FastFold

News 🚩

• [2023/01] Compatible with AlphaFold v2.3
• [2023/01] Added support for inference and training of AlphaFold on Intel Habana platform. For usage instructions, see here.

Optimizing Protein Structure Prediction Model Training and Inference on Heterogeneous Clusters

FastFold provides a high-performance implementation of Evoformer with the following characteristics.

1. Excellent kernel performance on GPU platform
2. Supporting Dynamic Axial Parallelism(DAP)
   • Break the memory limit of single GPU and reduce the overall training time
   • DAP can significantly speed up inference and make ultra-long sequence inference possible
3. Ease of use
   • Huge performance gains with a few lines changes
   • You don't need to care about how the parallel part is implemented
4. Faster data processing, about 3x times faster on monomer, about 3Nx times faster on multimer with N sequence.
5. Great Reduction on GPU memory, able to inference sequence containing more than 10000 residues.

Installation

To install FastFold, you will need:

• Python 3.8 or 3.9.
• NVIDIA CUDA 11.3 or above
• PyTorch 1.12 or above

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

Advanced

To leverage the power of FastFold, we recommend you to install Triton.

pip install triton==2.0.0.dev20221005

Using PyPi

You can download FastFold with pre-built CUDA extensions.

Warning, only stable versions available.

pip install fastfold -f https://release.colossalai.org/fastfold

Use Docker

Build On Your Own

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

Usage

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)

Download the dataset

You can down the dataset used to train FastFold by the script download_all_data.sh:

./scripts/download_all_data.sh data/

Inference

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 ./ \
    --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`

or run the script ./inference.sh, you can change the parameter in the script, especisally those data path.

./inference.sh

inference with data workflow

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, you should install the package and add parameter --enable_workflow to cmdline or shell script ./inference.sh

pip install ray==2.0.0 pyarrow

python inference.py target.fasta data/pdb_mmcif/mmcif_files/ \
    --output_dir ./ \
    --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 

inference with lower memory usage

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] and --inplace 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:15000 to inference such an extreme long sequence.

python inference.py target.fasta data/pdb_mmcif/mmcif_files/ \
    --output_dir ./ \
    --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`  \
    --chunk_size N \
    --inplace

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.

Once you have prepared your dataset and installed fastfold, you can use the following scripts:

bash habana/inference.sh
bash habana/train.sh

Performance Benchmark

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 us

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}
}

Acknowledgments

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.