Problem when building

[JeremieDona]

Hi,

I am trying to get to use your work, but it seems that your conda env create -f environment.yaml

with the error:

Collecting package metadata (repodata.json): done
Solving environment: failed

I suspect that the root cause is that your foldtoken/environment.yaml includes a lot packages that might conflict when creating an env.

[Mistletoe-git]

Hi, I encountered the same issue as you. May I ask if you managed to resolve it? :)

[dandingsky]

I modified foldtoken/environment.yml(A LOT!!!), added a few procedures and got it to work (kind of).

Step 1: Install via a modified environment.yml

See the end of this comment for the modified file.

conda env create -f foldtoken/environment.yml

Step 2: Install the following packages from here:

pip install pyg-lib -f https://data.pyg.org/whl/torch-2.0.0+cu117.html
pip install https://data.pyg.org/whl/torch-2.0.0%2Bcu117/torch_cluster-1.6.1%2Bpt20cu117-cp39-cp39-linux_x86_64.whl
pip install https://data.pyg.org/whl/torch-2.0.0%2Bcu117/torch_scatter-2.1.1%2Bpt20cu117-cp39-cp39-linux_x86_64.whl
pip install https://data.pyg.org/whl/torch-2.0.0%2Bcu117/torch_sparse-0.6.17%2Bpt20cu117-cp39-cp39-linux_x86_64.whl
pip install https://data.pyg.org/whl/torch-2.0.0%2Bcu117/torch_spline_conv-1.2.2%2Bpt20cu117-cp39-cp39-linux_x86_64.whl

Step 3: Install flash-attn following the official guide

Depending on your machine you may need to manually install cuda-11.7 first.

Step 4: Run into the same issue I'm facing (maybe)

See #4.

Here's the modified environment.yml:

