Linear Algebra Libraries

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Linear Algebra Libraries

Sylvestre Ledru-6
Hello,

I am planning to upload some modifications in the way Linear Algebra
Libraries BLAS / LAPACK and ATLAS are handle in Debian. These libraries
are very used by many scientific software.
They didn't have many attentions during the last few years and ATLAS in
unstable is in a pretty bad shape (old version, plenty of bugs, hard to
use ...)
I described what I am planning to do in this wiki page:
http://wiki.debian.org/DebianScience/LinearAlgebraLibraries
and my changes have been tested.

There will be no need of transition since the ABI remains the same and
is pretty stable (it is very common to switch between BLAS and LAPACK
implementation) and the the impact should be low.

I would like your opinion on these uploads.

Sylvestre


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Re: Linear Algebra Libraries

Marc 'HE' Brockschmidt-3
Sylvestre Ledru <[hidden email]> writes:
> I am planning to upload some modifications in the way Linear Algebra
> Libraries BLAS / LAPACK and ATLAS are handle in Debian. These libraries
> are very used by many scientific software.
> They didn't have many attentions during the last few years and ATLAS in
> unstable is in a pretty bad shape (old version, plenty of bugs, hard to
> use ...)
> I described what I am planning to do in this wiki page:
> http://wiki.debian.org/DebianScience/LinearAlgebraLibraries
> and my changes have been tested.

I have to admit that I'm a bit uncomfortable with using
update-alternatives to switch between libary implementations. I am not
aware of any other package doing this. Is there a reason for not doing
it on the package level, allowing users to just install the package
fitting their needs and machine? Is it really common to switch
implementations on the same machine very often?

Marc
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Re: Linear Algebra Libraries

Sylvestre Ledru-6
Le samedi 20 mars 2010 à 13:49 +0100, Marc 'HE' Brockschmidt a écrit :

> Sylvestre Ledru <[hidden email]> writes:
> > I am planning to upload some modifications in the way Linear Algebra
> > Libraries BLAS / LAPACK and ATLAS are handle in Debian. These libraries
> > are very used by many scientific software.
> > They didn't have many attentions during the last few years and ATLAS in
> > unstable is in a pretty bad shape (old version, plenty of bugs, hard to
> > use ...)
> > I described what I am planning to do in this wiki page:
> > http://wiki.debian.org/DebianScience/LinearAlgebraLibraries
> > and my changes have been tested.
>
> I have to admit that I'm a bit uncomfortable with using
> update-alternatives to switch between libary implementations. I am not
> aware of any other package doing this.
This is done with the different MPI implementation (openmpi, mpich2,
etc)

> Is there a reason for not doing
> it on the package level, allowing users to just install the package
> fitting their needs and machine?
Yes, it does improve the performance of software based this libraries.

> Is it really common to switch
> implementations on the same machine very often?
Yes, it is. This kind of library are used by Scilab, R or Octave. They
relies strongly on these libraries and for precision, confirmation of
the result and performances, it is common to switch between the
different implementation.
Now, it has to be managed by upstream (which is pretty hard and boring)
or by the user with LD_LIBRARY_PATH (if upstream allows that)

Sylvestre






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Re: Linear Algebra Libraries

Thomas Weber-8
On Sat, Mar 20, 2010 at 06:00:04PM +0100, Sylvestre Ledru wrote:

> Le samedi 20 mars 2010 à 13:49 +0100, Marc 'HE' Brockschmidt a écrit :
> > Sylvestre Ledru <[hidden email]> writes:
> > > I am planning to upload some modifications in the way Linear Algebra
> > > Libraries BLAS / LAPACK and ATLAS are handle in Debian. These libraries
> > > are very used by many scientific software.
> > > They didn't have many attentions during the last few years and ATLAS in
> > > unstable is in a pretty bad shape (old version, plenty of bugs, hard to
> > > use ...)
> > > I described what I am planning to do in this wiki page:
> > > http://wiki.debian.org/DebianScience/LinearAlgebraLibraries
> > > and my changes have been tested.
> >
> > I have to admit that I'm a bit uncomfortable with using
> > update-alternatives to switch between libary implementations. I am not
> > aware of any other package doing this.
> This is done with the different MPI implementation (openmpi, mpich2,
> etc)
>
> > Is there a reason for not doing
> > it on the package level, allowing users to just install the package
> > fitting their needs and machine?
> Yes, it does improve the performance of software based this libraries.
>
> > Is it really common to switch
> > implementations on the same machine very often?
> Yes, it is. This kind of library are used by Scilab, R or Octave. They
> relies strongly on these libraries and for precision, confirmation of
> the result and performances, it is common to switch between the
> different implementation.

As Octave maintainer, I can confirm that switching the libraries is a
routine[1]. Having a reference implementation and some highly tuned (but
occasionally buggy) implementation is extremely valuable.

Example of such a case on upstream's list:
http://www-old.cae.wisc.edu/pipermail/bug-octave/2010-January/010231.html

Example in Debian:
http://bugs.debian.org/570231

[1] Actually, I'm pretty sad that ATLAS isn't allowed any more to ship a
configuration file in /etc/ld.so.conf.d/ .
        Thomas


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Re: Linear Algebra Libraries

Sylvestre Ledru-6
Le samedi 20 mars 2010 à 20:21 +0100, Thomas Weber a écrit :
> On Sat, Mar 20, 2010 at 06:00:04PM +0100, Sylvestre Ledru wrote:
> > Le samedi 20 mars 2010 à 13:49 +0100, Marc 'HE' Brockschmidt a écrit :
> > > Sylvestre Ledru <[hidden email]> writes:
> > > > I am planning to upload some modifications in the way Linear Algebra
> > > > Libraries BLAS / LAPACK and ATLAS are handle in Debian. These libraries
> > > > are very used by many scientific software.
[...]

> > > Is it really common to switch
> > > implementations on the same machine very often?
> > Yes, it is. This kind of library are used by Scilab, R or Octave. They
> > relies strongly on these libraries and for precision, confirmation of
> > the result and performances, it is common to switch between the
> > different implementation.
>
> As Octave maintainer, I can confirm that switching the libraries is a
> routine[1]. Having a reference implementation and some highly tuned (but
> occasionally buggy) implementation is extremely valuable.
Thanks for the confirmation.

> Example in Debian:
> http://bugs.debian.org/570231
>
> [1] Actually, I'm pretty sad that ATLAS isn't allowed any more to ship a
> configuration file in /etc/ld.so.conf.d/ .
I am too. It is why I had to come up with the alternatives solution.

Sylvestre





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Re: Linear Algebra Libraries

Marc 'HE' Brockschmidt-3
Hi,

Sylvestre Ledru <[hidden email]> writes:

> Le samedi 20 mars 2010 à 20:21 +0100, Thomas Weber a écrit :
>> On Sat, Mar 20, 2010 at 06:00:04PM +0100, Sylvestre Ledru wrote:
>> > Le samedi 20 mars 2010 à 13:49 +0100, Marc 'HE' Brockschmidt a écrit :
>> > > Sylvestre Ledru <[hidden email]> writes:
>> > > > I am planning to upload some modifications in the way Linear Algebra
>> > > > Libraries BLAS / LAPACK and ATLAS are handle in Debian. These libraries
>> > > > are very used by many scientific software.
> [...]
>> > > Is it really common to switch
>> > > implementations on the same machine very often?
>> > Yes, it is. This kind of library are used by Scilab, R or Octave. They
>> > relies strongly on these libraries and for precision, confirmation of
>> > the result and performances, it is common to switch between the
>> > different implementation.
>> As Octave maintainer, I can confirm that switching the libraries is a
>> routine[1]. Having a reference implementation and some highly tuned (but
>> occasionally buggy) implementation is extremely valuable.
> Thanks for the confirmation.
OK, so I guess we will have to go to this way. Upload whenever you want,
this shouldn't break anything, at least I hope so.

Marc
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