From chemistry-request@server.ccl.net Wed May 2 10:50:22 2001 Received: from gate.syntem-sa.fr ([146.19.248.65]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42EoLI29219 for ; Wed, 2 May 2001 10:50:21 -0400 Received: (from uucp@localhost) by gate.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) id QAA04466 for <@firewall.syntem-sa.fr:chemistry@ccl.net>; Wed, 2 May 2001 16:49:13 +0200 (MDT) Received: from syntem-sa.fr(10.0.0.2) by gate.syntem-sa.fr via smap (4.1) id xma004448; Wed, 2 May 01 16:48:31 +0200 Received: from victoria.syntem-sa.fr (victoria.syntem-sa.fr [10.0.0.44]) by laetitia.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id QAA02447 for <@laetitia.syntem-sa.fr:chemistry@ccl.net>; Wed, 2 May 2001 16:45:48 +0200 (MDT) Received: from syntem-sa.fr (localhost [127.0.0.1]) by victoria.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id QAA11752 for ; Wed, 2 May 2001 16:51:57 +0200 (MDT) Sender: dturner@syntem-sa.fr Message-ID: <3AF01F0D.1EA63F8A@syntem-sa.fr> Date: Wed, 02 May 2001 16:51:57 +0200 From: David Turner Reply-To: dturner@syntem.com Organization: Computational Drug Design, Syntem X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "'chemistry@ccl.net'" Subject: Critical T scores References: <45EE82EFB176D311815F0000F8CD235402C78168@fszhtv48.ml.wpafb.af.mil> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does anyone know where I can get a table of critical student's t-scores in electronic format? Thanks Dave -- ________________________________________________________________ David Turner Synt:em Senior Modeling Scientist Parc Scientifique G.Besse Computational Drug Discovery 30000 Nimes email: dturner@syntem.com France Tel: Switchboard: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 Direct Line: +33 (0)4 66 04 22 85 ________________________________________________________________ Discover New Drugs, Discover Synt:em http://www.syntem.com ________________________________________________________________ From chemistry-request@server.ccl.net Wed May 2 12:23:32 2001 Received: from mail-d.bcc.ac.uk ([144.82.100.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42GNVI29964; Wed, 2 May 2001 12:23:31 -0400 Received: from dns (actually host oganov-jpb98.geol.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (Mailer); Wed, 2 May 2001 17:23:28 +0100 Reply-To: "a.oganov" From: "Artem R. Oganov" To: chemistry Cc: chemistry-request Subject: CCL: energy levels of Fe atom and Fe2+ ion Date: Wed, 2 May 2001 17:21:47 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 1 (Highest) X-MSMail-Priority: High X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: High X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear CCLers, I would be very happy to hear about any available tables of energy levels of Fe atom (ground state) and Fe2+ ion - both experimental and theoretical. I need a quantitative information about d-level splitting associated with spin polarisation. I will summarise on request. Thanks a lot, Artem ----------------------------------------------------- Artem R. Oganov Department of Geological Sciences University College London Gower Street London WC1E 6BT tel: +44 (020)-7679-3344 fax: +44 (020)-7387-1612 email: a.oganov@ucl.ac.uk http://slamdunk.geol.ucl.ac.uk/~artem --------------------------------------------------- From chemistry-request@server.ccl.net Wed May 2 01:26:50 2001 Received: from mercury.chem.nwu.edu (root@[129.105.116.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f425QoI24404 for ; Wed, 2 May 2001 01:26:50 -0400 Received: from [129.105.186.208] (pistachio-32-186208.nuts.nwu.edu [129.105.186.208]) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id f425Qfv12721; Wed, 2 May 2001 00:26:41 -0500 (CDT) Mime-Version: 1.0 X-Sender: hutchisn@mercury.chem.northwestern.edu (Unverified) Message-Id: In-Reply-To: <3AEF0D6E.56D1051D@dedalus.lcc.ufmg.br> References: <3AEF0D6E.56D1051D@dedalus.lcc.ufmg.br> Date: Wed, 2 May 2001 00:19:08 -0500 To: irwin From: Geoff Hutchison Subject: Re: CCL:Where obtain the g++ compiler free? Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" At 4:24 PM -0300 5/1/01, irwin wrote: >and/or can help me with these things? Where obtain the g++ compiler free? g++, g77, gcc, gcj and company are all part of the GCC package (GNU Compiler Collection) and is free in just about all senses of the word since they're covered by the GNU GPL. You may find the latest version at Cheers, -- -- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.nwu.edu/ From chemistry-request@server.ccl.net Wed May 2 07:30:37 2001 Received: from chemik.chem.univ.gda.pl ([153.19.29.