From chemistry-request@server.ccl.net Mon Jan 29 04:28:37 2001 Received: from power.curtin.edu.au ([134.7.118.91]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0T9SZw10894 for ; Mon, 29 Jan 2001 04:28:36 -0500 Received: from [134.7.118.25] ([134.7.118.25]) by power.curtin.edu.au (8.10.2/8.10.2/SuSE Linux 8.10.0-0.3) with ESMTP id f0T9QK102051 for ; Mon, 29 Jan 2001 17:26:20 +0800 Mime-Version: 1.0 Message-Id: Date: Mon, 29 Jan 2001 17:26:17 +0800 To: chemistry@ccl.net From: Andrew Rohl Subject: java applet for teaching intermolecular forces Content-Type: text/plain; charset="us-ascii" ; format="flowed" Is anyone aware of a java applet which allows a student to interact with two particles under short range forces? I was thinking of the situation where two particles interact with each other and by moving the mouse, the student can add energy to the system and see how the paricles behave. Andrew -- ------------------------------------------------------------------------------ Andrew Rohl Email: A.Rohl@curtin.edu.au Senior Lecturer in Computational Chemistry School of Applied Chemistry Phone: +61 8 9266 7317 (Office) Curtin University of Technology +61 8 9266 3780 (Lab) PO Box U 1987 Perth, 6845 FAX: +61 8 9266 2300 WESTERN AUSTRALIA WWW: http://chemistry.curtin.edu.au/staff/alr ------------------------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Jan 29 09:19:41 2001 Received: from bbhm.na.pg.com (bbhm.na.pg.com [192.44.184.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0TEJfw13850 for ; Mon, 29 Jan 2001 09:19:41 -0500 X-ExtMailInfo: pandora.na.pg.com [155.118.176.101] Received: from pandora.na.pg.com (pandora.na.pg.com [155.118.176.101]) by bbhm.na.pg.com (8.8.8/8.10.1/D1r2) with ESMTP id f0TEB0B02433; Mon, 29 Jan 2001 09:11:01 -0500 (EST) Received: from morpheus.na.pg.com (morpheus.na.pg.com [143.5.24.124]) by pandora.na.pg.com (SGI-8.9.3/8.9.3) with ESMTP id JAA15486 for <@pandora.na.pg.com:chemistry@ccl.net>; Mon, 29 Jan 2001 09:14:25 -0500 (EST) Received: from pg.com by morpheus.na.pg.com via ESMTP (980427.SGI.8.8.8/930416.SGI.AUTO) for id JAA11612; Mon, 29 Jan 2001 09:17:06 -0500 (EST) Sender: laidig@pg.com Message-ID: <3A757B62.8B09BFE0@pg.com> Date: Mon, 29 Jan 2001 09:17:06 -0500 From: Bill Laidig X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: PBS vs. PBS Pro Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit All, While checking into the PBS (Portable Batch System) references I was recently sent, I discovered that there is a free version PBS and a commercial version PBS Pro. Does anyone know if there are any real advantages to the PBS Pro product? Thanks, Bill -- ************************************************************************ * "Like jewels in a crown, the precious stones glittered in the * * queen's round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 laidig.wd@pg.com * * Cincinnati, OH 45253-8707 * ************************************************************************ From chemistry-request@server.ccl.net Mon Jan 29 09:16:52 2001 Received: from bbhm.na.pg.com (bbhm.na.pg.com [192.44.184.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0TEGpw13823 for ; Mon, 29 Jan 2001 09:16:51 -0500 X-ExtMailInfo: pandora.na.pg.com [155.118.176.101] Received: from pandora.na.pg.com (pandora.na.pg.com [155.118.176.101]) by bbhm.na.pg.com (8.8.8/8.10.1/D1r2) with ESMTP id f0TE8BB00371; Mon, 29 Jan 2001 09:08:11 -0500 (EST) Received: from morpheus.na.pg.com (morpheus.na.pg.com [143.5.24.124]) by pandora.na.pg.com (SGI-8.9.3/8.9.3) with ESMTP id JAA92947; Mon, 29 Jan 2001 09:11:35 -0500 (EST) Received: from pg.com by morpheus.na.pg.com via ESMTP (980427.SGI.8.8.8/930416.SGI.AUTO) id JAA11875; Mon, 29 Jan 2001 09:14:16 -0500 (EST) Sender: laidig@pg.com Message-ID: <3A757AB8.149D12F@pg.com> Date: Mon, 29 Jan 2001 09:14:16 -0500 From: Bill Laidig X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net CC: stein.pandora@pg.com Subject: Summary: Batch Queuing Systems Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Yesterday, I posted a question about batch queueing systems: > All, > > We have been looking into and testing queuing software for a while and > found nothing very satisfactory. All have drawbacks such as price, lack > of adequate cross-platform support or features. I am interested in what > queuing software CCL users USE on their systems and how they like this > software. I will summarize responses to the list. By the