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From: "S.I.Gorelsky" <gorelsky -()- stanford.edu>
To: chemistry -()- ccl.net
cc: ed.gasiorowski -()- amd.com, <mike -()- colfax-intl.com>
Subject: dual-core Opteron 275 performance
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To add to the discussion about the performance of new dual-core
processors for computational chemistry applications,

the comparison of Intel and AMD dual-CPU based computers is shown at:

http://www.sg-chem.net/cluster/

As can be seen from the graph, the Gaussian 03 execution speed (test job
397) on dual-core dual-CPU Opteron 275 workstation is faster by a factor of 1.95
as compared to the dual-CPU Xeon 3.2GHz 800MHz FSB machine.

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

I would like to thank Ed Gasiorowski (AMD) and Mike Fay (Colfax
International) for their support.

Serge Gorelsky

----------------------------------------------------------------
 Dr S.I. Gorelsky, Department of Chemistry, Stanford University
 Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA
 Phone: (650) 723-0041. Fax: (650) 723-0852.
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From: "Rino Ragno" <rinoragno !! libero.it>
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Subject: R: SUMMARY - Software for combinatorial generation of structures
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Dear Dr. Peter Bladon,
=20
This is really interesting, I wonder if you can manage to convert also =
the
other software to linux environment, tis would be a good choice to have =
your
software used broadly in the academic world and more to have the bug =
fixed.
=20
Please let me  know if you decide to do the job.
=20
Rino Ragno
=20
=20
++------------------------------------------++
|| Dr. Rino Ragno                           ||
||                                          ||
|| Dip. Studi Farmaceutici                  ||
|| Facolta' di Farmacia                     ||
|| Universita' "La Sapienza"                ||
|| P.le Aldo Moro, 5 - 00185                ||
|| Roma/Italia                              ||
|| PO BOX 36 ROMA 62                        ||
||                                          ||
|| Phone: 39-06-49913152                    ||
||                                          ||
|| Fax: 39-06-491491                        ||
||                                          ||
|| E-mail: rino.ragno !! uniroma1.it           ||
|| WWW: http://w3.uniroma1.it/rcmd          ||
++------------------------------------------++

-----Messaggio originale-----
Da: Computational Chemistry List [mailto:chemistry-request !! ccl.net] Per
conto di Dr. Peter Bladon
Inviato: mercoled=EC 29 giugno 2005 19.21
A: chemistry !! ccl.net; gustavo !! mercury.chem.pitt.edu; Dr. Peter Bladon
Oggetto: CCL:SUMMARY - Software for combinatorial generation of =
structures


Dear Gustavo,

I have been following with some interest the discussions you have been
having in CCL
with regard to generating structures combinatorially.  I was pleased to =
see
that you
have considered AUTOBUILD but I can understand that there could be =
problems
in conversion
> from the IRIX platform to LINUX.

However, I have risen to the challenge and there is now a version of =
this
program for LINUX.
It is present as a gzipped tar file on my (anonymous ftp) file server =
at:
    81.178.7.83  in the directory pub/interchem_linux_programs
and you are welcome to download it and try it out.

There were not many real problems in the porting, but I have taken the
opportunity to
cast the program as a Fortran-90 version.  (g77 will take care of these
modifications).

Yours sincerely

Peter Bladon


 =20

 =20


  _____ =20

<< ella for Spam Control >> has removed 21502 Spam messages and set =
aside
1598 Newsletters for me
You can use it too - and it's FREE!  www.ellaforspam.com=09

------=_NextPart_000_002A_01C57E48.3049B890
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<HTML><HEAD>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Diso-8859-1">
<TITLE>Messaggio</TITLE>

