Hi MMTKers and NUMPYers,
Bill's answer to my inquiry about the problem I'm having with Collection.findTransformation() (and also, incidentally, with the dgesvd call in Subspace.getBasis(), has convinced me that I can no long use MMTK without changing some of the code over to numpy. I have already been able to determine that invoking numpy.oldnumeric.alter_code1.convertall() over the MMTK directory tree is not the answer. Has anyone on either of these lists ever tried this before and, if so, can it be done (without destroying my sanity)?
Cheers,
Seth
On 9/19/06, Dr. Seth Olsen <[EMAIL PROTECTED]> wrote:
Hi Bill,
MMTK has not made the conversion over to the new numpy module. It is built against the old Numeric code, and the word from its developers is that changing to numpy cannot be a priority now.
Cheers,
SethOn 9/19/06, Bill Baxter < [EMAIL PROTECTED]> wrote:Hey there,
I don't see anything called "LinearAlgegra.eigenvectors()". Do you
maybe mean numpy.linalg.eig?
Which version of numpy are you using?
The latest release is 1.0b5.
>>> import numpy
>>> numpy.__version__
'1.0b5'
>>> numpy.linalg.eig([[2,1],[1,2]])
(array([ 3., 1.]),
array([[ 0.70710678, -0.70710678],
[ 0.70710678, 0.70710678]]))
I'm on WindowsXP, though.
Regards,
Bill
On 9/19/06, Dr. Seth Olsen <[EMAIL PROTECTED]> wrote:
>
> Hi Numpyers,
>
> I recently sent the message below to the MMTK mailing list, but it's really
> a problem with LinearAlgebra.py. The routine LinearAlgebra.eigenvectors()
> never stops, even when I try to diagonalize a very simple 2x2 matrix. I've
> tried this on two machines with completely standard FC4 and FC5
> installations using the default libraries and atlas libraries downloaded and
> installed via yum. Does anyone on this list have any experience with this
> problem?
>
> Cheers,
>
> Seth
>
> ---------- Forwarded message ----------
> From: Dr. Seth Olsen <[EMAIL PROTECTED] >
> Date: Sep 19, 2006 10:38 AM
> Subject: Re: Collection.findTransformation() never stops
> To: [EMAIL PROTECTED], [EMAIL PROTECTED]
>
>
> Hi MMTKers,
>
> The problem with Collection.findTransformation() that I reported earlier is
> due to a problem with LinearAlgebra.eigenvectors(). This algortithm does
> not seem to stop - it can't even manage to find the eigenvectors of the 2x2
> square matrix [[2,1],[1,2]]. Asking for this causes a long wait followed by
> CPU overheat warnings. Moreover, I have recompiled Numeric23.8 with newly
> installed atlas libraries, but it still won't work. I have had this problem
> now on 2 machines (one running FC4 with , the other FC5, both pentium 4
> machines), with atlas lapack/blas libraries installed freshly via yum and
> linked as per the recommendations found in setup.py . THE FEDORA
> INSTALLATIONS ON BOTH MACHINES IS STANDARD - everything has been downloaded
> and installed via the fedora yum repositories.
>
> As the eigenvectors() routine in LinearAlgebra.py is obviously going to be a
> heavily used algorithm (not just in MMTK), is it really possible that no one
> has had this problem before?
>
> Cheers,
>
> Seth
>
>
> On 9/18/06, Dr. Seth Olsen < [EMAIL PROTECTED]> wrote:
> >
> >
> > Hi MMTKers,
> >
> > I'm having a bit of trouble with
> MMTK.Collection.findTransformation . When I use this member
> function, the computer never stops thinking until I kill the process. I've
> waited a couple of hours and still nothing. I get the same thing if I try
> to take a step back and use
> Collection.findTransformationAsQuaternion. Has anyone had
> this problem before?
> >
> > Cheers,
> >
> > Seth
> >
> > --
> >
> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> >
> > Dr Seth Olsen, PhD
> > Postdoctoral Fellow, Biomolecular Modeling Group
> > Centre for Computational Molecular Science
> > Australian Institute for Bioengineering and Nanotechnology (Bldg. 75)
> > The University of Queensland
> > Qld 4072, Brisbane, Australia
> >
> > tel (617) 3346 3976
> > fax (617) 33654623
> > email: [EMAIL PROTECTED]
> > Web: www.ccms.uq.edu.au
> >
> >
> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> > The opinions expressed here are my own and do not reflect the positions of
> the University of Queensland.
>
>
>
> --
> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
>
> Dr Seth Olsen, PhD
> Postdoctoral Fellow, Biomolecular Modeling Group
> Centre for Computational Molecular Science
> Australian Institute for Bioengineering and Nanotechnology (Bldg. 75)
> The University of Queensland
> Qld 4072, Brisbane, Australia
>
> tel (617) 3346 3976
> fax (617) 33654623
> email: [EMAIL PROTECTED]
> Web: www.ccms.uq.edu.au
>
> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> The opinions expressed here are my own and do not reflect the positions of
> the University of Queensland.
>
> --
> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
>
> Dr Seth Olsen, PhD
> Postdoctoral Fellow, Biomolecular Modeling Group
> Centre for Computational Molecular Science
> Australian Institute for Bioengineering and Nanotechnology (Bldg. 75)
> The University of Queensland
> Qld 4072, Brisbane, Australia
>
> tel (617) 3346 3976
> fax (617) 33654623
> email: [EMAIL PROTECTED]
> Web: www.ccms.uq.edu.au
>
> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> The opinions expressed here are my own and do not reflect the positions of
> the University of Queensland.
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Dr Seth Olsen, PhD
Postdoctoral Fellow, Biomolecular Modeling Group
Centre for Computational Molecular Science
Australian Institute for Bioengineering and Nanotechnology (Bldg. 75)
The University of Queensland
Qld 4072, Brisbane, Australia
tel (617) 3346 3976
fax (617) 33654623
email: [EMAIL PROTECTED]
Web: www.ccms.uq.edu.au
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
The opinions expressed here are my own and do not reflect the positions of the University of Queensland.
--
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
Dr Seth Olsen, PhD
Postdoctoral Fellow, Biomolecular Modeling Group
Centre for Computational Molecular Science
Australian Institute for Bioengineering and Nanotechnology (Bldg. 75)
The University of Queensland
Qld 4072, Brisbane, Australia
tel (617) 3346 3976
fax (617) 33654623
email: [EMAIL PROTECTED]
Web: www.ccms.uq.edu.au
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
The opinions expressed here are my own and do not reflect the positions of the University of Queensland.
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