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42BUVI27882 for ; Wed, 2 May 2001 07:30:35 -0400 Received: from localhost (adam@localhost) by chemik.chem.univ.gda.pl (8.9.3+Sun/8.9.3) with ESMTP id NAA21905; Wed, 2 May 2001 13:30:36 +0200 (CEST) Date: Wed, 2 May 2001 13:30:36 +0200 (CEST) From: Adam Liwo To: cc: Adam Liwo Subject: Summer school on "Parallel computing in biomolecular simulations" in Gdansk Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ___________________________________________________________________________ | | | SUMMER SCHOOL ON | | | | PARALLEL COMPUTING IN BIOMOLECULAR SIMULATIONS | | | | | | organized by | | | | | | Faculty of Chemistry, University of Gdansk, Poland | | | | Academic Computer Center in Gdansk TASK, Poland | | | | Interdisciplinary Center of Mathematical and Computer Modeling | | (ICM) University of Warsaw, Poland | | | | INTEL Poland | | | | | | Held in conjunction with the annual meeting of the | | Polish Society of Computational Simulations, 28.08 - 01.09, 2001. | | | | | | | | Saturday, September 1 - Monday, September 3, 2001 | | Technical University of Gdansk, Gdansk, Poland | | | | | |___________________________________________________________________________| | | | Second Announcement | | | | Registration Form - Call for Contributed Papers | | | | ________________________________________________________________________ | | | | Web page: http://www.task.gda.pl/ptsk-2001/biomol.html | |___________________________________________________________________________| AIMS Computational molecular biology and computational chemistry play a still increasing role in contemporary science, medicine, agriculture, and industry. With the advent of high-speed parallel computers it appears now possible to calculate the pathways of complex chemical reactions, predict the reactivity of chemical compounds, predict the structure and properties of crystalline, glassy and metallic systems, predict the structure of proteins and nucleic acids, and simulate cellular processes at the molecular level. This finds numerous applications in the design of novel drugs, materials, fuels, etc. The purpose of this summer school is to give an overview of the techniques and software used in modern computational chemistry and molecular biology, as well as to give an insight into the problems that are currently being investigated by the scientists working in this field. Special attention will be devoted to the use of parallel computers. The formula of the summer school should encourage participation of researchers, students and industry engineers. LOCATION The Summer school on "Parallel computing in biomolecular simulations" will be held on 01-03.09.2001 on the premises of the Technical University of Gdansk. The town of Gdansk is situated at the coast of the Baltic Sea, with an international airport 20 minutes driving > from the city, good rail and road connections with major cities in Poland and Europe, and ferry links with Scandinavia. Gdansk is one of the most impressive industrial, historic and tourist sites in Poland. It is a center of shipping, ship-building, commerce as well as chemical, electronic, telecommunication and food industry. In 1997, Gdansk celebrated its Millennium. Throughout turbulent times of the twentieth century, Gdansk was a bone of contention at the eve of the second world war. More recently, it was a cradle of the Solidarity movement which inspired the process of political and economic transformations in Central and Eastern Europe. Gdansk offers a variety of places of cultural interest, including old town architecture, museums, churches, and also places for shopping and leisure. TOPICS The topics of the summer school "Parallel computing in biomolecular simulations" will include the following: 1. Quantum chemistry (ab initio and semiempirical methods): o prediction of properties of inorganic and organic compounds and materials; o reaction path calculations; o quantum mechanics of biomolecular systems; o photochemical and radiative processes, including DNA damage and repair. 2. Global optimization in the prediction of the structure of peptides, proteins, and crystals. 3. Inclusion of solvation in quantum-mechanical calculations and empirical force fields. 4. Effect of pH on protein conformation. 5. Homology modeling and threading in the prediction of protein structure. 6. Software demonstration: AMBER, ECEPPAK, CRYSTALG, UNRES, GAMESS, MCSYM, and other. KEYNOTE AND INVITED LECTURES Dr. Piotr Bala, Nicholas Copernicus University, Poland - "Parallelism in classical and quantum-classical molecular dynamics". Prof. Maciej S. Gutowski, Pacific National Laboratories, USA - "Stabilization of the zwitterionic forms of amino acids by an excess electron in the gas phase". Prof. Jooyoung Lee, Korea Institute for Advanced Study, Korea - "Massively parallel computation and conformational space annealing method". Prof. Bogdan Lesyng, ICM, Poland - TBA. Prof. Andrzej Kolinski, University of Warsaw, Poland - "Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, lattice and off-lattice modeling for protein structure prediction". Prof. Gregory V. Nikiforovich, Washington University, USA - "Restoring small, medium and large (up to 60 residues) loops in proteins". Dr. Krzysztof Olszewski, Molecular Simulations Inc., USA - "Automated knowledge extraction from predictive structural models". Prof. Lucjan Piela, University of Warsaw, Poland - "Deformation methods in global optimization". Dr. Jaroslaw Pillardy, Cornell University, USA - "Structure prediction by global optimization of a potential function: proteins, polypeptides, and crystals". Dr. Daniel R. Ripoll, Cornell University, USA - "The ECEPPAK program for conformational analysis of peptides and proteins". Prof. Irena Roterman, Jagiellonian University, Poland - "Capabilities and restrictions of molecular dynamics". Prof. Harold A. Scheraga, Cornell University, USA - TBA. Dr. Mark D. Shenderovich, Structural Bioinformatics Inc., USA - "Computational phenotyping of HIV protease - inhibitor complexes". Prof. Jeffrey Skolnick, Danforth Plant Sciences Center, USA - "Genome scale prediction of protein structure and function". Prof. Andrzej Sokalski, Technical University of Wroclaw, Poland - "Modeling interactions in large molecular systems and inhibitor design". Prof. Jorge A. Vila, Universidad Nacional de San Luis, Argentina - "Theoretical study of linear tetrapeptides in solution. A test of different solvation models". SCIENTIFIC COMMITTEE Prof. Andrzej Kolinski, University of Warsaw, Poland; Prof. Jooyoung Lee, Korea Institute for Advanced Study, Korea; Prof. Bogdan Lesyng, ICM, Poland; Prof. Adam Liwo, University of Gdansk, Poland; Prof. Gregory V. Nikiforovich, Washington University, USA; Prof. Lucjan Piela, University of Warsaw, Poland; Dr. Daniel R. Ripoll, Cornell University, USA; Prof. Irena Roterman, Jagiellonian University, Poland; Prof. Harold A. Scheraga, Cornell University, USA; Dr. Mark D. Shenderovich, Structural Bioinformatics Inc., USA; Prof. Jeffrey Skolnick, Danforth Plant Sciences Center, USA; Prof. Jorge A. Vila, Universidad Nacional de San Luis, Argentina. ORGANIZING COMMITTEE Prof. Adam Liwo, Gdansk, Poland (Chairman); Dr. Jaroslaw Rybicki, Gdansk, Poland (V-ce Chairman); Dr. Sylwia Rodziewicz-Motowidlo, MSc. Bartosz Pliszka, Gdansk, Poland (Secretaries); Dr. Cezary Czaplewski, Gdansk, Poland; Dr. Stanislaw Oldziej, Gdansk, Poland; Prof. Bogdan Lesyng, Warsaw, Poland. LANGUAGE The official language of the Summer School will be English. ABSTRACT SUBMISSION Abstracts can be submitted by one of the following three ways: o By regular mail to: Dr. Sylwia Rodziewicz-Motowidlo, Faculty of Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk, Poland. Please submit two copies of your abstract. The sheet(s) must not be folded to enable direct reproduction. LATEX and Word templates for abstract preparation are available on the Conference web site. An ASCII version of the template with instructions is also attached to this announcement. o By e-mail to biomol@task.gda.pl. The subject line should begin with the word ABSTRACT and contain the name of the corresponding author. The electronic version of the abstract, together with all pertaining graphics files, should be included as an attachment. Virtually all mailers, such as pine or Netscape Mail contain the attachment utility. If you use an old-style mailer, encode the binary files for for 7-bit transmission, using the UNIX or DOS uuencode utility and include the uuencoded files in the body of the message. Abstracts prepared with LATEX, which are in ASCII format can be included in the message body directly. Any DOS, Windows or Unix-compatible word processor can be used. Using MacIntosh word processors is discouraged to avoid the risk of misconversion. Microsoft Word, LATEX, and WordPerfect are recommended. All non-standard stylevles used when preparing the abstract with LATEX must be included with the abstract. o On-line submission using the Conference web site: (http://www.task.gda.pl /ptsk-2001/biomol/submit.html). Follow the instructions of the submission form. PUBLICATION Both lecturers and other participants will be asked to contribute a paper to a special issue of TASK Quarterly. All manuscripts will undergo regular peer-reviewing process. See http://www.task.gda.pl/quart/ for instructions for authors. ACCOMMODATION For participants who wish so accommodation will be provided in Student Hostel DS1 (hotel standard; located within walking distance from the Technical University of Gdansk) at a cost of 55 zl (approximately $14) per night. The address is: ul. Traugutta 115 80-266 Gdansk Wrzeszcz, tel. +48 58 347-15-97. The participants of the PTSK (Polish Society of Computer Simulation) Workshops who wish to take part in the School can be accommodated in the Workshops site at Sobieszewo or in the DS1 Students Hostel. For participants who prefer to stay elsewhere, the organizers can assist in arranging hotel accommodation; please indicate in the registration form, if you wish so. Below are the addresses and phone numbers of the hotels located near the School site. "SZYDLOWSKI" ul. Grunwaldzka 114, (+48 58) tel. 345-70-40 - 370 zl single room, 420 zl double room. "HEVELIUS" Orbis S.A. ul. Heweliusza 22, tel. 321-00-00 - 420 zl single room, 515 zl double room. "HOLIDAY INN" ul. Podwale Grodzkie 9, tel. 