Optimizing Protein Structure Prediction Model Training and Inference on Heterogeneous Clusters
FastFold provides a high-performance implementation of Evoformer with the following characteristics.
To install FastFold, you will need:
For now, You can install FastFold:
Using Conda (Recommended)We highly recommend installing an Anaconda or Miniconda environment and install PyTorch with conda. Lines below would create a new conda environment called "fastfold":
git clone https://github.com/hpcaitech/FastFold cd FastFold conda env create --name=fastfold -f environment.yml conda activate fastfold python setup.py install
To leverage the power of FastFold, we recommend you to install Triton.
NOTE: Triron needs CUDA 11.4 to run.
pip install -U --pre triton
Run the following command to build a docker image from Dockerfile provided.
Building FastFold from scratch requires GPU support, you need to use Nvidia Docker Runtime as the default when doing
docker build. More details can be found here.
cd FastFold docker build -t fastfold ./docker
Run the following command to start the docker container in interactive mode.
docker run -ti --gpus all --rm --ipc=host fastfold bash
You can use Evoformer as nn.Module in your project after from fastfold.model.fastnn import Evoformer:
from fastfold.model.fastnn import Evoformer evoformer_layer = Evoformer()
If you want to use Dynamic Axial Parallelism, add a line of initialize with fastfold.distributed.init_dap.
from fastfold.distributed import init_dap init_dap(args.dap_size)
You can down the dataset used to train FastFold by the script download_all_data.sh:
./scripts/download_all_data.sh data/
You can use FastFold with inject_fastnn. This will replace the evoformer from OpenFold with the high performance evoformer from FastFold.
from fastfold.utils import inject_fastnn model = AlphaFold(config) import_jax_weights_(model, args.param_path, version=args.model_name) model = inject_fastnn(model)
For Dynamic Axial Parallelism, you can refer to ./inference.py. Here is an example of 2 GPUs parallel inference:
python inference.py target.fasta data/pdb_mmcif/mmcif_files/ \
--output_dir .outputs/ \
--gpus 2 \
--uniref90_database_path data/uniref90/uniref90.fasta \
--mgnify_database_path data/mgnify/mgy_clusters_2022_05.fa \
--pdb70_database_path data/pdb70/pdb70 \
--uniref30_database_path data/uniref30/UniRef30_2021_03 \
--bfd_database_path data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--jackhmmer_binary_path `which jackhmmer` \
--hhblits_binary_path `which hhblits` \
--hhsearch_binary_path `which hhsearch` \
--kalign_binary_path `which kalign` \
--enable_workflow \
--inplace
or run the script ./inference.sh, you can change the parameter in the script, especisally those data path.
Alphafold's data pre-processing takes a lot of time, so we speed up the data pre-process by ray workflow, which achieves a 3x times faster speed. To run the inference with ray workflow, we add parameter --enable_workflow by default. To reduce memory usage of embedding presentations, we also add parameter --inplace to share memory by defaul.
Alphafold's embedding presentations take up a lot of memory as the sequence length increases. To reduce memory usage, you should add parameter --chunk_size [N] to cmdline or shell script ./inference.sh. The smaller you set N, the less memory will be used, but it will affect the speed. We can inference a sequence of length 10000 in bf16 with 61GB memory on a Nvidia A100(80GB). For fp32, the max length is 8000.
You need to set
PYTORCH_CUDA_ALLOC_CONF=max_split_size_mb:15000to inference such an extreme long sequence.
python inference.py target.fasta data/pdb_mmcif/mmcif_files/ \
--output_dir .outputs/ \
--gpus 2 \
--uniref90_database_path data/uniref90/uniref90.fasta \
--mgnify_database_path data/mgnify/mgy_clusters_2022_05.fa \
--pdb70_database_path data/pdb70/pdb70 \
--uniref30_database_path data/uniref30/UniRef30_2021_03 \
--bfd_database_path data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--jackhmmer_binary_path `which jackhmmer` \
--hhblits_binary_path `which hhblits` \
--hhsearch_binary_path `which hhsearch` \
--kalign_binary_path `which kalign` \
--enable_workflow \
--inplace
--chunk_size N \ inference multimer sequence
Alphafold Multimer is supported. You can the following cmd or shell script ./inference_multimer.sh. Workflow and memory parameters mentioned above can also be used.
python inference.py target.fasta data/pdb_mmcif/mmcif_files/ \
--output_dir ./ \
--gpus 2 \
--model_preset multimer \
--uniref90_database_path data/uniref90/uniref90.fasta \
--mgnify_database_path data/mgnify/mgy_clusters_2022_05.fa \
--pdb70_database_path data/pdb70/pdb70 \
--uniref30_database_path data/uniref30/UniRef30_2021_03 \
--bfd_database_path data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--uniprot_database_path data/uniprot/uniprot.fasta \
--pdb_seqres_database_path data/pdb_seqres/pdb_seqres.txt \
--param_path data/params/params_model_1_multimer.npz \
--model_name model_1_multimer \
--jackhmmer_binary_path `which jackhmmer` \
--hhblits_binary_path `which hhblits` \
--hhsearch_binary_path `which hhsearch` \
--kalign_binary_path `which kalign` Inference or Training on Intel Habana
To run AlphaFold inference or training on Intel Habana, you can follow the instructions in the Installation Guide to set up your environment on Amazon EC2 DL1 instances or on-premise environments, and please use SynapseAI R1.7.1 to test as it was verified internally.
Once you have prepared your dataset and installed fastfold, you can use the following scripts:
cd fastfold/habana/fastnn/custom_op/; python setup.py build (this is for Gaudi, for Gaudi2 please use setup2.py) ; cd - bash habana/inference.sh bash habana/train.sh
We have included a performance benchmark script in ./benchmark. You can benchmark the performance of Evoformer using different settings.
cd ./benchmark torchrun --nproc_per_node=1 perf.py --msa-length 128 --res-length 256
Benchmark Dynamic Axial Parallelism with 2 GPUs:
cd ./benchmark torchrun --nproc_per_node=2 perf.py --msa-length 128 --res-length 256 --dap-size 2
If you want to benchmark with OpenFold, you need to install OpenFold first and benchmark with option --openfold:
torchrun --nproc_per_node=1 perf.py --msa-length 128 --res-length 256 --openfold
Cite this paper, if you use FastFold in your research publication.
@misc{cheng2022fastfold,
title={FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours},
author={Shenggan Cheng and Ruidong Wu and Zhongming Yu and Binrui Li and Xiwen Zhang and Jian Peng and Yang You},
year={2022},
eprint={2203.00854},
archivePrefix={arXiv},
primaryClass={cs.LG}
}
We would like to extend our special thanks to the Intel Habana team for their support in providing us with technology and resources on the Habana platform.
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