[gentoo-science] status of lapack install

[gentoo-science] status of lapack install

[de Almeida, Valmor F.]

Hello,

Is lapack ready for gcc-4.1.1? On my system profile 2006.1, these are
the options for lapack install

->emerge --search lapack

*  sci-libs/lapack-atlas
      Latest version available: 3.7.11
      Latest version installed: [ Not Installed ]
      Size of files: 6,924 kB
      Homepage:      http://math-atlas.sourceforge.net/
      Description:   Full LAPACK implementation using available ATLAS
routines
      License:       BSD

*  sci-libs/lapack-config
      Latest version available: 1.0.1
      Latest version installed: [ Not Installed ]
      Size of files: 0 kB
      Homepage:      http://www.gentoo.org/
      Description:   Utility to change the default LAPACK library
      License:       GPL-2

*  sci-libs/lapack-reference
      Latest version available: 3.0-r1
      Latest version installed: [ Not Installed ]
      Size of files: 4,934 kB
      Homepage:      http://www.netlib.org/lapack/index.html
      Description:   FORTRAN reference implementation of LAPACK Linear
Algebra PACKage
      License:       lapack

I've checked the homepage of lapack-atlas and it says

At present, it provides C and Fortran77 interfaces to a portably
efficient BLAS implementation, as well as a few routines from LAPACK.

This does not seem as a *full* lapack implementation as called for in
the Description field above.

Therefore I am leaning towards the installation of the lapack-reference
package instead. This what an emerge for lapack-reference would do

->emerge --pretend --verbose lapack-reference

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  N    ] sci-libs/lapack-config-1.0.1  0 kB 
[ebuild  N    ] sci-libs/blas-atlas-3.7.11  USE="doc -debug" 1,991 kB 
[ebuild  N    ] sci-libs/lapack-reference-3.0-r1  USE="-debug -ifc"
4,935 kB

I suppose since the -ifc flag is the default, the intel compiler will
not be called and that the gcc gfortran (G95) compiler will. Is this a
correct assumption? Also what is the lapack-config package doing exactly
since the blas-config package is not pulled in.

Thanks,

--
Valmor

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Re: [gentoo-science] status of lapack install

[Adam Piątyszek]

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Dear Valmor,

* de Almeida, Valmor F. [2007-03-19 21:17]:
> Is lapack ready for gcc-4.1.1? On my system profile 2006.1, these are
> the options for lapack install

Yes, it is ready and working well. I personally use testing ~x86 versions,
so I can not say much about the stable ones, which are usually a bit
outdated. ;-)

[...]

> I've checked the homepage of lapack-atlas and it says
> 
> At present, it provides C and Fortran77 interfaces to a portably
> efficient BLAS implementation, as well as a few routines from LAPACK.
> 
> This does not seem as a *full* lapack implementation as called for in
> the Description field above.
> 
> Therefore I am leaning towards the installation of the lapack-reference
> package instead. This what an emerge for lapack-reference would do

In Gentoo, lapack-atlas is a joint package of a few optimised LAPACK
routines from ATLAS and the rest from NetLib's reference LAPACK. So, it
includes everything LAPACK has. If you care for performance, you should
give lapack-atlas a try.

> ->emerge --pretend --verbose lapack-reference
> 
> These are the packages that would be merged, in order:
> 
> Calculating dependencies... done!
> [ebuild  N    ] sci-libs/lapack-config-1.0.1  0 kB 
> [ebuild  N    ] sci-libs/blas-atlas-3.7.11  USE="doc -debug" 1,991 kB 
> [ebuild  N    ] sci-libs/lapack-reference-3.0-r1  USE="-debug -ifc"
> 4,935 kB

If you do not want to use lapack-atlas, you might consider installing
blas-reference (and optionally cblas-reference) instead of blas-atlas.

> I suppose since the -ifc flag is the default, the intel compiler will
> not be called and that the gcc gfortran (G95) compiler will. Is this a
> correct assumption?

Correct.

> Also what is the lapack-config package doing exactly
> since the blas-config package is not pulled in.

lapack-config and blas-config are used for setting /usr/lib/lib* links to
a particular blas/lapack library (reference, atlas, mkl, etc.). These are
outdated tools and eselect {blas,lapack,cblas} are their replacement in
testing ~ARCH.

Besides, blas-config is a runtime dependency for blas-atlas-3.7.11:
RDEPEND="sci-libs/blas-config",
so you should have it already installed on your system.

BR,
/Adam


-- 
-=#=-  Adam Piatyszek - "ediap"  -=#=-  JID: ediap (at) jabber.org  -=#=-
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Re: [gentoo-science] status of lapack install

[Markus Dittrich]

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On Mon, 19 Mar 2007, de Almeida, Valmor F. wrote:
>
> Hello,
> Calculating dependencies... done!
> [ebuild  N    ] sci-libs/lapack-config-1.0.1  0 kB
> [ebuild  N    ] sci-libs/blas-atlas-3.7.11  USE="doc -debug" 1,991 kB
> [ebuild  N    ] sci-libs/lapack-reference-3.0-r1  USE="-debug -ifc"
> 4,935 kB
>

The currently stable lapack-atlas and blas-atlas (3.7.11) compile
fine with gcc-4.x.
Should you go with lapack-reference you will need the most
recent lapack-reference-3.1.1 not lapack-reference-3.0-r1. 
The reference ebuilds (both lapack and blas) take less time
to compile but provide less optimized routines. Hence, you have
to decide what is more important to you.

cheers,
Markus


- -- 
Markus Dittrich (markusle)
Gentoo Linux Developer
Scientific applications
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RE: [gentoo-science] status of lapack install

[de Almeida, Valmor F.]

> -----Original Message-----
> From: Adam Piątyszek [mailto:ediap@ET.PUT.Poznan.PL]
> Sent: Monday, March 19, 2007 4:42 PM
> To: gentoo-science@lists.gentoo.org
> Subject: Re: [gentoo-science] status of lapack install

[lines deleted]

> In Gentoo, lapack-atlas is a joint package of a few optimised LAPACK
> routines from ATLAS and the rest from NetLib's reference LAPACK. So, it
> includes everything LAPACK has. If you care for performance, you should
> give lapack-atlas a try.

Thanks for the prompt info.

--
Valmor

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RE: [gentoo-science] status of lapack install

[de Almeida, Valmor F.]

> -----Original Message-----
> From: Markus Dittrich [mailto:markusle@gentoo.org]
> Sent: Monday, March 19, 2007 5:00 PM
> To: gentoo-science@lists.gentoo.org
> Subject: Re: [gentoo-science] status of lapack install

[lines deleted]

> 
> The currently stable lapack-atlas and blas-atlas (3.7.11) compile
> fine with gcc-4.x.
> Should you go with lapack-reference you will need the most
> recent lapack-reference-3.1.1 not lapack-reference-3.0-r1.
> The reference ebuilds (both lapack and blas) take less time
> to compile but provide less optimized routines. Hence, you have
> to decide what is more important to you.
> 
> cheers,
> Markus

Hi I went for lapack-atlas and the required blas-atlas did not compile.
It suggested an interactive approach so I did

interactive=1 emerge blas-atlas

and answered the questions. Finally it died here. Looks like sed is
looking for an input file.

++++++++++++++++++++++++++++++++++++
Configuration completed successfully.  You may want to examine the make
include
file (Make.xeon_dual) for accuracy before starting the install with the
command:
   make install arch=xeon_dual

rm -f ./xconfig
sed: no input files

!!! ERROR: sci-libs/blas-atlas-3.7.11 failed.
Call stack:
  ebuild.sh, line 1614:   Called dyn_compile
  ebuild.sh, line 971:   Called qa_call 'src_compile'
  environment, line 3681:   Called src_compile
  blas-atlas-3.7.11.ebuild, line 123:   Called reconfigure
  blas-atlas-3.7.11.ebuild, line 110:   Called die

++++++++++++++++++++++++++++++++++++

Any suggestions? Thanks,

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RE: [gentoo-science] status of lapack install

[Markus Dittrich]

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On Mon, 19 Mar 2007, de Almeida, Valmor F. wrote:
>> -----Original Message-----
>> From: Markus Dittrich [mailto:markusle@gentoo.org]
>> Sent: Monday, March 19, 2007 5:00 PM
>> To: gentoo-science@lists.gentoo.org
>> Subject: Re: [gentoo-science] status of lapack install
>
> [lines deleted]
>
>>
>> The currently stable lapack-atlas and blas-atlas (3.7.11) compile
>> fine with gcc-4.x.
>> Should you go with lapack-reference you will need the most
>> recent lapack-reference-3.1.1 not lapack-reference-3.0-r1.
>> The reference ebuilds (both lapack and blas) take less time
>> to compile but provide less optimized routines. Hence, you have
>> to decide what is more important to you.
>>
>> cheers,
>> Markus
>
> Hi I went for lapack-atlas and the required blas-atlas did not compile.
> It suggested an interactive approach so I did
>
> interactive=1 emerge blas-atlas
>
> and answered the questions. Finally it died here. Looks like sed is
> looking for an input file.
>

You probably have a newer CPU type on which blas-atlas'
configure routine is chocking. I'd try the most recent versions
in ~ARCH, i.e., blas/lapack-atlas-3.7.24.

Good luck,
Markus


- -- 
Markus Dittrich (markusle)
Gentoo Linux Developer
Scientific applications
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RE: [gentoo-science] status of lapack install

[de Almeida, Valmor F.]

> -----Original Message-----
> From: Markus Dittrich [mailto:markusle@gentoo.org]
> Sent: Monday, March 19, 2007 6:16 PM
> To: gentoo-science@lists.gentoo.org
> Subject: RE: [gentoo-science] status of lapack install
> 
> >
> > interactive=1 emerge blas-atlas
> >
> > and answered the questions. Finally it died here. Looks like sed is
> > looking for an input file.
> >
> 
> You probably have a newer CPU type on which blas-atlas'


The machine has two 2.6 MHz Xeon CPU's.


> configure routine is chocking. I'd try the most recent versions
> in ~ARCH, i.e., blas/lapack-atlas-3.7.24.
> 
> Good luck,
> Markus
> 
> 
> - --
> Markus Dittrich (markusle)
> Gentoo Linux Developer
> Scientific applications
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