From chemistry-request@server.ccl.net Thu Jul 4 13:42:22 2002 Received: from mail.anbi.ethz.ch ([129.132.117.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g64HgMS26861 for ; Thu, 4 Jul 2002 13:42:22 -0400 Received: from pharma.anbi.ethz.ch (unkel.ethz.ch [129.132.117.164]) by mail.anbi.ethz.ch (Postfix) with ESMTP id 9C7431E3106; Thu, 4 Jul 2002 19:42:21 +0200 (CEST) Message-ID: <3D2488CB.844ABD78@pharma.anbi.ethz.ch> Date: Thu, 04 Jul 2002 19:41:31 +0200 From: "C. Klein" X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Jianhui Wu Cc: chemistry@ccl.net, amber@heimdal.compchem.ucsf.edu Subject: Re: Origin300, Linux Cluster References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, take a look at this: ............. ~/bin> uptime 7:32pm up 50 days, 4:10, 7 users, load average: 0.01, 0.09, 0.06 ............. That is the front end of our linux cluster, a bunch of athlons with a dual PIII front end machine. This all came for maybe 15000 USD and the performance is extremely good. The uptimes of the compute nodes are equally high. So do not worry about stability. The price/performance ratio is much much better for linux clusters than for SGI systems. I do not have a lot of time to write, but there is one very important issue: Once you get your cluster hardware, check it thoroughly. Check if all the hardware meets the specification (amounts of RAM, NIC types etc.). I had some surprises with that. And even more important: Do test runs of your software, if possible in parallel, for maybe a week. I had to send back 10 dual PIIIs because they would give unexplainable crashes!!!!! Do not pay the bill before everything is up and running... Take care not to buy cheap NICs. Best regards, Chris -- Dr. C. Klein; cklein(at)pharma.anbi.ethz.ch Dept. of Applied Biosciences, Pharmaceutical Chemistry Swiss Federal Institute of Technology / ETH Zuerich Winterthurerstr. 190 CH-8057 Zuerich Phone: +41 1 6356062 FAX : +41 1 6356884 From chemistry-request@server.ccl.net Thu Jul 4 12:12:40 2002 Received: from web21109.mail.yahoo.com ([216.136.227.111]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g64GCdS24735 for ; Thu, 4 Jul 2002 12:12:40 -0400 Message-ID: <20020704161239.46226.qmail@web21109.mail.yahoo.com> Received: from [193.205.210.2] by web21109.mail.yahoo.com via HTTP; Thu, 04 Jul 2002 18:12:39 CEST Date: Thu, 4 Jul 2002 18:12:39 +0200 (CEST) From: =?iso-8859-1?q?Michele=20Lunelli?= Subject: Dual Athlon with G98W To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi all, do you think a dual Athlon MP is good choice to run the Windows version of Gaussian98? Or may be the second processor will be unused, and so a single processor machine is a more logical choice? thanks in advance, Michele Lunelli University of Trento, Italy ______________________________________________________________________ Scarica il nuovo Yahoo! Messenger: con webcam, nuove faccine e tante altre novità. http://it.yahoo.com/mail_it/foot/?http://it.messenger.yahoo.com/ From chemistry-request@server.ccl.net Fri Jul 5 09:48:00 2002 Received: from mailhub.health.nb.ca ([207.179.181.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g65Dm0S19334 for ; Fri, 5 Jul 2002 09:48:00 -0400 Received: from onco_irmb.health.nb.ca ([10.10.100.12]) by mailhub.health.nb.ca (Post.Office MTA v3.5.3 release 223 ID# 607-57574U3000L300S0V35) with ESMTP id ca for ; Fri, 5 Jul 2002 10:47:54 -0300 Message-Id: <5.1.0.14.0.20020705104555.009fcb80@mailhub.health.nb.ca> X-Sender: miroslavac@mailhub.health.nb.ca X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 05 Jul 2002 10:51:36 -0300 To: CCL From: miroslavac@health.nb.ca (Miroslava Cuperlovic-Culf) Subject: protein isoforms Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All, I would like to find out more about molecular simulations of protein isoforms (structural differences, docking to isoforms etc.). Good references and experiences will be greatly appreciated. Thanks for on-going help, Mira Miroslava Cuperlovic-Culf Research Scientist Beausejour Medical Research Institute 37 Providence Street Moncton, NB E1C 8X3 Canada fax: 506-862-4222 tel: 506-862-4848 e-mail: miroslavac@health.nb.ca From chemistry-request@server.ccl.net Fri Jul 5 04:36:48 2002 Received: from ns.ice.mpg.de ([195.37.47.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g658amS13666 for ; Fri, 5 Jul 2002 04:36:48 -0400 Received: from [10.10.11.61] (helo=ice.mpg.de) by ns.ice.mpg.de with esmtp (Exim 3.14 #17) id 17QOa7-00072k-00 for chemistry@ccl.net; Fri, 05 Jul 2002 10:36:47 +0200 Message-ID: <3D255A99.4020308@ice.mpg.de> Date: Fri, 05 Jul 2002 10:36:41 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max Planck Institute of Chemical Ecology User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.0) Gecko/20020530 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Origin300, Linux Cluster References: <3D2488CB.844ABD78@pharma.anbi.ethz.ch> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit C. Klein wrote: > > ~/bin> uptime > 7:32pm up 50 days, 4:10, 7 users, load average: 0.01, 0.09, 0.06 That's nothing. Check this out: [stein@cn01 stein]$ uptime 10:47am up 161 days, 20:19, 11 users, load average: 0.87, 0.94, 0.96 This is the front machine of our 16-nodes linux cluster. :-) But seriously: > The price/performance ratio is much much better for linux clusters than > for SGI systems. I can only support this. And I would also suggest using no no-name, garage-built hardware. There are lots of good x86-based systems available which are specially made for 19'' racks (see for example http://www.fujitsu-siemens.com/rl/products/primergy/rackservers.html). We are running Siemens hardware and we are very satisfied, but I think there are tons of comparable systems from other major producers. Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 Jena, Germany Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Fri Jul 5 04:49:52 2002 Received: from mefteh.dsi.univ-paris5.fr ([193.51.86.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g658npS13884 for ; Fri, 5 Jul 2002 04:49:51 -0400 Received: (from root@localhost) by mefteh.dsi.univ-paris5.fr (8.11.6) id g658ngF26807; Fri, 5 Jul 2002 10:49:42 +0200 (MEST) Received: from alpha.univ-paris5.fr (alpha.univ-paris5.fr [193.51.86.2]) by mefteh.dsi.univ-paris5.fr (8.11.6) with ESMTP id g658neQ26787; Fri, 5 Jul 2002 10:49:40 +0200 (MEST) Received: from there (pcumr70.biomedicale.univ-paris5.fr [172.20.101.107]) by alpha.univ-paris5.fr (8.9.3/jtpda-5.3.1) with SMTP id KAA29635 ; Fri, 5 Jul 2002 10:49:35 +0200 (MET DST) Message-Id: <200207050849.KAA29635@alpha.univ-paris5.fr> Content-Type: text/plain; charset="iso-8859-15" From: =?iso-8859-15?q?St=E9phane=20Teletch=E9a?= Organization: UMR 8601 To: "C. Klein" , Jianhui Wu Subject: Re: Origin300, Linux Cluster Date: Fri, 5 Jul 2002 10:48:03 +0200 X-Mailer: KMail [version 1.3.2] Cc: chemistry@ccl.net, amber@heimdal.compchem.ucsf.edu References: <3D2488CB.844ABD78@pharma.anbi.ethz.ch> In-Reply-To: <3D2488CB.844ABD78@pharma.anbi.ethz.ch> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by AMaViS perl-11 Le Jeudi 4 Juillet 2002 19:41, C. Klein a écrit : > Hi, > > take a look at this: > ............. > ~/bin> uptime > 7:32pm up 50 days, 4:10, 7 users, load average: 0.01, 0.09, 0.06 > ............. > > > That is the front end of our linux cluster, a bunch of athlons with a > dual PIII front end machine. This all came for maybe 15000 USD and the > performance is extremely good. The uptimes of the compute nodes are > equally high. So do not worry about stability. > > The price/performance ratio is much much better for linux clusters than > for SGI systems. > > I do not have a lot of time to write, but there is one very important > issue: Once you get your cluster hardware, check it thoroughly. Check if > all the hardware