MPI is the new standard for multicomputer and cluster message passing introduced by the Message-Passing Interface Forum (MPIF) in April 1994. This paper describes the current inter-communicator interface found in MPI and the reasons for its current design. We also motivate the need for additional inter-communicator operations and introduce the extensions we have included in MPIX (MPI eXtension ...

The Message Passing Interface (MPI) provides a common high-level Application Programming Interface (API) to implement parallel programs on commodity off-the-shelf (COTS) clusters. Recently, increasing attention has been shown in using Java-based MPI implementations. The reason for this growing interest is that the Java language offers a potentially machine-independent method of distributing the...

The paper discusses use of the Java object serialization model for marshalling communication data in Java bindings of the Message Passing Interface standard, MPI. This approach is compared with a Java transcription of the derived datatype mechanism used for bu er description in C and Fortran bindings of MPI. We describe an implementation of the mpiJava interface to MPI incorporating automatic o...

SUMMARY TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has ...

Collective communication is one of the most powerful message passing concepts, enabling parallel applications to express complex communication patterns while allowing the underlying MPI to provide efficient implementations to minimize the cost of the data movements. However, with the increase in the heterogeneity inside the nodes, more specifically the memory hierarchies, harnessing the maximum...

This thesis describes a high-performance implementation of the Message Passing Interface (MPI) library based on a shared memory communication mechanism. Our implementation, called MPI/MBCF, combines two protocols to utilize the shared memory communication mechanism: the write protocol and the eager protocol. In the write protocol, Remote Write is used for communication with no bu ering. In the ...

The Open MPI implementation provides a high performance MPI-2 implementation for a wide variety of platforms. Open MPI has recently been ported to the Cray XT3 platform. This paper discusses the challenges of porting and describes important implementation decisions. A comparison of performance results between Open MPI and the Cray supported implementation of MPICH2 are also presented.

This paper describes the Java MPI bindings that have been included in the Open MPI distribution. Open MPI is one of the most popular implementations of MPI, the Message-Passing Interface, which is the predominant programming paradigm for parallel applications on distributed memory computers. We have added Java support to Open MPI, exposing MPI functionality to Java programmers. Our approach is ...

A hybrid performance monitor is presented. The hardware and software components of the system are discussed. The design of the probes to support MPI is presented along with some example displays generated by the system. This system has been successfully used to monitor several MPI applications with minimal in-trusiveness.