300-60-00, fax 300-60-11 e-mail: smm@holidayinn.gdansk.pl, web page: http://www.holidayinn.pl/gdansk/ - 150 ECU (550 zl) single room, 180 ECU (650 zl) double room; the rates on weekends are 180 ECU (380 zl) and 126 ECU (450 zl), respectively. "JANTAR" ul. Dlugi Targ 19, tel. (+48 58) 301-95-32 - 80 zl per person (single and double rooms; breakfast included). "RO-KO" ul. Traugutta 29, (+48 58) tel. 347-77-88 - 100 zl double room, 132 zl triple room. Follow the "Turystyka" link of http://www.gdansk.pl/ for more hotel information. SOCIAL EVENTS Welcome Party and Conference Dinner are planned on September 1 and September 3, respectively. Depending on the number of those interested, a sightseeing trip to the Old Town of Gdansk and/or other interesting places (the curort of Sopot, the Marine Life Museum in Gdynia) will be organized. A special sightseeing program for accompanying persons will be organized (costs included in accompanying persons' registration fee). TRAVEL Gdansk (Danzig) is a part of the Gdansk-Sopot-Gdynia Tricity chain located at southern Baltic. Gdansk's airport Rebiechowo is ~10-15 km away > from the city center and serves limited international `ights (e.g., from and to London, Hamburg, and Copenhagen), as well as domestic `ights from and to Warsaw, whose international Okecie airport serves worldwide connections by air. There is also a reliable express and InterCity train service between Warsaw and Gdansk (4 h trip) and direct train connections with Berlin (9 h trip). Trains between Warsaw and Gdansk run every hour during daytime. FEE The complete fee is 700 zl (180 USD) and 415 zl (104 USD) for undergraduate and graduate students, as well as academic employees below Ph.D. degree. The fee covers regi stration, accommodation in DS1 Students Hostel (see "Accommodation"), and meals at the Technical University of Gdansk caffeteria. Participants who do not wish to stay at the DS1 Students Hostel pay 535 zl (138 USD) or 250 zl (63 USD), respectively. Important: Participants of PTSK Workshops (August 30, September 1, 2001) can participate in this Summer School at a fee of 400 zl covering the cost of additional accommodation in the Workshops site at Sobieszewo or in the vicinity of the School site. Those persons DO NOT pay the registration and accommodation fee specived above. For information about the Workshops see http://www.task.gda.pl/ptsk-2001/ Payment should be made by bank transfer to Wydzial FTiMS PG, ul. Narutowicza 11/12, 80-952 Gdansk, Poland Summer school on "Parallel computing in biomolecular simulations" bank account: Wielkopolski Bank Kredytowy SA, Oddzial Gdansk 10901098-2903-128-00-0. with the annotation "Zadanie nr 014772" (very important!). Also, indicate the names of persons paid for. REGISTRATION Participants can register by filling out the attached form. Mail the form together with a copy of bank transfer record to: Dr. Sylwia Rodziewicz-Motowidlo Secretary, Summer School "Parallel computing in biomolecular simulations" Faculty of Chemistry, University of Gdansk ul. Sobieskiego 18, 80-952 Gdansk, Poland tel. +48 58 345 0361, fax +48 58 341 0357 The other option is to register on line at http://www.task.gda.pl/ptsk-2001/biomol/registration.html. If so, mail or fax the copy of bank transfer record to the address given above. On-line registration will open on May 9, 2001. CORRESPONDENCE All regular-mail correspondence should be directed to the address printed above. E-mail should be sent to biomol@task.gda.pl. The web page of the School is: http://www.task.gda.pl/ptsk-2001/biomol.html PRESENTATIONS Poster stands will be provided for poster sessions. Visual equipment: overhead and slide projectors, as well as a computer projector will be provided for oral presentations. An IMB PC machine with Windows/Linux systems will be available for computer presentations. IMPORTANT DEADLINES o Abstract submission - July 15, 2001. o Registration & Payment - July 22, 2001. ________________________________cut here_____________________________________ Registration and Accommodation Form SUMMER SCHOOL ON Parallel computing in biomolecular simulations September 1 - September 3, 2001, Gdansk, Poland Family Name ______________________________________________________________ Given Name _______________________________________________________________ Title: Prof.___ Dr.___ MSc.___ Mr.___ Mrs.___ Ms.