In-depth Analysis On Parallel Processing Patterns for High-Performance Dataframes

The Data Science domain has expanded monumentally in both research and industry communities during the past decade, predominantly owing to the Big Data revolution. Artificial Intelligence (AI) and Machine Learning (ML) are bringing more complexities to data engineering applications, which are now integrated into data processing pipelines to process terabytes of data. Typically, a significant amount of time is spent on data preprocessing in these pipelines, and hence improving its e fficiency directly impacts the overall pipeline performance. The community has recently embraced the concept of Dataframes as the de-facto data structure for data representation and manipulation. However, the most widely used serial Dataframes today (R, pandas) experience performance limitations while working on even moderately large data sets. We believe that there is plenty of room for improvement by taking a look at this problem from a high-performance computing point of view. In a prior publication, we presented a set of parallel processing patterns for distributed dataframe operators and the reference runtime implementation, Cylon [1]. In this paper, we are expanding on the initial concept by introducing a cost model for evaluating the said patterns. Furthermore, we evaluate the performance of Cylon on the ORNL Summit supercomputer.

Analyzing the Performance of Deep Encoder-Decoder Networks as Surrogates for a Diffusion Equation

Neural networks (NNs) have proven to be a viable alternative to traditional direct numerical algorithms, with the potential to accelerate computational time by several orders of magnitude. In the present paper we study the use of encoder-decoder convolutional neural network (CNN) as surrogates for steady-state diffusion solvers. The construction of such surrogates requires the selection of an appropriate task, network architecture, training set structure and size, loss function, and training algorithm hyperparameters. It is well known that each of these factors can have a significant impact on the performance of the resultant model. Our approach employs an encoder-decoder CNN architecture, which we posit is particularly well-suited for this task due to its ability to effectively transform data, as opposed to merely compressing it. We systematically evaluate a range of loss functions, hyperparameters, and training set sizes. Our results indicate that increasing the size of the training set has a substantial effect on reducing performance fluctuations and overall error. Additionally, we observe that the performance of the model exhibits a logarithmic dependence on the training set size. Furthermore, we investigate the effect on model performance by using different subsets of data with varying features. Our results highlight the importance of sampling the configurational space in an optimal manner, as this can have a significant impact on the performance of the model and the required training time. In conclusion, our results suggest that training a model with a pre-determined error performance bound is not a viable approach, as it does not guarantee that edge cases with errors larger than the bound do not exist. Furthermore, as most surrogate tasks involve a high dimensional landscape, an ever increasing training set size is, in principle, needed, however it is not a practical solution.

GTrans: Spatiotemporal Autoregressive Transformer with Graph Embeddings for Nowcasting Extreme Events

Spatiotemporal time series nowcasting should preserve temporal and spatial dynamics in the sense that generated new sequences from models respect the covariance relationship from history. Conventional feature extractors are built with deep convolutional neural networks (CNN). However, CNN models have limits to image-like applications where data can be formed with high-dimensional arrays. In contrast, applications in social networks, road traffic, physics, and chemical property prediction where data features can be organized with nodes and edges of graphs. Transformer architecture is an emerging method for predictive models, bringing high accuracy and efficiency due to attention mechanism design. This paper proposes a spatiotemporal model, namely GTrans, that transforms data features into graph embeddings and predicts temporal dynamics with a transformer model. According to our experiments, we demonstrate that GTrans can model spatial and temporal dynamics and nowcasts extreme events for datasets. Furthermore, in all the experiments, GTrans can achieve the highest F1 and F2 scores in binary-class prediction tests than the baseline models.

Earthquake Nowcasting with Deep Learning

We review previous approaches to nowcasting earthquakes and introduce new approaches based on deep learning using three distinct models based on recurrent neural networks and transformers. We discuss different choices for observables and measures presenting promising initial results for a region of Southern California from 1950-2020. Earthquake activity is predicted as a function of 0.1-degree spatial bins for time periods varying from two weeks to four years. The overall quality is measured by the Nash Sutcliffe Efficiency comparing the deviation of nowcast and observation with the variance over time in each spatial region. The software is available as open-source together with the preprocessed data from the USGS.

MLPerf HPC: A Holistic Benchmark Suite for Scientific Machine Learning on HPC Systems

Scientific communities are increasingly adopting machine learning and deep learning models in their applications to accelerate scientific insights. High performance computing systems are pushing the frontiers of performance with a rich diversity of hardware resources and massive scale-out capabilities. There is a critical need to understand fair and effective benchmarking of machine learning applications that are representative of real-world scientific use cases. MLPerf is a community-driven standard to benchmark machine learning workloads, focusing on end-to-end performance metrics. In this paper, we introduce MLPerf HPC, a benchmark suite of large-scale scientific machine learning training applications driven by the MLCommons Association. We present the results from the first submission round, including a diverse set of some of the world's largest HPC systems. We develop a systematic framework for their joint analysis and compare them in terms of data staging, algorithmic convergence, and compute performance. As a result, we gain a quantitative understanding of optimizations on different subsystems such as staging and on-node loading of data, compute-unit utilization, and communication scheduling, enabling overall $>10 \times$ (end-to-end) performance improvements through system scaling. Notably, our analysis shows a scale-dependent interplay between the dataset size, a system's memory hierarchy, and training convergence that underlines the importance of near-compute storage. To overcome the data-parallel scalability challenge at large batch sizes, we discuss specific learning techniques and hybrid data-and-model parallelism that are effective on large systems. We conclude by characterizing each benchmark with respect to low-level memory, I/O, and network behavior to parameterize extended roofline performance models in future rounds.

Scientific Machine Learning Benchmarks

The breakthrough in Deep Learning neural networks has transformed the use of AI and machine learning technologies for the analysis of very large experimental datasets. These datasets are typically generated by large-scale experimental facilities at national laboratories. In the context of science, scientific machine learning focuses on training machines to identify patterns, trends, and anomalies to extract meaningful scientific insights from such datasets. With a new generation of experimental facilities, the rate of data generation and the scale of data volumes will increasingly require the use of more automated data analysis. At present, identifying the most appropriate machine learning algorithm for the analysis of any given scientific dataset is still a challenge for scientists. This is due to many different machine learning frameworks, computer architectures, and machine learning models. Historically, for modelling and simulation on HPC systems such problems have been addressed through benchmarking computer applications, algorithms, and architectures. Extending such a benchmarking approach and identifying metrics for the application of machine learning methods to scientific datasets is a new challenge for both scientists and computer scientists. In this paper, we describe our approach to the development of scientific machine learning benchmarks and review other approaches to benchmarking scientific machine learning.

HPTMT Parallel Operators for High Performance Data Science & Data Engineering

Data-intensive applications are becoming commonplace in all science disciplines. They are comprised of a rich set of sub-domains such as data engineering, deep learning, and machine learning. These applications are built around efficient data abstractions and operators that suit the applications of different domains. Often lack of a clear definition of data structures and operators in the field has led to other implementations that do not work well together. The HPTMT architecture that we proposed recently, identifies a set of data structures, operators, and an execution model for creating rich data applications that links all aspects of data engineering and data science together efficiently. This paper elaborates and illustrates this architecture using an end-to-end application with deep learning and data engineering parts working together.

HPTMT: Operator-Based Architecture for Scalable High-Performance Data-Intensive Frameworks

Data-intensive applications impact many domains, and their steadily increasing size and complexity demands high-performance, highly usable environments. We integrate a set of ideas developed in various data science and data engineering frameworks. They employ a set of operators on specific data abstractions that include vectors, matrices, tensors, graphs, and tables. Our key concepts are inspired from systems like MPI, HPF (High-Performance Fortran), NumPy, Pandas, Spark, Modin, PyTorch, TensorFlow, RAPIDS(NVIDIA), and OneAPI (Intel). Further, it is crucial to support different languages in everyday use in the Big Data arena, including Python, R, C++, and Java. We note the importance of Apache Arrow and Parquet for enabling language agnostic high performance and interoperability. In this paper, we propose High-Performance Tensors, Matrices and Tables (HPTMT), an operator-based architecture for data-intensive applications, and identify the fundamental principles needed for performance and usability success. We illustrate these principles by a discussion of examples using our software environments, Cylon and Twister2 that embody HPTMT.

HPTMT: Operator-Based Architecture for ScalableHigh-Performance Data-Intensive Frameworks

Data-intensive applications impact many domains, and their steadily increasing size and complexity demands high-performance, highly usable environments. We integrate a set of ideas developed in various data science and data engineering frameworks. They employ a set of operators on specific data abstractions that include vectors, matrices, tensors, graphs, and tables. Our key concepts are inspired from systems like MPI, HPF (High-Performance Fortran), NumPy, Pandas, Spark, Modin, PyTorch, TensorFlow, RAPIDS(NVIDIA), and OneAPI (Intel). Further, it is crucial to support different languages in everyday use in the Big Data arena, including Python, R, C++, and Java. We note the importance of Apache Arrow and Parquet for enabling language agnostic high performance and interoperability. In this paper, we propose High-Performance Tensors, Matrices and Tables (HPTMT), an operator-based architecture for data-intensive applications, and identify the fundamental principles needed for performance and usability success. We illustrate these principles by a discussion of examples using our software environments, Cylon and Twister2 that embody HPTMT.

Multidimensional Scaling for Gene Sequence Data with Autoencoders

Multidimensional scaling of gene sequence data has long played a vital role in analysing gene sequence data to identify clusters and patterns. However the computation complexities and memory requirements of state-of-the-art dimensional scaling algorithms make it infeasible to scale to large datasets. In this paper we present an autoencoder-based dimensional reduction model which can easily scale to datasets containing millions of gene sequences, while attaining results comparable to state-of-the-art MDS algorithms with minimal resource requirements. The model also supports out-of-sample data points with a 99.5%+ accuracy based on our experiments. The proposed model is evaluated against DAMDS with a real world fungi gene sequence dataset. The presented results showcase the effectiveness of the autoencoder-based dimension reduction model and its advantages.