From owner-chemistry@ccl.net Fri Oct 28 00:22:00 2005 From: "George Fitzgerald gxf%x%accelrys.com" To: CCL Subject: CCL: Frequencies + intensities (IR, Raman) Message-Id: <-29804-051027172434-2236-g1+awv9xGYHVSQVScouMSA[#]server.ccl.net> X-Original-From: George Fitzgerald Content-Type: multipart/alternative; boundary="=_alternative 00759636882570A7_=" Date: Thu, 27 Oct 2005 14:24:42 -0700 MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [gxf _ accelrys.com] This is a multipart message in MIME format. --=_alternative 00759636882570A7_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable CASTEP will do this in version 4.0, which will be released at the end of=20 this year. It already computes phonon frequencies and some related response=20 properties such as dielectric constants, polarizability and the like. =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F George Fitzgerald, Ph.D. gxf!=!accelrys.com Accelrys, Inc. Tel: +1 858 799 5360 10188 Telesis Court Fax: +1 858 799 5100 Suite 100 Mobile: +1 858 692 8722 San Diego, CA 92121 "BOUYER Fr=E9d=E9ric 153746 FB153746]-[ATIL.CEA.FR" =20 Sent by: owner-chemistry!=!ccl.net 10/27/2005 04:48 AM Please respond to "CCL Subscribers" To "Fitzgerald, George " cc Subject CCL: Frequencies + intensities (IR, Raman) Dear CCLers, =20 I would like to know if there is software that can calculate frequencies=20 (phonons) of solids AND intensities (IR and Raman). =20 Many thanks to let me known if those software exist. =20 With best regards, =20 Frederic =20 Click here to report this email as spam. --=_alternative 00759636882570A7_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
CASTEP will do this in version 4.0, which will be released at the end of this year.
It already computes phonon frequenci= es and some related response properties such as dielectric constants, polariza= bility and the like.
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F
George Fitzgerald, Ph.D.       gxf!=!accelrys.com
Accelrys, Inc.                             Tel:  +1 858 799 5360
10188 Telesis Court                 Fax: +1 858 799 5100
Suite 100                                     Mobile: +1 858 692 8722
San Diego, CA 92121


"BOUYER Fr=E9d= =E9ric 153746 FB153746]-[ATIL.CEA.FR" <owner-chemistry!=!ccl.net>
Sent by: owner-chemistry!=!ccl.net

10/27/2005 04:48 AM
Please respond to
"CCL Subscribers" <chemistry!=!ccl.net>
To
"Fitzgerald, George &qu= ot; <gxf!=!accelrys.com>
cc
Subject
CCL: Frequencies + intensities (IR, Raman)





Dear CCLers,
 
I would like to know if there is software that can calculate frequencies (phonons) of solids AND intensities (IR and Raman).
 
Many thanks to let me known if those soft= ware exist.
 
With best regards,
 
Frederic
 

Click <= font size=3D3 color=3Dblue>here to report this email as spam.

--=_alternative 00759636882570A7_=-- From owner-chemistry@ccl.net Fri Oct 28 00:57:00 2005 From: "Arindam Ganguly arindamganguly^^^gmail.com" To: CCL Subject: CCL: help needed Message-Id: <-29805-051027180310-4810-MTxAZt+X4LwM6c4pQFPJpA#server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary="----=_Part_7929_20116301.1130450584746" Date: Thu, 27 Oct 2005 17:03:04 -0500 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly]![gmail.com] ------=_Part_7929_20116301.1130450584746 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Perry, could you suggest some more refernces where a clear distinction espcially i= n terms of the diffrences between the architectural differences of windows an= d lInux is highlighted. thanks, Arindam On 10/26/05, Perry E. Metzger perry[#]piermont.com wrote: > > > Sent to CCL by: "Perry E. Metzger" [perry]=3D[piermont.com > ] > > "Nuno A. G. Bandeira" writes: > > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[]ist.utl.pt] > > Perry E. Metzger perry^piermont.com wrote: > > > >> Microsoft also has a similar offering that they give away called > >> (inexplicably) "Services for Unix". I've heard they're getting rid of > >> it though. > >> Performance under Cygwin will not rival performance on a real Linux > >> box -- Windows has architectural issues that make it perform pretty > >> badly in general, and Cygwin is just a POSIX scrim over Windows. > > > > This is a false issue. If the program were natively compiled in > > Windows the performance would be different. Problem is not many take > > the trouble to make their programs transferable to microsoft > > platforms. Many have never heard of Visual Studio .NET or even care to > > think of anything non-unix. Tha fault is on them not the OS itself. > > Sadly, you are wrong on this. Windows has a number of very serious > design flaws, especially in things like the virtual memory management > subsystem, which seriously compromise performance. For example, it is > difficult to do the sort of "memory for disk I/O" tradeoff that you do > on most Unix systems under Windows because the ability to tune buffer > cache policy is extremely limited. It is easy to put Windows into > situations where it becomes I/O bound even though there is enormous > amounts of memory available for caching. > > If you insist on arguing about this with me, I suggest you do it off > the list -- most of the people here aren't going to be interested in > the intimate details. However, the fact here are straightforward. I've > studied the issue very carefully. Windows just doesn't perform well in > a wide variety of cases interesting to people who do computational > chemistry. It is also expensive. There is no good reason to use it on > machines that crunch numbers for a living, and there are excellent > reasons *not* to use it. > > Perry > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_7929_20116301.1130450584746 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Perry,
could you suggest some more refernces where a clear distinction espcially in terms of the diffrences between the architectural differences of windows and lInux is highlighted. thanks,
Arindam

On 10/26/05, Perry E. Metzger perry[#]piermont.com <owner-chemistry_+_ccl.net> wrote:=

Sent to CCL by: "Perry E. Metzger" [perry]=3D[piermont.com]

"Nuno A. G. Bandeira" w= rites:
> Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandei= ra []ist.utl.pt]
> Perry E. Metzger perry^piermont.com wrote:
>>> Microsoft also has a similar offering that they give away called<= br>>> (inexplicably) "Services for Unix". I've heard they'r= e getting rid of
>> it though.
>> Performance under Cygwin will not rival= performance on a real Linux
>> box -- Windows has architectural i= ssues that make it perform pretty
>> badly in general, and Cygwin = is just a POSIX scrim over Windows.
>
> This is a false issue. If the program were natively compil= ed in
> Windows the performance would be different. Problem is not ma= ny take
> the trouble to make their programs transferable to microsof= t
> platforms. Many have never heard of Visual Studio .NET or even car= e to
> think of anything non-unix. Tha fault is on them not the OS it= self.

Sadly, you are wrong on this. Windows has a number of very ser= ious
design flaws, especially in things like the virtual memory managementsubsystem, which seriously compromise performance. For example, it is
= difficult to do the sort of "memory for disk I/O" tradeoff that y= ou do
on most Unix systems under Windows because the ability to tune buffercache policy is extremely limited. It is easy to put Windows into
situ= ations where it becomes I/O bound even though there is enormous
amounts = of memory available for caching.

If you insist on arguing about this with me, I suggest you do it of= f
the list -- most of the people here aren't going to be interested inthe intimate details. However, the fact here are straightforward. I've
studied the issue very carefully. Windows just doesn't perform well in<= br>a wide variety of cases interesting to people who do computational
ch= emistry. It is also expensive. There is no good reason to use it on
machines that crunch numbers for a living, and there are excellent
reaso= ns *not* to use it.

Perry



-=3D This is automatically = added to each message by the mailing script =3D-
To recover the email ad= dress of the author of the message, please change l= ook up the X-Original-From: line in the mail header.

