From chemistry-request@ccl.net Tue May 10 09:45:52 2005
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Date: Tue, 10 May 2005 15:45:47 +0200
From: Marius Retegan <retegan.marius * gmail.com>
Reply-To: Marius Retegan <retegan.marius * gmail.com>
To: chemistry * ccl.net
Subject: more about NBO analysis
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Hello again
I would like to thank all the people that responded to my previous
question. Although I've got some interesting suggestions none helped
in solving my problem.
I tried to perform a NBO analysis on a simpler compound, that is
tungsten hexacarbonyl, but again only three of the CO units are
bounded to W, and I get an error message " WARNING:  4 low occupancy
(<1.9990e) core orbitals found on  W 3". I've tried to use resonance
and  3cbond but didn't help.
So, I am asking if anyone has a succesfull NBO analysis on tungsten
carbonyls  or any carbonyls in general to give me the input for
Gaussian.
Thank you.
Marius Retegan



From chemistry-request@ccl.net Tue May 10 03:54:11 2005
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Date: Tue, 10 May 2005 07:54:09 +0100 (BST)
From: akila iyer <akil_chem * yahoo.co.in>
Subject: Wiberg Bond order analysis
To: CHEMISTRY * ccl.net
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Dear Chemists,
           During reaction modelling, wiberg bond
orders were computed using NBO in G98.One such
calculation (for a Transtion state) at
b3lyp/6-31+g(d,p) level ended with an error " NBO
cannot handle linearly dependent basis set".But
successful bond order calculations were possible for
the reactants at the same level.It would be of great
help if someone helps me in knowing the reason of the
error and how to get out of it.
Advanced Thanks

sincerely
L.Akila
India

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From chemistry-request@ccl.net Tue May 10 05:41:58 2005
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From: Christian Boehme <Christian.Boehme * gwdg.de>
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To: Luigi Cavallo <cavallo * chemistry.unina.it>
CC: chemistry * ccl.net
Subject: Re: CCL:Opteron or Nocona ?
References: <Pine.OSF.4.44.0505070914350.31601-100000 * main.chemistry.unina.it>
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Dear Luigi,

Luigi Cavallo schrieb:
> we are going to invest some money for a few computers, and we have to
> make a decision between the AMD-Opterons and the Intel-Nocona. What's
> better ? We are experienced with the Opterons, but we have no idea about
> 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.

We recently purchased a 32 dual-processor Opteron (2GHz) cluster. We 
used CPMD and several artificial benchmarks on Opteron and Xeon (3GHz) 
machines to come to this decision. With CPMD we found that the advantage 
of the Opteron over the Xeon was very significant for 32-bit memory 
intensive applications running on both processors of a dual processor 
box (Intel compiler on both architectures). When using just one 
processor, the Xeon scored much better. As Intel has not changed the 
memory interface of the Nocona, I do not think this trend would be 
different for 64-bit applications. Regarding Fortran compilers, from our 
experience both the Intel and the Portland can now be used to make 
production quality 64-bit binaries for the Opterons. Best wishes

Christian

-- 
Dr. Christian Boehme
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From chemistry-request@ccl.net Tue May 10 06:11:18 2005
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From: Eugen Leitl <eugen :a: leitl.org>
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Subject: Re: [Beowulf] CCL:Opteron or Nocona ? (fwd from m.somers :a: chem.leidenuniv.nl) (fwd from lindahl :a: pathscale.com)
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----- Forwarded message from Greg Lindahl <lindahl :a: pathscale.com> -----

From: Greg Lindahl <lindahl :a: pathscale.com>
Date: Tue, 10 May 2005 00:03:11 -0700
To: Beowulf :a: beowulf.org
Cc: 
Subject: Re: [Beowulf] CCL:Opteron or Nocona ? (fwd from
	m.somers :a: chem.leidenuniv.nl)
User-Agent: Mutt/1.4.1i

On Mon, May 09, 2005 at 08:05:28PM -0400, Mark Hahn wrote:

> I would very much like to see a good comparison of Intel compilers
> versus the alternatives.  I know good things about Pathscale, for instance,
> and gcc 4.0 and 4.1 seem pretty impressive.

