From owner-chemistry@ccl.net Sat Oct 29 02:26:00 2005 From: "Mark Zottola mzottola::gmail.com" To: CCL Subject: CCL: help needed Message-Id: <-29830-051028234258-32544-++6jXE/YOA/nYVClny3sqA;;server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary="----=_Part_10117_1187237.1130553696243" Date: Fri, 28 Oct 2005 22:41:36 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola**gmail.com] ------=_Part_10117_1187237.1130553696243 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I am a person who codes because he needs to, not because it is my profession. So I do not want (and cannot intelligently) comment on the aspects of coding on Windows as opposed to Linux being discussed in this thread. However, I would like to point out that the real test of any OS is not how a code runs, but rather the price to performance ratio for that cod= e using a certain OS. While it is still not clear to me that a Windows box will perform as well as a Linux box, I will assume such to be the case. Thus one has to calculat= e the cost of a multi-processor license. For a given cluster size n, there ar= e n copies of Windows to be bought at x dollars a piece. Even with a price discount, the value of n*x increases rather rapidly. Next there is the issu= e of compilers. I do not know of a gcc equivalent for Windows, so there is th= e cost of the compilers with their generally ridiculous pricing schemes. While I suppose there is a cost for downloading and burning Debian, SuSe o= r Fedora to CD, that cost is negligible compared to even a single seat of Windows. There is finally movement to make a real FORTRAN compiler system for Linux to compliment gcc. So the compiler systems are essentially free. In that regard, the price performance ratio of Windows (1 divided by a large number) compared to that for Linux (1 divided by a very small number) is greatly in favor of Linux. While this analysis might be oversimplified (to a point), the vast number of clusters running Linux as compared to Windows validates the conclusion that Windows is an inferior OS for running comp. chem codes. I frankly do not ever see Windows being anything more than an OS for the desktop regardless any improvements they may make in memory. I/O, or elsewhere. Mark Zottola ------=_Part_10117_1187237.1130553696243 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
 
I am a person who codes because he needs to, not because it is my prof= ession.  So I do not want (and cannot intelligently) comment on t= he aspects of coding on Windows as opposed to Linux being discussed in this= thread.  However, I would like to point out that the real test of any= OS is not how a code runs, but rather the price to performance ratio for t= hat code using a certain OS. =20
 
While it is still not clear to me that a Windows box will perform as w= ell as a Linux box, I will assume such to be the case.  Thus one has t= o calculate the cost of a multi-processor license.  For a given cluste= r size n, there are n copies of Windows to be bought at x dollars a piece.&= nbsp; Even with a price discount, the value of n*x increases rather rapidly= .  Next there is the issue of compilers.  I do not know of a gcc = equivalent for Windows, so there is the cost of the compilers with their ge= nerally ridiculous pricing schemes. =20
 
While I suppose there is a cost for downloading and burning Debian, Su= Se or Fedora to CD, that cost is negligible compared to even a single seat = of Windows.  There is finally movement to make a real FORTRAN compiler= system for Linux to compliment gcc.  So the compiler systems are esse= ntially free. =20
 
In that regard, the price performance ratio of Windows (1 divided by a= large number) compared to that for Linux (1 divided by a very small number= ) is greatly in favor of Linux.  While this analysis might be oversimp= lified (to a point), the vast number of clusters running Linux as compared = to Windows validates the conclusion that Windows is an inferior OS for runn= ing comp. chem codes.
 
I frankly do not ever see Windows being anything more than an OS for t= he desktop regardless any improvements they may make in memory. I/O, or els= ewhere. 
 

