[gentoo-science] Fwd: sci-lib/atlas, static libraries, cblas, lapack

[gentoo-science] Fwd: sci-lib/atlas, static libraries, cblas, lapack

[jody]

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Hi
I have successfully installed sci-libs/atlas from the science overlay.

Now there are some points which are somewhat unclear.
I have been redirected here from the gentoo forum.

1. cblas implementation
Even though
 # eselect cblas list
Available providers for cblas:
  [1]   atlas *
  [2]   atlas-threads

all cblas libraries are pointing to gsl implementations:
 ls -l /usr/lib64/libcblas.*
lrwxrwxrwx 1 root root 13 Aug 20 10:54 /usr/lib64/libcblas.a ->
libgslcblas.a
lrwxrwxrwx 1 root root 14 Aug 20 10:54 /usr/lib64/libcblas.so ->
libgslcblas.so
lrwxrwxrwx 1 root root 16 Aug 20 10:54 /usr/lib64/libcblas.so.0 ->
libgslcblas.so.0

Shouldn't the '/usr/lib64/libcblas.so' point to '/usr/lib64/libatlcblas.so'
etc.?


2. static libs for cblas
The installation of sci-libs/atlas did not create any static libs:
  ls -l /usr/lib64/libatl*
lrwxrwxrwx 1 root root      13 Aug 22 09:11 /usr/lib64/libatlas.so ->
libatlas.so.3
-rwxr-xr-x 1 root root 5961968 Aug 22 09:11 /usr/lib64/libatlas.so.3
lrwxrwxrwx 1 root root      16 Aug 22 09:11 /usr/lib64/libatlcblas.so ->
libatlcblas.so.3
-rwxr-xr-x 1 root root  142504 Aug 22 09:11 /usr/lib64/libatlcblas.so.3

And i have at least one 3rd party code which requires the cblas libraries
to be linked statically.


3. eselect lapack
I found that 'app-admin/eselect-lapack' is blocking 'sci-libs/atlas',
but atlas did not pull in eselect for lapack:
  # eselect lapack list
!!! Error: Can't load module lapack
exiting
eselect-cblas is also blocking 'sci-libs/atlas', but apparently atlas pulls
in eselect for cblas.

4. Shouldn't there also be a lapack implementation from atlas?

Could somebody clarify or help out?
Jody

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Re: [gentoo-science] Fwd: sci-lib/atlas, static libraries, cblas, lapack

[François Bissey]

Hi Jody,

The mechanism for handling multiple BLAS/LAPACK in the science overlay
is incompatible with the one used in the main tree.
In particular the science overlay stack doesn't create link link to 
libcblas,
libblas and liblapack.
You have to unmask eselect from the science overlay as well as the 
virtuals
(cblas,blas and lapack) and remove all the tree eselect-blas, 
eselect-cblas
and eselect-lapack modules.
No packages in Gentoo, in the tree or the overlay, should use libblas, 
libcblas or
liblapack directly but configure it throught pkg-config.
All BLAS/LAPACK implementation in Gentoo provide .pc file for that 
purpose. With
the new science overlay structure you create a link for which .pc file 
is the default.

So once you have completed your move to the science overlay stack you 
need to remove
those links if they still exist.

Francois

On 2013-09-02 19:04, jody wrote:
> Hi
> I have successfully installed sci-libs/atlas from the science overlay.
> 
> Now there are some points which are somewhat unclear.
> 
> I have been redirected here from the gentoo forum.
> 
>  1. cblas implementation
>  Even though
> 
>  # eselect cblas list
>  Available providers for cblas:
>    [1]   atlas *
>    [2]   atlas-threads
> 
>  all cblas libraries are pointing to gsl implementations:
> 
>  ls -l /usr/lib64/libcblas.*
>  lrwxrwxrwx 1 root root 13 Aug 20 10:54 /usr/lib64/libcblas.a ->
> libgslcblas.a
>  lrwxrwxrwx 1 root root 14 Aug 20 10:54 /usr/lib64/libcblas.so ->
> libgslcblas.so
>  lrwxrwxrwx 1 root root 16 Aug 20 10:54 /usr/lib64/libcblas.so.0 ->
> libgslcblas.so.0
> 
>  Shouldn't the '/usr/lib64/libcblas.so' point to
> '/usr/lib64/libatlcblas.so' etc.?
> 
>  2. static libs for cblas
>  The installation of sci-libs/atlas did not create any static libs:
> 
>  ls -l /usr/lib64/libatl*
>  lrwxrwxrwx 1 root root      13 Aug 22 09:11 /usr/lib64/libatlas.so
> -> libatlas.so.3
>  -rwxr-xr-x 1 root root 5961968 Aug 22 09:11 /usr/lib64/libatlas.so.3
>  lrwxrwxrwx 1 root root      16 Aug 22 09:11
> /usr/lib64/libatlcblas.so -> libatlcblas.so.3
>  -rwxr-xr-x 1 root root  142504 Aug 22 09:11
> /usr/lib64/libatlcblas.so.3
> 
>  And i have at least one 3rd party code which requires the cblas
> libraries to be linked statically.
> 
>  3. eselect lapack
>  I found that 'app-admin/eselect-lapack' is blocking 'sci-libs/atlas',
> 
>  but atlas did not pull in eselect for lapack:
> 
>   # eselect lapack list
>  !!! Error: Can't load module lapack
>  exiting
> 
> eselect-cblas is also blocking 'sci-libs/atlas', but apparently atlas
> pulls in eselect for cblas.
> 
> 4. Shouldn't there also be a lapack implementation from atlas?
> 
>  Could somebody clarify or help out?
>  Jody

Re: [gentoo-science] Fwd: sci-lib/atlas, static libraries, cblas, lapack

[jody]

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Hi Francois
Thanks for your reply.

I already had eselect from the science overlay: version 1.3.7-r100[1] ([1]
refers to the science overlay)
and eselect-blas, eselect-cblas and eselect-lapack were already removed (i
had to do this to emerge atlas).

Now I unmasked and emerged the virtuals cblas, blas and lapack from the
science overlay.

when i look at the lib64 directory, i see
aim-octopus ~ # ls -l /usr/lib64/liblapack.*
lrwxrwxrwx 1 root root 28 Aug 20 09:43 /usr/lib64/liblapack.a ->
lapack/reference/liblapack.a
lrwxrwxrwx 1 root root 29 Aug 20 09:43 /usr/lib64/liblapack.so ->
lapack/reference/liblapack.so
lrwxrwxrwx 1 root root 31 Aug 20 09:43 /usr/lib64/liblapack.so.0 ->
lapack/reference/liblapack.so.0
aim-octopus ~ # ls -l /usr/lib64/libcblas.*
lrwxrwxrwx 1 root root 13 Aug 20 10:54 /usr/lib64/libcblas.a ->
libgslcblas.a
lrwxrwxrwx 1 root root 14 Aug 20 10:54 /usr/lib64/libcblas.so ->
libgslcblas.so
lrwxrwxrwx 1 root root 16 Aug 20 10:54 /usr/lib64/libcblas.so.0 ->
libgslcblas.so.0
aim-octopus ~ # ls -l /usr/lib64/libblas.*
lrwxrwxrwx 1 root root 24 Aug 19 18:07 /usr/lib64/libblas.a ->
blas/reference/libblas.a
lrwxrwxrwx 1 root root 25 Aug 19 18:07 /usr/lib64/libblas.so ->
blas/reference/libblas.so
lrwxrwxrwx 1 root root 27 Aug 19 18:07 /usr/lib64/libblas.so.0 ->
blas/reference/libblas.so.0

I found .pc files in /usr/lib64/blas/reference/ and
/usr/lib64/lapack/reference/ but there is no directory
/usr/lib64/cblas/reference. How can i get the cblas from the science
overlay?

I noticed that i have sci-libs/*-reference for blas and lapack emerged
(even though none of them are from the science overlay) but no
sci-libs/cblas-reference:
aim-octopus ~ # eix blas-reference
[I] sci-libs/blas-reference
     Available versions:  20070226 ~20070226-r2 **20070226-r3 ~20120925[1]
**99999999[1] {{doc static-libs test}}
     Installed versions:  20070226(18:07:30 08/19/13)(-doc)
     Homepage:            http://www.netlib.org/lapack/
     Description:         Reference implementation of BLAS

aim-octopus ~ # eix lapack-reference
[I] sci-libs/lapack-reference
     Available versions:  3.1.1-r1 ~3.2.1-r1 **3.2.1-r3 ~3.4.2[1] **9999[1]
{{doc static-libs test xblas}}
     Installed versions:  3.1.1-r1(09:43:40 08/20/13)(-doc)
     Homepage:            http://www.netlib.org/lapack/
     Description:         Reference implementation of LAPACK

[1] "science" /var/lib/layman/science

aim-octopus ~ # eix cblas-reference
* sci-libs/cblas-reference
     Available versions:  20030223-r4 ~20030223-r5 ~20110218[1]
{{static-libs}}
     Homepage:            http://www.netlib.org/blas/
     Description:         C wrapper interface to the F77 reference BLAS
implementation

[1] "science" /var/lib/layman/science


Do i need to emerge sci-libs/cblas-reference?
Do i need to unmask and emerge the overlay versions for all
sci-libs/*-reference as well?


