Scientific Computing Meets Big Data Technology: An Astronomy Use Case

Scientific analyses commonly compose multiple single-process programs into a dataflow. An end-to-end dataflow of single-process programs is known as a many-task application. Typically, tools from the HPC software stack are used to parallelize these analyses. In this work, we investigate an alternate approach that uses Apache Spark -- a modern big data platform -- to parallelize many-task applications. We present Kira, a flexible and distributed astronomy image processing toolkit using Apache Spark. We then use the Kira toolkit to implement a Source Extractor application for astronomy images, called Kira SE. With Kira SE as the use case, we study the programming flexibility, dataflow richness, scheduling capacity and performance of Apache Spark running on the EC2 cloud. By exploiting data locality, Kira SE achieves a 2.5x speedup over an equivalent C program when analyzing a 1TB dataset using 512 cores on the Amazon EC2 cloud. Furthermore, we show that by leveraging software originally designed for big data infrastructure, Kira SE achieves competitive performance to the C implementation running on the NERSC Edison supercomputer. Our experience with Kira indicates that emerging Big Data platforms such as Apache Spark are a performant alternative for many-task scientific applications

RELEASE: A High-level Paradigm for Reliable Large-scale Server Software

Erlang is a functional language with a much-emulated model for building reliable distributed systems. This paper outlines the RELEASE project, and describes the progress in the rst six months. The project aim is to scale the Erlang's radical concurrency-oriented programming paradigm to build reliable general-purpose software, such as server-based systems, on massively parallel machines. Currently Erlang has inherently scalable computation and reliability models, but in practice scalability is constrained by aspects of the language and virtual machine. We are working at three levels to address these challenges: evolving the Erlang virtual machine so that it can work effectively on large scale multicore systems; evolving the language to Scalable Distributed (SD) Erlang; developing a scalable Erlang infrastructure to integrate multiple, heterogeneous clusters. We are also developing state of the art tools that allow programmers to understand the behaviour of massively parallel SD Erlang programs. We will demonstrate the e ectiveness of the RELEASE approach using demonstrators and two large case studies on a Blue Gene

Holistic debugging - enabling instruction set simulation for software quality assurance

We present holistic debugging, a novel method for observing execution of complex and distributed software. It builds on an instruction set simulator, which provides reproducible experiments and non-intrusive probing of state in a distributed system. Instruction set simulators, however, only provide low-level information, so a holistic debugger contains a translation framework that maps this information to higher abstraction level observation tools, such as source code debuggers. We have created Nornir, a proof-of-concept holistic debugger, built on the simulator Simics. For each observed process in the simulated system, Nornir creates an abstraction translation stack, with virtual machine translators that map machine-level storage contents (e.g. physical memory, registers) provided by Simics, to application-level data (e.g. virtual memory contents) by parsing the data structures of operating systems and virtual machines. Nornir includes a modified version of the GNU debugger (GDB), which supports non-intrusive symbolic debugging of distributed applications. Nornir's main interface is a debugger shepherd, a programmable interface that controls multiple debuggers, and allows users to coherently inspect the entire state of heterogeneous, distributed applications. It provides a robust observation platform for construction of new observation tools

RELEASE: A High-level Paradigm for Reliable Large-scale Server Software

Erlang is a functional language with a much-emulated model for building reliable distributed systems. This paper outlines the RELEASE project, and describes the progress in the first six months. The project aim is to scale the Erlang’s radical concurrency-oriented programming paradigm to build reliable general-purpose software, such as server-based systems, on massively parallel machines. Currently Erlang has inherently scalable computation and reliability models, but in practice scalability is constrained by aspects of the language and virtual machine. We are working at three levels to address these challenges: evolving the Erlang virtual machine so that it can work effectively on large scale multicore systems; evolving the language to Scalable Distributed (SD) Erlang; developing a scalable Erlang infrastructure to integrate multiple, heterogeneous clusters. We are also developing state of the art tools that allow programmers to understand the behaviour of massively parallel SD Erlang programs. We will demonstrate the effectiveness of the RELEASE approach using demonstrators and two large case studies on a Blue Gene

Iso-energy-efficiency: An approach to power-constrained parallel computation

Future large scale high performance supercomputer systems require high energy efficiency to achieve exaflops computational power and beyond. Despite the need to understand energy efficiency in high-performance systems, there are few techniques to evaluate energy efficiency at scale. In this paper, we propose a system-level iso-energy-efficiency model to analyze, evaluate and predict energy-performance of data intensive parallel applications with various execution patterns running on large scale power-aware clusters. Our analytical model can help users explore the effects of machine and application dependent characteristics on system energy efficiency and isolate efficient ways to scale system parameters (e.g. processor count, CPU power/frequency, workload size and network bandwidth) to balance energy use and performance. We derive our iso-energy-efficiency model and apply it to the NAS Parallel Benchmarks on two power-aware clusters. Our results indicate that the model accurately predicts total system energy consumption within 5% error on average for parallel applications with various execution and communication patterns. We demonstrate effective use of the model for various application contexts and in scalability decision-making