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------=_Part_7929_20116301.1130450584746-- From owner-chemistry@ccl.net Fri Oct 28 01:32:00 2005 From: "frisch:_:gaussian.com (Michael Frisch)" To: CCL Subject: CCL:G: filters Message-Id: <-29806-051027181602-12233-DIK9Ju75feG3wVPzXYiR7g:server.ccl.net> X-Original-From: frisch**gaussian.com (Michael Frisch) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 27 Oct 2005 18:12:22 -0400 Mime-Version: 1.0 Sent to CCL by: frisch#%#gaussian.com (Michael Frisch) On Thu, Oct 27, 2005 at 06:26:32PM +0200, Mehdi Bounouar mehdi.bounouar .. ch.tum.de wrote: > > Sent to CCL by: Mehdi Bounouar [mehdi.bounouar[]ch.tum.de] > > Sorry for my 2 cents, but what you said previously, is exactly why people > defend and would like to see more open source programs. > If G.inc don't care about implementing or correcting something for > comercial reason or other you would have basically to pay them to do so > (Mr. Frisch previous mail). No. Given very finite resources, we add the features which appear to be most important for the largest number of customers. In general we don't solicit and don't accept requests to do features for individual customers, because we're trying to provide the features which will have the most general benefit. In the one case where someone paid for us to do something, the customer wanted a feature which was important to them and interesting to me but was not widely requested and so was a low priority for us. They covered some travel expenses to facilitate the work (not by any means all the costs) to motivate us to make this feature a higher priority. The customer had source code, but the feature was not something they could have trivially added themselves. In fact, it required new research which was subsequently published (CPL 250, 373 (1996)). (Specifically, the customer paid for Mike Robb to travel for a visit to Gaussian, where he and I worked out what to do. Coding was done in his group, supported by Gaussian, Inc. The feature was included in a subsequent revision of our software; we would never consider adding a feature unless it was to be added for the use of all our customers.) Mike Frisch From owner-chemistry@ccl.net Fri Oct 28 02:07:00 2005 From: "Brian Salter-Duke b_duke^-^octa4.net.au" To: CCL Subject: CCL: Filters Message-Id: <-29807-051027190425-2864-g5ekSJORNpPB41zw5oZ2EA^server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 28 Oct 2005 08:20:26 +1000 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke=-=octa4.net.au] On Thu, Oct 27, 2005 at 06:17:25PM +0200, Eugen Leitl eugen__leitl.org wrote: > > Sent to CCL by: Eugen Leitl [eugen(-)leitl.org] > On Thu, Oct 27, 2005 at 12:13:30PM -0300, Cory Pye cpye{}crux.smu.ca wrote: > > > It is comments such as this that could convince the Gordon group to decide > > to switch from available source to binary distribution (or none at all). > > I'm not sure this would change a lot. The code is purely complimentary, > as no one can change a line of it and share it but within their group. This is techically correct but it is not the whole story. Mike Schmidt will accept bug fixes and sometimes he accepts new code. Have you asked him ever to accept changes that you want? I have on many occassions and he has always been extremely friendly and helpfull. For example, the hooks in the latest July Gamess version to our VB2000 code are much better because Mike took my changes to three gamess modules and then spent time improving my code. If you do not like the build process, which I agree is prehistoric, write a makefile for your own use and then ask Mike whether he wants to distribute it. He may, I do not know. There is another point about code release. It may not be "free", as in free software foundation definition, but you can look at it and see if it really does what it claims to in all circumstances and you can check how it does it. That sure beats "binary only" releases. Brian. > > Why are people complaining about getting something for free? If you don't like > > Because being merely free (as in beer) is not enough. The license must > offer the freedom of being able to contribute, and, preferrably, to > fork (under a different name). > > > aspects about the distribution the package of group X, write your own > > open-source package, or improve upon someone elses. Any volunteers to write an > > I would gladly start hacking on GAMESS, such as improving the build > process (which is frankly prehistoric), and porting to gcc4.0. The license > doesn't allow me to. No other package under a less restrictive license > plays in the same league. I'm sure there are lots more of users which > share this frustration. > > > efficient integral package? OK. Uh-oh, it works on Suns and IBMs, but not on > > SGIs or HP. It works with RedHat, but not with Mandrake or Debian. I can't find > > If you want it to work on Debian, change the license. > > > optimized BLAS libraries. How come it core dumps every time I try to do an > > f-type integral? Version 4.2.3 of compiler X on machine Y has a bug. Are you > > willing to provide support for this free program in perpetuity? In biology, > > The point of open source under a nonrestrictive license is that the user > fix the bugs they find, and offer support. The GAMESS mailing list is such > a place. > > > most mutations are non-viable. > > If somebody fails to support a mutated fork, of what concern is this > to the authors maintaining the original code line? If they don't > fork, but contribute to the main tree, there are submission privileges > and regression unit tests which will quickly weed out the weak. > > > Sounds to me like downloading from Kazaa and then complaining about the audio > > quality. > > It sounds to me as if you don't understand the impact of a license > on a fate of a project. > > The license alone does not grant a blessing. But no open source project > will be successful without a good license. > > This is getting off-topic for the list, so no more in this thread from me. > > -- > Eugen* Leitl leitl > ______________________________________________________________ > ICBM: 48.07100, 11.36820 http://www.leitl.org > 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE> > > -- Brian Salter-Duke (Brian Duke) b_duke]~[octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher, Chem., Melbourne Univ. & Med. Chem., Monash Univ. From owner-chemistry@ccl.net Fri Oct 28 02:43:01 2005 From: "Derosa-Latech pderosa_-_latech.edu" To: CCL Subject: CCL:G: Filters; really Gaussian, Inc. and funding Message-Id: <-29808-051027211334-5971-28LKxnDA+OEom0goIgQ42Q-.-server.ccl.net> X-Original-From: "Derosa-Latech" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 27 Oct 2005 19:10:04 -0500 MIME-Version: 1.0 Sent to CCL by: "Derosa-Latech" [pderosa(!)latech.edu] I am reading all this discussion about Gaussian and every e-mail I read sound reasonable so I certainly do not know who is right. however I'd like to make a couple of comments. This started by a request for CCL to filter out e-mails requesting help for problems with Gaussian, the argument was that Gaussian is developed with taxpayer money, yet we have to pay to get it and we do not even get appropriate support when problems arise. Although I can see some logic in this request as a Gaussian user I believe it is unfair that another resource to get some help closes for us, there should be other ways to make Gaussian hear our voice than forcing their users to change codes because nobody wants answers their questions to complain about Gaussian policies. However the discussion is now about whether is legal, ethical, moral, or whatever to pay for a software developed with taxpayers money. I think the topic is not that easy to deal with. The response to Mike's Frisch claim that Gaussian finance itself was a list of papers introducing some of the methods implemented in Gaussian that were not financed by Gaussian but is most cases by taxpayer money through grants. Well, isn't every computational chemistry software the implementation of a theory that all or in part was developed by somebody that got a grant to do that? does that mean not computer chemistry code should be commercial? As a young Faculty (meaning no money to buy anything) it would be great, but what if nobody wants to spend their time writing and optimizing a code and (even more difficult) taking calls or e-mails from users that cannot make it work? I have developed codes and use codes developed by somebody else, my research is about getting results from simulation methods, most of the time I cannot afford the time it would take for me to write my own code, thus I pay for somebody else to implement, in an optimize code, the theory or theories I want to use to study a problem. Even if all the theories behind a software was developed out of government money, writing a code certainly does add a value. We could certainly discuss how much would it be reasonable to pay for that service. Anyway, I am probably totally wrong, I was just trying to get away from a proposal I need to write. Pedro ----- Original Message ----- > From: "Jim Kress ccl_nospam---kressworks.com" To: "Derosa, Pedro " Sent: Thursday, October 27, 2005 12:30 PM Subject: CCL:G: G: Filters; really Gaussian, Inc. and funding > > Sent to CCL by: "Jim Kress" [ccl_nospam##kressworks.com] > With regard to the claims made about Gaussian self funding, let us look at > a > few excerpts from > > http://www.gaussian.com/g_brochures/g03_new.htm > > entitled "What's New in Gaussian 03" taken from the Gaussian web site. > The > numbers to the left with the ) are the references listed on the page from > the Gaussian web site. > > > 3) B. Mennucci, E. Cancès, and J. Tomasi, J. Phys. Chem. B 101, 10506 > (1997). > > Evaluation of Solvent Effects in Isotropic and Anisotropic Dielectrics and > in Ionic Solutions > with a Unified Integral Equation Method: Theoretical Bases, Computational > Implementation, and Numerical Applications > > The authors acknowledge