installation error #462
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Hello, (base) ➜ openfold git:(main) ✗ sudo docker build -t openfold .
[+] Building 223.4s (12/21) docker:default
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 1.92kB 0.0s
=> [internal] load metadata for docker.io/nvidia/cuda:11.3.1-cudnn8-devel-ubuntu18.04 0.8s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [ 1/17] FROM docker.io/nvidia/cuda:11.3.1-cudnn8-devel-ubuntu18.04@sha256:69cd988555eabe116f76acc754b363eee75f37674c23adb2b523f5fa32543984 0.0s
=> [internal] load build context 0.0s
=> => transferring context: 8.71kB 0.0s
=> CACHED [ 2/17] RUN apt-key del 7fa2af80 0.0s
=> CACHED [ 3/17] RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub 0.0s
=> CACHED [ 4/17] RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub 0.0s
=> CACHED [ 5/17] RUN apt-get update && apt-get install -y wget libxml2 cuda-minimal-build-11-3 libcusparse-dev-11-3 libcublas-dev-11-3 libcusolver-dev-11-3 git 0.0s
=> CACHED [ 6/17] RUN wget -P /tmp "https://github.com/conda-forge/miniforge/releases/download/23.3.1-1/Miniforge3-Linux-x86_64.sh" && bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/cond 0.0s
=> [ 7/17] COPY environment.yml /opt/openfold/environment.yml 0.1s
=> ERROR [ 8/17] RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all 222.4s
------
> [ 8/17] RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all:
21.63
21.63
21.63 Looking for: ['python=3.9', 'libgcc=7.2', 'setuptools=59.5.0', 'pip', 'openmm=7.7', 'pdbfixer', 'pytorch-lightning', 'biopython', 'numpy', 'pandas', 'pyyaml==5.4.1', 'requests', 'scipy==1.7', 'tqdm==4.62.2', 'typing-extensions==4.0', 'wandb', 'modelcif==0.7', 'awscli', 'ml-collections', 'aria2', 'mkl=2024.0', 'git', 'bioconda::hmmer==3.3.2', 'bioconda::hhsuite==3.3.0', 'bioconda::kalign2==2.04', 'bioconda::mmseqs2', 'pytorch::pytorch=1.13.1']
21.63
21.63
38.14 Transaction
38.14
38.14 Prefix: /opt/conda
38.14
38.14 Updating specs:
38.14
38.14 - libgcc=7.2
38.14 - openmm=7.7
38.14 - pdbfixer
38.14 - pytorch-lightning
38.14 - biopython
38.14 - numpy
38.14 - pandas
38.14 - pyyaml==5.4.1
38.14 - scipy==1.7
38.14 - typing-extensions==4.0
38.14 - wandb
38.14 - modelcif==0.7
38.14 - awscli
38.14 - ml-collections
38.14 - aria2
38.14 - mkl=2024.0
38.14 - git
38.14 - bioconda::hmmer==3.3.2
38.14 - bioconda::hhsuite==3.3.0
38.14 - bioconda::kalign2==2.04
38.14 - bioconda::mmseqs2
38.14 - pytorch::pytorch=1.13.1
38.14 - python=3.9
38.14 - setuptools=59.5.0
38.14 - pip
38.14 - requests
38.14 - tqdm==4.62.2
38.14
38.14
38.15 Package Version Build Channel Size
38.15 ───────────────────────────────────────────────────────────────────────────────────────────────────
