From owner-chemistry@ccl.net Wed Mar 29 04:17:00 2006 From: "Jens Thomas j.m.h.thomas/./dl.ac.uk" To: CCL Subject: CCL: Comparison of Athelon and Pentium 4M ? Message-Id: <-31349-060329040431-24181-EUHSIZJ0NH8yFYOKuZpMkA::server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 Mar 2006 10:04:00 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas\a/dl.ac.uk] Hi Mark, Mark Thompson mark::arguslab.com wrote: >Sent to CCL by: Mark Thompson [mark,,arguslab.com] > >I have to compare some performance numbers between a couple of processors. >Specifically, the Athelon MP 1800+ and a 2.4 GHz Pentium 4M laptop. > >I'm only interested in rough comparisons (e.g. "P4M is ~1.5x faster on >the XXX benchmark than Athelon", etc.) > >I've poked around the web and have not found any good resources for >these numbers. > >Any ideas or suggestions would be welcome. > >Thanks, >Mark > > The Distributed Computing group at Daresbury has a range of benchmarking data, including some focusing on chemistry codes that you might find helpful. You can find their website at: http://www.cse.clrc.ac.uk/disco/ Follow the link to "Hardware Performance" halfway down the left-hand side to get to the benchmark data. I hope that you will find something that's useful to you there. If not, they also have a forum where you can post specific questions. Best wishes, Jens From owner-chemistry@ccl.net Wed Mar 29 08:32:00 2006 From: "Mark Hahn hahn]^[physics.mcmaster.ca" To: CCL Subject: CCL: Comparison of Athelon and Pentium 4M ? Message-Id: <-31350-060329023405-13481-FDAHXLtQDd1FvdKyLJQ18A],[server.ccl.net> X-Original-From: Mark Hahn Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 29 Mar 2006 00:49:07 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Mark Hahn [hahn#%#physics.mcmaster.ca] > I have to compare some performance numbers between a couple of processors. > Specifically, the Athelon MP 1800+ and a 2.4 GHz Pentium 4M laptop. > > I'm only interested in rough comparisons (e.g. "P4M is ~1.5x faster on > the XXX benchmark than Athelon", etc.) specFP is a pretty reasonable, widely-reported benchmark. here are some scores: cpu clock specFP pentium-m 2260 1375 athlonxp/1800 1533 671 this is pretty reasonable- the athlonxp is several years old, with slower memory, small caches, lower clock, no sse2, etc. (vs the pentium-m which is a pretty agressive (if originally laptop-targetted) cpu with large cache, higher clock, lots of replicated functional units, etc). for comparison: pentium4 3733 2118 opteron 2800 2344 the latter is a nice workstation/compute-server CPU, and you could legitimately expect it to be at ~3-4x faster than the athlonxp. regards, mark hahn. From owner-chemistry@ccl.net Wed Mar 29 09:07:00 2006 From: "Paul Fleurat-Lessard Paul.Fleurat-Lessard*_*ens-lyon.fr" To: CCL Subject: CCL: question about Gaussian03 PCM calculation Message-Id: <-31351-060329031109-18059-03mAG6gF/d1xZLt3CHWgYQ**server.ccl.net> X-Original-From: Paul Fleurat-Lessard Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 Mar 2006 09:11:30 +0200 MIME-Version: 1.0 Sent to CCL by: Paul Fleurat-Lessard [Paul.Fleurat-Lessard(!)ens-lyon.fr] Dear Yu, It might be of great help if you give us the full input file, as it seems that the PCM subroutine tries to read something that is clearly not what you want (ie RADII=UAKS). It might be that there is one blank line somewhere that should not be. Regards, Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard\a/ens-lyon.fr Laboratoire de Chimie Ecole Normale Supérieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allée d'Italie Fax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07 From owner-chemistry@ccl.net Wed Mar 29 09:51:01 2006 From: "Gopakumar gopakumar++chem.kuleuven.be" To: CCL Subject: CCL: Ghemical and Fedora3 Message-Id: <-31352-060329092912-3543-F2JIA6eUJV6KOwBG5mUIrQ##server.ccl.net> X-Original-From: Gopakumar Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 29 Mar 2006 15:24:59 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Gopakumar [gopakumar%chem.kuleuven.be] Hello members, I was trying to compile ghemical-1.02 under fedora core 3. And when I run configure script I am getting an error message checking for gdk_gl_query in -lgtkgl... no configure: error: Cannot find gtkgl library Any help is highly appreciated -Gopa Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Wed Mar 29 10:30:01 2006 From: "John McKelvey jmmckel]|[attglobal.net" To: CCL Subject: CCL: Comparison of Athelon and Pentium 4M ? Message-Id: <-31353-060329101500-4519-T08lkNJdpyCC7L2T68jD7A]~[server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 Mar 2006 10:08:55 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel() attglobal.net] CCLers Provided to me by a friend: You may be interested in this article on dual CPU vs dual core: http://www.pugetsystems.com/articles.php?id=23 Cheers, John McKelvey Jens Thomas j.m.h.thomas/./dl.ac.uk wrote: >Sent to CCL by: Jens Thomas [j.m.h.thomas\a/dl.ac.uk] >Hi Mark, > >Mark Thompson mark::arguslab.com wrote: > > >>Sent to CCL by: Mark Thompson [mark,,arguslab.com] >> >>I have to compare some performance numbers between a couple of processors. >>Specifically, the Athelon MP 1800+ and a 2.4 GHz Pentium 4M laptop. >> >>I'm only interested in rough comparisons (e.g. "P4M is ~1.5x faster on >>the XXX benchmark than Athelon", etc.) >> >>I've poked around the web and have not found any good resources for >>these numbers. >> >>Any ideas or suggestions would be welcome. >> >>Thanks, >>Mark >> >> >> >> >The Distributed Computing group at Daresbury has a range of benchmarking >data, including some focusing on chemistry codes that you might find >helpful. > >You can find their website at: > >http://www.cse.clrc.ac.uk/disco/ > >Follow the link to "Hardware Performance" halfway down the left-hand >side to get to the benchmark data. > >I hope that you will find something that's useful to you there. If not, >they also have a forum where you can post specific questions. > >Best wishes, > >Jens> > > > > > > From owner-chemistry@ccl.net Wed Mar 29 11:47:00 2006 From: "David A Case case\a/scripps.edu" To: CCL Subject: CCL: Announcement: Amber 9 is now available Message-Id: <-31354-060329114158-15488-TNnFDgQi2k9KpBXwgExo1A(0)server.ccl.net> X-Original-From: "David A Case" Date: Wed, 29 Mar 2006 11:41:54 -0500 Sent to CCL by: "David A Case" [case:+:scripps.edu] The Amber development team is pleased to announce the release of Amber 9. This is a major update from version 8, which was released in March of 2004. The main changes involve updated force fields and new QM/MM capability, but there are other enhancements and speedups as well. For information on what is new, and how to obtain Amber, please visit our web site: http://amber.scripps.edu ..thanks....dave case From owner-chemistry@ccl.net Wed Mar 29 13:52:00 2006 From: "=?iso-8859-1?Q?Gon=E7alo_Deira_Duarte_de_Campos_Justino?= goncalo.justino.##.zmail.pt" To: CCL Subject: CCL: Ghemical and Fedora3 Message-Id: <-31355-060329124354-13803-cbV0rbiQ1m7TA+HWI8aHlA##server.ccl.net> X-Original-From: =?iso-8859-1?Q?Gon=E7alo_Deira_Duarte_de_Campos_Justino?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 29 Mar 2006 18:08:13 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?Gon=E7alo_Deira_Duarte_de_Campos_Justino?= [goncalo.justino-.-zmail.pt] Dear Gopa, I tried a few months ago to compile ghemical under fedora and under suse. Both required several libraries to be present, and sometimes each of those libraries required another few libraries. This using the full install CD's. The "problem" is that Ghemical requires several libraries that were developed within a scientific frame that are common in suse and fedora. After a few weeks of the make / make install tango it got to work, albeit at the same speed as using cygwin under WinXP Pro :(. Persisitence is what it takes ... Good luck Gonçalo _________________________________ Gonçalo C. Justino Molecule Chiseler and Radical Tinderer http://depoisdos25.blogspot.com -----Original Message----- > From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net] Sent: quarta-feira, 29 de Março de 2006 16:02 To: Justino, Gonçalo Subject: CCL: Ghemical and Fedora3 Sent to CCL by: Gopakumar [gopakumar%chem.kuleuven.be] Hello members, I was trying to compile ghemical-1.02 under fedora core 3. And when I run configure script I am getting an error message checking for gdk_gl_query in -lgtkgl... no configure: error: Cannot find gtkgl library Any help is highly appreciated -Gopa Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htmhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Mar 29 14:27:00 2006 From: "Joe Corkery jcorkery]^[eyesopen.com" To: CCL Subject: CCL: Free Conformational Analysis Software Message-Id: <-31356-060329140052-28163-wNUAIM/EenTCT6eLn78Wig%a%server.ccl.net> X-Original-From: Joe Corkery Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 Mar 2006 14:00:38 -0500 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery|*|eyesopen.com] Omega from OpenEye Scientific Software (www.eyesopen.com) is available for free for non-commercial use. Joe Corkery OpenEye Scientific Software, Inc. Roger Kevin Robinson r.robinson-#-imperial.ac.uk wrote: > Sent to CCL by: Roger Kevin Robinson [r.robinson()imperial.ac.uk] > Hi, > > I was wondering if any one knew if there is any free conformation > analysis software either for Linux or Windows. > Ive been used to using Cerius2 (drieding) but this is no longer > available to me. > > I tried Dynamol but it doesnt seem to be able to choose the lowest > energy confermer. Although it can generate all confermers. > > Any advice would be appreciated. > > Roger> > > From owner-chemistry@ccl.net Wed Mar 29 15:02:00 2006 From: "Yu Adam Zhang yzhang*_*chem.ubc.ca" To: CCL Subject: CCL: question about Gaussian03 PCM calculation Message-Id: <-31357-060329143406-13374-mtFPxK2BtqZhSIRTJ5gzpQ(-)server.ccl.net> X-Original-From: "Yu Adam Zhang" Date: Wed, 29 Mar 2006 14:34:06 -0500 Sent to CCL by: "Yu Adam Zhang" [yzhang|chem.ubc.ca] < Sent to CCL by: Paul Fleurat-Lessard [Paul.Fleurat-Lessard(!)ens-lyon.fr] < Dear Yu, < < To: CCL Subject: CCL: Free Conformational Analysis Software Message-Id: <-31358-060329122702-4003-x3mP5+jP8Fd5l0jGtHKbAA^-^server.ccl.net> X-Original-From: Zsolt Mohacsi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 Mar 2006 18:29:10 +0200 MIME-Version: 1.0 Sent to CCL by: Zsolt Mohacsi [zsolt.mohacsi=-=chemaxon.hu] Hi, Try Marvin from ChemAxon. This is a Java based chemistry software, so it can be used on Linux, Windows and several other platforms. It can generate the lowest energy conformer as well as all conformers, for calculations Dreiding is used. Marvin Beans package can be downloaded at the Marvin site (locate the Download link at http://www.chemaxon.com/marvin/). This package contains MarvinSketch, MarvinView, MarvinSpace and MolConverter applications. MarvinSketch and MarvinView are also available as Java applet, so you can use them even from your web browser (Demo->Applets link at http://www.chemaxon.com/marvin/). To generate the lowest energy conformer sketch a molecule in MarvinSketch and choose "Edit->Clean->3D->Clean in 3D" (Fine build) from menu. A command line tool named MolConverter is also available. For generating lowest energy conformer with this tool use command "molconvert mol -3:S{fine} test.mol > leconformer.mol", supposing that your input molecule is stored in file test.mol; the output molecule is written to file leconformer.mol. In the 4.1 alpha release of Marvin (http://www.chemaxon.com/shared/alpha) a new conformer plugin is also available. To try this plugin sketch a molecule and choose "Tools->Conformers" from the menu. An other command line tool, cxcalc is also available in the Marvin Beans 4.1 alpha release package. For generating lowest energy conformer with cxcalc use command "cxcalc leconformer -f mol test.mol > leconformer.mol" (supposing that input and output files are same as above). Our software tools are free for academic users and non-commercial websites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html I hope this helps. Zsolt > Sent to CCL by: Roger Kevin Robinson [r.robinson()imperial.ac.uk] > Hi, > > I was wondering if any one knew if there is any free conformation analysis software either for Linux or Windows. > Ive been used to using Cerius2 (drieding) but this is no longer available to me. > > I tried Dynamol but it doesnt seem to be able to choose the lowest energy confermer. Although it can generate all confermers. > > Any advice would be appreciated. > > Roger From owner-chemistry@ccl.net Wed Mar 29 16:56:00 2006 From: "Eike Huebner eike.huebner=-=uni-konstanz.de" To: CCL Subject: CCL: Comparison of Athelon and Pentium 4M ? Message-Id: <-31359-060329165122-19473-RT4Si+m962urx9F1vNkByQ(!)server.ccl.net> X-Original-From: "Eike Huebner" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 29 Mar 2006 23:51:02 +0200 Mime-Version: 1.0 Sent to CCL by: "Eike Huebner" [eike.huebner{:}uni-konstanz.de] Hello, some time ago we did some benchmarking on different OS, programs and CPU's. While a lot of it was concentrated on our needs, this small table may be of interest in this context: Gamess(W): CPU socket CPU-speed RAM-speed time A64 X2 4600+ 2cores S939 2400 MHz DDR-400 1077 Seconds 2x Xeon(P4) 3,06GHz S604 3066 MHz DDR-266 1588 Seconds 2x Athlon MP 2800+ S.A. 2133 MHz DDR-266 1889 Seconds 1x A64 3800+ S.A. 2400 MHz DDR-400 1882 Seconds 1x A64 3500+ S.A. 2200 MHz DDR-490 1944 Seconds 1x Pentium-4 3,0GHz S755 3000 MHz DDR2-533 2267 Seconds 1x Athlon XP 3200+ S.A. 2200 MHz DDR-400 2412 Seconds 1x Xeon(P4) 3,06GHz S604 3066 MHz DDR-266 2496 Seconds 1x Athlon MP 2800+ S.A. 2133 MHz DDR-266 2902 Seconds 1x Sempron 3000+ S.A 2000 MHz DDR-333 3130 Seconds 1x Pentium-M 1400 S479 1400 MHz DDR-266 4331 Seconds 1x VIA (C3 Nehemia) S370 800 MHz DDR-400 29132 Seconds The direct calculations were performed using PC GAMESS version 6.4, build number 2606. The caclulation was a geometry optimization of naphtaline on the N311G6 basis set and the B3LYP DFT functional. The operating system in these benchmarks was Windows XP SP2 and the most optimized binaries for each system were used. Parallel runs (1-3) were performed with wMPI v1.3. Of course, there is a lot to discuss on these data. The results will differ if you choose a different calculation (HF instead of DFT or maybe even CI), a different molecule, one should take into account that the whole computer systems differs (disk speed (although it is a direct calculation there will be some influence), chipset, maybe some driver "helper service" or whatever...) but one can have a fast look at the approximate speeds. Regards, Eike Huebner *********** REPLY SEPARATOR *********** On 29.03.2006 at 10:41 John McKelvey jmmckel]|[attglobal.net wrote: >Sent to CCL by: John McKelvey [jmmckel() attglobal.net] >CCLers > >Provided to me by a friend: > >You may be interested in this article on dual CPU vs dual core: > >http://www.pugetsystems.com/articles.php?id=23 > > >Cheers, > >John McKelvey > >Jens Thomas j.m.h.thomas/./dl.ac.uk wrote: > >>Sent to CCL by: Jens Thomas [j.m.h.thomas\a/dl.ac.uk] >>Hi Mark, >> >>Mark Thompson mark::arguslab.com wrote: >> >> >>>Sent to CCL by: Mark Thompson [mark,,arguslab.com] >>> >>>I have to compare some performance numbers between a couple of >processors. >>>Specifically, the Athelon MP 1800+ and a 2.4 GHz Pentium 4M laptop. >>> >>>I'm only interested in rough comparisons (e.g. "P4M is ~1.5x faster on >>>the XXX benchmark than Athelon", etc.) >>> >>>I've poked around the web and have not found any good resources for >>>these numbers. >>> >>>Any ideas or suggestions would be welcome. >>> >>>Thanks, >>>Mark >>> >>> >>> >>> >>The Distributed Computing group at Daresbury has a range of benchmarking >>data, including some focusing on chemistry