From owner-chemistry@ccl.net Tue Dec 13 00:38:01 2005 From: "Jozsef Csontos jozsefcsontos]_[creighton.edu" To: CCL Subject: CCL:G: dual core opteron Message-Id: <-30300-051213003205-17156-c0A+02B88kAoo0HagHVThg-.-server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 12 Dec 2005 23:31:47 -0600 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos[-]creighton.edu] G03+Suse9.3+2.6.11.4-21.7-smp kernel+linda(7.1)+pgf77(PGI 6.0) are OK. On Mon, 2005-12-12 at 20:58 -0500, dedey*alumni.bilkent.edu.tr wrote: > Sent to CCL by: [dedey%%alumni.bilkent.edu.tr] > > Dear CCL members, > > We are about to build a cluster and trying to decide about the machine configurations. > I wonder if anyone performed parallel execution of Gaussian 98 or 03 > on clusters each of which has AMD Opteron-dual core processors, running Solaris or rpm Linux. > If yes, can you inform me about the operating system. Any diffucilties, or tricks -if present- is also requested. > > > Thanks in advance. > -- > Yavuz Dede> > > -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Tue Dec 13 04:30:01 2005 From: "Gert von Helden helden*|*fhi-berlin.mpg.de" To: CCL Subject: CCL:G: dual core opteron Message-Id: <-30301-051213042226-612-MEAxJg+sxvq2MVgktdvekA . server.ccl.net> X-Original-From: Gert von Helden Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Tue, 13 Dec 2005 09:31:00 +0100 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Gert von Helden [helden---fhi-berlin.mpg.de] Same config here (no Linda, however). Works great. Don't try Redhat. On our Sun V40z boxes (4x dual core), performance with Redhat was terrible. On Dec 13, 2005, at 6:45 AM, Jozsef Csontos jozsefcsontos]_[creighton.edu wrote: > Sent to CCL by: Jozsef Csontos [jozsefcsontos[-]creighton.edu] > G03+Suse9.3+2.6.11.4-21.7-smp kernel+linda(7.1)+pgf77(PGI 6.0) are OK. > > On Mon, 2005-12-12 at 20:58 -0500, dedey*alumni.bilkent.edu.tr wrote: >> Sent to CCL by: [dedey%%alumni.bilkent.edu.tr] >> >> Dear CCL members, >> >> We are about to build a cluster and trying to decide about the >> machine configurations. >> I wonder if anyone performed parallel execution of Gaussian 98 or 03 >> on clusters each of which has AMD Opteron-dual core processors, >> running Solaris or rpm Linux. >> If yes, can you inform me about the operating system. Any >> diffucilties, or tricks -if present- is also requested. >> >> >> Thanks in advance. >> -- >> Yavuz Dede> >> >> > -- > Jozsef Csontos, Ph.D. > > Department of Biomedical Sciences > Creighton University, > Omaha, NE > > ------------------------------------- Gert von Helden Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin tel.: +49-30-8413 5615 fax: +49-30-8413 5603 From owner-chemistry@ccl.net Tue Dec 13 05:04:00 2005 From: "roger robinson r.robinson : imperial.ac.uk" To: CCL Subject: CCL:G: dual core opteron Message-Id: <-30302-051213042150-493-dZAAYqL1AYVv6agw14YamQ/./server.ccl.net> X-Original-From: roger robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 13 Dec 2005 09:17:57 +0000 MIME-Version: 1.0 Sent to CCL by: roger robinson [r.robinson]|[imperial.ac.uk] Dear Yavuz, When i was compiling it on a dual processor opteron system, I had to change the file cachesize to this -> grep 'cache size' /proc/cpuinfo | uniq | tr -d "[:alpha:][:punct:]" its in the bsd directory. I used SUSE 9.3 the patch and pgi 6.0. roger >Sent to CCL by: [dedey%%alumni.bilkent.edu.tr] > >Dear CCL members, > >We are about to build a cluster and trying to decide about the machine configurations. >I wonder if anyone performed parallel execution of Gaussian 98 or 03 >on clusters each of which has AMD Opteron-dual core processors, running Solaris or rpm Linux. >If yes, can you inform me about the operating system. Any diffucilties, or tricks -if present- is also requested. > > >Thanks in advance. >-- >Yavuz Dede> > > > > From owner-chemistry@ccl.net Tue Dec 13 07:51:01 2005 From: "Marcel Drabbels Marcel.Drabbels-,-epfl.ch" To: CCL Subject: CCL:G: dual core opteron Message-Id: <-30303-051213074228-5650-zYvsLASn9misyiBgm1YzRw_._server.ccl.net> X-Original-From: Marcel Drabbels Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Tue, 13 Dec 2005 12:42:18 +0100 Mime-Version: 1.0 Sent to CCL by: Marcel Drabbels [Marcel.Drabbels/a\epfl.ch] We do not succeed running Gaussian on multiple processors on a SUSE 9.3 system with kernel 2.6.11.4-21.9-smp. However, colleagues get it to work on a SUSE system with kernel 2.6.11.4-21.7-smp. According to Gaussian there might be an issue with this newer kernel, but they have not yet offered a solution for the problem. Marcel ==================================================================== Dr. Marcel Drabbels Laboratoire de Chimie Physique Moléculaire (LCPM) École Polytechnique Fédérale de Lausanne (EPFL) Station 6 CH-1015 Lausanne Switzerland Tel: +41-21-693 3022/6131 Fax: +41-21-693 5170 http://lcpm.epfl.ch/ ==================================================================== From owner-chemistry@ccl.net Tue Dec 13 09:22:01 2005 From: "Vlad Cojocaru Vlad.Cojocaru-#-eml-r.villa-bosch.de" To: CCL Subject: CCL:G: openbabel question Message-Id: <-30304-051213090746-7905-Nhfj0TOPKwmJ37usGVcJzQ##server.ccl.net> X-Original-From: Vlad Cojocaru Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 13 Dec 2005 14:25:04 +0100 MIME-Version: 1.0 Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru=eml-r.villa-bosch.de] Dear CCL-ers, I have been using in the past babel to create gzmat files from mol2 or pdb. However, I noticed that openbabel doesnt support the gzmat file format anymore ... Is that correct? Second, I also noticed that openbabel doesnt convert Gaussian output anymore as babel used to do ... Is that also correct? Although I am not using Gaussian at the moment I am just wondering why openbabel doesnt support these file formats? Best wishes vlad -- Dr. Vlad Cojocaru EML Research gGmbH Molecular and Cellular Modeling Group Villa Bosch Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Germany Phone: +49-6221-533266 Fax: +49-6221-533298 e-mail: Vlad.Cojocaru()eml-r.villa-bosch.de Additional info: my home page From owner-chemistry@ccl.net Tue Dec 13 09:56:01 2005 From: "Andreas Klamt klamt-#-cosmologic.de" To: CCL Subject: CCL: New Release of COSMOtherm software for fluid phase thermodynamics based on DFT/COSMO Message-Id: <-30305-051213092150-8815-rFRPexv7AytkJeV34UV2SA{=}server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Tue, 13 Dec 2005 15:21:37 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt_+_cosmologic.de] Dear CCLer's I am pleased to announce a new release of our COSMOtherm software for fluid phase thermodynamics based on DFT/COSMO calculations. COSMOtherm is the most powerful implementation of my COSMO-RS method (COSMO for realistic solvation). It is able to calculate the free energy of almost arbitrary molecules in almost arbitrary liquid systems (pure and mixed solvents at variable temperature, even ionic liquids, and with some restrictions even polymers, blood/brain, soil, and similar less well defined matrices). Thus it is able to calculate solubilities, partition coefficients, activity coefficients, vapor pressures, and entire phase diagrams, just based on the DFT/COSMO calculations of the solutes and solvents. These capabilities go far beyond the scope of conventional solvation models. An exciting new feature is the ability to treat molecules at interfaces between liquid systems. COSMOtherm now comes with a graphical user interface for Windows and LINUX systems. A database of carefully precalculated COSMO files of more than 3000 common solvents and other common or important chemicals can be ordered in addition to COSMOtherm. Academic research licenses are available at very reduced prices. For the first time we even offer an academic educational license at just 800 EURO, which allows usage for teaching molecular thermodynamics and for doing excercises on thermodynamics by the students. It is exceptionally well suited to teach things as "Why some molecules like eachother and others do not". With best regards Andreas Klamt and the COSMOlogic team -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt++cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Dec 13 10:32:01 2005 From: "Alex Allardyce aa|*|chemaxon.hu" To: CCL Subject: CCL: Wiki-like Chemical Databases Message-Id: <-30306-051213090907-8036-B6iIRa4vPvLxYAGv1Hxl9Q=server.ccl.net> X-Original-From: "Alex Allardyce" Sent to CCL by: "Alex Allardyce" [aa*chemaxon.hu] HI Paul, For the cheminformatics functions feel free to check out ChemAxon's Java toolkits. Marvin, the chemical editor/viewer has always been free for freely accessible websites; the structure search/database manager (JChem Base or JChem Cartridge) and structure canonicalization toolkit (Standardizer) can be made available for free if the cause is good and non commercial. If you are concerned about causes and costs perhaps come back to me offline. Good luck More info, examples and links to download etc here: http://www.chemaxon.com/products.html From owner-chemistry@ccl.net Tue Dec 13 11:07:00 2005 From: "Carlos Lagos A. carlos+/-cgb.cl" To: CCL Subject: CCL: Is there any book/review/web to learn QSAR/QSAR-3D from the basis? Message-Id: <-30307-051213093025-15943-8Ox79JUWeX2Ohf0eAAAh/Q##server.ccl.net> X-Original-From: "Carlos Lagos A." Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 13 May 2005 10:50:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos Lagos A." [carlos:_:cgb.cl] I suggest you this 2 papers from Kubinyi QSAR and 3D QSAR in drug design Part 1: methodology Drug Discovery Today, Volume 2, Issue 11, November 1997, Pages 457-467 And QSAR and 3D QSAR in drug design Part 2: applications and problems Drug Discovery Today, Volume 2, Issue 12, December 1997, Pages 538-546 Carlos Lagos A. Centro de Genómica y Bioinformática CGB http://www.cgb.cl D.BIO- Gerard Pujadas gerard.pujadas(a)urv.net wrote: > Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas]^[urv.net] > > Dear CCL list members, > > I would appreciate if you could point me to a > book, review, etc. where I could learn > QSAR/3D-QSAR from the basis. > > With many thanks in advances for your help > > Yours sincerely > > Gerardhttp://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 Tue Dec 13 11:41:00 2005 From: "Alex Allardyce aa=-=chemaxon.hu" To: CCL Subject: CCL: Wiki-like Chemical Databases Message-Id: <-30308-051213103023-11462-6mMkEukKmG1GQ3qw8z3OOg/a\server.ccl.net> X-Original-From: "Alex Allardyce" Sent to CCL by: "Alex Allardyce" [aa a chemaxon.hu] HI Paul, For the cheminformatics functions feel free to check out ChemAxon's Java toolkits. Marvin, the chemical editor/viewer has always been free for freely accessible websites; the structure search/database manager (JChem Base or JChem Cartridge) and structure canonicalization toolkit (Standardizer) can be made available for free if the cause is good and non commercial. If you are concerned about causes and costs perhaps come back to me offline. Good luck More info, examples and links to download etc here: http://www.chemaxon.com/products.html From owner-chemistry@ccl.net Tue Dec 13 12:17:00 2005 From: "Geoffrey Hutchison grh25**cornell.edu" To: CCL Subject: CCL:G: openbabel question Message-Id: <-30309-051213104639-25479-z3lSiQOT11UlH+jNO7t6RA::server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Tue, 13 Dec 2005 10:46:20 -0500 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Geoffrey Hutchison [grh25-#-cornell.edu] Yes, it is correct that in Open Babel 2.0, we have not included the Gaussian z-matrix input format. Instead, we concentrated on two things: * Making sure the core library is flexible and robust * Making sure "key formats" work well So no, not all formats from the original babel are supported in Open Babel right now. Certainly if there seems to be a demand for gzmat, it can be added. Since it's a volunteer project, formats are added when people contribute them to us, or when developers like myself have a need (e.g., I start using WizzyChem). On the other hand, Gaussian cartesian input has been supported for ages. > Second, I also noticed that openbabel doesnt convert Gaussian > output > anymore as babel used to do ... Is that also correct? I use Open Babel to read Gaussian output every day. So I'm not sure how you decided that it doesn't convert Gaussian output -- for sure I don't have old Gaussian files so I can only test g98 and g03. Older Gaussian files or other formats can be contributed: http://sourceforge.net/tracker/?atid=447448&group_id=40728&func=browse http://sourceforge.net/tracker/?atid=740158&group_id=40728&func=browse Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruña Group http://abruna.chem.cornell.edu/ On Dec 13, 2005, at 9:39 AM, Vlad Cojocaru Vlad.Cojocaru-#-eml- r.villa-bosch.de wrote: > Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru=eml-r.villa-bosch.de] > Dear CCL-ers, > I have been using in the past babel to create gzmat files from mol2 > or pdb. However, I noticed that openbabel doesnt support the gzmat > file > format anymore ... Is that correct? > Second, I also noticed that openbabel doesnt convert Gaussian > output > anymore as babel used to do ... Is that also correct? > Although I am not using Gaussian at the moment I am just wondering > why openbabel doesnt support these file formats? > Best wishes > vlad > > > -- > > > Dr. Vlad Cojocaru > EML Research gGmbH > Molecular and Cellular Modeling Group > Villa Bosch > Schloss-Wolfsbrunnenweg 33 > 69118 Heidelberg > Germany > Phone: +49-6221-533266 > Fax: +49-6221-533298 > e-mail: Vlad.Cojocaru.:.eml-r.villa-bosch.de > > Additional info: my home page > From owner-chemistry@ccl.net Tue Dec 13 12:59:00 2005 From: "Vlad Cojocaru Vlad.Cojocaru=eml-r.villa-bosch.de" To: CCL Subject: CCL:G: openbabel question Message-Id: <-30310-051213125738-7523-FHIwgotlDKAzjE/ATwZh2Q[A]server.ccl.net> X-Original-From: Vlad Cojocaru Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 13 Dec 2005 18:57:14 +0100 MIME-Version: 1.0 Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru-$-eml-r.villa-bosch.de] Dear Geoffrey, Thanks for the answers to my questions ... I thought that the Gaussian output is not supported because when I type babel -H into the terminal, there is no g94, g98 or g03 input fyle type ... So, it was more like a guess .. I didnt test it. However, if it supports those files as input, I thought they should be listed by -H option... But, again at the moment I am not using Gaussian so it was a rather informative question, not based on encountered problems... Best vlad Geoffrey Hutchison grh25**cornell.edu wrote: >Sent to CCL by: Geoffrey Hutchison [grh25-#-cornell.edu] > >Yes, it is correct that in Open Babel 2.0, we have not included the >Gaussian z-matrix input format. Instead, we concentrated on two things: >* Making sure the core library is flexible and robust >* Making sure "key formats" work well > >So no, not all formats from the original babel are supported in Open >Babel right now. Certainly if there seems to be a demand for gzmat, >it can be added. Since it's a volunteer project, formats are added >when people contribute them to us, or when developers like myself >have a need (e.g., I start using WizzyChem). On the other hand, >Gaussian cartesian input has been supported for ages. > > > >> Second, I also noticed that openbabel doesnt convert Gaussian >>output >>anymore as babel used to do ... Is that also correct? >> >> > >I use Open Babel to read Gaussian output every day. So I'm not sure >how you decided that it doesn't convert Gaussian output -- for sure I >don't have old Gaussian files so I can only test g98 and g03. > >Older Gaussian files or other formats can be contributed: >http://sourceforge.net/tracker/?atid=447448&group_id=40728&func=browse >http://sourceforge.net/tracker/?atid=740158&group_id=40728&func=browse > >Cheers, >-Geoff > >-- >-Dr. Geoffrey Hutchison >Cornell University, Department of Chemistry and Chemical Biology >Abruña Group http://abruna.chem.cornell.edu/ > >On Dec 13, 2005, at 9:39 AM, Vlad Cojocaru Vlad.Cojocaru-#-eml- >r.villa-bosch.de wrote: > > > >>Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru=eml-r.villa-bosch.de] >>Dear CCL-ers, >> I have been using in the past babel to create gzmat files from mol2 >>or pdb. However, I noticed that openbabel doesnt support the gzmat >>file >>format anymore ... Is that correct? >> Second, I also noticed that openbabel doesnt convert Gaussian >>output >>anymore as babel used to do ... Is that also correct? >> Although I am not using Gaussian at the moment I am just wondering >>why openbabel doesnt support these file formats? >>Best