From chemistry-request@www.ccl.net Wed Feb 24 18:20:42 1999 Received: from diamin.chem.cinvestav.mx (root@diamin.chem.cinvestav.mx [148.247.11.63]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA25993 Wed, 24 Feb 1999 18:20:40 -0500 (EST) Received: from localhost by diamin.chem.cinvestav.mx via sendmail with smtp id (Debian Smail3.2.0.101) for ; Wed, 24 Feb 1999 17:23:16 -0600 (CST) Date: Wed, 24 Feb 1999 17:23:16 -0600 (CST) From: webmaster RelaQ X-Sender: kaiser@diamin.chem.cinvestav.mx To: "Jerry C.C. Chan" cc: chemistry@www.ccl.net Subject: Re: CCL:Summary: AMD-K6/linux for G98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by www.ccl.net id SAA25994 On Wed, 24 Feb 1999, Jerry C.C. Chan wrote: > > Sorry for any duplication, it seems the following summary didn't get > posted at the first time. > ------------------------- > > Many thanks for those who responsed to my post. In short, P-II is highly > recommended, DEC Alpha (21164) is a good alternative, Celeron-based > machine MAY be a good choice (see both positive and negative comments > below), AMD-K6 is not at all useful for numerical calculation. The 11th > response from Prof Teppen is very interesting that the performance of his > 4-processor-P-II linux box from Peter Pulay's company (cost $11,000) is > only 15% slower than a Cray T3E-1200 with 4 processors. Please excuse me > for removing some of the signatures in order to shorten this summary. > > Original post: > > We have a plan to get a linux box equipped with AMD-K6 for Gaussian 98 > > calculations. However, it seems that the recommended blas library and > > Portland Fortran compiler are optimized for Intel CPU only (I may be > > mistaken saying so). I would be grateful if anyone could share his/her > > experience concerning the following thoughts > > i. pay more money to buy Intel processor > > ii. go on with our plan (assuming that the performance of Linux/AMDK6-G98 > > won't be very different from Linux/IntelPII-G98) > > iii. keep the AMD but switch to NT/G98W instead of linux/G98 > > ++++++Responses++++++ > 1. From: Drake Diedrich > > BLAS isn't apparently heavily used in Gaussian (only in CI methods), > but... you may still be better off getting an Intel CPU. On heavy floating > point and memory bandwidth I have benchmarked a pentium-166 outperforming an > AMD K6/2-300. Pentiums (and later Intel processors) have pipelined floating > point units while AMD and Cyrix have only a single floating point execution > unit. AMD processors are not competitive with the pentium-II. > You should add the DEC Alpha (21164) to your shortlist of alternatives. > I haven't benchmarked Gaussian on it, but if you search the web you'll find > a hand coded BLAS library for the Alpha that achives 800 MFlops on a 600MHz > chip. The ASCI-Red BLAS library gets only 180 MFlops on our Pentium-II/266. > > -Drake > > 2. From fparnold@balihai.uchicago.edu Tue Feb 23 10:46:42 1999 > > If you follow the links through the Beowulf page (www.beowulf.org) to > their archive for February of 1999 (or possible Jan) there is a comparison > of CHARMm run times on the K6 vs. Celeron. Basically, CHARMm is slow on > the K6, but runs on teh Celeron at the same speed of the PII. So, if > you're not cache limited, this is a cheap option. IF you are, then the K6 > if probably ok. My personal results with GAMESS-US indicates that the > K6-233 is slightly faster than a P200 classic, and roughly 5% faster than > an SGI O2 with an R5000 processor and secondary cache. > > Unfortunately, the real answer therefore is, "buy one, and benchmark it > yourself". If you get good numbers, buy more and make a cluster out of > them. If you don't, you can probably return it and just be out the > shipping fee. > -fred > > 3. From pczyryca@smurf.chem.usu.edu Tue Feb 23 10:46:45 1999 > > K6 is slower than PentiumII (with the same clock). Especially on floating > point operations. This is not OS dependent, so I wouldn't expect better > performance with NT/G98W combination. > Probably it's the best option to spend some more money and buy PentiumII. > Regards, > > * Przemek Czyryca, pczyryca@smurf.chem.usu.edu * > > 4. From gammadas@telis.org Tue Feb 23 10:46:49 1999 > > I had the same questions and similar experiences for g94w/g98w as > mentioned in the message below---I would pay more and get the Intel > PII(PIII will be available in 2 wks!) Also check 2nd message (Jerry: the > next message). Hope it helps! > > 5. From: "Dr.Christian M¸ck-Lichtenfeld" > > I have a small number of PCs at hand, which are run under > Windows NT and Linux. Although the hardware is not exactly > the same, one can come to the overall conclusion that the > AMD processors are about 1.5 - 2 times slower than the > Intel machines. Even a PentiumII with 266 MHz was found to > run a moderate G98W-job in about 60% of the time that an > AMD K6/2 with 300 MHz needed (both with at least 128MB RAM). > A comparison of several Mopac jobs (Mopac93/Linux) on the > AMD K6/2 (300MHz) and on a PentiumII (333MHz) gave the same > result (t(AMD)/t(PII) = 1.5 ... 