Summary of Scalefold: Reducing Alphafold Initial Training Time to 10 Hours, by Feiwen Zhu et al.
ScaleFold: Reducing AlphaFold Initial Training Time to 10 Hours
by Feiwen Zhu, Arkadiusz Nowaczynski, Rundong Li, Jie Xin, Yifei Song, Michal Marcinkiewicz, Sukru Burc Eryilmaz, Jun Yang, Michael Andersch
First submitted to arxiv on: 17 Apr 2024
Categories
- Main: Machine Learning (cs.LG)
- Secondary: Artificial Intelligence (cs.AI); Distributed, Parallel, and Cluster Computing (cs.DC); Quantitative Methods (q-bio.QM)
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| Summary difficulty | Written by | Summary |
|---|---|---|
| High | Paper authors | High Difficulty Summary Read the original abstract here |
| Medium | GrooveSquid.com (original content) | Medium Difficulty Summary The AlphaFold2 protein folding model has achieved remarkable accuracy, but its implementation lacks the necessary training code. OpenFold is the first trainable public reimplementation of AlphaFold, aiming to overcome this limitation. However, the original AlphaFold training procedure exhibits inefficiencies, hindering scaling and performance improvements. This study analyzes the Openfold-based AlphaFold training procedure, identifying inefficient communication and overhead-dominated computations as key bottlenecks. To address these issues, ScaleFold is introduced, a systematic training method incorporating optimizations for these factors. ScaleFold successfully scales the AlphaFold training to 2080 NVIDIA H100 GPUs with high resource utilization, demonstrating significant speedup in the MLPerf HPC v3.0 benchmark. For training the AlphaFold model from scratch, ScaleFold reduces the pretraining time to just 10 hours, a substantial improvement over the original seven days. |
| Low | GrooveSquid.com (original content) | Low Difficulty Summary AlphaFold2 is a supercomputer that can quickly predict protein structures with high accuracy. However, it doesn’t come with instructions on how to train it. OpenFold is the first version of AlphaFold that you can train yourself. The researchers who made AlphaFold found that the way they trained it wasn’t very efficient and didn’t get much better when they used more powerful computers. They analyzed what was going wrong and came up with a new way of training, called ScaleFold. This new method uses computer power more efficiently and can even train AlphaFold2 itself in just 10 hours, which is much faster than the original seven days. |
Keywords
» Artificial intelligence » Pretraining
