Bug 405807 – sci-libs/blas-reference-20120215-r1 - eselect: Can't load module blas

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Martin Mokrejš 2012-02-25 19:11:08 UTC]

I am am not sure if this is a configuration issue or not but here is what happens to me on a recent Gentoo installation:


>>> Source compiled.
>>> Test phase [not enabled]: sci-libs/blas-reference-20120215-r1

>>> Install blas-reference-20120215-r1 into /var/tmp/portage/sci-libs/blas-reference-20120215-r1/image/ category sci-libs
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/blas-reference-20120215-r1/work/blas-reference-20120215_build"
make -j5 DESTDIR=/var/tmp/portage/sci-libs/blas-reference-20120215-r1/image/ -C BLAS install 
make: Entering directory `/var/tmp/portage/sci-libs/blas-reference-20120215-r1/work/blas-reference-20120215_build/BLAS'
make[1]: Entering directory `/var/tmp/portage/sci-libs/blas-reference-20120215-r1/work/blas-reference-20120215_build'
make[2]: Entering directory `/var/tmp/portage/sci-libs/blas-reference-20120215-r1/work/blas-reference-20120215_build'
make[2]: Leaving directory `/var/tmp/portage/sci-libs/blas-reference-20120215-r1/work/blas-reference-20120215_build'
[100%] Built target refblas
make[1]: Leaving directory `/var/tmp/portage/sci-libs/blas-reference-20120215-r1/work/blas-reference-20120215_build'
Install the project...
-- Install configuration: "Gentoo"
-- Installing: /var/tmp/portage/sci-libs/blas-reference-20120215-r1/image/usr/lib64/pkgconfig/refblas.pc
-- Installing: /var/tmp/portage/sci-libs/blas-reference-20120215-r1/image/usr/lib64/librefblas.so
make: Leaving directory `/var/tmp/portage/sci-libs/blas-reference-20120215-r1/work/blas-reference-20120215_build/BLAS'
>>> Completed installing blas-reference-20120215-r1 into /var/tmp/portage/sci-libs/blas-reference-20120215-r1/image/


>>> Installing (1 of 1) sci-libs/blas-reference-20120215-r1
!!! Error: Can't load module blas
exiting
!!! Error: Can't load module blas
exiting
 * Removed reference alternative module for blas, current is 
 * Creating reference alternative module for blas
!!! Error: Can't load module blas
exiting
>>> Auto-cleaning packages...

>>> No outdated packages were found on your system.

python-updater nor "revdep-rebuild -i" found anything to be recompiled. :(


However, my programs give me:

    from matplotlib import colors
  File "/usr/lib64/python2.7/site-packages/matplotlib/__init__.py", line 133, in <module>
    from matplotlib.rcsetup import (defaultParams,
  File "/usr/lib64/python2.7/site-packages/matplotlib/rcsetup.py", line 19, in <module>
    from matplotlib.colors import is_color_like
  File "/usr/lib64/python2.7/site-packages/matplotlib/colors.py", line 52, in <module>
    import numpy as np
  File "/usr/lib64/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
  File "/usr/lib64/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib64/python2.7/site-packages/numpy/lib/__init__.py", line 13, in <module>
    from polynomial import *
  File "/usr/lib64/python2.7/site-packages/numpy/lib/polynomial.py", line 17, in <module>
    from numpy.linalg import eigvals, lstsq
  File "/usr/lib64/python2.7/site-packages/numpy/linalg/__init__.py", line 48, in <module>
    from linalg import *
  File "/usr/lib64/python2.7/site-packages/numpy/linalg/linalg.py", line 23, in <module>
    from numpy.linalg import lapack_lite
ImportError: /usr/lib64/python2.7/site-packages/numpy/linalg/lapack_lite.so: undefined symbol: dpotrf_




Here is what I have at the moment installed:

