Python advocacy in scientific computation

Michael Tobis mtobis at gmail.com
Sat Mar 4 18:30:46 CET 2006


There is a range of folks doing scientific programming. Not all of them
are described correctly by your summary, but many are. The article is
aimed not at them, but rather at institutions that develop engineered
Fortran models using multipuurpose teams and formal methods. I
appreciate your comments, because I see that there should be another
article aimed at desktop programmers.

One of the things python addresses best is the division of labor, where
the subtle concepts are available to those who need them and hidden
from those who don't need them. From what I understand of your work
(and what I have seen of the work of two other neuroscientists,
actually) Python would be a good choice for you.

That said, the level of computational skill in many scientists is
alarming. Why do we expect to spend six semesters learning mathematics
and expect to pick up computing "on the side"? It baffles me.  Frankly,
saying "I don't need version control" sounds to me no less foolish than
 saying "I don't need logarithms". (Perhaps you don't but someday soon
you will.)

"Speed of excecution is an issue, regardless of what computer science
folks try to tell you." strikes me as nothing short of hallucinatory.
No informed person says that speed is never an issue, and a great deal
of effort is spent on  speed. Where do you suppose your Fortran
compiler came from in the first place?

For someone without legacy code to worry about, fussing with Fortran
for single-user one-off codes strikes me as a weak choice. If you are
hitting Matlab's performance or memory limits, you should take the time
to learn something about computation, not because you are idle, but
because you are busy. Or if you prefer, because your competitors will
be learning how to be more productive while you put all your efforts
into coping with crude tools.

The peculiar lack of communication between computer scientists and
application scientists is real; but I believe the fault is not all on
one side. The fact that you have a PhD does not prove that you know
everything you need to know, and I strongly recommend you reconsider
this attitude. For one thing, you misjudged which side of the divide I
started on.

Michael Tobis
(While I dislike credentialism on usenet, I will reply in kind. I hold
a Ph.D. in geophysical fluid dynamics.)




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