From chemistry-request@server.ccl.net Sat Nov 9 01:30:02 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA96U1Q26251 for ; Sat, 9 Nov 2002 01:30:01 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id E37EB91B7; Sat, 9 Nov 2002 07:30:00 +0100 (CET) To: chemistry@ccl.net Subject: gaussian98 compilation SGI r4400 Message-ID: <1036823400.3dccab68d77f5@webmail.u-picardie.fr> Date: Sat, 09 Nov 2002 07:30:00 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, I compiled g98 without problems on SGI r12000, r10000 and r5000 (IRIX 6.5.15). Then, I tried to compile g98 on r4400 and I got an error message relation to the -lscs library : 'error -lscs no found' I checked these scientific libraries, they are in the /usr/lib32/mips3 directory as in the r5000 machine. Why these library are found on the r5000 and not found on the r4400 by g98 ? Did someone was able to compile g98 on SGI r4400 ? Thanks, Kind regards, Francois From chemistry-request@server.ccl.net Sat Nov 9 02:33:51 2002 Received: from mail.staff.site.ntu.edu.au ([138.80.69.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA97XoQ27191 for ; Sat, 9 Nov 2002 02:33:51 -0500 Received: from mail.staff.site.ntu.edu.au ([138.80.49.20]) by mail.staff.site.ntu.edu.au with Microsoft SMTPSVC(5.0.2195.5329); Sat, 9 Nov 2002 17:03:40 +0930 Received: by mail.staff.site.ntu.edu.au (sSMTP sendmail emulation); Sat, 9 Nov 2002 17:02:34 +0930 Date: Sat, 9 Nov 2002 17:02:34 +0930 From: Brian Salter-Duke To: Comp Chem List Subject: Queueing systems for Comp Chem Message-ID: <20021109073234.GA4931@bsalterduke1> Mail-Followup-To: Comp Chem List Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i X-OriginalArrivalTime: 09 Nov 2002 07:33:40.0923 (UTC) FILETIME=[5335B8B0:01C287C2] For years, I and other quantum chemists, plus probably all computational chemists, have been using one of the queueing systems to submit jobs to run in an orderly fashion on our machines. I have used NQS for example. These systems seem to be losing support. I have had NQS not compiling on one system and earlier this year it looked as if the guy who supports it had dropped off the planet. I have not checked more recently. These systems are also large and contain many features we do not use. So earlier this year I started to write my own queueing system. I call it SQS - Simple Queueing System. It has developed considerably and the latest version - 2.2 - is now on SourceForge - http://sqs.sourceforge.net for details on my web pages. It can be downloaded from the project page - https://sourceforge.net/projects/sqs/ It runs jobs on a single machine, although this of course can be the master host for a job that is shared over other processors. The job submitted handles that. It allows more than one queue. Jobs submitted to the queue can be listed (like qstat in NQS), deleted, even if running, held or released. Non-running jobs can be moved from one queue to another. The system works by a set of queue files that are globally readable and writable, and a daemon, called qseek, which each user runs. qseek is started automatically, if not running, when jobs are submitted to the queue or held jobs are released. The user rarely has to start it manually, although routines are available to start and stop qseek. The whole is a set of about a dozen perl scripts, none of which, apart from the install script, is longer than 130 lines of perl. It does not allow the setting of priorities on jobs in the queue, although the next release to sourceforge will. It does not allow jobs to be submitted to run on remote machines, although this is being considered. The install script is also in perl and has just grown with the system. I have written man pages for all the scripts and there are web pages avaqilable on sourceforge. Please give it a go. My programming skills are not brilliant and I am sure the code can be improved. It may of course also contain bugs. It is sometimes difficult to find bugs that arise only in ways you yourself do not use the system and subconsciously one can run code in a way that does not cover all options. It would be nice to have a small team working to improve this system. SQS is released under the GNU GPL. Regards, Brian. -- Brian Salter-Duke (Brian Duke) b_duke@octa4.net.au Honorary Fellow in Chemistry, NT University, Darwin, NT 0909, Australia. Post: Box 1028, Humpty Doo, NT 0836, Australia. Phone 08-89881600. Fax 08-89881302. http://www.octa4.net.au/linden/brian/ From chemistry-request@server.ccl.net Sat Nov 9 00:54:07 2002 Received: from sccrmhc01.attbi.com ([204.127.202.61]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA95s7Q25829; Sat, 9 Nov 2002 00:54:07 -0500 Received: from daveg-lifebook.cachesoftware.com ([12.224.252.136]) by sccrmhc01.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20021109055407.ZYMR25908.sccrmhc01.attbi.com@daveg-lifebook.cachesoftware.com>; Sat, 9 Nov 2002 05:54:07 +0000 Message-Id: <5.1.0.14.0.20021108121415.02421650@pop3.norton.antivirus> X-Sender: (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 08 Nov 2002 12:24:17 -0800 To: chemistry@ccl.net From: David Gallagher Subject: CAChe & MOPAC New Release Cc: chemistry-request@ccl.net Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_958003==_.ALT" --=====================_958003==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed The CAChe Group of Fujitsu is pleased to announce a new Windows release of CAChe and BioMedCAChe, version 5.04. This Windows release has many important enhancements including those listed below. CAChe 5.04 Enhancements: 1. An enhanced PDB filter now saves all essential PDB data in the file 2. New "rubber-bonding" and "snap-to-atoms" making drawing easier 3. New Tool-tips and Fly-By menus make learning CAChe faster 4. Faster Workspace operations speed selection and viewing 5. New Right-click Cursor Menu in WorkSpace adds convenience 6. Several new WorkSpace View commands make editing and viewing easier 7. New Transition metals in MOPAC PM5, AM1 and PM3 include: Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Zr, Mo, Pd, Ag, and Pt 8. MOPAC PM5 has parameters for ALL main group elements (except Po, At, Fr, Pa, and inert gases) 9. Linear scaling MOPAC-COSMO for solvated proteins, etc. up to 20,000 atoms. 10. Faster computation using less memory for frontier orbitals of large molecules 11. MOPAC displays changing partial charges and bond orders on maps and reaction paths 12. Many tweaks and bug-fixes in Workspace and MOPAC improve reliability. For further information please contact Sales@CACheSoftware.com or visit www.CACheSoftware.com The CAChe Group Team --=====================_958003==_.ALT Content-Type: text/html; charset="us-ascii" The CAChe Group of Fujitsu is pleased to announce a new Windows release of CAChe and BioMedCAChe, version 5.04. This Windows release has many important enhancements including those listed below.

