From chemistry-request@server.ccl.net Wed Mar 29 01:49:44 2000 Received: from mail.virco.be ([195.207.78.10]) by server.ccl.net (8.8.7/8.8.7) with SMTP id BAA07799 for ; Wed, 29 Mar 2000 01:49:17 -0500 Received: from [192.168.2.168] by mail.virco.be (CommuniGate SMTP 2.7.2) with ESMTP id S.001841210212 for ; Wed, 29 Mar 2000 08:39:04 +0100 Sender: jan@ccl.net Message-ID: <38E1A80A.BF7B0CD8@tibotec.be> Date: Wed, 29 Mar 2000 08:51:54 +0200 From: jan de kerpel Organization: Tibotec X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:Clustering compounds from large databases Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL members, I would like to know the availability (both freeware as commercial) of software able to cluster chemical compounds based on physical (e.g. logP), structural (smiles string/2D/SDF) and biological screening data. The number of compounds in the database is typically 100.000 to 150.000 or larger. The questions are : 1) available software based on 2D clustering and, is there already software capable to work in 3D on this large amount of compounds (or smaller databases)? 2) where can I find information about the algorithms, and are there other than SMILES strings used to generate structure keys? 3) has anybody an idea of the ratio of cpu usage when doing 2D versus 3D clustering on this amount of compounds, and what are the expected bottlenecks? Thanks! Jan -- ************************************************************* TIBOTEC Dep. Medicinal Chemistry Gen. De Wittelaan 11B 3 B-2800 Mechelen (BELGIUM) tel : (32) 15 286.300 fax : (32) 15 286.349 email : jan.dekerpel@tibotec.be ************************************************************* From chemistry-request@server.ccl.net Wed Mar 29 00:46:32 2000 Received: from post.webmailer.de (natmail2.webmailer.de [192.67.198.65]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA07486 for ; Wed, 29 Mar 2000 00:46:31 -0500 Received: from cosmologic.de (0-39.K.dial.o-tel-o.net [212.144.0.39]) by post.webmailer.de (8.9.3/8.8.7) with ESMTP id HAA02521 for ; Wed, 29 Mar 2000 07:46:25 +0200 (MET DST) Message-ID: <38E1988D.9332B20D@cosmologic.de> Date: Wed, 29 Mar 2000 07:45:49 +0200 From: "A.Klamt" X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: de MIME-Version: 1.0 To: chemistry@ccl.net Subject: routines for substructure decomposition Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, does anyone know about a commonly available set of FORTRAN subroutines allowing for the handling of structures, structure analysis (ring percetion, aromaticity, etc.) and decomposition of structures into substructures? -- Regards Andreas Klamt COSMOlogic GmbH&Co.KG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de From chemistry-request@server.ccl.net Wed Mar 29 03:44:09 2000 Received: from coch11.chm.tu-dresden.de (mann@coch11.chm.tu-dresden.de [141.30.9.111]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA08377 for ; Wed, 29 Mar 2000 03:44:08 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by coch11.chm.tu-dresden.de (8.9.3/8.9.3) id KAA11123 for chemistry@ccl.net; Wed, 29 Mar 2000 10:45:05 +0200 From: Matthias Mann Reply-To: Matthias.Mann@chemie.tu-dresden.de To: chemistry@ccl.net Subject: Re: CCL:Athlon vs Intel performance Date: Wed, 29 Mar 2000 10:26:24 +0200 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain References: <4.2.0.58.20000328184133.00ad79a0@mbi.ucla.edu> MIME-Version: 1.0 Message-Id: <00032910450501.11106@coch11> Content-Transfer-Encoding: 8bit On Wed, 29 Mar 2000, you wrote: >1GHz PC's will be shipping in May (Athlon) and June (PIII). > >Performance comparison: >PIII 1GHz with 133MHz bus (anyone know when 200MHz bus is expected ?) >vs >Athlon 1GHz with 200MHz bus (anyone know of dual Athlon mobo with 200MHz bus ?) > >Any comments or links would be appreciated. > >Any comments on CPU comparison of PIII 1GHz vs Athlon 1G (FPU and cache >size/speed are the main issues ?). > >Discussion welcome. > >Laurence I have only comparisions of PII-450, PIII-500 and AMD Athlon 550. Look at: http://www.chm.tu-dresden.de/edv/bench/bench9.html for GAMESS(US) benchmarks, and at: http://www.chm.tu-dresden.de/edv/bench/bench10.html for GAUSSIAN98 A7 benchmarks. Normally the relation of relative performance looks as expected; however, in some cases the Pentium-III system is extremly slow: this is the case in MP2 and QCISD(T) calculations with Gaussian and in CASSCF calculations with Gamess. I'm not sure about the reason, maybe this is the cache, or the architecture specific optimization (the code was compiled in both cases with pgf77 on an PII system, and in the Gaussian case maybe the optimized BLAS plays a role). Matthias -- Dr. Matthias Mann Institut fuer Organische Chemie, TU Dresden D-01069 Dresden, Mommsenstr. 13 Tel.: +49 (351) 463-4286 / Fax: -7030 Email: Matthias.Mann@chemie.tu-dresden.de From chemistry-request@server.ccl.net Wed Mar 29 05:52:34 2000 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA08995 for ; Wed, 29 Mar 2000 05:52:33 -0500 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/05) with ESMTP id MAA16807; Wed, 29 Mar 2000 12:52:22 +0200 (MET DST) From: "Dr. Peter Burger" Received: [(chburger@localhost) by zisgi.unizh.ch (8.9.3/SMI-IRIX6.2/USAR_MAIL_V2) id MAA62332; Wed, 29 Mar 2000 12:52:22 +0200 (MDT)] Message-Id: <200003291052.MAA62332@zisgi.unizh.ch> Subject: Re: CCL:Athlon vs Intel performance To: Matthias.Mann@chemie.tu-dresden.de (Matthias Mann) Date: Wed, 29 Mar 2000 12:52:22 +0200 (CEST) Cc: CHEMISTRY@ccl.net In-Reply-To: <00032910450501.11106@coch11> from "Matthias Mann" at Mar 29, 0 10:26:24 am X-Mailer: ELM [version 2.4 PL25 PGP2] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi, just worth my 0.02 cents The numbers I have. show that at the same clock freq. the Athlon is roughly 0-10 % faster on my benchmarks compared to the PIII (ADF, Turbomole, Jaguar). Things are different for Dmol which make heavy usage of Blas-3 dgemm, which is substantially faster on the Athlon using the fabulous Atlas (cudos to Clint Whaley!) libarary, e.g. 860 MFlops at 800 MHz for the Athlon compared to 825 MFlops at 750 " " 440 MFlops at 550 MHz on a PIII (still Katmai core) for dgemm based matrix multiplications (independent of the matrix size) Based on figures by Intel for their new math kernel library, peformance of a 733 MHz Coppermine is below 600 MFlops. For Dmol this helps alot and gives a 30% performance edge for the Athlon. But I guess most vendors that use Blas-3 libs will provide only one version of their commercial software which is quite likely to be based on the Intel library. For Gaussian & Gamess etc. you can obviously choose yourself, but then it depends how much your code depends on Blas-3. For Jaguar, there was a tremendous speedup in their new Linux 4.0 version (factor 2x over 3.5) which to the best of my knowledge is at least in parts due to the usage of dgemm. I will post an updated version of my Linux quantumchemistry software comparison shortly which includes new results for Jaguar 4.0 and Dmol on the Athlon/Linux. The Athlon has still alot more potential and needs better compilers to support its second FP pipeline (not present in the PIII) and a faster memory bus. Compaq I heard is working on an Athlon version of their DVF NT Fortran compiler and supposedly they see good speedup (taken from ct' a German computer magazine) already. Supposedly it is due in 3 months. The memory bus is already slightly improved with the event of the new KX133 chipset supporting 133 MHz SDRAM. Ought to get still better though through the usage of DDR RAM aware chipset in the second half of this year. Nevertheless stream memory bandwith benchmarks went up from 500 MB/sec on the 100 MHz bus to 600-700 MHz on the 133 memory bus in the new KX133 based boards. Also, one can expect alot good things from the new Thunderbird core which has the L2 cache ondie running at the core clock speed and which should be out soon. At least Intels Coppermine with 256 K ondie L2 cache seems to have a 20% performance edge over the Katmai core with 512 K L2 cache running a 1/2 clockrate. Regards, Peter P.S. May I ask users of the Portland group (pgi) Linux pgf77/90 Fortran compiler (e.g. Gaussian G98 users!) to request at pgi for Athlon optimizations in that pgi notices that there definitely is a market. ------------------------------------------- Peter Burger Anorg.-chem. Institut Winterthurerstr. 190 Universitaet Zuerich From chemistry-request@server.ccl.net Wed Mar 29 12:10:44 2000 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA11345 for ; Wed, 29 Mar 2000 12:10:38 -0500 Received: from higia.qui.ufmg.br (higia.qui.ufmg.br [150.164.20.135]) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id OAA52893; Wed, 29 Mar 2000 14:09:20 -0300 Sender: andre@dedalus.lcc.ufmg.br Message-ID: <38E28B98.167E@dedalus.lcc.ufmg.br> Date: Wed, 29 Mar 2000 15:02:48 -0800 From: Andre de Oliveira Organization: UFMG X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) MIME-Version: 1.0 To: Keisuke Ishida CC: chemistry@ccl.net Subject: Re: CCL:How to build PC clusters for MD simulation References: <006001bf8cdf$cdb5c2a0$7bce9ed2@taiho.co.jp> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Prof. Ishida, Please forward all replies. I am also interested in PC clusters. Keisuke Ishida wrote: > > Hi everyone, > > I want to build PC cluster for MD simulation. > Please let me know how to build PC cluster > and which MD programs can I get for parallel computers. > > Thanks. > ---------- > Keisuke Ishida > Chemistry Laboratory, Taiho Pharmaceutical Co.,Ltd. > Hanno 357-8527 Japan > TEL. +81-429-72-8900 > FAX. +81-429-72-8913 > E-mail. ishida@taiho.co.jp > ---------- > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Andre Mauricio de oliveira Nucleo de Estudos em Quimica Meducinal Federal University of Minas Gerais VOICE: +55-31-499-5765 FAX: +55-31-499-5700 ZIP CODE 31270901 Belo Horizonte, MG Brazil From chemistry-request@server.ccl.net Wed Mar 29 06:07:42 2000 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA09093 for ; Wed, 29 Mar 2000 06:07:41 -0500 Received: (qmail 4028 invoked from network); 29 Mar 2000 11:07:00 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 29 Mar 2000 11:07:00 -0000 Received: (qmail 25894 invoked from network); 29 Mar 2000 11:02:01 -0000 Received: from demokritos.physics.upatras.gr (HELO demokritos) (150.140.158.10) by pythagoras.physics.upatras.gr with SMTP; 29 Mar 2000 11:02:01 -0000 Message-ID: <003801bf996e$e8197ce0$0a9e8c96@demokritos.physics.upatras.gr> From: "garoufal" To: Subject: PVM and quantum chemistry Date: Wed, 29 Mar 2000 14:07:00 +0300 Dear CCLers Are there any quantum chemistry programs (preferably free) which can run in parallel on linux clusters using PVM or maybe some other free program? Thanks in advance -------------------------------------------------------------------------= Christos S. Garoufalis department of Physics, University of Patras, Greece -------------------------------------------------------------------------= From chemistry-request@server.ccl.net Wed Mar 29 09:18:07 2000 Received: from sp81.msi.umn.edu (sp81.msi.umn.edu [128.101.135.81]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA10698 for ; Wed, 29 Mar 2000 09:18:07 -0500 Received: from sp67.msi.umn.edu (sp67.msi.umn.edu [128.101.135.67]) by sp81.msi.umn.edu (8.9.3/8.9.3) with SMTP id IAA31436 for ; Wed, 29 Mar 2000 08:17:55 -0600 Date: Wed, 29 Mar 2000 08:17:55 -0600 (CST) From: William Johnson X-Sender: wtgj@sp67.msi.umn.edu To: "CHEMISTRY@ccl.net" Subject: CCL:Huckel energies for buckminsterfullerene In-Reply-To: <200003290144.JAA05133@ms.dicp.ac.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, A while ago someone asked for the Huckel energies for the MOs of buckminsterfullerene. Unfortunately, I deleted the message before I realized how simple it would be to obtain them. If you search on Yahoo! for Huckel theory, the second hit takes you to a JAVA based simple Huckle MO calculator. Since simple Huckel theory doesn't care about the geometry, only the connectivity, you can draw in the flattened buckminsterfullerene and obtain the eigenvalues and eigenvectors for that particular connectivity matrix. It takes a little time to draw in the 60 carbons, but it'll draw the MOs right on the structure for you when you're done. So, anyway, here are the results you asked for. The coeffs. for beta are listed (remember that beta's a negative quantitiy, so the bottom thirty MOs are occupied): Degeneracy Coeffs. ---------- ------- 3 -2.618 4 -2.562 4 -2.000 5 -1.618 3 -1.438 5 -1.303 3 -0.382 3 -0.139 5 0.618 9 1.000 4 1.562 3 1.820 5 2.303 3 2.757 1 3.000 If you go to the site, be careful with the minimization button near the end of your construction. Hope this helps. William T. Johnson Post-Doc, Univ. of Minnesota, Twin Cities wtgj@pollux.chem.umn.edu From chemistry-request@server.ccl.net Wed Mar 29 12:23:45 2000 Received: from lrz.uni-muenchen.de (root@lsanca1-ar99-078-042.biz.dsl.gtei.net [4.3.78.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA11440 for ; Wed, 29 Mar 2000 12:23:44 -0500 Received: from localhost (eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) with ESMTP id JAA05143; Wed, 29 Mar 2000 09:23:17 -0800 Date: Wed, 29 Mar 2000 09:23:17 -0800 (PST) From: "eugene.leitl" To: Andre de Oliveira cc: Keisuke Ishida , chemistry@ccl.net Subject: Re: CCL:How to build PC clusters for MD simulation In-Reply-To: <38E28B98.167E@dedalus.lcc.ufmg.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 29 Mar 2000, Andre de Oliveira wrote: > Dear Prof. Ishida, > > Please forward all replies. I am also interested in PC clusters. Such questions are more likely to be answered at the Beowulf list (which has an searchable archive at http://supercomputer.org). I have forwarded the original request there. Regards, Eugene Leitl From chemistry-request@server.ccl.net Wed Mar 29 15:15:03 2000 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA12688 for ; Wed, 29 Mar 2000 15:15:03 -0500 Received: (from mn1@localhost) by helix.nih.gov (8.9.3/8.9.3) id PAA1761713; Wed, 29 Mar 2000 15:15:02 -0500 (EST) Date: Wed, 29 Mar 2000 15:15:02 -0500 From: "M. Nicklaus" To: Laurence Lavelle cc: CCL , "M. Nicklaus" Subject: Re: CCL:Athlon vs Intel performance In-Reply-To: <4.2.0.58.20000328184133.00ad79a0@mbi.ucla.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For what it's worth: We've run one single direct speed comparison (I wouldn't call it a benchmark) so far, running the same Titan calculation on both a 600 MHz Pentium III (non-Coppermine) and an 800 MHz AMD K7 (Athlon) system, both running under Windows 98. (The job was a single point energy calculation at the LMP2/6-31G** level for a nucleoside analog.) Time for completion (as per program output, but in agreement with wall time): 600 MHz Pentium III - 7:05 h 800 MHz Athlon - 2:25 h Correcting (linearly) for the difference in clock rate, the Athlon is still faster (for this job!) by a factor of 2.2. Specs: 600 MHz Pentium III - 100 MHz FSB, 512 MB PC100 RAM, 27 GB ATA/66 7,200rpm HD 800 MHz Athlon - 100 MHz FSB, 256 MB PC100 RAM, 27 GB ATA/66 7,200rpm HD However, we've had quite a few stability problems with the Athlon system so far (both in Titan and in general), but we think these are more likely related to hardware driver problems in Windows 98 than to true hardware instability. All in all, YMMV. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 402-2275 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Wed Mar 29 16:18:53 2000 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA12989 for ; Wed, 29 Mar 2000 16:18:53 -0500 Received: from red5 (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id NAA22379; Wed, 29 Mar 2000 13:18:51 -0800 (PST) Message-Id: <4.2.0.58.20000329133454.00ae25f0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Wed, 29 Mar 2000 13:36:54 -0800 To: "M. Nicklaus" From: Laurence Lavelle Subject: Re: CCL:Athlon vs Intel performance Cc: CCL In-Reply-To: References: <4.2.0.58.20000328184133.00ad79a0@mbi.ucla.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Well that answers that. Are there any dual Athlon's expected this year ? Thanks for all the replies. Laurence At 03:15 PM 03/29/2000 -0500, M. Nicklaus wrote: >For what it's worth: > >We've run one single direct speed comparison (I wouldn't call it a >benchmark) so >far, running the same Titan calculation on both a 600 MHz Pentium III >(non-Coppermine) and an 800 MHz AMD K7 (Athlon) system, both running under >Windows 98. (The job was a single point energy calculation at the >LMP2/6-31G** >level for a nucleoside analog.) > >Time for completion (as per program output, but in agreement with wall time): > >600 MHz Pentium III - 7:05 h >800 MHz Athlon - 2:25 h > >Correcting (linearly) for the difference in clock rate, the Athlon is still >faster (for this job!) by a factor of 2.2. > >Specs: > >600 MHz Pentium III - 100 MHz FSB, 512 MB PC100 RAM, 27 GB ATA/66 >7,200rpm HD >800 MHz Athlon - 100 MHz FSB, 256 MB PC100 RAM, 27 GB ATA/66 >7,200rpm HD > >However, we've had quite a few stability problems with the Athlon system >so far >(both in Titan and in general), but we think these are more likely related to >hardware driver problems in Windows 98 than to true hardware instability. >All in >all, YMMV.