2). > > I am not a hardware expert but I would suppose that the different > architecture of the CPUs clearly favours Intel over AMD, due to the better > performance in floating point operations. For the aquisition of new > machines I therefore would strongly suggest Intel over AMD. > > I would be very interested to hear from the experiences of other > users, so please forward their answers or summarize if possible. > > Best wishes > > Christian Mueck-Lichtenfeld > > 7. From Steven.Creve@dsm-group.com Tue Feb 23 10:46:52 1999 > > do anything but the last suggestion. WindowsNT is really a *bad* choice for > doing (any kind of) calculations. > I would suggest you contact the people at Gaussian with this problem. > Steven > > 8. From: val > > > i. pay more money to buy Intel processor > > It seems yes, see comments below. > > > ii. go on with our plan (assuming that the performance of Linux/AMDK6-G98 > > won't be very different from Linux/IntelPII-G98) > > Using GAMESS ab-initio program under Linux we found that Intel PII-350 > is significantly faster then AMDK6-350 (in order of 50%) even without > any specific blas libraries. If your budget allows, go to the PII CPU. > > On the other hand, Celeron shows very good performance: Celeron-300A is > close to AMDK6-350, Celeron 333 expected to be a little faster. Both are > really cheap now. > > I have a small collection of GAMESS/ab-initio benchmarks under linux on > my homepage: http://nmr.ioc.ac.ru/Staff/AnanikovVP/ > > > iii. keep the AMD but switch to NT/G98W instead of linux/G98 > > This is very old (and dangerous ;) question, you may look to the CCL > archives, the last discussion finished not long ago. > > For example, a part of the email from Mike Frisch ; > CCL Tue, 5 Jan 1999: > ".. We use the same compiler (Portand) and blas libraries on both Windows/NT > and Linux, and performance is similar. The differences in reported times > are a few percent and probably reflect Linux reporting system time > overhead (as other unix versions do) while this isn't included on a > per-process basis under NT. Elapsed times are sometimes a bit better > under Linux because of better I/O, but the best summary of the situation > is that there isn't a signficant performance diffence for running a > single, stand-alone job under one OS or the other." > > best regards, > Valentin. > > 9. From ivan@lipid.biocomp.unibo.it Tue Feb 23 10:46:57 1999 > > > i. pay more money to buy Intel processor > > That is the way to go. AMD K6 is a great cpu, but NOT for scientific and > technical applications. Its Floating-point unit is VERY slow when compared > to intel one. Get a real PII, the fastest you can afford, don't buy a > Celeron-based machine. > > BTW i tested both CPU with G94. > > > ii. go on with our plan (assuming that the performance of Linux/AMDK6-G98 > > won't be very different from Linux/IntelPII-G98) > > Once more, just to stress it.... > > I don't think the small saving is absolutely worth the the performance > penalty that you have with K6 with scientific and technical programs. > > > > iii. keep the AMD but switch to NT/G98W instead of linux/G98 > > linux is more stable. go for it. > > -- > Dr. Ivan Rossi - CIRB Biocomputing Unit > e-mail: ivan@lipid.biocomp.unibo.it WWW: http://www.biocomp.unibo.it/ivan > > 10. From daniels@kemi.uu.se Tue Feb 23 10:47:00 1999 > > I haven't tried gaussian on the AMD-k6, but from my experiences I would *not* > recommend using the K6 for floating point stuff. I really like the performance > of the K6 for regular stuff like editing, compiling, but the fp perfomance is > simply not good enough. my experience is that the pii is about 50 % faster than > the k6 with the same frequency. the processor is only part of the computer > anyway, you still have to pay the same money for case, monitor, disks etc, so > if the final computer is perhaps 20 % more expensive with the PII, it is still > worth it for fp stuff. What may break down my argument is that in my > calculations, the fp is the bottleneck. In your case it may be the disk, so... > > best regards > Daniel Spångberg > Inorganic Chemistry > Uppsala University > Sweden. > > 11. From teppen@pilot.msu.edu Tue Feb 23 10:47:05 1999 > > If I may propose a fourth option in addition to the three you posted: > > Peter Pulay at the University of Arkansas is a true pioneer of quantum > chemistry - for example, his contributions were cited in Pople's official > Nobel Prize announcement this past fall. He is a former professor of mine > and I like him very much, but I have no other interest in promoting his new > company. > > Pulay has been working on optimized quantum codes since the 1960s and he > just started a company to sell them this past year. He has 5-6 coworkers > including Jon Baker, another master of optimization methods. Several years > ago, Pulay began to parallelize his program for cheap PCs running Linux, > and they now have a system they can sell. Their company is "Parallel > Quantum Solutions" and pulay's e-mail is "pulay@pqs-chem.com". They build > their own PCs and sell a software-hardware bundle. > > I paid $11,000 for a 4-processor (400 MHz Pentium IIs) machine with Linux > and the quantum software installed. I have just got the machine, but > benchmarks indicate that this machine has exceedingly good > performance/price. For pinene using DFT/B3LYP with large basis sets, for > example, the machine i bought for $11,000 was faster than a Cray T3E-600 > with 4 processors and only 15% slower than a Cray T3E-1200 with 4 > processors, both running parallel Gaussian 94. (The G94 calculations were > done by Sosa and Frisch, so were probably pretty well optimized for the > machine, see last July 15 number of J. Comput. Chem. Sosa et al. Vol 19, p. > 1053). I haven't priced those machines but they must be >$100k. If you want > to benchmark against one of your own machines, Pulay would be happy to do > some calculations for you. > > Again, I have no financial interest in telling you this, but it seems like > a great product for working quantum chemists. The graphical interface is > not great, but it is adequate. They put their time into optimizing code. > > Best wishes, > > Brian > > ********************** > Dr. Brian J. Teppen > Assistant Professor > Department of Crop and Soil Sciences > Plant and Soil Science Building, Room 538 > Michigan State University > East Lansing, MI 48824-1325 > > phone: 517-353-5215 > fax: 517-355-0270 > e-mail: teppen@pilot.msu.edu > > 12. From haasj@ubaclu.unibas.ch Tue Feb 23 10:47:08 1999 > > i am a chemistry student in the very last three weeks of studying. I am > using g98 /molden /k6-2-300 and RH 5.2 Linux and 96MB of RAM. I have > encountered that the speed is ok, but not as fast compared to a PII. If i > might I would recon you to buy the K7 (will probably come out this year) > with the EV6 bus protocol of a DEC ALPHA processor 21264. In later times > you would have the opportunity to exchange the proc against an 21264 - > what ever clockspeed... nice option i think. With a PII you are at the > limit of only increasing clockspeed if even possible, although PII are > better in floating point operations. DEC Alpha is for sure a good choice > for later. K6-3 (sharptooth) is also quite nice proc to think of cheaper > than PII but should be equally fast.. (I can only assume that NT system is > equally fast)... > > greetings juergen haas > uni basel > org. chem dep. > > > feel free to contact me again > > 13. From eugene.leitl@lrz.uni-muenchen.de Tue Feb 23 10:47:10 1999 > > AMD K6 ist voll kompatibel zu PPro/P II CPU. Allerdings koennte > Celeron das bessere Preis/Leistungsverhaeltnis bieten. Vielleicht auf > K6-3 oder sogar K7 warten? > > MfG, > Eugen > > 14. From RedAndr@anrb.ru Tue Feb 23 10:47:12 1999 > > It is not good idea buying AMD/K6 CPU for floating point calculations. > Intel processors with same price as AMD have more powerful FPU > performance. In addition all compilers can do optimization only for > Pentium/Pentium Pro unlike AMD or Cyrix. Therefore you have to forget > about using AMD in numerical purposes. You can also buy multiprocessor > station with Intel processors unlike AMD. About Linux and NT. Our > experiments shows that Linux haven't advantage over Windows 95/NT in > numerical calculations. > > > Best regards, > Andrew mailto:RedAndr@anrb.ru > > > 15. From gaussian.com!fox@lorentzian.com Tue Feb 23 10:47:15 1999 > > At this point I cannot vouch for proper operation of G98 on an > AMD processor. We do not have plans for supporting this as a platform. > While most things work on AMD I have at least one site with a problem > trying to run G98W and have several sites that have demonstrated problems > with Cyrix processors which make it impossible to run G98. > > In short I recommend you get Intel. > > Douglas J. Fox > Director of Technical Support > help@gaussian.com > > -----end of summary------ > > > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > >