From chugunovamar@yahoo.ca Wed Mar 31 22:30:01 2004 Return-Path: Received: from postal.ac.brocku.ca (postal.ac.BrockU.CA [139.57.65.18]) by abacus.ac.BrockU.CA (8.9.3p2/8.9.3) with ESMTP id WAA20152476 for ; Wed, 31 Mar 2004 22:30:01 -0500 (EST) Received: from smtp011.mail.yahoo.com (smtp011.mail.yahoo.com [216.136.173.31]) by postal.ac.brocku.ca (8.12.10/8.12.10) with SMTP id i313UEua017129 for ; Wed, 31 Mar 2004 22:30:14 -0500 Received: from unknown (HELO mainxp) (chugunovamar@65.49.60.163 with login) by smtp011.mail.yahoo.com with SMTP; 1 Apr 2004 03:30:15 -0000 X-AntiVirus: Checked by Dr.Web [version: 4.31a, engine: 4.31b, virus records: 47933, updated: 28.03.2004] Message-ID: <003901c417b2$c47d9ac0$a33c3141@mainxp> From: "Chugunova Marina" To: "Thomas Wolf" References: <200402260350.WAA9682308@abacus.ac.BrockU.CA> <200403281557.KAA19452252@abacus.ac.BrockU.CA> <200403290419.XAA19526066@abacus.ac.BrockU.CA> Subject: Re: MPI Day Date: Wed, 31 Mar 2004 22:30:02 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=-4.8 required=6.0 tests=BAYES_00,RCVD_IN_SORBS autolearn=no version=2.63-brock-0.4 X-Spam-Checker-Version: SpamAssassin 2.63-brock-0.4 (2004-01-11) on postal.ac.BrockU.CA Status: R Hello Thomas, I have added below list of parallel libraries which my friends in Far East State University of Russia are using now for their parallel applications. Maybe it's useful for someone in Brock University. Danke schon for your kind meeting Marina a.. iPETSc PETSc, the Portable, Extensible Toolkit for Scientific computation, is a suite of uni- and parallel-processor codes for solving large-scale problems modeled by partial differential equations. PETSc employs the MPI standard for all message-passing communication. The code is written in a data-structure-neutral manner to enable easy reuse and flexibility. PETSc has been used for a variety of large-scaled applications, including transonic flow, modeling vortex dynamics in high-temperature superconductors, parallelization of a 3D magnetostatics code, and study of compressible flows at low and transonic Mach number. http://www.mcs.anl.gov/petsc/ a.. TAO. Toolkit for Advanced Optimization. The Toolkit for Advanced Optimization (TAO) is aimed at the solution of large-scale optimization problems on high-performance architectures. Our main goals are portability, performance, scalable parallelism, and an interface independent of the architecture. TAO is suitable for both single-processor and massively-parallel architectures. The current version of TAO has algorithms for unconstrained and bound-constrained optimization. We are working on extending the toolkit to nonlinearly constrained problems. http://www.mcs.anl.gov/tao/ a.. NAMD. NAMD, recipient of a 2002 Gordon Bell Award, is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. http://www.ks.uiuc.edu/Research/namd/ a.. XPLOR. X-PLOR is a program system for computational structural biology. X-PLOR stands for exploration of conformational space of macromolecules restrained to regions allowed by combinations of empirical energy functions and experimental data. But it also stands for exploration of modern concepts of structured programming in macromolecular simulation. ... X-PLOR's main focus is the three-dimensional structure determination of macromolecules using crystallographic diffraction or nuclear magnetic resonance (NMR) data. The program is based on an energy function approach: arbitrary combinations of empirical, geometric and effective energy terms describing experimental data may be used. The combined energy function can be minimized by a variety of gradient descent, simulated annealing, and conformational search procedures. http://xplor.csb.yale.edu/xplor/ > > Hope I will not get lost. > > Once you are in St Catharines, everyone knows Brock. > Once you are at Brock, everyone knows the Computer Commons :) > > Thomas >