the Consiglio Nazionale delle Ricerche (CNR) for > financial support. No Gaussian Inc. here. > > 5) M. Cossi, N. Rega, G. Scalmani and V. Barone, J. Chem. Phys. 114, 5691 > (2001). > > Polarizable dielectric model of solvation with inclusion of charge > penetration effects > > The authors acknowledge - no one > > 6) M. Cossi, G. Scalmani, N. Rega, and V. Barone, J. Chem Phys. 117, 43 > (2002). > > New developments in the polarizable continuum model for quantum mechanical > and classical calculations on molecules in solution > > The authors wish to thank M. J. Frisch ~Gaussian, Inc.! for helpful > discussions (not money). The technical support by the CIMCF ~Centro > Interdipartimentale di Metodologie Chimico-Fisiche, University of Naples! > is > also acknowledged. No Gaussian Inc. here. > > 18) H. B. Schlegel, J. M. Millam, S. S. Iyengar, G. A. Voth, A. D. > Daniels, > G. E. Scuseria, and M. J. Frisch, J. Chem. Phys. 114, 9758 (2001). > > Ab initio molecular dynamics: Propagating the density matrix with Gaussian > orbitals > > This work was supported by the Natural Science Foundation (CHE-9982156 and > CHE-9874005), the Office of Naval Research (GAV), and Gaussian, Inc. We > would like to acknowledge Professor Jack Simons for his input on a > preliminary version of this manuscript. Note the use of government > funding. > > 20) H. B. Schlegel, S. S. Iyengar, X. Li, J. M. Millam, G. A. Voth, G. E. > Scuseria, and M. J. Frisch, J. Chem. Phys. 117, 8694 (2002). > > Ab initio molecular dynamics: Propagating the density matrix with Gaussian > orbitals. III. Comparison with Born-Oppenheimer dynamics > > This work was supported by the National Science Foundation (Grants Nos. > CHE-9982156, CHE-9874005, and CHE-0131157), the Office of Naval Research > ~GAV! and Gaussian, Inc. An allocation of computer time from the Center of > High Performance Computing at the University of Utah is gratefully > acknowledged. Note the use of government funding. > > 23) M. Klene, M. A. Robb, M. J. Frisch, and P. Celani, J. Chem. Phys. 113, > 5653 (2000). > > Parallel implementation of the CI-vector evaluation in full CIÕCAS-SCF > > This work was supported in part by Gaussian Inc., PA, USA. All > computations > were carried out on an IBM SP2 funded jointly by IBM UK and HEFCE ~U.K.!. > Note the 'in part' funding reference to Gaussian Inc. > > 52) F. Neese, J. Chem. Phys. 115, 11080 (2001). > > Prediction of electron paramagnetic resonance g values using coupled > perturbed Hartree-Fock and Kohn-Sham theory > > The author acknowledges - no one > > 55) B. Mennucci, J. Tomasi, R. Cammi, J. R. Cheeseman, M. J. Frisch, F. J. > Devlin, S. Gabriel, and P. J. Stephens, J. Phys. Chem. A 106, 6102 (2002). > > Polarizable Continuum Model (PCM) Calculations of Solvent Effects on > Optical > Rotations > of Chiral Molecules > > One of us (P.J.S.) is grateful to the National Science Foundation for > financial support (Grant CHE- > 9902832). B.M and J.T are grateful to the Italian CNR (through Agenzia > 2000 > project) for financial support. Note the use of government funding. No > Gaussian Inc. here. > > > These are just a few of the examples I could easily acquire. The more > recent references are either listed 'in prep' or in journals to which I do > not have access. > > In any case, it would appear the claim of 'pure Gaussian funding' is > overstated. So, Federal Government funding IS being used to develop > Gaussian products, even if it is 'indirect', Gaussian still directly > benefits from others being forced to provide money for this 'indirect' > support. > > Jim > > > >> -----Original Message----- >> From: frisch_+_gaussian.com (Michael Frisch) >> [mailto:owner-chemistry,ccl.net] >> Sent: Thursday, October 27, 2005 9:13 AM >> To: Kress, Jim >> Subject: CCL:G: Filters; really Gaussian, Inc. and funding >> >> >> Sent to CCL by: frisch{:}gaussian.com (Michael Frisch) >> >> People are certainly entitled to their own opinions about our >> company, but I think this discussion is based on some >> assumptions which are just plain wrong. >> >> Gaussian, Inc. has been around for 18 years and has never >> received any direct government grants. We were a >> subcontractor in one SBIR grant given to another company ten >> years ago, and we once received a small contract which paid >> travel expenses for one person we work with to spend a few >> weeks with us and put in a feature which a government lab >> particularly wanted. We've paid for about 75 man-years of >> work on our software over the past 15 years, and these two >> small contracts account for about 1/2 man-year of that. The >> rest, including absolutely everything we've done in the last >> 10 years and 99.5% of what we've done in the last 15 years, >> has been paid for out of license fees. >> >> Personally, I've worked on the software for over 20 years >> without any government support for either my salary or >> equipment I used. >> >> We do collaborate with various academic research groups, but >> we subsidize their research both with cash (again coming from license >> fees) and with the time of scientists employed by Gaussian, Inc. >> who are paid from license fees. >> >> Thus, the implication that Gaussian's products have been >> produced substantially or primarily with government funding >> is simply wrong. >> >> This was an accurate statement about Gaussian 82, but I don't >> see many questions on this list about that program -- people >> seem to be using the versions we've produced in the last two >> decades, for which the implication is false. >> >> Michael Frisch >> >> >> >> -= This is automatically added to each message by the mailing >> script =- To recover the email address of the author of the >> message, please change the strange characters on the top line >> to the , sign. You can also look up the X-Original-From: line >> in the mail header.> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> -+-+-+-+-+> > > > From owner-chemistry@ccl.net Fri Oct 28 03:18:01 2005 From: "M. L. Dodson bdodson*|*scms.utmb.EDU" To: CCL Subject: CCL:G: Filters Message-Id: <-29809-051027232122-25404-BN0hQIvIHpz6NO4f/akd6A|a|server.ccl.net> X-Original-From: "M. L. Dodson" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 27 Oct 2005 22:21:17 -0500 Mime-Version: 1.0 Sent to CCL by: "M. L. Dodson" [bdodson . scms.utmb.EDU] On Thu, Oct 27, 2005 at 09:13:21AM -0500, Aaron Deskins ndeskins(~)purdue.edu wrote: > > Sent to CCL by: Aaron Deskins [ndeskins[]purdue.edu] > Jim Kress ccl_nospam.:.kressworks.com wrote: > > >Sent to CCL by: "Jim Kress" [ccl_nospam%a%kressworks.com] > >They're not working for free. Their using the government as an agent to > >take money from their neighbors to pay for their work (i.e. government > >grants). Then they sell the results of that work to the people who paid > >for > >it originally (i.e. taxpayers). > > > >That's called double dipping and it's immoral. > > > >Remember, all government money comes from us taxpayers. No matter what any > >government employee tells you, there is no money tree in Washington. > > > >Jim > > > > > > > This topic seems mostly to come down to a discussion of the merits of > free-market capitalism versus socialism. Who does work better: > profit-minded citizens or government paid workers? Of course it depends, > but I think if Gaussian was never commercialized, then we all very well > could have been stuck using Gaussian 86. > Why don't we all cool down a little bit and avoid words like immoral and socialism. The discussion might gain some civility in the process. I'll only say that if you think open source is socialism, you have missed the point about open source. Think of peer review as a better analogy or descriptor. The advantage of open source consumer s/w is the increase in the number of "eyeballs" looking at the code, and the substantially better debugging (and maybe, just maybe, an increase in the efficiency of the algorithms) that follows from that "peer review". As I see it this advantage would not carry over into computational chemistry s/w IN A SIMPLE WAY for two conflicting reasons: (1) most computational chemistry s/w is in fact open source (whether or not you pay for it), so theoretically that benefit should hold, HOWEVER (2) due to the small "market" the people looking at the code are not, by and large, computer scientists, so debugging is not as good as, e.g., apache, BSD unix, Linux, etc. And, in any case, if the "purveyers" of CC s/w are not willing to take patches from the community, that benefit will not be realized. And that is the only way you get YOUR ideas implemented in most projects: describing a better algorithm on an email list is not enough; you must submit patches. Most open source projects have multiple email lists, some devoted to support (in the sense of the "Gaussian questions"), others to discussion of the algorithms ("theory"), and still others to the development process itself. So the "Gaussian question" problem does not occur. Only people wanting to ask or answer "Gaussian questions" subscribe to that particular list. I'm just trying to inject a little reality about open source into this discussion which has been filled with a lot of misinformation and almost complete lack of appreciation of the real user benefits of the open source s/w movement (far beyond the cost of the s/w). -- M. L. Dodson Personal: mldodson-at-houston-dot-rr-dot-com Work: bdodson-at-scms-dot-utmb-dot-edu Work: four_zero_nine-772-2178 FAX: four_zero_nine-772-1790 From owner-chemistry@ccl.net Fri Oct 28 07:38:01 2005 From: "Ulrike Salzner salzner^fen.bilkent.edu.tr" To: CCL Subject: CCL:G: Filters; really Gaussian, Inc. and funding Message-Id: <-29810-051028064217-20835-iM9bJ+Tcx8fz3SgFPJj/4A^^server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 28 Oct 2005 12:38:33 +0300 Mime-Version: 1.0 (Apple Message framework v734) Sent to CCL by: Ulrike Salzner [salzner]^[fen.bilkent.edu.tr] On Oct 28, 2005, at 3:10 AM, Derosa-Latech pderosa_-_latech.edu wrote: > This started by a request for CCL to filter out e-mails requesting > help for problems with Gaussian, the argument was that Gaussian is > developed with taxpayer money, yet we have to pay to get it and we > do not even get appropriate support when problems arise. When I was on my first faculty position, I had to compile Gaussian98 for the first time by myself with no one in the university able or willing to help. The Gaussian people coatched me through every single compiling error until the program was running on a SUN cluster and under Linux. The answers were always quick and to the point. This was done although the SUN cluster the university had, had outdated libraries and although I was a total moron with these things. I think the customer support was excellent. Whenever I am asking a question to the Gaussian people, I get answers. I do try not to bother them (and CCL) with things I can find in the manual or on their webpage. I agree that CCL should not be overloaded with question about Gaussian keywords but scientific questions about methods, their applicability and shortcomings should be allowed. I have learnt a lot in this way through CCL and I do not see why some people want to censor the list. Assoc. Prof. Dr. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey salzner.^^.fen.bilkent.edu.tr From owner-chemistry@ccl.net Fri Oct 28 09:28:01 2005 From: "Barbault Florent florent.barbault(-)paris7.jussieu.fr" To: CCL Subject: CCL: COMFA =?ISO-8859-1?Q?q=B2?= Message-Id: <-29811-051028050900-14807-SCGD2TGrDVTtUWtLMgZpKg(a)server.ccl.net> X-Original-From: "Barbault Florent" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Fri, 28 Oct 2005 03:23:48 +0200 MIME-Version: 1.0 Sent to CCL by: "Barbault Florent" [florent.barbault(a)paris7.jussieu.fr] Hi Antoine, When you do a cross-validation the r² in SYBYL represent the q². So you have to do a cross-validation analysis first, and if it is correct a non-cross-validation analysis. Best regards On Thu, 27 Oct 2005 13:50:48 +0200 "Antoine FORTUNE Antoine.Fortune^_^ujf-grenoble.fr" wrote: > > Sent to CCL by: Antoine FORTUNE [Antoine.Fortune- -ujf-grenoble.fr] > Hi all, > I'm working with sybyl MSS to do comfa study. As I run a PLS, sybyl >gives r² value in the report. Where / how can i get the q² value ? >It's not in the report log. > Thank's > > Antoine > > > > -= This is automatically added to each message by the mailing script >=- > To recover the email address of the author of the message, please >change> > Before posting check wait time for next message at: >http://www.ccl.net> > > From owner-chemistry@ccl.net Fri Oct 28 10:56:00 2005 From: "Derosa-Latech pderosa|a|latech.edu" To: CCL Subject: CCL:G: Filters; really Gaussian, Inc. and funding Message-Id: <-29812-051028103325-13354-4LbMvLQvEjDbrUBflauxDg ~ server.ccl.net> X-Original-From: "Derosa-Latech" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Fri, 28 Oct 2005 08:41:45 -0500 MIME-Version: 1.0 Sent to CCL by: "Derosa-Latech" [pderosa=latech.edu] I was not planning on sending more e-mails to this discussion, I am really working on a proposal I need to send out (I want my cut on taxpayers money:-), but in the e-mail below one of my statements was taken out of context, in my e-mail I did NOT express any opinion about Gaussian customer service, for good or bad, I just brought up the argument expressed on the e-mail that opened this discussion, and voice my opinion about that. Dr Salner's answer is a good piece of information, but he shouldn't have associated my name to the statement he commented since I was just quoting the e-mail that started this discussion. I needed to clarify that Just to add my personal opinion I am not 100% satisfied with Gaussian customer support but I am not in the group of people that seems to want Gaussian banned from the face of the earth either, my last interaction with Gaussian customer service was painful, took months and includes an unreal confrontation between Gaussian and the company that sold me my computers, at the end after tons of mails (Including some I sent to CCL when I thought Gaussian was not responding any longer) Gaussian technical support found the problem and even sent me the set of libraries that G03 needed to work in my system. My general impression is that Gaussian technical support work wonderful and are extremely helpful unless they determine your combination processor+OS+compiler is not supported by them. In order to be fair I need to add that I had one of such combination, as I said it was painful but at the end they helped me solve my problem. I hope nothing in here is taken out of context this time I do need to finish my proposal. Regards, Pedro ----- Original Message ----- > From: "Ulrike Salzner salzner^fen.bilkent.edu.tr" To: "Derosa, Pedro " Sent: Friday, October 28, 2005 4:38 AM Subject: CCL:G: Filters; really Gaussian, Inc. and funding > > Sent to CCL by: Ulrike Salzner [salzner]^[fen.bilkent.edu.tr] > On Oct 28, 2005, at 3:10 AM, Derosa-Latech pderosa_-_latech.edu wrote: > >> This started by a request for CCL to filter out e-mails requesting help >> for problems with Gaussian, the argument was that Gaussian is developed >> with taxpayer money, yet we have to pay to get it and we do not even get >> appropriate support when problems arise. > > > When I was on my first faculty position, I had to compile Gaussian98 for > the first time by myself with no one in the university able or willing to > help. The Gaussian people coatched me through every single compiling > error until the program was running on a SUN cluster and under Linux. The > answers were always quick and to the point. This was done although the > SUN cluster the university had, had outdated libraries and although I was > a total moron with these things. I think the customer support was > excellent. > Whenever I am asking a question to the Gaussian people, I get answers. I > do try not to bother them (and CCL) with things I can find in the manual > or on their webpage. I agree that CCL should not be overloaded with > question about Gaussian keywords but scientific questions about methods, > their applicability and shortcomings should be allowed. I have learnt a > lot in this way through CCL and I do not see why some people want to > censor the list. > > > > Assoc. Prof. Dr. Ulrike Salzner > Department of Chemistry > Bilkent University > 06800 Bilkent, Ankara > Turkey > salzner,;,fen.bilkent.edu.trhttp://www.ccl.net/chemistry/sub_unsub.shtml> > > > From owner-chemistry@ccl.net Fri Oct 28 11:33:00 2005 From: "Nuno A. G. Bandeira nuno.bandeira-$-ist.utl.pt" To: CCL Subject: CCL:G: Filters Message-Id: <-29813-051028113116-28861-US07bTqC0sLcLFA0Qci7hA{}server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 28 Oct 2005 16:31:05 +0100 Mime-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira^ist.utl.pt] Jim Kress ccl_nospam+*+kressworks.com wrote: > Work derived from taxpayer funding should be freely available to those > taxpayers who have paid for it. That is the case with GAMESS, with NCARS > CAM3 and MAGICC, Jay Ponder's Tinker, and other codes. That is the way it > should be. > > Profiteering by Gaussian and the other commercial entities should not be > allowed. I will be speaking to my congressman to explore current law as > well as proposing future law that will remedy this issue. You can speak to your congressman about it and you may even be successful in changing the law but what you mention is standard practice the world over. From Beijing to Western Europe and the US you'll find a handful of companies that provide scientific software with post-graduate staff on their payroll. Some argue that education should be free for everyone but the fact remains some people still prefer private education and the same goes for health... It's all about choice, market laws and whether your product satisfies the needs of the (in this case) chemical community. The discussion of who owns intellectual property has always been controversial and will not end here. I accept Dr Frisch's explanation and I view his position as perfectly valid. I have no reason to doubt him so far. You complained about Gaussian giving bad support to its users. Do the developers of open source volunteer to give any at all ? If they do it's solely out of their generosity which I commend... at least with paid software you can always ask for something in return. Again it's not for me to judge which is the best option. That always lies with the user. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student ]_[ IST,Lisbon -- -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.362 / Virus Database: 267.12.5/150 - Release Date: 27-10-2005 From owner-chemistry@ccl.net Fri Oct 28 12:07:01 2005 From: "Perry E. Metzger perry[-]piermont.com" To: CCL Subject: CCL: Filters Message-Id: <-29814-051028102545-12766-CvfYaKjXDQt5ufTCxTAHLA[]server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Fri, 28 Oct 2005 10:25:39 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry^piermont.com] "Konstantin Kudin konstantin_kudin||yahoo.com" writes: > In heated discussions like this it helps a bit to understand the > realities of producing a polished software package. As such, "The > Mythical Man-Month" by Fred Brooks is highly recommended as a good > introduction. > > Here is a relevant piece from the book review taken from > { http://www.glenmccl.com/misc_005.htm } > > "A program is something you might quickly put together in a few hours > or days or weeks. But to take the additional two steps of coming up > with a programming system or programming product is a lot of additional > work, on the order of 3X as Brooks describes it. Each of these steps is > independent, therefore Brooks talks about a 9X ratio of cost between a > program and a programming systems product." > > Now, the important question is who is going to cover the 8/9th (or > even only 2/3rds) of the total development cost of a highly integrated > package. Somehow no grants usually cover such efforts ... That is why Linux does not exist -- because it is impossible for a large piece of software to be developed in this manner. This is also why gcc, which is far larger than ANY computational chemistry package ever built and far more complicated, doesn't exist. This is also why PyMol doesn't exist -- because it is far too difficult for computational chemistry software to be written in an open source manner. Perry From owner-chemistry@ccl.net Fri Oct 28 12:42:00 2005 From: "david.giesen~!