Mark Zottola
------=_Part_10117_1187237.1130553696243-- From owner-chemistry@ccl.net Sat Oct 29 03:01:01 2005 From: "David Gallagher dgallagher[#]us.fujitsu.com" To: CCL Subject: CCL: ZINDO parameters for Rubidium Message-Id: <-29831-051028232708-31392-7s2glx0U4MVwqZfrWI7/Aw[a]server.ccl.net> X-Original-From: "David Gallagher" Sent to CCL by: "David Gallagher" [dgallagher/./us.fujitsu.com] Can anyone point me towards any published spectroscopic ZINDO parameters for Rubidium? Thank you in anticipation, David Gallagher Fujitsu From owner-chemistry@ccl.net Sat Oct 29 03:43:00 2005 From: "Dr. N. SUKUMAR nagams ~~ rpi.edu" To: CCL Subject: CCL: Summary Message-Id: <-29832-051029030903-5637-JxfPet096jIPMe/coLv40A=-=server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Sat, 29 Oct 2005 3:08:58 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams[]rpi.edu] On Fri, 28 Oct 2005 20:52:28 EDT "Jim Kress ccl_nospam-.-kressworks.com" wrote: ... 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... Most of us believe that academia serves a public purpose and thus deserves public funding. (Some of us even hold to the scandalous belief that academia serves a higher public purpose than politics, the clergy or the military). Anyway there is no compulsion; most scientists are unarmed and you are free to lobby your legislators. Indeed, successive administrations have repeatedly cut non-defense research funding in real dollars, partly because the voting public has not been pursuaded as to the public purpose of science. Such trends will very likely accelerate under the force of arguments as yours. Brave new worlds! And some wonder why we are no longer competitive or even able to teach biology in schools. Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From owner-chemistry@ccl.net Sat Oct 29 11:26:00 2005 From: "Perry E. Metzger perry|a|piermont.com" To: CCL Subject: CCL: help needed Message-Id: <-29833-051029112024-3984-wmDWvC0Qmu1nqHtRNFh0Jw(~)server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Sat, 29 Oct 2005 11:20:16 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry-,-piermont.com] "Alex. A. Granovsky gran++classic.chem.msu.su" writes: >> 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, You perhaps do, but I don't. The comparison seems perfectly fair. The architecture of Windows makes it handle file caching in an extremely inefficient manner. This simply demonstrated it. > but it is much more unfair to give such an incorrect examples > with respect to people who do not. There is nothing even remotely incorrect about the example. > 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... It was a four processor machine running Windows 2003, with 4G of memory -- I can't remember the specific Xeon model being used or the speed, but each of the four were substantially faster than the 1.6Ghz processor in my laptop which none the less beat the heck out of the Windows box even though it had four times the memory and four processors. The Windows box also had much faster disks, and had drivers written by the manufacturers of the various pieces of hardware, unlike the machine that beat it up, which had drivers written by hobbyists in their spare time without original manufacturer specs. > You must also provide enough details on the particular benchmark > used. Both the Windows machine and the NetBSD box were compiling about 4000 files of Java code, using the identical Sun supplied Java SDK, both compilations driven by Ant, using identical files, identical versions of Ant, etc. The performance of the compilers themselves was not at issue, though, because the reason the NetBSD box beat the Windows box wasn't that the NetBSD box had "faster compilers" or some such, but because the Windows box was running an OS with totally a worthless VM subsystem incapable of doing proper file caching. If the Windows machine had been running its processors flat out, it would have beaten the hell out of the NetBSD machine, but since it could not provide data to the processors fast enough for them to remain even at 10% of capacity, they were unable to finish the task as quickly. > In your case, you should specify compilers used on NetBSD and > Windows system, indicate compiler options of significant impact on > the compiler performance, None of that had the least impact. Although the systems were compiling absolutely identical codebases (both compilations were driven from identical versions of Ant as well), CPU performance was NOT a factor, code quality of the compilers was NOT a factor. The only factor was that the Windows VM subsystem sucks dingo kidneys, and thus no matter how much money one spent on the processors, the speed of the Windows system was completely bound on disk read performance, whereas the NetBSD box quickly cached all the data, so it was at 100% CPU at all times. > 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. As it turns out, the Windows machine had essentially identical performance when running with only one processor. That's because it was I/O bound because of the exceptionally bad design of the Windows VM subsystem. > Next, if you used Cygwin to compile on Windows system, No, I didn't. > Finally, you must admit that this is not the type of benchmark of > interest/importance for typical computational chemist. I disagree. Many CC problems involve far more I/O than you would think IF THE OPERATING SYSTEM IS BADLY DESIGNED. Certainly not *all* programs behave this way, but many, in fact, are badly impacted by it. There are, as I said, also many other flaws in Windows. For example, network performance is badly impacted by the architecture of the Windows NDIS and TCP/IP layers. If you are running a tightly coupled compute cluster, that will hurt you. There are many other flaws, too. These are just a couple of examples. On top of that, there is the fact that (and I realize this is subjective) Windows is simply unmanageable. There is too much state stored in too many places. If