[Beowulf] CCL:Opteron or Nocona ? (fwd from m.somers at chem.leidenuniv.nl)

Mikhail Kuzminsky kus at free.net
Wed May 11 11:26:04 PDT 2005

In message from Eugen Leitl <eugen at leitl.org> (Mon, 9 May 2005 
23:24:11 +0200):
>----- Forwarded message from mark somers 
><m.somers at chem.leidenuniv.nl> -----
>From: mark somers <m.somers at chem.leidenuniv.nl>
>Date: Mon, 9 May 2005 09:38:06 +0200
>To: Luigi Cavallo <cavallo at chemistry.unina.it>
>Cc: chemistry at ccl.net
>Subject: CCL:Opteron or Nocona ?
>User-Agent: KMail/1.6.2
>Dear Luigi Cavallo,
>we have recently purchased and setup a new Beowulf cluster here in 
>dedicated to run ADF and other DFT codes (Dacapo and Vasp) on it. We 
>found the Nocona's, in combination with the Intel compilers, to be 
>the best 
>combination especially for ADF and ADF-BAND.
>Before we decided to go for the Nocona's, we did try with two test 
>one being a dual-cpu AMD Opteron 246 (2.0 GHz) and the other being a 
>Nocona (3.0 GHz). Tests showed that the AMD has, in general, a 
>better cache hierarchy and a better memory scalability, but also that 
>lack of compilers able to tune for the Opterons is severe. Of course 
>we took 
>the differences in cpu clocks into account.
>As it turns out, after having contacted the SCM people in Amsterdam, 
>ADF can 
>effectively use the SSE3 registers and cpu intruction set and that 
>makes it 
>run fast on the Nocona's. This, together with the prices being 
>roughly the 
>same, made us decide to go for the Nocona's. 
>BTW, maybe this is known to you already, but Intel offers you their 
>capable compilers for free for academic use.

Sorry for big delay w/answer: today is 1st working day after May's 
holidays here in Russia ;-)

I've no doubts that in average Opteron is today better, in particular 
for computational chemistry codes. The reasons is both performance 
"top frequency" chips) and price/performance ratio. We stop to use 
Intel x86 for computational chemistry and began to use AMD from 
times" - because of price/performance reason. But now Opteron is in
average absolutely better due to

a) single CPU performance (See, for example, SPECfp2000 which includes 
also some molecular dynamics codes)
b) power dissipation (which is lower for AMD)
c) dual (and higher also:-)) CPU system architecture: 2 Opteron's
have 2 independed pathes to main memory instead of common system bus
in the case of Nocona. As a result, Opteron's have much more good 
memory throughput scalability. 

Pls take into account that many modern quantum chemistry codes (like 
G03) are "restricted" by memory throughput !

What is about compilers, it was answered in a set of previous messages

IMHO, the only HPC area where Nocona has clear advantage over Opteron, 
is floating point applications reaching performance close to peak 
value (like Linpack). In that case it should be take into account that 
Peak_Performance = 2*frequency for both processors, and Nocona
has therefore higher values. But it's not typically for computational

Mikhail Kuzminsky
Zelinsky Institute of Organic Chemistry


>The machine is up and running now in 64 bit mode and doing fine ;-). 
>Maybe the information can help you in your decision.
>Best regards, 
>Mark Somers.
>> Hi,
>> we are going to invest some money for a few computers, and we have 
>> make a decision between the AMD-Opterons and the Intel-Nocona. 
>> better ? We are experienced with the Opterons, but we have no idea 
>> the Noconas...
>> Major codes to run on them will be classical QM packages as ADF, 
>>G03, TM,
>> some AIMD as CPMD, and possibly some classical MD as gromacs.
>> Thanks,
>> Luigi
>Dr. M. F. Somers
>Theoretical Chemistry - Leiden Institute of Chemistry  - Leiden 
>Einsteinweg 55, P.B. 9502, 2300 RA Leiden, The Netherlands
>tel: +31715274437
>mail: m.somers at chem.leidenuniv.nl
>web:  http://rulgla.leidenuniv.nl/Researchers/Somers.htm
>room: HB322
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