meets the specification (amounts of RAM, NIC types > etc.). I had some surprises with that. And even more important: Do test > runs of your software, if possible in parallel, for maybe a week. I had > to send back 10 dual PIIIs because they would give unexplainable > crashes!!!!! Do not pay the bill before everything is up and running... > Take care not to buy cheap NICs. > > Best regards, > > Chris I agree with Chris about stability and performance (you can even get athlons instead of PII/PIV, you will get a much more efficiency on your calculation: for example amber is 30% rapidlyer on an athlon 1.0Ghz than a 1.0Ghz pentium). The only problem you will need to solve is the definition of your needs : - first; will you use your cluster as a superparallel computer ? in that case for example, you will not get a good speedup with explicit water in sander, but a good one in GB. For PME on, you will better dedicate one node per person. - second: do your programs run under linux ? you talked about some virtual screening, and if you think of Accelrys'product, they do not run under linux for the moment. Stef From chemistry-request@server.ccl.net Fri Jul 5 09:15:32 2002 Received: from jubilantbiosys.com ([202.144.86.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g65DFUS18862 for ; Fri, 5 Jul 2002 09:15:31 -0400 Received: from parthiban ( [192.168.1.56] (may be forged)) (authenticated) by jubilantbiosys.com (8.11.6/8.11.6) with ESMTP id g65DGie30346 for ; Fri, 5 Jul 2002 18:46:45 +0530 Message-ID: <01b701c22425$c6651b60$3801a8c0@parthiban> From: "Parthiban Srinivasan" To: Subject: HotDock/Babel Date: Fri, 5 Jul 2002 18:43:36 +0530 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01B4_01C22453.DF3B82E0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 This is a multi-part message in MIME format. ------=_NextPart_000_01B4_01C22453.DF3B82E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Friends... I am finding some problem while installing the HotDock and Babel... While tring to read a PDB file, it gives an error -ip is not a supported input file type Could u plz help me to resolve this. Thanks in advance S Parthiban Jubilant Biosys=20 ------=_NextPart_000_01B4_01C22453.DF3B82E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Friends...
I am finding some problem while = installing the=20 HotDock and Babel...
While tring to read a PDB file, it = gives an=20 error
-ip is not a supported input file = type
Could u plz help me to resolve this. = Thanks in=20 advance
S Parthiban
Jubilant Biosys =
------=_NextPart_000_01B4_01C22453.DF3B82E0-- From chemistry-request@server.ccl.net Fri Jul 5 22:15:25 2002 Received: from hevensgate.org ([24.209.32.91]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g662FOp09285 for ; Fri, 5 Jul 2002 22:15:25 -0400 Message-Id: <200207060215.g662FOp09285@server.ccl.net> From: "A.Stranger" To: Subject: Pray for the Children Sender: "A.Stranger" Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Date: Fri, 5 Jul 2002 22:16:55 -0700 Reply-To: "A.Stranger" Content-Transfer-Encoding: 8bit Blessed Saviour, please hear my prayer; Father of mine, Son, of the father Saviour of all mankind Let them fear not, Lord, as satan strike's them down as we return there small bodys, to the ground for they are faithfull servents Lord satan dosen't want around and in your wisdom Lord, you allow this to be..... When you send them back , Lord With faithfull heart and mind Let them have some happiness to pay them for there time A loving Mother and Father that gives there love for free a son or a daughter,to know how love shoud be your grace and guidance, you gave to me and lots of LOVE Lord, Lots of LOVE in Christs name I pray amen I Pledge Allegiance to the flag of the United States of America and to the Republic for which it stands,one Nation under God, indivisible, with liberty and justice for all. A.Stranger,U.S.Vet http://goldenegg.ws