~kodak.com" To: CCL Subject: CCL:G: Filters; really Gaussian, Inc. and funding Message-Id: <-29815-051028102606-12815-Y6ZhkU4Aps5erekMRqS3PQ[*]server.ccl.net> X-Original-From: david.giesen-x-kodak.com Content-Type: text/plain; charset="US-ASCII" Date: Fri, 28 Oct 2005 09:01:43 -0400 MIME-Version: 1.0 Sent to CCL by: david.giesen:_:kodak.com I must confess to being completely confused by this discussion. It attempts to somehow create two groups - those who receive government funding and should give away their products for free, and those who don't receive funding and may charge for their services/products. It baffles me that anyone thinks there is a single product on the market in the United States that hasn't benefitted in some way from government funding. First and foremost, corporations frequently apply for, and receive, government research grants. I doubt anyone truly expects IBM, Phillips or Ford Motor Company to give away their products. Thus, there really is no distinction between academic groups (or scientific corporations such as Gaussian, Inc.) and your friendly local Fortune 500 company. To treat one differently than the other makes no sense to me. Secondly, companies are often the happy beneficiaries of tax breaks, "economic incentives" or whatever else you want to call them. Sure, this type of government funding is very slightly more opaque in that the company only gets to keep its own money. But ultimately the other tax payers have to pay more taxes to make up for the money not paid by the company, and the result is the same: the "little guy" pays more money, and the "big guy" has a little more money. And finally, we all understand that the government paid for the roads that a company's employees must drive on to get to work, the sewers that carry water into and out of the company, the police that keep the employees safe and also the consumers safe so they can buy the company's products, the Social Security checks that allow the company to pay artificially low wages because the employees don't need to truly fully fund their own retirement, etc. etc. etc. If the government doesn't pay for these things, the company must, so these things are also clearly "government funding" of the company. Drawing some line in the air and saying that software produced using some sort of government funding MUST be free but it is OK to sell government funded computers, razors, cameras and cars just doesn't make any sense to me. Also, drawing a line in the air and saying research grants are government funding that matters, but other types of government funding don't matter just doesn't make any sense to me either. Dave Giesen (An employee of the Eastman Kodak Company expressing his own private opinions) From owner-chemistry@ccl.net Fri Oct 28 13:17:00 2005 From: "Perry E. Metzger perry.~!~.piermont.com" To: CCL Subject: CCL: help needed Message-Id: <-29816-051028102224-12582-VRt7CYWKD936Sa29ycPsjA~!~server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Fri, 28 Oct 2005 10:22:14 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry~~piermont.com] "Arindam Ganguly arindamganguly^^^gmail.com" writes: > could you suggest some more refernces where a clear distinction espcially in > terms of the diffrences between the architectural differences of windows and > lInux is highlighted. thanks, Unfortunately, a lot of this stuff is hard. The problem is that issues like virtual memory subsystem architecture aren't any more easily understood by non-specialist than an ab initio computational chemistry system is easily understood by the non-specialist. Really understanding the issues requires that you have an operating systems class under your belt, or the equivalent. There are also a *lot* of different issues in performance differences between Windows and various Unix flavors, not just the VM subsystems. I picked that just because seeing the difference made there is particularly easy. there are many others. Anyway, trying to answer your point more directly: For Linux, there is apparently a book on the virtual memory subsystem -- you can find it by doing a google for "linux virtual memory". I have to admit, though, that the best way to *really* understand the architecture of the system is to look at the code and play with it. There is also some documentation that comes with the kernel sources themselves, including a bunch of stuff on tuning associated with the proc filesystem documentation. For NetBSD (the Unix I tend to use the most, but which I suspect no one here uses or will be using any time soon), there is a longish paper on the design of the VM subsystem, which you can find off of here: http://netbsd.org/Documentation/kernel/uvm.html Unfortunately, Chuck's original papers don't include a description of the way that the unified buffer cache works or the internal tuning mechanisms it employs. Those can be found out about in other pieces of system documentation. For Windows, the easiest way to learn about the VM system and its tuning is by reading through the MSDN documentation on the subject -- the information from Microsoft's old NT architecture books is quite out of date at this point. The MSDN info is, however, quite opaque, including the obscure references to the several variables in the registry that you actually can flip to alter performance a bit. There are also some good open source tools to let you monitor Windows VM behavior in real time, including from www.sysinternals.com. Perry From owner-chemistry@ccl.net Fri Oct 28 13:52:00 2005 From: "Perry E. Metzger perry%%piermont.com" To: CCL Subject: CCL: help needed Message-Id: <-29817-051028101157-11806-ra3WsrpGm4Yl62hh+nlzpw]*[server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Fri, 28 Oct 2005 10:11:47 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry_._piermont.com] "Alex. A. Granovsky gran ~~ classic.chem.msu.su" writes: >> Sadly, you are wrong on this. Windows has a number of very serious >> design flaws, especially in things like the virtual memory management >> subsystem, which seriously compromise performance. For example, it is >> difficult to do the sort of "memory for disk I/O" tradeoff that you do >> on most Unix systems under Windows because the ability to tune buffer >> cache policy is extremely limited. It is easy to put Windows into >> situations where it becomes I/O bound even though there is enormous >> amounts of memory available for caching. > > The statements above are no more than lore, which are definitely not > based on the results of any serious comparison, and only show that > people usually do not know and do not make use of advanced Windows > memory management and I/O features. Oh, really? I've personally conducted extensive benchmarking on this specific topic, and I've read enormous amounts of Microsoft documentation. The page cache policy in Windows is utterly primitive. As a result of this, file pages are evicted from cache long before they need to be. You can, of course, set the registry key to tell the box to behave as a file server, at which point, executable pages are evicted from cache long before they need to be. There is no in between. There are no pluggable policies. You can't even tune the policy that is there. About a year ago I conducted a demonstration in which a single processor machine running NetBSD (not Linux, but the principle would apply to Linux as well) successfully rebuilt a large software system many times faster than a four processor Windows server. The Windows machine had more memory, and each individual processor was faster than the NetBSD machine's one processor. The reason? The Windows machine was unable to keep enough pages in memory to be able to keep its four processors running at 100%. The NetBSD box more or less put everything it needed into memory once and barely touched the disk again, so its processor hit 100% and stayed pinned there. If the Windows machine had been able to this, it would have easily outperformed the NetBSD machine, but since it could not, most of its four expensive processors were sitting idle most of the time. I can easily conduct a demonstration like this for anyone who likes in the New York area, where I'm based. I've done it multiple times before, and I can happily do it again. To make it fair, I'll let whomever wants tune the Windows machine any way they like. This specific issue comes down to this: Windows does not have a true unified VM subsystem architecture in which the buffer cache is properly integrated into the virtual memory subsystem. It also does not have a flexible, self tuning mechanism for managing the tradeoff between using memory for executable pages, data pages and file cache pages. The result of this is that it does lots of I/O when it doesn't need to, drastically hurting performance. You can argue all you like about how much nicer Windows is. Perhaps it is. That is subjective. The OBJECTIVE benchmarks, however, show that it is trivial to drive a Windows box out of page cache and make it stall. > If one would be really interested in Windows vs. Linux performance, > it is a good idea to use PC GAMESS as the benchmark No, actually, that isn't a particularly good benchmark. Proper benchmarking requires that you use a variety of tasks that exercise a variety of operating conditions. A single program can never be a good benchmark. In a computational chemistry context, a variety of loads are needed to properly assess the differences between the two systems. > It is not the problem at all to create an input file which will put > Linux