Accelerating Spark Genome Sequencing in Cloud—A Data Driven Approach, Case Studies and Beyond

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Spark data processing is shifting from on-premises to cloud service to take advantage of its horizontal resource scalability, better data accessibility and easy manageability. However, fully utilizing the computational power, fast storage and networking offered by cloud service can be challenging without deep understanding of workload characterizations and proper software optimization expertise. In this presentation, we will use a Spark based programing framework – Genome Analysis Toolkit version 4 (GATK4, under development), as an example to present a process of configuring and optimizing a proficient Spark cluster on Google Cloud to speed up genome data processing. We will first introduce an in-house developed data profiling framework named PAT, and discuss how to use PAT to quickly establish the best combination of VM configurations and Spark configurations to fully utilize cloud hardware resources and Spark computational parallelism. In addition, we use PAT and other data profiling tools to identify and fix software hotspots in application. We will show a case study in which we identify a thread scalability issue of Java Instanceof operator. The fix in Scala language hugely improves performance of GATK4 and other Spark based workloads.

About Yingqi (Lucy) Lu

Yingqi (Lucy) Lu is a Senior Software Performance Engineer in the Software Solution Group. She has been at Intel for over 8 years working on performance optimizations of Virtualization, Power Efficiency, Webservers and Java Virtual Machine. She is currently focusing on enabling and optimizing Big Data frameworks such as Hadoop* and Spark* for Intel Architecture. She earned a MS degree in Computer Science from University of Colorado at Boulder.

About Eric Kaczmarek

Eric Kaczmarek is a Senior Java Performance Architect in the Software Solution Group. He has been at Intel for over 20 years. For the better part of the last 10 years, he focused on optimizing the Java Virtual Machine for Intel Architectures. Because of his deep and broad Java Virtual Machine expertise, Eric leads the effort to enable and optimize Big Data frameworks such as Hadoop* and HBase* for Intel based platforms. He earned a BS degree in Computer Science and Engineering for the University of California Los Angeles (UCLA).