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habana imporvement #189

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habana imporvement #189

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31a2066
use a more general path
KimBioInfoStudio Feb 23, 2024
6e80826
fix a error; simplify code
KimBioInfoStudio Feb 23, 2024
f6ceea4
add 1.14.0 habana docker
KimBioInfoStudio Feb 23, 2024
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7 changes: 2 additions & 5 deletions fastfold/habana/fastnn/custom_op/fusedsoftmax.py
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Expand Up @@ -4,13 +4,10 @@

import torch
import os
from glob import glob
import habana_frameworks.torch.core

custom_fusedsoftmax_op_lib_path = "./build/lib.linux-x86_64-3.8/hpu_fusedsoftmax.cpython-38-x86_64-linux-gnu.so"
my_dir = os.path.realpath(__file__)
my_len = my_dir.rfind('/')
base_dir = my_dir[:my_len]
torch.ops.load_library(os.path.join(base_dir, custom_fusedsoftmax_op_lib_path))
torch.ops.load_library(glob.glob(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'build/lib.*/*.so'))[0])

class FusedSoftmaxFunction(torch.autograd.Function):
@staticmethod
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15 changes: 15 additions & 0 deletions habana/docker/Dockerfile
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@@ -0,0 +1,15 @@
FROM vault.habana.ai/gaudi-docker/1.14.0/ubuntu22.04/habanalabs/pytorch-installer-2.1.1:latest

RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash Miniconda3-latest-Linux-x86_64.sh -b
RUN source ${HOME}/miniconda3/etc/profile.d/conda.sh && conda create -n habana python=3.10.12 && conda activate habana && conda install openmm=7.7.0 pdbfixer -c conda-forge -y \
&& conda install hmmer==3.3.2 hhsuite=3.3.0 kalign2=2.04 -c bioconda -y

RUN source ${HOME}/miniconda3/etc/profile.d/conda.sh && conda activate habana && python -m pip install biopython==1.79 dm-tree==0.1.6 ml-collections==0.1.0 \
scipy==1.7.1 ray pyarrow pandas einops colossalai

ENV PYTHONPTAH=$PYTHONPATH:/usr/local/lib/python3.10/dist-packages

Run source ${HOME}/miniconda3/etc/profile.d/conda.sh && conda activate habana && git clone https://github.com/hpcaitech/FastFold.git \
&& cd ./FastFold \
&& python setup.py install \
&& cd fastfold/habana/fastnn/custom_op/ && python ./setup2.py build && cd -