<META content=3D"MSHTML 6.00.2900.2668" name=3DGENERATOR></HEAD>
<BODY text=3D#000000 bgColor=3D#ffffff>
<DIV><SPAN class=3D718201912-01072005><FONT face=3DArial color=3D#0000ff =
size=3D2>Dear=20
Dr. Peter Bladon,</FONT></SPAN></DIV>
<DIV><SPAN class=3D718201912-01072005><FONT face=3DArial color=3D#0000ff =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D718201912-01072005><FONT face=3DArial color=3D#0000ff =
size=3D2>This=20
is really interesting, I wonder if you can manage to convert also the =
other=20
software to linux environment, tis would be a good choice to have your =
software=20
used broadly in the academic world and more to have the bug=20
fixed.</FONT></SPAN></DIV>
<DIV><SPAN class=3D718201912-01072005><FONT face=3DArial color=3D#0000ff =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D718201912-01072005><FONT face=3DArial color=3D#0000ff =
size=3D2>Please=20
let me&nbsp; know if you decide to do the job.</FONT></SPAN></DIV>
<DIV><SPAN class=3D718201912-01072005><FONT face=3DArial color=3D#0000ff =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D718201912-01072005><FONT face=3DArial color=3D#0000ff =
size=3D2>Rino=20
Ragno</FONT></SPAN></DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>
<DIV align=3Dleft><FONT face=3DCourier=20
size=3D2>++------------------------------------------++</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>|| Dr. Rino=20
Ragno&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier=20
size=3D2>||&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>|| Dip. Studi=20
Farmaceutici&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>|| Facolta' di=20
Farmacia&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>|| Universita' "La=20
Sapienza"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>|| P.le Aldo Moro, 5 -=20
00185&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>||=20
Roma/Italia&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>||&nbsp;PO BOX 36 ROMA=20
62&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier=20
size=3D2>||&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>|| Phone:=20
39-06-49913152&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier=20
size=3D2>||&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>|| Fax:=20
39-06-491491&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier=20
size=3D2>||&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>|| E-mail: <A=20
href=3D"mailto:rino.ragno !! uniroma1.it">rino.ragno !! uniroma1.it</A>&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier size=3D2>|| WWW: <A=20
href=3D"http://w3.uniroma1.it/rcmd">http://w3.uniroma1.it/rcmd</A>&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
||</FONT></DIV>
<DIV align=3Dleft><FONT face=3DCourier=20
size=3D2>++------------------------------------------++</FONT><FONT=20
face=3D"Courier New" size=3D2></DIV></FONT></FONT></DIV>
<BLOCKQUOTE dir=3Dltr=20
style=3D"PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px =
solid; MARGIN-RIGHT: 0px">
  <DIV></DIV>
  <DIV class=3DOutlookMessageHeader lang=3Dit dir=3Dltr =
align=3Dleft><FONT face=3DTahoma=20
  size=3D2>-----Messaggio originale-----<BR><B>Da:</B> Computational =
Chemistry=20
  List [mailto:chemistry-request !! ccl.net] <B>Per conto di </B>Dr. Peter=20
  Bladon<BR><B>Inviato:</B> mercoled=EC 29 giugno 2005 =
19.21<BR><B>A:</B>=20
  chemistry !! ccl.net; gustavo !! mercury.chem.pitt.edu; Dr. Peter=20
  Bladon<BR><B>Oggetto:</B> CCL:SUMMARY - Software for combinatorial =
generation=20
  of structures<BR><BR></FONT></DIV><FONT size=3D+1><TT>Dear =
Gustavo,<BR><BR>I=20
  have been following with some interest the discussions you have been =
having in=20
  CCL<BR>with regard to generating structures combinatorially.&nbsp; I =
was=20
  pleased to see that you<BR>have considered AUTOBUILD but I can =
understand that=20
  there could be problems in conversion<BR>&gt; from the IRIX platform =
to=20
  LINUX.<BR><BR>However, I have risen to the challenge and there is now =
a=20
  version of this program for LINUX.<BR>It is present as a gzipped tar =
file on=20
  my (anonymous ftp) file server at:<BR>&nbsp;&nbsp;&nbsp; =
81.178.7.83&nbsp; in=20
  the directory pub/interchem_linux_programs<BR>and you are welcome to =
download=20
  it and try it out.<BR><BR>There were not many real problems in the =
porting,=20
  but I have taken the opportunity to<BR>cast the program as a =
Fortran-90=20
  version.&nbsp; (g77 will take care of these =
modifications).<BR><BR>Yours=20
  sincerely<BR><BR>Peter Bladon<BR><BR><BR></TT></FONT>&nbsp;=20
  <BLOCKQUOTE=20
  =
cite=3Dmid4971.200.165.141.250.1119920416.squirrel !! mercury.chem.pitt.edu =

  type=3D"cite"><PRE wrap=3D"">  =
</PRE></BLOCKQUOTE></BLOCKQUOTE><BR><!--Ella123-->
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From chemistry-request@ccl.net Fri Jul  1 06:09:34 2005
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From: "Xin Liu" <liuxin_dut *o* hotmail.com>
To: chemistry *o* ccl.net
Subject: RE: CCL:dual-core Opteron 275 performance
Date: Fri, 01 Jul 2005 09:22:23 +0000
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I'm wondering if there is some performance tests carried out on Daul core 
Xeon.