way, we are > looking for a queuing system that: > > a) Works across both SGI Irix and Linux clusters (NQS works well on > linux, but we are having problems getting it work well on SGI's if I > remember the problems our systems manager mentioned). > b) Is not extremely expensive (LSF, for example, is quite nice, but > would be rather expensive to implement across our whole system) > c) Is full featured in terms of queue control (priority, job limits, > processor limits, time limits, ability to suspend and track jobs...) > d) Can treat a group of machines as a single queue (for our cluster) > Since then I have received a lot of useful responses. Thanks to everyone for their quick, detailed responses. This is what I learned: ********************************************************************************* PBS, the portable batch system (http://www.openpbs.org/ or .com or .net - all work), was recommended by most of the respondents. It seems to by flexible, free and work across many platforms. It also has a scheduling module that can easily be extended/replaced and several mentioned other, more flexible schedulers that could be substituted. This is the system we will be trying out first. DQS was also recommended by several list members. If we have problems with PBS we will try DQS out. LSF also received a couple of positive responses and we may reconsider this if the other choices do not work and we can get the budget. I also recieved one response favoring generic NQS and one pointing to a soon to be released free system from Sun, the Grid engine. Thanks again to everyone and the detailed responses are listed below. ********************************************************************************* Did you look at PBS? http://pbs.mrj.com/ http://hpc.sissa.it/pbs/ http://www.chpc.utah.edu/policies/pbs.html Jan K. Labanowski ********************************************************************************* Did you look at PBS (Portable Batch System)? http://www.openpbs.org/ Bill Ross ********************************************************************************* Try DQS. However, LSF has become sort of a standard in the commercial world. -P. ********************************************************************************* PBS is the answer. It is free/cheap, should work on more than one machine, is very flexible in terms of queue control, can treat a group of machines as a single queue. The downside of the flexibility is that one has to work on the scheduler (which is just FIFO by default), but K.Visser@rc.rug.nl has done a fine job of writing his own version (the Fair Share model), which works very well. He probably can also point you to some more documentation. Most sincerely, Marcel Swart. ********************************************************************************* www.openpbs.net Groeten, David. ********************************************************************************* Hi Bill, PBS is the free queing system of choice. We run it on SGIs and LINUX clusters. NQS is crap, LSF is ok but costs mucho. PBS, is choice and you get the source. -Matt ********************************************************************************* Bill, The following maybe of interest as SUN says that they will be releasing free versions for both IRIX and Linux, although they are not ready yet :- http://www.sun.com/software/gridware/ Bye Jeff. ********************************************************************************* On Sun, 28 Jan 2001, Bill Laidig wrote: > We have been looking into and testing queuing software for a while and > found nothing very satisfactory. All have drawbacks such as price, lack > of adequate cross-platform support or features. I am interested in what > queuing software CCL users USE on their systems and how they like this > software. We use Open PBS (www.openpbs.com) here and it works well for our needs (distribution of single-processor and MPI jobs across a network of Linux-based workstations and compute nodes). It is available under a fairly liberal licence, and is free for both commercial and non-commercial use provided you are registered with its owners. The "P" in PBS stands for "portable" and as such it works on a variety of platforms (although we've only tried it on Intel and Alpha Linux boxes so far here). It is fairly feature-rich by default, but since the source code is available, you can augment its features (or "bugs" if you like ;) with your own. If that's still not enough, you can get the "full" version, PBS Pro, but that costs money... > a) Works across both SGI Irix and Linux clusters (NQS works well on > linux, but we are having problems getting it work well on SGI's if I > remember the problems our systems manager mentioned). If you've used NQS in the past, PBS should be relatively easy to pick up, as it's based (at least in part) on NQS. There are even utilities for converting NQS job scripts to PBS format. > c) Is full featured in terms of queue control (priority, job limits, > processor limits, time limits, ability to suspend and track jobs...) This is all possible by default, I believe, with the exception of processor limits (you can restrict jobs by nodes - machines - but not by processors). Patches are available for this functionality, however (for instance, from our own site, http://bellatrix.pcl.ox.ac.uk/~ben/pbs/). PBS is flexible in that this kind of thing is generally determined by a dedicated scheduler program, which you can either provide from scratch (in one of three different languages) or can derive from the example "FIFO" scheduler. > d) Can treat a group of machines as a single queue (for our cluster) This is the default behaviour. More complex behaviour can be obtained by tinkering with the scheduler. Most "unusual" requirements have already been addressed by other researchers, however, and you can usually find patches that do something similar to what you want on the mailing list, which is generally quite responsive. Ben ********************************************************************************* Bill, we are using Generic NQS with GAMESS-US on SGI Indigo2 (Irix 6.5.9), which is working fine. Wolfgang ********************************************************************************* hi bill, we use DQS on SGI, linux and DEC. There are about 20 machines in our system, and most of the time it runs stable - well to be honest it can't remember a breakdown caused by that part of the whole installation ;). We used NQS before, but when we renewed allmost all our hardware in 1998 it wasn't as easy to learn and showed not enough hardware flexibility to me. I also remember some comiling problems expecially on SGI. DQS worked fine after only a few hours of reading, compiling and installation - and i have only been a beginner on administration of UNIX-Systems at that time ;). We still use same version today - after about 2 years running time, I just did not see any need of upgrading. let me know if you need some more information or config filed of our system - good luck, c. ps. oops, did I mention: we use DQS3.2.7 from http://www.scri.fsu.edu/~pasko/dqs.html ********************************************************************************* Hi Bill Try the Distributed Queueing System (DQS). We use it on SGI Irix and Linux Workstations without problems and it is free software. Look at www.scri.fsu.edu/~pasko/dqs.html Greetings from Darmstadt, Germany Bernd ********************************************************************************* Bill, You might remember me as a grad student who worked for Dan Edwards. We met at Sanibel a few years ago. I am now at a pharmaceutical company and have been managing a queue for a couple of years that is now made up of SGI's, Linux and a new IBM SP. I think you will find that LSF is the product to meet all your needs and it is not as expensive as first appears when you consider the increase in efficiency of use of the systems. I had Eric Deumens here a few weeks back installing our SP and he has been trying DQS, NQE, etc. but was very impressed (I think) with LSF. I'd be happy to talk with you more about this if you want some more info. Bob -- ************************************************************************ * "Like jewels in a crown, the precious stones glittered in the * * queen's round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 laidig.wd@pg.com * * Cincinnati, OH 45253-8707 * ************************************************************************ From chemistry-request@server.ccl.net Mon Jan 29 11:50:05 2001 Received: from coltrane.dichi.unina.it (coltrane.dichi.unina.it [143.225.167.154]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0TGo5w14639 for ; Mon, 29 Jan 2001 11:50:05 -0500 Received: from localhost (cavallo@localhost) by coltrane.dichi.unina.it (8.9.3/8.9.3) with ESMTP id RAA21842 for ; Mon, 29 Jan 2001 17:48:02 GMT X-Authentication-Warning: coltrane.dichi.unina.it: cavallo owned process doing -bs Date: Mon, 29 Jan 2001 17:48:01 +0000 (GMT) From: Luigi Cavallo X-Sender: cavallo@coltrane.dichi.unina.it To: chemistry@ccl.net Subject: Teaching water Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi there, I friend of mine, who teaches chemistry at high school, asked me about web-sites concerned with water simulations. The purpose is educational, clearly, thus clarity and "fancy" things would be appreciated. Any suggestions ? TIA Luigi ------------------------------------------------------------------------------ | Dr. Luigi Cavallo Department of Chemistry | | Ph: ++39-81-674448 University of Naples | | Fax: ++39-81-674442 Complesso Monte S.Angelo | | Email cavallo@chemistry.unina.it Via Cintia, I-80126 Napoli, ITALY | ------------------------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Jan 29 13:08:16 2001 Received: from tbaytel.net (tbaytel3.tbaytel.net [206.47.150.229]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0TI8Fw15215 for ; Mon, 29 Jan 2001 13:08:15 -0500 Received: from rjohns (vickesh01-69.tbaytel.net [206.186.170.69]) by tbaytel.net (8.11.2/8.11.2) with SMTP id f0TI8C552798 for ; Mon, 29 Jan 2001 13:08:13 -0500 Message-ID: <004001c08a1e$9d9ae540$45aabace@norlink.net> From: "Richard Johns" To: "ccl_posting" Subject: DLPOLY & SGI Origin 2000 Date: Mon, 29 Jan 2001 13:09:24 -0500 I have been having some problems compiling DLPOLY.X. We are running irix 6.5.5m on an SGI Origin 2000 with R12000 processors. I would appreciate hearing from anyone who has been successful in this regard. Thanks RIchard Johns Research Associate, Chemistry Department Lakehead University 955 Oliver Road, Thunder Bay, ON. P7B 5E1 rjohns@tbaytel.net From chemistry-request@server.ccl.net Mon Jan 29 13:49:24 2001 Received: from hotmail.com (f104.law10.hotmail.com [64.4.15.104]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0TInOw15511 for ; Mon, 29 Jan 2001 13:49:24 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 29 Jan 2001 10:47:24 -0800 Received: from 128.97.139.222 by lw10fd.law10.hotmail.msn.com with HTTP; Mon, 29 Jan 2001 18:47:24 GMT X-Originating-IP: [128.97.139.222] From: "hu eric" To: chemistry@ccl.net Subject: Annihilation Date: Mon, 29 Jan 2001 10:47:24 -0800 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312; format=flowed Message-ID: X-OriginalArrivalTime: 29 Jan 2001 18:47:24.0287 (UTC) FILETIME=[EB51D0F0:01C08A23] Hi, In DFT singlet or triplet diradical g98 output, there's a S**2 after annihilation. What is annihilation for? Does that mean I should use the new S**2 value as the reference? Thanks! Eric _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From chemistry-request@server.ccl.net Mon Jan 29 13:57:31 2001 Received: from server5.safepages.com ([216.127.146.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0TIvVw15567 for ; Mon, 29 Jan 2001 13:57:31 -0500 Received: from kressj (5131-196-251.008.popsite.net [209.69.196.251]) by server5.safepages.com (Postfix) with SMTP id 65C767103C; Mon, 29 Jan 2001 18:55:54 +0000 (GMT) Message-ID: <001601c08a25$1d31cd40$0100a8c0@webrise.net> From: "Jim Kress" To: "Luigi Cavallo" , References: Subject: Re: CCL:Teaching water Date: Mon, 29 Jan 2001 13:55:55 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Look here: http://www.sbu.ac.uk/water/index.html Jim ----- Original Message ----- From: "Luigi Cavallo" To: Sent: Monday, January 29, 2001 12:48 PM Subject: CCL:Teaching water > > Hi there, > > I friend of mine, who teaches chemistry at high school, asked me about > web-sites concerned with water simulations. The purpose is educational, > clearly, thus clarity and "fancy" things would be appreciated. > > Any suggestions ? > > TIA > > Luigi > > -------------------------------------------------------------------------- ---- > | Dr. Luigi Cavallo Department of Chemistry | > | Ph: ++39-81-674448 University of Naples | > | Fax: ++39-81-674442 Complesso Monte S.Angelo | > | Email cavallo@chemistry.unina.it Via Cintia, I-80126 Napoli, ITALY | > -------------------------------------------------------------------------- ---- > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Mon Jan 29 18:14:09 2001 Received: from mserve1.acs.ucalgary.ca (postfix@mserve1.acs.ucalgary.ca [136.159.34.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0TNE9w16792 for ; Mon, 29 Jan 2001 18:14:09 -0500 Received: from ucalgary.ca (acs1.acs.ucalgary.ca [136.159.34.221]) by mserve1.acs.ucalgary.ca (Postfix) with ESMTP id BB411136D; Mon, 29 Jan 2001 16:13:25 -0700 (MST) Received: from localhost (patchkov@localhost) by ucalgary.ca (AIX4.3/8.9.3/8.8.8) with ESMTP id QAA42922; Mon, 29 Jan 2001 16:13:25 -0700 Date: Mon, 29 Jan 2001 16:13:20 -0700 (MST) From: Serguei Patchkovskii X-Sender: patchkov@acs1.acs.ucalgary.ca To: hu eric Cc: chemistry@ccl.net Subject: Re: CCL:Annihilation In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 29 Jan 2001, hu eric wrote: > In DFT singlet or triplet diradical g98 output, there's a S**2 after > annihilation. What is annihilation for? Does that mean I should use the new > S**2 value as the reference? Thanks! You should keep in mind that the "" expectation value, printed by Gaussian at the end of DFT calculations is not particularly meaningful in any case. This value is computed for the non-interacting Kohn-Sham reference wavefunction, and has no relation to the of the real, interacting system. The Gaussians' "" may be useful as a qualitative indication of the degree of spin-contamination, but that's about it. /Serge.P --- Home page: http://www.cobalt.chem.ucalgary.ca/ps/ From chemistry-request@server.ccl.net Mon Jan 29 20:47:38 2001 Received: from bnpi.com (bnpi.com [208.188.148.225] (may be forged)) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0U1lcw17271 for ; Mon, 29 Jan 2001 20:47:38 -0500 Received: from BNPISRV2 by bnpi.com via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 30 Jan 2001 01:54:37 UT Received: from bnpi.com (b27 [198.213.32.6]) by bnpisrv2.bnpi.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id D79ZA2X5; Mon, 29 Jan 2001 19:42:46 -0600 Sender: jeff@ccl.net Message-ID: <3A761CB0.FEE865E3@bnpi.com> Date: Mon, 29 Jan 2001 19:45:20 -0600 From: Jeff Saxe X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: curves5.3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Earlier this month I asked a question about the Curves5.3 program. I asked if anyone knew what the variable 'mv' in the eigen subroutine should be since it was never initialized. I finally figured it out on my own by finding the nearly identical eigen subroutine elsewhere. In the Curves5.3 program only 3 values are passed into the eigen subroutine, however in other programs a 4th value is passed in, and this value is 'mv'. Apparently in the Curves5.3 program the only value ever used for 'mv' was 0, and I guess someone removed it from the call to eigen, but never actually removed 'mv' itself from the routine. As long as the program is compiled such that all uninitialized variables are 0 there will be no problem, though I would recommend that you fix this if you are using the program. If anyone is really interested in having this program even cleaner, in the subroutine 'locate' there is actually a 'go to 64' statement which jumps right into the middle of an 'if-then-else' block. It seems to actually be okay, but I rewrote it to avoid this. Jeff Saxe -- Jeffrey D. Saxe BioNumerik Pharmaceuticals, Inc. Suite 400, 8122 Datapoint Dr., San Antonio, TX 78229 email jeff.saxe@bnpi.com phone 210-614-1701 x225 fax 210-614-2892 From chemistry-request@server.ccl.net Mon Jan 29 23:03:26 2001 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0U43Qw17962 for ; Mon, 29 Jan 2001 23:03:26 -0500 Received: from localhost (renxiao@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id UAA16763 for ; Mon, 29 Jan 2001 20:03:25 -0800 (PST) X-Authentication-Warning: neon.chem.ucla.edu: renxiao owned process doing -bs Date: Mon, 29 Jan 2001 20:03:25 -0800 (PST) From: Renxiao Wang To: Comp Chem List Subject: An article worth reading Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I highly recommend you to read the article appearing on the latest issue of Chemical and Engineering News: 2001, Jan 29, p37-38, which is entitled as "Drowning in a sea of refereed publications". The author challenged the out-of-control scientific publication realm and made some good wishes. I think I agree with most of his points. Yes we are definitely flooded with too many junk papers. Here I would like to give you an example. I read a paper before, in which the author cited about 100 references. 60 or 70 of them are the previous work of his own and here is how he cited them (something like that): "we have also applied this method to other systems [20-80], ...". Ooops. So what do you say? Dr. Renxiao Wang Georgetown University, Medical Center