in get_basis
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/contextlib.py", line 113, in enter
return next(self.gen)
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/cuda/nvtx.py", line 86, in range
range_push(msg.format(*args, **kwargs))
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/site-packages/torch/cuda/nvtx.py", line 28, in range_push
return _nvtx.rangePushA(msg)
File "/home/katja/anaconda3/envs/RF2NA/lib/python3.8/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?
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