# emerge -pv blas lapack blas-reference blas-atlas

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

Calculating dependencies... done!
[ebuild   R    ] virtual/lapack-3.3::science  USE="-doc" 0 kB
[ebuild   R    ] sci-libs/blas-reference-20120215-r1::science  USE="-static-libs -test" 0 kB
[ebuild   R    ] virtual/blas-2.1::science  USE="-doc" 0 kB
[ebuild  N     ] app-admin/eselect-blas-0.1  0 kB
[ebuild  N     ] app-admin/eselect-cblas-0.1  0 kB
[uninstall     ] sci-libs/gsl-1.15-r2::science  USE="-static-libs" 
[ebuild  N     ] sci-libs/blas-atlas-3.9.23-r4  USE="-doc" 4,776 kB
[blocks B      ] app-admin/eselect-blas ("app-admin/eselect-blas" is blocking sci-libs/gsl-1.15-r2, sci-libs/blas-reference-20120215-r1, sci-libs/lapack-reference-3.4.0_p20120215-r1)
[blocks B      ] app-admin/eselect-cblas ("app-admin/eselect-cblas" is blocking sci-libs/gsl-1.15-r2, sci-libs/blas-reference-20120215-r1, sci-libs/lapack-reference-3.4.0_p20120215-r1)

Total: 6 packages (3 new, 3 reinstalls, 1 uninstall), Size of downloads: 4,776 kB
Conflict: 2 blocks (2 unsatisfied)

[Comment 1 Martin Mokrejš 2012-02-26 10:16:45 UTC]

(In reply to comment #0)
>     from numpy.linalg import lapack_lite
> ImportError: /usr/lib64/python2.7/site-packages/numpy/linalg/lapack_lite.so:
> undefined symbol: dpotrf_

Reinstalling numpy does not help, "revdep-rebuild -i" does not find any problems. Interesting. ;-)

# equery belongs /usr/lib64/python2.7/site-packages/numpy/linalg/lapack_lite.so
 * Searching for /usr/lib64/python2.7/site-packages/numpy/linalg/lapack_lite.so ... 
dev-python/numpy-1.6.1-r1 (/usr/lib64/python2.7/site-packages/numpy/linalg/lapack_lite.so)
#

[Comment 2 François Bissey 2012-02-27 01:25:47 UTC]

If you are installing this version of blas-reference, it looks to me like you are trying to migrate to the new blas infrastructure from the science overlay.

Now for your symbols in numpy, would you happen to have atlas installed and have it eselected as your lapack provider? If so which version?

Other infos, what do
eselect blas list
eselect cblas list
eselect lapack list
return?

[Comment 3 Justin Lecher (RETIRED) 2012-02-27 07:15:32 UTC]

You need the eselect from sci overlay.

[Comment 4 Martin Mokrejš 2012-02-27 10:16:38 UTC]

(In reply to comment #2)
> If you are installing this version of blas-reference, it looks to me like you
> are trying to migrate to the new blas infrastructure from the science overlay.

Well, personally I do not use any of them, I just added USE="lapack blas" to my make.conf. So at this stage I expected the system to install stuff automatically for me. ;)

> 
> Now for your symbols in numpy, would you happen to have atlas installed and
> have it eselected as your lapack provider? If so which version?

Neither of sci-libs/atlas, sci-libs/blas-atlas, sci-libs/lapack-atlas is installed.

> 
> Other infos, what do
> eselect blas list
> eselect cblas list
> eselect lapack list
> return?

# eselect blas list
Available providers for blas:
  [1]   reference *
# eselect cblas list
Available providers for cblas:
  [1]   gsl *
# eselect lapack list
Available providers for lapack:
  [1]   reference
#

[Comment 5 Martin Mokrejš 2012-02-27 10:17:29 UTC]

(In reply to comment #3)
> You need the eselect from sci overlay.

Looks I do have it.

# emerge -pv eselect

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

Calculating dependencies... done!
[ebuild   R    ] app-admin/eselect-1.3.1-r1::science  USE="-doc" 0 kB
#

[Comment 6 Sébastien Fabbro (RETIRED) 2012-02-27 15:25:26 UTC]

this might be an issue with an older tar ball. it should be fixed now. remove the lapack-3.4.0* tar balls from /usr/portage/distfiles and re-install blas-reference, gsl, and lapack-reference all from the sci overlay, then numpy.