From prs@organik.uni-erlangen.de Tue Sep 23 10:26:07 1997 Received: from faui45.informatik.uni-erlangen.de for prs@organik.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id JAA28528; Tue, 23 Sep 1997 09:31:37 -0400 (EDT) Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by uni-erlangen.de with SMTP id PAA28645 (8.7.6/7.5c-FAU); Tue, 23 Sep 1997 15:31:18 +0200 (MET DST) Received: (from prs@localhost) by organik.uni-erlangen.de id PAA14223 (8.6.12/7.4f-FAU);; Tue, 23 Sep 1997 15:17:50 +0200 From: "Peter R. Schreiner" Message-Id: <199709231317.PAA14223@derioc1.organik.uni-erlangen.de> Subject: Pentium Pro vs. Pentium II To: kim@traj.chem.wayne.edu (Kim Bolton) Date: Tue, 23 Sep 1997 15:17:49 +0200 (MET) Cc: chemistry@www.ccl.net In-Reply-To: <9709231138.AA14511@traj.chem.wayne.edu> from "Kim Bolton" at Sep 23, 97 07:38:27 am Return-Receipt-To: prs@organik.uni-erlangen.de Organization: Institut fuer Organische Chemie, Universitaet Goettingen Postal-Address: Tammannstr. 2, D-37077 Goettingen, Bundesrepublik Deutschland Fax: +49-(0) 551-399475 X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Dear CCLers, The question "Does anyone have experience with numerical applications (Ab initio codes etc.) on Pentium Pro vs. Pentium II under Linux systems?" triggered quite a number of useful responses. It looks like PCs are finally replacing average type workstations. It is still not clear whether or not the Pentium II series really is better that the Pentium Pros - at least they are different in price. Here are the responses: You can find some timings concerning PC GAMESS benchmarks on Pentium Pro and Pentium II systems under Windows NT on the URLs: http://classic.chem.msu.su/gran/gamess/index.html http://classic.chem.msu.su/gran/gamess/performance.html May be these can somewhat help to estimate performance under Linux. Regards, Alex. A. Granovsky Moscow State University ----------------------------------------------------------- gran@classic.chem.msu.su %%%%%%%%% I am really interested in any informations you will receive. My personal experience, up to now, is only with the Pro 256kb cache. I used it to run DFT programs, and the performance, with big systems (30 atoms or more) are excellent. It is 85% of an IBM rs6000 Mod. 3CT with 1MB of L2 cache memory. And it costs roughly 20%. Remarkable! As for the PII, I have no experience. Anyhow, I "think" that the Pro even if the clock is slower, should perform better. The L2 cache in the Pro is fully integrated on the processor and thus run at the same speed of the processor itself. On the PII, instead, the the L2 memory runs at 1/2 of the speed of the processor. Finally, the Pro is somewhat cheaper than the PII 266 MHz. Hope it helps, Best regards Luigi Luigi Cavallo Dept. of Chemistry Univ. of Naples, ITALY Email cavallo@chemna.dichi.unina.it %%%%%%%%%% While I don't have any timings or benchmarks for Pentium II systems, I suggest you have a look at http://www.specbench.org/ for SPECint95 and SPECfp95 results. From what I've seen the pentium II is much better in floating point and better in integer than the pentium pro. Also direct your web browser at http://www.intel.com/procs/perf/PentiumII/spec95int.htm and http://www.intel.com/procs/perf/PentiumII/cpumark32.htm and http://www.intel.com/procs/perf/PentiumII/nortonsi32.htm To the bottom of this email I've attached the output of cpu benchmarks I ran on a dual PPRO 200 (the fact that it is dual means nothing; the SMP code for Linux is bad right now and the benchmarks are not multithreading). good luck, Rich BBBBBB YYY Y TTTTTTT EEEEEEE BBB B YYY Y TTT EEE BBB B YYY Y TTT EEE BBBBBB YYY Y TTT EEEEEEE BBB B YYY TTT EEE BBB B YYY TTT EEE BBBBBB YYY TTT EEEEEEE BYTEmark (tm) Native Mode Benchmark ver. 2 (10/95) NUMERIC SORT : Iterations/sec.: 70.24 Index: 1.80 STRING SORT : Iterations/sec.: 4.35 Index: 1.94 BITFIELD : Iterations/sec.: 16976692.52 Index: 2.91 FP EMULATION : Iterations/sec.: 3.90 Index: 1.87 FOURIER : Iterations/sec.: 1393.26 Index: 1.58 ASSIGNMENT : Iterations/sec.: 0.71 Index: 2.71 IDEA : Iterations/sec.: 138.29 Index: 2.12 HUFFMAN : Iterations/sec.: 63.19 Index: 1.75 NEURAL NET : Iterations/sec.: 0.71 Index: 1.13 LU DECOMPOSITION: Iterations/sec.: 52.81 Index: 2.74 ...done... ===========OVERALL============= INTEGER INDEX: 2.119 FLOATING-POINT INDEX: 1.700 (90 MHz Dell Pentium = 1.000) =============================== %%%%%%%%%%%%%% I don't have any real quantitative answers for you, but thought I might pass along my experience with running Gaussian 94 under Linux on a single Pentium Pro 200MHz with 64MB RAM and a fast/wide SCSI hard drive. The couple of runs that I did to compare the speed with an Indigo2 (single R8000 75MHz processor) seemed to give a factor of about 3-4 in cpu time. That is, the Pentium Pro 200 was 3-4 times slower than the SGI. Considering the relative costs this is pretty good in my opinion. I compiled Gaussian94 using f2c/gcc. I sometimes wonder if Gaussian would run faster if compiled with a good commercial fortran compiler (e.g. Absoft). But even the educational price ($524.25 US) is too pricey for me right now. My guess is that you will not see much of an improvement with the Pentium II for these types of floating point intensive calculations. I believe that most of the advantage of the Pentium II comes from MMX capabilities which you will find useless with Linux. At least this is what I recall reading in Linux Journal or Unix Review. Floating point is probably only marginally faster than a Pentium Pro. Hope this helps - John Bushnell bushnell@gaucho.ucsb.edu %%%%%%%%%%%%%% We are implementing a system called LoBoS, short for Lots of Boxes on Shelves, which consists of 64 dual Pentium Pro machines. We organize them to do supercomputing with molecular dynamics calculations. We tested the Pentium Pro and the Pentium II prior to selecting the Pentium Pro. 1. The Pentium Pro gives equivalent performance. Our benchmark which consists of extensive floating point (CHARMM) took 2 hours on a 200 MHz Pentium Pro. On a 266 MHz Pentium II the time was 2 hours times (200/266). This is not surprising since a PentiumII is a Pentium Pro core with the MMX instructions added on. MMX, which is entirely integer operations, doesn't do anything for floating point operations. It might do something for pointer references and integer math but compilers do not currently use MMX for these operations. The PentiumII has some new features. One which improves performance is better IO to the system bus. However, this is essentially offset by the fact that the L2 cache runs at half the CPU speed. Essentially we saw a wash between these two design changes. Buy the Pentium Pro ! It gives you MUCH more for the money. Eric Billings LoBoS Project NIH %%%%%%%%%%%% I tested calculations using Gaussian 94, Revision D.4 1. #N b3p86/gen 5d freq : ClO2 calculation using 79 basis Pentium Pro 200MHz : 256 mins Pentium II 233MHz : 192 mins CrayT3E (DEC Alpha EV5.6 450MHz, 900MFLOPS, not parallelized) : 39 mins 2. #N b3p86/gen 5d opt=z-matrix : Cl2O calculation using 131 basis Pentium 133MHz : 336 mins Pentium Pro 200MHz : 149 mins Pentium II 233MHz : 130 mins CrayT3E (DEC Alpha EV5.6 450MHz, 900MFLOPS, not parallelized) : 56 mins ----------------------------------------------------------------------- Son, Sang-kil zannavi@orbit.kaist.ac.kr \\____// (. .) | Quantum Chemistry Laboratory | " | | Dept. of Chemistry, KAIST, South Korea CC|___/CCC http://cmsrisc.kaist.ac.kr/qclab/ U ----------------------------------------------------------------------- ...Peter -- //// ___|--00___________________________________________________________________ C ^ Dr. Peter R. Schreiner \ ~/ Institut fuer Organische Chemie <><> Georg-August Universitaet Goettingen Tammannstr. 