README.md

![](/assets/fold.jpg)

# FastFold

![](https://img.shields.io/github/v/release/hpcaitech/FastFold)
[![GitHub license](https://img.shields.io/github/license/hpcaitech/FastFold.svg)](https://github.com/hpcaitech/FastFold/blob/master/LICENSE)
![](https://img.shields.io/badge/Made%20with-ColossalAI-blueviolet?style=flat)

Optimizing Protein Structure Prediction Model Training and Inference on GPU 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
    * Distributed inference can significantly speed up inference and make extremely long sequence inference possible
3. Ease of use
    * Replace a few lines and you can use FastFold in your project
    * You don't need to care about how the parallel part is implemented

## Installation

You will need Python 3.8 or later and [NVIDIA CUDA](https://developer.nvidia.com/cuda-downloads) 11.1 or above when you are installing from source. 

We highly recommend installing an Anaconda or Miniconda environment and install PyTorch with conda:

```
conda create -n fastfold python=3.8
conda activate fastfold
conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch
```

You can get the FastFold source and install it with setuptools:

```shell
git clone https://github.com/hpcaitech/FastFold
cd FastFold
python setup.py install --cuda_ext
```

## Performance Benchmark

We have included a performance benchmark script in `./benchmark`. You can benchmark the performance of Evoformer using different settings.

```shell
cd ./benchmark
torchrun --nproc_per_node=1 perf.py --msa-length 128 --res-length 256
```

If you want to benchmark with [OpenFold](https://github.com/aqlaboratory/openfold), you need to install OpenFold first and benchmark with option `--openfold`:

```shell
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.

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