[Insight-users] ITK and netlab

[Kaveh Kohan]

Hi Luis,

Thank you for the answer.

I am looking for linear algebra functionally because part of my algorithm has massive iterative matrix-matrix product and I am looking for an efficient way of performing matrix-matrix product.

I did not find VNL sparse matrix strong enough thus I ended up using gmm++. I thought (also they mentioned in their website) that gmm++ is an interface to blas/lapck/atlas but unfortunately I see a huge gap between effciency of matrix-matrix prodcut between MATLAB and gmm (for matrix size I have: 17sec  vs. 0.5sec). Hence, I am tryig to close the gap by using various libraries including vnl (only for dense matrix-matrix operation). I do not expect to be as fast as MATLAB but I feel that I am doing something wrong since the gap is too big.

Any help or idea is highly appreciated.

Regards,
Kaveh




________________________________
From: Luis Ibanez <luis.ibanez at kitware.com>
To: Kaveh Kohan <kaveh.kohan at yahoo.com>
Cc: insight-users at itk.org
Sent: Tuesday, March 31, 2009 7:42:58 PM
Subject: Re: [Insight-users] ITK and netlab

Hi Kaveh,


Your first two questions will be better addressed if you post them to
the VXL users list.

(it is a kind way to say that : we don't really know....)    :-)

--

In the context of ITK, we use VXL mainly for providing the following
functionalities

    A) Linear algebra solutions
    B) Optimization

most of the methods for (A) and (B) will be provided by vnl throught
the vnl_matrix
and vnl_vector classes. You will find the most used method under the directory

                                Insight/Utilities/vxl/core/vnl/algo


Some of these algorithms are implemented in VXL by making calls to functions
provided by blas, while others are provided by lapack.


When we make use of vxl, we rarely expose the internal implementations of the
methods. That is, we never call  the blas or lapack routines directly.
Instead we
do this through the C++ API defined by VXL.


What specific functionalities do you have in mind ?

Are you looking for Linear Algebra ? or for Optimizations  ? or something else ?


   Please let us know,


         Thanks


--------------------------------------------------------------------------------------------------------
On Tue, Mar 31, 2009 at 10:56 AM, Kaveh Kohan <kaveh.kohan at yahoo.com> wrote:
> Dear All,
>
> I have a question about using and linking ITK programs to the netlib
> libraries already available in the following folder inside of the ITK
> directory tree:
>
> $ITKDIR/Utilities/vxl/v3p/netlib/blas
> $ITKDIR/Utilities/vxl/v3p/netlib/lapack
> $ITKDIR/Utilities/vxl/v3p/netlib/linpack
> $ITKDIR/Utilities/vxl/v3p/netlib/sparse
> $ITKDIR/Utilities/vxl/v3p/netlib/libf2c
> ...
>
> Here is my question and I would be thankful if you can help:
>
> 1) Does VXL by default uses blas for its operations or one needs to activate
> special flag to activate it? If yes, does anybody know how I can activate
> using blas, lapck?
>
> 2) When one calls VNL class, does it use lapack, blas or one needs to set a
> flag for it?
>
> 3) Is there any example about using blas, lack inside of itk programs?
>
> Thanks,
> Kaveh
>
>
>
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