memory & I/O subsystems down. That actually is false. If you have conditions in which the default settings of the Linux algorithms are working incorrectly, then by a simple tuning process you can alter the tradeoff between executable, data and file pages and optimize your performance. It may be true that if you don't know what you are doing, you can't make a Linux box perform properly, but at least there is stuff you can do if you know what you're doing. Even if you know what you are doing, there is little you can do to tune Windows properly. > The same is true for Windows to some degree. I personally do > not aware of any (and doubt if it is possible at all) good > implementation of memory management in any OS for the case of > simultaneous heavy I/O and memory load. Then you aren't paying close attention to the work that people have done in the last 20 years in operating system design. > Nevertheless, Windows has much more advanced memory and I/O API than > Linux Oh, really? Can you explain, then, why it is that Unix systems easily beat Windows on high performance network I/O, why there is no ability to tune the Windows page cache, why Windows doesn't have a unified VM model, why Windows is so much worse at context switches, etc? If Windows is so fast, one might ask why it is that the record for fastest TCP transmission rates is not held by Windows hardware, and why researchers on networking performance rarely do their work under Windows. Sure, Cutler stole a lot of VMS code to build NT. If you assume VMS nearly 20 years ago was the best model of how to do I/O on earth, I'm sure you're a Windows fan. The benchmarks don't agree. Anyway, the proof is in the pudding. In the real world, benchmarks don't favor Windows. Claim otherwise if you like -- I'm happy to show people if they're in my vicinity. Perry From owner-chemistry@ccl.net Fri Oct 28 14:28:01 2005 From: "Nuno A. G. Bandeira nuno.bandeira!^!ist.utl.pt" To: CCL Subject: CCL: Filters Message-Id: <-29818-051028113209-29019-ukmDfRAygrSsv20jSTA2JA,;,server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 28 Oct 2005 16:32:03 +0100 Mime-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira!A!ist.utl.pt] Cory Pye cpye{}crux.smu.ca wrote: > Please don't trivialize a crippling disability such as autism on the list (or > anywhere, for that matter.) I think you know the meaning of metaphor. > It is comments such as this that could convince the Gordon group to decide > to switch from available source to binary distribution (or none at all). > > Why are people complaining about getting something for free? If you don't like > aspects about the distribution the package of group X, write your own > open-source package, or improve upon someone elses. Any volunteers to write an > efficient integral package? OK. Uh-oh, it works on Suns and IBMs, but not on > SGIs or HP. It works with RedHat, but not with Mandrake or Debian. I can't find > optimized BLAS libraries. How come it core dumps every time I try to do an > f-type integral? Version 4.2.3 of compiler X on machine Y has a bug. Are you > willing to provide support for this free program in perpetuity? In biology, > most mutations are non-viable. Well the "program it yourself like I had to do also, stupid!" attitude does not go down well with some people I'm afraid. I think the collaborative spirit that many so blatantly preach in the open source movement suddenly seems hypocritical with views like that. In any way I meant no offense to the Gordon group. Apologies if my words were too harsh. I just meant to underline my pessimism about the future of the code. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student ^_^ IST,Lisbon -- -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.362 / Virus Database: 267.12.5/150 - Release Date: 27-10-2005 From owner-chemistry@ccl.net Fri Oct 28 15:02:00 2005 From: "Igor Filippov Contr igorf*helix.nih.gov" To: CCL Subject: CCL: Filters Message-Id: <-29819-051028122156-21023-JlOA4M4wJZnnt4F7XuOKdg=-=server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 28 Oct 2005 12:21:50 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf[-]helix.nih.gov] > Do the > developers of open source volunteer to give any at all ? If they do it's > solely out of their generosity which I commend... They do, and quite often it's way better than what you get from the people who're in it only for the money. This very mail list is a proof to that. > at least with paid > software you can always ask for something in return. You can ask. Whether you get a meaningful reply is another matter altogether. Whether you get a reply which does not require you to purchase yet another license is something even more rare yet. Igor From owner-chemistry@ccl.net Fri Oct 28 15:37:00 2005 From: "Francisco Rodriguez-Ropero francisco.rodriguez-ropero^^^upc.edu" To: CCL Subject: CCL: Problems with GAMESS Message-Id: <-29820-051028114606-8863-fE7tG0lkSCTbly3TLJjdoA() server.ccl.net> X-Original-From: "Francisco Rodriguez-Ropero" Sent to CCL by: "Francisco Rodriguez-Ropero" [francisco.rodriguez-ropero(~)upc.edu] I need to run a parallel job with GAMESS program (MP2 calculation) in a given number of nodes. I need to estimate the values of both MEMORY and MEMDDI to write them in SYSTEM but I dont know how to do it for more than 1 node. Could anybody help me with it? Thanks in advanced. From owner-chemistry@ccl.net Fri Oct 28 16:12:01 2005 From: "Aaron Deskins ndeskins%x%purdue.edu" To: CCL Subject: CCL:G: Filters Message-Id: <-29821-051028115331-9429-tDtoY66VnUOFbklu+PJdng_+_server.ccl.net> X-Original-From: Aaron Deskins Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 28 Oct 2005 10:53:26 -0500 MIME-Version: 1.0 Sent to CCL by: Aaron Deskins [ndeskins#,#purdue.edu] M. L. Dodson bdodson*|*scms.utmb.EDU wrote: >>This topic seems mostly to come down to a discussion of the merits of >>free-market capitalism versus socialism. Who does work better: >>profit-minded citizens or government paid workers? Of course it depends, >>but I think if Gaussian was never commercialized, then we all very well >>could have been stuck using Gaussian 86. >> >> >> > >Why don't we all cool down a little bit and avoid words like >immoral and socialism. The discussion might gain some civility in >the process. > > >I'll only say that if you think open source is socialism, you have >missed the point about open source. Think of peer review as a > > > ...... >I'm just trying to inject a little reality about open source into >this discussion which has been filled with a lot of misinformation >and almost complete lack of appreciation of the real user benefits >of the open source s/w movement (far beyond the cost of the s/w). > > My apologies for use of the "S" word. There was no attempt to imply that open source software is to be equated with socialism; open source is a great idea for many software packages. The discussion (as I saw it) however was not about the merits of open source software, but whether commercialization of computational chemistry software that may have involved government funding at some point is illegal, immoral, etc. I am in the camp that believes that some commercialization of academic research is not necessarily a bad thing and in many cases beneficial to the most amount of people. Aaron Deskins Purdue University From owner-chemistry@ccl.net Fri Oct 28 16:47:00 2005 From: "Nuno A.G. Bandeira nuno.bandeira!^!ist.utl.pt" To: CCL Subject: CCL: Windows v. Linux Message-Id: <-29822-051028154945-10257-njT3KtWNZeCtjSWrXTHl4Q{=}server.ccl.net> X-Original-From: "Nuno A.G. Bandeira" Sent to CCL by: "Nuno A.G. Bandeira" [nuno.bandeira_+_ist.utl.pt] Perry E. Metzger perry%%piermont.com wrote: > No, actually, that isn't a particularly good benchmark. Proper > benchmarking requires that you use a variety of tasks that exercise a > variety of operating conditions. A single program can never be a > good benchmark. In a computational chemistry context, a variety of > loads are needed to properly assess the differences between the two > systems. Isn't this implying that some programs can perform better in one OS environment rather than the other ? A peer-reviewed publication for what you are saying would be a nice thing too. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student -*- IST,Lisbon -- From owner-chemistry@ccl.net Fri Oct 28 17:40:01 2005 From: "Prashanth Athri athriprashanth,yahoo.com" To: CCL Subject: CCL: COMFA q² Message-Id: <-29823-051028162047-5981-pHDsReG8D4F4ySgQbhdLdQ!^!server.ccl.net> X-Original-From: Prashanth Athri Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 28 Oct 2005 12:53:58 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Prashanth Athri [athriprashanth!=!yahoo.com] Hi, On the Partial Least Squares Analysis dialog box: 1. Click on the SAMPLS button and set the number of components to a value higher than what you would expect the dimensionality of your data to be. Then click on "Run PLS". 