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My installation of scipy cannot import scipy.stats (and a number of other
modules) due to an undefined symbol clapack_sgesv in clapack.so.  The output
from scipy.test(), the stack trace from ">>> import scipy.stats", my "emerge
info" are below.  Let me know if I can help more.

Arch = ~86
scipy.__version__ == 0.4.8

cowboy ~ # blas-config -p
Current profiles:
F77 BLAS: /usr/lib/blas/f77-reference
C BLAS: /usr/lib/blas/c-reference

cowboy ~ # lapack-config -p
Current profile:
F77 LAPACK: /usr/lib/lapack/f77-reference


In [13]: scipy.test()
import signal -> failed:
/usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so: undefined symbol:
clapack_sgesv
import lib.lapack -> failed:
/usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so: undefined symbol:
clapack_sgesv
import cluster -> failed:
/usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so: undefined symbol:
clapack_sgesv
import integrate -> failed:
/usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so: undefined symbol:
clapack_sgesv
import special -> failed:
/usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so: undefined symbol:
clapack_sgesv
import linalg -> failed:
/usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so: undefined symbol:
clapack_sgesv
import maxentropy -> failed:
/usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so: undefined symbol:
clapack_sgesv
import stats -> failed:
/usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so: undefined symbol:
clapack_sgesv
  Found 4 tests for scipy.io.array_import
  Found 397 tests for scipy.ndimage
  Found 89 tests for scipy.sparse.sparse
  Found 20 tests for scipy.fftpack.pseudo_diffs
  Found 6 tests for scipy.optimize.optimize
  Found 5 tests for scipy.interpolate.fitpack
  Found 12 tests for scipy.io.mmio
  Found 18 tests for scipy.fftpack.basic
  Found 1 tests for scipy.optimize.zeros
  Found 4 tests for scipy.fftpack.helper
Warning: FAILURE importing tests for <module 'scipy.special.basic' from
'...ckages/scipy/special/basic.pyc'>
/usr/lib/python2.4/site-packages/scipy/lib/lapack/__init__.py:16: ImportError:
/usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so: undefined symbol:
clapack_sgesv (in ?)
  Found 128 tests for scipy.lib.blas.fblas
  Found 1 tests for scipy.optimize.cobyla
  Found 16 tests for scipy.lib.blas
  Found 0 tests for __main__

Don't worry about a warning regarding the number of bytes read.
Warning: 1000000 bytes requested, 20 bytes read.
...E.............................................................................................................................................................................................................................................................................................................................................................................................................
2 3 1 2 2
 3 2 1 3 3
 3 3 1 3 3
. 3 3 1 3 3
...........Use minimum degree ordering on A'+A.
.....................Use minimum degree ordering on A'+A.
.....................Use minimum degree ordering on A'+A.
.......................Use minimum degree ordering on A'+A.
.........................................................................TESTING
CONVERGENCE

zero should be 1

function f2

cc.bisect :    1.0000000000001952
cc.ridder :    1.0000000000004658
cc.brenth :    0.9999999999999997
cc.brentq :    0.9999999999999577



function f3

cc.bisect :    1.0000000000001952
cc.ridder :    1.0000000000000000
cc.brenth :    1.0000000000000009
cc.brentq :    1.0000000000000011



function f4

cc.bisect :    1.0000000000001952
cc.ridder :    1.0000000000001452
cc.brenth :    0.9999999999993339
cc.brentq :    0.9999999999993339



function f5

cc.bisect :    1.0000000000001952
cc.ridder :    1.0000000000004574
cc.brenth :    0.9999999999991442
cc.brentq :    0.9999999999991442



function f6

cc.bisect :    1.0000000000001952
cc.ridder :    0.9999999999998919
cc.brenth :    1.0000000000014924
cc.brentq :    1.0000000000007443



........caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
..Result: [ 4.957975    0.64690335] (exact result = 4.955356249106168,
0.666666666666666)
.................
======================================================================
ERROR: check_integer (scipy.io.tests.test_array_import.test_read_array)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.4/site-packages/scipy/io/tests/test_array_import.py",
line 55, in check_integer
    from scipy import stats
  File "/usr/lib/python2.4/site-packages/scipy/stats/__init__.py", line 7, in ?
    from stats import *
  File "/usr/lib/python2.4/site-packages/scipy/stats/stats.py", line 193, in ?
    import scipy.special as special
  File "/usr/lib/python2.4/site-packages/scipy/special/__init__.py", line 10,
in ?
    import orthogonal
  File "/usr/lib/python2.4/site-packages/scipy/special/orthogonal.py", line 66,
in ?
    from scipy.linalg import eig
  File "/usr/lib/python2.4/site-packages/scipy/linalg/__init__.py", line 8, in
?
    from basic import *
  File "/usr/lib/python2.4/site-packages/scipy/linalg/basic.py", line 18, in ?
    from scipy.lib.lapack import get_lapack_funcs
  File "/usr/lib/python2.4/site-packages/scipy/lib/lapack/__init__.py", line
16, in ?
    import clapack
ImportError: /usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so:
undefined symbol: clapack_sgesv

----------------------------------------------------------------------
Ran 701 tests in 22.651s

FAILED (errors=1)


In [15]: import scipy.stats
---------------------------------------------------------------------------
exceptions.ImportError                               Traceback (most recent
call last)

/root/<ipython console>

/usr/lib/python2.4/site-packages/scipy/stats/__init__.py
      5 from info import __doc__
      6
----> 7 from stats import *
      8 from distributions import *
      9 from rv import *

/usr/lib/python2.4/site-packages/scipy/stats/stats.py
    191 import numpy.core.umath as math
    192 from numpy.core.umath import *
--> 193 import scipy.special as special
    194 import scipy.linalg as linalg
    195

/usr/lib/python2.4/site-packages/scipy/special/__init__.py
      8 from basic import *
      9 import specfun
---> 10 import orthogonal
     11 from orthogonal import legendre, chebyt, chebyu, chebyc, chebys, \
     12      jacobi, laguerre, genlaguerre, hermite, hermitenorm, gegenbauer, \

/usr/lib/python2.4/site-packages/scipy/special/orthogonal.py
     64 import _cephes as cephes
     65 _gam = cephes.gamma
---> 66 from scipy.linalg import eig
     67
     68 def poch(z,m):

/usr/lib/python2.4/site-packages/scipy/linalg/__init__.py
      6 from linalg_version import linalg_version as __version__
      7
----> 8 from basic import *
      9 from decomp import *
     10 from matfuncs import *

/usr/lib/python2.4/site-packages/scipy/linalg/basic.py
     16 #from lapack import get_lapack_funcs
     17 from flinalg import get_flinalg_funcs
---> 18 from scipy.lib.lapack import get_lapack_funcs
     19 from numpy import
asarray,zeros,sum,newaxis,greater_equal,subtract,arange,\
     20      conjugate,ravel,r_,mgrid,take,ones,dot,transpose,sqrt,add,real

/usr/lib/python2.4/site-packages/scipy/lib/lapack/__init__.py
     14
     15 import flapack
---> 16 import clapack
     17
     18 _use_force_clapack = 1

ImportError: /usr/lib/python2.4/site-packages/scipy/lib/lapack/clapack.so:
undefined symbol: clapack_sgesv

