[MMTK] Re: Collection.findTransformation() never stops

Dr. Seth Olsen seth.olsen at gmail.com
Tue Sep 19 13:38:06 CEST 2006


Hi Konrad,

Thank you for pointing me towards the previous discussion.  The last time I
searched my archives I don't think I understood where the problem was coming
from, and so I overlooked them because I searched for the wrong key terms.
I apologize to the list if I sounded frustrated earlier - it is a testament
to MMTK's utility that I expected the task ahead of me to be quite easy and
fun, and quickly became frustrated when I encountered this hiccup.  Thank
you for your advice.

Cheers,

Seth

On 9/19/06, Konrad Hinsen <hinsen at cnrs-orleans.fr> wrote:
>
> On Sep 19, 2006, at 2:38, Dr. Seth Olsen wrote:
>
> > 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?
>
> This is a well-known problem and has been discussed on this list
> before. It concerns most (if not all) Linux distributions that use
> GCC 4. GCC 4 does not translate CLAPACK code correctly when used with
> its default options, though I can't say if this is GCC's or f2c's
> fault (CLAPACK is LAPACK translated to C using f2c). Both Numeric and
> MMTK contain CLAPACK code.
>
> The solution is to install both Numeric and MMTK using
>
>         CFLAGS='-ffloat-store' python setup.py build
>
> in place of the simple
>
>         python setup.py build
>
> With MMTK 2.5.14, this is included already in setup.py, but you will
> still have to apply the fix for Numeric.
>
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: hinsen at cnrs-orleans.fr
> ---------------------------------------------------------------------
>
>
>


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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: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au

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The opinions expressed here are my own and do not reflect the positions of
the University of Queensland.
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