High-Performance Cloud Computing: A View of Scientific Applications

Scientific computing often requires the availability of a massive number of computers for performing large scale experiments. Traditionally, these needs have been addressed by using high-performance computing solutions and installed facilities such as clusters and super computers, which are difficult to setup, maintain, and operate. Cloud computing provides scientists with a completely new model of utilizing the computing infrastructure. Compute resources, storage resources, as well as applications, can be dynamically provisioned (and integrated within the existing infrastructure) on a pay per use basis. These resources can be released when they are no more needed. Such services are often offered within the context of a Service Level Agreement (SLA), which ensure the desired Quality of Service (QoS). Aneka, an enterprise Cloud computing solution, harnesses the power of compute resources by relying on private and public Clouds and delivers to users the desired QoS. Its flexible and service based infrastructure supports multiple programming paradigms that make Aneka address a variety of different scenarios: from finance applications to computational science. As examples of scientific computing in the Cloud, we present a preliminary case study on using Aneka for the classification of gene expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape

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

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

Scalable Persistent Storage for Erlang

The many core revolution makes scalability a key property. The RELEASE project aims to improve the scalability of Erlang on emergent commodity architectures with 100,000 cores. Such architectures require scalable and available persistent storage on up to 100 hosts. We enumerate the requirements for scalable and available persistent storage, and evaluate four popular Erlang DBMSs against these requirements. This analysis shows that Mnesia and CouchDB are not suitable persistent storage at our target scale, but Dynamo-like NoSQL DataBase Management Systems (DBMSs) such as Cassandra and Riak potentially are. We investigate the current scalability limits of the Riak 1.1.1 NoSQL DBMS in practice on a 100-node cluster. We establish for the first time scientifically the scalability limit of Riak as 60 nodes on the Kalkyl cluster, thereby confirming developer folklore. We show that resources like memory, disk, and network do not limit the scalability of Riak. By instrumenting Erlang/OTP and Riak libraries we identify a specific Riak functionality that limits scalability. We outline how later releases of Riak are refactored to eliminate the scalability bottlenecks. We conclude that Dynamo-style NoSQL DBMSs provide scalable and available persistent storage for Erlang in general, and for our RELEASE target architecture in particular

The BioLighthouse: Reusable Software Design for Bioinformatics

Advances in next-generation sequencing have accelerated the field of microbiology by making accessible a wealth of information about microbiomes. Unfortunately, microbiome experiments are among the least reproducible in terms of bioinformatics. Software tools are often poorly documented, under-maintained, and commonly have arcane dependencies requiring significant time investment to configure them correctly. Microbiome studies are multidisciplinary efforts but communication and knowledge discrepancies make accessibility, reproducibility, and transparency of computational workflows difficult. The BioLighthouse uses Ansible roles, playbooks, and modules to automate configuration and execution of bioinformatics workflows. The roles and playbooks act as virtual laboratory notebooks by documenting the provenance of a bioinformatics workflow. The BioLighthouse was tested for platform dependence and data-scale dependence with a microbial profiling pipeline. The microbial profiling pipeline consisted of Cutadapt, FLASH2, and DADA2. The pipeline was tested on 3 canola root and soil microbiome datasets with differing orders of magnitude of data: 1 sample, 10 samples, and 100 samples. Each dataset was processed by The BioLighthouse with 10 unique parameter sets and outputs were compared across 8 computing environments for a total of 240 pipeline runs. Outputs after each step in the pipeline were tested for identity using the Linux diff command to ensure reproducible results. Testing of The BioLighthouse suggested no platform or data-scale dependence. To provide an easy way of maintaining environment reproducibility in user-space, Conda and the channel Bioconda were used for virtual environments and software dependencies for configuring bioinformatics tools. The BioLighthouse provides a framework for developers to make their tools accessible to the research community, for bioinformaticians to build bioinformatics workflows, and for the broader research community to consume these tools at a high level while knowing the tools will execute as intended

Enhancing Job Scheduling of an Atmospheric Intensive Data Application

Nowadays, e-Science applications involve great deal of data to have more accurate analysis. One of its application domains is the Radio Occultation which manages satellite data. Grid Processing Management is a physical infrastructure geographically distributed based on Grid Computing, that is implemented for the overall processing Radio Occultation analysis. After a brief description of algorithms adopted to characterize atmospheric profiles, the paper presents an improvement of job scheduling in order to decrease processing time and optimize resource utilization. Extension of grid computing capacity is implemented by virtual machines in existing physical Grid in order to satisfy temporary job requests. Also scheduling plays an important role in the infrastructure that is handled by a couple of schedulers which are developed to manage data automaticall