From Kurt.Hillig@um.cc.umich.edu Tue Apr 27 07:07:18 1993
Date: Tue, 27 Apr 93 11:07:18 EDT
From: Kurt.Hillig@um.cc.umich.edu
To: chemistry@ccl.net
Message-Id: <22506386@um.cc.umich.edu>
Subject: Gaussina 9x memory/disk requirements
I've often seen the claim that memory (for in-core) or disk space
needed by Gaussian 9x scales as N^4/4 (SCF). I expect a first-order
approximation to the memory needs can be given by M = A + B N^4,
where A is the "overhead" and B is a scale factor (words per integral?).
I've occasionally seen some very rough estimates - for example today,
the claim (paraphrased) 100 basis functions:100 MWords, 200 BF's:200 MW,
300 BF's:>1GW - but it's hard to fit this to a fourth-order polynomial
with any accuracy (;-) and it doesn't match M = N^4/4 (i.e. A=0, B=.25)
particularly well.
Can anyone supply more accurate numbers so I can better advise my users?
Dr. Kurt Hillig
Dept. of Chemistry I always tell the khillig@umich.edu
University of Michigan absolute truth Telephone (313)747-2867
Ann Arbor, MI 48109-1055 as I see it. hillig@chem.lsa.umich.edu
From richard@TC.Cornell.EDU Tue Apr 27 06:47:17 1993
Date: Tue, 27 Apr 1993 10:47:17 -0400
From: Richard Gillilan <richard@TC.Cornell.EDU>
Message-Id: <199304271447.AA20137@theory.TC.Cornell.EDU>
To: chemistry@ccl.net
Subject: Visualization Summer School
--- Scientific Visualization of Chemical Systems ---
Cornell Theory Center Summer School
Offered through the Cornell School of
Continuing Education and Summer Sessions
Course Description
Within the past ten years, the simulation and modeling of
molecules has evolved from an esoteric academic subject into
a international industry. Computer graphics has played a
decisive role in this transformation by allowing chemists to
build, visualize and interact with complex geometrical objects.
While computer scientists are conversant in the language of their
own discipline, they are often unfamiliar with the terminology,
simulation techniques and practical needs of research chemists.
Similarly, chemists are often unfamiliar with the latest paradigms
and technological advances in graphical computing.
This interdisciplinary course is intended to bridge the gap
between computer science and chemistry and to equip chemistry
researchers who wish to be more than just casual users of
prepackaged graphics software. Although this is not intended to
be a course in computational chemistry or drug design, data sets
>from chemical research problems will be used in lab and students
will be encouraged to bring data sets of their own. Lab exercises
and projects will be carried out using data-flow programming
(IBM Visualization Data Explorer software) and students will have
access to Cornell Theory Center computing resources, including video
recording equipment.
Audience: researchers and students in the chemical and biological
sciences interested in integrating state-of-the-art
computer graphics into their research; computer scientists
wishing to gain familiarity with a major application of
scientific visualization.
The class size will be limited to 25 participants on a
first-come first-served basis.
Level: Graduate/advanced undergraduate, 1 or 2 Credits. May be taken
without credit as a workshop. Calculus, linear algebra
and introductory chemistry required. Familiarity with Unix,
X-windows and C is useful but not required.
Date: June 14-25, 1993 (2 Credits)
June 14-18, 1993 (1 or 0 credits)
Time: Mon-Fri 9:00 am to 12:00 pm and 1:00 pm to 4:00 pm
Cost: 0 or 1 credit $410
2 credits $820
Format
The course will be held in the Theory Center training facility
where computer workstations will be available. Daily lectures will be
interspersed with laboratory exercises and ample time will be provided
for project enablement and familiarization with the new computing
environment. Students enrolled for one credit will be graded on the basis
of their laboratory exercises and short final project. Those enrolled
for a second credit will receive more advanced lectures, be given
more time for project development and meet daily to share experience
and discuss problems encountered.
Content (may vary)
Elements of computer graphics
polygonal rendering, lighting models, ray tracing, volumetric
rendering, stereo graphics, animation, introduction to data-flow
programming (DX), interactivity.
Representing the atom
size, time and energy scales
basic classical and quantum mechanics
Important categories of molecules
small molecules, biopolymers, surfaces and catalysts,
miscellaneous current applications
Data formats and conversions
Advanced molecular graphics techniques
Types of simulation and experiment
electronic structure, molecular dynamics/mechanics
electrostatics, X-ray crystallography, NMR, quantum
dynamics and spectroscopy.
Instructors
The course will be taught by two instructors. Topics related to computer
graphics will be handled by Dr. Bruce Land, Project Leader of Visualization,
Cornell National Supercomputing Facility. Chemistry-specific aspects
of the course will be handled by Dr. Richard E. Gillilan, Visualization
Specialist and Research Scientist, Cornell National Supercomputing Facility
TO REGISTER: mail completed form to
Cornell University
School of Continuing Education
and Summer Sessions
B20 Day Hall
Ithaca, NY 14853-2801
Questions: Richard Gillilan (607) 254-8757
richard@tc.cornell.edu
IMPORTANT: Acceptance will be first-come, first-served and based
on a target class size of 15 full-credit and 10 single
or non-credit participants.
DEADLINE: May 20, 1993
----------------------- Application Form ----------------------
Scientific Visualization of Chemical Systems
Chemistry 782 Computer Science 718
U.S. Social Security number (if available) _____ - ___ - _______
Cornell ID number (if available) ________________
Name: _______________________________________________________________
Last First Middle Suffix (Jr, etc)
Address: _____________________________________________________________
_____________________________________________________________
_____________________________________________________________
Home Address (where grades will be mailed):
_____________________________________________________________
_____________________________________________________________
_____________________________________________________________
Local Phone ________________ Home Phone _______________
Academic Discipline _____________________________
Course number (check one): __ Chemistry __ Computer Science
Credits: __.__
Status: __ Undergraduate Student __ Smart Node Consultant
__ Graduate Student __ Smart Node Advisor
__ Post-Doctoral
__ Faculty __ Other (explain) _______________
Corporate Commercial
__ Research Staff __ Other (explain) ______________
Name of Firm ___________________________________________________________
Indicate which of the following best describes you (optional):
__ African American __ Alaskan Native __ Asian American
__ Caucasian __ Hispanic American __ Native American
List special needs (e.g. mobility impaired): ____________________________
----------------------------------------------------------------------------
Accommodations:
Blocks of rooms are available at the Sheraton. Reservations
must be made no later than May 17. Be sure to tell them you
are here for the "Cornell Theory Center Visualization Workshop".
Sheraton Inn
One Sheraton Drive, Ithaca
(607) 257-2000
FAX: 607-257-398
Rates starting at $64.00
Other local motels (Make your reservation early! Our
workshop coincides with other Cornell events)
Econo Lodge
Cayuga Mall 2303 N. Triphammer Rd. Ithaca
(607) 257-1400
(800) 466-6900
FAX: (607) 257-6359
Rates from $35.10 (ask for the Cornell Rate)
Dorm rooms have also been reserved participants
(both credit and non-credit). Participants who
are interested in dorm rooms should call (below)
for registration information:
Jeanne Miller (607) 254-8813 or Donna Smith (607) 254-8614
email: jeanne@tc.cornell.edu or donna@tc.cornell.edu
---------------------------------------------------------------------------
From mail Tue Apr 27 12:42:46 1993
From: hyper!slee (Thomas Slee)
Message-Id: <9304271623.AA12347@hyper.hyper.com>
Subject: PC's and workstations
To: chemistry@ccl.net
Date: Tue, 27 Apr 1993 12:23:11 -0400
Dear OSC-ers,
Following the "Gaussian for Windows" announcement, there has been a
flurry of discussion about the relative merits or otherwise of
PC's, workstations, and supercomputers. I thought I would add a
couple of pieces of fairly elementary information to the pile as
I haven't seen them posted yet.
First, relative cpu speeds of workstations and PC's with real applications.
We find that for the semi-empirical and molecular mechanics programs in
HyperChem the relative speeds of a high-end, but not quite top-of-the-line,
PC (486-50MHz model) and an R3000 SGI Indigo are about 1 to 2.5.
An R4000 SGI Crimson is just over 2 times faster again. So, a
reasonably fast PC certainly has the cpu speed to do useful
calculations.
The memory requirements for semi-empirical and molecular mechanics
calculations are much less than those for (indirect) ab initio methods,
of course: a 100-orbital AM1 calculation can be done in around 5Mb,
making it quite easily within reach of standard PCs. I can make no
comment on Gaussian 92 in this context.
A couple of other things for those who are new to thinking about
PC's for computational chemistry. Workstations have, of course,
the advantage of being multi-user platforms, while PC's are single-user.
Windows does not do time-slicing by itself: it will share CPU time
among applications only if those programs give up the CPU. Thus,
the ability to run other programs without too much interference from
a big calculation depends on program implementation,
rather than on the operating system. It will be interesting to
see how easily Gaussian can be put "in the background".
One of the big advantages of Windows is, apart of course from having
lots of commercial programs available for all kinds of purposes,
the ability of different programs to communicate with each other
through Dynamic Data Exchange (DDE). I certainly find this one of
the most attractive and powerful tools when working in Windows.
Anyone know if G92 has any facility to share its results by DDE?
FInally, to those who say you can't do anything worthwhile with less
than a gigabyte of scratch space (or whatever): you make me feel very
old. I felt like starting this posting by saying "When I were a lad,
we only had 80Mb of disk space, and 4Mb of memory, TOTAL. And we
STILL did ab initio calculations. Times were tough then..." And it
wasn't that long ago, either. Really. Sigh...
Tom Slee
--
Tom Slee
Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2
Internet: slee@hyper.com Tel. (519) 725-4040
From rbw@msc.edu Tue Apr 27 08:29:47 1993
Date: Tue, 27 Apr 93 13:29:47 -0500
From: rbw@msc.edu (Richard Walsh)
Message-Id: <9304271829.AA25192@uh.msc.edu>
To: Kurt.Hillig@um.cc.umich.edu, chemistry@ccl.net
Subject: Re: Gaussina 9x memory/disk requirements
Hello,
I made a mistatement in my previous note .. I got my divisors
mixed up and stated that closed shell systems scale as N^4/4
when this is actually the number for open shell systems. Here is
the correct information:
open shell incore scf memory needs scale as N^4/4
closed shell incore scf memory needs scale as N^4/8
So, for closed shell systems, explicitly:
50*50*50*50/8 = 781250 MWs
100*100*100*100/8 = 12500000 MWs
200*200*200*200/8 = 200000000 MWs
300*300*300*300/8 = 1012500000 MWs
I usually give my jobs a additional 1 or 2 MWs to
to be sure their is enough room for the instuctions
and static data.
Sorry about the mistake,
Richard Walsh
Minnesota Supercomputer Center
From srheller@asrr.arsusda.gov Sat Apr 27 10:11:00 1993
Message-Id: <199304271814.AA14237@oscsunb.ccl.net>
Date: 27 Apr 93 14:11:00 EDT
From: "STEPHEN R. HELLER" <srheller@asrr.arsusda.gov>
Subject: Software for review
To: "chemed-l" <chemed-l%uwf.bitnet@cunyvm.cuny.edu>
27 April, 1993
Subject: Computer Software for Review
As the Software Review Editor for the ACS Journal of
Chemical Information and Computer Science (JCICS) I often get
software for review in the journal. I now have some packages in
hand (see below) and I am looking for people who are willing to
review the software. In return for the review you get to keep
the software. The review should be completed in 1-2 months. The
length of the review is 4-10 double spaced typed pages. Sample
reviews can be found in most of the recent issues of JCICS.
I have tried this approach with some software for review in
the past few months and it is working reasonably well. (For those
who haven't finished your reviews of software sent a few months
ago, this last sentence does not apply to you!) As a result, I
am continuing this new method to find reviewers using this e-
mail/user group system. I hope it continues to work. I reserve
the right to abandon this if it is a problem, or inappropriate.
I will not notify people if I have found a reviewer. If you
don't hear from me I have chosen someone else to review the
particular package.
As I get many, many, (too many) replies to this message,
please do not respond after 28 April, as I am sure the software
will be gone by then.
I can be reached on INTERNET (SRHELLER@ASRR.ARSUSDA.GOV),
or if necessary, by phone at 301-504-6055 or FAX at 301-946-2704.
PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE and FAX
NUMBER!!! (I send the software by Federal Express.)
Steve Heller
The packages I now have are:
1. LabAdvisor - IBM PC Regulatory Information database from the
ACS. This is the complete LabADVISOR package with all modules.
This helps you keep track of regulatory requirements for
chemicals in the lab.
2. Ami-Pro 3.0 for windows.
From wsonnen@rcf.usc.edu Tue Apr 27 06:42:51 1993
Date: Tue, 27 Apr 93 13:42:51 PDT
From: wsonnen@alnitak.usc.edu (Wayne Sonnen)
Message-Id: <9304272042.AA24285@alnitak.usc.edu>
To: chemistry@ccl.net
Subject: dna-ligand studies
Dear computational chemists,
I would appreciate any directions (references, etc.) as to where
to find data on dna-ligand studies. In particular i would like to
find a series of ligands (or a ligand and several of its derivatives)
which bind to the same dna sequence.
Any references to thermodynamic, biochemical and of course simulation
studies would be most welcome. My interest is in studing the binding
of these ligands via md.
Regardless of the number of replies to my question, i will post
a summary of the replies i receive to this network.
Thank you,
Wayne Sonnen
wsonnen@alnitak.usc.edu