you want to run 100 or 500 or 1000 Windows machines in a compute cluster you can devote your life to keeping the machines running and operating smoothly and not get anywhere, whereas with a bit of proper scripting you can make a cluster of Linux or other Unix systems sing while spending your real effort on your research and not on systems management. I've seen this hurt very hard in the real world. > In CC, building the project is not the most time-consuming step, So what? If you have to do lots of unneeded I/O with a data set that will not conveniently fit in buffer cache, you'll have the same problem. The compilation example was just an exemplar. The truth is, you hit exactly the same sorts of problems in large cluster situations all the time. The compiler example is something I'm quoting purely because it was dramatic, but you can get similar issues with all sorts of other kinds of tasks, including computational chemistry. > It seems you are not very familiar with typical Quantum Chemistry > codes, If you wish to believe that. By the way, the word is PROGRAMS, not CODES. "Code" can be used in certain idioms, but it is a mass noun or a verb. It is never correct English to pluralize a mass noun. I realize many computational chemists do that, but it is not correct grammar. Do not do it. >> I've personally conducted extensive benchmarking on this specific >> topic, and I've read enormous amounts of Microsoft documentation. > > So did I too. Well, then people will have to decide if they think you know what you're doing or if they think I do. Perry From owner-chemistry@ccl.net Sat Oct 29 12:01:01 2005 From: "Perry E. Metzger perry*|*piermont.com" To: CCL Subject: CCL: help needed Message-Id: <-29834-051029112309-4163-NoVL6820ztFLVAa9994j6w{:}server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Sat, 29 Oct 2005 11:23:06 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry^piermont.com] "Mark Zottola mzottola::gmail.com" writes: > There is finally movement to make a real FORTRAN compiler system > for Linux to compliment gcc. As an aside, "gcc" is not a C compiler (or at least is not any more). It stands for "Gnu Compiler Collection" (yes, that's not what it originally stood for) and includes compilers for many languages besides C, including FORTRAN. The standard FORTRAN compiler on most Linux boxes is, in fact, part of gcc. (It also works reasonably well.) Perry From owner-chemistry@ccl.net Sat Oct 29 12:36:00 2005 From: "Jim Kress ccl_nospam*_*kressworks.com" To: CCL Subject: CCL: Summary Message-Id: <-29835-051029122306-7364-2oXbOm0F2aQkF6fXxgessg=-=server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Sat, 29 Oct 2005 12:23:00 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam++kressworks.com] > Most of us believe that academia serves a public purpose and > thus deserves public funding. (Some of us even hold to the Stalin believed his blockade and subsequent deaths of the Kulaks served a public purpose - those arrogant peasants didn't deserve to keep the grain they worked to grow because Stalin wanted to redistribute it to those he thought were more deserving of it (i.e. for a 'public purpose'). Calling upon 'a public purpose' has been historically shown to be a pretext for the imposition of the desires of a few upon the rest of an unwilling population. > purpose than politics, the clergy or the military). Anyway > there is no compulsion; most scientists are unarmed and you Try not paying your taxes and see how Government compulsion is applied. Taxpayer funded grants originate from the taxes people are compelled to pay. At the end of the day you cannot say to the government, "I think I'll just skip paying taxes this year". If you do you'll find yourself at the business end of a gun held by a government official. That, my friend, is the definition of compulsion - "Your money or your life/ freedom" Jim > -----Original Message----- > From: Dr. N. SUKUMAR nagams ~~ rpi.edu > [mailto:owner-chemistry(~)ccl.net] > Sent: Saturday, October 29, 2005 3:09 AM > To: Kress, Jim > Subject: CCL: Summary > > > Sent to CCL by: "Dr. N. SUKUMAR" [nagams[]rpi.edu] On Fri, 28 > Oct 2005 20:52:28 EDT "Jim Kress ccl_nospam-.-kressworks.com" wrote: > > .. 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... > > Most of us believe that academia serves a public purpose and > thus deserves public funding. (Some of us even hold to the > scandalous belief that academia serves a higher public > purpose than politics, the clergy or the military). Anyway > there is no compulsion; most scientists are unarmed and you > are free to lobby your legislators. Indeed, successive > administrations have repeatedly cut non-defense research > funding in real dollars, partly because the voting public has > not been pursuaded as to the public purpose of science. Such > trends will very likely accelerate under the force of > arguments as yours. Brave new worlds! And some wonder why we > are no longer competitive or even able to teach biology in schools. > > > Dr. N. Sukumar > Center for Biotechnology and Interdisciplinary Studies > Rensselaer Polytechnic Institute > > > > -= 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 Sat Oct 29 13:32:01 2005 From: "Nuno A. G. Bandeira nuno.bandeira(-)ist.utl.pt" To: CCL Subject: CCL: help needed Message-Id: <-29836-051029133102-28156-B8wCCyWKriKNzpWHVDtERQ!=!server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Sat, 29 Oct 2005 18:30:48 +0100 Mime-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira/a\ist.utl.pt] Mark Zottola mzottola::gmail.com wrote: > > I am a person who codes because he needs to, not because it is my > profession. So I do not want (and cannot intelligently) comment on the > aspects of coding on Windows as opposed to Linux being discussed in this > thread. However, I would like to point out that the real test of any OS > is not how a code runs, but rather the price to performance ratio for > that code using a certain OS. There's another thing you don't equate and which is often forgotten and it is user-machine interface. Do you expect to seduce students into computational chemistry through a unix command shell ?? I got into this business through the use of wonderful graphic interfaces which showed me the marvels of molecular modelling. I was hooked on it ever since. I'm still waiting for someone to develop a completely integrated system of GUI/QM modules (the only program that comes close to that is Spartan). I grew up with Windows and it is something I frequently use for routine calculations such as geometry optimizations and the like. Many young students are probably more familiar with this kind of intuitive interface and would rather use it than say use something as abstract and boring as a unix prompt and torture them to the extreme with the wise old ways of the VI editor ! Your experience is probably different, you probably had to learn the hard way and in a sense I was privileged. This is probably a generation gap (hope you don't think I'm calling you old). And as we're talking of user-machine interface another OS which is becoming increasingly popular (and I believe it's very popular in the US) is the Mac. There are a growing number of chemistry software being produced/ported for the MacOS environment. It's not for free so have you wondered why ? Another question I mean to ask you is this: you mention that you are an amateur programmer (like indeed most comp. chem. developers are). Have you ever considered porting your applications to Windows ? Has that even crossed your mind ? > While it is still not clear to me that a Windows box will perform as > well as a Linux box, I will assume such to be the case. Thus one has to > calculate the cost of a multi-processor license. For a given cluster > size n, there are n copies of Windows to be bought at x dollars a > piece. Even with a price discount, the value of n*x increases rather > rapidly. Microsoft offers major discounts for academia. Many institutions are short of money but they never cease to upgrade Windows so it can't be all that expensive. > Next there is the issue of compilers. I do not know of a gcc > equivalent for Windows, so there is the cost of the compilers with their > generally ridiculous pricing schemes. There are plenty of free compilers for Windows (there's mingw/gcc, LCC and OpenWatcom for instance...). The open source movement is not bound to any single OS. > I frankly do not ever see Windows being anything more than an OS for the > desktop regardless any improvements they may make in memory. I/O, or > elsewhere. There are Windows clusters in this world. You may think they're a rarity but they're out there. -- 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: 267.12.6/151 - Release Date: 28-10-2005 From owner-chemistry@ccl.net Sat Oct 29 15:12:00 2005 From: "Philip Barnett phibarn%x%sci.ccny.cuny.edu" To: CCL Subject: CCL: Speaker Needed on Careers in Computational Chemistry Message-Id: <-29837-051029131915-20572-Y6ZhkU4Aps5erekMRqS3PQ .. server.ccl.net> X-Original-From: "Philip Barnett" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Sat, 29 Oct 2005 12:19:11 -0400 MIME-Version: 1.0 Sent to CCL by: "Philip Barnett" [phibarn : sci.ccny.cuny.edu] On Fri, 28 Oct 2005 19:28:58 -0400 "Andy Holder holdera^umkc.edu" wrote: 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 Barnett has requested a speaker for the Careers Symposium at the Atlanta National Meeting in the area of computational chemistry. Please reply directly to him.... ------------------------------------ As a follow up to Andy Holder's posting of yesterday, here are the details: Previously posted on CHMINF-L |-|LISTSERV.INDIANA.EDU Folks, We all enjoy our careers in the information side of chemistry, and now you have an opportunity to share your enthusiasm with others. At the American Chemical Society National Meeting, next spring in Atlanta (Sunday March 26 to Thursday March 30, 2006) the Division of Chemical Information will be presenting a symposium on Careers in Chemical Information, and we need speakers. Randy Ward of Brigham Young University and I are organizing this session. The aim of this symposium is to introduce students to the various kinds of both chemical and science information careers, and to provide guidance to chemists who may be considering a career change. We aim to give a complete view of the chemical and related science information professions, covering all the different types of information careers in which chemists or chemistry majors can apply their training, experience, talent, and skills. The format of the symposium will be 25 or 30 minute talks (this includes time for questions and answers). The exact date and time of this half-day symposium has not yet been set. We are still looking for a speaker on computational chemistry. Are you interested in being this speaker, or do you know a colleague who may be interested. If so, please let me know, and I will provide you with all the necessary details, hints on preparing a talk, and answer any questions you may have. A web page featuring previous talks and other resources on careers in chemical information is available to give you some ideas, and guidance to help you prepare a talk: http://mail.sci.ccny.cuny.edu/~phibarn/careers.html While there is plenty of time to prepare your talk, the deadline for submission of abstracts is November 23. So if you are interested please let me know as soon as possible. Unfortunately, the American Chemical Society cannot reimburse travel expenses for speakers. Speakers who are not American Chemical Society members can usually have their meeting registration fee waived. Please respond to me privately, not to the list. Thanks, Phil ----------------------- (Dr.) Philip Barnett Careers Chair, ACS Division of Chemical Information 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 E-Mail: phibarn|-|sci.ccny.cuny.edu http://mail.sci.ccny.cuny.edu/~phibarn From owner-chemistry@ccl.net Sat Oct 29 15:47:00 2005 From: "Bill Ross ross{}cgl.ucsf.edu" To: CCL Subject: CCL: help needed Message-Id: <-29838-051029143050-11825-1TX1ljP7QbCSnUe4f9MR0w^^server.ccl.net> X-Original-From: Bill Ross Date: Sat, 29 Oct 2005 10:53:42 -0700 (PDT) Sent to CCL by: Bill Ross [ross,cgl.ucsf.edu] > By the way, the word is PROGRAMS, not CODES. Depends on culture, I believe. Viva la difference, in this case :-) Bill Ross From owner-chemistry@ccl.net Sat Oct 29 16:22:00 2005 From: "Greg Landrum Landrum=RationalDiscovery.com" To: CCL Subject: CCL: help needed Message-Id: <-29839-051029143119-12065-1wCKvmSnU7tlag1c+f4wEQ_-_server.ccl.net> X-Original-From: Greg Landrum Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 29 Oct 2005 10:31:15 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Landrum [Landrum~!~RationalDiscovery.com] Perry E. Metzger perry|a|piermont.com wrote: > > Both the Windows machine and the NetBSD box were compiling about 4000 > files of Java code, using the identical Sun supplied Java SDK, both > compilations driven by Ant, using identical files, identical versions > of Ant, etc. > Given that this "conversation" is being carried out on the computational chemistry mailing list, I'd suggest that the benchmark proposed by Alex Granovsky is far more appropriate. This community does, after all, spend much more time waiting for computational chemistry software to run than it does waiting for java code to compile. The stresses placed on the system by a computational chemistry program are far more relevant than those placed by a compiler. > By the way, the word is PROGRAMS, not CODES. "Code" can be used in > certain idioms, but it is a mass noun or a verb. It is never correct > English to pluralize a mass noun. I realize many computational > chemists do that, but it is not correct grammar. Do not do it. Oh, please. Now we're stooping to grammar flames? Use of the word "code" in the plural to refer to multiple pieces of software is widespread in this community. -greg From owner-chemistry@ccl.net Sat Oct 29 16:57:00 2005 From: "Rick Venable rvenable|*|pollux.cber.nih.gov" To: CCL Subject: CCL: New Element Discovered Message-Id: <-29840-051029160917-26108-UP1pVvE8MvjmwdYTJ91/VQ-$-server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sat, 29 Oct 2005 16:04:40 -0400 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable|pollux.cber.nih.gov] Does anyone recall that most modern electronics are derived from the government funded space program, and that the Internet was started as a government research project? We interrupt the debates on M$ vs. Linux and commercial products derived from government funding to introduce a bit of levity-- NEW ELEMENT DISCOVERED: "Governmentium" A major research institution has recently announced the discovery of the heaviest element yet known to science. The new element has been named "Governmentium." Governmentium has 1 neutron, 12 deputy neutrons, 75 assistant neutrons, and 224 deputy assistant neutrons, giving it an atomic mass of 312. These 312 particles are held together by forces called morons, which are surrounded by vast quantities of lepton-like particles called peons. A minute amount of Governmentium causes a reaction to take 4 days to complete, when it would normally take less than a second. It does not decay, but instead undergoes a reorganization in which a portion of the assistant neutrons and deputy neutrons exchange places. In fact, governmentium's mass will actually increase over time since each reorganization will cause more morons to become neutrons, forming isodopes. Governmentium is formed whenever morons reach a certain quantity in concentration. This hypothetical quantity is referred to as "Critical Morass." When catalyzed with money, Governmentium becomes Administratium, an element that radiates just as much energy as Governmentium since it has half as many peons but twice as many morons. ------------------------------------- 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 AT nih*gov ALT email: rvenable AT speakeasy*org ------------------------------------- www.redcross.org From owner-chemistry@ccl.net Sat Oct 29 17:31:00 2005 From: "David F. Green dfgreen,ams.sunysb.edu" To: CCL Subject: CCL: Recent disturbing behavior on the CCL. Message-Id: <-29841-051029161354-2049-G37svMopWrxRz6tPpuWe3Q__server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 29 Oct 2005 13:57:53 -0400 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen]=[ams.sunysb.edu] To all members of the list: I've been a subscriber to the CCL for close to ten years, and have never considered dropping it until now. However, I have noticed that in the past month or so, several threads have degraded into very unprofessional diatribes involving personal insults to both posters and uninvolved individuals or groups. I find this trend very disturbing, and the behavior is completely inappropriate in what is meant to be a scientific forum. I think that the majority of the community would agree would me in requesting that people make every effort to remain respectful of the other members of the list, and to keep posts on topic. Given the amount of effort that Jan has put into creating and maintaining this important resource for the community (and we all know > from recent posts how much work this has involved), we ought to do our part to help it continue to be successful. If this type of behavior continues, however, I'm afraid the list is going to have no future, as many subscribers will be driven away. Thank you, David ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== From owner-chemistry@ccl.net Sat Oct 29 18:07:00 2005 From: "Mark Zottola mzottola]-[gmail.com" To: CCL Subject: CCL: help needed Message-Id: <-29842-051029172246-22805-Iy2XdyyYuzVn9VL/n29VOg:-:server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary="----=_Part_14733_11566328.1130620961110" Date: Sat, 29 Oct 2005 17:22:41 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola|gmail.com] ------=_Part_14733_11566328.1130620961110 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline On 10/29/05, Nuno A. G. Bandeira nuno.bandeira(-)ist.utl.pt < owner-chemistry**ccl.net> wrote: > > > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira/a\ist.utl.pt] > Mark Zottola mzottola:: gmail.com wrote: > > > There's another thing you don't equate and which is often forgotten and > it is user-machine interface. Do you expect to seduce students into > computational chemistry through a unix command shell ?? While I believe this issue has religous elements to it, I will endeavour t= o steer clear of those danger areas as I try to answer you. Knowledge seduces scientists, not a GUI. How does one get that knowledge? Well a GUI is certainly one way and a command shell is another. Both have their roles and uses. In terms of the Windows interface being "superior" to a Linux desktop GUI, well that seems to border on religion. I can only say that well-designed GUI is a well designed GUI. Both Unix and Windows do have well-designed desktop GUIs. So I see no obvious benefit here either. In fact, I have a problem with students' over-reliance on a GUI. A command shell is simply superior to a GUI when it comes to modifying your environment. You do have the full functionality with a command shell that i= s simply impossible to fully implement with a GUI. Yes, I do value a GUI when there are tasks that require are repetitive (hence can be automated). But a decent script writer (Korne or C-shell), can also accomplish those things. Knowing how to get "under the hood" is an important facet of moving from being a technician to being an independent researcher. But this last statement is rather religious, so I am not going to push this argument any further. I grew up with Windows and it is something I frequently use for routine > calculations such as geometry optimizations and the like. Many young > students are probably more familiar with this kind of intuitive > interface and would rather use it than say use something as abstract and > boring as a unix prompt and torture them to the extreme with the wise > old ways of the VI editor ! Actually vi is probably one of the most useful (and powerful) text editing tools outside of the old VMS editors. We can both certainly agree that MS Word and its counterparts are certainly better for document creation (dissertations, publications, etc.) than any UNIX tool. But I am uncertain as to how learning to use a tool like vi could be considered torture. Notepad is similar in functionality to jot, so again, I cannot find much to bolster your assertion here. Your experience is probably different, you probably had to learn the > hard way and in a sense I was privileged. This is probably a generation > gap (hope you don't think I'm calling you old). > And as we're talking of user-machine interface another OS which is > becoming increasingly popular (and I believe it's very popular in the > US) is the Mac. There are a growing number of chemistry software being > produced/ported for the MacOS environment. It's not for free so have you > wondered why ? The current Mac OS is based on UNIX, IIRC. It is the ability to move back and forth seamlessly between the MAC and UNIX environments that makes peopl= e enjoy it. Also, Macs tend to have a loyal and devoted following. Talk to an older Mac user and outside of the day the current American president stole Florida, the blackest day in history was when Windows 3.1 came out with the first incarnation of their desktop graphical interface that co-opted the advantage Mac had at that time. Another question I mean to ask you is this: you mention that you are an > amateur programmer (like indeed most comp. chem. developers are). Have > you ever considered porting your applications to Windows ? Has that even > crossed your mind ? Actually - no. I do not mind producing source code and allowing people "port" it to non-Unix environments. > While it is still not clear to me that a Windows box will perform as > > well as a Linux box, I will assume such to be the case. Thus one has to > > calculate the cost of a multi-processor license. For a given cluster > > size n, there are n copies of Windows to be bought at x dollars a > > piece. Even with a price discount, the value of n*x increases rather > > rapidly. > > Microsoft offers major discounts for academia. Many institutions are > short of money but they never cease to upgrade Windows so it can't be > all that expensive. Since I do not have hard numbers, all I can say is that Microsoft is not known to be generous, although Red Hat is certainly not above squeezing the market either. Since MS owns the desktop productivity market, large institutions like colleges and universities will make substantive long term deals with MS for cheaper prices on software and upgrades. More over, while I believe that there are MS clusters out there (I think NCSA has one funded by MS and I am certain there are others), the marketplace speaks for itself. And I believe the staggering majority use Linux/Unix as their cluster OS. So price must certainly factor into this. N= o one in academics or industry makes large capital expenditures without considering their ROI. If MS had a cluster software that was as competitive as an open source OS in terms of both cost and maintenance, I am certain people would buy it (assuming the actual software performance was essentially identical). The fact that MS clusters are not ubiquitous in academia seems to cast a significant shadow upon the point you are making. > > There are plenty of free compilers for Windows (there's mingw/gcc, LCC > and OpenWatcom for instance...). The open source movement is not bound > to any single OS. Thanks for the info. I do use MS on my desktop and having the ability to run some calculations on my windows box would be useful. Best Regards, MZ ------=_Part_14733_11566328.1130620961110 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