2. A dialog informing you about SAMPLS pops up- click OK. 3. On the terminal window, you will eventually see crossvalidated r-squared [alias q-squared]. The number of components you will choose for the final run will be the one for which the q-squared is the highest. Hope this helps. -Prashanth --- "Antoine FORTUNE Antoine.Fortune^_^ujf-grenoble.fr" wrote: > > Sent to CCL by: Antoine FORTUNE [Antoine.Fortune- > -ujf-grenoble.fr] > Hi all, > I'm working with sybyl MSS to do comfa study. As I > run a PLS, sybyl > gives r² value in the report. Where / how can i get > the q² value ? It's > not in the report log. > Thank's > > Antoine > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the +*+ > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST+*+ccl.net > or use> > Before posting check wait time for next message at: > http://www.ccl.net> > If your mail bounces from CCL with 5.7.1 error, > check:> > > > __________________________________ Start your day with Yahoo! - Make it your home page! http://www.yahoo.com/r/hs From owner-chemistry@ccl.net Fri Oct 28 18:15:01 2005 From: "M. L. Dodson bdodson**scms.utmb.edu" To: CCL Subject: CCL:G: Filters Message-Id: <-29824-051028173828-17265-2Z2evf40bvRHciCvbCNepA(-)server.ccl.net> X-Original-From: "M. L. Dodson" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 28 Oct 2005 16:38:16 -0500 MIME-Version: 1.0 Sent to CCL by: "M. L. Dodson" [bdodson__scms.utmb.edu] On Friday 28 October 2005 10:53, Aaron Deskins ndeskins%x%purdue.edu wrote: > > Sent to CCL by: Aaron Deskins [ndeskins#,#purdue.edu] > M. L. Dodson bdodson*|*scms.utmb.EDU wrote: > > >>This topic seems mostly to come down to a discussion of the merits of > >>free-market capitalism versus socialism. Who does work better: > >>profit-minded citizens or government paid workers? Of course it depends, > >>but I think if Gaussian was never commercialized, then we all very well > >>could have been stuck using Gaussian 86. > >> > >> > >> > > > >Why don't we all cool down a little bit and avoid words like > >immoral and socialism. The discussion might gain some civility in > >the process. > > > > > >I'll only say that if you think open source is socialism, you have > >missed the point about open source. Think of peer review as a > > > > > > > ...... > > >I'm just trying to inject a little reality about open source into > >this discussion which has been filled with a lot of misinformation > >and almost complete lack of appreciation of the real user benefits > >of the open source s/w movement (far beyond the cost of the s/w). > > > > > My apologies for use of the "S" word. There was no attempt to imply that > open source software is to be equated with socialism; open source is a > great idea for many software packages. The discussion (as I saw it) > however was not about the merits of open source software, but whether > commercialization of computational chemistry software that may have > involved government funding at some point is illegal, immoral, etc. I > am in the camp that believes that some commercialization of academic > research is not necessarily a bad thing and in many cases beneficial to > the most amount of people. > > Aaron Deskins > Purdue University > I don't think apologies are needed. I was just trying to shutdown a potential flamefest. I think I made my position reasonably clear (although using mutt over a ssh link is not as good as my gui email system). I think commercialization is probably necessary, so I also do not think it is necessarily a bad thing either. My email was only incidentally aimed at you, my main beef was the subrosa assertions that open source = bad, commercial = good (because of support issues, etc). As a contributor to the FreeBSD project, I can tell you that in my experience open source COMMODITY software is of much higher quality than closed. Of course, IMO. My additional point was that there are not enough expert programmers among the CC s/w users for that assertion to be brought over into this field in some sort of general way. Bud Dodson -- M. L. Dodson Personal: mldodson-at-houston-dot-rr-dot-com Work: bdodson-at-scms-dot-utmb-dot-edu Work: four_zero_nine-772-2178 FAX: four_zero_nine-772-1790 From owner-chemistry@ccl.net Fri Oct 28 18:50:00 2005 From: "Prashanth Athri athriprashanth|yahoo.com" To: CCL Subject: CCL:G: Filters; really Gaussian, Inc. and funding Message-Id: <-29825-051028163557-19890-FQSa2B4ZdnbBa1+ThqYlDQ|a|server.ccl.net> X-Original-From: Prashanth Athri Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 28 Oct 2005 12:35:53 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Prashanth Athri [athriprashanth.:.yahoo.com] **************My opinion**************************** How is all this so important? *I* believe exploration/ discovery or whatever else of science is the primary motive. Credit assigment, $$, are peripheral by products, necessary and important but thats really not the end goal...right? I say take it easy, Gaussian or for that matter so many other s/w applications (Sybyl-Tripos, and probably all) use acedemic research. Big deal guys just use what YOU want to use and let others use what they want to use and lets all just keep our eyes on the ball. __________________________________ Yahoo! FareChase: Search multiple travel sites in one click. http://farechase.yahoo.com From owner-chemistry@ccl.net Fri Oct 28 19:24:01 2005 From: "Andy Holder holdera^umkc.edu" To: CCL Subject: CCL: COMP: Careers Symposium at the Atlanta Message-Id: <-29826-051028180103-31322-6wKlPeCehOBljORFADvong---server.ccl.net> X-Original-From: "Andy Holder" Sent to CCL by: "Andy Holder" [holdera(-)umkc.edu] Hello All, Here is an opportunity for someone from the ranks of computational chemistry-land to help out that next generation take your job when you are old. (That's a joke!) Phil Barnette has requested a speaker for the Careers Symposium at the Atlanta National Meeting in the area of computational chemistry. Please reply directly to him at: Philip Barnett ACS-CINF Careers Chair Science/Engineering Library, Room J-29 City College of New York (CUNY) Convent Avenue and 138th Street New York, NY 10031 Voice: 212-650-8243 FAX: 212-650-7626 http://mail.sci.ccny.cuny.edu/~phibarn E-Mail: phibarn _ sci.ccny.cuny.edu pbarnett _ ccny.cuny.edu From owner-chemistry@ccl.net Fri Oct 28 19:59:01 2005 From: "Andrew Good Andrew.Good||bms.com" To: CCL Subject: CCL: CCG award - deadine extension to Fri Nov 4th. Message-Id: <-29827-051028180109-31385-cIJXanajna8XTEPZRTYTjQ[-]server.ccl.net> X-Original-From: Andrew Good Content-transfer-encoding: 7BIT Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Fri, 28 Oct 2005 16:59:03 -0400 MIME-version: 1.0 Sent to CCL by: Andrew Good [Andrew.Good**bms.com] 5 $1150 CCG Excellence Student Travel Award Stipends Available for the Spring 2006 Atlanta ACS* The CCG Excellence Awards have been created to stimulate graduate student participation in COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are American graduate students in good standing who present work within the COMP program, either in oral or poster format. Winners receive $1,150, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session For details of application requirments visit the CCG Award url at http://membership.acs.org/C/COMP/CCG/ccg.html From owner-chemistry@ccl.net Fri Oct 28 20:35:01 2005 From: "Alex. A. Granovsky gran++classic.chem.msu.su" To: CCL Subject: CCL: help needed Message-Id: <-29828-051028184742-18535-Gzu8soePLJnvShIiu/AS6g*o*server.ccl.net> X-Original-From: "Alex. A. Granovsky" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 29 Oct 2005 02:47:54 +0400 MIME-Version: 1.0 Sent to CCL by: "Alex. A. Granovsky" [gran]~[classic.chem.msu.su] Hi Perry, > About a year ago I conducted a demonstration in which a single > processor machine running NetBSD (not Linux, but the principle would > apply to Linux as well) successfully rebuilt a large software system > many times faster than a four processor Windows server. The Windows > machine had more memory, and each individual processor was faster than > the NetBSD machine's one processor. The reason? The Windows machine > was unable to keep enough pages in memory to be able to keep its four > processors running at 100%. The NetBSD box more or less put everything > it needed into memory once and barely touched the disk again, so its > processor hit 100% and stayed pinned there. If the Windows machine had > been able to this, it would have easily outperformed the NetBSD > machine, but since it could not, most of its four expensive processors > were sitting idle most of the time. This is unfair comparison. In fact, we both know this, but it is much more unfair to give such an incorrect examples with respect to people who do not. First of all, describing any benchmark, you must avoid any qualitative statements. You must fully specify hardware configurations, OS versions and relevant settings, any nonstandard drivers used, etc..., etc... You must also provide enough details on the particular benchmark used. In your case, you should specify compilers used on NetBSD and Windows system, indicate compiler options of significant impact on the compiler performance, provide sufficient details on the software system which was rebuilt, explain the way how additional processors were used (if used at all) during compilation on Windows system, etc... Second, we all know that there are many situations when running I/O or memory-limited tests on SMP system in parallel results in worse performance than using only single thread or single process. Next, if you used Cygwin to compile on Windows system, you must agree that there are many situations when it causes significant overhead, e.g., process initialization, forking, etc... This overhead is not usually of significance for typical computational chemistry programs, but certainly is for compilers. Also, nothing was made to change Cygwin version of gcc to optimize it for Windows OS. On the other hand, if you used different compiler, it is incorrectly to compare compilation times at all, as nobody knows how much additional time was spent generating/optimizing the code. Finally, you must admit that this is not the type of benchmark of interest/importance for typical computational chemist. In CC, building the project is not the most time-consuming step, using the program for number-crunching is. This is why I suggested to use PC GAMESS as the benchmark. It seems you are not very familiar with typical Quantum Chemistry codes, otherwise, you would easily recognize that any non-trivial high quality QC program can be used to impose (or model) almost any desired scenario of loads on OS and computer hardware. > I've personally conducted extensive benchmarking on this specific > topic, and I've read enormous amounts of Microsoft documentation. So did I too. > The page cache policy in Windows is utterly primitive. As a result of > this, file pages are evicted from cache long before they need to > be. > You can, of course, set the registry key to tell the box to behave as > a file server, at which point, executable pages are evicted from cache > long before they need to be. There is no in between. There are no > pluggable policies. You can't even tune the policy that is there. This is only partially true. Windows API provides standard ways for any particular application to optimize its memory and I/O usage. Most of these API calls do not require any nonstandard rights to be used, some (potentially having system-wide effects) do require them but these rights can always be granted on per-user or per-group basis. What is important is to use this API and to use it properly. This is simply quite a different philosophy - to allow application itself to optimize his execution strategy. Well, it is evident that only application itself knows the best way of how it should be executed, and how OS resources should be managed for the best performance. One can spent lots of years improving OS kernels - and it is surely worth while - but there always be applications for which the default OS algorithms will perform badly. > This specific issue comes down to this: Windows does not have a true > unified VM subsystem architecture in which the buffer cache is > properly integrated into the virtual memory subsystem. It also does > not have a flexible, self tuning mechanism for managing the tradeoff > between using memory for executable pages, data pages and file cache > pages. The result of this is that it does lots of I/O when it doesn't > need to, drastically hurting performance. I do not agree with this. Certainly, Windows' caching algorithms differs from that of Linux or BSD derivatives. Sure there are situations when the performance of Unix-like strategies is better (or worse). Nevertheless, this is almost irrelevant to real computational chemistry, where we typically have one of two scenario - either huge data files (to be handled either sequentially or randomly), or very compact data files. The intermediate case is exotic. Aggressive data caching can (and often does) seriously reduce performance if working with really large datasets. Just an example - did you ever try to perform any non-trivial work with the file twice as large as the system memory under Linux (or any other OS)? If not, just try and you'll most likely find that the default system strategy is not perfect. > You can argue all you like about how much nicer Windows is. Perhaps it > is. That is subjective. The OBJECTIVE benchmarks, however, show that > it is trivial to drive a Windows box out of page cache and make it > stall. This is true for some aggressive badly-written applications. On the other hand, it is very trivial to put any 2.4.x Linux kernel to the same state as well. Do you know that there are many cases when swapoff -a is the only way to perform the calculations not damaging your HDDs and spending finite time waiting for results? It is less trivial to do this with 2.6.x, but it is still possible. Once again, you simply should reckon that Windows is quite a different world and has somewhat different rules how to write efficient programs. The point is that it is typically a very good idea to allow programmer to control how his program will be executed, his files cached, etc... This is what Windows allows. > > If one would be really interested in Windows vs. Linux performance, > > it is a good idea to use PC GAMESS as the benchmark > > No, actually, that isn't a particularly good benchmark. Proper > benchmarking requires that you use a variety of tasks that exercise a > variety of operating conditions. A single program can never be a > good benchmark. In a computational chemistry context, a variety of > loads are needed to properly assess the differences between the two > systems. See above. > > > It is not the problem at all to create an input file which will put > > Linux memory & I/O subsystems down. > > That actually is false. If you have conditions in which the default > settings of the Linux algorithms are working incorrectly, then by a > simple tuning process you can alter the tradeoff between executable, > data and file pages and optimize your performance. What you forgot to say here is that a) you must be a root, and b) the changes for any particular program will have system-wide effect. Do not you believe that allowing some API here (as Windows does for years) to be used by any non-privileged user would be of great help here? > It may be true that if you don't know what you are doing, you can't > make a Linux box perform properly, but at least there is stuff you can > do if you know what you're doing. Even if you know what you are doing, > there is little you can do to tune Windows properly. Well, there is no much need to tune Windows as there is much I can do to write high-performance Windows programs. Nevertheless, there are some things I can do system-wide with Windows, although I agree that you have more options under Linux. > > The same is true for Windows to some degree. I personally do > > not aware of any (and doubt if it is possible at all) good > > implementation of memory management in any OS for the case of > > simultaneous heavy I/O and memory load. > > Then you aren't paying close attention to the work that people have > done in the last 20 years in operating system design. Then where are these Operating Systems causing any QC code to fly? > > Nevertheless, Windows has much more advanced memory and I/O API than > > Linux > Oh, really? Can you explain, then, why it is that Unix systems easily > beat Windows on high performance network I/O, > If Windows is so fast, one might ask why it is that the record for > fastest TCP transmission rates is not held by Windows hardware, and > why researchers on networking performance rarely do their work under > Windows. You can look at http://www.tpc.org/tpcc/results/tpcc_perf_results.asp > why there is no ability to tune the Windows page cache as there is no need to do this system-wide :-) >why Windows is so much worse at context switches, etc? Oh, really? Would you like to discuss the threading API/implementation/performance under Linux vs. Windows? > Sure, Cutler stole a lot of VMS code to build NT. If you assume VMS > nearly 20 years ago was the best model of how to do I/O on earth, I'm > sure you're a Windows fan. The benchmarks don't agree. VMS was really good OS in many senses - I used to work under VMS... > This is also why gcc, which is far larger than ANY computational > chemistry package ever built and far more complicated, doesn't exist. It seems you are simply not familiar with QC codes. Good QC package is _at least_ as complex as gcc, both in the sense of nontrivial algorithms, size of sources, know hows used, etc... > Unfortunately, a lot of this stuff is hard. The problem is that issues > like virtual memory subsystem architecture aren't any more easily > understood by non-specialist than an ab initio computational chemistry > system is easily understood by the non-specialist. Really > understanding the issues requires that you have an operating systems > class under your belt, or the equivalent. Is the statement above ethical? Should we assume you are the only guy around knowing both CC and OS kernels programming? Should your opinion be the only law for us? Best regards, Alex Granovsky From owner-chemistry@ccl.net Fri Oct 28 21:09:00 2005 From: "Jim Kress ccl_nospam-.-kressworks.com" To: CCL Subject: CCL:G: Summary Message-Id: <-29829-051028205236-28654-ngohC6k91GvMtBQWpl00pQ(_)server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Fri, 28 Oct 2005 20:52:28 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam^^^kressworks.com] The point that was being made is that Gaussian (or other private entities) should not be allowed to profit (i.e. make money) by using property (i.e. taxes) taken by force from other parties (i.e. taxpayers). Remember, taxpayers are being made to do without in order to provide the money for these grants being used in Academia or Industry. I understand that this is a threatening concept to many in Academia or Industry that choose to depend on government money. However, it's a moral issue with which the scientific community needs to deal. In addition, just because this behavior has been accepted for many years does not vindicate its continuing imposition on people who have better uses for their own money. The money belongs to the taxpayer, not members of Academia or Industry. Academia or Industry have no right to compel their neighbors, friends, families, and citizens who live far away to fund their salaries or other activities. In addition, with regard to Mr. Frisch's remarks, the itemized listing I provided was presented in response to his claim that Gaussian 'fully funded' all development activity for the Gaussian programs. The list of examples (including the Italian ones) clearly demonstrate that Mr. Frisch's assertion was false and, if he would read further down the list he would see that the US Government (i.e., taxpayers) did provide funding for at least the listed additions to Gaussian 03 and probably many more. Anyway, I've made my point and said all I believe I need to say on this topic. However, it is a problem that needs to be dealt with within the overall scientific community since, as has been recently noted in the press, the dependence of our community on funding from political organizations (i.e. the government) is making us susceptible to preferential funding of work based on specific political agendas. This is a situation we cannot tolerate if we hope to retain an image of impartiality (which is already eroding - e.g. the refusal of C&E News, Science, Nature, and other journals to publish peer reviewed articles (or summaries thereof) that refute claims of catastrophic anthropogenic climate change, etc.) Regards, Jim Kress "The reformation was preceded by the discovery of America, as if the Almighty graciously meant to open a sanctuary to the persecuted in future years, when home should afford neither friendship nor safety." -- Thomas Paine (Common Sense, 1776)