Re: CCL:Summary: AMD-K6/linux for G98
- From: webmaster RelaQ <kaiser (- at -) relaq.mx>
- Subject: Re: CCL:Summary: AMD-K6/linux for G98
- Date: Wed, 24 Feb 1999 17:23:16 -0600 (CST)
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 <Drake.Diedrich (- at -) anu.edu.au>
>
> 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 (- at -) 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 (- at -) 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 (- at -) smurf.chem.usu.edu *
>
> 4. From gammadas (- at -) 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" <cml (- at -)
lipari.uni-muenster.de>
>
> 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 (- at -) 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 <val (- at -) cacr.ioc.ac.ru>
>
> > 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 <frisch (- at -)
lorentzian.com>;
> 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 (- at -) 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 (- at -) lipid.biocomp.unibo.it WWW: http://www.biocomp.unibo.it/ivan
>
> 10. From daniels (- at -) 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 (- at -) 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 (- at -)
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 (- at -) pilot.msu.edu
>
> 12. From haasj (- at -) 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 (- at -) 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 (- at -) 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 (- at -)
anrb.ru
>
>
> 15. From gaussian.com!fox (- at -) 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 (- at -) gaussian.com
>
> -----end of summary------
>
>
>
>
>
>
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