/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

物件導向軟體之架構(Object-Oriented Software Construction)探討

A large number of MPI implementations are currently available, each of which emphasize different aspects of high-performance computing or are intended to solve a specific research problem. The result is a myriad of incompatible MPI implementations, all of which require separate installation, and the combination of which present significant logistical challenges for end users. Building upon prior research, and influenced by experience gained from the code bases of the LAM/MPI, LA-MPI, and FT-MPI projects, Open MPI is an all-new, production-quality MPI-2 implementation that is fundamentally centered around component concepts. Open MPI provides a unique combination of novel features previously unavailable in an open-source, production-quality implementation of MPI. Its component architecture provides both a stable platform for third-party research as well as enabling the run-time composition of independent software add-ons. This paper presents a high-level overview the goals, design, and implementation of Open MPI.

/pdf/open-mpi-goals-concept-and-design-of-a-next-generation-mpi-16i41y4jp9.pdf

Open MPI: Goals, Concept, and Design of a Next Generation MPI Implementation

[서평]「Component Software」 - Beyond Object-Oriented Programming -

The ability of performance technology to keep pace with the growing complexity of parallel and distributed systems depends on robust performance frameworks that can at once provide system-specific performance capabilities and support high-level performance problem solving Flexibility and portability in empirical methods and processes are influenced primarily by the strategies available for instrmentation and measurement, and how effectively they are integrated and composed This paper presents the TAU (Tuning and Analysis Utilities) parallel performance sytem and describe how it addresses diverse requirements for performance observation and analysis

/pdf/the-tau-parallel-performance-system-3fr3lax14z.pdf

The Tau Parallel Performance System

With support for C/C++, Fortran, MPI, OpenMP, and performance tools, the Eclipse integrated development environment (IDE) is a serious contender as a programming environment for parallel applications. There is interest in adding capabilities in Eclipse for conducting workflows where an application is executed under different scenarios and its outputs are processed. For instance, parametric studies are a requirement in many benchmarking and performance tuning efforts, yet there was no experiment management support available for the Eclipse IDE. In this paper, we describe an extension of the Parallel Tools Platform (PTP) plugin for the Eclipse IDE. The extension provides a graphical user interface for selecting experiment parameters, launches build and run jobs, manages the performance data, and launches an analysis application to process the data. We describe our implementation, and discuss three experiment examples which demonstrate the experiment management support.

/pdf/parametric-studies-in-eclipse-with-tau-and-perfexplorer-2j1u3yv98a.pdf

Parametric Studies in Eclipse with TAU and PerfExplorer

Hands-on Practical Hybrid Parallel Application Performance Engineering

There is a growing awareness that high-end performance evaluation and tuning requires holistic program analysis. In addition to CPU performance characterization, observation of memory, network, and input/output (I/O) performance can help to identify execution bottlenecks related to these factors. Correctness of memory and communication operations is also an issue and can affect performance indirectly. This paper describes extensions to the TAU performance system to incorporate direct source-level code instrumentation for tracking dynamic memory management in FORTRAN codes that use allocate and de-allocate statements. TAU's lightweight profiling can then generate a detailed report of memory usage including the sizes of memory blocks allocated and de-allocated with precise program attribution: variable name, source line number, and file name. We report on results and experiences in applying TAU to the PTURBO application.

Memory Leak Detection in FORTRAN Applications Using TAU

The recent development of a unified SHMEM framework, OpenSHMEM, has enabled further study in the porting and scaling of applications that can benefit from the SHMEM programming model. This paper focuses on non-numerical graph algorithms, which typically have a low FLOPS/byte ratio. An overview of the space and time complexity of Kruskal's and Prim's algorithms for generating a minimum spanning tree (MST) is presented, along with an implementation of Kruskal's algorithm that uses OpenSHEM to generate the MST in parallel without intermediate communication. Additionally, a procedure for applying the TAU Performance System to OpenSHMEM applications to produce indepth performance profiles showing time spent in code regions, memory access patterns, and network load is presented. Performance evaluations from the Cray XK7 "Titan" system at Oak Ridge National Laboratory and a 48 core shared memory system at University of Maryland, Baltimore County are provided.

/pdf/profiling-non-numeric-openshmem-applications-with-the-tau-sbtlw6do1n.pdf

Sameer Shende

Papers

Parametric Studies in Eclipse with TAU and PerfExplorer

Hands-on Practical Hybrid Parallel Application Performance Engineering

Memory Leak Detection in FORTRAN Applications Using TAU

Profiling Non-numeric OpenSHMEM Applications with the TAU Performance System

Performance Analysis and Debugging Tools at Scale