From chemistry-request@server.ccl.net Wed Nov 27 04:00:57 2002 Received: from mail-b.bcc.ac.uk ([144.82.100.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAR90ui21958 for ; Wed, 27 Nov 2002 04:00:57 -0500 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Wed, 27 Nov 2002 09:00:56 +0000 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.6+Sun/8.9.3) id gAR90tG00601; Wed, 27 Nov 2002 09:00:55 GMT From: uccatvm Message-Id: <200211270900.gAR90tG00601@socrates-a.ucl.ac.uk> Subject: Re: G98 + Linda Linux Cluster Scheduler To: chemistry@ccl.net (CCL) Date: Wed, 27 Nov 2002 09:00:55 +0000 (GMT) Cc: T.vanMourik@ucl.ac.uk (Tanja van Mourik) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Daniel, I have no experience in running G98 in parallel with Linda, but I encountered the Shmmax Failed problem when running G98 over 2 prcessors with shared memory and when running NWChem in parallel over different nodes, so I assume it is the same problem. The Linux kernel has traditionally fairly small limit for the shared memory segment size (SHMMAX), and this needs to be increased. On my dual Xeon (with 2 Gb memory) I have set it to 0.5 Gig, while on some other 2Gb Xeons in our department it is set to 1Gb. The way to do it permanently is to put (as root) the lines # Increase max shared memory kernel.shmmax=536870912 into /etc/sysctl.conf before rebooting. The temporary solution is echo 536870912 > /proc/sys/kernel/shmmax Hope this helps, Tanja -- ===================================================================== Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik@ucl.ac.uk London WC1H 0AJ, UK home: tanja_van_mourik@btopenworld.com http://www.chem.ucl.ac.uk/people/vanmourik/index.html ===================================================================== From chemistry-request@server.ccl.net Wed Nov 27 04:10:26 2002 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAR9APi22837 for ; Wed, 27 Nov 2002 04:10:25 -0500 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr@ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id KAA25013 for ; Wed, 27 Nov 2002 10:09:51 +0100 Received: (qmail 1703 invoked by uid 525); 27 Nov 2002 09:09:51 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 27 Nov 2002 09:09:51 -0000 Date: Wed, 27 Nov 2002 10:09:51 +0100 (CET) From: To: chemistry@ccl.net Subject: Ki database Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Could anyone suggest me free Ki (inhibition constant) databases on the net? Thanks for any reply. Best wishes, Csaba ------ Csaba Hetenyi, MSc, PhD Dept. of Medical Chemistry, University of Szeged, 8 Dom ter, Szeged 6720, Hungary From chemistry-request@server.ccl.net Wed Nov 27 04:14:50 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAR9Eni23253 for ; Wed, 27 Nov 2002 04:14:49 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18GyCy-00022w-00; Wed, 27 Nov 2002 09:10:12 +0000 Date: Wed, 27 Nov 2002 09:10:12 +0000 (GMT) From: Szilveszter Juhos To: Reinaldo Pis Diez cc: chemistry@ccl.net Subject: Re: CCL:Tools for administrating a linux cluster In-Reply-To: <5.1.0.14.2.20021126143333.00a10cb0@dalton.quimica.unlp.edu.ar> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 26 Nov 2002, Reinaldo Pis Diez wrote: > I'd like to hear your opinions on the current tools you're > using to administrate a (heterogeneous) linux cluster. I have no any confidence in pre-written tools (sorry) but even using them a thing you will need for Linux is the Bash guide: http://www.tldp.org/LDP/abs/html/index.html Szilva From chemistry-request@server.ccl.net Wed Nov 27 05:20:54 2002 Received: from anor.ics.muni.cz ([147.251.4.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gARAKri27919 for ; Wed, 27 Nov 2002 05:20:53 -0500 Received: from bilbo.chemi.muni.cz (bilbo.chemi.muni.cz [147.251.28.2]) by anor.ics.muni.cz (8.12.1/8.12.1) with ESMTP id gARAKrRF027293 for ; Wed, 27 Nov 2002 11:20:53 +0100 Received: from ncbr.chemi.muni.cz (ncbr.chemi.muni.cz [147.251.28.55]) by bilbo.chemi.muni.cz (8.9.3/8.8.5) with ESMTP id LAA15239 for ; Wed, 27 Nov 2002 11:20:53 +0100 (MET) Received: from ncbr.chemi.muni.cz (ncbr.chemi.muni.cz [147.251.28.55]) by ncbr.chemi.muni.cz (8.11.3nb1/8.10.1) with ESMTP id gARAKqJ11389 for ; Wed, 27 Nov 2002 11:20:52 +0100 (MET) Date: Wed, 27 Nov 2002 11:20:52 +0100 (MET) From: Jana Precechtelova To: "CCL.NET" Subject: CCL:g98-optimizing more variables to the same final value Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Muni-Virus-Test: Clean Dear CCL users, I want to perform a geometry optimization in which several couples of dihedral angles have the same starting value and I`d like to let these couples optimize so that both dihedral angles within each couple can have the same value at the end of the optimization. How can I achieve such a course of optimization? Best regards, Jana Precechtelova ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jana Precechtelova (MSc. student) NMR Laboratory National Centre for Biomolecular Research (NCBR) Faculty of Science, Masaryk University Kotlarska 2, 611 37 Brno, Czech Republic email: janap@ncbr.chemi.muni.cz phone: +420-5-41129588 fax: +420-5-411 29 506 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Nov 27 06:02:59 2002 Received: from piimsdm11.univ-mrs.fr ([194.57.196.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gARB2wi30809 for ; Wed, 27 Nov 2002 06:02:58 -0500 Received: from mf242u09 (piimsdm19.univ-mrs.fr [194.57.196.109]) by piimsdm11.univ-mrs.fr (8.9.3/jtpda-5.3.3) with SMTP id MAA00980 for ; Wed, 27 Nov 2002 12:03:07 +0100 (MET) Message-ID: <001101c29604$be5b8660$011811ac@u3mrs.fr> From: "olivier Maresca" To: Subject: ONIOM and multiplicity Date: Wed, 27 Nov 2002 12:03:53 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000E_01C2960D.0E044FA0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_000E_01C2960D.0E044FA0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi , we are performing ONIOM (b3LYP:UFF) calculations on graphite compounds. The low and the high level have not the same multiplicity and = consequently the computation stops. The problem arises from the UFF. Does anybody know how to : wether specify two different multiplicities for the two levels or = suppress the multiplicity test in the molecular mechanics computation. Best Regards Olivier ------=_NextPart_000_000E_01C2960D.0E044FA0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi ,
we are performing ONIOM (b3LYP:UFF) = calculations=20 on
graphite compounds.
The low and the high level have not the = same=20 multiplicity and consequently the computation stops.
The problem arises from the UFF. Does=20 anybody know how to :
wether specify two different = multiplicities for the=20 two levels or suppress the multiplicity test in the molecular mechanics=20 computation.
 
Best Regards
 
Olivier
 
------=_NextPart_000_000E_01C2960D.0E044FA0-- From chemistry-request@server.ccl.net Tue Nov 26 23:09:32 2002 Received: from mail531.nifty.com ([202.248.37.220]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAR49Vi02484 for ; Tue, 26 Nov 2002 23:09:31 -0500 Received: from TP-R32.mb.infoweb.ne.jp by mail531.nifty.com (8.12.6/3.7W-07/15/02) with ESMTP id gAR46ExD005499; Wed, 27 Nov 2002 13:06:17 +0900 Message-Id: <5.0.2.7.2.20021127125704.00e6a2d0@pop.nifty.com> X-Sender: fwip5390@pop.nifty.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.0.2-Jr2 Date: Wed, 27 Nov 2002 13:05:19 +0900 To: , From: Aaron Subject: Re: CCL:G98 + Linda Linux Cluster problem In-Reply-To: <32909.148.223.46.28.1038367552.squirrel@www3.cimav.edu.mx> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi, I think you have to check the size of shmmax for the kernel. By default, the size of shmmax is quite small. You should take a look "/proc/sys/kernel/shmmax". You can change it like this, echo 1073741824 > /proc/sys/kernel/shmmax "1073741824" means 1GB for the maximum size of shared memory. Regards, At 20:25 02/11/26 -0700, daniel.glossman@cimav.edu.mx wrote: >Dear Netters: > >Following with my last question about G98+Linda on Linux Clusters, >I have made some progress: Linda was installed and the paralell >version has been built. Now I have g98l command to run jobs in >paralell. When I tried g98l with a simple job, with 1 proccesor, >the job ran fine. when I tried with more that 1 processor, the >run stops with the following error: > >After Link 1: > >shmget failed >shmget failed - invalid argument > > >Any idea of what can be happening? > >Thanks in advance > > Dr. Daniel Glossman-Mitnik > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net