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* [gentoo-user] Problem with cblas libraries
@ 2011-08-26 12:12 denis cohen
  2011-08-26 15:36 ` Helmut Jarausch
                   ` (3 more replies)
  0 siblings, 4 replies; 11+ messages in thread
From: denis cohen @ 2011-08-26 12:12 UTC (permalink / raw
  To: gentoo-user

Hello,

I recently removed some packages like blas-reference, cblas-reference,
and lapack-reference to get emerge to run (some blocking issues).
Not sure that was a good idea because now, even if I've reinstalled
these packages,
I am having several new problems:

- compiling gcc with the gsl library spits out errors like:
g++ -L/usr/local/lib -lm -lgsl  exact.o
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
undefined reference to `cblas_ctrmv'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
undefined reference to `cblas_zswap'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
undefined reference to `cblas_zsymm'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
undefined reference to `cblas_cgeru'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
undefined reference to `cblas_sgemm'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
undefined reference to `cblas_ctrsv'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
undefined reference to `cblas_sgemv'
and so on.......

- still can't re-emerge packages like gsl and gmsh. For example, for gmsh I get;
.....
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshDraw.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshQuad.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshWrite.cpp.o
[100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o
make[2]: *** No rule to make target `/usr/lib64/libcblas.so', needed
by `gmsh'.  Stop.
make[2]: *** Waiting for unfinished jobs....
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/SetOfE4.cpp.o
make[1]: *** [CMakeFiles/gmsh.dir/all] Error 2
make: *** [all] Error 2
emake failed
 * ERROR: sci-libs/gmsh-2.5.0 failed (compile phase):
 *   Make failed!
 *
 * Call stack:
 *     ebuild.sh, line   56:  Called src_compile
 *   environment, line 2995:  Called cmake-utils_src_compile
 *   environment, line  866:  Called _execute_optionaly 'src_compile'
 *   environment, line  291:  Called enable_cmake-utils_src_compile
 *   environment, line 1105:  Called cmake-utils_src_make
 *   environment, line  885:  Called die
 * The specific snippet of code:
 *           emake "$@" || die "Make failed!";
 *
 * If you need support, post the output of 'emerge --info =sci-libs/gmsh-2.5.0',
 * the complete build log and the output of 'emerge -pqv =sci-libs/gmsh-2.5.0'.
 * This ebuild is from an overlay named 'science': '/var/lib/layman/science/'
 * The complete build log is located at
'/var/tmp/portage/sci-libs/gmsh-2.5.0/temp/build.log'.
 * The ebuild environment file is located at
'/var/tmp/portage/sci-libs/gmsh-2.5.0/temp/environment'.
 * S: '/var/tmp/portage/sci-libs/gmsh-2.5.0/work/gmsh-2.5.0-source'

>>> Failed to emerge sci-libs/gmsh-2.5.0, Log file:

>>>  '/var/tmp/portage/sci-libs/gmsh-2.5.0/temp/build.log'


/usr/lib64/libcblas.so is present:


Does anyone have an idea of how solve this problem?

I'd be glad to provide more details.

Thanks

Denis



^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: [gentoo-user] Problem with cblas libraries
  2011-08-26 12:12 [gentoo-user] Problem with cblas libraries denis cohen
@ 2011-08-26 15:36 ` Helmut Jarausch
  2011-08-26 17:41 ` [gentoo-user] " Gene Hannan
                   ` (2 subsequent siblings)
  3 siblings, 0 replies; 11+ messages in thread
From: Helmut Jarausch @ 2011-08-26 15:36 UTC (permalink / raw
  To: gentoo-user

On 08/26/2011 02:12:35 PM, denis cohen wrote:
> Hello,
> 
> I recently removed some packages like blas-reference, cblas-
> reference,
> and lapack-reference to get emerge to run (some blocking issues).
> Not sure that was a good idea because now, even if I've reinstalled
> these packages,


I cannot say anything about sci-libs/gmsh since this is not in my 
portage tree. Are you using an overlay for that?

As gsl is concerned I have

sci-libs/gsl with the -cblas-external USE flag here.

Helmut.



^ permalink raw reply	[flat|nested] 11+ messages in thread

* [gentoo-user] Re: Problem with cblas libraries
  2011-08-26 12:12 [gentoo-user] Problem with cblas libraries denis cohen
  2011-08-26 15:36 ` Helmut Jarausch
@ 2011-08-26 17:41 ` Gene Hannan
  2011-08-26 21:20 ` [gentoo-user] " Alex Schuster
  2011-08-27 15:27 ` Valmor de Almeida
  3 siblings, 0 replies; 11+ messages in thread
From: Gene Hannan @ 2011-08-26 17:41 UTC (permalink / raw
  To: gentoo-user

On 08/26/2011 05:12 AM, denis cohen wrote:
> Hello,
>
> I recently removed some packages like blas-reference, cblas-reference,
> and lapack-reference to get emerge to run (some blocking issues).
> Not sure that was a good idea because now, even if I've reinstalled
> these packages,
> I am having several new problems:
>
> - compiling gcc with the gsl library spits out errors like:
> g++ -L/usr/local/lib -lm -lgsl  exact.o
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
> undefined reference to `cblas_ctrmv'
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
> undefined reference to `cblas_zswap'
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
> undefined reference to `cblas_zsymm'
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
> undefined reference to `cblas_cgeru'
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
> undefined reference to `cblas_sgemm'
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
> undefined reference to `cblas_ctrsv'
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
> undefined reference to `cblas_sgemv'
> and so on.......
>
> - still can't re-emerge packages like gsl and gmsh. For example, for gmsh I get;
> .....
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshDraw.cpp.o
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshQuad.cpp.o
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshWrite.cpp.o
> [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o
> make[2]: *** No rule to make target `/usr/lib64/libcblas.so', needed
> by `gmsh'.  Stop.
> make[2]: *** Waiting for unfinished jobs....
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/SetOfE4.cpp.o
> make[1]: *** [CMakeFiles/gmsh.dir/all] Error 2
> make: *** [all] Error 2
> emake failed
>   * ERROR: sci-libs/gmsh-2.5.0 failed (compile phase):
>   *   Make failed!
>   *
>   * Call stack:
>   *     ebuild.sh, line   56:  Called src_compile
>   *   environment, line 2995:  Called cmake-utils_src_compile
>   *   environment, line  866:  Called _execute_optionaly 'src_compile'
>   *   environment, line  291:  Called enable_cmake-utils_src_compile
>   *   environment, line 1105:  Called cmake-utils_src_make
>   *   environment, line  885:  Called die
>   * The specific snippet of code:
>   *           emake "$@" || die "Make failed!";
>   *
>   * If you need support, post the output of 'emerge --info =sci-libs/gmsh-2.5.0',
>   * the complete build log and the output of 'emerge -pqv =sci-libs/gmsh-2.5.0'.
>   * This ebuild is from an overlay named 'science': '/var/lib/layman/science/'
>   * The complete build log is located at
> '/var/tmp/portage/sci-libs/gmsh-2.5.0/temp/build.log'.
>   * The ebuild environment file is located at
> '/var/tmp/portage/sci-libs/gmsh-2.5.0/temp/environment'.
>   * S: '/var/tmp/portage/sci-libs/gmsh-2.5.0/work/gmsh-2.5.0-source'
>
>>>> Failed to emerge sci-libs/gmsh-2.5.0, Log file:
>
>>>>   '/var/tmp/portage/sci-libs/gmsh-2.5.0/temp/build.log'
>
>
> /usr/lib64/libcblas.so is present:
>
>
> Does anyone have an idea of how solve this problem?
>
> I'd be glad to provide more details.
>
> Thanks
>
> Denis
>
>

Perhaps you need to run eselect cblas after re-emerging?



^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: [gentoo-user] Problem with cblas libraries
  2011-08-26 12:12 [gentoo-user] Problem with cblas libraries denis cohen
  2011-08-26 15:36 ` Helmut Jarausch
  2011-08-26 17:41 ` [gentoo-user] " Gene Hannan
@ 2011-08-26 21:20 ` Alex Schuster
  2011-08-27 15:27 ` Valmor de Almeida
  3 siblings, 0 replies; 11+ messages in thread
From: Alex Schuster @ 2011-08-26 21:20 UTC (permalink / raw
  To: gentoo-user

denis cohen writes:

> I recently removed some packages like blas-reference, cblas-reference,
> and lapack-reference to get emerge to run (some blocking issues).

I unmerged eselect-cblas and eselect-blas when I had similar problems, and I 
think also {blas,cblas}-reference. The eselect packages got remerged 
automatically, and some block I do not remember remained, but after some 
days, a deep world update finally was working again.

> Not sure that was a good idea because now, even if I've reinstalled
> these packages,
> I am having several new problems:
> 
> - compiling gcc with the gsl library spits out errors like:
> g++ -L/usr/local/lib -lm -lgsl  exact.o
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
> undefined reference to `cblas_ctrmv'
[...]
> and so on.......
> 
> - still can't re-emerge packages like gsl and gmsh. For example, for gmsh
> I get; .....
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshDraw.cpp.o
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshQuad.cpp.o
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshWrite.cpp.o
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o [100%] Building CXX
> object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o
> make[2]: *** No rule to make target `/usr/lib64/libcblas.so', needed
> by `gmsh'.  Stop.

This looks strange. A target in the root file system? Here the log continues 
like this:

[100%] Building CXX object 
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o
[100%] Building CXX object 
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o
[100%] Building CXX object 
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/SetOfE4.cpp.o
Linking CXX executable gmsh
[100%] Built target gmsh
>>> Source compiled.
>>> Test phase [not enabled]: sci-libs/gmsh-2.5.0



> Does anyone have an idea of how solve this problem?

No. All I can say is that I just emerged gmsh without problems on ~amd64,  
both with and without the blas USE flag. The other USE flags are those:
     Installed versions:  2.5.0{tbz2}(23:10:59 26.08.2011)(X blas jpeg png 
zlib -cgns -chaco -doc -examples -lua -med -metis -mpi -netgen -opencascade 
-petsc -taucs -tetgen)                                             

	Wonko



^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: [gentoo-user] Problem with cblas libraries
  2011-08-26 12:12 [gentoo-user] Problem with cblas libraries denis cohen
                   ` (2 preceding siblings ...)
  2011-08-26 21:20 ` [gentoo-user] " Alex Schuster
@ 2011-08-27 15:27 ` Valmor de Almeida
  2011-08-27 16:34   ` Michael Mol
  3 siblings, 1 reply; 11+ messages in thread
From: Valmor de Almeida @ 2011-08-27 15:27 UTC (permalink / raw
  To: gentoo-user

On 08/26/2011 08:12 AM, denis cohen wrote:
> Hello,
> 
> I recently removed some packages like blas-reference, cblas-reference,
> and lapack-reference to get emerge to run (some blocking issues).
> Not sure that was a good idea because now, even if I've reinstalled
> these packages,
> I am having several new problems:
> 
[snip]
> 
> 
> Does anyone have an idea of how solve this problem?
> 
> I'd be glad to provide more details.
> 
> Thanks
> 
> Denis
> 

Hi Denis,

Have you done revdep-rebuild ? followed by a emerge --depclean ? before
doing anything else after you removed the blas/lapack packages?


--
Valmor




^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: [gentoo-user] Problem with cblas libraries
  2011-08-27 15:27 ` Valmor de Almeida
@ 2011-08-27 16:34   ` Michael Mol
  2011-08-30 22:15     ` denis cohen
  0 siblings, 1 reply; 11+ messages in thread
From: Michael Mol @ 2011-08-27 16:34 UTC (permalink / raw
  To: gentoo-user

On Sat, Aug 27, 2011 at 11:27 AM, Valmor de Almeida
<val.gentoo@gmail.com> wrote:
> On 08/26/2011 08:12 AM, denis cohen wrote:
>> Hello,
>>
>> I recently removed some packages like blas-reference, cblas-reference,
>> and lapack-reference to get emerge to run (some blocking issues).
>> Not sure that was a good idea because now, even if I've reinstalled
>> these packages,
>> I am having several new problems:
>>
> [snip]
>>
>>
>> Does anyone have an idea of how solve this problem?
>>
>> I'd be glad to provide more details.
>>
>> Thanks
>>
>> Denis
>>
>
> Hi Denis,
>
> Have you done revdep-rebuild ? followed by a emerge --depclean ? before
> doing anything else after you removed the blas/lapack packages?

revdep-rebuild
emerge --depclean
revdep-rebuild # Since emerge --depclean will warn that you should do
a revdep-rebuild after it.


-- 
:wq



^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: [gentoo-user] Problem with cblas libraries
  2011-08-27 16:34   ` Michael Mol
@ 2011-08-30 22:15     ` denis cohen
  2011-08-30 22:27       ` Michael Mol
  2011-08-30 23:02       ` Alex Schuster
  0 siblings, 2 replies; 11+ messages in thread
From: denis cohen @ 2011-08-30 22:15 UTC (permalink / raw
  To: gentoo-user

Thanks to all that responded. I've tried

revdep-rebuild
emerge --depclean
revdep-rebuild

with no progress on the errors I have.
I've unmerged cblas* blas* gsl, synced, and "emerge -uDN world "also
without success (also tried cblas-external USE flag but could not see
it with eix).
eselect cblas also gave no results.

One problem I may have is with eselect. eselect-cblas has been
unmerged but trying to re-emerge it gives this block.


emerge -vp eselect-cblas

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

Calculating dependencies... done!
[ebuild  N     ] app-admin/eselect-cblas-0.1  0 kB
[blocks B      ] app-admin/eselect-cblas ("app-admin/eselect-cblas" is
blocking sci-libs/lapack-reference-3.3.1-r1, sci-libs/gsl-1.15-r1)

Total: 1 package (1 new), Size of downloads: 0 kB
Conflict: 1 block (1 unsatisfied)

 * Error: The above package list contains packages which cannot be
 * installed at the same time on the same system.

 (app-admin/eselect-cblas-0.1::gentoo, ebuild scheduled for merge) pulled in by
   eselect-cblas

 (sci-libs/lapack-reference-3.3.1-r1::science, installed) pulled in by
   >=sci-libs/lapack-reference-3.3 required by
(virtual/lapack-3.3::science, installed)

 (sci-libs/gsl-1.15-r1::science, installed) pulled in by
   sci-libs/gsl required by (media-gfx/inkscape-0.48.2::gentoo, installed)
   >=sci-libs/gsl-1.14-r2 required by (virtual/cblas-2.0::science, installed)


For more information about Blocked Packages, please refer to the following
section of the Gentoo Linux x86 Handbook (architecture is irrelevant):

http://www.gentoo.org/doc/en/handbook/handbook-x86.xml?full=1#blocked



Similar problem with eselect-blas and eselect-lapack. Any ideas before
I try some more unmerging?

Thanks

Denis

On Sat, Aug 27, 2011 at 18:34, Michael Mol <mikemol@gmail.com> wrote:
> On Sat, Aug 27, 2011 at 11:27 AM, Valmor de Almeida
> <val.gentoo@gmail.com> wrote:
>> On 08/26/2011 08:12 AM, denis cohen wrote:
>>> Hello,
>>>
>>> I recently removed some packages like blas-reference, cblas-reference,
>>> and lapack-reference to get emerge to run (some blocking issues).
>>> Not sure that was a good idea because now, even if I've reinstalled
>>> these packages,
>>> I am having several new problems:
>>>
>> [snip]
>>>
>>>
>>> Does anyone have an idea of how solve this problem?
>>>
>>> I'd be glad to provide more details.
>>>
>>> Thanks
>>>
>>> Denis
>>>
>>
>> Hi Denis,
>>
>> Have you done revdep-rebuild ? followed by a emerge --depclean ? before
>> doing anything else after you removed the blas/lapack packages?
>
> revdep-rebuild
> emerge --depclean
> revdep-rebuild # Since emerge --depclean will warn that you should do
> a revdep-rebuild after it.
>
>
> --
> :wq
>
>



^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: [gentoo-user] Problem with cblas libraries
  2011-08-30 22:15     ` denis cohen
@ 2011-08-30 22:27       ` Michael Mol
  2011-08-30 23:02       ` Alex Schuster
  1 sibling, 0 replies; 11+ messages in thread
From: Michael Mol @ 2011-08-30 22:27 UTC (permalink / raw
  To: gentoo-user

On Tue, Aug 30, 2011 at 6:15 PM, denis cohen <denis.cohen@gmail.com> wrote:
> Thanks to all that responded. I've tried
>
> revdep-rebuild
> emerge --depclean
> revdep-rebuild
>
> with no progress on the errors I have.
> I've unmerged cblas* blas* gsl, synced, and "emerge -uDN world "also
> without success (also tried cblas-external USE flag but could not see
> it with eix).
> eselect cblas also gave no results.
>
> One problem I may have is with eselect. eselect-cblas has been
> unmerged but trying to re-emerge it gives this block.
>
>
> emerge -vp eselect-cblas
>
> These are the packages that would be merged, in order:
>
> Calculating dependencies... done!
> [ebuild  N     ] app-admin/eselect-cblas-0.1  0 kB
> [blocks B      ] app-admin/eselect-cblas ("app-admin/eselect-cblas" is
> blocking sci-libs/lapack-reference-3.3.1-r1, sci-libs/gsl-1.15-r1)
>
> Total: 1 package (1 new), Size of downloads: 0 kB
> Conflict: 1 block (1 unsatisfied)
>
>  * Error: The above package list contains packages which cannot be
>  * installed at the same time on the same system.
>
>  (app-admin/eselect-cblas-0.1::gentoo, ebuild scheduled for merge) pulled in by
>   eselect-cblas
>
>  (sci-libs/lapack-reference-3.3.1-r1::science, installed) pulled in by
>   >=sci-libs/lapack-reference-3.3 required by
> (virtual/lapack-3.3::science, installed)
>
>  (sci-libs/gsl-1.15-r1::science, installed) pulled in by
>   sci-libs/gsl required by (media-gfx/inkscape-0.48.2::gentoo, installed)
>   >=sci-libs/gsl-1.14-r2 required by (virtual/cblas-2.0::science, installed)
>
>
> For more information about Blocked Packages, please refer to the following
> section of the Gentoo Linux x86 Handbook (architecture is irrelevant):
>
> http://www.gentoo.org/doc/en/handbook/handbook-x86.xml?full=1#blocked
>
>
>
> Similar problem with eselect-blas and eselect-lapack. Any ideas before
> I try some more unmerging?

Are there newer versions of cblas, lapack-reference and gsl which you
could unmask and update to? Grasping at straws, but maybe the block is
caused by a of particular set of versions?


-- 
:wq



^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: [gentoo-user] Problem with cblas libraries
  2011-08-30 22:15     ` denis cohen
  2011-08-30 22:27       ` Michael Mol
@ 2011-08-30 23:02       ` Alex Schuster
  2011-08-30 23:14         ` denis cohen
  1 sibling, 1 reply; 11+ messages in thread
From: Alex Schuster @ 2011-08-30 23:02 UTC (permalink / raw
  To: gentoo-user

denis cohen writes:

> I've unmerged cblas* blas* gsl, synced, and "emerge -uDN world "also
> without success (also tried cblas-external USE flag but could not see
> it with eix).

What's your problem with the world update? Adding --tree to the emerge 
command might show what pulls in what. I had to unmerge clapack and lapack-
reference yesterday, but I cannot remember the details - it all started with 
digikam not building because some blas stuff was missing. But finally the 
@world update was possible. And both got re-installed.

> eselect cblas also gave no results.

Here it is set to the only option gsl.

> One problem I may have is with eselect. eselect-cblas has been
> unmerged but trying to re-emerge it gives this block.

I get the very same blocker as you. eselect cblas is working, though. So is 
eselect-cblas being needed at all?

	Wonko



^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: [gentoo-user] Problem with cblas libraries
  2011-08-30 23:02       ` Alex Schuster
@ 2011-08-30 23:14         ` denis cohen
  2011-08-30 23:27           ` denis cohen
  0 siblings, 1 reply; 11+ messages in thread
From: denis cohen @ 2011-08-30 23:14 UTC (permalink / raw
  To: gentoo-user

Following Michael Mol's advice I masked these in /etc/portage/package.mask:

>=virtual/blas-2.0
>=virtual/cblas-2.0
>=virtual/lapack-3.1
>=sci-libs/cblas-reference-20030223-r5
>=sci-libs/lapack-reference-3.2.1
>=sci-libs/gsl-1.14

and did an "emerge -uD world".

All blocks were gone and after the emerge I got gsl working again.
I am also not sure what use is eselect-cblas since eselect blas works
without it.

gmsh still won't emerge with these types of errors:
...
[100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/SetOfE4.cpp.o
Linking CXX executable gmsh
CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function
`fullMatrix<double>::invertInPlace()':
fullMatrix.cpp:(.text+0xcc): undefined reference to `dgesv_'
CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function
`fullMatrix<double>::gemm(fullMatrix<double> const&,
fullMatrix<double> const&, double, double)':
fullMatrix.cpp:(.text+0x1e9): undefined reference to `dgemm_'
CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function
`fullVector<double>::axpy(fullVector<double> const&, double)':
fullMatrix.cpp:(.text+0x260): undefined reference to `daxpy_'
...

So making some progress.

Denis



On Wed, Aug 31, 2011 at 01:02, Alex Schuster <wonko@wonkology.org> wrote:
> denis cohen writes:
>
>> I've unmerged cblas* blas* gsl, synced, and "emerge -uDN world "also
>> without success (also tried cblas-external USE flag but could not see
>> it with eix).
>
> What's your problem with the world update? Adding --tree to the emerge
> command might show what pulls in what. I had to unmerge clapack and lapack-
> reference yesterday, but I cannot remember the details - it all started with
> digikam not building because some blas stuff was missing. But finally the
> @world update was possible. And both got re-installed.
>
>> eselect cblas also gave no results.
>
> Here it is set to the only option gsl.
>
>> One problem I may have is with eselect. eselect-cblas has been
>> unmerged but trying to re-emerge it gives this block.
>
> I get the very same blocker as you. eselect cblas is working, though. So is
> eselect-cblas being needed at all?
>
>        Wonko
>
>



^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: [gentoo-user] Problem with cblas libraries
  2011-08-30 23:14         ` denis cohen
@ 2011-08-30 23:27           ` denis cohen
  0 siblings, 0 replies; 11+ messages in thread
From: denis cohen @ 2011-08-30 23:27 UTC (permalink / raw
  To: gentoo-user

Just an update: gmsh build with USE="-blas"
Denis


On Wed, Aug 31, 2011 at 01:14, denis cohen <denis.cohen@gmail.com> wrote:
> Following Michael Mol's advice I masked these in /etc/portage/package.mask:
>
>>=virtual/blas-2.0
>>=virtual/cblas-2.0
>>=virtual/lapack-3.1
>>=sci-libs/cblas-reference-20030223-r5
>>=sci-libs/lapack-reference-3.2.1
>>=sci-libs/gsl-1.14
>
> and did an "emerge -uD world".
>
> All blocks were gone and after the emerge I got gsl working again.
> I am also not sure what use is eselect-cblas since eselect blas works
> without it.
>
> gmsh still won't emerge with these types of errors:
> ...
> [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o
> [100%] Building CXX object
> CMakeFiles/gmsh.dir/contrib/bamg/bamglib/SetOfE4.cpp.o
> Linking CXX executable gmsh
> CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function
> `fullMatrix<double>::invertInPlace()':
> fullMatrix.cpp:(.text+0xcc): undefined reference to `dgesv_'
> CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function
> `fullMatrix<double>::gemm(fullMatrix<double> const&,
> fullMatrix<double> const&, double, double)':
> fullMatrix.cpp:(.text+0x1e9): undefined reference to `dgemm_'
> CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function
> `fullVector<double>::axpy(fullVector<double> const&, double)':
> fullMatrix.cpp:(.text+0x260): undefined reference to `daxpy_'
> ...
>
> So making some progress.
>
> Denis
>
>
>
> On Wed, Aug 31, 2011 at 01:02, Alex Schuster <wonko@wonkology.org> wrote:
>> denis cohen writes:
>>
>>> I've unmerged cblas* blas* gsl, synced, and "emerge -uDN world "also
>>> without success (also tried cblas-external USE flag but could not see
>>> it with eix).
>>
>> What's your problem with the world update? Adding --tree to the emerge
>> command might show what pulls in what. I had to unmerge clapack and lapack-
>> reference yesterday, but I cannot remember the details - it all started with
>> digikam not building because some blas stuff was missing. But finally the
>> @world update was possible. And both got re-installed.
>>
>>> eselect cblas also gave no results.
>>
>> Here it is set to the only option gsl.
>>
>>> One problem I may have is with eselect. eselect-cblas has been
>>> unmerged but trying to re-emerge it gives this block.
>>
>> I get the very same blocker as you. eselect cblas is working, though. So is
>> eselect-cblas being needed at all?
>>
>>        Wonko
>>
>>
>



^ permalink raw reply	[flat|nested] 11+ messages in thread

end of thread, other threads:[~2011-08-30 23:28 UTC | newest]

Thread overview: 11+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2011-08-26 12:12 [gentoo-user] Problem with cblas libraries denis cohen
2011-08-26 15:36 ` Helmut Jarausch
2011-08-26 17:41 ` [gentoo-user] " Gene Hannan
2011-08-26 21:20 ` [gentoo-user] " Alex Schuster
2011-08-27 15:27 ` Valmor de Almeida
2011-08-27 16:34   ` Michael Mol
2011-08-30 22:15     ` denis cohen
2011-08-30 22:27       ` Michael Mol
2011-08-30 23:02       ` Alex Schuster
2011-08-30 23:14         ` denis cohen
2011-08-30 23:27           ` denis cohen

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