2 Phone: +49-(0)551-393287 D-37077 Goettingen, Germany FAX: +49-(0)551-399475 http://www.gwdg.de/~pschrei ___________________________________________________________________________ From jstewart@fai.com Tue Sep 23 12:26:08 1997 Received: from fujitsuI.fujitsu.com for jstewart@fai.com by www.ccl.net (8.8.3/950822.1) id MAA00237; Tue, 23 Sep 1997 12:01:44 -0400 (EDT) Received: from 169-185-21.ipt.aol.com (169-185-21.ipt.aol.com [152.169.185.21]) by fujitsuI.fujitsu.com (8.8.5/8.7.3) with SMTP id JAA06645 for ; Tue, 23 Sep 1997 09:01:10 -0700 (PDT) Message-Id: <3.0.16.19691231170000.43ffbf36@iti2.net> X-Sender: jstewart@iti2.net X-Mailer: Windows Eudora Pro Version 3.0 (16) Date: Tue, 23 Sep 1997 11:01:35 -0600 To: CHEMISTRY@www.ccl.net From: "James J. P. Stewart" Subject: A problem in quantum chemistry. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I have the following problem. While I think I know the answer, input from different people would be very helpful. In other words, HELP!!! Given a diatomic A-B, with the derivative of the dipole with respect to distance = 1.2345 Debye/Angstrom, and mass A = mass B, what is the value of the vibrational transition dipole? If mass A = 1, mass B = 1000, what is the value of the transition dipole? Jimmy Stewart From schneider@msbcs.ENET.dec.com Tue Sep 23 16:26:09 1997 Received: from mail11.digital.com for schneider@msbcs.ENET.dec.com by www.ccl.net (8.8.3/950822.1) id PAA02819; Tue, 23 Sep 1997 15:52:58 -0400 (EDT) Received: from us8rmc.bb.dec.com (us8rmc.bb.dec.com [16.53.0.44]) by mail11.digital.com (8.7.5/UNX 1.5/1.0/WV) with SMTP id PAA13228 for ; Tue, 23 Sep 1997 15:43:15 -0400 (EDT) Received: from msbcs.enet by us8rmc.bb.dec.com (5.65/rmc-17Jan97) id AA22916; Tue, 23 Sep 97 15:21:33 -0400 Message-Id: <9709231921.AA22916@us8rmc.bb.dec.com> Received: from msbcs.enet; by us8rmc.enet; Tue, 23 Sep 97 15:43:14 EDT Date: Tue, 23 Sep 97 15:43:14 EDT From: "Chuck (aka chazix), 508-493-1399 (DTN 223-1399)" To: chemistry@www.ccl.net Cc: loha@mail.dec.com, schneider@msbcs.ENET.dec.com Apparently-To: loha@mail.dec.com, chemistry@www.ccl.net Subject: re: Perf. of Alpha vs. R10k Greetings, I don't follow this forum, but a colleague forwarded Dr. van der Spoel's notes. Was the Fortran code that was posted (routine FORLJC, with a test harness) the same code that produced a timing of 31 seconds on a 400MHz Alpha? On my system, it runs in less than 4 seconds, either with the options Dr. van der Spoel gave, or with just "f90 -fast -tune host -non_shared". (The simpler command is a wee bit better for the given code on my system, mostly because the rather speculative optimizations at the -O5 level are not attempted. As the man page suggests, it's best to test -O5 to make sure it's an improvement. That's why -O4 is the default.) I assume from the cache size that Dr. van der Spoel's system is an AlphaStation 500/400. My system is an AlphaServer 4100 5/400, which has a 4MB backup cache. Both use an EV5 generation Alpha chip at the same clock speed, so the bcache and main memory system are the main differences that would affect the given code. But I don't think that the larger bcache could account for the near order of magnitude difference between Dr. van der Spoel's timings and mine. Either I'm timing something different, or some other interesting factor remains hidden. Regards, Chuck Schneider Digital High Performance Computing Expertise Center Maynard, Massachusetts (e-mail me directly for best response) From pino@jsbach.dichi.unina.it Wed Sep 24 07:26:25 1997 Received: from jsbach.dichi.unina.it for pino@jsbach.dichi.unina.it by www.ccl.net (8.8.3/950822.1) id GAA05986; Wed, 24 Sep 1997 06:45:10 -0400 (EDT) From: Received: by jsbach.dichi.unina.it (AIX 3.2/UCB 5.64/4.03) id AA09954; Fri, 8 Mar 1996 12:44:11 +0100 Date: Fri, 8 Mar 1996 12:44:11 +0100 Message-Id: <9603081144.AA09954@jsbach.dichi.unina.it> To: chemistry@www.ccl.net Subject: Molecular Graphic Software for O2 Dear Netters, I would appreciate to receive informations about molecular graphic FREE software compatible and tested for O2 Silicon Graphics. Thanx in Advance Pino ========================== Pino Milano Universita' degli Studi di SALERNO e-mail pino@jsbach.dichi.unina.it ========================== From Erdem.Buyukbingol@pharmacy.ankara.edu.tr Wed Sep 24 10:26:20 1997 Received: from io.pharmacy.ankara.edu.tr for Erdem.Buyukbingol@pharmacy.ankara.edu.tr by www.ccl.net (8.8.3/950822.1) id JAA06861; Wed, 24 Sep 1997 09:49:52 -0400 (EDT) Received: from 194.27.25.26.erdem (erdem.pharmacy.ankara.edu.tr [194.27.25.26]) by io.pharmacy.ankara.edu.tr (8.8.5/8.8.5) with SMTP id QAA01625 for ; Wed, 24 Sep 1997 16:50:34 +0300 Message-Id: <1.5.4.32.19970924135140.006c1758@pharmacy.ankara.edu.tr> X-Sender: erdem@pharmacy.ankara.edu.tr X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 24 Sep 1997 16:51:40 +0300 To: chemistry@www.ccl.net From: Erdem Buyukbingol Subject: New Computational Chemistry Lab. Dear Netter, We would like to set up a new computational chemistry lab. for both education and research with unix-based machines. However, due to the limitations of financial sources, it seems difficult to buy unix-based computer systems such as SGI, IRIX, IBM/R6000. I am asking if there will be an availability of such systems as donation. Your benefit would be much appreciated. Dr. Erdem Buyukbingol Ankara University, Faculty of Pharmacy, Tandogan 06100, Ankara, Turkey Tel: +90 312 212 6805 ext. 165 Fax: +90 312 222 6543 E-mail: erdem@pharmacy.ankara.edu.tr From bruno@antas.agraria.uniss.it Wed Sep 24 10:37:03 1997 Received: from ICINECA.CINECA.IT for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id KAA06949; Wed, 24 Sep 1997 10:02:28 -0400 (EDT) Received: from cinymp.cineca.it by ICINECA.CINECA.IT (IBM VM SMTP V2R2) with TCP; Wed, 24 Sep 97 16:03:29 ITA Received: from antas.agraria.uniss.it by cinymp.cineca.it with SMTP (5.61/CRI-80.1) id AA88325; Wed, 24 Sep 97 16:01:36 +0200 Date: Wed, 24 Sep 1997 16:00:08 +0100 (NFT) From: "Dr. Bruno Manunza" To: pino@jsbach.dichi.unina.it Cc: chemistry@www.ccl.net Subject: Re: CCL:Molecular Graphic Software for O2 In-Reply-To: <9603081144.AA09954@jsbach.dichi.unina.it> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 8 Mar 1996 pino@jsbach.dichi.unina.it wrote: > > Dear Netters, > I would appreciate to receive informations about > molecular graphic FREE software compatible and tested > for O2 Silicon Graphics. > Thanx in Advance > Pino > > ========================== > Pino Milano > Universita' degli Studi di > SALERNO > > e-mail pino@jsbach.dichi.unina.it > ========================== Dear Pino, I've used the following softwares on SGI O2: PDBtool molden gopenmol VMD (Visual Molecular Dynamics) rasmol msms (M. Sammer Molecular Surface)a all freeware If you want the sites have a look to the software pages on our website at http://antas.agraria.uniss.it Hope it helps regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From elewars@alchemy.chem.utoronto.ca Wed Sep 24 12:26:40 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id LAA08169; Wed, 24 Sep 1997 11:37:53 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id LAA09431 for chemistry@www.ccl.net; Wed, 24 Sep 1997 11:37:52 -0400 (EDT) Date: Wed, 24 Sep 1997 11:37:52 -0400 (EDT) From: "E. Lewars" Message-Id: <199709241537.LAA09431@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: SOURCE OF EYRING QUOTE 1997 Sept 24 Hello, Does any one heve the actual literature reference for this quotation (which reminds us that reacting molecules stray outside the intrinsic reaction coordinate)? : ---------------------- ... A MOLECULAR SYSTEM ... (PASSES) ... FROM ONE STATE OF EQUILIBRIUM TO ANOTHER ... BY MEANS OF ALL POSSIBLE INTERMEDIATE PATHS, BUT THE PATH MOST ECONOMICAL OF ENERGY WILL BE THE MORE OFTEN TRAVELED. -- HENRY EYRING, 1945 ------------------- Thanks E. Lewars ======================= From dan@sage.pal.roche.com Wed Sep 24 13:26:22 1997 Received: from chub1.pal.roche.com for dan@sage.pal.roche.com by www.ccl.net (8.8.3/950822.1) id MAA08675; Wed, 24 Sep 1997 12:42:11 -0400 (EDT) Received: from sage.pal.roche.com (sage.syntex.com) by Roche.COM (PMDF V5.0-8 #15454) id <01IO0LH8A9PC000CK3@Roche.COM>; Wed, 24 Sep 1997 09:37:54 -0700 (PDT) Received: by sage.pal.roche.com (950413.SGI.8.6.12/951211.SGI.AUTO) id JAA09997; Wed, 24 Sep 1997 09:36:30 -0700 Date: Wed, 24 Sep 1997 09:36:30 -0700 From: dan@sage.pal.roche.com (Dr. Daniel L. Severance) Subject: Re: CCL:re: Perf. of Alpha vs. R10k In-reply-to: "Chuck (aka chazix), 508-493-1399 (DTN 223-1399)" <"CCL:re: Perf. of Alpha vs. R10k"@Roche.COM> (Sep 23, 3:43pm) To: "Chuck (aka chazix), 508-493-1399 (DTN 223-1399)" Cc: chemistry@www.ccl.net Message-id: <9709240936.ZM9995@sage.pal.roche.com> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT References: <9709231921.AA22916@us8rmc.bb.dec.com> On Sep 23, 3:43pm, Chuck (aka chazix), 508-493-1399 (DTN 223-1399) wrote: > Subject: CCL:re: Perf. of Alpha vs. R10k > > I don't follow this forum, but a colleague forwarded Dr. van der Spoel's > notes. Was the Fortran code that was posted (routine FORLJC, with a test > harness) the same code that produced a timing of 31 seconds on a 400MHz > Alpha? > On my system, it runs in less than 4 seconds, either with the options > Dr. van der Spoel gave, or with just "f90 -fast -tune host -non_shared". Hi, It runs in 1.3 seconds on an Indigo2 R10K machine (1 MB cache) with -Ofast, or 1.8 seconds using the compile options listed. His 30 second time was presumably for the whole program. It sounds like the R10K SGI machines are still significantly faster than the alpha machines even with the test code. The R10K chips were a BIG jump in performance over the previous R4xxx series >from SGI, so this isn't that far from possibility. Take care, Dan -- Dr. Daniel L. Severance dan@sage.syntex.com ***************** Research Scientist Work phone:(650) 354-7509 Note the Change Roche Bioscience (Syntex) Fax (Work):(650) 852-1875 in area code! R6W-201, 3401 Hillview Ave Palo Alto, CA 94304 ***************** From choic@gusun.georgetown.edu Wed Sep 24 22:26:27 1997 Received: from gusun.georgetown.edu for choic@gusun.georgetown.edu by www.ccl.net (8.8.3/950822.1) id VAA10869; Wed, 24 Sep 1997 21:35:08 -0400 (EDT) Received: from localhost (choic@localhost) by gusun.georgetown.edu (8.8.5/8.8.5) with SMTP id VAA06147 for ; Wed, 24 Sep 1997 21:34:39 -0400 (EDT) Date: Wed, 24 Sep 1997 21:34:39 -0400 (EDT) From: Cheol Choi X-Sender: choic@gusun To: chemistry@www.ccl.net Subject: No unpruned grid is available for this atom.? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I was doing DFT-SCF for a compound containing Iodine with G94 which gave me " No unpruned grid is available for this atom." Would it affect the numerical accuracy of SCF result? In fact, the compound also has Mn and the SCF failed. The initial geometry was taken from experiment. How can I improve the SCF convergency for this compound? Thanks in advance. Cheol-Ho Choi Georgetown Univ.