ScaleFold: Reducing AlphaFold Initial Training Time to 10 Hours

AlphaFold2 has been hailed as a breakthrough in protein folding. It can rapidly predict protein structures with lab-grade accuracy. However, its implementation does not include the necessary training code. OpenFold is the first trainable public reimplementation of AlphaFold. AlphaFold training procedure is prohibitively time-consuming, and gets diminishing benefits from scaling to more compute resources. In this work, we conducted a comprehensive analysis on the AlphaFold training procedure based on Openfold, identified that inefficient communications and overhead-dominated computations were the key factors that prevented the AlphaFold training from effective scaling. We introduced ScaleFold, a systematic training method that incorporated optimizations specifically for these factors. ScaleFold successfully scaled the AlphaFold training to 2080 NVIDIA H100 GPUs with high resource utilization. In the MLPerf HPC v3.0 benchmark, ScaleFold finished the OpenFold benchmark in 7.51 minutes, shown over $6\times$ speedup than the baseline. For training the AlphaFold model from scratch, ScaleFold completed the pretraining in 10 hours, a significant improvement over the seven days required by the original AlphaFold pretraining baseline.

Reducing Activation Recomputation in Large Transformer Models

Training large transformer models is one of the most important computational challenges of modern AI. In this paper, we show how to significantly accelerate training of large transformer models by reducing activation recomputation. Activation recomputation is commonly used to work around memory capacity constraints. Rather than storing activations for backpropagation, they are traditionally recomputed, which saves memory but adds redundant compute. In this work, we show most of this redundant compute is unnecessary because we can reduce memory consumption sufficiently without it. We present two novel yet very simple techniques: sequence parallelism and selective activation recomputation. In conjunction with tensor parallelism, these techniques almost eliminate the need to recompute activations. We evaluate our approach on language models up to one trillion parameters in scale and show that our method reduces activation memory by 5x, while reducing execution time overhead from activation recomputation by over 90%. For example, when training a 530B parameter GPT-3 style model on 2240 NVIDIA A100 GPUs, we achieve a Model Flops Utilization of 54.2%, which is 29% faster than the 42.1% we achieve using recomputation. Our implementation will be available in both Megatron-LM and NeMo-Megatron.

Sparse Persistent RNNs: Squeezing Large Recurrent Networks On-Chip

Recurrent Neural Networks (RNNs) are powerful tools for solving sequence-based problems, but their efficacy and execution time are dependent on the size of the network. Following recent work in simplifying these networks with model pruning and a novel mapping of work onto GPUs, we design an efficient implementation for sparse RNNs. We investigate several optimizations and tradeoffs: Lamport timestamps, wide memory loads, and a bank-aware weight layout. With these optimizations, we achieve speedups of over 6x over the next best algorithm for a hidden layer of size 2304, batch size of 4, and a density of 30%. Further, our technique allows for models of over 5x the size to fit on a GPU for a speedup of 2x, enabling larger networks to help advance the state-of-the-art. We perform case studies on NMT and speech recognition tasks in the appendix, accelerating their recurrent layers by up to 3x.