Sincerely yours
Xin, Liu

>From: "S.I.Gorelsky" <gorelsky *o* stanford.edu>
>Reply-To: chemistry *o* ccl.net
>To: chemistry *o* ccl.net
>CC: ed.gasiorowski *o* amd.com, <mike *o* colfax-intl.com>
>Subject: CCL:dual-core Opteron 275 performance
>Date: Thu, 30 Jun 2005 23:00:42 -0700 (PDT)
>
>
>To add to the discussion about the performance of new dual-core
>processors for computational chemistry applications,
>
>the comparison of Intel and AMD dual-CPU based computers is shown at:
>
>http://www.sg-chem.net/cluster/
>
>As can be seen from the graph, the Gaussian 03 execution speed (test job
>397) on dual-core dual-CPU Opteron 275 workstation is faster by a factor of 
>1.95
>as compared to the dual-CPU Xeon 3.2GHz 800MHz FSB machine.
>
>-----------------
>
>I would like to thank Ed Gasiorowski (AMD) and Mike Fay (Colfax
>International) for their support.
>
>Serge Gorelsky
>
>----------------------------------------------------------------
>  Dr S.I. Gorelsky, Department of Chemistry, Stanford University
>  Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA
>  Phone: (650) 723-0041. Fax: (650) 723-0852.
>----------------------------------------------------------------
>
>
>
>
>
>
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From chemistry-request@ccl.net Fri Jul  1 08:57:33 2005
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From: john furr <john.furr *o* gmail.com>
Reply-To: john furr <john.furr *o* gmail.com>
To: chemistry *o* ccl.net
Subject: Re: CCL:dual-core Opteron 275 performance
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Thanks for the review.

While the results are very impressive I wonder  what the results would
have been if you compared 4 3.2 Xeon's against the two opterons.

A quick look at pricewatch.com shows the Xeon 3.2 selling for USD $310
were as the opteron 275's are going for USD $1328.

Also I would be interested to know if the Xeon processors had 1 or 2 M
of cache.  I have found this to make a difference on certain
calculations.

Anyhow thaks for posting the review.  I am looking into building a new
test system and I will certainly be looking into AMD processors.

John Furr
Dynamol Inc.

On 7/1/05, S.I.Gorelsky <gorelsky *o* stanford.edu> wrote:
> 
> To add to the discussion about the performance of new dual-core
> processors for computational chemistry applications,
> 
> the comparison of Intel and AMD dual-CPU based computers is shown at:
> 
> http://www.sg-chem.net/cluster/
> 
> As can be seen from the graph, the Gaussian 03 execution speed (test job
> 397) on dual-core dual-CPU Opteron 275 workstation is faster by a factor of 1.95
> as compared to the dual-CPU Xeon 3.2GHz 800MHz FSB machine.
> 
> -----------------
> 
> I would like to thank Ed Gasiorowski (AMD) and Mike Fay (Colfax
> International) for their support.
> 
> Serge Gorelsky
> 
> ----------------------------------------------------------------
>  Dr S.I. Gorelsky, Department of Chemistry, Stanford University
>  Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA
>  Phone: (650) 723-0041. Fax: (650) 723-0852.
> ----------------------------------------------------------------
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From chemistry-request@ccl.net Fri Jul  1 05:41:37 2005
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From: C J Kenneth Tan -- OptimaNumerics <cjtan *o* OptimaNumerics.com>
To: chemistry *o* ccl.net
cc: ed.gasiorowski *o* amd.com, mike *o* colfax-intl.com
Subject: Re: CCL:dual-core Opteron 275 performance
In-Reply-To: <Pine.LNX.4.44.0506302246510.26093-100000 *o* cardinal3.Stanford.EDU>
Message-ID: <Pine.LNX.4.62.0507010841320.14321 *o* kontrovich.OptimaNumerics.com>
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Serge,

Do you have the data for:

- 1-CPU, with 2 cores
- 2-CPU, running 1 core each (with 2 cores on chip)

for the Opteron?

Thanks a lot!


Ken
--------------------------------------------------------------------------
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On 2005-06-30 23:00 -0700 S.I.Gorelsky (gorelsky *o* stanford.edu) wrote:

> Date: Thu, 30 Jun 2005 23:00:42 -0700 (PDT)
> From: S.I.Gorelsky <gorelsky *o* stanford.edu>
> Reply-To: chemistry *o* ccl.net
> To: chemistry *o* ccl.net
> Cc: ed.gasiorowski *o* amd.com, mike *o* colfax-intl.com
> Subject: CCL:dual-core Opteron 275 performance
> 
> 
> To add to the discussion about the performance of new dual-core
> processors for computational chemistry applications,
> 
> the comparison of Intel and AMD dual-CPU based computers is shown at:
> 
> http://www.sg-chem.net/cluster/
> 
> As can be seen from the graph, the Gaussian 03 execution speed (test job
> 397) on dual-core dual-CPU Opteron 275 workstation is faster by a factor of 1.95
> as compared to the dual-CPU Xeon 3.2GHz 800MHz FSB machine.
> 
> -----------------
> 
> I would like to thank Ed Gasiorowski (AMD) and Mike Fay (Colfax
> International) for their support.
> 
> Serge Gorelsky
> 
> ----------------------------------------------------------------
>  Dr S.I. Gorelsky, Department of Chemistry, Stanford University
>  Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA
>  Phone: (650) 723-0041. Fax: (650) 723-0852.
> ----------------------------------------------------------------
> 
> 
> 
> 
> 
> 
> -= This is automatically added to each message by the mailing script =-
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From chemistry-request@ccl.net Fri Jul  1 04:29:14 2005
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No

Regards,
Arvydas
*******************************************************************
                   Arvydas Tamulis

Doctor of Natural Sciences, senior researcher

Institute of Theoretical Physics and Astronomy, Vilnius University,
Theoretical Molecular Electronics and Spintronics Research Group,
A. Gostauto 12, Vilnius 01108, Lithuania
e-mails: tamulis *o* itpa.lt  or  arvydas_tamulis *o* yahoo.com
WEBsite: http://www.itpa.lt/~tamulis/
fax: +370-5-2125361 
Phone: +370-5-2620861 
Home address: Didlaukio 27-40, Vilnius 2057, Lithuania
Mobile phone: +370-69919397
*******************************************************************

On Tue, 28 Jun 2005, Pablo Albores wrote:

> Hi,
>
> I would like to know if it is possible to calculate g-tensors with Gaussian98 
> or 03.
>
> Thanks for your time!
> Lic. Pablo Alboris
>
> INQUIMAE-FCEyN-UBA-ARGENTINA
> Ciudad Universitaria-Pab II-3 Piso
> Tel. 45763343 int. 127
> Fax 45763341
>
>
>
>
>
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From chemistry-request@ccl.net Fri Jul  1 06:13:49 2005
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Subject: Re: CCL:dual-core Opteron 275 performance
To: chemistry %x% ccl.net
Date: Fri, 1 Jul 2005 12:13:32 +0200 (CEST)
In-Reply-To: <Pine.LNX.4.44.0506302246510.26093-100000 %x% cardinal3.Stanford.EDU> from "S.I.Gorelsky" at Jun 30, 5 11:00:42 pm
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Hi,

are these the values for the Gaussian provided binary version
or pgroup compiled?

In my own tests I saw a 2x+ performance advantage of the Xeon over the 
Opteron using a binary compiled with the Intel Fortran compiler on the 
Xeon and the Gaussian provided binary on the Opteron. Unfortunately
I could not achieve a more fair comparison so far, since the Opteron 
binary would not run on an EM64T Xeon and I have been unable so far
to compile G03 for the Opteron with the Intel compiler (I do not have
a current version of the pgroup compiler).

Regards,

Peter

P.S. Did you receive my fax & money for your AOMIX program 
(burger %x% chemie.uni-hamburg.de)? This is still my old account from
Zuerich.
> 
> To add to the discussion about the performance of new dual-core
> processors for computational chemistry applications,
> 
> the comparison of Intel and AMD dual-CPU based computers is shown at:
> 
> http://www.sg-chem.net/cluster/
> 
> As can be seen from the graph, the Gaussian 03 execution speed (test job
> 397) on dual-core dual-CPU Opteron 275 workstation is faster by a factor of 1.95
> as compared to the dual-CPU Xeon 3.2GHz 800MHz FSB machine.
> 
> -----------------
> 
> I would like to thank Ed Gasiorowski (AMD) and Mike Fay (Colfax
> International) for their support.
> 
> Serge Gorelsky
> 
> ----------------------------------------------------------------
>  Dr S.I. Gorelsky, Department of Chemistry, Stanford University
>  Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA
>  Phone: (650) 723-0041. Fax: (650) 723-0852.
> ----------------------------------------------------------------
> 
> 
> 
> 
> 
> 
> -= This is automatically added to each message by the mailing script =-
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From chemistry-request@ccl.net Fri Jul  1 11:22:42 2005
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Accelrys Inc. are holding the following training workshops during August.  
These events are designed to help you get more value from your Accelrys 
software, helping you to better accomplish your research goals.

