From chemistry-request@server.ccl.net Thu Jun  6 03:35:33 2002
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From: Szilveszter Juhos <szilva@ribotargets.com>
To: "Peterson,Brian K." <PETERSBK@apci.com>
cc: chemistry@ccl.net
Subject: Re: CCL:EIDE vs SCSI & backup in Linux clusters
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> current perspectives on disk solutions for Intel based Linux clusters?  

IMHO it is better to have a central RAID NFS server and good network
connections than managing individual HDs on the cluster. (You do not need
a HD at all on a cluster node though in practice most people buy nodes
with HD since it is cheaper or just because that is easily available from
vendors. Booting can be solved using network cards with EPROM). For RAID
arrays I would recommend SCSI with a good controller and fine tuned kernel
(summary here:
http://server.ccl.net/cgi-bin/ccl/message.cgi?2002+05+07+009 ). Than
backup becames easier since you have to backup only the RAID array not the
individual nodes.

Hope it helps:
Szilva



From chemistry-request@server.ccl.net Thu Jun  6 03:47:32 2002
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From: Ingo Brunberg <ib@oc30.uni-paderborn.de>
To: kckyung@inha.ac.kr
CC: chemistry@ccl.net
In-reply-to: <254361A45F4AD311B42900104B1343926656C9@inha.ac.kr> (message from
	=?euc-kr?B?sejC+bDm?= on Thu, 6 Jun 2002 01:22:54 +0900)
Subject: Re: CCL:G98 : Printing isodensity surface
References:  <254361A45F4AD311B42900104B1343926656C9@inha.ac.kr>

Dear Chan,

you can use cube=density as a keyword to calculate the electron
density at points in space distibuted on a regular cubic grid around a
molecule. To find the points with an electron density of 0.001 au you
have to do, what most graphics packages do: Calculate an isosurface at
0.001 au.
There are a lot of programs which can calculate isosurfaces. A pure
graphics application is OpenDX. From a chemists point of view programs
like molden, gOpenMol or molekel come to mind. These are all free.
An easy approach would be to use molden to import a Gaussian cube
file, build the isosurface and save it as a vrml file. From that you
can easily get the points on the surface.

Regards,
Ingo Brunberg

> Dear Computational Chemists:
> 
>     I would like to print a set of points(x,y,z coordinates) on the
> (molecular) surface of electron density 0.001 au of a molecule. Using this
> points, I want to calculate electrostatic potential on this surface. But I
> could not find an option to print this in the Gaussian 98 manual. Many
> programs are available for the graphic representation of the surface. But I
> need the cartesian coordinates of the surface.
> 
>    How can I do that? If not, do I need any other programs to generate such
> coordinates?
> 
> Thanks in advance.
> 
> Chan.

From chemistry-request@server.ccl.net Thu Jun  6 14:29:02 2002
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From: "Jim Kress" <kresslists@kressworks.com>
To: "CCL" <chemistry@ccl.net>
Subject: Summary of CCL:guess=cards in G98W
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There was only one response.  It was from Doug Fox of Gaussian.  His
response was:

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

   There may be a buffer limitation.  Some of the limitations
needed to support Windows 3.1 may have survived.  How big is the
actual input file with all the MO's, over 512MB?

   On the workaround side, the SCF only cares about occupied
orbitals as any set of orthogonal virtual orbitals will work.  Do
you actually have 281 occupied orbitals?  Otherwise just truncate
the list to the occupieds and you should be set.

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

The truncation worked.

Jim



From chemistry-request@server.ccl.net Thu Jun  6 16:23:21 2002
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Date: Thu, 6 Jun 2002 15:23:12 -0500 (CDT)
From: COREY ALLEN RICE <corrice@siue.edu>
To: chemistry@ccl.net
Subject: NiF CI calculation
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TO WHOM THIS MAY CONCERN:

I WAS WONDERING WHAT AN ERROR ON G98 MEANT. FAILURE BECAUSE OF LNK1E VIA
I502.EXE.

CAN ANYONE TELL ME WHAT THIS MEANS?

