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Register a new userScaling Distributed Training of Flood-Filling Networks on HPC Infrastructure for Brain Mapping
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Wushi Dong
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Mapping all the neurons in the brain requires automatic reconstruction of entire cells from volume electron microscopy data. The flood-filling network (FFN) architecture has demonstrated leading performance for segmenting structures from this data. However, the training of the network is computationally expensive. In order to reduce the training time, we implemented synchronous and data-parallel distributed training using the Horovod library, which is different from the asynchronous training scheme used in the published FFN code. We demonstrated that our distributed training scaled well up to 2048 Intel Knights Landing (KNL) nodes on the Theta supercomputer. Our trained models achieved similar level of inference performance, but took less training time compared to previous methods. Our study on the effects of different batch sizes on FFN training suggests ways to further improve training efficiency. Our findings on optimal learning rate and batch sizes agree with previous works.
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Modern deep learning systems like PyTorch and Tensorflow are able to train enormous models with billions (or trillions) of parameters on a distributed infrastructure. These systems require that the internal nodes have the same memory capacity and compute performance. Unfortunately, most organizations, especially universities, have a piecemeal approach to purchasing computer systems resulting in a heterogeneous infrastructure, which cannot be used to compute large models. The present work describes HetSeq, a software package adapted from the popular PyTorch package that provides the capability to train large neural network models on heterogeneous infrastructure. Experiments with transformer translation and BERT language model shows that HetSeq scales over heterogeneous systems. HetSeq can be easily extended to other models like image classification. Package with supported document is publicly available at https://github.com/yifding/hetseq.
The modern deep learning method based on backpropagation has surged in popularity and has been used in multiple domains and application areas. At the same time, there are other -- less-known -- machine learning algorithms with a mature and solid theoretical foundation whose performance remains unexplored. One such example is the brain-like Bayesian Confidence Propagation Neural Network (BCPNN). In this paper, we introduce StreamBrain -- a framework that allows neural networks based on BCPNN to be practically deployed in High-Performance Computing systems. StreamBrain is a domain-specific language (DSL), similar in concept to existing machine learning (ML) frameworks, and supports backends for CPUs, GPUs, and even FPGAs. We empirically demonstrate that StreamBrain can train the well-known ML benchmark dataset MNIST within seconds, and we are the first to demonstrate BCPNN on STL-10 size networks. We also show how StreamBrain can be used to train with custom floating-point formats and illustrate the impact of using different bfloat variations on BCPNN using FPGAs.
Stochastic gradient descent (SGD) is an inherently sequential training algorithm--computing the gradient at batch $i$ depends on the model parameters learned from batch $i-1$. Prior approaches that break this dependence do not honor them (e.g., sum the gradients for each batch, which is not what sequential SGD would do) and thus potentially suffer from poor convergence. This paper introduces a novel method to combine gradients called Adasum (for adaptive sum) that converges faster than prior work. Adasum is easy to implement, almost as efficient as simply summing gradients, and is integrated into the open-source toolkit Horovod. This paper first provides a formal justification for Adasum and then empirically demonstrates Adasum is more accurate than prior gradient accumulation methods. It then introduces a series of case-studies to show Adasum works with multiple frameworks, (TensorFlow and PyTorch), scales multiple optimizers (Momentum-SGD, Adam, and LAMB) to larger batch-sizes while still giving good downstream accuracy. Finally, it proves that Adasum converges. To summarize, Adasum scales Momentum-SGD on the MLPerf Resnet50 benchmark to 64K examples before communication (no MLPerf v0.5 entry converged with more than 16K), the Adam optimizer to 64K examples before communication on BERT-LARGE (prior work showed Adam stopped scaling at 16K), and the LAMB optimizer to 128K before communication on BERT-LARGE (prior work used 64K), all while maintaining downstream accuracy metrics. Finally, if a user does not need to scale, we show LAMB with Adasum on BERT-LARGE converges in 30% fewer steps than the baseline.
The exponential growth in use of large deep neural networks has accelerated the need for training these deep neural networks in hours or even minutes. This can only be achieved through scalable and efficient distributed training, since a single node/card cannot satisfy the compute, memory, and I/O requirements of todays state-of-the-art deep neural networks. However, scaling synchronous Stochastic Gradient Descent (SGD) is still a challenging problem and requires continued research/development. This entails innovations spanning algorithms, frameworks, communication libraries, and system design. In this paper, we describe the philosophy, design, and implementation of Intel Machine Learning Scalability Library (MLSL) and present proof-points demonstrating scaling DL training on 100s to 1000s of nodes across Cloud and HPC systems.
The recent Natural Language Processing techniques have been refreshing the state-of-the-art performance at an incredible speed. Training huge language models is therefore an imperative demand in both industry and academy. However, huge language models impose challenges to both hardware and software. Graphical processing units (GPUs) are iterated frequently to meet the exploding demand, and a variety of ASICs like TPUs are spawned. However, there is still a tension between the fast growth of the extremely huge models and the fact that Moores law is approaching the end. To this end, many model parallelism techniques are proposed to distribute the model parameters to multiple devices, so as to alleviate the tension on both memory and computation. Our work is the first to introduce a 3-dimensional model parallelism for expediting huge language models. By reaching a perfect load balance, our approach presents smaller memory and communication cost than existing state-of-the-art 1-D and 2-D model parallelism. Our experiments on 64 TACCs V100 GPUs show that our 3-D parallelism outperforms the 1-D and 2-D parallelism with 2.32x and 1.57x speedup, respectively.
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