Closed GoogleCodeExporter closed 9 years ago
Thanks for reporting this. I think this is due to recent changes in Numpy.
We'll take a look.
Original comment by luke.ol...@gmail.com
on 10 Jan 2012 at 5:22
Hi,
Thanks for reporting this. I had some trouble reproducing this warning, so I
was hoping that you could share a short code snippet that produces the warning
on your machine.
Also, could you report what
>>> import numpy
>>> numpy.version.version
produces on your machine?
and what
>>> import scipy
>>> A = scipy.sparse.csr_matrix( 1.0j*scipy.rand(3,3))
>>> print(A.dtype == complex)
produces on your machine?
Last, do you know if any of the matrices that you're using are of a complex
data type? If they are, then this may not be a spurious warning, but hopefully
it is just spurious.
Thanks again,
Jacob
Original comment by jacob.b....@gmail.com
on 18 Jan 2012 at 5:51
Hi Jacob,
The call that causes the warning is:
self.create_amg_hierarchy(G)
Where G is a laplacian graph with one of the diagonal elements set to 0.
Numpy version produces 1.6.1. The scipy code produces True. None of
our matrices are complex.
-Brad
--
------------------------------------------------------------------------------
Brad McRae, Ph.D.
The Nature Conservancy
1917 1st Avenue
Seattle, WA 98101
Cell: 541-223-1170
Office: 206-436-6206
Fax: 206-343-5608
email: bmcrae@tnc.org
http://www.nceas.ucsb.edu/~mcrae/
Original comment by mc...@circuitscape.org
on 24 Jan 2012 at 4:11
My bad- I forgot to mention that create_amg_hierarchy calls this function:
def create_amg_hierarchy(self, G):
ml = []
ml = smoothed_aggregation_solver(G)
So, the problematic call boils down to the last line above, where G is
a laplacian graph with one of the diagonal elements set to 0.
-Brad
--
------------------------------------------------------------------------------
Brad McRae, Ph.D.
The Nature Conservancy
1917 1st Avenue
Seattle, WA 98101
Cell: 541-223-1170
Office: 206-436-6206
Fax: 206-343-5608
email: bmcrae@tnc.org
http://www.nceas.ucsb.edu/~mcrae/
Original comment by mc...@circuitscape.org
on 24 Jan 2012 at 7:40
Hey Brad,
Thanks for the reply. Since your matrix is not actually complex, my
suspicion is that this warning isn't a big deal. But, I'm still not
able to reproduce the warning on my system. I just tried some simple
graph Laplacian examples, but couldn't get it.
If it's easy, could you email me (jacob.b.schroder - gmail) an example
G that gives you this warning when you call
smoothed_aggregation_solver(G)? You probably already know this, but
scipy.io.savemat() is an easy way to store sparse matrices to disk.
Thanks again,
Jacob
Original comment by jacob.b....@gmail.com
on 25 Jan 2012 at 6:28
Update: I think that I have this figured out. In v2.0, we have this line in
linalg.py:approximate_spectral_radius
H = numpy.zeros((maxiter+1,maxiter), dtype=A.dtype)
But this was changed later in r815 in the trunk to
H = numpy.zeros((maxiter+1,maxiter), dtype=v0.dtype)
Basically, the approximate_spectral_radius routine can generate an imaginary
part for the approximate eigenvectors/values for nonsymmetric matrices (like
DinvA). When these approximate eigenvectors are then fed back into
_approximate_eigenvalues as initial guesses during the adaptive cycling in
approximate_spectral_radius, then A.dtype is no longer the right type to use
for H. H needs to be complex.
So, I think if circuitscape switches to the trunk this Warning will disappear.
If not, then please let us know.
Skipping over all the techno gibberish, if circuitscape continues to use v2.0,
I don't think that this is too big of an issue. The spectral radius estimates
just might be a little less accurate because the adaptive cycling will be a
little off.
Pending any feedback from Brian, I think this ticket can eventually be closed.
- Jacob
Original comment by jacob.b....@gmail.com
on 10 Feb 2012 at 11:44
Thank you Jacob! I'm sorry I didn't get back to you before on the
residual norm, as I haven't had time to dive in deeper. We'll give
the trunk a try.
Best,
Brad
--
------------------------------------------------------------------------------
Brad McRae, Ph.D.
The Nature Conservancy
1917 1st Avenue
Seattle, WA 98101
Cell: 541-223-1170
Office: 206-436-6206
Fax: 206-343-5608
email: bmcrae@tnc.org
http://www.nceas.ucsb.edu/~mcrae/
Original comment by mc...@circuitscape.org
on 11 Feb 2012 at 12:01
Hi Brad,
I just noticed that this ticket was still open. Has this issue been resolved
on your end, so that it can be closed?
Thanks,
Jacob
Original comment by jacob.b....@gmail.com
on 5 Aug 2012 at 6:59
Hi Jacob,
I installed the most recent release, and have not noticed the problem. So
yes, I believe it is resolved. Thanks!
Brad
--
------------------------------------------------------------------------------
Brad McRae, Ph.D.
The Nature Conservancy
North America Region
1917 1st Avenue
Seattle, WA 98101
Cell: 541-223-1170
Fax: 206-343-5608
email: bmcrae@tnc.org
http://www.nceas.ucsb.edu/~mcrae/
Original comment by mc...@circuitscape.org
on 5 Aug 2012 at 3:39
Original comment by jacob.b....@gmail.com
on 5 Aug 2012 at 4:30
moved to github:
https://github.com/pyamg/pyamg/issues
Original comment by luke.ol...@gmail.com
on 8 Jul 2013 at 3:51
Original issue reported on code.google.com by
mc...@circuitscape.org
on 10 Jan 2012 at 5:18