Corey A Rice
Southern Illinois University at Edwardsville
Chemistry Department
corrice@siue.edu
http://www.siue.edu/~corrice


From chemistry-request@server.ccl.net Thu Jun  6 16:40:00 2002
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Date: Thu, 06 Jun 2002 21:30:29 +0100
From: Michael Brunsteiner <m.brunsteiner@ucl.ac.uk>
Organization: University College London
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dear all,

  I plan do do a couple of classical MD simulations of systems with a 
net charge (aqueous ionic solution above a surface). When using a 
conventional Ewald summation algorithm  the so called self term 
(which is usually included in standard implementations of Ewald) 
provides in such cases an effective background charge that takes 
care of the charge neutralisation more or less automatically.

My questions: 
Is this (entirely) true ?
What are possible artefacts introduced by using a charged system
Any methodological problems I might encounter ?
Any other known problems/pitfalls I might face with charged systems ?

Any hints and/or references appreciated!
cheers!
Michael



==========================================================================
According to convention there is a sweet and a bitter, a hot and a cold,
and according to convention, there is an order.  In truth, there are
atoms
and a void.
                -- Democritus, 400 B.C.

--------------------------------------------------------------------------
Michael Brunsteiner
Centre for Theoretical and Computational Chemistry
University College London
mailto:m.brunsteiner@ucl.ac.uk
http://www.ucl.ac.uk/~uccambr/
--------------------------------------------------------------------------

From chemistry-request@server.ccl.net Thu Jun  6 18:06:16 2002
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Date: Thu, 6 Jun 2002 18:05:54 -0400
From: Rick Venable <rvenable@gandalf.cber.nih.gov>
To: Szilveszter Juhos <szilva@ribotargets.com>
cc: "Peterson,Brian K." <PETERSBK@apci.com>, chemistry@ccl.net
Subject: Re: CCL:EIDE vs SCSI & backup in Linux clusters
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> > current perspectives on disk solutions for Intel based Linux clusters?  

On Thu, 6 Jun 2002, Szilveszter Juhos wrote:
> IMHO it is better to have a central RAID NFS server and good network
> connections than managing individual HDs on the cluster. (You do not need
> a HD at all on a cluster node though in practice most people buy nodes
> with HD since it is cheaper or just because that is easily available from
> vendors. Booting can be solved using network cards with EPROM). For RAID
> arrays I would recommend SCSI with a good controller and fine tuned kernel
> (summary here:
> http://server.ccl.net/cgi-bin/ccl/message.cgi?2002+05+07+009 ). Than
> backup becames easier since you have to backup only the RAID array not the
> individual nodes.

However, for large scratch files such as one might need for QM
calculations, a local disk would be preferred (faster access) over an
NFS mounted RAID server, which has network overhead.  I do agree that
one doesn't want to use the cluster nodes for any other type of storage.

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   Rick_Venable@nih.gov
ALT email:  rvenable@speakeasy.org
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=



From chemistry-request@server.ccl.net Thu Jun  6 02:55:57 2002
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Dear Friends:
I am looking for downloadable programs (trivial to sophisticated) =
applicable in=20
various stages of drug discovery pipeline. Kindly send me the URL and/or =

any other helpful info. As an useful prcatice, I will summarise the =
replies.
Thanks and Regards
S Parthiban
Jubilant Biosys


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<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear Friends:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I am looking for downloadable programs =
(trivial to=20
sophisticated) applicable&nbsp;in </FONT></DIV>
<DIV><FONT face=3DArial size=3D2>various stages of</FONT><FONT =
face=3DArial size=3D2>=20
drug discovery pipeline. Kindly send me the URL and/or </FONT></DIV>
<DIV><FONT face=3DArial size=3D2>any other helpful info. As an useful =
prcatice, I=20
will summarise the replies.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Thanks and Regards</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>S Parthiban</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Jubilant Biosys</FONT></DIV>
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From chemistry-request@server.ccl.net Thu Jun  6 11:11:18 2002
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Date: Thu, 06 Jun 2002 10:11:13 -0500
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Dear Friends:

    Could you please tell me how to calculate and get a contour map of the 
deformation electron densities of a plannar molecule?
    I was trying to produce such a contour map using the gaussian 98 and AIM 
(atoms in molecules) package.  I have tried both ghost atom with basis set 
and real atom without basis set techniques, but the results were not good 
enough.
    Best Wishes,

    JIM











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From chemistry-request@server.ccl.net Thu Jun  6 10:12:28 2002
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Date: Thu, 06 Jun 2002 07:16:53 -0700
To: Roy Jensen <royj@uvic.ca>
From: David Gallagher <dgallagher@cachesoftware.com>
Subject: Re: singlet-triplet crossings...
Cc: chemistry@ccl.net
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Hi Roy,

Angalda and Bofill have developed a method for locating intersystem 
crossing geometries which is now incorporated into MOPAC 2002 and CAChe. 
The reference below may provide more insight, and there is additional 
information in the MOPAC manual at 
http://www.cachesoftware.com/techsupport/mopac/

J. M. Anglada and J. M. Bofill, "A Reduced Restricted-Quasi-Newton-Raphson 
Method for Locating and Optimizing Energy Crossing Points Between Two 
Potential Energy Surfaces", J. Comp. Chem., 1997, 18, 992-1003 (1997).

Regards,
David Gallagher

At 11:13 AM 6/5/2002 -0700, Roy Jensen wrote:
>All
>
>I would like to understand how states of different multiplicity are
>coupled together AND how to determine the probability of surface-crossing.
>
>Coupling is, I believe, a spin-orbit interaction. CASSCF can apparently
>optimize to a singlet-triplet crossing -- has anyone attempted this?
>I am aware of the work by Landau and Zener in the 1930s on surface
>crossing probabilities.
>
>Roy Jensen
>
><I will summarize to the List.>
>
>
>-= This is automatically added to each message by mailing script =-
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<html>
Hi Roy,<br><br>
Angalda and Bofill have developed a method for locating intersystem
crossing geometries which is now incorporated into MOPAC 2002 and CAChe.
The reference below may provide more insight, and there is additional
information in the MOPAC manual at
<a href=3D"http://www.cachesoftware.com/techsupport/mopac/"=
 eudora=3D"autourl">http://www.cachesoftware.com/techsupport/mopac/<br><br>
</a><font face=3D"Century Schoolbook, New Century Schoolbook">J. M. Anglada
and J. M. Bofill, &quot;A Reduced Restricted-Quasi-Newton-Raphson Method
for Locating and Optimizing Energy Crossing Points Between Two Potential
Energy Surfaces&quot;, <i>J. Comp. Chem., </i>1997, <b>18</b>, 992-1003
(1997).<br><br>
</font>Regards,<br>
David Gallagher<br><br>
At 11:13 AM 6/5/2002 -0700, Roy Jensen wrote:<br>
<blockquote type=3Dcite class=3Dcite cite>All<br><br>
I would like to understand how states of different multiplicity are<br>
coupled together AND how to determine the probability of
surface-crossing.<br><br>
Coupling is, I believe, a spin-orbit interaction. CASSCF can
apparently<br>
optimize to a singlet-triplet crossing -- has anyone attempted=20
this?<br>
I am aware of the work by Landau and Zener in the 1930s on surface<br>
crossing probabilities.<br><br>
Roy Jensen<br><br>
&lt;I will summarize to the List.&gt;<br><br>
<br>
-=3D This is automatically added to each message by mailing script =3D-<br>
CHEMISTRY@ccl.net -- To Everybody&nbsp; | CHEMISTRY-REQUEST@ccl.net -- To
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<a href=3D"http://www.ccl.net/chemistry/%A0%A0" eudora=3D"autourl">http://ww=
w.ccl.net/chemistry/&nbsp;
</a> | Jan: jkl@ccl.net</blockquote></html>

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From chemistry-request@server.ccl.net Thu Jun  6 04:21:17 2002
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Date: Thu, 6 Jun 2002 10:21:15 +0200
To: chemistry@ccl.net
Cc: "Peterson,Brian K." <PETERSBK@apci.com>
Subject: Re: CCL:EIDE vs SCSI & backup in Linux clusters
Message-ID: <20020606102115.K301@tr4.ok.dtu.dk>
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In-Reply-To: <B2029542231CD3118A3F0008C75D15AE10A9F804@naex001m.apci.com>; from PETERSBK@apci.com on Wed, Jun 05, 2002 at 04:37:02PM -0400
From: Malcolm Gillies <malcolm@kemi.dtu.dk>

On Wed, Jun 05, 2002 at 04:37:02PM -0400, Peterson,Brian K. wrote:
> We are specifying a Linux Cluster to use for a variety of codes including
> computational chemistry- both quantum and molecular simulations.  I've
> looked at the CCL archives to see what people have said about SCSI vs EIDE
> drives in such a cluster and the results are a bit ambiguous.  What are the
> current perspectives on disk solutions for Intel based Linux clusters?  Are
> EIDE drives sufficient?  Does one need to tune parameters to get good
> performance?  

SCSI vs IDE can turn into a bit of religious issue, so you are likely
to run into some conflicting opinions. The technology is also changing
quickly, with various different generations of interface available
on the market simultaneoulsy, which makes matters more confusing.

The general opinion seems to be that with the more recent generations
of IDE interfaces (UDMA 66 and up), IDE no longer has a systematic
transfer rate disadvantage compared to SCSI, i.e. for both SCSI and IDE,
interface transfer rates are well above the maximum physical transfer
rates of the available drives.
 
However, new drive technology usually appears first with a SCSI
interface. For instance, I believe that 15 000 rpm drives are currently
only available as SCSI. If you need the highest possible performance,
then SCSI is the only option. On the other hand, SCSI drives tend to be
larger, noisier and dissipate more heat.

The remaining advantage of SCSI for me is the ability to swap drives
easily, and to connect drives in an external enclosure. As far as I
know, hot-swapping of IDE drives is currently impossible.  While this
is useful for file servers, or when configuring machines, it's less
important for scratch disks on cluster machines.

We have a cluster here with both SCSI-based and IDE-based nodes. If
we buy new nodes in the future, I would recommend IDE, as the price
advantage is quite convincing. If disk performance is a limiting
factor, a RAID setup may also be solution.

As for tuning parameters, this will depend on your hardware. For most
chipsets, with a recent Linux kernel (2.4.*) it is no longer necessary.
Ideally, you should test before you buy. With Intel x86-based hardware,
it should be easy enough to find an alternative if a particular type of
motherboard/chipset turns out to be problematic. The rule of thumb
here is to stick with hardware that has been on the market for
a while, say six months to a year.

> Second question.  What are you doing about backup of disks on your Linux
> clusters?  Do you just move output files to another machine which is backed
> up?

We don't back up anything on the compute nodes. The queuing system
(OpenPBS) is responsible for moving output files back to the master
node, which is backed up.

cheers,

Malcolm
--
Malcolm Gillies <malcolm.gillies@kemi.dtu.dk>
Post-doctoral researcher
Organic Chemistry, Dept Chemistry,
Technical University of Denmark


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Date: Thu, 6 Jun 2002 22:05:14 +0400
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Hello Szilveszter,

Thursday, June 06, 2002, 11:31:47 AM, you wrote:

>> current perspectives on disk solutions for Intel based Linux clusters?  

SJ> IMHO it is better to have a central RAID NFS server and good
SJ> network connections than managing individual HDs on the cluster.

For common parallel qchemistry packages (say, GAMESS) for diskless
cluster you will need _very_ good connections for multigigabyte NFS
disk I/O. I'm not sure that Ethernet (even Gigabit Ethernet) will be
fast enough.

SJ> (You do not need  a HD at all on a cluster node though in practice
SJ> most people buy nodes  with HD since it is cheaper or just because
SJ> that is easily available from vendors. Booting can be solved using
SJ> network cards with EPROM). For RAID  arrays I would recommend SCSI
SJ> with a good controller and fine tuned kernel (summary here:
SJ> http://server.ccl.net/cgi-bin/ccl/message.cgi?2002+05+07+009 ).
SJ> Than  backup becames easier since you have to backup only the RAID
SJ> array not the  individual nodes.



-- 
Best regards,
 Gregory                            mailto:gas5x@bancorp.ru