codes that you might find >>helpful. >> >>You can find their website at: >> >>http://www.cse.clrc.ac.uk/disco/ >> >>Follow the link to "Hardware Performance" halfway down the left-hand >>side to get to the benchmark data. >> >>I hope that you will find something that's useful to you there. If not, >>they also have a forum where you can post specific questions. >> >>Best wishes, >> >>Jens From owner-chemistry@ccl.net Wed Mar 29 19:09:00 2006 From: "renyanliang yanliangren_2002|yahoo.com.cn" To: CCL Subject: CCL:G: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20CCL:G:=20question=20about=20Gaussian03=20?= =?gb2312?q?PCM=20calculation?= Message-Id: <-31360-060328210106-1076-+gA8Eam0qFCSFnFgsNmH1Q:server.ccl.net> X-Original-From: renyanliang Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1227049094-1143594057=:68556" Date: Wed, 29 Mar 2006 09:00:57 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: renyanliang [yanliangren_2002(0)yahoo.com.cn] --0-1227049094-1143594057=:68556 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear zhang: I think that you are too careless, there are "#" before the keywords, as following: # b3lyp/6-31g** scrf=(pcm,solvent=h2o,read) opt Best regards! "Yu Adam Zhang yzhang[]chem.ubc.ca" дµÀ£º Sent to CCL by: "Yu Adam Zhang" [yzhang[-]chem.ubc.ca] hi, all I want to do some pcm calculations with Gaussian03. As many people complained on ccl, my opt calculation failed. Once I learned from one post on ccl that specifying the molecular cavity might help (using scrf=(read,...) and an additional input line). So I wrote my input file as following: %mem=500mb %nproc=2 b3lyp/6-31g** scrf=(pcm,solvent=h2o,read) opt title 0 1 C C 1 B1 . ... D32 -1.25323616 D33 -121.20303534 end of molecular geometry specification RADII=UAKS (blank line) (end of input file) but this input file didn't work:(. It always gave a error message like: ..... Using the following non-standard input for PCM: 1 2 1.5 5 1.0 9 1.0 ------------------------------------------------------------------------------ The following wrong keyword(s) have been found: 1.0 ------------------------------------------------------------------------------ Error termination via Lnk1e in /usr/apps/g03_c02/g03/l301.exe at Mon Mar 27 17:26:26 2006. ..... What can I do to get out of mistake? Thank you very much if you can give me hand! Yuhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- ÑÅ»¢1GÃâ·ÑÓÊÏä°Ù·Ö°Ù·ÀÀ¬»øÐÅ ÑÅ»¢ÖúÊÖ-ËÑË÷¡¢É±¶¾¡¢·ÀɧÈÅ --0-1227049094-1143594057=:68556 Content-Type: text/html; charset=gb2312 Content-Transfer-Encoding: 8bit
Dear zhang:
      I think that you are too careless, there are "#" before the keywords, as following:
       # b3lyp/6-31g** scrf=(pcm,solvent=h2o,read) opt
  Best regards!


"Yu Adam Zhang yzhang[]chem.ubc.ca" <owner-chemistry#ccl.net> дµÀ£º
Sent to CCL by: "Yu Adam Zhang" [yzhang[-]chem.ubc.ca]
hi, all
I want to do some pcm calculations with Gaussian03. As many people complained on ccl, my opt calculation failed. Once I learned from one post on ccl that specifying the molecular cavity might help (using scrf=(read,...) and an additional input line). So I wrote my input file as following:
%mem=500mb
%nproc=2
b3lyp/6-31g** scrf=(pcm,solvent=h2o,read) opt

title

0 1
C
C 1 B1
. ...
D32 -1.25323616
D33 -121.20303534 end of molecular geometry specification

RADII=UAKS
(blank line)
(end of input file)

but this input file didn't work:(. It always gave a error message like:
.....
Using the following non-standard input for PCM:
1 2 1.5 5 1.0 9 1.0
------------------------------------------------------------------------------
The following wrong keyword(s) have been found:






1.0
------------------------------------------------------------------------------
Error termination via Lnk1e in /usr/apps/g03_c02/g03/l301.exe at Mon Mar 27 17:26:26 2006.
.....

What can I do to get out of mistake? Thank you very much if you can give me hand!
Yu


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