Life Sciences Molecular Dynamics Applications on the IBM System Blue Gene Solution: Performance Overview

نویسندگان

  • Carlos P. Sosa
  • Tom Milledge
  • Jeffrey McAllister
  • Gaolin Zheng Milledge
چکیده

This IBM® System Blue Gene® Solution Applications Guide provides a brief overview of the performance characteristics of a selected set of computational chemistry applications. Classical Molecular Mechanics/Molecular Dynamics (MM/MD) are commonly used to simulate large biomolecules that cannot be treated with more accurate methods. This guide is intended to help applications users in computational chemistry area evaluate(?) applications that are running on Blue

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system

dynamics with NAMD on the IBM Blue Gene/L system S. Kumar C. Huang G. Zheng E. Bohm A. Bhatele J. C. Phillips H. Yu L. V. Kalé NAMD (nanoscale molecular dynamics) is a production molecular dynamics (MD) application for biomolecular simulations that include assemblages of proteins, cell membranes, and water molecules. In a biomolecular simulation, the problem size is fixed and a large number of ...

متن کامل

Overview of molecular dynamics techniques and early scientific results from the Blue Gene project

The Blue Genet project involves the development of a highly parallel supercomputer, the coding of scalable applications to run on it, and the design of protein simulations that take advantage of the power provided by the new machine. This paper provides an overview of analysis techniques applied to scientific results obtained with Blue Matter, the software framework for performing molecular dyn...

متن کامل

Understanding Checkpointing Overheads on Massive-Scale Systems: Analysis of the IBM Blue Gene/P System

Providing fault tolerance in high-end petascale systems, consisting of millions of hardware components and complex software stacks, is becoming an increasingly challenging task. Checkpointing continues to be the most prevalent technique for providing fault tolerance in such high-end systems. Considerable research has focussed on optimizing checkpointing; however, in practice, checkpointing stil...

متن کامل

Enabling Loosely-Coupled Serial Job Execution on the IBM BlueGene/P Supercomputer and the SiCortex SC5832

Our work addresses the enabling of the execution of highly parallel computations composed of loosely coupled serial jobs with no modifications to the respective applications, on largescale systems. This approach allows new-and potentially far larger-classes of application to leverage systems such as the IBM Blue Gene/P supercomputer and similar emerging petascale architectures. We present here ...

متن کامل

Custom math functions for molecular dynamics

functions for molecular dynamics R. F. Enenkel B. G. Fitch R. S. Germain F. G. Gustavson A. Martin M. Mendell J. W. Pitera M. C. Pitman A. Rayshubskiy F. Suits W. C. Swope T. J. C. Ward While developing the protein folding application for the IBM Blue Genet/L supercomputer, some frequently executed computational kernels were encountered. These were significantly more complex than the linear alg...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2006