38.15 Install:
38.15 ───────────────────────────────────────────────────────────────────────────────────────────────────
38.15
38.15 + absl-py 2.1.0 pyhd8ed1ab_0 conda-forge/noarch 107kB
38.15 + appdirs 1.4.4 pyh9f0ad1d_0 conda-forge/noarch 13kB
38.15 + aria2 1.37.0 h347180d_1 conda-forge/linux-64 2MB
38.15 + aws-c-auth 0.7.22 h9137712_5 conda-forge/linux-64 106kB
38.15 + aws-c-cal 0.6.15 h88a6e22_0 conda-forge/linux-64 47kB
38.15 + aws-c-common 0.9.19 h4ab18f5_0 conda-forge/linux-64 226kB
38.15 + aws-c-compression 0.2.18 h83b837d_6 conda-forge/linux-64 19kB
38.15 + aws-c-event-stream 0.4.2 h0cbf018_13 conda-forge/linux-64 54kB
38.15 + aws-c-http 0.8.2 h360477d_2 conda-forge/linux-64 195kB
38.15 + aws-c-io 0.14.9 h2d549f9_2 conda-forge/linux-64 158kB
38.15 + aws-c-mqtt 0.10.4 hf85b563_6 conda-forge/linux-64 164kB
38.15 + aws-c-s3 0.5.10 h679ed35_3 conda-forge/linux-64 110kB
38.15 + aws-c-sdkutils 0.1.16 h83b837d_2 conda-forge/linux-64 55kB
38.15 + aws-checksums 0.1.18 h83b837d_6 conda-forge/linux-64 50kB
38.15 + awscli 2.17.5 py39hf3d152e_0 conda-forge/linux-64 12MB
38.15 + awscrt 0.20.10 py39hdd0344b_6 conda-forge/linux-64 172kB
38.15 + biopython 1.83 py39hd1e30aa_0 conda-forge/linux-64 3MB
38.15 + blas 2.121 mkl conda-forge/linux-64 15kB
38.15 + blas-devel 3.9.0 21_linux64_mkl conda-forge/linux-64 14kB
38.15 + click 8.1.7 unix_pyh707e725_0 conda-forge/noarch 84kB
38.15 + contextlib2 21.6.0 pyhd8ed1ab_0 conda-forge/noarch 16kB
38.15 + cudatoolkit 11.8.0 h4ba93d1_13 conda-forge/linux-64 716MB
38.15 + distro 1.8.0 pyhd8ed1ab_0 conda-forge/noarch 41kB
38.15 + docker-pycreds 0.4.0 py_0 conda-forge/noarch 11kB
38.15 + docutils 0.19 py39hf3d152e_1 conda-forge/linux-64 760kB
38.15 + fftw 3.3.10 nompi_hf1063bd_110 conda-forge/linux-64 2MB
38.15 + fsspec 2024.6.1 pyhff2d567_0 conda-forge/noarch 133kB
38.15 + gawk 5.3.0 ha916aea_0 conda-forge/linux-64 1MB
38.15 + gettext 0.22.5 h59595ed_2 conda-forge/linux-64 475kB
38.15 + gettext-tools 0.22.5 h59595ed_2 conda-forge/linux-64 3MB
38.15 + git 2.45.1 pl5321hef9f9f3_0 conda-forge/linux-64 10MB
38.15 + gitdb 4.0.11 pyhd8ed1ab_0 conda-forge/noarch 53kB
38.15 + gitpython 3.1.43 pyhd8ed1ab_0 conda-forge/noarch 157kB
38.15 + gmp 6.3.0 hac33072_2 conda-forge/linux-64 460kB
38.15 + hhsuite 3.3.0 py39pl5321h0dd7abe_11 bioconda/linux-64 28MB
38.15 + hmmer 3.3.2 hdbdd923_4 bioconda/linux-64 10MB
38.15 + ihm 1.2 py39hd3abc70_1 conda-forge/linux-64 303kB
38.15 + jmespath 1.0.1 pyhd8ed1ab_0 conda-forge/noarch 21kB
38.15 + kalign2 2.04 h031d066_6 bioconda/linux-64 106kB
38.15 + libabseil 20240116.2 cxx17_h59595ed_0 conda-forge/linux-64 1MB
38.15 + libasprintf 0.22.5 h661eb56_2 conda-forge/linux-64 43kB
