From owner-chemistry@ccl.net Tue Jul 18 04:40:26 1995 Received: from spider.chemie.fu-berlin.de for sschulz@chemie.fu-berlin.de by www.ccl.net (8.6.10/930601.1506) id EAA10173; Tue, 18 Jul 1995 04:29:21 -0400 Message-Id: <199507180829.EAA10173@www.ccl.net> Received: by spider.chemie.fu-berlin.de (1.37.109.16/16.2) id AA245656145; Tue, 18 Jul 1995 10:29:05 +0200 From: Stefan Schulz Subject: Re: CCL:GAMESS graphics programs To: chemistry@ccl.net Date: Tue, 18 Jul 95 10:29:04 MESZ X-Hpvue$Revision: 1.8 $ Mime-Version: 1.0 Content-Type: Message/rfc822 X-Vue-Mime-Level: 4 Mailer: Elm [revision: 70.85] Hi CCLers, here are some of the answers I got when asking for a program to visualize orbitals from GAMESS_US output files. I had alreadsy tried out PLTORB but was not exactly excited about the poor quality of the generated plots. Even if MolDen, as it turned out, is not compatible with the GAMESS_US version it does a nice job when supplied with GAUSSIAN or GAMESS_UK output files. I also think that Viewmol is a very nice visualization program for all those who are currently working with GAUSSIAN 92. Thanks for all your help! Stefan Schulz =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | | Stefan Schulz | | schulz@chemie.fu-berlin.de | FU Berlin - Theoretical Chemistry | | Tel. ++49/30/838 5384 (2351) | Takustrasse 3 | | FAX. ++49/30/838 4792 | D-14195 Berlin | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Answer 1 ======== From dfq.ufrj.br!jomal Wed Jul 12 19:54:47 1995 From pecos.rc.arizona.edu!jaimeco Wed Jul 12 01:17:23 1995 From ibm12.biosym.com!jxh Wed Jul 12 01:42:44 1995 From prades.cesca.es!cadi.cesca.es!hal6000.qf.ub.es!work Wed Jul 12 10:28:34 1995 Return-Path: <@prades.cesca.es,@cadi.cesca.es:work@hal6000.qf.ub.es> Received: by ki1.chemie.fu-berlin.de (Smail3.1.28.1) from prades.cesca.es (192.94.163.152) with smtp id ; Wed, 12 Jul 95 10:28 MEST Received: from cadi.cesca.es by prades.cesca.es with SMTP (1.38.193.4/16.2) id AA09980; Wed, 12 Jul 1995 10:25:35 +0200 Received: from hal6000.qf.ub.es by cadi.cesca.es with SMTP id AA33651; 5.61/CRI-61.3; Wed, 12 Jul 95 10:30:03 +0200 Received: by hal6000.qf.ub.es (AIX 3.2/UCB 5.64/4.03) id AA12412; Wed, 12 Jul 1995 10:26:01 GMT Date: Wed, 12 Jul 1995 10:26:01 GMT From: work@hal6000.qf.ub.es (Francesc Illas) Message-Id: <9507121026.AA12412@hal6000.qf.ub.es> To: <@cadi.cesca.es:sschulz@chemie.fu-berlin.de> Subject: plots Status: RO X-Status: Hi Stefan, Yo may try to use KGNGRAF, it is a graphic interface which works with HONDO, Gaussian and Mopac. HONDO is very similar to GAMESS so you should have no problems. HONDO + KGNGRAF are distributed by IBM as a product called CHEM-STATION I'm using it and I think it is a good code. You may contact MICHEL DUPUIS IBM Corporation Department MLM/078 Neighborhood Road Kingston, NY 12401 USA tel. (914) 385-4965 fax. (914) 385-4372 MICHEL @ KGNVMT.VNET.IBM.COM Best regards, Francesc ======================================================================== Prof. Francesc Illas, Facultat de Quimica, Departament de Quimica Fisica, Universitat de Barcelona, C/ Marti i Franques 1, 08028 Barcelona, SPAIN e-mail: work@hal6000.qf.ub.es phone : 34-3-402 1229 FAX : 34-3-402 1231 or 34-3-411 1492 ======================================================================== Answer 2 ======== Return-Path: Received: by ki1.chemie.fu-berlin.de (Smail3.1.28.1) from bioc1.biosym.com (146.202.0.2) with smtp id ; Wed, 12 Jul 95 01:42 MEST Received: from ibm12.biosym.com by bioc1.biosym.com (5.64/0.0) id AA07917; Tue, 11 Jul 95 16:42:41 -0700 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA18129; Tue, 11 Jul 1995 16:42:32 -0700 Received: from Messages.8.5.N.CUILIB.3.45.SNAP.NOT.LINKED.ibm12.biosym.com.rs.aix3 via MS.5.6.ibm12.biosym.com.rs_aix3; Tue, 11 Jul 1995 16:42:32 -0700 (PDT) Message-Id: Date: Tue, 11 Jul 1995 16:42:32 -0700 (PDT) From: Joerg Hill To: Stefan Schulz Subject: Re: CCL:GAMESS graphics programs Cc: Joerg Hill In-Reply-To: <199507112304.TAA18412@www.ccl.net> References: <199507112304.TAA18412@www.ccl.net> Status: RO X-Status: Hallo, Viewmol kann MO's dreidimensional zeichnen, als TIFF oder HPGL ausgeben und laueft auf SGI-Workstation. Allerdings verfuegt es ueber keine Funktion zum Einlesen von GAMESS-Outputs (nur Gaussian + Turbomole fuer Orbitale). Viewmol ist verfuegbar auf ftp.ask.uni-karlsruhe.de unter /pub/education/chemistry/viewmol.tar.gz. Eine Beschreibung zum Schreiben eines neuen Input-Filters ist in der Dokumentation vorhanden und ich glaube, dass es nicht allzu schwer waere. Ich bin gewaertig dabei, Viewmol umzuschreiben (unter anderem fuer Linux) und das Einlesen anderer Formate einfacher zu machen, das wird aber noch eine Weile dauern. Ich hoffe, das hilft. Viele Gruesse nach Berlin Joerg-R. Hill ------------------------------------------------------------------------------- - Dr. Joerg-Ruediger Hill | Every attempt to employ mathematical methods in the Biosym Technologies, Inc. | study of chemical questions must be considered pro- 9685 Scranton Road | foundly irrational and contrary to the spirit of San Diego, CA 92121-2777 | chemistry ... If mathematical analysis should ever USA | hold a prominent place in chemistry - an aberration | which is happily almost impossible - it would Phone (619) 546-5508 | occasion a rapid and widespread degeneration of Fax (619) 458-0136 | that science. E-mail jxh@biosym.com | A. Comte, 1838 ------------------------------------------------------------------------------- - The opinions expressed in this message are my personal opinions and no offical statements of Biosym Technologies, Inc. For informations about Biosym products take a look at: http://www.biosym.com/. ------------------------------------------------------------------------------- - Answer 3 ======== Return-Path: Received: by ki1.chemie.fu-berlin.de (Smail3.1.28.1) from Arizona.EDU (128.196.128.217) with smtp id ; Wed, 12 Jul 95 01:17 MEST Received: from pecos.rc.arizona.edu by Arizona.EDU (PMDF V5.0-3 #2381) id <01HSR0JTP734BESTW4@Arizona.EDU> for sschulz@chemie.fu-berlin.de; Tue, 11 Jul 1995 16:17:08 -0700 (MST) Received: by pecos.rc.arizona.edu (5.x/SMI-SVR4) id AA12701; Tue, 11 Jul 1995 16:16:12 -0700 Date: Tue, 11 Jul 1995 16:16:12 -0700 From: jaimeco@pecos.rc.arizona.edu (Jaime E. Combariza) Subject: Re: CCL:GAMESS graphics programs To: sschulz@chemie.fu-berlin.de Message-id: <9507112316.AA12701@pecos.rc.arizona.edu> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Content-MD5: Aoh7+5o3XYwDwGUI//feOg== Status: RO X-Status: Hi. I tried before PSI88 for this type of plots. You are limuted to the basis sets and you have to do some reformating of files but it worked just fine. You can get PSI88 from the CCL archives. JAime Combariza Answer 4 ======== Return-Path: Received: by ki1.chemie.fu-berlin.de (Smail3.1.28.1) from mozart.iq.ufrj.br (146.164.30.3) with smtp id ; Wed, 12 Jul 95 19:54 MEST Received: (jomal@localhost) by mozart.iq.ufrj.br (8.6.12/8.3) id OAA16735; Wed, 12 Jul 1995 14:51:56 GMT Date: Wed, 12 Jul 1995 14:51:56 GMT From: "Joao Otavio M.A. Lins / DFQ-IQ-UFRJ" Message-Id: <199507121451.OAA16735@mozart.iq.ufrj.br> To: sschulz@chemie.fu-berlin.de Subject: Re: CCL:GAMESS graphics programs Status: RO Hi Stefan, I suggest you to take a look at the MolDen program. It seems to do what you want. Take the latest version (2.5) on ftp://camms1.caos.kun.nl/pub/molgraph/molden But, I would like to know from you how to use Barchetta, since I have compiled it here but it shows me just the QUIT option when I run it. Cheers, Joao O.M.A. Lins System Manager Quantum Chemistry Group ______________________________________________________________________ Instituto de Quimica da U.F.R.J. email: jomal@dfq.ufrj.br Centro de Tecnologia, bloco A, sala 412 voice: +55-21-590-9890 Cidade Universitaria fax : +55-21-290-4746 21949-900 - Rio de Janeiro - RJ BRAZIL ______________________________________________________________________ Answer 5 ======== From dfq.ufrj.br!jomal Wed Jul 12 19:54:47 1995 Return-Path: Received: by ki1.chemie.fu-berlin.de (Smail3.1.28.1) from mozart.iq.ufrj.br (146.164.30.3) with smtp id ; Wed, 12 Jul 95 19:54 MEST Received: (jomal@localhost) by mozart.iq.ufrj.br (8.6.12/8.3) id OAA16735; Wed, 12 Jul 1995 14:51:56 GMT Date: Wed, 12 Jul 1995 14:51:56 GMT From: "Joao Otavio M.A. Lins / DFQ-IQ-UFRJ" Message-Id: <199507121451.OAA16735@mozart.iq.ufrj.br> To: sschulz@chemie.fu-berlin.de Subject: Re: CCL:GAMESS graphics programs Status: RO X-Status: Hi Stefan, I suggest you to take a look at the MolDen program. It seems to do what you want. Take the latest version (2.5) on ftp://camms1.caos.kun.nl/pub/molgraph/molden But, I would like to know from you how to use Barchetta, since I