From gene@eastrg1.cray.com Wed Apr 28 05:01:57 1993 Date: Wed, 28 Apr 93 09:01:57 EDT From: gene@eastrg1.cray.com (Eugene Fleischmann) Message-Id: <9304281301.AA06069@sodium.cray.com> To: rbw@msc.edu Subject: Re: direct vs. in-core calculations > From chemistry-request@ccl.net Mon Apr 26 19:10:44 1993 > To: DSMITH@uoft02.utoledo.edu, chemistry@ccl.net > Subject: Re: direct vs. in-core calculations > Sender: chemistry-request@ccl.net > > Doug, > > If the memory is free and sufficient for the problem, you should > always use INCORE (although I am not sure if this option is available > on non-CRAY versions of the code). For closed shell systems memory > requirements scale as N^4/4 where N is the number of basis functions. > If you pay extra for memory then you need to consider the performance > boost you get from running INCORE. On a CRAY-2 it can be as much as > a factor of four. On the C90 it appears that it is a factor of three. > At some point the DIRECT algorithm overcomes the INCORE algorithm, > but this seems to be far beyond the basis function count that can > be fit INCORE on todays machines reasonably ... some 'memorable' data > points on the basis function memory relationship for closed shell > systems are 100 basis function or fewer fit inside 100+ MWs (64 bit > words, 200 basis needs 200 MWs (64 bit words), 300 basis needs 1+ GWs > (again 64 bit words). Open shell systems need twice as much space. > > Sincerely, > > Richard Walsh > Minnesota Supercomputer Center > > > --- > Richard, I beg to differ with your numbers. Using N^4/4 one calculates: # functions memory ----------- ------ 100 -> 25 MW 200 -> 400 MW 300 -> 2025 MW However, the Gaussian manual says, and my own experience support it, that for closed shell RHF calculations memory scales as N^4/8 plus some additional memory, say 500,000 words. (G92 User's Guide p.88.) My own experience has been that the additional .5 MW is too small, a more realistic number is 100N*N. Using this formula one calculates: # functions memory ----------- ------ 100 -> 12.5 + 1 = 13.5 MW 200 -> 200 + 4 = 204 MW 300 -> 1012.5 + 9 = 1021.5 MW A recent calculation of mine ran INCORE with 61 MW for 147 functions. ( 147 -> 58.4 + 2.2 = 60.6 MW ) Even this memory requirement for 300 functions (i.e. 2025 MW) is tractable on today's Cray systems. I might also point out that use of the DIRECT keyword can still cause an INCORE calculation to run if sufficient memory has been provided using the %mem=???? directive in conjunction with the # QSUB lM ???mw option for NQS (if it is a batch job) and having no additional limits imposed on the job by the system. My opinion is that the INCORE is not warranted for production work at a site where no charge is incurred for memory, since the job may sit in a queue for some time, then fail due to lack of memory, whereas a DIRECT job will test for memory availability and run DIRECT if there is a lack of memory. The trade off, of course, is that you will then pay for the EXTRA CPU time incurred running DIRECT instead of INCORE. Regards, Gene ++++++++++++++++++++++++++++++++++++++++ Eugene D. Fleischmann, Ph.D. Computational Chemist Cray Research, Inc. (301)595-2695 gene@eastrg2.cray.com ++++++++++++++++++++++++++++++++++++++++ From NMUELLER@EDVZ.UNI-LINZ.AC.AT Wed Apr 28 21:02:32 1993 Message-Id: <199304281757.AA05458@oscsunb.ccl.net> Date: Wed, 28 Apr 1993 20:02:32 +0100 To: chemistry@ccl.net From: NMUELLER@edvz.uni-linz.ac.at (Norbert Mueller) Subject: Proteus-C Hello, I was just aked by one of our students if I knew a molecular modelling pacakage called Proteus-C, which seems to be partly in the public domain. Does anyone have more specific information? Thanks for any help Norbert Mueller Institut fuer Chemie Johannes Kepler Universitaet A-4040 Linz Austria Please take notice of my changed e-mail address! ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From farnold@wotan.duch.udel.edu Wed Apr 28 13:37:22 1993 Date: Wed, 28 Apr 1993 17:37:22 EDT From: "System Manager, and VAX Gopher" To: chemistry@ccl.net Message-Id: <0096BB74.3D76E180.10874@wotan.duch.udel.edu> Subject: Molecular Visualization. Hello all. Not to continue a thread beyond it's time, but I have been looking for a package to allow the visualization of molecular orbitals and electron densities, either on a PC or workstation. I found a reference in the literature to a program called _Interactive MOPLOT_, which contains the routines MOPLOT, PLOTDEN, SCHUSS, and EXTREM, and was published by P. Sherwood and P.J. MacDougall in 1989. No further references, such as where were provided. Does anybody have any details on this program, such as who to contact about obtaining it, or whether there are any licensing details? Thank you. -Fred farnold@wotan.duch.udel.edu From mw@crystal.uwa.edu.au Wed Apr 28 20:14:19 1993 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9304290017.AA05601@hewl.crystal.uwa.edu.au> Subject: G90-Time To: chemistry@ccl.net Date: Thu, 29 Apr 93 8:17:58 WST Dear G90 users, This might be a very trivial question, but I was wondering if any one knows how to get G90 to display CPU time at the end of a job in the output file. Thank you very much fo your help. M. Wajrak (e-mail: mw@crystal.uwa.edu.au) From root@stardent.chem.UTOLEDO.edu Wed Apr 28 16:37:33 1993 Date: Wed, 28 Apr 1993 16:37:52 -0400 (EDT) From: root@stardent.chem.UTOLEDO.edu (Charles W. Ulmer II) Subject: Gaussian NFS problems To: chemistry@ccl.net Message-Id: <9304282038.AA00987@stardent.chem.utoledo.edu> Since Doug Fox is out of town until May 4th, the Gaussian Help Line is unavailable until then. So, I am asking for help from any Gaussian users out there. Correct me if I am wrong, but shouldn't I be able to use any file system, whether NFS mounted or not, as my scratch space? I have set the environment variable "GAUSS_SCRDIR" in the g90.login to point to an NFS mounted disk (exported from a DEC ALPHA running OSF/1) and Gaussian core dumps with the following error: ********************************************** Gaussian 90: Stardent-Unix-G90RevJ 4-Jun-1990 27-Apr-1993 ********************************************** %CHK=COMPLX1.chk lock-new-file: Invalid argument sh: 924 Illegal instruction - core dumped G90 is running on a Stardent/Kubota Titan 3000 and the ALPHA exports the filesystem with the root uid set equal to 0. I have no problems writing to the NFS mounted file system from either machine, only Gaussian seems to have the problems. I have also tried making Gaussian write to other NFS mounted disks which are exported from DECstation 3100's with the same error. Is there something that I have missed, a problem with Gaussian, or a problem with Digital's NFS? Thanks in advance, Chuck -- Charles W. Ulmer, II root@stardent.chem.utoledo.edu A&S System Manager culmer@uoft02.utoledo.edu D.A.Smith Group University of Toledo Toledo, OH, 43606 WE ARE PERHAPS NOT FAR REMOVED FROM THE TIME WHEN WE SHALL BE ABLE TO SUBMIT THE BULK OF CHEMICAL PHENOMENA TO CALCULATION. -- JOSEPH LOUIS GAY-LUSSAC MEMOIRES DE LA SOCIETE D'ARCUEIL, 2, 207 (1808)