A Network Monitoring system is a vital component of a Grid; however, its scalability is a challenge. We propose a network monitoring approach that combines passive monitoring, a domain oriented overlay network, and an attitude for demand driven monitoring sessions. In order to keep into account the demand for extreme scalability, we introduce a solution for two problems that are inherent to the proposed approach: security and group membership maintenance.

Euro-Par 2006 Parallel Processing

The computation of ever larger as well as more accurate phylogenetic (evolutionary) trees with the ultimate goal to compute the tree of life represents one of the grand challenges in High Performance Computing (HPC) Bioinformatics. Unfortunately, the size of trees which can be computed in reasonable time based on elaborate evolutionary models is limited by the severe computational cost inherent to these methods. There exist two orthogonal research directions to overcome this challenging computational burden: First, the development of novel, faster, and more accurate heuristic algorithms and second, the application of high performance computing techniques. The goal of this chapter is to provide a comprehensive introduction to the field of computational evolutionary biology to an audience with computing background, interested in participating in research and/or commercial applications of this field. Moreover, we will cover leading-edge technical and algorithmic developments in the field and discuss open problems and potential solutions.

Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions

We report on the performance of our cold dark matter cosmological N-body simulation that was carried out concurrently using supercomputers across the globe. We ran simulations on 60–750 cores distributed over a variety of supercomputers in Amsterdam (The Netherlands, Europe), in Tokyo (Japan, Asia), Edinburgh (UK, Europe) and Espoo (Finland, Europe). Regardless of the network latency of 0.32 s and the communication over 30 000 km of optical network cable, we are able to achieve ~87% of the performance compared to an equal number of cores on a single supercomputer. We argue that using widely distributed supercomputers in order to acquire more compute power is technically feasible and that the largest obstacle is introduced by local scheduling and reservation policies.

High-performance gravitational N-body simulations on a planet-wide-distributed supercomputer

One embodiment of the present invention can include a computer program product comprising one or more computer readable media storing a set of computer instructions that are executable by one or more computer processors, wherein the set of computer instructions comprise instructions executable to generate a command according to a generic command structure, forward the command to a remote computer, receive the command at the remote computer and translate the command to platform specific format.

System and method of command processing

We present MPWide, a platform independent communication library for performing message passing between computers. Our library allows coupling of several local MPI applications through a long distance network and is specifically optimized for such communications. The implementation is deliberately kept light-weight, platform independent and the library can be installed and used without administrative privileges. The only requirements are a C++ compiler and at least one open port to a wide area network on each site. In this paper we present the library, describe the user interface, present performance tests and apply MPWide in a large scale cosmological N-body simulation on a network of two computers, one in Amsterdam and the other in Tokyo.

A Light-Weight Communication Library for Distributed Computing

The revolution in life sciences research brought about by the sequencing of the human genome creates new challenges for scientists and new opportunities for computing support organizations. This may involve significant shifts in computing support strategies, particularly as regards interacting with life sciences researchers who maintain a medical practice. This paper describes Indiana University's experience in a large-scale initiative in supporting life sciences research, as well as several strategies and suggestions relevant to colleges and universities of any size. Computing organizations and support professionals have many opportunities to facilitate and accelerate life sciences research.

Advanced information technology support for life sciences research

A barrier deters Windows users from evaluating graphical scientific software that runs only on remote UNIX systems. Graphical UNIX applications are based on X Windows. To make use of X applications, Windows users must install an X server, install communications software for connecting to remote UNIX systems, and configure their systems to display graphics from remote systems. This barrier can be removed by making use of an X server and communications software that run live from CD-ROM. This poster presents such a CD-ROM known as XLiveCD. XLiveCD appears to users as an application that provides a command-prompt that allows them to log in to remote computers. Windows XP/NT/ 2000 users insert the CD into a drive and click twice in response to a wizard. A terminal window appears on the screen and provides a command prompt. From the command prompt users run the secure shell (ssh) to connect to a remote computer and launch applications. X graphics windows are forwarded automatically. XLiveCD is based entirely on open source software and is available free for download. It is a Cygwin environment (from Red Hat, Inc.), including the X.org X server and openssh installed and modified to be run from CD-ROM. The home page is http://xlivecd.indiana.edu/.

Easy access to remote graphical UNIX applications for windows users

The facilities described in this document were made possible in part through funding from Indiana University, the Indiana University Office of the Vice President for
Information Technology, the State of Indiana, Shared University Research Grants from IBM, Inc., and from the Lilly Endowment through their support o f the Indiana Genomics Initiative. The Indiana Genomics Initiative (INGEN) of Indiana University is supported in part by Lilly Endowment Inc.

/pdf/ingen-s-advanced-it-facilities-the-least-you-need-to-know-1qcwphw12u.pdf

INGEN's advanced IT facilities: The least you need to know

Like many large institutions, Indiana University has thousands of desktop computers devoted primarily to running office productivity applications on the Windows operating system, tasks which are necessary but that do not use the computers’ full capacity. This is a resource worth pursuing. However, the individual desktop systems do not offer enough processing power for a long enough period of time to complete large scientific computing applications. Some form of distributed, parallel programming is required, to make them worth the chase. They must be instantly available to their primary users, so they are available only intermittently. This has been a serious stumbling block: currently available communications libraries for distributed computing do not support such a dynamic communications world well. This paper introduces Simple Message Broker Library (SMBL), which provides the flexibility needed to take advantage of such ephemeral resources. Condor [1] offers an approach to managing jobs on scattered computing resources that is well suited to this situation; there is a Windows version of Condor, although it does not at the time of this writing provide support for parallel computing. There are other systems for managing jobs in a distributed environment, such as Globus [2]. SMBL addresses a different problem: performing extended computations using a continually changing collection of small computers. We could not find a sufficiently fault-tolerant and wellbehaved PVM [3] implementation for Windows. MPI [4] implementations expect the same machines at the end of a job as at the beginning. This is only reasonable, since these libraries are generally used on dedicated systems. DOGMA [5] supports the desired type of computing, but only for applications written in Java. SETI@Home [6] does not provide a general-purpose framework. SMBL enables parallel computing on sporadically-available desktop systems by introducing a server to keep track of the processing nodes and route messages between them. The SMBL server acts as a communications broker for processes associated with a particular parallel job running on many different processors. SMBL is designed to work with heterogeneous systems. It is not a part of Condor, but they work well together. In conjunction, they can be used to run parallel jobs on Windows computers in an opportunistic fashion, without interfering with the computers’ primary users. Available as open source, SMBL is scalable, flexible and robust enough for a highly constrained and highly dynamic distributed computing environment, using ephemeral resources for massive computations.

Distributed parallel computing using windows desktop systems

Technical Report: Distributed Parallel Computing Using Windows Desktop Systems

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