Friday, February 29, 2008

Molecular Simulations And Applications In Environmental Chemistry

Randall T. Cygan, Geochemistry Department, Sandia National Laboratories


The fate of chemical and radioactive wastes in the environment is linked to the ability of natural phases to attenuate and immobilize contaminants through chemical adsorption and precipitation processes. Our ability to understand the molecular control of these processes is provided by a few experimental and analytical methods such as X-ray absorption, vibrational, and NMR spectroscopies. However, due to complexities in the structure and composition of clay and other hydrated minerals, and the inherent uncertainties of the experimental methods, it is important to apply theoretical molecular models for a fundamental understanding and interpretation of these phenomena. In this effort, we have developed a general force field suitable for the simulation of hydrated and multicomponent mineral systems. Interatomic potentials were derived from parameterizations incorporating structural and spectroscopic data from a variety of simple hydrated compounds. A flexible water model is used to describe the water and hydroxyl behavior. Bulk structures, interfacial behavior, and intercalation processes are evaluated and compared to experimental and spectroscopic findings. Classical molecular dynamics methods and ab initio molecular dynamics using quantum approaches provide additional insights into the structure, dynamics, and reactivity of these complex materials.

Thursday, February 28, 2008

SUN OpenxVM

xVM is the intersection of virtualization and management. OpenxVM is a community hub for a number of related open source projects that together create the next generation of data center infrastructure.

By combining virtualization software and data center automation tools, OpenxVM technology provides the technologies to operate data centers at radically reduced costs.

Friday, February 22, 2008

Challenges For The Message-Passing Interface In The PetaFLOPS Era

William D. Gropp

MPI has been a successful parallel programming model. The combination of performance, scalability, composability, and support for libraries has made it relatively easy to build complex parallel applications. Further, these applications scale well, with some applications already running on systems with over 128000 processors. However, MPI is by no means the perfect parallel programming model. This talk will review the strengths of MPI with respect to other parallel programming models and discuss some of the weaknesses and limitations of MPI in the areas of performance, productivity, scalability, and interoperability. The impact of recent developments in computing, such as multicore (and manycore), better networks, and global view programming models on both MPI and applications that use MPI will be covered, as well as lessons from the success of MPI that are relevant to furture progress in parallel computing. The talk will conclude with a discussion of what extensions (or even changes) may be needed in MPI, and what issues should be addressed by combining MPI with other parallel programming models.


Challenges for the Message Passing Interface in the Petaflops Era, University of Illinois at Urbana-Champaign, March 26, 2007.

OSG All Hands Consortium Meeting

OSG All Hands Consortium Meeting


from Monday 03 March 2008 (08:00)
to Thursday 06 March 2008 (18:00)
at
RENCI

Fermilab

>>>> Timetable:

Tuesday 04 March 2008 toptop


09:00->17:00 US ATLAS Transparent Distributed Facility workshop (Convener: Michael Ernst (Brookhaven National Laboratory) , Robert Gardner (University of Chicago) ) files agenda

09:00->17:00 US CMS Tier-3 workshop (Convener: Burt Holzman (Fermilab) , Brian Bockelman (University of Nebraska–Lincoln) ) files agenda

09:00->12:30 Biology Applications workshop (Convener: Maxim Potekhin (Brookhaven National Laboratory) , Mats Rynge (Renaissance Computing Institute) )
Description:
This workshop will have presentations on current biology efforts that use the Open Science Grid, discussions on what has worked well, obstacles, and ideas future improvements and better support for large scale computational efforts in the biosciences.

09:00 Biology Applications Workshop Introductions (15')
09:15 CompBioGrid (15')
09:45 SBGrid: Ian Stokes-Rees (15')
10:15 CHARMM (15')
10:45 GLOW (15')
11:00 Biology Applications Workshop Discussion (1h30')

Friday, February 15, 2008

WideShark: network protocol analyzer

Wireshark is the world's foremost network protocol analyzer, and is the de facto (and often de jure) standard across many industries and educational institutions.

Wireshark development thrives thanks to the contributions of networking experts across the globe. It is the continuation of a project that started in 1998.

Features

Wireshark has a rich feature set which includes the following:

  • Deep inspection of hundreds of protocols, with more being added all the time
  • Live capture and offline analysis
  • Standard three-pane packet browser
  • Multi-platform: Runs on Windows, Linux, OS X, Solaris, FreeBSD, NetBSD, and many others
  • Captured network data can be browsed via a GUI, or via the TTY-mode TShark utility
  • The most powerful display filters in the industry
  • Rich VoIP analysis
  • Read/write many different capture file formats: tcpdump (libpcap), Catapult DCT2000, Cisco Secure IDS iplog, Microsoft Network Monitor, Network General Sniffer® (compressed and uncompressed), Sniffer® Pro, and NetXray®, Network Instruments Observer, Novell LANalyzer, RADCOM WAN/LAN Analyzer, Shomiti/Finisar Surveyor, Tektronix K12xx, Visual Networks Visual UpTime, WildPackets EtherPeek/TokenPeek/AiroPeek, and many others
  • Capture files compressed with gzip can be decompressed on the fly
  • Live data can be read from Ethernet, IEEE 802.11, PPP/HDLC, ATM, Bluetooth, USB, Token Ring, Frame Relay, FDDI, and others (depending on your platfrom)
  • Decryption support for many protocols, including IPsec, ISAKMP, Kerberos, SNMPv3, SSL/TLS, WEP, and WPA/WPA2
  • Coloring rules can be applied to the packet list for quick, intuitive analysis
  • Output can be exported to XML, PostScript®, CSV, or plain text

http://www.wireshark.org/

Friday, February 8, 2008

GNOME Glib

_____________________________________________________

GNOME Glib Reference Manual:

http://library.gnome.org/devel/glib/stable/


String: http://library.gnome.org/devel/glib/stable/glib-String-Utility-Functions.html


Error Reporting:http://library.gnome.org/devel/glib/stable/glib-Error-Reporting.html


Glob-style pattern matching: http://library.gnome.org/devel/glib/stable/glib-Glob-style-pattern-matching.html


String Chunks: http://library.gnome.org/devel/glib/stable/glib-String-Chunks.html

_____________________________________________________



GNOME GLIB - GNU C library - C++ tutorial

GNOME Glib Library Reference:

http://library.gnome.org/devel/glib/stable/


GNU C library:

http://www.cs.utah.edu/dept/old/texinfo/glibc-manual-0.02/library_toc.html


GNU C Library Pattern Matching

http://www.gnu.org/software/libc/manual/html_node/Pattern-Matching.html#Pattern-Matching


GNU C Library Wildcard Matching

http://www.gnu.org/software/libc/manual/html_node/Wildcard-Matching.html#Wildcard-Matching


C++ tutorial:

http://www.cplusplus.com/doc/tutorial/inheritance.html


C++ reference:

http://www.cppreference.com/


C++ String:

http://www.cppreference.com/cppstring/index.html


C++ standard Components

http://uw713doc.sco.com/en/SDK_c++/CONTENTS.html


C++ string parse:

http://www.cprogramming.com/faq/cgi-bin/smartfaq.cgi?answer=1057105750&id=1044780608

Regular expression in C - regexex regcomp fnmatch

Parsing URL with regex: how it is done in apache

http://www.divms.uiowa.edu/~luke/xls/projects/regexp/regexp.html#NWcite-welch97:_pract_progr_tcl_tk

http://www.divms.uiowa.edu/~luke/xls/projects/regexp/regexp.html


Unix Programming Examples: Parsing Command Line - Regular expressions

http://mij.oltrelinux.com/devel/unixprg/#regex_notes


Regexex / regcomp

http://www.opengroup.org/onlinepubs/000095399/functions/regcomp.html


Fnmatch:

http://docs.hp.com/en/36430-90007/ch04s20.html


C++ string parse:

http://www.cprogramming.com/faq/cgi-bin/smartfaq.cgi?answer=1057105750&id=1044780608






#include
#include
#include
#include
#include
/* max error message length */
#define MAX_ERR_LENGTH 80

bool match( char * pattern, char * string );bool match( char * pattern, char * string ){
regex_t myre;
int err;
char err_msg[MAX_ERR_LENGTH];

/* compiles the RE. If this step fails, reveals what's wrong with the RE */
if ( (err = regcomp(&myre, pattern, REG_EXTENDED)) != 0 ) {
regerror(err, &myre, err_msg, MAX_ERR_LENGTH);
printf("Error analyzing regular expression '%s': %s - %s:%d\n", pattern, err_msg, __FILE__,__LINE__);
regfree(&myre);
return false;
}
if ( (err = regexec(&myre, string, 0, NULL, 0)) == 0 ) {
regfree(&myre);
return true;
}
if ( err != REG_NOMATCH ) {
/* this is when errors have been encountered */
regerror(err, &myre, err_msg, MAX_ERR_LENGTH);
printf("Error analyzing regular expression '%s' over '%s': %s - %s:%d\n", pattern, string, err_msg, __FILE__,__LINE__);

}
regfree(&myre);
return false;
}//match

Test_parseURL (){

regex_t re;
int error;
char *buffer="gsiftp://alo:90/lls/lsld/l";
regmatch_t pm[8];
(void) regcomp (&re, "^(([^:]+)://)?([^:/]+)(:([0-9]+))?(/.*)", REG_EXTENDED);
error = regexec (&re, &buffer[0], 6, &pm[0], 0);
printf("%d %d\n",pm[3].rm_so, pm[3].rm_eo);
}

GNU C Library Pattern Matching

http://www.gnu.org/software/libc/manual/html_node/Pattern-Matching.html#Pattern-Matching

GNU C Library Wildcard Matching

http://www.gnu.org/software/libc/manual/html_node/Wildcard-Matching.html#Wildcard-Matching

Thursday, February 7, 2008

Migol: A Fault Tolerant Grid Service Framework for Computational Applications in the Grid

A major challenge in a distributed, inherently dynamic Grid is fault tolerance. The more resources and components involved, the more complicated and error-prone becomes the system. In a Grid with potentially thousands of machines connected to each other the reliability of individual resources cannot be guaranteed. This talk discusses how the fault tolerance of long-running Grid applications can be ensured. Migol is a Grid middleware, which supports the fault tolerance of Grid applications. A key feature of Migol is the ability to transparently migrate parallel applications in the Grid. Migol comprises of different services for resource allocation, selection, and application and resource monitoring. The framework is based on open standards and is built on top of the Globus Toolkit 4. In addition, this talk will discuss methods to ensure the fault tolerance of critical infrastructure services. For example, Migol replicates critical services, such as the central information service and the monitoring services, using a ring-based replication protocol to achieve data consistency.

http://www.cct.lsu.edu/events/talks/314

Andre Luckow, University of Potsdam, Germany
February 07 2008 3:00 pm
Johnston Hall Room 338 CCT


Wednesday, February 6, 2008

High Performance SSH/SCP - HPN-SSH

SCP and the underlying SSH2 protocol implementation in OpenSSH is network performance limited by statically defined internal flow control buffers. These buffers often end up acting as a bottleneck for network throughput of SCP, especially on long and high bandwith network links. Modifying the ssh code to allow the buffers to be defined at run time eliminates this bottleneck. We have created a patch that will remove the bottlenecks in OpenSSH and is fully interoperable with other servers and clients. In addition HPN clients will be able to download faster from non HPN servers, and HPN servers will be able to receive uploads faster from non HPN clients. However, the host receiving the data must have a properly tuned TCP/IP stack.

HPN-SSH
- from Pitsburg SuperComputing Center - PSC
- presented in Mardi Gras Conference 2008