Problem on scripts/install_third_party_dependencies.sh

[tryumanshow]

When it comes to installation on Linux, scripts/install_third_party_dependencies.sh, which is the very first code that I should execute, does not work correctly.

It shows

Pip subprocess error:
 
failed

CondaEnvException: Pip failed

Thereafter, all the codes are useless. Can you tell me how to solve this problem on the most recent version?

---

conda update -n base -c defaults conda

which is suggested as a solution does not work.

[anpanche]

I am also facing same problem. Are there any requirements to be fulfilled for installation of openfold? Is GPU necessary?

[gahdritz]

Hm I just tried reinstalling OpenFold from scratch and am unable to reproduce this behavior. Could you share:

1. The full output of the command
2. Details about your environment (incl. CUDA installation, etc.)

[gahdritz]

@anpanche you too.

[fglaser]

Same problem here:

mamba env create -n openfold_env -f environment.yml Channels:

• conda-forge
• bioconda
• pytorch Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: done

==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.5.0

Please update conda by running

$ conda update -n base -c conda-forge conda

Downloading and Extracting Packages:

Preparing transaction: done Verifying transaction: done Executing transaction: - By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html

done Installing pip dependencies: / Ran pip subprocess with arguments: ['/home/fabian/miniforge3/envs/openfold_env/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/fabian/openfold/condaenv.v3nskj_k.requirements.txt', '--exists-action=b'] Pip subprocess output: Collecting git+https://github.com/NVIDIA/dllogger.git (from -r /home/fabian/openfold/condaenv.v3nskj_k.requirements.txt (line 3)) Cloning https://github.com/NVIDIA/dllogger.git to /tmp/pip-req-build-5qi5j6us Resolved https://github.com/NVIDIA/dllogger.git to commit 0540a43971f4a8a16693a9de9de73c1072020769 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting git+https://github.com/Dao-AILab/flash-attention.git@5b838a8 (from -r /home/fabian/openfold/condaenv.v3nskj_k.requirements.txt (line 4)) Cloning https://github.com/Dao-AILab/flash-attention.git (to revision 5b838a8) to /tmp/pip-req-build-coan6uef Resolved https://github.com/Dao-AILab/flash-attention.git to commit 5b838a8 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error'

Pip subprocess error: Running command git clone --filter=blob:none --quiet https://github.com/NVIDIA/dllogger.git /tmp/pip-req-build-5qi5j6us Running command git clone --filter=blob:none --quiet https://github.com/Dao-AILab/flash-attention.git /tmp/pip-req-build-coan6uef WARNING: Did not find branch or tag '5b838a8', assuming revision or ref. Running command git checkout -q 5b838a8 Running command git submodule update --init --recursive -q error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [13 lines of output] Traceback (most recent call last): File "", line 2, in File "", line 34, in File "/tmp/pip-req-build-coan6uef/setup.py", line 105, in raise_if_cuda_home_none("flash_attn") File "/tmp/pip-req-build-coan6uef/setup.py", line 55, in raise_if_cuda_home_none raise RuntimeError( RuntimeError: flash_attn was requested, but nvcc was not found. Are you sure your environment has nvcc available? If you're installing within a container from https://hub.docker.com/r/pytorch/pytorch, only images whose names contain 'devel' will provide nvcc.

  torch.__version__  = 1.12.1
  
  
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details.

failed

CondaEnvException: Pip failed