In addition to the usual benchmarks like SPECfp and Polyhedron, there
is a computational chemistry comparison done by Daresbury Labs in the
UK.  Opteron+PathScale does quite well.

http://www.polyhedron.co.uk/compare/linux/f77bench_AMD.html
http://www.polyhedron.co.uk/compare/linux/f90bench_AMD.html

http://www.cse.clrc.ac.uk/disco/index.shtml, especially
http://www.cse.clrc.ac.uk/disco/Benchmarks/IntelProj.Serial.update1.pdf

We're looking forward to Daresbury testing with our newest compilers,
as we've made some substantial performance improvements since the
version they used (1.2).

-- greg

_______________________________________________
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To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf

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From chemistry-request@ccl.net Mon May  9 23:01:06 2005
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Date: Mon, 9 May 2005 19:01:04 -0700 (PDT)
From: Konstantin Kudin <konstantin_kudin * yahoo.com>
Subject: Re: CCL:Opteron or Nocona ?
To: mark somers <m.somers * chem.leidenuniv.nl>,
        Luigi Cavallo <cavallo * chemistry.unina.it>
Cc: chemistry * ccl.net
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 Actually, highly optimizing compilers for Opteron do exist (such as
Pathscale). Even Intel Fortran 8.1 (either 32 or 64 bits) produces
decent code for Opteron since Opteron is not as fragile as Pentium 4 in
terms of which code it likes and which it does not.

 There is  one specific situation where Nocona could come as a clear
winner, but such cases are not too common. Basically, codes that run
BLAS routines such as DGEMM for the majority of their runtime gain a
lot on Nocona when the correct libraries are used. This is because both
Opteron and Nocona run BLAS proportionally to the clock speed, so the
much higher clocked Nocona wins (~3 vs ~2 Ghz). On the other hand,
multi-processor Noconas can choke because of limited memory bandwidth,
whereas Opterons under such circumstances do just fine.

 Last, here are some last year's Gaussian03 benchmarks, where both
Opterons and Noconas were comparable:
http://www.princeton.edu/~kkudin/g03_b5_tests_1.txt

 YMMV ...

 Kostya
 
 


--- mark somers <m.somers * chem.leidenuniv.nl> wrote:
> Dear Luigi Cavallo,
> 
> we have recently purchased and setup a new Beowulf cluster here in
> Leiden, 
> dedicated to run ADF and other DFT codes (Dacapo and Vasp) on it. We
> have 
> 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
> machines, 
> one being a dual-cpu AMD Opteron 246 (2.0 GHz) and the other being a
> dual-cpu 
> Nocona (3.0 GHz). Tests showed that the AMD has, in general, a
> slightly 
> better cache hierarchy and a better memory scalability, but also that
> the 
> 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
> OpenMP 
> capable compilers for free for academic use. 
> 
> 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
> to
> > make a decision between the AMD-Opterons and the Intel-Nocona.
> What's
> > better ? We are experienced with the Opterons, but we have no idea
> about
> > 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
> University
> Einsteinweg 55, P.B. 9502, 2300 RA Leiden, The Netherlands
> tel: +31715274437
> mail: m.somers * chem.leidenuniv.nl
> web:  http://rulgla.leidenuniv.nl/Researchers/Somers.htm
> room: HB322
> 
> 
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From chemistry-request@ccl.net Tue May 10 15:35:39 2005
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From: "Bardon, Alma" <Alma.Bardon #%# nrc-cnrc.gc.ca>
To: "'chemistry #%# ccl.net'" <chemistry #%# ccl.net>
Subject: diatomic vibrations
Date: Tue, 10 May 2005 13:51:52 -0400
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I have access to Gaussian 98 and I want to look at vibrating homonuclear diatomic molecules. I'd like to see the maximum and minimum distance between the nuclei for the different vibrational levels, as well as a superposition of several vibrational states. I would also like to view the orbitals as the molecules stretch. How can I do this with Gaussian?

 

Thanks,

Alma

Alma.Bardon #%# nrc.ca


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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I have access to Gaussian 98 and I want to look at vibrating
homonuclear diatomic molecules. I'd like to see the maximum and minimum
distance between the nuclei for the different vibrational levels, as well as a
superposition of several vibrational states. I would also like to view the orbitals
as the molecules stretch. How can I do this with Gaussian?</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thanks,</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
  font-family:Arial'>Alma</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Alma.Bardon #%# nrc.ca</span></font></p>

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