Costs for the scheduled workshops are $500 per day for all customers.  For 
the on-line presentations, the price is $175 per three hour session for 
all customers.

SAN DIEGO, CA

Pharmacophore Generation with Catalyst               16-17 Aug
Structure Based Drug Design with Cerius2             18-19 Aug
Library Design and Analysis with Cerius2             22-23 Aug
QSAR with Cerius2                                    24-25 Aug
 
BURLINGTON. MA

Introduction to MS Modeling                          3 August
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ONLINE TRAINING

Modeling of GPCR's with Insight II                   2 August (7am PDT)
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and http://www.accelrys.com/training/general/calendar_online.html

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From chemistry-request@ccl.net Fri Jul  1 11:45:58 2005
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Date: Fri, 01 Jul 2005 11:00:45 -0400
From: "Andrew D. Fant" <fant :: pobox.com>
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Subject: Two Questions about finding code
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Good Morning all,

I have two questions about source code I am looking for and would
appreciate any help that anyone can offer.

1)  Can anyone recommend a good source for code that can calculate
various molecular descriptors (a la QSAR/QSPR use)?  Open Source would
be really nice, though I would settle for anything that I don't actually
have to pay for.  Fortran or Python would be easiest for me to read, but
I am not fussy.  This is just for a personal project of mine where I
would rather borrow code for the descriptors that has already been
tested to some degree than roll my own from scratch

2)   Has anyone got any knowledge of the python bindings for openbabel?
 I keep hearing rumors of their existence but confirmed sightings are
rare.  Any pointers to actual code and download sites would be really
spiffy if possible.

Thanks for your time and help.

Andy Fant


From chemistry-request@ccl.net Fri Jul  1 11:43:49 2005
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To: chemistry :a: ccl.net
From: Laurence Lavelle <lavelle :a: mbi.ucla.edu>
Subject: Re: CCL:dual-core Opteron 275 performance
In-Reply-To: <Pine.LNX.4.44.0506302246510.26093-100000 :a: cardinal3.Stanfor
 d.EDU>
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A valid comparison is dual-core dual-CPU Opteron 275 workstation versus 
dual-core dual-CPU Xeon 3.X GHz workstation.



At 11:00 PM 6/30/2005, you wrote:

>To add to the discussion about the performance of new dual-core
>processors for computational chemistry applications,
>
>the comparison of Intel and AMD dual-CPU based computers is shown at:
>
>http://www.sg-chem.net/cluster/
>
>As can be seen from the graph, the Gaussian 03 execution speed (test job
>397) on dual-core dual-CPU Opteron 275 workstation is faster by a factor 
>of 1.95
>as compared to the dual-CPU Xeon 3.2GHz 800MHz FSB machine.
>
>-----------------
>
>I would like to thank Ed Gasiorowski (AMD) and Mike Fay (Colfax
>International) for their support.
>
>Serge Gorelsky
>
>----------------------------------------------------------------
>  Dr S.I. Gorelsky, Department of Chemistry, Stanford University
>  Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA
>  Phone: (650) 723-0041. Fax: (650) 723-0852.
>----------------------------------------------------------------
>
>
>
>
>
>
>-= This is automatically added to each message by the mailing script =-
>To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
>and send your message to:  CHEMISTRY :a: ccl.net
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From chemistry-request@ccl.net Fri Jul  1 13:45:13 2005
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Subject: Re: CCL:Two Questions about finding code
From: Rajarshi Guha <rxg218!at!psu.edu>
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On Fri, 2005-07-01 at 11:00 -0400, Andrew D. Fant wrote:
> Good Morning all,
> 
> I have two questions about source code I am looking for and would
> appreciate any help that anyone can offer.
> 
> 1)  Can anyone recommend a good source for code that can calculate
> various molecular descriptors (a la QSAR/QSPR use)?  Open Source would
> be really nice, though I would settle for anything that I don't actually
> have to pay for.  Fortran or Python would be easiest for me to read, but
> I am not fussy.  This is just for a personal project of mine where I
> would rather borrow code for the descriptors that has already been
> tested to some degree than roll my own from scratch

The CDK (http://almost.cubic.uni-koeln.de/cdk/) has a number of
descriptor routines - the list is not complete by any means, but more
are being added.

You can find example code to calculate descriptors using the CDK at
http://blue.chem.psu.edu/~rajarshi/code/java/#desc

JOELib (http://www-ra.informatik.uni-tuebingen.de/software/joelib/) also
has quite a comprehensive collcetion of descriptor routines

HTH,

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Rajarshi Guha <rxg218!at!psu.edu> <http://jijo.cjb.net>
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Writing software is more fun than working.