Subject: PC/Linux-Workstation:Summary

From: Eric HENON <[email-masked]>
Date: Wed, 10 Jan 2001 09:40:48 +0000

Dear CCLers,

I would like to thank all people who replied to my question !

Original Question:

> Hello,

> We have a plan to get a workstation with 4 processors to do

> some ab initio calculations (g98, Molcas). The "Linux/xeon" platform

> seems to be an interesting alternative but, unfortunately, we have
not

> found recent benchmarks for current xeon.

> Thus, I would be grateful if anyone could share his/her

> experience concerning the performance of Linux/current Xeon-PIII
vs

> Power 3-II  (IBM RS6000).

> Thank you in advance.

First of all, it is not easy to find very recent benchmarks for

the last CPU processors, concerning computational chemistry.

It seems however that the Xeon performances are pretty close to

its parents (PII/PII) ones, and it has a bad price/performance ratio.

That is the reason why we gave up the idea of buying such a configuration.

It was next difficult to decide without any doubt

from the answers what was the best

alternative : "Linux/PIII" (or "Linux/Athlon") platform

or Unix work station (such IBM Power 3-II) platform.

The reason is probably that PC machines are

faster and faster and their performances are now

relatively close to some Unix workstations. It seems from

recent benchmarks that Athlon is now faster that its

corresponding Pentium processor.

However,  the performance of computational chemistry programs

are not only determined  by the CPU,  and other criteria
must be

taken into account:

- I/O system

- memory size

- cache memory size !

- Libraries and compiler choice !

...

PC has the best price/performance ratio but building PC

requires carefull choice of hardware

(e.g. SCSI configuration, good motherboard and

memory, etc.) and software (e.g. good compiler and optimized BLAS for
G9X

compilation).

One has to consider also that

PC has limit on RAM and number of CPUs.

Moreover it was recently suggest that

that if you test LINUX boxes, you need a reasonable size problem,

as small test jobs run very fast, while real size problems may easyly
be a

factor of 10 slower than the real UNIX machine

I present the following numbers.

These are timings from using Gaussian with a set of four jobs, using

either PC_Athlon/Linux or IBM Power III-2 (many thanks
to D. Rinaldi

for CPU times facilities on the IBM machine !).

(Fortran 7.1, C++, IBM 44p-270,375MHz, one processor used, %MEM=90MB)

(the first number corresponds to Athlon 800MHz/Linux Mandrake
release 7.1

Kernel 2.2.15-4, running G94)

(the last number corresponds to RISC Power3-II running
G98

using Fortran 7.1, C++, IBM 44p-270,375MHz, one processor, %MEM=90MB)

*********************************************

SP B3LYP   33mn 42s ------> 17mn
(4mn21 with scf=incore)

81 basis functions
451 primitive gaussians

17 alpha electrons
16 beta electrons

*********************************************

*********************************************

FREQ  UHF    13mn 28s ------>  5mn30

52 basis functions
298 primitive gaussians

12 alpha electrons
11 beta electrons

*********************************************

*********************************************

H2S molecule CCSD(T)   2mn 26s ------>
32s

62 basis functions
145 primitive gaussians

9 alpha electrons
9 beta electrons

*********************************************

*********************************************

H2S molecule  CCSD(T)  42mn ------> 8mn

119 basis functions      226 primitive
gaussians

9 alpha electrons
9 beta electrons

*********************************************

Here is a summary.

hi,

we have obtained verny good results by unsing a linux cluster with the

amd athlon processor. the new thunderbird core almost reaches the power3

processor of our sp. take a look at

"http://topas.chemie.uni-dortmund.de/mg98b.html"
for benchmark results.

hope this will help

michael braunschweig

department of chemistry

university of dortmund

germany

Hi Eric,

We have some experience running Molcas on RS6000 model 270 workstations.

One thing that you should to bear in mind is that the performance of

Molcas is determined not so much by the CPU as by the I/O system.
A

modest sized CASPT2, for example, chokes even a uniprocessor machine:
the

I/O system simply cannot feed the CPU quickly enough.  And if
it can't

keep one satisified, having four CPUs would be pointless...

So your choice depends partly on how much you intend to use Molcas.
The

IBM is otherwise a very impressive beast and we are very happy with
ours.

Certainly we have had no problems running other QM codes on them.
One

possibility you might want to consider is to buy a multiprocessor RS6K
for

Gaussian, etc., and keep a cheap and cheerful Pentium (with a decent
disk,

etc.) exclusively for Molcas.

Hope this helps, and good luck!

Chris Page

Università di Siena

From Stanislaw OldZiej

Hi all,

As usual all is about $$$$$.

First of all the g98 is not very well scalable on the multiprocesor

machines in my opinion is better (and cheaper) to buy four machines

(1CPU) than one 4xCPUs.

I'm not using g98 however and I do not have acess to Power-3-II IBM

machine but, I have some benchmark for GAMESS on PC-like processors

(single point MP2 energy calculations), the results are below (time
in seconds):

DURON 600MHz
-       1227.9

K-7 ATHLON 600MHz
-       1093.0

PIII CELERON 433MHz
-       2029.2 (app 600Mhz 1462.1)

PIII 650MHz
-       1195.0 (app 600MHz 1294.2)

PIII XEON 700Mhz/1MB Cache      -
1081.1 (app 600MHz 1261.1)

I do not have access to the T-Bird AMD but I'm sure that T-Bird AMD
will

be the best.

The second point is that Xeon is very expensive. If you want to have

4-way motherboard the XEON 700Mhz/1MB Cache will cost you 1349 USD,

XEON 550MHz/512K 975 USD. If you will buy 1-way motherboards you can

get XEON 933/256k for 670 USD.

The 4-way motherboard for Xeon is SC450NX and it cost c.a. 1800USD,
or

S2QR6 c.a 2500 USD. It is mean that 4-way motherboards + 4 XEONs 700MHz

is ~7000 USD and you should add memory disks and all another stuff.

For comparison the 1000Mhz T-Bird + motherboard ASUSTek, 1GB RAM, 18
GB HD

SCSII cost ~1600 USD.

Have fun,

Stan

P.S. All prices are from: www.pricewatch.com.

===============================================================================

Dr Stanislaw Oldziej

Faculty of Chemistry,

University of Gdansk,
"Plucie to nie to samo co wolnosc wypowiedzi"

Molecular Modelling Group

Sobieskiego 18, 80-952 Gdansk

POLAND

tel:(048-58)-345-0361

fax:(048-58)-341-0357

===============================================================================

Hi,

Xeon .... I dont know. It would be better Athlon, in my mind. It runs
Linux also,

but has better performance and is cheaper. But consider other answers.

A.Ziemys

From Frederick. P. Arnold, Jr

Hello:

First, try http://www.dl.ac.uk/CFS/benchmarks/compchem.html
for a thorough

and well-balanced overview.

The basic take-home lesson is that the PowerIII is a nice chip, but
an

Athlon 800 should be even with it for Hessian runs, and faster otherwise,

at a fraction of the price.  Xeon numbers I've seen in the past
track the

parent PII/PIII pretty closely; i.e. even with the larger cache, their

performance doesn't jump by much, and their price is high.  If
you're

willing to pay Xeon prices, you should probably be looking at Alphas.
Note

that Alpha near the top of the list is a generation and a half ago.
Newer

ones at 2-3 times faster for the same clock-frequency.

Hi!

This doesn't answer your question, but have you considered using a
beowulf

instead of a four-way smp machine?  It would be a far cheaper
solution to

implement and works rather well for g98 (speaking from experience with
both

dual-smp PIIs versus beowulfs).

Resepectfully,

Phillip Matz

[email-masked]

From Cédric Merlot:

Links to computational chemistry benchmarks:

http://www.emsl.pnl.gov:2080/docs/tms/abinitio-v4/cover.html

http://www.ccl.net/cgi-bin/ccl/message.cgi?1998+03+31+010

http://www.ccl.net/cgi-bin/ccl/message.cgi?1999+08+12+011

http://www.ccl.net/cgi-bin/ccl/message.cgi?1999+02+25+011

Cédric Merlot

ChemCAD - 120, rue du Général Gouraud - 67210 OBERNAI
- France

Tel : 03 88 95 68 52 - Fax : 03 88 95 07 92

http://www.chemcad.fr

mailto:[email-masked]

From Vincent KRIEF:

http://www.compaq.com/hpc/apps/app_chem.html

----------------------------------------------------------

Eric HENON - Maitre de Conférences

Groupe de Spectrometrie Moleculaire et Atmospherique (GSMA)

Equipe Associee au CNRS UMR 6089

UFR Sciences Exactes et Naturelles B.P. 1039

51687 REIMS Cedex 2

Tel  : 03 26 91 33 66

email: [email-masked]

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