wishes >>vlad >> >> >>-- >> >> >> Dr. Vlad Cojocaru >> EML Research gGmbH >> Molecular and Cellular Modeling Group >> Villa Bosch >> Schloss-Wolfsbrunnenweg 33 >> 69118 Heidelberg >> Germany >> Phone: +49-6221-533266 >> Fax: +49-6221-533298 >> e-mail: Vlad.Cojocaru.:.eml-r.villa-bosch.de >> >> Additional info: my home page >> > > > > > -- Dr. Vlad Cojocaru EML Research gGmbH Molecular and Cellular Modeling Group Villa Bosch Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Germany Phone: +49-6221-533266 Fax: +49-6221-533298 e-mail: Vlad.Cojocaru/./eml-r.villa-bosch.de Additional info: my home page From owner-chemistry@ccl.net Tue Dec 13 13:52:00 2005 From: "Geoffrey Hutchison grh25(!)cornell.edu" To: CCL Subject: CCL:G: openbabel question Message-Id: <-30311-051213134950-11119-bp19kU4CXFImbhAxlK1Mmw _ server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Tue, 13 Dec 2005 13:49:35 -0500 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Geoffrey Hutchison [grh25+*+cornell.edu] Dear Vlad, I don't know what version of Open Babel you're using if it doesn't list g98 or g03 as input options: [ghutchis~!~Alumina] ghutchis: babel -H | grep Gaussian com -- Gaussian 98/03 Cartesian Input [Write-only] g03 -- Gaussian98/03 Output [Read-only] g98 -- Gaussian98/03 Output [Read-only] gau -- Gaussian 98/03 Cartesian Input [Write-only] Have you checked out the latest version (2.0)? http://openbabel.sourceforge.net/ Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruña Group http://abruna.chem.cornell.edu/ On Dec 13, 2005, at 1:01 PM, Vlad Cojocaru Vlad.Cojocaru=eml-r.villa- bosch.de wrote: > Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru-$-eml-r.villa-bosch.de] > Dear Geoffrey, > > Thanks for the answers to my questions ... I thought that the > Gaussian output is not supported because when I type babel -H into the > terminal, there is no g94, g98 or g03 input fyle type ... So, it was > more like a guess .. I didnt test it. However, if it supports those > files as input, I thought they should be listed by -H option... But, > again at the moment I am not using Gaussian so it was a rather > informative question, not based on encountered problems... > > Best > vlad From owner-chemistry@ccl.net Tue Dec 13 14:26:01 2005 From: "S.I.Gorelsky gorelsky.\a/.stanford.edu" To: CCL Subject: CCL: dual core opteron Message-Id: <-30312-051213135539-19623-3Bgv28Vz/0h018aNY8dyaA\a/server.ccl.net> X-Original-From: "S.I.Gorelsky" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 13 Dec 2005 09:56:36 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "S.I.Gorelsky" [gorelsky*stanford.edu] I do not have any bad experiences with RedHat Fedora Core 4 on dual CPU dual core servers. I am running 64-bit SUSE Linux version 9.3 (2.6.11.4-20a-smp) and 64-bit RedHat Fedora Core 4 Linux (2.6.11-1.1369_FC4smp) on the Opteron-275 CPU server (AMD Opteron 275, 8GB PC3200 RAM with ECC, Tyan S2882G3NR-D motherboard, 80-120GB SATA HD), check http://www.sg-chem.net/cluster for details The OS performance of SuSe and RedHat is almost identical. Serge On Tue, 13 Dec 2005, Gert von Helden helden*|*fhi-berlin.mpg.de wrote: > Sent to CCL by: Gert von Helden [helden---fhi-berlin.mpg.de] > > Same config here (no Linda, however). Works great. Don't try Redhat. On > our Sun V40z boxes (4x dual core), performance with Redhat was > terrible. > From owner-chemistry@ccl.net Tue Dec 13 15:06:01 2005 From: "Hongbing Fu hongbing.f=gmail.com" To: CCL Subject: CCL:G: Freq cal error Message-Id: <-30313-051213114343-380-+GhX4eaWQ3iMthEwCRFPIQ^-^server.ccl.net> X-Original-From: "Hongbing Fu" Sent to CCL by: "Hongbing Fu" [hongbing.f*gmail.com] Hi, I have a problem completing a gaussian98 frequency job. I have a system with ~600 basis functions and the freq job quits with the following message: "Compute integral second derivatives. ... and contract with generalized density number 0. FileIO operation on non-existent file. FileIO: IOper= 2 IFilNo(1)= -690 Len= 1 IPos= 1 Q= 1089289192 dumping /fiocom/, unit = 1 NFiles = 78 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 667585536 FType=2 FMxFil=10000 .... (similar lists as below)... Number 989 993 997 998 Base 788700 791200 791300 23677 End 791200 791300 911304 23727 End1 791200 791300 911304 23727 Wr Pntr 788700 791200 791300 23677 Rd Pntr 788700 791200 791300 23677 dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 65536 FType=2 FMxFil=10000 Number 0 Base 20480 End 65536 End1 65536 Wr Pntr 20480 Rd Pntr 20480 Error termination in NtrErr: NtrErr Called from FileIO." Anyone has any idea about this? Any help will be appreciated. Thank you, From owner-chemistry@ccl.net Tue Dec 13 17:14:00 2005 From: "krishna kiyer25|*|yahoo.com" To: CCL Subject: CCL: [Fwd: irix fortran 77 compiler] Message-Id: <-30314-051213162925-27836-lo3r82maKJwdAR7cCbdPJg^server.ccl.net> X-Original-From: krishna Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 13 Dec 2005 12:29:20 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: krishna [kiyer25]~[yahoo.com] hi all I would like to know is there any free fortran F77 compiler for irix 6.5, I like to compile a program on SGI, but not willing to buy the compiler it is expensive for out of date SGI. really appreciate the help thanks venkat > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam > protection around > http://mail.yahoo.com > > > -- > Computational Chemistry List > Attn. Jan K. Labanowski > Columbus, OH 43221 > http://www.ccl.net > E-mail: chemistry-request__ccl.net or ccl__ccl.net > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Tue Dec 13 17:58:00 2005 From: "Rick Venable rvenable,+,pollux.cber.nih.gov" To: CCL Subject: CCL: [Fwd: irix fortran 77 compiler] Message-Id: <-30315-051213175439-28814-VRt7CYWKD936Sa29ycPsjA---server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 13 Dec 2005 17:53:47 -0500 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable- -pollux.cber.nih.gov] > Sent to CCL by: krishna [kiyer25]~[yahoo.com] > I would like to know is there any free fortran F77 > compiler for irix 6.5, I like to compile a program > on SGI, but not willing to buy the compiler it is > expensive for out of date SGI. The gcc-3.3 package at freeware.sgi.com includes the g77 compiler ------------------------------------- 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 ------------------------------------- From owner-chemistry@ccl.net Tue Dec 13 19:44:01 2005 From: "jle jle _ theworld.com" To: CCL Subject: CCL:G: dual core opteron Message-Id: <-30316-051213194059-875-7gF1RwK0KjnGfBLGYDePHQ###server.ccl.net> X-Original-From: jle Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Tue, 13 Dec 2005 19:39:46 -0500 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: jle [jle[a]theworld.com] On Dec 13, 2005, at 7:53 AM, Marcel Drabbels Marcel.Drabbels-,- epfl.ch wrote: > Sent to CCL by: Marcel Drabbels [Marcel.Drabbels/a\epfl.ch] > We do not succeed running Gaussian on multiple processors on a SUSE > 9.3 > system with kernel 2.6.11.4-21.9-smp. However, colleagues get it to > work on > a SUSE system with kernel 2.6.11.4-21.7-smp. According to Gaussian > there > might be an issue with this newer kernel, but they have not yet > offered a > solution for the problem. A question for the CCL community. Are the software "vendors" (commercial or otherwise) responsible for these kinds of problem or are the users responsible for keeping at or too near the bleeding edge? Given the sheer number of distributions, graphics options, ..., would not the community do better by standardizing on a number of hardware/software configurations which would change relatively slowly? This might let the software providers (especially those lacking big budgets) create more stable code. I know that at least some providers list supported configurations - does anybody pay attention to them? Joe Leonard jle]^[theworld.com > > Marcel > > ==================================================================== > Dr. Marcel Drabbels > Laboratoire de Chimie Physique Moléculaire (LCPM) > École Polytechnique Fédérale de Lausanne (EPFL) > Station 6 > CH-1015 Lausanne > Switzerland > > Tel: +41-21-693 3022/6131 > Fax: +41-21-693 5170 > http://lcpm.epfl.ch/ > ==================================================================== > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > >