[Numpy-discussion] Fwd: Collection.findTransformation() never stops

Dr. Seth Olsen seth.olsen at gmail.com
Mon Sep 18 22:11:35 CDT 2006


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 <seth.olsen at gmail.com> 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,
>
> Seth
>
>
> On 9/19/06, Bill Baxter <wbaxter at gmail.com> 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 <seth.olsen at gmail.com> 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 <seth.olsen at gmail.com >
> > > Date: Sep 19, 2006 10:38 AM
> > > Subject: Re: Collection.findTransformation() never stops
> > > To: mmtk at python.net, mmtk at starship.python.net
> > >
> > >
> > > 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 < seth.olsen at gmail.com> 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: s.olsen1 at uq.edu.au
> > > > 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: s.olsen1 at uq.edu.au
> > > 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: s.olsen1 at uq.edu.au
> > > 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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> --
>
> 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: s.olsen1 at uq.edu.au
> 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: s.olsen1 at uq.edu.au
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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