___ Institution________________________________________________________________ Mailing address____________________________________________________________ ___________________________________________________________________________ Country_____________Postal Code____________________________________________ E-mail ____________________________________________________________________ * Presentation preference oral ___ poster ___ # Regular registration fee _______________________________________ 535zl ___ or student's & young scientist registration _____________________ 250zl ___ Accompanying person(s) _______________________________________ x 200 zl ___ Accommodation at DS1 Students Hostel (Sept.1-Sept.3, 2001) ___ x 165 zl ___ Extra night Aug. 29/Sept. 1 + supper __________________________ x 70 zl ___ Total payment ______________________________________________________ zl ___ Please pay by bank transfer to Wielkopolski Bank Kredytowy SA, Oddzial Gdansk, 10901098-2903-128-00-0; account owner: Wydzia_l FTiMS PG ul. Narutowicza 11/12 80-952 Gdansk, Poland with annotation "Zadanie nr 014772" (very important!). Include the list of persons paid for. Need hotel reservation ___ Preferred hotel (list in decreasing order; see p .5 for hotels located closely to the School site) ___________________ ___________________________________________________________________________ Date of Arrival________________________________Date of Departure___________ If you will arrive by plane in Gdansk, give arrival time and flight number ___________________________________________________________________________ Sightseeing tours: Old Town of Gdansk ___ Westerplatte ___ Oliva Cathedral (including organ concert) ___ Sopot curor ___ Marine Life Museum in Gdynia ___ (tours will be paid on site) Food preferences: Kosher ___ Vegetarian ___ Diet ___ Other (please describe): ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ Special wishes/Remarks ____________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ Date________________Signature______________________________________________ MAIL OR FAX THE FORM & A COPY OF BANK-TRANSFER RECORD TO: Dr. Sylwia Rodziewicz-Motowidlo, Secretary, Summer School "Parallel computing in biomolecular simulations", Faculty of Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk, Poland, FAX: +48 58 341 0357 or e-mail the form to biomol@task.gda.pl (this address will become active on May 9, 2000) and mail or fax a copy of bank-transfer record to the address above. ----- * For those interested in presenting a contribution. Final selection of contributions for oral presentations will be made by the Scientific Committee. # Registered participants of PTSK workshops (August 30 - September 1, 2001) do not pay the above fee; instead they add 400 zl to their PTSK workshop registration fee. See http://www.task.gda.pl/ptsk-2001/ for more information. _____________________________________________________________________________ Web page: http://www.task.gda.pl/ptsk-2001/biomol.html e-mail: biomol@task.gda.pl (will become active on May 9, 2001) ------------------------------------- Dr. Adam Liwo Faculty of Chemistry University of Gdansk Sobieskiego 18 80-952 Gdansk, Poland phone: +48 58 345-0361 fax: +48 58 341-0357 e-mail: adam@chemik.chem.univ.gda.pl From chemistry-request@server.ccl.net Wed May 2 13:52:10 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42HqAI30545 for ; Wed, 2 May 2001 13:52:10 -0400 Received: from sun1.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Wed, 2 May 2001 19:52:08 +0200 Received: from localhost (ui22204@localhost) by sun1.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id TAA10821 for ; Wed, 2 May 2001 19:52:06 +0200 (MET DST) X-Authentication-Warning: sun1.lrz-muenchen.de: ui22204 owned process doing -bs Date: Wed, 2 May 2001 19:52:06 +0200 (MET DST) From: Eugene Leitl X-X-Sender: To: Subject: Re: Athlon SDR/DDR stats for *specific* gaussian98 jobs (fwd) Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Wed, 2 May 2001 12:53:17 -0400 (EDT) From: Mark Hahn To: Velocet Cc: beowulf@beowulf.org Subject: Re: Athlon SDR/DDR stats for *specific* gaussian98 jobs > the same duron on a DDR board w/256Mb DDR RAM (talk about a waste! :) well, a duron has the same dram performance as a tbird at the same FSB. so in that sense, it's actually a better match for a lot of computational codes that sneer at cache. otoh, tbirds are dirt cheap, not much more than durons. > I havent had a chance to run any of these on a P4 with SSE3 (is that the sse2. gcc 3.0 snapshots apparently can generate sse2 code... > in contributing such stats I'm very interested.) My stats here were generated > with ATLAS compiled for each change in config. does ATLAS include prefetching? it's fairly astonishing how big a difference prefetching (and movntq) can make on duron/athlon code. for an extreme case (Arjan van de Ven's optimized page-copy and -zero): 600.044 MHz clear_page 'normal_clear_page' took 8429 cycles (278.0 MB/s) clear_page 'slow_zero_page' took 8451 cycles (277.3 MB/s) clear_page 'fast_clear_page' took 7341 cycles (319.3 MB/s) clear_page 'faster_clear_page' took 2576 cycles (909.7 MB/s) clear_page 'even_faster_clear' took 2573 cycles (910.8 MB/s) copy_page 'normal_copy_page' took 8237 cycles (284.5 MB/s) copy_page 'slow_copy_page' took 8238 cycles (284.5 MB/s) copy_page 'fast_copy_page' took 5798 cycles (404.2 MB/s) copy_page 'faster_copy' took 3046 cycles (769.3 MB/s) copy_page 'even_faster' took 3077 cycles (761.6 MB/s) that's on a duron/600 (100 ddr fsb), kt133, cas2 PC133. I haven't seen results from a ddr dram system yet. > There are some caveats and other environmental factors discussed on > the page as well. error bars would be nice. > I am not trying to start a jihad here against high speed Thunderbird > and Dual Thunderbird proponents; this is just what i've found for *MY* maybe I'm being dense, but how would these results be interpreted jihadically? in general, they show two things: high-end machines bear a price-premium that decreases their speed/cost merit, and that freebsd's page coloring sometimes has a measurable benefit. I'm dubious about further interpretation, though. for instance, you seem to show a significant benefit to tbird's larger cache (384 vs 192K), but surely you chose this workload to be bandwidth intensive, didn't you? if not, then the DDR comparison is rather specious... thanks for posting the numbers! regards, mark hahn. _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf From chemistry-request@server.ccl.net Wed May 2 14:58:26 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42IwQI31064 for ; Wed, 2 May 2001 14:58:26 -0400 Received: from demetrio.ifi.unicamp.br (128.196.86.129) by deimos.email.Arizona.EDU (5.1.056) id 3AD79C9600178B59 for CHEMISTRY@ccl.net; Wed, 2 May 2001 11:58:25 -0700 Message-Id: <5.0.2.1.0.20010502233646.00b2acb0@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Wed, 02 May 2001 23:46:57 -0700 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: CI-S geometry optimizations Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, I want to optimize the geometry of the ground state, the first excited triplet state and the first excited singlet state of a molecule. I tried to do that using G98 and the CI-S methodology. I specified the following keywords: #p opt cis=(direct,Root=0)/3-21G* -> for ground state (GS). #p opt cis=(direct,Root=1,Singlets)/3-21G* -> for first excited singlet state (S1). #p opt cis=(direct,Root=1,Triplets)/3-21G* -> for first excited triplet state (T1). Is that right? I am confused because as result I got : E(GS) = E(S1) > E(T1) and it is completely different that what I expected (i.e E(T1) > E(S1) > E(GS) ). I don't know if I can expect that CI-S will give me the right order of those states. Does anybody have experience with this problem? As I have the geometries for those states, I can do a single point calculation and try to get a reasonable energy. Does anybody have a suggestion on which methodology I should use? Thanks in advance, Demetrio Filho From chemistry-request@server.ccl.net Wed May 2 15:18:37 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42JIbI31244 for ; Wed, 2 May 2001 15:18:37 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id PAA60555; Wed, 2 May 2001 15:06:22 -0400 (EDT) Date: Wed, 2 May 2001 15:06:22 -0400 From: Rick Venable To: David Turner cc: "'chemistry@ccl.net'" Subject: Re: CCL:Critical T scores In-Reply-To: <3AF01F0D.1EA63F8A@syntem-sa.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 2 May 2001, David Turner wrote: > Does anyone know where I can get a table of critical student's > t-scores in electronic format? I have a set of Fortran routines which can do both the F test (for the equivalence of 2 variances) and the T test (equivalence of 2 means). =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Wed May 2 16:29:58 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42KTvI32229 for ; Wed, 2 May 2001 16:29:57 -0400 Received: from [129.187.26.11] by mailout.lrz-muenchen.de with ESMTP; Wed, 2 May 2001 22:29:56 +0200 Sender: Eugene.Leitl@lrz.uni-muenchen.de Message-Id: <3AF089B7.948E6B84@lrz.uni-muenchen.de> Date: Thu, 03 May 2001 00:27:03 +0200 From: Eugene.Leitl@lrz.uni-muenchen.de X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.17-21mdksecure i586) X-Accept-Language: en, de-DE, ru MIME-Version: 1.0 To: chemistry@ccl.net Subject: [Fwd: Athlon SDR/DDR stats for *specific* gaussian98 jobs] Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit -------- Original Message -------- From: Velocet Subject: Athlon SDR/DDR stats for *specific* gaussian98 jobs To: beowulf@beowulf.org I've run a few select G98 jobs (as provided by my brother, who's the researcher) through a number of different configurations of CPUs and mainboards, ranging from a duron 750 on a regular old board with PC133 ram, to the same duron on a DDR board w/256Mb DDR RAM (talk about a waste! :) right up to a 1.3Ghz Tbird I able to borrow and put on the DDR board. I havent had a chance to run any of these on a P4 with SSE3 (is that the term?) optimized and recompiled gaussian and ATLAS. (If anyone is interested in contributing such stats I'm very interested.) My stats here were generated with ATLAS compiled for each change in config. The freeBSD stats were with ATLAS and G98 compiled on Linux and run on FreeBSD in Linux emulation mode (I had alot of trouble getting ATLAS *AND* G98 to compile in FreeBSD, so I just gave up). There are some caveats and other environmental factors discussed on the page as well. I am not trying to start a jihad here against high speed Thunderbird and