On 10/29/05, Nuno A. G. Bandeira nuno.bandeira(-)ist.utl.pt < owner-chemistry**ccl.net> wrote:=20

Sent to CCL by: "Nuno A= . G. Bandeira" [nuno.bandeira/a\ist.utl.pt]
Mark Zottola mzottola::= =20 gmail.com wrote:


There's anoth= er thing you don't equate and which is often forgotten and
it is user-ma= chine interface. Do you expect to seduce students into
computational chemistry through a unix command shell ??
 
While I believe this issue has religous elements to it, I will endeavo= ur to steer clear of those danger areas as I try to answer you.  Knowl= edge seduces scientists, not a GUI.  How does one get that knowledge?&= nbsp; Well a GUI is certainly one way and a command shell is another. = Both have their roles and uses.  In terms of the Windows interface be= ing "superior" to a Linux desktop GUI, well that seems to border = on religion.  I can only say that well-designed GUI is a well designed= GUI.  Both Unix and Windows do have well-designed desktop GUIs.&= nbsp; So I see no obvious benefit here either.=20
 
In fact, I have a problem with students' over-reliance on a GUI. = A command shell is simply superior to a GUI when it comes to modifying you= r environment.  You do have the full functionality with a command shel= l that is simply impossible to fully implement with a GUI.  Yes, I do = value a GUI when there are tasks that require are repetitive (hence can be = automated).  But a decent script writer (Korne or C-shell), can also a= ccomplish those things.  Knowing how to get "under the hood"= is an important facet of moving from being a technician to being an indepe= ndent researcher.  But this last statement is rather religious, so I a= m not going to push this argument any further.=20

