installation problem, what is wrong ?

[KatjaM2020]

ld2NA/RoseTTAFold2NA/example$ ../runRF2NA.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], alphat, "%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, alphaprev, , 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?

[rgogal]

I am having the same issue despite installing it a few times. Were you able to find a resolution?

[KatjaM2020]

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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[leiloull]

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.

[KatjaM2020]

Probably not. We started with CUDA 10 and Ubuntu 19.01. Then upgraded everything and got the same error.

From: Alvin LOU @.> Reply to: uw-ipd/RoseTTAFold2NA @.> Date: Thursday, 8 December 2022 at 07:04 To: uw-ipd/RoseTTAFold2NA @.> Cc: Ekaterina Morgunova @.>, Author @.***> Subject: Re: [uw-ipd/RoseTTAFold2NA] installation problem, what is wrong ? (Issue #33)

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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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[rgogal]

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. conda install pytorch==1.9.0 torchvision==0.10.0 torchaudio==0.9.0 cudatoolkit=11.3 -c pytorch -c conda-forge

[sa-minami]

I had the same error as KatjaM2020 and the solution by rgogal worked for me as well.

[leiloull]

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.

[leiloull]

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. conda install pytorch==1.9.0 torchvision==0.10.0 torchaudio==0.9.0 cudatoolkit=11.3 -c pytorch -c conda-forge

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.

[sa-minami]

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. conda install pytorch==1.9.0 torchvision==0.10.0 torchaudio==0.9.0 cudatoolkit=11.3 -c pytorch -c conda-forge

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.

[rgogal]

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. conda install pytorch==1.9.0 torchvision==0.10.0 torchaudio==0.9.0 cudatoolkit=11.3 -c pytorch -c conda-forge

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 don't have access to change my CUDA version (working on university HPC) so had no choice but to use 11.3.

[i-l-sokolov]

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. conda install pytorch==1.9.0 torchvision==0.10.0 torchaudio==0.9.0 cudatoolkit=11.3 -c pytorch -c conda-forge

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

[dpretorius]

I have the same error when trying to run my script as @KatjaM2020

I am running it on: Ubantu 20.4 Nvidia Driver version 470.161.03 CUDA version 11.4

Any developments on this?

[aylindmm]

What worked for me was uninstalling PyTorch and installing the Preview (Nightly) build acording to my OS and CUDA version.

https://pytorch.org/get-started/locally/

[SuhasSrinivasan]

Hello everyone, please see #105 for potential solution.