From chemistry-request@server.ccl.net Wed May 31 03:10:59 2000 Received: from mailsrv.engr.uconn.edu (mailsrv.engr.uconn.edu [137.99.21.179]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA12434 for ; Wed, 31 May 2000 03:10:59 -0400 Received: from engr.uconn.edu (IDENT:bhupen@genius [137.99.9.36]) by mailsrv.engr.uconn.edu (8.9.1a/8.9.1) with ESMTP id DAA15342 for ; Wed, 31 May 2000 03:11:00 -0400 (EDT) Sender: bhupen@mailsrv.engr.uconn.edu Message-ID: <3934BAD2.8F330236@engr.uconn.edu> Date: Wed, 31 May 2000 03:10:10 -0400 From: Bhupendra Wakankar Organization: University of Connecticut X-Mailer: Mozilla 4.73 [en] (X11; U; Linux 2.2.5-15smp i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL_posting Subject: GAMESS Hessian Calculation crashes Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Netters, I am trying to calculate hessian of a Rhodium complex with 40 atoms when GAMESS crashes towards the end calculation. Here is a transcript of the output file ---------------------------------------------- TWO ELECTRON INTEGRAL DERIVATIVE CONTRIBUTIONS ---------------------------------------------- 1367030 WORDS REQUIRED, 7000000 WORDS AVAILABLE ...... END OF 2-ELECTRON GRAD+HESS+FOCKDER ...... ON NODE 0, STEP CPU TIME = 3832.40 TOTAL CPU TIME = 4896.9 ( 81.6 MIN) TOTAL WALL CLOCK TIME= 4927.7 SECONDS, CPU UTILIZATION IS 99.38% endfile: truncation failed in endfile apparent state: unit 16 named /usr/tmp/bhupen/6a7cpme3hess.F16 lately writing sequential unformatted external IO ------------------------------------------- COUPLED-PERTURBED CLOSED SHELL HARTREE-FOCK ------------------------------------------- THE CPHF HAS 4752 INDEPENDENT ORBITAL ROTATIONS. CHOOSING OUT OF MEMORY CPHF ALGORITHM, -WXY- WILL BE FORMED IN 7 SLICES OF 744 COLUMNS. -FA- WILL USE 1565092 WORDS, -TA- WILL USE 2875265 WORDS, -FCK- WILL USE 2793004 WORDS, -WXY- AND -YA- WILL USE 6996484 WORDS, THERE ARE 7000000 WORDS AVAILABLE. IN MEMORY FORMATION OF -WXY- WOULD REQUIRE 26022336 WORDS TIME FOR -FA- = 0.370 TIME FOR -TA- = 6.780 TIME FOR -FCK- = 472.550 ddikick: Trapped SIGCHLD: Unexpected termination of a child process. ddikick: A signal has been sent to interrupt all child processes. ddikick: terminated abnormally. child process 2: interrupted by parent child process 1: interrupted by parent child process 3: interrupted by parent unset echo ----- accounting info ----- Tue May 30 13:53:09 EDT 2000 Files used on the master node twin2.engr.uconn.edu were: -rwxr-xr-x 1 bhupen bhupen 2187 May 30 12:03 /usr/tmp/bhupen/6a7cpme3hess.F05* -rw-rw-r-- 1 bhupen bhupen 246877684 May 30 12:20 /usr/tmp/bhupen/6a7cpme3hess.F09 -rw-rw-r-- 1 bhupen bhupen 261557436 May 30 12:20 /usr/tmp/bhupen/6a7cpme3hess.F09.001 -rw-rw-r-- 1 bhupen bhupen 2741024 May 30 13:25 /usr/tmp/bhupen/6a7cpme3hess.F10 -rw-rw-r-- 1 bhupen bhupen 76546048 May 30 13:53 /usr/tmp/bhupen/6a7cpme3hess.F16 -rw-rw-r-- 1 bhupen bhupen 9747840 May 30 13:25 /usr/tmp/bhupen/6a7cpme3hess.F18 Files from twin2 are: ls: /usr/tmp/bhupen/6a7cpme3hess.*: No such file or directory 0.070u 0.470s 1:50:25.48 0.0% 0+0k 0+0io 3113pf+87w The hessian calculations with smaller number of atoms works fine. What could be the cause of this problem? Thanks in advance, Bhupendra From chemistry-request@server.ccl.net Wed May 31 03:49:30 2000 Received: from kali01.fh-nb.de (root@[195.37.133.173]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA12633 for ; Wed, 31 May 2000 03:49:27 -0400 Received: (from kali@localhost) by kali01.fh-nb.de (8.9.3/8.9.3) id KAA03035; Wed, 31 May 2000 10:31:02 -0700 Date: Wed, 31 May 2000 10:31:02 -0700 From: Michael Harig Message-Id: <200005311731.KAA03035@kali01.fh-nb.de> To: CHEMISTRY@ccl.net Reply-To: m.harig@gmx.de Subject: Probs with Linux Rasmol 24/32 Bit X-Mailer: XCmail 1.0.0 - with PGP support, PGP engine version 0.5 (Linux) X-Mailerorigin: http://www.fsai.fh-trier.de/~schmitzj/Xclasses/XCmail/ MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit Hi CCLers, Rasmol 2.6.2B2 & 2.7.1 24/32 bit versions do not display molecules on a 800x600x24 TFT. I tried precompiled and self compiled executables. There appear several 'insinuated' instances of the loaded molecule (PDB) on the screen. They can be rotated etc., so it seems to be a problem of the 3D graphics routines. I didn't find anything about this in the net, does someone here experienced this, too? Tia, Michael --- Michael Harig m.harig@gmx.de From chemistry-request@server.ccl.net Wed May 31 06:19:12 2000 Received: from fir.lif.icnet.uk (fir.lif.icnet.uk [143.65.53.138]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA13448 for ; Wed, 31 May 2000 06:19:11 -0400 Received: (from turcotte@localhost) by fir.lif.icnet.uk (8.9.3/8.9.3) id LAA1519117; Wed, 31 May 2000 11:12:50 +0100 (BST) X-Authentication-Warning: fir.lif.icnet.uk: turcotte set sender to turcotte@fir.lif.icnet.uk using -f To: Valentine Ananikov Cc: CCL_post Subject: Re: CCL:Queueing System and Linux cluster References: <39335A61.7367DE04@cacr.ioc.ac.ru> From: Marcel Turcotte Date: 31 May 2000 11:12:49 +0100 In-Reply-To: Valentine Ananikov's message of "Tue, 30 May 2000 10:06:25 +0400" Message-ID: Lines: 85 User-Agent: Gnus/5.0802 (Gnus v5.8.2) Emacs/20.4 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi Valentine, We selected PBS (Portable Batch System) http://pbs.mrj.com/ because, * It's free. * Works well with PVM and MPI. It's more flexible than the traditional NQS. You don't have to create queues on each node, you don't have to pre-partition the nodes, each job requests the number of nodes it needs; as the nodes are seen as a collection and this makes it easier to work with PVM and MPI. * Since version 2.2, the notion of virtual processors has been introduced which allows to take advantage of cheap dual- or quad-processors machines. Prior to 2.2 there was two kinds of nodes: single processor or time shared, but time shared is inadequate for machines with a small number of processors. * File staging. * Comes with a library of schedulers, but the user can also write his/her own scheduler in C, BASL (PBS's own C-like language) or tcl. * Properties to nodes, for example one can ask for a node with large memory and a local copy of some database. * It's got nice tcl/tk management tools. * Well supported and open source. * Comes with API. * Used by SGI. Here we've been using it for about a year or so and we're quite happy about it, we've got one cluster of about 15 SGIs and one Linux cluster of 25 x 500MHz PIII. Hope this helps, Marcel Valentine Ananikov writes: > Dear CCl members, > > We are going to create a cluster from Linux PC's for quantum > chemistry calculations. The question arose what kind of > Queueing System should be used. > > As I know, NQS and DQS are very popular queueing system, but > may be some others as well. Of course, an ideal version > should be easy to install, menage and use. > > Which system would be preferred for Linux based PC's ? > Is the answer the same from users' and administrators' points > of view? > > will be summarized, > Valentin. -- Marcel Turcotte Biomolecular Modelling Laboratory M.Turcotte@icrf.icnet.uk Imperial Cancer Research Fund Phone/Fax +[44]-(020)-7269-3348/3258 PO Box 123, 44 Lincoln's Inn Fields http://www.bmm.icnet.uk/people/turcotte London WC2A 3PX, England New address effective July 1st 2000, School of Information Technology and Engineering University of Ottawa 150 Louis Pasteur P.O. Box 450, Station A Ottawa, Ontario K1N 6N5 Canada Tel: (613) 562-5826 Fax: (613) 562-5187 Generic e-mail address: info@site.uottawa.ca Web site: http://www.site.uottawa.ca From chemistry-request@server.ccl.net Wed May 31 08:17:49 2000 Received: from batata.fh.huji.ac.il (batata.fh.huji.ac.il [132.64.96.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA14828 for ; Wed, 31 May 2000 08:17:47 -0400 Received: from orion.fh.huji.ac.il (orion.fh.huji.ac.il [132.64.96.6]) by batata.fh.huji.ac.il (8.8.8/8.8.8) with ESMTP id PAA24891 for <@batata.fh.huji.ac.il:chemistry@ccl.net>; Wed, 31 May 2000 15:18:21 +0300 (IDT) Received: from localhost (galinac@localhost) by orion.fh.huji.ac.il (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id PAA01713 for ; Wed, 31 May 2000 15:18:20 +0300 (IDT) Date: Wed, 31 May 2000 15:18:18 +0300 From: Galina Chaban To: chemistry@ccl.net Subject: OPLS-AA in Tinker Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everyone, I would like to do a calculation of glycine molecule using Tinker program and OPLS-AA potential. I wanted to use these atom types for glycine carboxyl group: atom 107 21 C "COOH Carboxylic Acid" 6 12.000 3 atom 108 26 OH "OH Carboxylic Acid" 8 15.999 2 atom 109 22 O "C=O Carboxylic Acid" 8 15.999 1 atom 110 8 HO "COOH Carboxylic Acid" 1 1.008 1 and these for amine group: atom 70 19 NT "NH2 Primary Amine" 7 14.007 3 atom 71 20 H2 "HN Primary Amine" 1 1.008 1 However, when I try to run it, the program stops with the message that some parameters are not found. When I check the parameters file, I can see that indeed many parameters are missing: for example, bond parameters for atom pairs 21-26, 26-8, 19-20. Has anyone experienced this problem? How could I get the missing parameter values? I would appreciate any suggestions and references that could help. Galina ------------------------------------------------------------------- Dr. Galina Chaban Fritz Haber Research Center for Molecular Dynamics. Hebrew University of Jerusalem Jerusalem, Israel 91904 Tel: 972-2-6585936 Fax: 972-2-6513742 e-mail: galinac@fh.huji.ac.il