From chemistry-request@ccl.net Tue May 25 04:38:56 2004 Received: from probity.mcc.ac.uk (probity.mcc.ac.uk [130.88.200.94]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4P9ct7a014620 for ; Tue, 25 May 2004 04:38:56 -0500 Received: from photon.ch.man.ac.uk ([130.88.80.70]) by probity.mcc.ac.uk with esmtp (Exim 4.20) id 1BSYRY-000HCy-Aw for chemistry[at]ccl.net; Tue, 25 May 2004 10:41:56 +0100 Subject: PED calculations From: Gopalan Rajaraman To: chemistry[at]ccl.net Content-Type: text/plain Organization: Message-Id: <1085478115.17153.4.camel[at]photon.ch.man.ac.uk> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.2 (1.2.2-5) Date: 25 May 2004 10:41:56 +0100 Content-Transfer-Encoding: 7bit X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *1BSYRY-000HCy-Aw*/eAPGZcdhRw* X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All I would like to do PED (Potential energy distribution) analysis for some systems. Is there any way of doing it using Gaussian or is there any free software available to do that ? Any publication related to this work will also be helpful. Thank you all in advance Regards Rajaraman. -- Gopalan Rajaraman Post graduate Student Department of Chemistry The University of Manchester U.K Email:gopalan.rajaraman[at]stud.man.ac.uk rajachemist[at]yahoo.com WWW: http://www.rajaraman.0catch.com From chemistry-request@ccl.net Tue May 25 12:38:05 2004 Received: from mx10.uop.edu (mx10.uop.edu [138.9.240.95]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4PHc37a027531 for ; Tue, 25 May 2004 12:38:04 -0500 Received: from unix1.cc.uop.edu (unix1.cc.uop.edu [138.9.1.1]) by mx10.uop.edu (8.12.10/8.12.10) with ESMTP id i4PHetNI051515; Tue, 25 May 2004 10:40:56 -0700 (PDT) (envelope-from mmccallum)at(pacific.edu) Received: from [10.10.160.19] (merckx.cop.uop.edu [10.10.160.19]) by unix1.cc.uop.edu (8.12.10/8.12.10) with ESMTP id i4PHetLo014091; Tue, 25 May 2004 10:40:55 -0700 (PDT) In-Reply-To: <20040520085433.GZ16732)at(leitl.org> References: <20040520085433.GZ16732)at(leitl.org> Mime-Version: 1.0 (Apple Message framework v613) Content-Type: text/plain; charset=US-ASCII; format=flowed Message-Id: Content-Transfer-Encoding: 7bit Cc: Eugen Leitl From: Mike McCallum Subject: Re: CCL:[Beowulf] Question regarding Mac G5 performance Date: Tue, 25 May 2004 10:40:55 -0700 To: chemistry)at(ccl.net X-Mailer: Apple Mail (2.613) X-PMX-Version: 4.6.0.99824, Antispam-Core: 4.6.0.99824, Antispam-Data: 2004.5.24.101456 X-PerlMx-Spam: Gauge=IIIIIIII, Probability=8%, Report='__IN_REP_TO 0, __REFERENCES 0, __MIME_VERSION 0, __MIME_VERSION_APPLEMAIL 0, __EVITE_CTYPE 0, __CT_TEXT_PLAIN 0, __CT 0, __MSGID_APPLEMAIL 0, __HAS_MSGID 0, __SANE_MSGID 0, __CTE 0, __TO_MALFORMED_2 0, __HAS_X_MAILER 0, __X_MAILER_APPLEMAIL 0, __C230066_P2 0, EMAIL_ATTRIBUTION 0, QUOTED_EMAIL_TEXT 0, SIGNATURE_SHORT_DENSE 0, __MIME_TEXT_ONLY 0, __USER_AGENT_APPLEMAIL 0, REFERENCES 0.000, IN_REP_TO 0' X-Spam-Status: No, hits=2.0 required=7.5 tests=IMPRONONCABLE_1, IMPRONONCABLE_2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I'm sorry that this response is so long in coming --- I had forgotten that I was filtering messages to a different mbox! On May 20, 2004, at 01:54, Eugen Leitl wrote: > > Any actual numbers would be very useful, ideally with the compilers, > compiler options, motherboard, and similar. Did you compare 1 job per > node vs 1 job per node? Or 2 jobs per node vs 2 jobs per node? 4 or 8 > dimms? Which kind of memory PC2700? PC3200? > The numbers I have are for NAMD2, using one of my own jobs. This was with the stock PC3200, 512M. I'm asking Rick V. for his input files for his benchmarks, so we can make a more direct comparison in the types of stuff I'm interested in. I'm going to try and borrow another dual G5 or two so I can test the gigabit enet scaling. >> The built-in Gigabit enet is attractive, also, as charmm and NAMD >> scale >> very well with gigabit, and it makes myrinet less price-effective >> (when >> used on any platform, wintel included, see >> http://biobos.nih.gov/apps/charmm/charmmdoc/Bench/c30b1.html for >> example). I decided that dual G5 xserve cluster nodes with gigabit > > I come to a different conclusion based on those graphs. In the first > graph myrinet improves by a factor of 2.6 (250 -> 95 seconds) from 2 > processors to 8, where gige improves by only 20% (255 -> 210). In the > second graph gigE gets SLOWER from 2 to 8 processors. Do you think in > either case the 8 node (let alone 16) gige cluster would have better > price/performance then a myrinet cluster? I realize after actually looking at that URL that that wasn't the data I was thinking about when I wrote that message. I'm struggling to find the URL I was thinking of --- it mentioned the very poor performance of wintel systems with gigE, and mentioned that the G5 system architecture didn't suffer from the same. I realize this is useful information, so I'll find it! > > Seems like for applications like shown on that page you shouldn't > really bother with a cluster over 2 nodes with gigE, not many people > would be willing to pay a factor of 4 more for 20% or even negative > scaling. > >> switches were much more cost-effective for me than any other >> processor, > > Cost effective = price/performance? Can you make any numbers > available? It boiled down to the cost of the smallest myrinet switch + cards cost almost as much as 5 more 2.0GHz G5s. Add that to the comparable price of the wintel hardware (P4s, I'm not talking itaniums here, those guys are even more expensive), and it was a no brainer, even with the slightly poorer scaling. Also realize that I'm talking about small clusters, here, not > 16 nodes. > >> especially any high-bandwidth specialty comm method (apple's gigabit >> has a pretty low latency also). > > Oh? Can you share the apple gigabit numbers? What is "pretty low"? > >> Additional considerations for us were the BSD environment which is >> more >> secure than windows, and the OS is arguably more stable and supported > > I'd agree with more stable and supported for use as a desktop, I'd > disagree with stable and supported as computational node. OSX is the > new player on the block in this space. Do you really think you would > get a good response from calling apple's tech support line when the > scheduler or network stack isn't performing to your performance > expectations? > > Certainly a very reasonable thing. > Actually, Apple has been very responsive and interested in making things work. I've already been over to Cupertino twice, and met with engineers here(on my campus) twice. I don't even have a cluster yet. To be fair, I don't have the resources (time, students or $$) to analyze the code to the nth degree, and find out why the network stack isn't doing 100 mph. I'm pretty much forced to analyze stock situations, because that is all my situation allows me to do. This clearly puts much more weight on the "familiarity" aspect, as I can't afford a whole lot of time spent under the hood, so to speak. Cheers, Mike -- C. Michael McCallum http://chem.cop.uop.edu/cmmccallum.html Associate Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax