VMD: Visual molecular dynamics

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

/pdf/scalable-molecular-dynamics-with-namd-51o1z7rwp8.pdf

Scalable molecular dynamics with NAMD

The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

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

Scalable Molecular Dynamics with NAMD

The proliferation of mobile computing devices and local-area wireless networks has fostered a growing interest in location-aware systems and services. In this paper we present RADAR, a radio-frequency (RF)-based system for locating and tracking users inside buildings. RADAR operates by recording and processing signal strength information at multiple base stations positioned to provide overlapping coverage in the area of interest. It combines empirical measurements with signal propagation modeling to determine user location and thereby enable location-aware services and applications. We present experimental results that demonstrate the ability of RADAR to estimate user location with a high degree of accuracy.

/pdf/radar-an-in-building-rf-based-user-location-and-tracking-ow0on2sogt.pdf

RADAR: an in-building RF-based user location and tracking system

This paper presents a new technique for disk storage management called a log-structured file system. A log-structured file system writes all modifications to disk sequentially in a log-like structure, thereby speeding up both file writing and crash recovery. The log is the only structure on disk; it contains indexing information so that files can be read back from the log efficiently. In order to maintain large free areas on disk for fast writing, we divide the log intosegmentsand use a segment cleaner to compress the live information from heavily fragmented segments. We present a series of simulations that demonstrate the efficiency of a simple cleaning policy based on cost and benefit. We have implemented a prototype log-structured file system called Sprite LFS; it outperforms current Unix file systems by an order of magnitude for small-file writes while matching or exceeding Unix performance for reads and large writes. Even when the overhead for cleaning is included, Sprite LFS can use 70% of the disk bandwidth for writing, whereas Unix file systems typically can use only 5–10%.

The design and implementation of a log-structured file system

Copyright © 1993 Addison-Wesley Publishing Company, Inc. All rights reserved. Duplication of this draft is permitted by individuals for personal use only. Any other form of duplication or reproduction requires prior written permission of the author or publisher. This statement must be easily visible on the first page of any reproduced copies. The publisher does not offer warranties in regard to this draft.

http://tcltk.co.kr/files/Tcl_and_The_Tk_Toolkit.pdf

Tcl and the Tk Toolkit

Raft is a consensus algorithm for managing a replicated log. It produces a result equivalent to (multi-)Paxos, and it is as efficient as Paxos, but its structure is different from Paxos; this makes Raft more understandable than Paxos and also provides a better foundation for building practical systems. In order to enhance understandability, Raft separates the key elements of consensus, such as leader election, log replication, and safety, and it enforces a stronger degree of coherency to reduce the number of states that must be considered. Results from a user study demonstrate that Raft is easier for students to learn than Paxos. Raft also includes a new mechanism for changing the cluster membership, which uses overlapping majorities to guarantee safety.

/pdf/in-search-of-an-understandable-consensus-algorithm-2tvnovxuiu.pdf

In search of an understandable consensus algorithm

This paper presents a new technique for disk storage management called a log-structured file system. A log-structured file system writes all modifications to disk sequentially in a log-like structure, thereby speeding up both file writing and crash recovery. The log is the only structure on disk; it contains indexing information so that files can be read back from the log efficiently. In order to maintain large free areas on disk for fast writing, we divide the log into segments and use a segment cleaner to compress the live information from heavily fragmented segments. We present a series of simulations that demonstrate the efficiency of a simple cleaning policy based on cost and benefit. We have implemented a prototype log-structured file system called Sprite LFS; it outperforms current Unix file systems by an order of magnitude for small-file writes while matching or exceeding Unix performance for reads and large writes. Even when the overhead for cleaning is included, Sprite LFS can use 70% of the disk bandwidth for writing, whereas Unix file systems typically can use only 5--10%.

/pdf/the-design-and-implementation-of-a-log-structured-file-2cyewxts7p.pdf

The Design and Implementation of a Log-structured file system

A fundamental change is occurring in the way people write computer programs, away from system programming languages such as C or C++ to scripting languages such as Perl or Tcl. Although many people are participating in the change, few realize that the change is occurring and even fewer know why it is happening. This article explains why scripting languages will handle many of the programming tasks in the next century better than system programming languages. System programming languages were designed for building data structures and algorithms from scratch, starting from the most primitive computer elements. Scripting languages are designed for gluing. They assume the existence of a set of powerful components and are intended primarily for connecting components.

/pdf/scripting-higher-level-programming-for-the-21st-century-1mstgj89iu.pdf

John Ousterhout

Papers

The design and implementation of a log-structured file system

Tcl and the Tk Toolkit

In search of an understandable consensus algorithm

The Design and Implementation of a Log-structured file system

Scripting: higher level programming for the 21st Century