[SciPy-dev] eig, eigh, and symeig in scipy
Tiziano Zito
opossumnano@gmail....
Tue Oct 28 12:30:57 CDT 2008
dear list,
I have started to work on the integration of symeig in scipy. I am
unfortunately unavailable for the sprint on november 1st and 2nd,
but I hope to make up for lost time during next week. This mail is
mainly directed to robert, who was assigned the task of helping me
with this issues, but other devs may have something to say
nonetheless. This is a looong message, be aware!
I've tried to understand the organization of the symmetric
eigenproblem routines in numpy and scipy, and came up with this:
- numpy.linalg.eigh:
- only standard problems ( Ax = lx)
- wraps (or uses its own lapack_lite version) EVD routines
- scipy.linalg.eigh:
- only standard problems (Ax = lx)
- wraps EV routines
- signature differs from numpy.linalg.eigh
- symeig:
- for standard problems (Ax = lx) wraps EVR routines
- for generalized problems (Ax = lBx) wraps GV, GVX, and GVD routines
- the routine is chosen depending on some flags and depending on
the type of problem
Those, who don't know the corresponding LAPACK routines, can find a
description here:
http://www.netlib.org/lapack/lug/node30.html
and here:
http://www.netlib.org/lapack/lug/node34.html
Basically, for the standard problems
- the EV routines are the oldest one (less optimized and less
precise)
- the EVD are faster than the EV but require more memory
- the EVX offer the possibility to extract just a subset of the
eigenvectors/eigenvalues
- the EVR are the fastest and use less memory than all others
for the generalized problems:
- the GV routines are the oldest one
- the GVX offer the possibility to extract just a subset of the
eigenvectors/eigenvalues
- the GVD are faster then GV but require more memory
This is the status quo, now:
- why are numpy and scipy wrapping different routines?
I think numpy should keep on wrapping the EVD routines (unless
someone manages to add the EVR routines to lapack_lite.c) and I
see no reason for scipy to wrap the old EV routines instead of the
EVD or EVR ones.
- In my opinion, scipy.linalg.eigh should take over the
functionality now offered by symeig. Note that this would be
consistent with what is already done with linalg.eig: the scipy
version adds generalized problem functionality to the standard
problem functionality already available in numpy (as a plus eigh
would also grow the possibility to request just
a subset of the eigenvs).
- While developing symeig with tested the EVR routines: they are
really better, so I see no reason not to use them by default. On
top of that, they fail when a matrix is nearly singular, while EV
and EVD tend to give wrong results without failing. When an EVR
routine fails the user can be advised that linalg.svd may be
better for his case.
- The pyf description files are (if I am not mistaken) automatically
generated. Should I try to let the generator create pyf files for
our routines, or do you want to have the little (?) inconsistency
of having some hand-made pyf in the distribution?
- In the symeig test suite we use two very useful routines:
random_rot and symrand. Their docstrings:
random_rot:
"""Return a random rotation matrix, drawn from the Haar distribution
(the only uniform distribution on SO(n)).
The algorithm is described in the paper
Stewart, G.W., "The efficient generation of random orthogonal
matrices with an application to condition estimators", SIAM Journal
on Numerical Analysis, 17(3), pp. 403-409, 1980.
For more information see
http://en.wikipedia.org/wiki/Orthogonal_matrix#Randomization"""
symrand:
"""Return a random symmetric (Hermitian) matrix.
If 'dim_or_eigv' is an integer N, return a NxN matrix, with eigenvalues
uniformly distributed on (0,1].
If 'dim_or_eigv' is 1-D real array 'a', return a matrix whose
eigenvalues are sort(a)."""
Do you think these routines may be a useful addition to scipy, or
should I keep them hidden in the tests?
let me know what do you think!
ciao,
tiziano
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