I grew up with Windows and it is= something I frequently use for routine
calculations such as geometry op= timizations and the like. Many young=20
students are probably more familiar with this kind of intuitive
inte= rface and would rather use it than say use something as abstract and
bor= ing as a unix prompt and torture them to the extreme with the wise
old w= ays of the VI editor !=20
 
Actually vi is probably one of the most useful (and powerful) text edi= ting tools outside of the old VMS editors.  We can both certainly agre= e that MS Word and its counterparts are certainly better for document creat= ion (dissertations, publications, etc.) than any UNIX tool.  But = I am uncertain as to how learning to use a tool like vi could be considered= torture.  Notepad is similar in functionality to jot, so again, I can= not find much to bolster your assertion here.=20
 

Your experience is probably diff= erent, you probably had to learn the
hard way and in a sense I was privi= leged. This is probably a generation=20
gap (hope you don't think I'm calling you old).
And as we're talking= of user-machine interface another OS which is
becoming increasingly pop= ular (and I believe it's very popular in the
US) is the Mac. There are a= growing number of chemistry software being=20
produced/ported for the MacOS environment. It's not for free so have yo= u
wondered why ?
 
The current Mac OS is based on UNIX, IIRC.  It is the abilit= y to move back and forth seamlessly between the MAC and UNIX environments t= hat makes people enjoy it.  Also, Macs tend to have a loyal and devote= d following.  Talk to an older Mac user and outside of the day the cur= rent American president stole Florida, the blackest day in history was when= Windows=20 3.1 came out with the first incarnation of their desktop graphical interfac= e that co-opted the advantage Mac had at that time. 

Another question I mean to ask y= ou is this: you mention that you are an
amateur programmer (like indeed = most comp. chem. developers are). Have=20
you ever considered porting your applications to Windows ? Has that eve= n
crossed your mind ?
 
Actually - no.  I do not mind producing source code and allowing = people "port" it to non-Unix environments.

> While it is still not clear= to me that a Windows box will perform as
> well as a Linux box, I wi= ll assume such to be the case.  Thus one has to=20
> calculate the cost of a multi-processor license.  For a = given cluster
> size n, there are n copies of Windows to be bought at= x dollars a
> piece.  Even with a price discount, the valu= e of n*x increases rather=20
> rapidly.

Microsoft offers major discounts for academia. Man= y institutions are
short of money but they never cease to upgrade Window= s so it can't be
all that expensive.
 
Since I do not have hard numbers, all I can say is that Microsoft is n= ot known to be generous, although Red Hat is certainly not above squeezing = the market either.  Since MS owns the desktop productivity market, lar= ge institutions like colleges and universities will make substantive long t= erm deals with MS for cheaper prices on software and upgrades.  = =20
 
More over, while I believe that there are MS clusters out there (I thi= nk NCSA has one funded by MS and I am certain there are others), the m= arketplace speaks for itself.  And I believe the staggering majority u= se Linux/Unix as their cluster OS.  So price must certainly factor int= o this.  No one in academics or industry makes large capital expenditu= res without considering their ROI.  If MS had a cluster software that = was as competitive as an open source OS in terms of both cost and maintenan= ce, I am certain people would buy it (assuming the actual software performa= nce was essentially identical).  The fact that MS clusters a= re not ubiquitous in academia seems to cast a significant shadow upon the p= oint you are making.  =20
 

There are plenty of free com= pilers for Windows (there's mingw/gcc, LCC
and OpenWatcom for instance..= .). The open source movement is not bound=20
to any single OS.
 
Thanks for the info.  I do use MS on my desktop and having the ab= ility to run some calculations on my windows box would be useful.
 
 
Best Regards,
 
 
MZ
 
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