name: flash
channels:
  - pytorch
  - nvidia
  - conda-forge
  - anaconda
  - https://software.repos.intel.com/python/conda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - blas=1.0=mkl
  - brotlipy=0.7.0=py39h27cfd23_1003
  - bzip2=1.0.8
  - ca-certificates=2023.5.7=hbcca054_0
  - certifi=2023.7.22=py39h06a4308_0
  - cffi=1.15.1=py39h5eee18b_3
  - charset-normalizer=2.0.4=pyhd3eb1b0_0
  - cryptography=41.0.2=py39h22a60cf_0
  - cuda-cudart=11.7.99=0
  - cuda-cupti=11.7.101=0
  - cuda-libraries=11.7.1=0
  - cuda-nvrtc=11.7.99=0
  - cuda-nvtx=11.7.91=0
  - cuda-runtime=11.7.1=0
  - nvidia/label/cuda-11.7.1::cuda-nvcc
  - nvidia/label/cuda-11.7.1::cuda-toolkit
  - ffmpeg=4.3=hf484d3e_0
  - filelock=3.9.0=py39h06a4308_0
  - freetype=2.12.1=h4a9f257_0
  - giflib=5.2.1=h5eee18b_3
  - gmp=6.2.1=h295c915_3
  - gmpy2=2.1.2=py39heeb90bb_0
  - gnutls=3.6.15=he1e5248_0
  - idna=3.4=py39h06a4308_0
  - intel-openmp
  - intelpython
  - jinja2=3.1.2=py39h06a4308_0
  - jpeg=9e=h5eee18b_1
  - lame=3.100=h7b6447c_0
  - lcms2=2.12=h3be6417_0
  - ld_impl_linux-64=2.38=h1181459_1
  - lerc=3.0=h295c915_0
  - libcublas=11.10.3.66=0
  - libcufft=10.7.2.124=h4fbf590_0
  - libcufile=1.7.0.149=0
  - libcurand=10.3.3.53=0
  - libcusolver=11.4.0.1=0
  - libcusparse=11.7.4.91=0
  - libdeflate=1.17=h5eee18b_0
  - libffi=3.4.2=h7f98852_5
  - libgcc-ng=12.2.0=h65d4601_19
  - libgomp=12.2.0=h65d4601_19
  - libiconv=1.16=h7f8727e_2
  - libidn2=2.3.4=h5eee18b_0
  - libnpp=11.7.4.75=0
  - libnsl=2.0.0=h7f98852_0
  - libnvjpeg=11.8.0.2=0
  - libpng=1.6.39=h5eee18b_0
  - libstdcxx-ng=12.2.0=h46fd767_19
  - libtasn1=4.19.0=h5eee18b_0
  - libtiff=4.5.0=h6a678d5_2
  - libunistring=0.9.10=h27cfd23_0
  - libuuid=2.38.1=h0b41bf4_0
  - libwebp=1.2.4=h11a3e52_1
  - libwebp-base=1.2.4=h5eee18b_1
  - lz4-c=1.9.4=h6a678d5_0
  - markupsafe=2.1.1=py39h7f8727e_0
  - mkl=2023.1.0=h6d00ec8_46342
  - mkl-service=2.4.0=py39h5eee18b_1
  - mkl_fft=1.3.6=py39h417a72b_1
  - mkl_random=1.2.2=py39h417a72b_1
  - mpc=1.1.0=h10f8cd9_1
  - mpfr=4.0.2=hb69a4c5_1
  - mpmath=1.2.1=py39h06a4308_0
  - ncurses=6.4=hcb278e6_0
  - nettle=3.7.3=hbbd107a_1
  - networkx=2.8.4=py39h06a4308_1
  - numpy=1.25.0=py39h5f9d8c6_0
  - numpy-base=1.25.0=py39hb5e798b_0
  - openh264=2.1.1=h4ff587b_0
  - openssl=3.1.1=hd590300_1
  - pillow=9.4.0=py39h6a678d5_0
  - pip=23.1.2=pyhd8ed1ab_0
  - pycparser=2.21=pyhd3eb1b0_0
  - pyopenssl=23.2.0=py39h06a4308_0
  - pysocks=1.7.1=py39h06a4308_0
  - python=3.9.17=h955ad1f_0
  - pytorch=2.0.1=py3.9_cuda11.7_cudnn8.5.0_0
  - pytorch-cuda=11.7=h778d358_5
  - pytorch-mutex=1.0=cuda
  - readline=8.2=h8228510_1
  - requests=2.29.0=py39h06a4308_0
  - setuptools=67.7.2=pyhd8ed1ab_0
  - sqlite=3.41.2=h5eee18b_0
  - sympy=1.11.1=py39h06a4308_0
  - tbb=2021.8.0=hdb19cb5_0
  - tk=8.6.12=h1ccaba5_0
  - torchaudio=2.0.2=py39_cu117
  - torchtriton=2.0.0=py39
  - torchvision=0.15.2=py39_cu117
  - typing_extensions=4.7.1=py39h06a4308_0
  - urllib3=1.26.16=py39h06a4308_0
  - wheel=0.40.0=pyhd8ed1ab_0
  - xz=5.4.2=h5eee18b_0
  - zlib=1.2.13=h5eee18b_0
  - zstd=1.5.5=hc292b87_0
  - packaging
  - pip:
    - absl-py==2.0.0
    - aiohttp==3.8.5
    - aiosignal==1.3.1
    - antlr4-python3-runtime==4.9.3
    - appdirs==1.4.4
    - async-timeout==4.0.2
    - attrs==23.1.0
    - bio==1.5.9
    - biopython==1.81
    - biothings-client==0.3.0
    - biotite==0.37.0
    - click==8.1.6
    - contextlib2==21.6.0
    - contourpy==1.2.0
    - cycler==0.12.1
    - deepspeed==0.10.3
    - dm-tree==0.1.8
    - docker-pycreds==0.4.0
    - easydict==1.10
    - einops==0.6.1
    - fair-esm==2.0.0
    # - flash-attn==2.0.1
    - fonttools==4.47.2
    - frozenlist==1.4.0
    - fsspec==2023.6.0
    - gitdb==4.0.10
    - gitpython==3.1.32
    - gprofiler-official==1.0.0
    - hjson==3.1.0
    - huggingface-hub==0.25.1
    - imageio==2.35.1
    - importlib-resources==6.1.1
    - joblib==1.3.1
    - kiwisolver==1.4.5
    - lazy-loader==0.4
    - lightning-utilities==0.9.0
    - lmdb==1.4.1
    - lpips==0.1.4
    - matplotlib==3.8.2
    - ml-collections==0.1.1
    - msgpack==1.0.5
    - multidict==6.0.4
    - mygene==3.2.2
    - ninja==1.11.1
    - omegaconf==2.3.0
    - opencv-python==4.10.0.84
    - opencv-python-headless==4.10.0.84
    - packaging==23.1
    - pandas==2.0.3
    - pathtools==0.1.2
    - platformdirs==3.11.0
    - pooch==1.7.0
    - protobuf==4.23.4
    - psutil==5.9.5
    - ptflops==0.7
    - py-cpuinfo==9.0.0
    - pydantic==1.10.12
    - pyparsing==3.1.0
    - python-dateutil==2.8.2
    - pytorch-lightning==1.9.0
    - pytz==2023.3
    - pyyaml==6.0.1
    - regex==2023.6.3
    - safetensors==0.4.5
    - scikit-image==0.24.0
    - scikit-learn==1.3.0
    - scipy==1.11.1
    - seaborn==0.13.1
    - sentry-sdk==1.28.1
    - sequence-models==1.7.0
    - setproctitle==1.3.2
    - six==1.16.0
    - smmap==5.0.0
    - tensorboardx==2.6.2.2
    - threadpoolctl==3.2.0
    - tifffile==2024.8.30
    - tokenizers==0.20.0
    - torch-geometric==2.3.1
    - torcheval==0.0.7
    - torchmetrics==1.0.1
    - tqdm==4.65.0
    - transformers==4.45.1
    - tzdata==2023.3
    - wandb==0.15.7
    - yacs==0.1.8
    - yarl==1.9.2
    - zipp==3.17.0
prefix: /opt/conda/flash