Dual Thunderbird proponents; this is just what i've found for *MY* jobs (which themselves are a very small subset of what most people would use G98 for) in *my* particular environment. They probably have very little to do with most people's cluster designs. http://trooper.velocet.net/~math/giocomms/benchmarks/ /kc -- Ken Chase, math@velocet.ca * Velocet Communications Inc. * Toronto, CANADA _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf From chemistry-request@server.ccl.net Wed May 2 16:15:15 2001 Received: from mailrelay2.lrz-muenchen.de ([129.187.254.102]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42KFEI32110 for ; Wed, 2 May 2001 16:15:14 -0400 Received: from [129.187.26.219] by mailout.lrz-muenchen.de with ESMTP; Wed, 2 May 2001 22:15:13 +0200 Sender: Eugene.Leitl@lrz.uni-muenchen.de Message-Id: <3AF08644.8471C19C@lrz.uni-muenchen.de> Date: Thu, 03 May 2001 00:12:20 +0200 From: Eugene.Leitl@lrz.uni-muenchen.de X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.17-21mdksecure i586) X-Accept-Language: en, de-DE, ru MIME-Version: 1.0 To: chemistry@ccl.net Subject: [Fwd: Re: Athlon SDR/DDR stats for *specific* gaussian98 jobs] Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit -------- Original Message -------- From: Velocet Subject: Re: Athlon SDR/DDR stats for *specific* gaussian98 jobs To: beowulf@beowulf.org On Wed, May 02, 2001 at 12:53:17PM -0400, Mark Hahn's all... > > the same duron on a DDR board w/256Mb DDR RAM (talk about a waste! :) > > well, a duron has the same dram performance as a tbird at the same FSB. > so in that sense, it's actually a better match for a lot of computational > codes that sneer at cache. > > otoh, tbirds are dirt cheap, not much more than durons. The thing is for the cost levels Im working with, the price diff between a Duron and a Thunderbird does matter. As does the cost of a videocard being needed to get a system booted or not. For gaussian98, for my jobs (specifically) the cache seems to really matter quite alot. Thats the only thing that I can guess that accounts for the very high speed of my K7-700, which performs, for most jobs, very close to a Tbird 900. I really wish I could find some old K7s that people are tossing out for cheap. Problem is the board ends up being huge - wont fit into a 1U case for sure obviously. > > I havent had a chance to run any of these on a P4 with SSE3 (is that the > > sse2. gcc 3.0 snapshots apparently can generate sse2 code... Wonder if g77 can generate sse2 code. > does ATLAS include prefetching? it's fairly astonishing how big a > difference prefetching (and movntq) can make on duron/athlon code. > for an extreme case (Arjan van de Ven's optimized page-copy and -zero): Im not too up on the internals of atlas. Others on the list probably are. > > There are some caveats and other environmental factors discussed on > > the page as well. > > error bars would be nice. Heh, my stats are so unprofessionally done, you flatter me by even asking. I dont know what the factors of error are at all - does /usr/bin/time have problems? Is my clock accurate? Like I said, I just ran the jobs 5 times each minimum (in one case 90 times) and took the median performance. > > I am not trying to start a jihad here against high speed Thunderbird > > and Dual Thunderbird proponents; this is just what i've found for *MY* > > maybe I'm being dense, but how would these results be interpreted > jihadically? in general, they show two things: high-end machines Because I've mentioned that "perhaps buying an assload of Durons instead of dual Athlon DDR boards would give more bang for the buck overall" caused some consternation. Most were regarding increased switch costs for having so many more nodes, or possibly the cost of havving a boot hardrive for each box (which would increase the costs quite heavily). My advantages that probably apply to few others: - I dont need any high speed paralellism for this cluster. all jobs run singly by themselves on one node. - quality isnt even a massive factor - if a board crashes, the job is rescheduled. Obviously there's an acceptable threshhold, and we're way beyond that - two boards running for 12 days didnt crash on either OS. I am not putting together a mini prototype to start before the shipment of the rest of the parts comes and I finalize the cabinet design: Im gonna run 10 boards within a few inches of eachother in a stack (with proper cooling) and see how they fare - Im mainly curious about RF interference and cooling problems. I am pretty sure they'll be fine (a friend ran 4 of these boards even closer than I plan for 4 weeks with no prbolems). - we are running diskless nodes over NFS and we dont read or write to it often. (256kbps/node average during calculations) So I dont need a big switch, I dont need super reliable BrandName equipment with a service contract and I dont even need high performance network cards. Im actually somewhat interested in the power usage stats for different Athlon systems. Having fewer but faster nodes may well not save all that much power. Someone have wattage stats handy? > bear a price-premium that decreases their speed/cost merit, and > that freebsd's page coloring sometimes has a measurable benefit. Wonder how many people are using FreeBSD on their clusters instead of Linux... > I'm dubious about further interpretation, though. for instance, > you seem to show a significant benefit to tbird's larger cache > (384 vs 192K), but surely you chose this workload to be bandwidth > intensive, didn't you? if not, then the DDR comparison is rather > specious... I didnt. I chose it to be related to what we need the cluster for. Im trying to justify my design because it may come into question. Which is partly why I really need to check out a P4s stats, but Im pretty sure the price/performance is going to be lower than we can afford. The only question Im really trying to head off is why we didnt use the fastest Tbirds available and DDR ram. I am not going to read the G98 code, its horrid spaghetti ;) and my fortran isnt that great. And there's A LOT of code. Its not worth my time. Its much faster to just run the jobs on different boards and see what the results are, than to predict them by reading the code. Actually I have about 3x as many numbers for non-Atlas jobs, but they're kind of useless. However, they do indicate the speedup provided by the Thunderbirds as I managed to get both a Tbird and Duron 750, 800 and 850. I can dig up those stats if people care, but then again these are stats for *my* particular jobs running on non-optimal (non ATLAS) gaussian. > thanks for posting the numbers! No problem, sorry it wasnt more professionally done ;) I also apologize for not running standard G98 tests (Im not aware what would constitute such, or if there's a preset package of benchmarks available). /kc -- Ken Chase, math@velocet.ca * Velocet Communications Inc. * Toronto, CANADA _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf From chemistry-request@server.ccl.net Wed May 2 17:18:52 2001 Received: from eefus.Colorado.EDU ([128.138.134.21]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42LIqI32635 for ; Wed, 2 May 2001 17:18:52 -0400 Received: from localhost (horinek@localhost) by eefus.Colorado.EDU (8.9.3/8.9.3/UnixOps-Hesiod (PDH,JWD)) with ESMTP id PAA17992 for ; Wed, 2 May 2001 15:19:11 -0600 Date: Wed, 2 May 2001 15:19:11 -0600 (MDT) From: Dominik Horinek To: chemistry@ccl.net Subject: quartz glass structure Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I'm looking for an experimental quartz glass structure. Has anybody a pdb- or whatever file, or does anyone know where it could be available? Thanks for replies, Dominik -- please reply to one of the following addresses: horinek@eefus.colorado.edu horinek@gmx.net From chemistry-request@server.ccl.net Wed May 2 17:13:38 2001 Received: from flash7.flashmail.com ([207.173.216.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f42LDcI32602 for ; Wed, 2 May 2001 17:13:38 -0400 Received: (from nobody@localhost) by flash7.flashmail.com (8.9.3/8.9.3) id NAA26489 for chemistry@ccl.net; Wed, 2 May 2001 13:20:55 -0700 From: totanec@address.com X-Authentication-Warning: flash7.flashmail.com: nobody set sender to totanec@address.com using -f To: chemistry@ccl.net Subject: guide to Gaussian output archive Message-ID: <988834855.3af06c271bc34@newmail.address.com> Date: Wed, 02 May 2001 13:20:55 -0700 (PDT) MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.4 X-Originating-IP: 129.74.80.129 Hi all, In the online Gaussian documentation http://www.gaussian.com/00000417.htm it is mentioned a book or chapter "Quantum Chemistry Database System User’s Guide" However I cannot find any reference anywhere... Does anyone know where I can find either this particular reference or some web site which describe the archive entry of a Gaussian output in detail? Thank you in advance, Nicolas Saettel University of Notre Dame --------------------------------------------------------------- Get Free Internet Access And WebEmail At http://www.address.com From chemistry-request@server.ccl.net Wed May 2 22:56:53 2001 Received: from physics.msuiit.edu.ph ([202.78.82.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f432u8I02078 for ; Wed, 2 May 2001 22:56:47 -0400 Received: by physics.msuiit.edu.ph (Postfix, from userid 701) id 7662C6312A; Thu, 3 May 2001 10:56:49 +0800 (PHT) Received: from localhost (localhost [127.0.0.1]) by physics.msuiit.edu.ph (Postfix) with ESMTP id 6792857A6B for ; Thu, 3 May 2001 10:56:49 +0800 (PHT) Date: Thu, 3 May 2001 10:56:49 +0800 (PHT) From: Arnold Alguno To: Subject: Structure of Furan Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All: Is there anybody knows the experimental structure of furan (monomer and dimer)? e.g. bond length, bond angle. thank you! -- _________ Very truly yours, ARNOLD C. ALGUNO IITHEP, Department of Physics MSU-IIT, Iligan City Philippines alguno@physics.msuiit.edu.ph Fax: +63-63-221-4068 Mobile Phone No.:+63-919-427-8205