CAChe 5.04 Enhancements:
1.  An enhanced PDB filter now saves all essential PDB data in the file
2.  New "rubber-bonding" and "snap-to-atoms" making drawing easier
3.  New Tool-tips and Fly-By menus make learning CAChe faster
4.  Faster Workspace operations speed selection and viewing
5.  New Right-click Cursor Menu in WorkSpace adds convenience
6.  Several new WorkSpace View commands make editing and viewing easier
7.  New Transition metals in MOPAC PM5, AM1 and PM3 include:
            Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Zr, Mo, Pd, Ag, and Pt
8.  MOPAC PM5 has parameters for ALL main group elements
            (except Po, At, Fr, Pa, and inert gases)
9.  Linear scaling MOPAC-COSMO for solvated proteins, etc. up to 20,000 atoms.
10. Faster computation using less memory for frontier orbitals of large molecules
11. MOPAC displays changing partial charges and bond orders on maps and reaction paths
12. Many tweaks and bug-fixes in Workspace and MOPAC improve reliability.

For further information please contact Sales@CACheSoftware.com or visit www.CACheSoftware.com

The CAChe Group Team

--=====================_958003==_.ALT-- From chemistry-request@server.ccl.net Fri Nov 8 17:20:56 2002 Received: from chimail.cambridgehealth.com ([140.239.39.194]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA8MKtQ14144 for ; Fri, 8 Nov 2002 17:20:55 -0500 Received: from [140.239.39.147] by chimail.healthtech.com (NTMail 7.02.3032/XR3768.00.9f28be90) with ESMTP id owsmcaaa for chemistry@ccl.net; Fri, 8 Nov 2002 17:24:42 +0000 Message-Id: <4.1.20021108171912.00c9de80@140.239.39.194> X-Sender: eoregan@140.239.39.194 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Fri, 08 Nov 2002 17:21:31 -0500 To: chemistry@ccl.net From: "Edel O'Regan" Subject: Library Design and Organic Synthesis meeting Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_28848932==_.ALT" --=====================_28848932==_.ALT Content-Type: text/plain; charset="us-ascii" CHI will host The Library Design and Organic Synthesis meeting in La Jolla on Feb. 24-27, 2003. For more details go to http://www.healthtech.com/2003/lds/index.htm Edel O'Regan --=====================_28848932==_.ALT Content-Type: text/html; charset="us-ascii" CHI will host The Library Design and Organic Synthesis meeting in La Jolla on Feb. 24-27, 2003.

For more details go to http://www.healthtech.com/2003/lds/index.htm

Edel O'Regan
--=====================_28848932==_.ALT-- From chemistry-request@server.ccl.net Fri Nov 8 19:12:22 2002 Received: from zone.nchc.gov.tw ([140.110.60.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA90CKQ16760 for ; Fri, 8 Nov 2002 19:12:21 -0500 Received: from nchc.gov.tw (pavo028.nchc.gov.tw [140.110.60.92]) by zone.nchc.gov.tw (8.11.6+Sun/8.11.6) with ESMTP id gA90CEH06517 for ; Sat, 9 Nov 2002 08:12:14 +0800 (CST) Message-ID: <3DCC52DC.7D027863@nchc.gov.tw> Date: Sat, 09 Nov 2002 08:12:12 +0800 From: Jyh-Shyong Ho X-Mailer: Mozilla 4.75 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Gaussian 98 parallel jobs on RedHat 8.0 clusters Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit Dear colleagues, Has anyone installed and run parallel Gaussian 98 jobs successfully on Linux clusters running RedHat8.0? Parallel Gaussiam 98 jobs ran well on my Linux cluster with RedHat 7.3, both on single node with dual AMD MP processors (nproc=2) and on more than two nodes. However, after upgrade the OS to RedHat8.0 and PGI 4.0, parallel jobs with nproc=2 spwans two processes but only one of them is actually running, parallel job nproclinda=2 only spwans a process on the master node, the slave node has an idle l302.exel process and eventually the job fails. Any suggestion on how to fix this problem will be appreciated. Best Regards Jyh-Shyong Ho, PhD. Research Scientist National Center for High-Performacne Computing Hsinchu, Taiwan, ROC From chemistry-request@server.ccl.net Sat Nov 9 06:32:12 2002 Received: from suncom.rz.hu-berlin.de ([141.20.1.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA9BWCQ31130 for ; Sat, 9 Nov 2002 06:32:12 -0500 Received: from impact1.chemie.hu-berlin.de (impact1.chemie.hu-berlin.de [141.20.72.25]) by suncom.rz.hu-berlin.de (8.9.3/8.9.3) with ESMTP id MAA09302 for ; Sat, 9 Nov 2002 12:32:08 +0100 (MET) Received: (from ah@localhost) by impact1.chemie.hu-berlin.de (SGI-8.9.3/8.9.3) id MAA96826 for chemistry@ccl.net; Sat, 9 Nov 2002 12:32:07 +0100 (MEZ) Date: Sat, 9 Nov 2002 12:32:07 +0100 From: "Dr. Alexander Hofmann" To: "chemistry@ccl.net" Subject: G98/Linux and huge files Message-ID: <20021109123207.A395325@chemie.hu-berlin.de> Reply-To: ah@chemie.hu-berlin.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i Hello, are there possibilities to circumvent the 2 GB limit with Gaussian 98 under Linux (Suse 8.0 2.4.x Kernel). I know the rwf-splitting. My aim is to write really huge files (like 100 GB or so). Thanks Alex -- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Brook-Taylor-Strasse 2 12489 Berlin ah@chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35