have compiled it here but it shows me just the QUIT option when I run it. Cheers, Joao O.M.A. Lins System Manager Quantum Chemistry Group ______________________________________________________________________ Instituto de Quimica da U.F.R.J. email: jomal@dfq.ufrj.br Centro de Tecnologia, bloco A, sala 412 voice: +55-21-590-9890 Cidade Universitaria fax : +55-21-290-4746 21949-900 - Rio de Janeiro - RJ BRAZIL ______________________________________________________________________ From owner-chemistry@ccl.net Tue Jul 18 09:10:29 1995 Received: from shiva.jussieu.fr for bouyer@ext.jussieu.fr by www.ccl.net (8.6.10/930601.1506) id JAA12521; Tue, 18 Jul 1995 09:01:18 -0400 Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id PAA16206 for ; Tue, 18 Jul 1995 15:01:08 +0200 Received: from [134.157.11.12] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Tue, 18 Jul 1995 15:01:05 +0200 X-Sender: bouyer@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 18 Jul 1995 15:05:59 +0100 To: chemistry@ccl.net From: bouyer@ext.jussieu.fr (Frederic BOUYER) Subject: Re: CCL:powermac Hi Paul, More interesting than Mopac perhaps, is the PowerMac version of Gamess, MacGamess. See http://hackberry.chem.niu.edu/ChemistrySoftware.html and click on Gamess. Thanks to Brett Bode. Hope this helps. Frederic Bouyer ____________________________________________________________________ Frederic BOUYER Laboratoire d'Electrochimie et de Chimie Analytique Equipe "Reactivite en Milieux Ioniques Liquides" (G. PICARD) ENSCP 11, rue Pierre et Marie Curie 75231 PARIS Cedex 05 FRANCE Tel : (33)-1-43-54-53-84 ou (33)-1-44-27-67-51 ou (33)-1-44-27-66-94 Fax : (33)-1-44-27-67-50 E-mail : bouyer@ext.jussieu.fr http://alcyone.enscp.jussieu.fr/ created, in progress ... http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/FB/ From owner-chemistry@ccl.net Tue Jul 18 09:25:30 1995 Received: from sums1.rdg.ac.uk for A.W.J.Smith@reading.ac.uk by www.ccl.net (8.6.10/930601.1506) id JAA13217; Tue, 18 Jul 1995 09:23:20 -0400 Received: from scsscsc1.rdg.ac.uk by sums1.rdg.ac.uk with SMTP - Local (PP); Tue, 18 Jul 1995 14:23:08 +0100 Received: by scsscsc1.rdg.ac.uk (8.6.12/8.6.12) id OAA20280; Tue, 18 Jul 1995 14:23:01 +0100 Date: Tue, 18 Jul 1995 14:23:00 +0100 (BST) From: Andy Smith To: "Chem. Comp. List" Subject: CCL: dielectric constants Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does any one know of a more recent compilation of dielectric data than Young K.F., Frederikse P.R., J. Phys. Chem, 2 (1973). I am after dielectric constants and elastic constants for rutiles (in particular CrO2) and also ternary molybdenum oxides (in particular NiMoO4, CoMoO4 or CaMoO4). I'll post any useful replies. thanks, Andy ---------------------------------------------------------------------------- Andrew W.J. Smith Phone: 44 (0)1734-875123 ext. 7415 or 4195 Chemistry Dept. Email: A.W.J.Smith@rdg.ac.uk University of Reading, Fax : 44 (0)1734- 311610 Whiteknights, Reading, Berkshire, RG6 2AD, UK --------------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Jul 18 12:10:38 1995 Received: from itc.univie.ac.at for stephan.irle@itc.univie.ac.at by www.ccl.net (8.6.10/930601.1506) id MAA17527; Tue, 18 Jul 1995 12:09:00 -0400 Received: from retsina.itc.univie.ac.at. (retsina.itc.univie.ac.at) by itc.univie.ac.at (5.65c/ITC-Vie(tk)-1.1m) id AA20528; Tue, 18 Jul 1995 18:08:42 +0200 Received: by retsina.itc.univie.ac.at. (5.65c/ITC-Vie(tk)-1.1s) id AA13403; Tue, 18 Jul 1995 18:08:42 +0200 From: stephan.irle@itc.univie.ac.at (Stephan Irle) Message-Id: <199507181608.AA13403@retsina.itc.univie.ac.at.> Subject: ADF vs. G92/DFT energies To: chemistry@ccl.net (Post Articles to CCL) Date: Tue, 18 Jul 1995 18:08:42 +0100 (MESZ) Organization: Institute for Theoretical Chemistry, University of Vienna Phone: (+43/1) 40480-679, priv. 4898087 Postal-Address: Waehringer Str. 17, A-1090 Wien, Austria Private-Address: Speckbachergasse 30/23, A-1160 Wien, Austria X-Mailer: ELM [version 2.4 PL20] Content-Type: text Content-Length: 1209 Dear Netters, the bond energies from ADF/X-Alpha/DZP and Gaussian/X-Alpha/6-31G** for H2 at the LDA-equilibrium geometry in D(\inf h) symmetry (which is calculated to be R=0.770 Angstrom from both programs) are (in kcal/mol): ADF/X-Alpha/DZP G92/DFT/XAlpha/6-31G** -150.1 -84.8 (the G92-Value was obtained by subtracting the energy of 2 Hydrogen atoms from the total molecular energy, while the ADF value is just simply printed out; there is no error due to a mixup of unrestricted and restricted energies since H is a one-electron system). This large difference requires explanation, and most likely it is due to my ignorance that these two values do not match. Any comments or suggestions? A second question: In dissociating H2 at the restricted level of theory with same functionals and basis sets as above, Gaussian shows the correct, i.e. wrong dissociation limit. ADF however does it wrong, i.e. the bond energy approaches zero. Thank you very much for your time and efforts Stephan Irle (Stud. of Prof. Lischka) -Stephan-Irle--stephan@itc.univie.ac.at--------------------------------------- http://www.itc.univie.ac.at/~stephan/ voice:+43/1/40480-679 From owner-chemistry@ccl.net Tue Jul 18 13:40:33 1995 Received: from uscmail.usc.es for qfsaulo@usc.es by www.ccl.net (8.6.10/930601.1506) id NAA19040; Tue, 18 Jul 1995 13:33:41 -0400 Received: by uscmail.usc.es (5.67b/1.34) id AA20929; Tue, 18 Jul 1995 19:38:31 +0200 Date: Tue, 18 Jul 1995 19:38:31 +0200 From: qfsaulo@usc.es (Saulo Vazquez Rodriguez) Message-Id: <199507181738.AA20929@uscmail.usc.es> To: chemistry@ccl.net Subject: SUMMARY of SGI hardware question Dear netters: Here is the collection of responses for "SGI hardware question". Thanks for your help. My original question was: We are going to buy a computer to run GAUSSIAN94. We will probably choose one of the two following options from Silicon Graphics: (1) A two-processor (R8000's) PowerChallenge workstation with 128MB RAM (in total) and 6 GB hard disk. (2) Two single-processor PowerChallenge workstations, with 128MB RAM and 4GB hard disk each. Does anybody known which of the two options has a better performance for GAUSSIAN calculations?. Thanks in advance. Saulo A. Vazquez (qfsaulo@usc.es) Response 1: Hi, If you have enough jobs to keep both processors constantly busy, it doesn't matter so much. The two processor machine is nice since it makes scheduling much easier; you can either queue a third job and it will start when either one of the other jobs finish, or you can use npri to put it at a low priority and again, it will finish when either of the others is done. Alternatively you can just run all 3 together and each will run at 66% speed and again, when any one of them finishes, the other 2 will run at 100% speed. If you only have one job to run (especially a big one) you can set it to run in parallel mode and use both processors that way. Due to extra overhead in parallel, however, only run in parallel if you only have 1 job to run. (i.e. the time for 2 jobs running serial to finish will be faster than if they are both in parallel.) If you only have one job, however, use the extra CPU! Bottom line, the 2 processor machine is a LOT more flexible, as long as you can afford the price difference. I hope this helps! Dan -- Dr. Daniel L. Severance dan@sage.syntex.com Staff Researcher Work phone: (415) 354-7509 Syntex Discovery Research Home phone: (415) 969-5818 R6W-002 Fax (Work): (415) 354-7363 3401 Hillview Ave Palo Alto, CA 94303 Response 2: Which option is the best depends on what you are most eager to calculate: many smaller jobs or fewer but bigger calculations. For the bigger jobs the Power Challenge can use several processors in parallel. This works very well in Gaussian 92 as you can see from the enclosed numbers. There is also the possibility to install additional processors later on. The parallel performance is probably even better in Gaussian 94. In the latter there is also network parallelism through the Linda parallel environment but then you need additional software in order to run parallel computations, for this option I have no idea about the performance. .............................................................................. Gaussian 92 Test Job 178: TATB rhf/6-31g**//hf/6-31g**, 300 basis functions: SGI Indigo^2, R4000: 113.4 min SGI Challenge, 1* R4400: 74.3 min SGI Power Challenge, 1*R8000: 15.7 min 1.0 Cray Y-MP, 1 processor: 13.2 min SGI Power Challenge, 2*R8000: 8.9 min 1.76 * 1 CPU SGI Power Challenge, 4*R8000: 5.5 min 2.85 * 1 CPU ------------------------------------------------------- Values obtained from other sources: Cray C90 8/256, 1 processor: 4.25 min Cray C90 8/256 (incore), 1 P.: 1.5 min IBM 590/pwr2: 17 min IBM 390/pwr2: 41 min 90 MHz Pentium: 600 min .............................................................................. Best Regards /Johan Landin ___________________________________________________________________ Johan Landin Tel: +46 31 773 3767 Dept. of Medical Biochemistry Fax: +46 31 41 6108 Medicinaregatan 9 Home: +46 31 14 7554 S-413 90 Goteborg, Sweden Email: landin@mednet.gu.se Response 3: If one ignores cost, then the next question may well be how fast do you wish to get a given job done. On a 2 processor machine the effective speed-up is about 1.85,,or so. You might contact Roberto Gomperts at SGI in Boston, the "keeper" of G94 on SGI hardware. He knows more than most about your question. Regards, John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- Response 4: I am afraid I cannot speak from experience of GAUSSIAN. However I would go for the two separate workstations. This would give you two screens, more core memory, more disk space and two separate processors anyway. If by chance one of the machines has a fault you would most likely have the other one working. Yours sincerely Peter Bladon. Response 5: The answer will depend on how you use Gaussian. If you are going to only run one job at any given time, then the single machine with 2CPU's might give you better performance, since you can do some of the work in parallel. If you are going to be running lots of separate Gaussian runs, then you can run two separate jobs on the two machines at the same time. Each individual run takes longer, but a collection takes about the same time (maybe even less since you don't have to pay for the overhead of parallization). Most of the people here tend to run a "family" of Gaussian jobs at a time. (same molecule, with different basis sets, or different constraints, etc) I would tend to favor the second option, especially if the two options are about equal in cost. a) I seem to recall that Gaussian is another one of those memory hogs, so "more memory is better". (More disk is better too) b) Two separate machines is better if (when) one dies. c) Sharing two machines is easier. The things that I can come up with that favor the single machine are related to networking and administration. Essentially, it is easier to only have one machine to troubleshoot, upgrade, and administer. If you already have other machines that you plan to network with this (these) new machine(s), then the extra work for the new machine(s) sort of blends in, because "it is always hardest the first time". ------------------------------------------------------------- ("`-/")_.-'"``-._ Wendy W. Richardson, Ph.D. (. . `) -._ )-;-,_() Sr. Research Investigator (v_,)' _ )`-.\ ``-' Searle _;- _,-_/ / ((,' 4901 Searle Parkway ((,.-' ((,/ Skokie, IL 60077 wwrich@ddpi7.monsanto.com Response 6: Of the two hardware platforms you describe I would lean to the PowerChallenge with two processors over two single processor machines. The memory bandwidth is better than the PowerIndigo2 and G94 automatically compiles to run in parallel, if desired, on a PowerChallenge. Gaussian 94 defaults to 32MB of memory per process which is sufficient for the majority of calculations and so even with 2 processors 128 MB is sufficient. Also G94 can now use your full disk by splitting its scratch files into 2GB chunks until SGI upgrades IRIX 6 to support files larger than 2GB. Gaussian 94 uses a shared memory parallel model on the PowerChallenge and HF and DFT energies, gradients and frequencies run in parallel. Post-HF calculations take some advantage of parallel but less than spectacular at this time. There is no additional cost for this capablity. Let us know if you have additional questions. Doug Fox help@gaussian.com Response 7: It look that (for performance of ONE g94 task) you'll receive more high performance on 2-processor system than on 2 systems, connected in one cluster - if the memory requirements for your task will be not higher than you have on 2-processor system. This is due to more bad parallelization in cluster if compare with 2-processor system. For performance of mix of G94 jobs you must have more high throughput on 2 independent 1-processor systems due to more high summary memory and absense of bus competitions. In the sense of price/performance 2-processor system must be more attractive. Dr.Mikhail Kuzminsky, N.D.Zelinsky Institute of Organic Chemistry, Moscow Response 8: We have a Power Challenge L and 2 Power Indigo2 workstations: Power Challenge L 4xR8000, 512 MB, 2x8GB Gaussian scratch directories (we implemented switching in a script) striped across 2 Fast-Wide Differential SCSI-2 channels each with 2 4 GB disks (aggregate 40 MBs and we sustain about 36 MBs) Runs 2 Gaussian jobs simultaneously. Each with MEMEORY=30 (240 MB). Power Indigo2 96/128 MB, 2/4 GB dedicated Gaussian scratch space on a single Fast-Wide SCSI2 disk (10 MBs and we sustain 6-8 MBs) These systems are constrained to running only 1 Gaussian job at a time with "MEMORY=8" (64 MB). All Gaussian acratch disks are Seagate Baraccuda drives. As far as raw CPU speed, the Power Indigo2 is about 0.8-0.9x the speed of a single processor on the PowerChallenge because of smaller cache and more limited bus bandwidth. Paralell performance is very good over 2-4 processors for HF and DFT calculations (degree of parallelization is about 0.95-0.97). Parallel performance is also good for MP2 calculations but not as good as HF or DFT (degree of prallelization is about 0.90). However you will find I/O to be a bigger issue particularly with Gaussian codes even for DIRECT calculations. Minimizing I/O will be a major concern and will dramatically impact your throughput. If you can, use striped file systems for your Gaussian scratch directory; and it would be best to stripe across disks on multiple SCSI channels as we do on the Power Challenge. On the Power Indigo 2, I/O is typically 20-50% of the total job time while on the Power Challenge it's 5-15%. Note that striping across a single SCSI channel will only improve I/O by about 20%. If you can... Power Indigo 2: Stripe across an internal (bus 0) and external (bus 1) disk on the Power Indigo2 or use a bus extender to use external devices on both channels. This will effectively double your I/O. Power Challenge: You can stripe across both internal SCSI channels but one is differential (20 MBs) and the other isn't (10 MBs) so you'd be limited to aggregate transfer rates of 30 MBs. Alternatively, you could stripe across the internal differential bus and the external bus which may be set to differential to get 40 MBs. We chose to take another route which offers future expandability. We installed an additional HIO card and bus extenders which provide three additional external differential SCSI2 channels; cost about $3,000. We then used two of these together with external differential 4 GB disks to give us a striped array which sustains 36 MBs. We plan to upgrade to 6 processors and stripe across 4 fast-wide SCSI-2 channels as soon as possible. Note that as your processors get faster I/O will become a larger fraction of the total job time. Therefore you'll have to look to balance your system performance to maximize throughput. Good luck! _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ Response 9: It depends a bit on the type of jobs you are going to run. Option 1 would allow parallelization, which is done reasonably well for a number of runtypes (in particular HF and DFT). This would mean one job at a time. If you want to run one job per processor, then go for option 2: it has more RAM available for each calculation and I/O will not interfere. Regardless of which configuration you choose: make sure that the scratch space is spread over at least two disks, in the form of a striped device. This greatly improves the I/O performance. For example, in the case of option 2 this would mean 2 2Gb disks, with 1Gb of each combined into a striped scratch partition of 2Gb total. With 1 4Gb disk, I/O performance is significantly worse. Best wishes, Nico van Eikema Hommes -- Dr. N.J.R. van Eikema Hommes Computer-Chemie-Centrum hommes@ccc.uni-erlangen.de Universitaet Erlangen-Nuernberg Phone: +49-(0)9131-856532 Naegelsbachstr. 25 FAX: +49-(0)9131-856566 D-91052 Erlangen, Germany From owner-chemistry@ccl.net Tue Jul 18 15:25:38 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.10/930601.1506) id PAA21472; Tue, 18 Jul 1995 15:24:29 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id AAA26678 for chemistry@ccl.net; Wed, 19 Jul 1995 00:54:29 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA17278; Wed, 19 Jul 95 00:54:24+050 Message-Id: <9507181954.AA17278@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Tue, 18 Jul 95 22:28:04 +0530 Date: Tue, 18 Jul 95 22:28:04 +0530 From: Mrigank To: chemistry@ccl.net Subject: Omega databese: Where ? Long time back i saw a different database than PDB for protein structure called OMEGA or something similar to that. Does anybody there with any idea as to where can this be located ? Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From owner-chemistry@ccl.net Tue Jul 18 16:40:41 1995 Received: from mcmail.CIS.McMaster.CA for g8815205@mcmail.CIS.McMaster.CA by www.ccl.net (8.6.10/930601.1506) id QAA23908; Tue, 18 Jul 1995 16:39:09 -0400 Received: (from g8815205@localhost) by mcmail.CIS.McMaster.CA (8.6.9/8.6.9) id QAA29973; Tue, 18 Jul 1995 16:39:33 -0400 Date: Tue, 18 Jul 1995 16:39:32 -0400 (EDT) From: "S.G. Urquhart" Subject: Re: CCL:where to ftp Bader's program To: Shubin Liu cc: chemistry@ccl.net In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Email Bader at bader@mcmaster.ca Good luck! Stephen On Mon, 17 Jul 1995, Shubin Liu wrote: > > Dear All: > I need to compute the density, its gradient and Laplacian of a few > molecules lately. I was told that the program by Professor Bader in McMaster > University does the job. And it is said that it is for free and available > at some ftp address. Can somebody let me know where I can get one? Thanks > a lot! > > Shubin > ............................................................................. > Shubin Liu > > Department of Chemistry Email: shubin@email.unc.edu > University of North Carolina sliu@mulliken.chem.unc.edu > Chapel Hill, NC 27599-3290 Tel : (919) 962-0150(O) > USA (919) 914-6923(H) > ............................................................................. > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: owner-chemistry@ccl.net > -- Original Sender From: Address: shubin@email.unc.edu > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > > From owner-chemistry@ccl.net Tue Jul 18 17:10:38 1995 Received: from audumla.students.wisc.edu for patterson@chem.wisc.edu by www.ccl.net (8.6.10/930601.1506) id QAA24496; Tue, 18 Jul 1995 16:56:47 -0400 Received: from [144.92.91.188] by audumla.students.wisc.edu; id PAA35571; 8.6.9W/42; Tue, 18 Jul 1995 15:56:43 -0500 Message-Id: <199507182056.PAA35571@audumla.students.wisc.edu> Date: Tue, 18 Jul 1995 15:56:52 -0600 To: chemistry@ccl.net From: patterson@chem.wisc.edu (Eric V. Patterson) Subject: G94 warning against LANL1DZ Dear Netters- In the G94 User's Reference (pg. 23), a small footnote warns that the use of LANL1DZ is "strongly discouraged". Can someone tell me why? The best I can tell, LANL1DZ and LANL2DZ only differ in the use of D95V for the former and D95 for the latter on first row atoms. Is there some general flaw with LANL1DZ that I should be aware of? Any help is appreciated. Eric ============================================================================== From the desk of: Eric Patterson voice: (608) 262-0599 Department of Chemistry FAX: (608) 262-0381 University of Wisconsin - Madison email: patterson@chem.wisc.edu 1101 University Ave. Madison, WI 53706 ============================================================================ == From owner-chemistry@ccl.net Tue Jul 18 17:40:36 1995 Received: from hub.ucsb.edu for felice@bioorganic.ucsb.edu by www.ccl.net (8.6.10/930601.1506) id RAA25208; Tue, 18 Jul 1995 17:39:11 -0400 Received: from bioorganic (bioorganic.ucsb.edu) by hub.ucsb.edu; id AA12215 sendmail 4.1/UCSB-2.1-sun Tue, 18 Jul 95 14:39:07 PDT for chemistry@ccl.net Received: by bioorganic (931110.SGI/930416.SGI) for @hub.ucsb.edu:chemistry@ccl.net id AA14407; Tue, 18 Jul 95 14:37:31 -0700 From: "Felice Chu" Message-Id: <9507181437.ZM14405@bioorganic> Date: Tue, 18 Jul 1995 14:37:29 -0700 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: calculate pKas Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hello, I was wondering if someone out there would know of a program that could predict the pKas of carboxylic acids. For example, if a molecule had two carboxylates, is there a program that could calculate the 2 pKas. If you could provide the name of the program and where I could obtain it, I would appreciate it. Thanks, Felice Chu felice@bioorganic.ucsb.edu 805-893-2234 Dept. of Chemistry Univ. of California Santa Barbara, CA 93106 From owner-chemistry@ccl.net Tue Jul 18 17:46:38 1995 Received: from gusun.acc.georgetown.edu for choic@gusun.acc.georgetown.edu by www.ccl.net (8.6.10/930601.1506) id RAA25143; Tue, 18 Jul 1995 17:35:37 -0400 Received: by gusun.acc.georgetown.edu; (5.0/1.1.8.2/6Jan9518:19pm) id AA13675; Tue, 18 Jul 1995 17:34:06 +0500 Date: Tue, 18 Jul 1995 17:34:06 -0400 (EDT) From: Cheol Choi To: chemistry@ccl.net Subject: Conversion factor of IR intensity? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII content-length: 682 Hi! everyone. I have a problem with conversion factor of IR intensity . The followings are what I already knew: Intensity units conversion factor to km mole-1 ------------------------------------------- cm mole-1 10-5 cm millimole-1 10-2 cm-2 atm-1 at 273 K 0.224 cm-2 atm-1 at298 K 0.245 sec-1 cm-1 atm-1 at 273 K 7.477 X 10-12 cm2 mole-1 v0(cm-1) X 10-5 ------------------------------------------ where v0 is the center of band position. But I found another unit for IR intensity which is mol-1 cm-2. Please let me know how to convert it into km mole-1. Thank you, Cheol Ho Choi Georgetown Univ. From owner-chemistry@ccl.net Tue Jul 18 17:51:15 1995 Received: from kcvax3.kenyon.edu for mcclellane@kenyon.edu by www.ccl.net (8.6.10/930601.1506) id RAA25095; Tue, 18 Jul 1995 17:29:32 -0400 Received: by kenyon.edu (MX V4.1 VAX) id 125; Tue, 18 Jul 1995 17:30:59 EST Date: Tue, 18 Jul 1995 17:30:35 EST From: "Let's boogie" To: mrigank@imtech.ernet.in CC: chemistry@ccl.net Message-ID: <009938BC.A7B08160.125@kenyon.edu> Subject: Protein Structure Databases From: MX%"mrigank@imtech.ernet.in" 18-JUL-1995 16:57:24.66 To: MX%"chemistry@ccl.net" CC: Subj: CCL:Omega databese: Where ? Long time back i saw a different database than PDB for protein structure called OMEGA or something similar to that. Does anybody there with any idea as to where can this be located ? Mrigank ---- Mrigank-- I did a quick search for protein structure databases. Although I did not come up with a database with a name similar to Omega, I found a few other links that may prove helpful to you, or to other compchem.dis users. I did not test these links, but have been to most of them in the past and they have proved quite useful. Hope these help!! Eva McClellan Kenyon College ************* Pedro's Biomolecular Research Tool 1. Pedro's Biomolecular Research Tool Database relating Proteins Structures and Sequences http://www.public.iastate.edu/~pedro/rt_1.html 2. Biochem and Mol Bio Resources http://cctr.umkc.edu/user/dborza/Bioresources.html 3. SWISS-PROT Protein sequence database http://www.hgmp.mrc.ac.uk/PROTEIN-SEQ-DB.html 4. SESAM Database for protein structure http://www.ucmb.ulb.ac.be/UCMBdescription/databases_description.html 5. Protein Database and link to related services http://www.ibf.unige.it/ls/Proteins 6. FSSP database of structurally aligned protein fold families http://www.sander.embl-heidelberg.de/fssp/paper.html ********** From owner-chemistry@ccl.net Tue Jul 18 18:40:38 1995 Received: from mail.crl.com for sunger@crl.com by www.ccl.net (8.6.10/930601.1506) id SAA26546; Tue, 18 Jul 1995 18:33:07 -0400 Received: from crl5.crl.com by mail.crl.com with SMTP id AA19098 (5.65c/IDA-1.5 for ); Tue, 18 Jul 1995 15:32:10 -0700 Received: by crl5.crl.com id AA14153 (5.65c/IDA-1.5); Tue, 18 Jul 1995 15:31:10 -0700 Date: Tue, 18 Jul 1995 15:31:09 -0700 (PDT) From: Stefan Unger To: Felice Chu Cc: chemistry@ccl.net Subject: Re: CCL:calculate pKas In-Reply-To: <9507181437.ZM14405@bioorganic> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There is a program PKALC that will do this. I am a dealer. Please respond with full mailing address and I will send you literature. Thanks. BioSoftware Marketing On Tue, 18 Jul 1995, Felice Chu wrote: > Hello, > > I was wondering if someone out there would > know of a program that could predict the pKas > of carboxylic acids. For example, if a molecule > had two carboxylates, is there a program > that could calculate the 2 pKas. > > If you could provide the name of the > program and where I could obtain it, I > would appreciate it. > > Thanks, > > Felice Chu > felice@bioorganic.ucsb.edu > 805-893-2234 > > Dept. of Chemistry > Univ. of California > Santa Barbara, CA 93106 > > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: owner-chemistry@ccl.net > -- Original Sender From: Address: felice@bioorganic.mechanisms.ucsb.edu > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > >