Subject: Re: CCL:Large matrix diagonalization.

From: Jochen Kuepper <[email-masked]>
Date: Fri, 30 Jul 1999 09:29:56 +0200

On Don, 29 Jul 1999 Iraj Daizadeh wrote:

>For my phd dissertation, we spent quite some time diagonalizing SPARSE
>matrices of the order of 1000x1000 or so...The diagonalization process was
>performed by a routine called cboris (fortran code):

>It is included in the QCPE 

>This routine is not faster than the diagonalization packages that come
>with blas or something or that sort...

So why have you used it ? What's it advantage to LAPACK algorithms ?

-- Jochen
 Heinrich-Heine-Universität Düsseldorf          [email-masked]
 Institut für Physikalische Chemie I               phone ++49-211-8113681
 Universitätsstr. 26.43.02.29                      fax   ++49-211-8115195
 40225 Düsseldorf, Germany       www-public.rz.uni-duesseldorf.de/~jochen

---

From: "David E. Bernholdt" <[email-masked]>
Date: Fri, 30 Jul 1999 12:40:05 -0400

The LAPACK library deals only with dense matrices, and is a de facto
standard library for those operations on uniprocessors.  

Sparse linear algebra has a great deal of variation across fields and
even across different applications, and is a lot less standardized at
this point in time.  Likewise, parallel dense linear algebra is also a
lot less standardized, though that area seems to be consolidating of
late.

Mounting soapbox...

My (humble?) opinion is that chemists (speaking broadly) aren't very
smart about solving their linear algbra problems.  I think it is
getting better, along with the evolution of packages like LAPACK, but
historically our track record is pretty poor.  

Chemists are all too willing to "roll their own" solutions to linear
algebra problems, blithly ignoring the fact that there is an entire
field of research that devotes itself to such problems.  To the extent
possible, we should be (well-informed) consumers of the high quality,
often highly optimized mainstream linear algebra packages that one can
easily obtain from NETLIB or other sites.

To be sure, there will be problems that the standard linear algebra
tools don't handle well for one reason or another.  In that case, my
recommendation is to make frieds with a good numerical analyst in the
problem area.  My experience is that they like new challenges -- it
pushes their research & their field along just as chemical challenges
do ours, andby virute of their training, they're likely to come up
with a better solution than you can working in isolation.  The more we
chemists expose the numerical analysis community to our unique
problems (relative to other fields), the more help we'll get from
them, as chemically-derived problems become part of the standard test
suites they use when testing new algorithms & libraries.

Stepping off soapbox...
--
David E. Bernholdt                      | Email:  [email-masked]
Northeast Parallel Architectures Center | Phone:  +1 315 443 3857
111 College Place, Syracuse University  | Fax:    +1 315 443 1973
Syracuse, NY 13244-4100                 | URL:    http://www.npac.syr.edu

---

From: Matt Challacombe <[email-masked]>
Date: Fri, 30 Jul 1999 12:42:16 -0600

<<begin rant>>

Much of computational chemistry is applied mathematics, and if the field is
to move ahead at a reasonable pace, we should not shirk the responsiblilty of
pushing the related fields of applied mathematics, computational physics, etc.
ourselves.  Excellent examples of this spirit is White and Head-Gordon's
significant advancement of the Fast Multipole Method and Davidson's method.  

I've just about completed a parallel sparse atom-blocked linear algebra 
library for my linear scaling quantum chemistry code MondoSCF. 
This library allows sparse matrix manipulations with variable sized
dense blocks. When I  started, I looked carefully at all the available linear
algebra software,  and talked to many computer scientists and applied
mathematicians.  The upshot was that nothing like this existed.  Moreover, it
turns out that parallel methods for sparse matrix multiplies are (were)
totally undeveloped!  If I'd waited for a numerical analyst to help me,
I'd still be waiting ...

In my opinion, the CC community is already way to addicted to black box solutions 
and pre-fab science.  To those who do roll their own, I salute you. 

<<end rant>>

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