MPI and Java-MPI

SUMMARYCCJ is a communication library that adds MPI-like message passing and collective operations to Java. Rather than trying to adhere to the precise MPI syntax, CCJ aims at a clean integration of communication into Java's object-oriented framework. For example, CCJ uses thread groups to support Java's multithreading model and it allows any data structure (not just arrays) to be communicated. CCJ is implemented entirely in Java, on top of RMI, so it can be used with any Java virtual machine. The paper discusses three parallel Java applications that use collective communication. It compares the performance (on top of a Myrinet cluster) of CCJ, RMI and mpiJava versions of these applications and also compares their code complexity. A detailed performance comparison between CCJ and mpiJava is given using the Java Grande Forum MPJ benchmark suite. The results show that neither CCJ's object-oriented design nor its implementation on top of RMI impose a performance penalty on applications compared to their mpiJava counterparts. The source of CCJ is available from our Web site http://www.cs.vu.nl/manta.

Section: Application Programsmentioning

confidence: 99%

CCJ: object‐based message passing and collective communication in Java

Nelisse

Maassen

Kielmann

et al. 2003

Development of distributed bioinformatics applications with GMP

Schmidt

Lin

Laud

et al. 2004

SUMMARYWe present the design and use of gMP as a tool for developing distributed bioinformatics applications. gMP is a purely Java-based interface that adds MPI-like message-passing and collective communication to the genomics Research Network Architecture (gRNA). The gRNA is a highly programmable, modular environment specifically designed to invigorate the development of genome-centric tools for life science research. We demonstrate the development of a distributed application to detect regulatory elements using correlation with gene expression data. Its implementation with gMP leads to significant runtime savings on our distributed gRNA system.

Ibis: a flexible and efficient Java‐based Grid programming environment

Nieuwpoort

Maassen

Wrzesinska

et al. 2005

165

145

In computational grids, performance-hungry applications need to simultaneously tap the computational power of multiple, dynamically available sites. The crux of designing grid programming environments stems exactly from the dynamic availability of compute cycles: grid programming environments (a) need to be portable to run on as many sites as possible, (b) they need to be flexible to cope with different network protocols and dynamically changing groups of compute nodes, while (c) they need to provide efficient (local) communication that enables high-performance computing in the first place.Existing programming environments are either portable (Java), or they are flexible (Jini, Java RMI), or they are highly efficient (MPI). No system combines all three properties that are necessary for grid computing. In this paper, we present Ibis, a new programming environment that combines Java's "run everywhere" portability both with flexible treatment of dynamically available networks and processor pools, and with highly efficient, object-based communication. Ibis can transfer Java objects very efficiently by combining streaming object serialization with a zero-copy protocol. Using RMI as a simple test case, we show that Ibis outperforms existing RMI implementations, achieving up to 9 times higher throughputs with trees of objects.