From chemistry-request@server.ccl.net Wed Oct 3 03:58:24 2001 Received: from mr3.cc.ic.ac.uk ([155.198.5.113]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f937wOB08638 for ; Wed, 3 Oct 2001 03:58:24 -0400 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by mr3.cc.ic.ac.uk with esmtp (Exim 3.31 #1) id 15ogv9-00089y-00; Wed, 03 Oct 2001 08:58:23 +0100 Received: from hbtower.ch.ic.ac.uk ([155.198.226.132] helo=argon.ch.ic.ac.uk) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 15ogvP-008IQ6-00; Wed, 3 Oct 2001 08:58:39 +0100 Sender: krzys@ic.ac.uk Message-ID: <3BBAC4F5.81D00962@argon.ch.ic.ac.uk> Date: Wed, 03 Oct 2001 08:57:41 +0100 From: Krzysztof Radacki Reply-To: k.radacki@ic.ac.uk Organization: Imperial College X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.4.2-2smp i686) X-Accept-Language: en MIME-Version: 1.0 To: Gerardo Andres Cisneros , CHEMISTRY@ccl.net Subject: Re: CCL:parallel g98 on AMD? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, it looks so that your computer does not see shared memmory in ammount you requested with %MEM. Have you tried to calculate some small job like H2 with %MEM=10MB %PROC=2? If it complete successfully nearly sure that that the reason and you should add to your system-starting scripts some were how much memory should be shared. In case of RedHat I sugesst to add as last line in /etc/rc.d/rc.local f.e for 1Gb computer echo 955306300 > /proc/sys/kernel/shmmax It should solve your problem. MfG K.Radacki Gerardo Andres Cisneros wrote: > > Hello > > I've managed to compile and run g98 on an AMD platform using the blas > libraries for intel (recomended by gaussian). However this machine is > dual processor but every time I try to run the same job in parallel I get > the following error message: > > %g98 tim0_2pAMD > shmget failed.: Invalid argument > > I have no problem running this job using a single processor. > > I haven't installed Linda on this machine but since it's dual processor I > don't see the need for it, or should I?. > > Thanks in advance, > > Andres > > -- > G. Andres Cisneros > Department of Chemistry > Duke University > andres@chem.duke.edu From chemistry-request@server.ccl.net Wed Oct 3 07:20:54 2001 Received: from cns.FTA-Berlin.de ([141.16.244.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93BKrB12767 for ; Wed, 3 Oct 2001 07:20:53 -0400 Received: from langmuir.aca-berlin.de (langmuir.ACA-Berlin.de [141.16.16.120]) by cns.FTA-Berlin.de (8.11.3/8.11.0/SuSE Linux 8.11.0-0.4) with ESMTP id f93BKok22610; Wed, 3 Oct 2001 13:20:50 +0200 Date: Wed, 3 Oct 2001 13:26:52 +0200 (MEST) From: Alexander Hofmann To: William Wei cc: chemistry@ccl.net Subject: Re: CCL:Help for ssh! In-Reply-To: <3BBA1A4D.134247AE@phm.utoronto.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi William, look at SGI's webpage ftp://freeware.sgi.com/index-by-alpha.html for precompiled versions of openssh and openssl, or use the IRIX Freeware 6.5 CD of your IRIX distribution (recommended due to security problems only, if you've got maintenance). Yours Alex --- Dr. Alexander Hofmann Institute for Applied Chemistry Berlin-Adlershof P.O. Box 96 11 56 Richard-Willstaetter-Str. 12 D-12474 Berlin D-12489 Berlin hofmann@aca-berlin.de Tel.: +49-30-6392-4408 Fax.: +49-30-6392-4350 http://www.aca-berlin.de From chemistry-request@server.ccl.net Wed Oct 3 08:54:50 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93CsoB14741 for ; Wed, 3 Oct 2001 08:54:50 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id IAA09271; Wed, 3 Oct 2001 08:54:48 -0400 (EDT) Date: Wed, 3 Oct 2001 08:54:47 -0400 (EDT) From: Jan Labanowski To: William Wei cc: chemistry@ccl.net Subject: Re: Help for ssh! In-Reply-To: <3BBA1A4D.134247AE@phm.utoronto.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On the CCL Web site there are my notes on installation of Web servers and servlets/JSP stuff in http://www.ccl.net/cca/software/UNIX/apache/ Among them, there are my notes on installing Apache on IRIX. In the IRIX notes, there is a blurb on ssh installation on IRIX. You can have a look at these. Note that the notes are a few months old, i.e., obsolete. But the principles hopefully still apply. Jan Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ On Tue, 2 Oct 2001, William Wei wrote: > Hi, Dear CClers, > > I want a free software of ssh server code for IRIX6.5 in SGI octane > workstation. I have download openssh and ossh, but they all can not be > compiled successfully in my machine. Any help is appreciated. Thanks. > > William. > From chemistry-request@server.ccl.net Wed Oct 3 07:09:55 2001 Received: from ccusv5.unical.it ([160.97.7.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93B9rB12587 for ; Wed, 3 Oct 2001 07:09:54 -0400 Received: from giorgio (chpcrs5.chimica.unical.it [160.97.42.131]) by ccusv5.unical.it (8.11.5/8.11.5) with SMTP id f93BEGb08564 for ; Wed, 3 Oct 2001 13:14:17 +0200 Message-ID: <00f801c14bfc$675bdd40$832a61a0@chimica.unical.it> From: "Giorgio De Luca" To: Subject: kernel 2.2 linux Date: Wed, 3 Oct 2001 13:13:17 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00F5_01C14C0D.2A6F2F20" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_00F5_01C14C0D.2A6F2F20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CCLers, I have a pentium III dual processors with linux 6.2 and kernel = 2.2.15-3SGI_32 smp-bigmen. With this system some gaussian98 input tests, like test338.com, give = this kind of error: Initial convergence to 1.0D-05 achieved. Increase integral accuracy. Warning! Spurious integrated density: NE=3D 42 NElCor=3D 0 Integral=3D 54.99274 Tolerance=3D1.00D-03 Consistency failure #2 in CalDSu. Error termination via Lnk1e in /home/gaussian/g98/l502.exe. Job cpu time: 0 days 0 hours 2 minutes 47.5 seconds. File lengths (MBytes): RWF=3D 36 Int=3D 0 D2E=3D 0 Chk=3D 2 = Scr=3D I have some informations that point out the kernel version as the = problem. Do you have experience to confirm this conclusion or not ? Thank you in advance. G. De luca. ps. I try several different optmization flags, but I don't obtain = results. ------=_NextPart_000_00F5_01C14C0D.2A6F2F20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi CCLers,
I have a pentium III dual = processors with=20 linux 6.2 and kernel 2.2.15-3SGI_32 smp-bigmen.
With this system some gaussian98 input = tests, like=20 test338.com, give this kind of error:
 
Initial convergence to 1.0D-05 = achieved. =20 Increase integral accuracy.
Warning!  Spurious integrated=20 density:
NE=3D   42 NElCor=3D    0 = Integral=3D  =20 54.99274 Tolerance=3D1.00D-03
Consistency failure #2 in = CalDSu.
Error=20 termination via Lnk1e in /home/gaussian/g98/l502.exe.
Job cpu = time:  0=20 days  0 hours  2 minutes 47.5 seconds.
File lengths = (MBytes): =20 RWF=3D   36 Int=3D    0 = D2E=3D    0=20 Chk=3D    2 Scr=3D
 
I have some informations that point out = the kernel=20 version as the problem.
Do you have experience to confirm this = conclusion=20 or not ?
Thank you in advance.
G. De luca.
 
 
ps. I try several different = optmization=20 flags, but I don't obtain results.
 
------=_NextPart_000_00F5_01C14C0D.2A6F2F20-- From chemistry-request@server.ccl.net Wed Oct 3 03:53:20 2001 Received: from iqe1.ethz.ch ([129.132.22.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f937rJB08555 for ; Wed, 3 Oct 2001 03:53:19 -0400 Received: from [129.132.22.89] (nlot89.ethz.ch [129.132.22.89]) by iqe1.ethz.ch (8.9.3/8.9.3) with ESMTP id JAA25529 for ; Wed, 3 Oct 2001 09:53:18 +0200 (MET DST) Mime-Version: 1.0 X-Sender: arashid@iqe1.ethz.ch (Unverified) Message-Id: Date: Wed, 3 Oct 2001 09:54:28 +0200 To: chemistry@ccl.net From: Ali Rashid Subject: Linear dichroism. Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hi, I was wandering if anyone knows of a way to simulate the absorption spectra of a system. What i am interested in is, starting > from a model of a molecules or molecules packed in a certain way, can i then calculate things like the dichroic ratio and the linear dichroism? Thank you in advance. -- ----------------------------------------------------------------------------- Dr. Ali N. Rashid arashid@iqe.phys.ethz.ch Nonlinear Optics Laboratory phone +41 1 6336953 Institute of Quantum Electronics fax +41 1 6331056 Swiss Federal Institute of Technology ETH-Honggerberg, CH-8093 Zurich, Switzerland From chemistry-request@server.ccl.net Wed Oct 3 10:02:30 2001 Received: from qtp.ufl.edu ([128.227.89.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93E2UB16994 for ; Wed, 3 Oct 2001 10:02:30 -0400 Received: from qtp.ufl.edu (dcream1 [192.168.5.129]) by qtp.ufl.edu (8.9.1a/8.9.1) with ESMTP id KAA05217 for ; Wed, 3 Oct 2001 10:02:54 -0400 (EDT) Message-ID: <3BBB1AAC.C2623F76@qtp.ufl.edu> Date: Wed, 03 Oct 2001 10:03:24 -0400 From: "Adrian E. Roitberg" X-Mailer: Mozilla 4.51 [en]C-CCK-MCD EBM-Compaq (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Call for papers, Enhanced sampling techniques Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit From: Carlos Simmerling and Adrian E. Roitberg "Enhanced Sampling Methods for Molecular Dynamics and Monte Carlo Simulations" A CALL FOR PAPERS 2002 Spring National ACS Meeting (April 7-11) !!! COMP Division ***** SUBMISSION DEADLINE: November 12, 2001 ***** The symposium "Enhanced Sampling Methods for Molecular Dynamics and Monte Carlo Simulations" will be held as part of the COMP division program at the 2002 Spring National ACS Meeting (April 7-11, 2002) in Orlando, FL. Advances in the areas of Monte Carlo and Molecular Dynamics permit the study of structures, their energetics and transitions between them on an almost routine basis. However, with energy barriers of several kcal/mol separating energy minima, the cost in computer time required to sample phase space in an appropiate way using traditional MC or MD is prohibitive. Hence, one must think of methods that "enhance" sampling, meaning improving this exploration of phase space. Some of these methods are approximate, while other solve exact equations of motions in more clever or efficient manner. This symposium will focus on both types of approaches. Some examples of relevent areas are Multiple Time Step approaches, Generalized Ensemble Simulations (e.g. Multicanonical Methods), Locally Enhanced Sampling, Replica Exchange, etc. We are asking for papers in any of these areas; they can describe development and testing of novel methods or application of these approaches to systems of interest. The on-line system at http://oasys.acs.org should be used to submit abstracts of suitable papers. Go to the COMP section for a complete list of symposia offered in Orlando. **** NOTE: THE SUBMISSION DEADLINE IS NOVEMBER 12, 2002 **** Please distribute this information to other researchers in industry, academia, and national labs. Thank you for your consideration. Dr Adrian E. Roitberg Dr. Carlos L. Simmerling Quantum Theory Project Department of Chemistry University of Florida SUNY at Stony Brook P.O.Box 118435 Stony Brook, NY 11794-3400 Gainesville, FL Web: http://comp.chem.stonybrook.edu/carlos Tel: (352) 392-6972 Tel: (631) 632-1336 Fax: (352) 392-8722 Fax: (631) 632-1555 Email: adrian@qtp.ufl.edu Email: carlos.simmerling@stonybrook.edu -- Dr. Adrian E. Roitberg Quantum Theory Project and Department of Chemistry University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email roitberg@qtp.ufl.edu ==================================================================== From chemistry-request@server.ccl.net Wed Oct 3 13:37:07 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93Hb7B23241 for ; Wed, 3 Oct 2001 13:37:07 -0400 Received: from trentu.ca ([204.225.12.60]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K92E5MRF3A0009N7@trentu.ca> for chemistry@ccl.net; Wed, 3 Oct 2001 13:34:48 EDT Date: Wed, 03 Oct 2001 13:35:52 -0400 From: elewars Subject: charges on a sphere; theorem? To: chemistry@ccl.net Message-id: <3BBB4C78.814B59FB@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2001 Oct 3 Hello, A colleague pose this question. Suppose you have two like point charges (e.g. two protons, considered dimensionless), which must be on or inside a sphere. The minimum energy geometry (MEG) is that they be on the surface, at the ends of a diameter of the sphere. For three charges, the MEG is on the surface, at the corners of an equilateral triangle. And so on for 4, 5, ...? charges, the MEG having all of them on the surface. Question: is there a number or numbers _n_ of charges for which migration of one or more charges _into_ the sphere would lower the energy? Is there some theorem in math or physics that deals with this? Thanks E. Lewars ============= From chemistry-request@server.ccl.net Wed Oct 3 18:37:38 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93MbUB28074 for ; Wed, 3 Oct 2001 18:37:38 -0400 Received: from Laurence.mbi.ucla.edu (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id f93MbTr01643 for ; Wed, 3 Oct 2001 15:37:29 -0700 (PDT) Message-Id: <5.1.0.14.2.20011003153246.03c8a530@127.0.0.1> X-Sender: lavelle/mbi.ucla.edu@127.0.0.1 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 03 Oct 2001 15:40:34 -0700 To: CCL From: Laurence Lavelle Subject: Average DNA-Protein binding (free) energy Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed I am looking for a (review ?) paper discussing DNA-protein binding energies. That is, experimental and calculated average delta G values (per DNA base pair) for: DNA + Protein <-----> DNA-Protein Comments and/or literature pointers. Appreciated. Laurence Lavelle From chemistry-request@server.ccl.net Wed Oct 3 23:20:29 2001 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f943KTB05228 for ; Wed, 3 Oct 2001 23:20:29 -0400 Received: from unix5.uvic.ca (unix5.uvic.ca [142.104.5.117]) by cascara.uvic.ca (8.11.3/8.11.3) with ESMTP id f943KSL135304; Wed, 3 Oct 2001 20:20:28 -0700 Date: Wed, 3 Oct 2001 20:20:28 -0700 (PDT) From: Roy Jensen To: Subject: Bond strength... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII All I am struggling to understand how bond strength is envisioned and how it can be extracted from an ab initio calculation. Bond strength is commonly discussed in terms of orbital overlap but I have not been able to find any quantitative explanations. An NBO analysis produces two-center orbitals, energies thereof, and the relative contribution from atomic orbitals. Can the two-center bond strength be extracted from this information? Thanks, Roy Jensen From chemistry-request@server.ccl.net Wed Oct 3 12:47:37 2001 Received: from ccmsi.jsums.edu ([143.132.103.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93GlbB22023 for ; Wed, 3 Oct 2001 12:47:37 -0400 Received: from ccmsi.jsums.edu [10.30.3.44] by ccmsi.jsums.edu with ESMTP (SMTPD32-7.04) id A12969C01BE; Wed, 03 Oct 2001 11:47:37 -0500 Message-ID: <3BBB4129.98B7726A@ccmsi.jsums.edu> Date: Wed, 03 Oct 2001 11:47:37 -0500 From: "Dr. Giju Thomas Kalathingal" Organization: Jackson State University X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: memory requirement with correlation consistent basis sets Content-Type: multipart/mixed; boundary="------------868A44FD04C655FA2226842A" This is a multi-part message in MIME format. --------------868A44FD04C655FA2226842A Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Could you please give me some info on the memory required for the geometry optimization and analytical frequency calculations using correlation consistent basis sets like cc-pVXZ, aug-ccpVXZ, etc.(X=2-6)? Thanks in advance. Giju Kalathingal --------------868A44FD04C655FA2226842A Content-Type: text/x-vcard; charset=us-ascii; name="giju.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Dr. Giju Thomas Kalathingal Content-Disposition: attachment; filename="giju.vcf" begin:vcard n:; tel;fax:++1-601-979-7823 tel;home:++1-601-979-2749 tel;work:++1-601-979-7824 x-mozilla-html:FALSE url:http://dogstar.duch.udel.edu/gijukt/welcome.html org:;Department of Chemistry version:2.1 email;internet:giju@ccmsi.jsums.edu adr;quoted-printable:;;Jackson State University=0D=0AP.O.Box 17910=0D=0A;Jackson, MS - 39217;;;USA fn:Dr. Giju T. Kalathingal end:vcard --------------868A44FD04C655FA2226842A-- From chemistry-request@server.ccl.net Wed Oct 3 11:43:52 2001 Received: from comm1.umaryland.edu ([134.192.1.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93FhpB20391 for ; Wed, 3 Oct 2001 11:43:51 -0400 Received: from winslow.umaryland.edu (winslow.umaryland.edu [134.192.72.40]) by comm1.umaryland.edu (8.9.3/8.9.3) with ESMTP id LAA04729 for ; Wed, 3 Oct 2001 11:43:50 -0400 (EDT) Received: (from strahan@localhost) by winslow.umaryland.edu (8.9.3/8.9.3) id LAA07138 for chemistry@ccl.net; Wed, 3 Oct 2001 11:49:05 -0400 (EDT) Date: Wed, 3 Oct 2001 11:49:03 -0400 From: Gary To: chemistry@ccl.net Subject: Re: CCL:Help for ssh! Message-ID: <20011003114903.B7079@winslow.umaryland.edu> References: <3BBA1A4D.134247AE@phm.utoronto.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: ; from jkl@ccl.net on Wed, Oct 03, 2001 at 08:54:47AM -0400 The IRIX compiler does have some well-documented quirks which cause problems with some versions of ssh. Some combinations of IRIX- and ssh-versions are easier to compile than others. In fact, sometimes even the older gcc compiler on IRIX works best... but not always. As I recall, the IRIX gcc does not work well with the commercial version of ssh-3.0. There are many excellent resources concerning SSH located on the web. One of the better places to start is: http://www.freessh.org/ . To actually get advice or to announce a bug, then one should sign up for the mailing list... it is a very active list, so don't expect to keep your mailbox empty. As always, be sure that you have read read the FAQs before posting questions. Here is an abridged list of sites: FAQs: http://www.employees.org/~satch/ssh/faq/ssh-faq.html http://www.tigerlair.com/ssh/faq/ List Archives: http://www.cs.hut.fi/ssh-archive/ http://www.securityfocus.com/archive/121 To subscribe send an empty e-mail from you present account to secureshell-subscribe@securityfocus.com -''- Or, if you want to subscribe some other address, then send an e-mail to: secureshell-unsubscribe-address=example.com@securityfocus.com - where = stands for @. Likewise, to unsubscribe, send an e-mail to secureshell-unsubscribe@securityfocus.com -''- Or, for a different address, then send an e-mail to secureshell-unsubscribe-address=example.com@securityfocus.com - where = stands for @. SSH works well with tcp-wrappers, and this combination provides a reasonable level of security. Gary _____________________________________________________________________ Gary Strahan, Ph.D. strahan@outerbanks.umaryland.edu Department of Pharmaceutical Sciences Phone: USA-410-706-3118 University of Maryland at Baltimore FAX: USA-410-706-0346 _____________________________________________________________________ Under US Code Title 47, Sec.227(b)(1)(C), Sec.227(a)(2)(B) This email address may not be added to any commercial mail list with out permission. Violation of this statute with advertisements, SPAM, or other unrequested mail will result in a suit for a MINIMUM of $500 damages/incident, $1500 for repeats. From chemistry-request@server.ccl.net Wed Oct 3 16:27:22 2001 Received: from france.chem.duke.edu ([152.3.169.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93KRMB26450 for ; Wed, 3 Oct 2001 16:27:22 -0400 Received: from mole.chem.duke.edu (mole.chem.duke.edu [152.3.169.102]) by france.chem.duke.edu (8.9.3/8.9.3) with ESMTP id QAA15658; Wed, 3 Oct 2001 16:27:21 -0400 (EDT) Received: from localhost (andres@localhost) by mole.chem.duke.edu (8.9.3+Sun/8.9.1) with ESMTP id QAA01846; Wed, 3 Oct 2001 16:27:20 -0400 (EDT) X-Authentication-Warning: mole.chem.duke.edu: andres owned process doing -bs Date: Wed, 3 Oct 2001 16:27:20 -0400 (EDT) From: Gerardo Andres Cisneros To: chemistry@ccl.net, hxt10@po.cwru.edu Subject: Summary CCL:parallel g98 on AMD? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Yesterday I posted a question to CCL about running gaussian in parallel using shared memory on a dual AMD/linux platform. Thank you very much to all who replied. I tried increasing the shmax variable as per everyone's suggestion and it worked like a charm (see below). I've summarized the responses below (including my original question): > Hello > >I've managed to compile and run g98 on an AMD platform using the blas >libraries for intel (recomended by gaussian). However this machine is >dual processor but every time I try to run the same job in parallel I get > the following error message: > >%g98 tim0_2pAMD >shmget failed.: Invalid argument > >I have no problem running this job using a single processor. > >I haven't installed Linda on this machine but since it's dual processor I >don't see the need for it, or should I?. > >Thanks in advance, > >Andres ########### >From bernd-schubert@web.de Wed Oct 3 16:14:22 2001 Date: Tue, 2 Oct 2001 21:25:35 +0200 From: Bernd Schubert Hi, have you increased your shmmax variable by doing an "echo "2147483648" >/proc/sys/kernel/shmmax"? If not you should have searched in the archives before asking this question. I hope it helps you, Bernd ########## >From szilva@ribotargets.com Wed Oct 3 16:14:26 2001 Date: Tue, 2 Oct 2001 19:35:34 +0000 (GMT) From: Szilveszter Juhos To: Gerardo Andres Cisneros Subject: Re: CCL:parallel g98 on AMD? Only guessing: Seems you have problem with Sys V IPCS (Inter Process Communication) routines (actually getting shared memory), ipcs (man ipcs) can help to show you what is acually happenning. I suppose you have a pre-compled kernel with both IPCS and SMP compiled in, but if they are missing that can cause problems. Or an incompatible glibc version that use a different shmget (taht is very unlikely). Hope it helps: Szilva ############ >From gio.deluca@unical.it Wed Oct 3 16:14:43 2001 Date: Wed, 3 Oct 2001 09:48:36 +0200 From: Giorgio De Luca To: Gerardo Andres Cisneros Subject: R: CCL:parallel g98 on AMD? Hi may be this is a memory problem. With linux or unix try this echo 67108864 >/proc/sys/kernel/shmmax may be you must put a dimension more great. SMP systems does'nt need Linda, then for you it's ok Giorgio ############ >From k.radacki@ic.ac.uk Wed Oct 3 16:14:53 2001 Date: Wed, 03 Oct 2001 08:57:41 +0100 From: Krzysztof Radacki To: Gerardo Andres Cisneros , CHEMISTRY@ccl.net Subject: Re: CCL:parallel g98 on AMD? Hi, it looks so that your computer does not see shared memmory in ammount you requested with %MEM. Have you tried to calculate some small job like H2 with %MEM=10MB %PROC=2? If it complete successfully nearly sure that that the reason and you should add to your system-starting scripts some were how much memory should be shared. In case of RedHat I sugesst to add as last line in /etc/rc.d/rc.local f.e for 1Gb computer echo 955306300 > /proc/sys/kernel/shmmax It should solve your problem. MfG K.Radacki ########### >From boris@oddy.irb.hr Wed Oct 3 16:15:03 2001 Date: Wed, 3 Oct 2001 19:45:50 +0000 (GMT) From: Borislav Kovacevic To: Gerardo Andres Cisneros Subject: Re: CCL:parallel g98 on AMD? Hi Andreas, Try with this: echo "500000000" > /proc/sys/kernel/shmmax You should do that as root. You can change the number (500000000) depending on amount of memory you have. Boris -- Borislav Kovacevic Institut Rugjer Boskovic Bijenicka 54, 10000 Zagreb tel. 4561-??? ############## Thanks again to all who replied. Andres -- G. Andres Cisneros Department of Chemistry Duke University andres@chem.duke.edu From chemistry-request@server.ccl.net Wed Oct 3 15:16:12 2001 Received: from ccmsi.jsums.edu ([143.132.103.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f93JGCB25367 for ; Wed, 3 Oct 2001 15:16:12 -0400 Received: from ccmsi.jsums.edu [10.30.3.44] by ccmsi.jsums.edu with ESMTP (SMTPD32-7.04) id A3FD7D901BE; Wed, 03 Oct 2001 14:16:13 -0500 Message-ID: <3BBB63FD.95F2968A@ccmsi.jsums.edu> Date: Wed, 03 Oct 2001 14:16:13 -0500 From: "Dr. Giju Thomas Kalathingal" Organization: Jackson State University X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: memory requirement with correlation consistent basis sets Content-Type: multipart/mixed; boundary="------------0ACF206C299460CC142C3F6F" This is a multi-part message in MIME format. --------------0ACF206C299460CC142C3F6F Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Could you please give me some info on the memory required for the geometry optimization and analytical frequency calculations using correlation consistent basis sets like cc-pVXZ, aug-ccpVXZ, etc.(X=2-6)? Thanks in advance. Giju Kalathingal --------------0ACF206C299460CC142C3F6F Content-Type: text/x-vcard; charset=us-ascii; name="giju.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Dr. Giju Thomas Kalathingal Content-Disposition: attachment; filename="giju.vcf" begin:vcard n:; tel;fax:++1-601-979-7823 tel;home:++1-601-979-2749 tel;work:++1-601-979-7824 x-mozilla-html:FALSE url:http://dogstar.duch.udel.edu/gijukt/welcome.html org:;Department of Chemistry version:2.1 email;internet:giju@ccmsi.jsums.edu adr;quoted-printable:;;Jackson State University=0D=0AP.O.Box 17910=0D=0A;Jackson, MS - 39217;;;USA fn:Dr. Giju T. Kalathingal end:vcard --------------0ACF206C299460CC142C3F6F--