From chemistry-request@server.ccl.net Wed Jul 25 08:57:02 2001 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6PCv1520037 for ; Wed, 25 Jul 2001 08:57:02 -0400 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.31) id 15PODe-0006Ve-00; Wed, 25 Jul 2001 14:56:54 +0200 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.31) id 15PODd-0005Qv-00; Wed, 25 Jul 2001 14:56:53 +0200 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: Date: Wed, 25 Jul 2001 14:56:52 +0200 To: chemistry@ccl.net From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: g98 compilation problems Cc: fox@gaussian.com Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f6PCv2520038 Some people reported to me that they cannot compile g98A7 under new LINUX versions, so I looked at it. There is indeed a problem in bsd/mdutil.c related to the constant CLK_TCK, which is not always defined by including . The "clean" solution is of course to use the getrusage interface, i.e. replace the lines #ifndef ETIME_DONE clock_t times(), wall; struct tms tbuf; wall = times(&tbuf); tarray[0] = (float) (((f77_wp) tbuf.tms_utime) / ((f77_wp) CLK_TCK)); tarray[1] = (float) (((f77_wp) tbuf.tms_stime) / ((f77_wp) CLK_TCK)); #endif by #ifndef ETIME_DONE struct rusage usage; getrusage(RUSAGE_SELF, &usage); tarray[0] = (double) usage.ru_utime.tv_sec + 0.000001 * (double) usage.ru_utime.tv_usec; tarray[1] = (double) usage.ru_stime.tv_sec + 0.000001 * (double) usage.ru_stime.tv_usec; #endif (near the bottom of function etime_). From chemistry-request@server.ccl.net Wed Jul 25 05:28:02 2001 Received: from spider.irb.hr ([161.53.131.146]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6P9S1511162 for ; Wed, 25 Jul 2001 05:28:01 -0400 Received: from localhost (boris@localhost) by spider.irb.hr (8.10.0/8.10.0) with ESMTP id f6PFUXJ13484 for ; Wed, 25 Jul 2001 11:30:33 -0400 Date: Wed, 25 Jul 2001 11:30:33 -0400 (EDT) From: Borislav Kovacevic To: chemistry@ccl.net Subject: motherboard for AMD processor (summary) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, I would like to say thanks to all people who helped me to make decision which computer configuration to buy. Here is the summary. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: David Konerding I have the A7A266 and it works great. I am running Windows 2000 on it but also spent some time running linux on it. I have the DDR and th emachine is a real screamer. DDR gets you maybe 15% better memory bandwidth, which would probably be seen while running gaussian. I would try the machine with the DDR RAM and then swap it out for SDRAM (that's the nice thing about the board- both are supported) and see how your timings differ. Yes, portland's compiler will run on the AMD. Dave ############################################################################ From: Scott Anderson I have an 1GHz thunderbird on an asus A7V socket 7 motherboard with PC 133 ram. It works find with gaussian and with the PGI compiler Prof. Scott L. Anderson Department of Chemistry University of Utah 315 S. 1400 E. Rm 1216 Salt Lake City, UT 84112 (801)585-7289 FAX(801)581-8433 ########################################################################## From: Niclas Andersson For what it's worth... I have no experience of DDR SDRAM yet. We have used ASUS Motherboards for a long time and are very pleased with the stability. I would go for the A7M266. The ALi Magik chipset on the A7A266 haven't shown that good performance. The VIA chipset for DDR (ASUS has no MB with that) also has problems. I am hoping VIA soon will fix their chipset. Their eariler versions for AMDs and SDRAM har performed very well. I assume if VIA can get a chipset working good for AMD and DDR, that will become the "default" chipset since AMD "... really don't want to produce chipsets". The best chipset for Thunderbird and DDR is now AMDs own which is mounted on the A7M266. With todays prices and derivatives of prices. DDR is the way to go. Unless you can prove you don't need the extra memory bandwidth. But with Gaussian and Games I reckon you do. The only nagging problem is the larger and larger non-ECC memory ... I can't see any problems using Portland Compilers in this setup. As I said, we've been using AMD in several clusters and Portland is the compiler to use for Fortran! It's stable, it is forgiving (easy to port), and the performace is good. It can generate 3DNow instructions but that's not that interesting unless you use singe precision. For