Subject: Summary: AMD-K6/linux for G98

From: "Jerry C.C. Chan" <[email-masked]>
Date: Wed, 24 Feb 1999 09:08:57 +0100 (MEZ)

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 <[email-masked]>

   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 [email-masked] 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 [email-masked] 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, [email-masked] *

4. From [email-masked] 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" <[email-masked]>

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 [email-masked] 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 <[email-masked]>

> 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 <[email-masked]>;
  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 [email-masked] 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: [email-masked]  WWW: http://www.biocomp.unibo.it/ivan 

10. From [email-masked] 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 [email-masked] 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 "[email-masked]". 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: [email-masked]

12. From [email-masked] 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 [email-masked] 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 [email-masked] 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:[email-masked]

15. From [email-masked] 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
  [email-masked]

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