I am sorry, but i don't understand what you said about the .pc files.
In what situation and how should i use the .pc file?

Thanks
  Jody



On Tue, Sep 3, 2013 at 12:57 AM, François Bissey <fbissey@slingshot.co.nz>wrote:

> Hi Jody,
>
> The mechanism for handling multiple BLAS/LAPACK in the science overlay
> is incompatible with the one used in the main tree.
> In particular the science overlay stack doesn't create link link to
> libcblas,
> libblas and liblapack.
> You have to unmask eselect from the science overlay as well as the virtuals
> (cblas,blas and lapack) and remove all the tree eselect-blas, eselect-cblas
> and eselect-lapack modules.
> No packages in Gentoo, in the tree or the overlay, should use libblas,
> libcblas or
> liblapack directly but configure it throught pkg-config.
> All BLAS/LAPACK implementation in Gentoo provide .pc file for that
> purpose. With
> the new science overlay structure you create a link for which .pc file is
> the default.
>
> So once you have completed your move to the science overlay stack you need
> to remove
> those links if they still exist.
>
> Francois
>
>
> On 2013-09-02 19:04, jody wrote:
>
>> Hi
>> I have successfully installed sci-libs/atlas from the science overlay.
>>
>> Now there are some points which are somewhat unclear.
>>
>> I have been redirected here from the gentoo forum.
>>
>>  1. cblas implementation
>>  Even though
>>
>>  # eselect cblas list
>>  Available providers for cblas:
>>    [1]   atlas *
>>    [2]   atlas-threads
>>
>>  all cblas libraries are pointing to gsl implementations:
>>
>>  ls -l /usr/lib64/libcblas.*
>>  lrwxrwxrwx 1 root root 13 Aug 20 10:54 /usr/lib64/libcblas.a ->
>> libgslcblas.a
>>  lrwxrwxrwx 1 root root 14 Aug 20 10:54 /usr/lib64/libcblas.so ->
>> libgslcblas.so
>>  lrwxrwxrwx 1 root root 16 Aug 20 10:54 /usr/lib64/libcblas.so.0 ->
>> libgslcblas.so.0
>>
>>  Shouldn't the '/usr/lib64/libcblas.so' point to
>> '/usr/lib64/libatlcblas.so' etc.?
>>
>>  2. static libs for cblas
>>  The installation of sci-libs/atlas did not create any static libs:
>>
>>  ls -l /usr/lib64/libatl*
>>  lrwxrwxrwx 1 root root      13 Aug 22 09:11 /usr/lib64/libatlas.so
>> -> libatlas.so.3
>>  -rwxr-xr-x 1 root root 5961968 Aug 22 09:11 /usr/lib64/libatlas.so.3
>>  lrwxrwxrwx 1 root root      16 Aug 22 09:11
>> /usr/lib64/libatlcblas.so -> libatlcblas.so.3
>>  -rwxr-xr-x 1 root root  142504 Aug 22 09:11
>> /usr/lib64/libatlcblas.so.3
>>
>>  And i have at least one 3rd party code which requires the cblas
>> libraries to be linked statically.
>>
>>  3. eselect lapack
>>  I found that 'app-admin/eselect-lapack' is blocking 'sci-libs/atlas',
>>
>>  but atlas did not pull in eselect for lapack:
>>
>>   # eselect lapack list
>>  !!! Error: Can't load module lapack
>>  exiting
>>
>> eselect-cblas is also blocking 'sci-libs/atlas', but apparently atlas
>> pulls in eselect for cblas.
>>
>> 4. Shouldn't there also be a lapack implementation from atlas?
>>
>>  Could somebody clarify or help out?
>>  Jody
>>
>
>

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Re: [gentoo-science] Fwd: sci-lib/atlas, static libraries, cblas, lapack

[jody]

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Hi
I think i begin to see how things have to work....
Just to make sure i understood correctly:
- the directories /usr/lib64/blas/reference/ and
/usr/lib64/lapack/reference/ and the libraries they contained are
irrelevant for the science overlay
- generally one compiles an application using cblas  with `pkg-config
--cflags cblas` and links it with `pkg-config --libs cblas` (and similarly
for blas and lapack)
Is this correct?

Thank You
  Jody


On Tue, Sep 3, 2013 at 11:57 AM, jody <jody.xha@gmail.com> wrote:

> Hi Francois
> Thanks for your reply.
>
> I already had eselect from the science overlay: version 1.3.7-r100[1] ([1]
> refers to the science overlay)
> and eselect-blas, eselect-cblas and eselect-lapack were already removed (i
> had to do this to emerge atlas).
>
> Now I unmasked and emerged the virtuals cblas, blas and lapack from the
> science overlay.
>
> when i look at the lib64 directory, i see
> aim-octopus ~ # ls -l /usr/lib64/liblapack.*
> lrwxrwxrwx 1 root root 28 Aug 20 09:43 /usr/lib64/liblapack.a ->
> lapack/reference/liblapack.a
> lrwxrwxrwx 1 root root 29 Aug 20 09:43 /usr/lib64/liblapack.so ->
> lapack/reference/liblapack.so
> lrwxrwxrwx 1 root root 31 Aug 20 09:43 /usr/lib64/liblapack.so.0 ->
> lapack/reference/liblapack.so.0
> aim-octopus ~ # ls -l /usr/lib64/libcblas.*
>
> lrwxrwxrwx 1 root root 13 Aug 20 10:54 /usr/lib64/libcblas.a ->
> libgslcblas.a
> lrwxrwxrwx 1 root root 14 Aug 20 10:54 /usr/lib64/libcblas.so ->
> libgslcblas.so
> lrwxrwxrwx 1 root root 16 Aug 20 10:54 /usr/lib64/libcblas.so.0 ->
> libgslcblas.so.0
> aim-octopus ~ # ls -l /usr/lib64/libblas.*
> lrwxrwxrwx 1 root root 24 Aug 19 18:07 /usr/lib64/libblas.a ->
> blas/reference/libblas.a
> lrwxrwxrwx 1 root root 25 Aug 19 18:07 /usr/lib64/libblas.so ->
> blas/reference/libblas.so
> lrwxrwxrwx 1 root root 27 Aug 19 18:07 /usr/lib64/libblas.so.0 ->
> blas/reference/libblas.so.0
>
> I found .pc files in /usr/lib64/blas/reference/ and
> /usr/lib64/lapack/reference/ but there is no directory
> /usr/lib64/cblas/reference. How can i get the cblas from the science
> overlay?
>
> I noticed that i have sci-libs/*-reference for blas and lapack emerged
> (even though none of them are from the science overlay) but no
> sci-libs/cblas-reference:
> aim-octopus ~ # eix blas-reference
> [I] sci-libs/blas-reference
>      Available versions:  20070226 ~20070226-r2 **20070226-r3 ~20120925[1]
> **99999999[1] {{doc static-libs test}}
>      Installed versions:  20070226(18:07:30 08/19/13)(-doc)
>      Homepage:            http://www.netlib.org/lapack/
>      Description:         Reference implementation of BLAS
>
> aim-octopus ~ # eix lapack-reference
> [I] sci-libs/lapack-reference
>      Available versions:  3.1.1-r1 ~3.2.1-r1 **3.2.1-r3 ~3.4.2[1]
> **9999[1] {{doc static-libs test xblas}}
>      Installed versions:  3.1.1-r1(09:43:40 08/20/13)(-doc)
>      Homepage:            http://www.netlib.org/lapack/
>      Description:         Reference implementation of LAPACK
>
> [1] "science" /var/lib/layman/science
>
> aim-octopus ~ # eix cblas-reference
> * sci-libs/cblas-reference
>      Available versions:  20030223-r4 ~20030223-r5 ~20110218[1]
> {{static-libs}}
>      Homepage:            http://www.netlib.org/blas/
>      Description:         C wrapper interface to the F77 reference BLAS
> implementation
>
> [1] "science" /var/lib/layman/science
>
>
> Do i need to emerge sci-libs/cblas-reference?
> Do i need to unmask and emerge the overlay versions for all
> sci-libs/*-reference as well?
>
>
> I am sorry, but i don't understand what you said about the .pc files.
> In what situation and how should i use the .pc file?
>
> Thanks
>   Jody
>
>
>
> On Tue, Sep 3, 2013 at 12:57 AM, François Bissey <fbissey@slingshot.co.nz>wrote:
>
>> Hi Jody,
>>
>> The mechanism for handling multiple BLAS/LAPACK in the science overlay
>> is incompatible with the one used in the main tree.
>> In particular the science overlay stack doesn't create link link to
>> libcblas,
>> libblas and liblapack.
>> You have to unmask eselect from the science overlay as well as the
>> virtuals
>> (cblas,blas and lapack) and remove all the tree eselect-blas,
>> eselect-cblas
>> and eselect-lapack modules.
>> No packages in Gentoo, in the tree or the overlay, should use libblas,
>> libcblas or
>> liblapack directly but configure it throught pkg-config.
>> All BLAS/LAPACK implementation in Gentoo provide .pc file for that
>> purpose. With
>> the new science overlay structure you create a link for which .pc file is
>> the default.
>>
>> So once you have completed your move to the science overlay stack you
>> need to remove
>> those links if they still exist.
>>
>> Francois
>>
>>
>> On 2013-09-02 19:04, jody wrote:
>>
>>> Hi
>>> I have successfully installed sci-libs/atlas from the science overlay.
>>>
>>> Now there are some points which are somewhat unclear.
>>>
>>> I have been redirected here from the gentoo forum.
>>>
>>>  1. cblas implementation
>>>  Even though
>>>
>>>  # eselect cblas list
>>>  Available providers for cblas:
>>>    [1]   atlas *
>>>    [2]   atlas-threads
>>>
>>>  all cblas libraries are pointing to gsl implementations:
>>>
>>>  ls -l /usr/lib64/libcblas.*
>>>  lrwxrwxrwx 1 root root 13 Aug 20 10:54 /usr/lib64/libcblas.a ->
>>> libgslcblas.a
>>>  lrwxrwxrwx 1 root root 14 Aug 20 10:54 /usr/lib64/libcblas.so ->
>>> libgslcblas.so
>>>  lrwxrwxrwx 1 root root 16 Aug 20 10:54 /usr/lib64/libcblas.so.0 ->
>>> libgslcblas.so.0
>>>
>>>  Shouldn't the '/usr/lib64/libcblas.so' point to
>>> '/usr/lib64/libatlcblas.so' etc.?
>>>
>>>  2. static libs for cblas
>>>  The installation of sci-libs/atlas did not create any static libs:
>>>
>>>  ls -l /usr/lib64/libatl*
>>>  lrwxrwxrwx 1 root root      13 Aug 22 09:11 /usr/lib64/libatlas.so
>>> -> libatlas.so.3
>>>  -rwxr-xr-x 1 root root 5961968 Aug 22 09:11 /usr/lib64/libatlas.so.3
>>>  lrwxrwxrwx 1 root root      16 Aug 22 09:11
>>> /usr/lib64/libatlcblas.so -> libatlcblas.so.3
>>>  -rwxr-xr-x 1 root root  142504 Aug 22 09:11
>>> /usr/lib64/libatlcblas.so.3
>>>
>>>  And i have at least one 3rd party code which requires the cblas
>>> libraries to be linked statically.
>>>
>>>  3. eselect lapack
>>>  I found that 'app-admin/eselect-lapack' is blocking 'sci-libs/atlas',
>>>
>>>  but atlas did not pull in eselect for lapack:
>>>
>>>   # eselect lapack list
>>>  !!! Error: Can't load module lapack
>>>  exiting
>>>
>>> eselect-cblas is also blocking 'sci-libs/atlas', but apparently atlas
>>> pulls in eselect for cblas.
>>>
>>> 4. Shouldn't there also be a lapack implementation from atlas?
>>>
>>>  Could somebody clarify or help out?
>>>  Jody
>>>
>>
>>
>

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Re: [gentoo-science] Fwd: sci-lib/atlas, static libraries, cblas, lapack

[François Bissey]

On 2013-09-04 03:29, jody wrote:
> Hi
> I think i begin to see how things have to work....
> 
> Just to make sure i understood correctly:
> 
> - the directories /usr/lib64/blas/reference/ and
> /usr/lib64/lapack/reference/ and the libraries they contained are
> irrelevant for the science overlay
> 
> - generally one compiles an application using cblas  with `pkg-config
> --cflags cblas` and links it with `pkg-config --libs cblas` (and
> similarly for blas and lapack)
> 
> Is this correct?
> 

Hi Jody,

This is correct. Once you have completely migrated to the science
overlay stack you should remove any of the leftover links as they can
have troublesome side effects.

Francois