From chemistry-request@server.ccl.net Sun Jan 9 12:13:45 2000 Received: from enterprise.cfu.net (root@enterprise.cfu.net [206.29.238.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA13887 for ; Sun, 9 Jan 2000 12:13:45 -0500 Received: from macmillan (dhcp70-152.vla2-e92.cfu.net [206.29.70.152]) by enterprise.cfu.net (8.9.3/8.9.3) with SMTP id LAA27391 for ; Sun, 9 Jan 2000 11:11:15 -0600 Reply-To: From: "James G. Macmillan" To: Subject: Summary on PC Cluster Software Date: Sun, 9 Jan 2000 11:11:13 -0600 Message-ID: <000301bf5ac4$893b06a0$98461dce@macmillan.cfu-cybernet.net> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2377.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Thanks to all that supplied information on software for parallel processing PC clusters. Several people show interest in a summary so here it is. I was very pleased with the number of responses. It appears that there are several commercial products. GAUSSIAN with the GaussView GUI (not required) HTTP://WWW.gaussian.com Schrodinger has TITAN (GUI) and Jaguar. TITAN is a SPARTAN GUI. HTTP://WWW.SCHRODINGER.COM Non-commercial products include GAMESS CHARM Peter Pulay's Parallel Quantum Solutions www.pqs-chem.com GROMACS parallel MD package http://md.chem.rug.nl/~gmx NWChem http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html There are many useful links to pages discussing Beowulf clusters. Again, Thanks to all, Jim ================= http://www.beowulf-underground.org http://sal.kachinatech.com/ These are two great sites that list a lot of applications that can run on a beowulf cluster. You might also want to search the boewulf/extreme linux mailing list archives as many announcements of applications have been made over both. -- Brian D. Haymore University of Utah Center for High Performance Computing 155 South 1452 East RM 405 Salt Lake City, Ut 84112-0190 Email: brian@chpc.utah.edu - Phone: (801) 585-1755 - Fax: (801) 585-5366 =============================== Hi Jim, I started a web site a couple of months back ( and haven't worked on it since ) dealing with "Beowulf clusters for chemists" you may find some useful information there. http://www.chem.arizona.edu/theochem/beowulf check the "what chemists are doing with their clusters" link Hope this helps -Don -- ++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Donald B. Kinghorn Theoretical and Computational Chemistry Group University of Arizona Tucson AZ 85721 kinghorn@u.arizona.edu (520)621-6761 ++++++++++++++++++++++++++++++++++++++++++++++++++ ======================================= Hi Jim, for Quantum Chemistry software running under Linux on our Cluster, take a look at http://www.chm.tu-dresden.de/edv/soft-lin.html (sorry, in german; but in most cases Links to Homepages are included). For real parallel computation, GAUSSIAN and GAMESS should work (but with different parallelization tools; LINDA vs. MPI or TCGMSG). Instead of this, we are using all the programs sequentially, managed by an batch system in our Linux cluster. Matthias -- Dr. Matthias Mann Fachrichtung Chemie der TU Dresden D-01069 Dresden, Mommsenstr. 13 Tel.: +49 (351) 463-4286 / Fax: -7030 Email: Matthias.Mann@chemie.tu-dresden.de ========================================= Dr. Macmillan, Gaussian 98 is supported on this type of cluster. We utilize the LINDA software from Scientific Computing Associates(SCA) to simulate shared memory and interprocess communication. The combination of G98 + Linda scales quite well for HF, DFT, CI-singles and even MP2 energies and gradients. We published a report about G94 on Cray T3E systems which demonstrates the scalability, of course the actual per CPU time varies by platform, in J. Comp. Chem. vol. 19, pp 1053 (1998) which will give you a good idea of what you can expect. The LINDA software is normally licensed on a per-process basis but we have made an arrangement with SCA which permits use of G98+Linda on any number of processors so it is a cost effective combination for this type of Parallel Cluster. If you would like a proper quote please send a request to fo@gaussian.com. If you have more specific technical questions let me know at help@gaussian.com. ======================================================= Schrodinger markets JAGUAR for Linux. Wavefunction markets TITAN, sort of Spartan with a hook to Jaguar,.. for NT, however. JAGUAR V4/Linux will be out at end of month. There is a Gui for it on the way. John McKelvey ======================================= Well for semi-empirical and ab initio modeling there's GAMESS, Gaussian, and Jaguar that all run under linux. You might check out the site http://chpc06.ch.unito.it/chem_linux.html, this gives a good listing of software running on linux. hope this helps, -david David Reichert, Ph.D. Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd@mir.wustl.edu voice: (314) 362-8461 fax: (314) 362-9940 =========================================================== Hello, James: For a good parallelized quantum package that is already optimized for PVM under Linux, I suggest the code from Peter Pulay's Parallel Quantum Solutions (www.pqs-chem.com). Best wishes, Brian Teppen ===================================== Dear Dr. Macmillan: Since you are working in the Dept. of Chemistry I thinks at least you can use CHARMM and GAMESS with the Beowulf cluster! Please check the link listed below, http://www.lobos.nih.gov/apps_frame.html Joe HCHuang@uh.edu ============================== GROMACS parallel MD package http://md.chem.rug.nl/~gmx Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ================================================== If the cluster is reasonably big, try NWChem. Single-node performance is not impressive, but it's very efficiently parallelized. Runs on Linux, and is free (subject to a user agreement). Have a look at http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html Don't know if parallel Gaussian is available for Linux. Check their web page (www.gaussian.com). Btw., I think it IS of general interest, so you might summarize some of the replies you get. Regards, Herbert ============================================== *********************************************** James G. Macmillan 1419 Laurel Cir. Cedar Falls, IA 50613 E-Mail macmillan@uni.edu Web http:\\www.cns.uni.edu\~macmilla ********************************************* "Making good wine is a science, making fine wine is an art" - Robert Mondavi From chemistry-request@server.ccl.net Sun Jan 9 18:24:06 2000 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA15334 for ; Sun, 9 Jan 2000 18:24:06 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id RAA10438 for ; Sun, 9 Jan 2000 17:22:39 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.1b+Sun/8.9.1) id RAA08911 for chemistry@www.ccl.net; Sun, 9 Jan 2000 17:22:39 -0600 (CST) Date: Sun, 9 Jan 2000 17:22:39 -0600 From: John Stone To: chemistry@server.ccl.net Subject: Announce: VMD 1.4 Released Message-ID: <20000109172239.A8881@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i VMD "Visual Molecular Dynamics" 1.4 Announcement ------------------------------------------------ The Theoretical Biophysics group at the Beckman Institute For Advanced Science and Technology, the University of Illinois (U-C), is proud to announce the public release of VMD 1.4. VMD is a package for the visualization and analysis of biomolecular systems. This software is distributed free of charge and includes source code, documentation, and precompiled binaries for IBM, HP, Linux, Sun, and SGI Unix systems, as well as Microsoft Windows 95/98/NT. The VMD documentation includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer. VMD development is supported by the NIH National Center for Research Resources. A full description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ The authors request that any published work which utilizes VMD includes a reference to the VMD web page and/or the following reference: Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. The Theoretical Biophysics group encourages VMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. We are eager to hear from you, and thank you for using our software! John Stone vmd@ks.uiuc.edu January 7, 2000 -- Theoretical Biophysics Group Email: johns at ks.uiuc.edu Beckman Institute http://www.ks.uiuc.edu/~johns/ University of Illinois Phone: (217) 244-3349 405 N. Mathews Ave FAX: (217) 244-6078 Urbana, IL 61801, USA Unix Is Good For You!!!