Early Observations on Performance of Google Compute Engine for Scientific Computing

Although Cloud computing emerged for business applications in industry, public Cloud services have been widely accepted and encouraged for scientific computing in academia. The recently available Google Compute Engine (GCE) is claimed to support high-performance and computationally intensive tasks, while little evaluation studies can be found to reveal GCE's scientific capabilities. Considering that fundamental performance benchmarking is the strategy of early-stage evaluation of new Cloud services, we followed the Cloud Evaluation Experiment Methodology (CEEM) to benchmark GCE and also compare it with Amazon EC2, to help understand the elementary capability of GCE for dealing with scientific problems. The experimental results and analyses show both potential advantages of, and possible threats to applying GCE to scientific computing. For example, compared to Amazon's EC2 service, GCE may better suit applications that require frequent disk operations, while it may not be ready yet for single VM-based parallel computing. Following the same evaluation methodology, different evaluators can replicate and/or supplement this fundamental evaluation of GCE. Based on the fundamental evaluation results, suitable GCE environments can be further established for case studies of solving real science problems.Comment: Proceedings of the 5th International Conference on Cloud Computing Technologies and Science (CloudCom 2013), pp. 1-8, Bristol, UK, December 2-5, 201

Predicting Intermediate Storage Performance for Workflow Applications

Configuring a storage system to better serve an application is a challenging task complicated by a multidimensional, discrete configuration space and the high cost of space exploration (e.g., by running the application with different storage configurations). To enable selecting the best configuration in a reasonable time, we design an end-to-end performance prediction mechanism that estimates the turn-around time of an application using storage system under a given configuration. This approach focuses on a generic object-based storage system design, supports exploring the impact of optimizations targeting workflow applications (e.g., various data placement schemes) in addition to other, more traditional, configuration knobs (e.g., stripe size or replication level), and models the system operation at data-chunk and control message level. This paper presents our experience to date with designing and using this prediction mechanism. We evaluate this mechanism using micro- as well as synthetic benchmarks mimicking real workflow applications, and a real application.. A preliminary evaluation shows that we are on a good track to meet our objectives: it can scale to model a workflow application run on an entire cluster while offering an over 200x speedup factor (normalized by resource) compared to running the actual application, and can achieve, in the limited number of scenarios we study, a prediction accuracy that enables identifying the best storage system configuration

A Factor Framework for Experimental Design for Performance Evaluation of Commercial Cloud Services

Given the diversity of commercial Cloud services, performance evaluations of candidate services would be crucial and beneficial for both service customers (e.g. cost-benefit analysis) and providers (e.g. direction of service improvement). Before an evaluation implementation, the selection of suitable factors (also called parameters or variables) plays a prerequisite role in designing evaluation experiments. However, there seems a lack of systematic approaches to factor selection for Cloud services performance evaluation. In other words, evaluators randomly and intuitively concerned experimental factors in most of the existing evaluation studies. Based on our previous taxonomy and modeling work, this paper proposes a factor framework for experimental design for performance evaluation of commercial Cloud services. This framework capsules the state-of-the-practice of performance evaluation factors that people currently take into account in the Cloud Computing domain, and in turn can help facilitate designing new experiments for evaluating Cloud services.Comment: 8 pages, Proceedings of the 4th International Conference on Cloud Computing Technology and Science (CloudCom 2012), pp. 169-176, Taipei, Taiwan, December 03-06, 201

It\u27s Fun, But Is It Science? Goals and Strategies in a Problem-Based Learning Course

