From jim at ks.uiuc.edu Wed Sep 6 18:00:53 2000 From: jim at ks.uiuc.edu (Jim Phillips) Date: Tue Nov 9 01:14:19 2010 Subject: [Beowulf-announce] NAMD 2.2b1 Release Announcement Message-ID: Hi, NAMD is free software for parallel biomolecular MD calculations. It uses latency tolerant algorithms, making it ideal for Beowulf class machines. -Jim +--------------------------------------------------------------------+ | | | NAMD 2.2b1 Release Announcement | | | +--------------------------------------------------------------------+ September 5, 2000 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.2b1 has several advantages over NAMD 2.1: - Parallelized particle mesh Ewald FFT and reciprocal space sum with demonstrated scaling to 128 processors for large systems. - Release binaries contain FFTW (under special license) for better serial performance when using particle mesh Ewald. - Much faster minimizer based on conjugate gradient method, also more stable when dealing with very bad initial contacts. - Improved load balancer with demonstrated scaling to over 1024 processors for large cutoff systems. This is a beta release! Please be on the lookout for bugs, memory leaks, and instabilities of all kinds and report them immediately. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From pls at takayama.jpl.nasa.gov Wed Sep 6 19:10:00 2000 From: pls at takayama.jpl.nasa.gov (Paul Springer) Date: Tue Nov 9 01:14:19 2010 Subject: [Beowulf-announce] Matpar: Parallel Extensions for MATLAB Message-ID: <200009062152.OAA08803@takayama.jpl.nasa.gov> Matpar version 1.2 is now publicly available. This version runs on Beowulf computers, and requires PVM 3.4.3 or later. Matpar is a client/server software package that allows a MATLAB user on a Sun to spawn certain lengthy MATLAB operations to a Beowulf computer for better speed. The web page for Matpar is http://hpc.jpl.nasa.gov/PS/MATPAR ------------------ Paul Springer High Performance Computing Group Jet Propulsion Laboratory pls@jpl.nasa.gov From jim at ks.uiuc.edu Tue Sep 19 12:39:34 2000 From: jim at ks.uiuc.edu (Jim Phillips) Date: Tue Nov 9 01:14:19 2010 Subject: [Beowulf-announce] NAMD 2.2b2 Release Announcement Message-ID: Hi, NAMD uses latency-tolerant algorithms, making it ideal for Beowulf-class machines. (It runs pretty well on the Cray T3E too.) This is the first release to include support for Windows NT (98 etc. are untested), not to imply that anyone on the Beowulf list would be interested in that. -Jim +--------------------------------------------------------------------+ | | | NAMD 2.2b2 Release Announcement | | | +--------------------------------------------------------------------+ September 15, 2000 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.2b2 has several advantages over NAMD 2.1: - New ports to the IBM RS/6000 SP and Windows NT. - Parallelized particle mesh Ewald FFT and reciprocal space sum with demonstrated scaling to 128 processors for large systems. - Release binaries contain FFTW (under special license) for better serial performance when using particle mesh Ewald. - Much faster minimizer based on conjugate gradient method, also more stable when dealing with very bad initial contacts. - Improved load balancer with demonstrated scaling to over 1024 processors for large cutoff systems. This is a beta release! Please be on the lookout for bugs, memory leaks, and instabilities of all kinds and report them immediately. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From pls at takayama.jpl.nasa.gov Tue Sep 19 20:45:52 2000 From: pls at takayama.jpl.nasa.gov (Paul Springer) Date: Tue Nov 9 01:14:19 2010 Subject: [Beowulf-announce] Support for Beowulf clusters in PVM 3.4.3 Message-ID: <200009192106.OAA13052@takayama.jpl.nasa.gov> There was some trouble in sending this out the first time, so I am repeating the post. I apologize if you've already received this. The latest release of PVM, 3.4.3, contains code I've written to support Beowulf clusters. In particular, it has been added in as one of the supported MPP architectures, under the name BEOLIN. This allows the Beowulf cluster to be seen by outside computers as a single parallel machine. When a user spawns tasks to the Beowulf, each task will automatically be put on its own node. This will work even when the main PVM host is running on a computer separate from the Beowulf, and the Beowulf nodes are on an internal network. Only the "front-end" Beowulf node needs to be visible to the outside world. Under this architecture pvmd daemons are not run on each node--only a single daemon runs on the "front-end" node. Additional details appear in a README file included with the release. Paul ------------------ Paul Springer High Performance Computing Group Jet Propulsion Laboratory From jim at ks.uiuc.edu Tue Sep 26 17:29:33 2000 From: jim at ks.uiuc.edu (Jim Phillips) Date: Tue Nov 9 01:14:19 2010 Subject: [Beowulf-announce] NAMD 2.2b3 Release Announcement Message-ID: Hi, NAMD runs on everything from workstation clusters to ASCI Red. This should be the last beta before 2.2 final. Please have a look. -Jim +--------------------------------------------------------------------+ | | | NAMD 2.2b3 Release Announcement | | | +--------------------------------------------------------------------+ September 25, 2000 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.2b3 has several advantages over NAMD 2.1: - New ports to the IBM RS/6000 SP and Windows NT. - Parallelized particle mesh Ewald FFT and reciprocal space sum with demonstrated scaling to 128 processors for large systems. - Release binaries contain FFTW (under special license) for better serial performance when using particle mesh Ewald. - Much faster minimizer based on conjugate gradient method, also more stable when dealing with very bad initial contacts. - Improved load balancer with demonstrated scaling to over 1024 processors for large cutoff systems. This is a beta release! Please be on the lookout for bugs, memory leaks, and instabilities of all kinds and report them immediately. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software!