FAQ Search Today's Posts Mark Forums Read
» Video Reviews

» Linux Archive

Linux-archive is a website aiming to archive linux email lists and to make them easily accessible for linux users/developers.


» Sponsor

» Partners

» Sponsor

Go Back   Linux Archive > Gentoo > Gentoo User

 
 
LinkBack Thread Tools
 
Old 08-26-2011, 12:12 PM
denis cohen
 
Default Problem with cblas libraries

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
 
Old 08-26-2011, 12:12 PM
denis cohen
 
Default Problem with cblas libraries

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
 
Old 08-26-2011, 03:36 PM
Helmut Jarausch
 
Default Problem with cblas libraries

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.
 
Old 08-26-2011, 05:41 PM
Gene Hannan
 
Default Problem with cblas libraries

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?
 
Old 08-26-2011, 09:20 PM
Alex Schuster
 
Default Problem with cblas libraries

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
 
Old 08-27-2011, 03:27 PM
Valmor de Almeida
 
Default Problem with cblas libraries

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
 
Old 08-27-2011, 04:34 PM
Michael Mol
 
Default Problem with cblas libraries

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
 
Old 08-30-2011, 10:15 PM
denis cohen
 
Default Problem with cblas libraries

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
>
>
 
Old 08-30-2011, 10:27 PM
Michael Mol
 
Default Problem with cblas libraries

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
 
Old 08-30-2011, 11:02 PM
Alex Schuster
 
Default Problem with cblas libraries

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
 

Thread Tools




All times are GMT. The time now is 11:39 AM.

VBulletin, Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.
Content Relevant URLs by vBSEO ©2007, Crawlability, Inc.
Copyright 2007 - 2008, www.linux-archive.org