38.15 + libasprintf-devel 0.22.5 h661eb56_2 conda-forge/linux-64 34kB
38.15 + libblas 3.9.0 21_linux64_mkl conda-forge/linux-64 15kB
38.15 + libcblas 3.9.0 21_linux64_mkl conda-forge/linux-64 15kB
38.15 + libexpat 2.6.2 h59595ed_0 conda-forge/linux-64 74kB
38.15 + libgcc 7.2.0 h69d50b8_2 conda-forge/linux-64 312kB
38.15 + libgettextpo 0.22.5 h59595ed_2 conda-forge/linux-64 171kB
38.15 + libgettextpo-devel 0.22.5 h59595ed_2 conda-forge/linux-64 37kB
38.15 + libgfortran-ng 13.2.0 h69a702a_0 conda-forge/linux-64 23kB
38.15 + libgfortran5 13.2.0 ha4646dd_0 conda-forge/linux-64 1MB
38.15 + libhwloc 2.10.0 default_h5622ce7_1001 conda-forge/linux-64 2MB
38.15 + libidn2 2.3.7 hd590300_0 conda-forge/linux-64 127kB
38.15 + liblapack 3.9.0 21_linux64_mkl conda-forge/linux-64 15kB
38.15 + liblapacke 3.9.0 21_linux64_mkl conda-forge/linux-64 15kB
38.15 + libprotobuf 4.25.3 h08a7969_0 conda-forge/linux-64 3MB
38.15 + libunistring 0.9.10 h7f98852_0 conda-forge/linux-64 1MB
38.15 + libxcrypt 4.4.36 hd590300_1 conda-forge/linux-64 100kB
38.15 + lightning-utilities 0.11.3.post0 pyhd8ed1ab_0 conda-forge/noarch 27kB
38.15 + llvm-openmp 18.1.7 ha31de31_0 conda-forge/linux-64 59MB
38.15 + mkl 2024.0.0 ha957f24_49657 conda-forge/linux-64 126MB
38.15 + mkl-devel 2024.0.0 ha770c72_49657 conda-forge/linux-64 32kB
38.15 + mkl-include 2024.0.0 ha957f24_49657 conda-forge/linux-64 768kB
38.15 + ml-collections 0.1.1 pyhd8ed1ab_0 conda-forge/noarch 67kB
38.15 + mmseqs2 15.6f452 pl5321h6a68c12_2 bioconda/linux-64 4MB
38.15 + modelcif 0.7 pyhd8ed1ab_0 conda-forge/noarch 36kB
38.15 + mpfr 4.2.1 h9458935_1 conda-forge/linux-64 643kB
38.15 + msgpack-python 1.0.8 py39h95fdab5_0 conda-forge/linux-64 96kB
38.15 + numpy 1.26.4 py39h474f0d3_0 conda-forge/linux-64 7MB
38.15 + ocl-icd 2.3.2 hd590300_1 conda-forge/linux-64 136kB
38.15 + ocl-icd-system 1.0.0 1 conda-forge/linux-64 4kB
38.15 + openmm 7.7.0 py39h15fbce5_1 conda-forge/linux-64 12MB
38.15 + pandas 2.2.2 py39hfc16268_1 conda-forge/linux-64 13MB
38.15 + pathtools 0.1.2 py_1 conda-forge/noarch 8kB
38.15 + pcre2 10.43 hcad00b1_0 conda-forge/linux-64 951kB
38.15 + pdbfixer 1.8.1 pyh6c4a22f_0 conda-forge/noarch 510kB
38.15 + perl 5.32.1 7_hd590300_perl5 conda-forge/linux-64 13MB
38.15 + prompt-toolkit 3.0.38 pyha770c72_0 conda-forge/noarch 269kB
38.15 + prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge/noarch 6kB
38.15 + protobuf 4.25.3 py39h1be52a0_0 conda-forge/linux-64 328kB
38.15 + psutil 6.0.0 py39hd3abc70_0 conda-forge/linux-64 365kB
38.15 + python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch 246kB
38.15 + python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge/noarch 144kB