C and C++, GCC is an alterative not because of performance but because it is the native compiler. Don't forget extra cooling fan in the box. 1.4GHz Thunderbirds run hot! Our current clusters: Regards, Niclas -- Niclas Andersson E-mail: nican@nsc.liu.se National Supercomputer Centre Phone: +46 13 281464 Linkoping University, S-581 83 Linkoping, Sweden Fax: +46 13 282535 ############################################################################ From: Antoine My PC is a T-bird 1.2GHz + 256 Mo DDR on a MSI K7T266Pro mobo and it works fine ! MSI mobo is linux certified and all reviews I saw present that mobo more reliable than A7A266 but a bit slower so they worth. It is fine for overclocking, Asus is better. It is based on a VIA chipset. If you look for pure performences you migh wait for the SIS735 chipset based mobo that should be released in a couple of monthes and should be better than AMD or VIA chipsets. DDR is the good choise if you want to upgrade your PC later, DDR is becoming the new RAM standard even if the speed gain is just about 15% (vs DRAM133). It is going cheaper and cheaper. AMD proc run Portland compiler without problems, they are i586 complients. Hope this help even if I don't really answer your question ... Antoine Antoine FORTUNE Ingenieur Modelisation Moleculaire Dept. Pharmacologie Moleculaire - UMR 5063 Universite Joseph Fourier Faculte de Pharmacie 38706 LA TRONCHE - FRANCE Tel: 04 76 63 71 40 Fax: 04 76 51 86 67 e-mail: Antoine.Fortune@ujf-grenoble.fr ############################################################################# From: a3arzi Im my mind, it is very good choice. I have no detail knowledge about your M/B, but take a look if it has VIA chipset. I have heard that VIA have made its chipsets well optimised for AMD CPU. RAM is extensively used in ab initio calculations. So DDRAM should increase the performance. Insure that your RAM and M/B both run 266 MHz FSB. Best regards Arturas Z. ############################################################################ From: Bruno Sopko we have used the configuration, you have mentioned, and encountered quite a few problems. However, the similar price is for two processor system (Intel PIII 750MHz) with normal 133 SDRAM 1Gb, which worked fine, in some cases even faster , without any problems, patches and so on. That's more or less all. If you have any other questions, do not hesitate to contact me Bruno Sopko Dept. of Biochemistry, Charles University - Faculty of Science, Albertov 2030 128 40 Praha 2, Czech Republic, Phone: +420-2-21952173 +420-607-836499 FAX: +420-2-21952331 ########################################################################## From: David van der Spoel I've just installed a MicroStar motherboard w 1.4 GHz Athlon. I did however get 1.5 Gb of SDRAM with it for Gaussian calculations, memory is cheap, 512 Mb < 100 US$. The amout of memory will have a large impact on Gaussian calculations, much more than the type of memory. I only regret I couldn't install more memory on the motherboard. As for Protland compiler, you have to have it because Gaussian will not compile without it. -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ########################################################################## From: Dr. Peter Burger yes, just skip it and do for the A7M266 or go for any other AMD760 chipset. SSR RAM is really rather nice. Stream bandwidth test on the A7M266 gives ca. 1 GB/sec and just 700 MB/sec on the A7A266. That really shows up in the quntum chemistry programs. > motherboard (for example A7M266)? Then, is it better to use DDR RAM or > SDRAM? I'm also interested to find out may I use Portland compiler on this DDR is ca. 10-15 faster. Pgroups compiler works nicely (including automatized prefetch for the Athlon). Hope thi helps. Peter ........................................ Peter Burger Anorg.-chem. Institut Universitaet Zuerich ########################################################################### From: jmmckel@attglobal.net There has been a benchmark posted on CCL about Gaussian and various cpu's and memory. I believe that it showed that DDR memory was better than SDR. At least in the US the price differential is small. John McKelvey =========================================================================== Boris Kovacevic Phone: (385) (1) 4561-117 Quantum chemistry group Fax: (385) (1) 4680-197 "Rudjer Boskovic" Institute e-mail: borislav.kovacevic@irb.hr Bijenicka 54, 10000 Zagreb Croatia ============================================================================ From chemistry-request@server.ccl.net Wed Jul 25 00:06:35 2001 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6P46Z531960 for ; Wed, 25 Jul 2001 00:06:35 -0400 Received: from ISOSIRRI (dhcp-28.csc.fi [193.166.2.28]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id HAA21213 for ; Wed, 25 Jul 2001 07:06:33 +0300 From: "Leif Laaksonen" To: Subject: Gaussian format question(s) Date: Wed, 25 Jul 2001 07:06:37 +0300 Message-ID: <000001c114bf$33ac1830$1c02a6c1@ISOSIRRI> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0001_01C114D8.58F95030" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C114D8.58F95030 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Hello, I'm writing some more code for gOpenMol to be able to display density gradients and Laplacians. However, I'm it bit puzzled by the different information in the different manuals and the (possible) difference between G94 and G98 input/output. First question: The coordinate and distance values in the CUBE file are they in Bohrs or Angstroms and how do I know in which they are? The manual says "Output-file-name Required in all Cubejobs. IFlag, X0, Y0, Z0 Output unit number and initial point. N1, X1, Y1, Z1 Number of points and step-size in the X-direction. N2, X2, Y2, Z2 Number of points and step-size in the Y-direction. N3, X3, Y3, Z3 Number of points and step-size in the Z-direction. If N1<0 the input cube coordinates are assumed to be in Bohr, otherwise, they are interpreted as Angstroms (this keyword is not affected by the setting of the Units keyword)." Does this mean that the output CUBE file is also in the same format as the input or can the input be in Angstroms and output in Bohrs? Is there a difference between the G94 and G98 versions in this respect? Second question: If I define Laplacian in the CUBE keyword I seem to get density+gradient+Laplacian norm for G94 but only the Laplacian norm for G98. Do these two version produce different output for the same input? Is there any way I can figure out what data there is in the CUBE file? I should somehow know what data is included in the CUBE file for parsing purposes without looking at the input files. Thank you very much for your help. Regards, -leif laaksonen ------=_NextPart_000_0001_01C114D8.58F95030 Content-Type: text/x-vcard; name="Leif Laaksonen.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Leif Laaksonen.vcf" BEGIN:VCARD VERSION:2.1 N:Laaksonen;Leif FN:Leif Laaksonen ORG:Center for Scientific Computing;CSC New Technologies TITLE:New Technologies Group Manager NOTE;ENCODING=QUOTED-PRINTABLE:My personal Web page: http://www.csc.fi/~laaksone/=0D=0A=0D=0AMy personal fa= x: +44-870-831-8909=0D=0A=0D=0A=0D=0A TEL;WORK;VOICE:+358 9 457 2378 TEL;CELL;VOICE:+358500425203 TEL;WORK;FAX:+358 9 457 2302 TEL;HOME;FAX:+44 870 831 8909 ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;Tekniikantie 15 a D=0D=0AP.O.Box 405;Espoo;;FIN-02101;Finland LABEL;WORK;ENCODING=QUOTED-PRINTABLE:Tekniikantie 15 a D=0D=0AP.O.Box 405=0D=0AEspoo FIN-02101=0D=0AFinland URL:http://laaksonen.csc.fi/ URL:http://www.csc.fi/ EMAIL;PREF;INTERNET:Leif.Laaksonen@csc.fi EMAIL;INTERNET:Leif.Laaksonen@iki.fi EMAIL;INTERNET:laaksone@csc.fi REV:20010502T202010Z END:VCARD ------=_NextPart_000_0001_01C114D8.58F95030-- From chemistry-request@server.ccl.net Wed Jul 25 11:52:55 2001 Received: from web20005.mail.yahoo.com ([216.136.225.68]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6PFqt523326 for ; Wed, 25 Jul 2001 11:52:55 -0400 Message-ID: <20010725155255.29948.qmail@web20005.mail.yahoo.com> Received: from [130.14.72.223] by web20005.mail.yahoo.com; Wed, 25 Jul 2001 08:52:55 PDT Date: Wed, 25 Jul 2001 08:52:55 -0700 (PDT) From: S Bear Subject: Re: CCL:Chemistry Databases/Services (Small Molecule) on the Web To: "M. Nicklaus" , CHEMISTRY@ccl.net Cc: mn1@helix.nih.gov In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii There's a collection of links to chem structures at the top of my chem page, of which some may meet your criteria http://geocities.com/soaringbear/biomed/chem.html Soaring Bear P.S. Let us know when you've got your collection ready. --- "M. Nicklaus" wrote: > I'm trying to compile a list of all the Web sites offering > chemical > structural databases (small molecule) that have at least one > of the > following capabilities: > > - Search by (sub-) structure > - Display of the structure, at least in 2D (not just a name) > - Download/save a structure in a computer-readable format > (SD, PDB...) > - Retrieve/dump large parts of the database (or even the > entire DB) in > bulk form, again in a computer-readable format > - Perform some kind of calculation on the structure (e.g. > physicochemical > properties etc.) > - At least 100 molecules available > - Accessible with just a Web browser, possibly with some > easily obtainable > plugin (this excludes services that require a special > application, such > as SciFinder) > > These sites may be academic, commercial, government, > non-profit. Required > fees or subscription is not a disqualifier, but should be > noted. > > I already have a certain number of such URLs; but I want to > make sure > that I don't overlook anything. I'll post a summary of > course. > > TIA, > > Marc > > ------------------------------------------------------------------------ > Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick > E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 > Phone: (301) 846-5903 376 Boyles Street > Fax: (301) 846-6033 FREDERICK, MD 21702 > USA > Head, Computer-Aided Drug Design MiniCore Facility > Laboratory of Medicinal Chemistry, Center for Cancer > Research, > National Cancer Institute at Frederick, National Institutes > of Health > > http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm > ------------------------------------------------------------------------ > > > > > -= 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 > > > > > ===== Soaring Bear Ph.D. Research Pharmacologist Scientific advisor to the health professions soaringbear@yahoo.com http://soaringbear.com or http://www.crosswinds.net/~soaringbear/ -- http://HERBMED.org was Science Magazine hotpick June 23, 2000 and Brit Med J netline Jan 20 2001 __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From chemistry-request@server.ccl.net Wed Jul 25 20:23:49 2001 Received: from post2.inre.asu.edu ([129.219.110.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6Q0Nn531057 for ; Wed, 25 Jul 2001 20:23:49 -0400 Received: from conversion.post2.inre.asu.edu by asu.edu (PMDF V6.0-24 #47347) id <0GH20000113N3Y@asu.edu> for chemistry@ccl.net; Wed, 25 Jul 2001 17:23:47 -0700 (MST) Received: from webmail1.asu.edu (webmail1.asu.edu [129.219.10.21]) by asu.edu (PMDF V6.0-24 #47347) with ESMTP id <0GH200N6V13N2N@asu.edu>; Wed, 25 Jul 2001 17:23:47 -0700 (MST) Received: (from nobody@localhost) by webmail1.asu.edu (8.9.3/8.9.3) id RAA32010; Wed, 25 Jul 2001 17:23:48 -0700 Date: Wed, 25 Jul 2001 17:23:48 -0700 (MST) From: Benjamin.Moritz@asu.edu Subject: Restarting a G98 Job X-Originating-IP: 149.169.38.28 To: chemistry@ccl.net, help@gaussian.com Message-id: <996107028.3b5f631410772@webmail1.asu.edu> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.3 Dear All, I am running a two step job in G98 using the STABLE keyword to find a wavefunction, and then running an OPT FREQ job. When I first started out my calculation ran out of time and I had to restart the job. So I added the following command in the second job route section...opt(restart,maxcycle=100), and G98 did the calculation, but optimized the structure and no freq were reported. I have included the resubmitted input file below, and I was hoping someone could help me on resubmitting the job so I get both the optimized structure and the frequencies. Thank you in advance. INPUT FILE %chk=cuOO %mem=3gb # HF/3-21G* stable(ruhf,opt) scf=maxcycle=500 nosymm cuOO optimization 1 3 Cu O,1,R2 O,1,R3,2,A3 O,1,R4,2,A4,3,D4,0 O,4,R5,1,A5,2,D5,0 H,3,R6,1,A6,2,D6,0 H,2,R7,1,A7,3,D7,0 H,2,R8,1,A8,7,D8,0 H,3,R9,1,A9,6,D9,0 Variables: R2=1.804 R3=1.88504075 R4=1.85527981 R5=1.244 R6=0.96673229 R7=0.96674287 R8=0.96615526 R9=0.96616383 A3=110.27970585 A4=124.81858691 A5=125.97567183 A6=122.29814425 A7=122.37407004 A8=128.33421827 A9=128.43244722 D4=179.88894814 D5=-80.69663424 D6=-170.33004164 D7=-167.17453856 D8=-176.29123573 D9=-176.66185433 --Link1-- %chk=cuOO %mem=3gb #b3lyp/tzvp opt(restart,maxcycle=100) freq=noraman geom=allcheck guess=read scf=maxcycle=500 gfprint pop=full nosymm ******************************************************************************** Benjamin J. Moritz Work: 480-965-8509 College of Engineering and Applied Sciences Mailto:bmoritz@asu.edu Dept. of Chemical & Materials Engineering PO Box 876006 Tempe, AZ 85287-6006 ********************************************************************************