All students at Hampshire College must complete a science requirement in which they demonstrate their understanding of how science is done, examine the work of science in larger contexts, and communicate their ideas effectively. Human Biology: Selected Topics in Medicine is one of 18-20 freshman seminars designed to move students toward completing this requirement. Students work in cooperative groups of 4-6 people to solve actual medical cases about which they receive information progressively. Students assign themselves homework tasks to bring information back for group deliberation. The goal is for case teams to work cooperatively to develop a differential diagnosis and recommend treatment. Students write detailed individual final case reports. Changes observed in student work over six years of developing this course include: increased motivation to pursue work in depth, more effective participation on case teams, increase in critical examination of evidence, and more fully developed arguments in final written reports. As part of a larger study of eighteen introductory science courses in two institutions, several types of pre- and post-course assessments were used to evaluate how teaching approaches might have influenced students’ attitudes about science, their ability to learn science, and their understanding of how scientific knowledge is developed [1]. Preliminary results from interviews and Likert-scale measures suggest improvements in the development of some students’ views of epistemology and in the importance of cooperative group work in facilitating that development

MPI-Vector-IO: Parallel I/O and Partitioning for Geospatial Vector Data

In recent times, geospatial datasets are growing in terms of size, complexity and heterogeneity. High performance systems are needed to analyze such data to produce actionable insights in an efficient manner. For polygonal a.k.a vector datasets, operations such as I/O, data partitioning, communication, and load balancing becomes challenging in a cluster environment. In this work, we present MPI-Vector-IO 1 , a parallel I/O library that we have designed using MPI-IO specifically for partitioning and reading irregular vector data formats such as Well Known Text. It makes MPI aware of spatial data, spatial primitives and provides support for spatial data types embedded within collective computation and communication using MPI message-passing library. These abstractions along with parallel I/O support are useful for parallel Geographic Information System (GIS) application development on HPC platforms

Optimizing I/O for Big Array Analytics

Big array analytics is becoming indispensable in answering important scientific and business questions. Most analysis tasks consist of multiple steps, each making one or multiple passes over the arrays to be analyzed and generating intermediate results. In the big data setting, I/O optimization is a key to efficient analytics. In this paper, we develop a framework and techniques for capturing a broad range of analysis tasks expressible in nested-loop forms, representing them in a declarative way, and optimizing their I/O by identifying sharing opportunities. Experiment results show that our optimizer is capable of finding execution plans that exploit nontrivial I/O sharing opportunities with significant savings.Comment: VLDB201

ArrayBridge: Interweaving declarative array processing with high-performance computing

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.Comment: 12 pages, 13 figure

PROFET: modeling system performance and energy without simulating the CPU

The approaching end of DRAM scaling and expansion of emerging memory technologies is motivating a lot of research in future memory systems. Novel memory systems are typically explored by hardware simulators that are slow and often have a simplified or obsolete abstraction of the CPU. This study presents PROFET, an analytical model that predicts how an application's performance and energy consumption changes when it is executed on different memory systems. The model is based on instrumentation of an application execution on actual hardware, so it already takes into account CPU microarchitectural details such as the data prefetcher and out-of-order engine. PROFET is evaluated on two real platforms: Sandy Bridge-EP E5-2670 and Knights Landing Xeon Phi platforms with various memory configurations. The evaluation results show that PROFET's predictions are accurate, typically with only 2% difference from the values measured on actual hardware. We release the PROFET source code and all input data required for memory system and application profiling. The released package can be seamlessly installed and used on high-end Intel platforms.Peer ReviewedPostprint (author's final draft

Ask a clearer question, get a better answer.

Many undergraduate students struggle to engage with higher order skills such as evaluation and synthesis in written assignments, either because they do not understand that these are the aim of written assessment or because these critical thinking skills require more effort than writing a descriptive essay. Here, we report that students who attended a freely available workshop, in which they were coached to pose a question in the title of their assignment and then use their essay to answer that question, obtained higher marks for their essay than those who did not attend. We demonstrate that this is not a result of latent academic ability amongst students who chose to attend our workshops and suggest this increase in marks was a result of greater engagement with ‘critical thinking’ skills, which are essential for upper 2:1 and 1st class grades. The tutoring method we used holds two particular advantages: First, we allow students to pick their own topics of interest, which increases ownership of learning, which is associated with motivation and engagement in ‘difficult’ tasks. Second, this method integrates the development of ‘inquisitiveness’ and critical thinking into subject specific learning, which is thought to be more productive than trying to develop these skills in isolation