38.15 + pytorch 1.13.1 py3.9_cpu_0 pytorch/linux-64 86MB
38.15 + pytorch-lightning 2.1.4 pyhd8ed1ab_0 conda-forge/noarch 427kB
38.15 + pytorch-mutex 1.0 cpu pytorch/noarch 3kB
38.15 + pytz 2024.1 pyhd8ed1ab_0 conda-forge/noarch 189kB
38.15 + pyyaml 5.4.1 py39hb9d737c_4 conda-forge/linux-64 189kB
38.15 + s2n 1.4.16 he19d79f_0 conda-forge/linux-64 350kB
38.15 + scipy 1.7.0 py39hee8e79c_1 conda-forge/linux-64 23MB
38.15 + sentry-sdk 2.7.1 pyhd8ed1ab_0 conda-forge/noarch 192kB
38.15 + setproctitle 1.3.3 py39hd1e30aa_0 conda-forge/linux-64 20kB
38.15 + six 1.16.0 pyh6c4a22f_0 conda-forge/noarch 14kB
38.15 + smmap 5.0.0 pyhd8ed1ab_0 conda-forge/noarch 22kB
38.15 + tbb 2021.12.0 h297d8ca_1 conda-forge/linux-64 194kB
38.15 + torchmetrics 1.4.0.post0 pyhd8ed1ab_0 conda-forge/noarch 350kB
38.15 + typing-extensions 4.0.0 hd8ed1ab_0 conda-forge/noarch 8kB
38.15 + typing_extensions 4.0.0 pyha770c72_0 conda-forge/noarch 27kB
38.15 + wandb 0.16.6 pyhd8ed1ab_0 conda-forge/noarch 2MB
38.15 + wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge/noarch 33kB
38.15 + wget 1.21.4 hda4d442_0 conda-forge/linux-64 770kB
38.15 + yaml 0.2.5 h7f98852_2 conda-forge/linux-64 89kB
38.15 + zlib 1.2.13 hd590300_5 conda-forge/linux-64 93kB
38.15
38.15 Change:
38.15 ───────────────────────────────────────────────────────────────────────────────────────────────────
38.15
38.15 - _openmp_mutex 4.5 2_gnu conda-forge
38.15 + _openmp_mutex 4.5 2_kmp_llvm conda-forge/linux-64 6kB
38.15 - brotli-python 1.1.0 py310hc6cd4ac_0 conda-forge
38.15 + brotli-python 1.1.0 py39h3d6467e_1 conda-forge/linux-64 350kB
38.15 - libarchive 3.6.2 h039dbb9_1 conda-forge
38.15 + libarchive 3.6.2 h039dbb9_1 conda-forge/linux-64 Cached
38.15 - ruamel.yaml.clib 0.2.7 py310h1fa729e_1 conda-forge
38.15 + ruamel.yaml.clib 0.2.7 py39hd1e30aa_2 conda-forge/linux-64 144kB
38.15
38.15 Reinstall:
38.15 ───────────────────────────────────────────────────────────────────────────────────────────────────
38.15
38.15 o boltons 23.0.0 pyhd8ed1ab_0 conda-forge
38.15 o certifi 2023.7.22 pyhd8ed1ab_0 conda-forge
38.15 o charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge
38.15 o colorama 0.4.6 pyhd8ed1ab_0 conda-forge
38.15 o conda-libmamba-solver 23.3.0 pyhd8ed1ab_0 conda-forge
38.15 o conda-package-handling 2.2.0 pyh38be061_0 conda-forge
38.15 o conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge
38.15 o idna 3.4 pyhd8ed1ab_0 conda-forge
38.15 o jsonpatch 1.32 pyhd8ed1ab_0 conda-forge
38.15 o jsonpointer 2.0 py_0 conda-forge
38.15 o packaging 23.1 pyhd8ed1ab_0 conda-forge
38.15 o pluggy 1.3.0 pyhd8ed1ab_0 conda-forge
38.15 o pycparser 2.21 pyhd8ed1ab_0 conda-forge
38.15 o pysocks 1.7.1 pyha2e5f31_6 conda-forge
38.15 o toolz 0.12.0 pyhd8ed1ab_0 conda-forge
38.15 o wheel 0.41.2 pyhd8ed1ab_0 conda-forge
38.15
38.15 Upgrade:
38.15 ───────────────────────────────────────────────────────────────────────────────────────────────────
38.15
38.15 - c-ares 1.19.1 hd590300_0 conda-forge
38.15 + c-ares 1.28.1 hd590300_0 conda-forge/linux-64 169kB
38.15 - cffi 1.15.1 py310h255011f_3 conda-forge
38.15 + cffi 1.16.0 py39h7a31438_0 conda-forge/linux-64 240kB
38.15 - conda 23.3.1 py310hff52083_0 conda-forge
38.15 + conda 23.5.2 py39hf3d152e_0 conda-forge/linux-64 1MB
38.15 - libcurl 8.2.1 hca28451_0 conda-forge
38.15 + libcurl 8.8.0 hca28451_0 conda-forge/linux-64 406kB
38.15 - libmamba 1.4.2 hcea66bb_0 conda-forge
38.15 + libmamba 1.5.0 h658169a_0 conda-forge/linux-64 2MB
38.15 - libmambapy 1.4.2 py310h1428755_0 conda-forge
38.15 + libmambapy 1.5.0 py39h78efd80_0 conda-forge/linux-64 297kB
38.15 - libnghttp2 1.52.0 h61bc06f_0 conda-forge
38.15 + libnghttp2 1.58.0 h47da74e_1 conda-forge/linux-64 632kB
38.15 - libnsl 2.0.0 h7f98852_0 conda-forge
38.15 + libnsl 2.0.1 hd590300_0 conda-forge/linux-64 33kB
38.15 - libsqlite 3.43.0 h2797004_0 conda-forge
38.15 + libsqlite 3.46.0 hde9e2c9_0 conda-forge/linux-64 865kB
38.15 - libxml2 2.11.5 h232c23b_1 conda-forge
38.15 + libxml2 2.12.7 hc051c1a_1 conda-forge/linux-64 705kB
38.15 - mamba 1.4.2 py310h51d5547_0 conda-forge
38.15 + mamba 1.5.0 py39hc5d2bb1_0 conda-forge/linux-64 51kB
38.15 - ncurses 6.4 hcb278e6_0 conda-forge
38.15 + ncurses 6.5 h59595ed_0 conda-forge/linux-64 887kB
38.15 - openssl 3.1.2 hd590300_0 conda-forge
38.15 + openssl 3.3.1 h4ab18f5_1 conda-forge/linux-64 3MB
38.15 - pip 23.2.1 pyhd8ed1ab_0 conda-forge
38.15 + pip 24.0 pyhd8ed1ab_0 conda-forge/noarch 1MB
38.15 - pycosat 0.6.4 py310h5764c6d_1 conda-forge
38.15 + pycosat 0.6.6 py39hd1e30aa_0 conda-forge/linux-64 85kB
38.15 - requests 2.31.0 pyhd8ed1ab_0 conda-forge
38.15 + requests 2.32.3 pyhd8ed1ab_0 conda-forge/noarch 59kB
38.15 - tk 8.6.12 h27826a3_0 conda-forge
38.15 + tk 8.6.13 noxft_h4845f30_101 conda-forge/linux-64 3MB
38.15 - zstandard 0.19.0 py310h5764c6d_0 conda-forge
38.15 + zstandard 0.22.0 py39h81c9582_1 conda-forge/linux-64 405kB
38.15 - zstd 1.5.5 hfc55251_0 conda-forge
38.15 + zstd 1.5.6 ha6fb4c9_0 conda-forge/linux-64 555kB
38.15
38.15 Downgrade:
38.15 ───────────────────────────────────────────────────────────────────────────────────────────────────
38.15
38.15 - cryptography 41.0.3 py310h75e40e8_0 conda-forge
38.15 + cryptography 40.0.2 py39h079d5ae_0 conda-forge/linux-64 2MB
38.15 - pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
38.15 + pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge/noarch 128kB
38.15 - python 3.10.12 hd12c33a_0_cpython conda-forge
38.15 + python 3.9.19 h0755675_0_cpython conda-forge/linux-64 24MB
38.15 - python_abi 3.10 3_cp310 conda-forge
38.15 + python_abi 3.9 4_cp39 conda-forge/linux-64 6kB
38.15 - ruamel.yaml 0.17.32 py310h2372a71_0 conda-forge
38.15 + ruamel.yaml 0.17.21 py39h72bdee0_3 conda-forge/linux-64 188kB
38.15 - setuptools 68.1.2 pyhd8ed1ab_0 conda-forge
38.15 + setuptools 59.5.0 py39hf3d152e_0 conda-forge/linux-64 1MB
38.15 - tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
38.15 + tqdm 4.62.2 pyhd8ed1ab_0 conda-forge/noarch 82kB
38.15 - urllib3 2.0.4 pyhd8ed1ab_0 conda-forge
38.15 + urllib3 1.26.19 pyhd8ed1ab_0 conda-forge/noarch 115kB
38.15
38.15 Summary:
38.15
38.15 Install: 102 packages
38.15 Change: 4 packages
38.15 Reinstall: 16 packages
38.15 Upgrade: 19 packages
38.15 Downgrade: 8 packages
38.15
38.15 Total download: 1GB
38.15
38.15 ───────────────────────────────────────────────────────────────────────────────────────────────────
38.15
38.15
155.6
155.6 Downloading and Extracting Packages
155.6
155.6 Preparing transaction: ...working... done
157.3 Verifying transaction: ...working... done
164.0 Executing transaction: ...working... 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
206.2
206.2 done
208.7 Installing pip dependencies: ...working... Pip subprocess error:
221.8 Running command git clone --filter=blob:none --quiet https://github.com/NVIDIA/dllogger.git /tmp/pip-req-build-j0fdx5x9
221.8 Running command git clone --filter=blob:none --quiet https://github.com/Dao-AILab/flash-attention.git /tmp/pip-req-build-dggcmzly
221.8 Running command git submodule update --init --recursive -q
221.8 error: subprocess-exited-with-error
221.8
221.8 × python setup.py egg_info did not run successfully.
221.8 │ exit code: 1
221.8 ╰─> [12 lines of output]
221.8 No CUDA runtime is found, using CUDA_HOME='/usr/local/cuda'
221.8 Traceback (most recent call last):
221.8 File "<string>", line 2, in <module>
221.8 File "<pip-setuptools-caller>", line 34, in <module>
221.8 File "/tmp/pip-req-build-dggcmzly/setup.py", line 115, in <module>
221.8 raise RuntimeError(
221.8 RuntimeError: FlashAttention is only supported on CUDA 11.6 and above. Note: make sure nvcc has a supported version by running nvcc -V.
221.8
221.8
221.8 torch.__version__ = 1.13.1
221.8
221.8
221.8 [end of output]
221.8
221.8 note: This error originates from a subprocess, and is likely not a problem with pip.
221.8 error: metadata-generation-failed
221.8
221.8 × Encountered error while generating package metadata.
221.8 ╰─> See above for output.
221.8
221.8 note: This is an issue with the package mentioned above, not pip.
221.8 hint: See above for details.
221.8
221.8 Ran pip subprocess with arguments:
221.8 ['/opt/conda/bin/python', '-m', 'pip', 'install', '-U', '-r', '/opt/openfold/condaenv.rat1mj4_.requirements.txt', '--exists-action=b']
221.8 Pip subprocess output:
221.8 Collecting git+https://github.com/NVIDIA/dllogger.git (from -r /opt/openfold/condaenv.rat1mj4_.requirements.txt (line 3))
221.8 Cloning https://github.com/NVIDIA/dllogger.git to /tmp/pip-req-build-j0fdx5x9
221.8 Resolved https://github.com/NVIDIA/dllogger.git to commit 0540a43971f4a8a16693a9de9de73c1072020769
221.8 Preparing metadata (setup.py): started
221.8 Preparing metadata (setup.py): finished with status 'done'
221.8 Collecting git+https://github.com/Dao-AILab/flash-attention.git (from -r /opt/openfold/condaenv.rat1mj4_.requirements.txt (line 4))
221.8 Cloning https://github.com/Dao-AILab/flash-attention.git to /tmp/pip-req-build-dggcmzly
221.8 Resolved https://github.com/Dao-AILab/flash-attention.git to commit 9486635c926ad1443c5c536d90e9cefaee3db9b4
221.8 Preparing metadata (setup.py): started
221.8 Preparing metadata (setup.py): finished with status 'error'
221.8
221.8 failed
221.8
221.8 CondaEnvException: Pip failed
221.8
------
5 warnings found (use --debug to expand):
- LegacyKeyValueFormat: "LABEL key=value" should be used instead of legacy "LABEL key value" format (line 4)
- LegacyKeyValueFormat: "LABEL key=value" should be used instead of legacy "LABEL key value" format (line 5)
- LegacyKeyValueFormat: "LABEL key=value" should be used instead of legacy "LABEL key value" format (line 6)
- LegacyKeyValueFormat: "LABEL key=value" should be used instead of legacy "LABEL key value" format (line 7)
- LegacyKeyValueFormat: "ENV key=value" should be used instead of legacy "ENV key value" format (line 19)
Dockerfile:24
--------------------
22 |
23 | # installing into the base environment since the docker container wont do anything other than run openfold
24 | >>> RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all
25 | RUN export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib:${LD_LIBRARY_PATH}
26 |
--------------------
ERROR: failed to solve: process "/bin/sh -c mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all" did not complete successfully: exit code: 1
Any idea how to fix this? |
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I was able to get it running in my high performance cluster with the following commands before installation: I also downloaded the CUDA12 version of the code with the following command: Then follow with "mamba env create -n openfold_env -f environment.yml" and so on and it worked. But I still could not fix this in my local workstation. I think the issue might be with incompatible versions of CUDA ??? |
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Thanks @abhinavb22, and some few adjusts to work:
If 11.8 or below, try to: I didn' use any Modify environment.yml file, using instead If sucess, |
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I addressed similar issues in PR #496. It also minimizes dependencies installed from the OS distribution. Maybe also see my comments in #494 where I describe what works for me . |
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PR #496 is now merged to |
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@abhinavb22 Hi, I'm trying to install openfold in a cluster. If you have documentation for that can you please share it with me? |
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I tried to install openfold with the command: mamba env create -n openfold_env -f environment.yml
and I get the following error:
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:
['/scratch/user/abhinav22/.conda/envs/openfold_env/bin/python', '-m', 'pip', 'install', '-U', '-r', '/scratch/user/abhinav22/openfold/openfold-main/condaenv.zagfsdj3.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting git+https://github.com/NVIDIA/dllogger.git (from -r /scratch/user/abhinav22/openfold/openfold-main/condaenv.zagfsdj3.requirements.txt (line 3))
Cloning https://github.com/NVIDIA/dllogger.git to /tmp/pip-req-build-hble364q
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 /scratch/user/abhinav22/openfold/openfold-main/condaenv.zagfsdj3.requirements.txt (line 4))
Cloning https://github.com/Dao-AILab/flash-attention.git (to revision 5b838a8) to /tmp/pip-req-build-lzk44cln
Resolved https://github.com/Dao-AILab/flash-attention.git to commit 5b838a8
Preparing metadata (setup.py): started
Preparing metadata (setup.py): still running...
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-hble364q
Running command git clone --filter=blob:none --quiet https://github.com/Dao-AILab/flash-attention.git /tmp/pip-req-build-lzk44cln
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-lzk44cln/setup.py", line 105, in
raise_if_cuda_home_none("flash_attn")
File "/tmp/pip-req-build-lzk44cln/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.
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
How can I fix this?
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