EMERGE INFO:
------------
cowboy ~ # emerge info
*** Deprecated use of action 'info', use '--info' instead
Portage 2.1_pre7-r5 (default-linux/x86/2005.0, gcc-3.3.6, glibc-2.3.6-r3,
2.6.11-gentoo-r9 i686)
=================================================================
System uname: 2.6.11-gentoo-r9 i686 AMD Athlon(tm) Processor
Gentoo Base System version 1.12.0_pre17
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632)
[disabled]
ccache version 2.4 [enabled]
dev-lang/python:     2.4.2-r1
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.59-r7
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2
sys-devel/binutils:  2.16.1-r2
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r3
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS=" -march=athlon -O2 -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config
/usr/lib/X11/xkb /usr/share/config /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/eselect/compiler /etc/gconf /etc/revdep-rebuild
/etc/terminfo /etc/texmf/web2c /etc/env.d"
CXXFLAGS=" -march=athlon -O2 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache distlocks metadata-transfer sandbox sfperms"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/linux/distributions/gentoo"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 X alsa apache2 apm arts avi berkdb bitmap-fonts blas crypt cups dba
dri eds emacs emboss encode f77 fftw foomaticdb fortran gdbm gif gnome gpm
gstreamer gtk gtk2 imlib ipv6 isdnlog jpeg kde libg++ libwww mad mikmod mime
mmap motif mp3 mpeg ncurses nls objc ogg oggvorbis opengl oss pam pdflib perl
png postgres pppd python qt quicktime readline sdl spell ssl svg tcltk tcpd
tidy truetype truetype-fonts type1-fonts unicode vorbis xml2 xmms xv zlib
elibc_glibc kernel_linux userland_GNU"
Unset:  ASFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL,
LDFLAGS, LINGUAS, MAKEOPTS

Hi,

In my experience, scipy is picky about blas/lapack implementations. (You will
notice that the dependecies in the ebuild are blas-atlas and lapack-atlas, and
not the virtual implementations, but that your system uses blas-reference and
lapack-reference.)

I suggest you try the following: Set your blas profile to f77-ATLAS/c-atlas,
set your lapack profile to f77-ATLAS, and reinstall scipy.

(In reply to comment #1)

> I suggest you try the following: Set your blas profile to f77-ATLAS/c-atlas,
> set your lapack profile to f77-ATLAS, and reinstall scipy.

That works, thanks.

Closing this for now, as there is no way to force a specific blas/lapack
profile to be used. (Reopen and correct me if I am wrong.)

Is there no way to check which implementation is in use during src_unpack()? If
not, the capability should be added to the eselect module.

It should also be easy enough to change implementations at build time and have
a very loud warning afterwards.

(In reply to comment #4)
> Is there no way to check which implementation is in use during src_unpack()?

That should be pkg_setup(), I suppose. ;-) Well, we should be able to, but it
does not seem to work. When I run 'eselect blas/lapack show' from inside an
ebuild, it reports the profiles as '(none)'. Does it work for anyone?

> It should also be easy enough to change implementations at build time and
> have a very loud warning afterwards.

I dislike changing the user's configuration without asking. It could break
other applications that were compiled against different BLAS/LAPACK profiles,
and might cause confusion. Better warn beforehand.

I used the old-fashioned {blas,lapack}-config instead of the eselect modules,
and added checks for ATLAS in scipy-0.4.8-r1.

(In reply to comment #6)

scipy-0.4.2-r1 fails to build when my blas profile is set to 'threaded-ATLAS:'

Calculating dependencies... done!
[ebuild   R   ] sci-libs/scipy-0.4.8-r1  USE="fftw -debug" 0 kB 

Total size of downloads: 0 kB

Would you like to merge these packages? [Yes/No] 
>>> Emerging (1 of 1) sci-libs/scipy-0.4.8-r1 to /
>>> checking ebuild checksums
>>> checking auxfile checksums
>>> checking miscfile checksums
>>> checking distfiles checksums

 * Checking active BLAS implementations for ATLAS.

Current profiles:
F77 BLAS: /usr/lib/blas/f77-threaded-ATLAS
C BLAS: /usr/lib/blas/c-threaded-ATLAS

 * Your F77 BLAS profile is not set to the ATLAS implementation,
 * which is required by scipy to compile and run properly.
 * Use: 'blas-config -f ATLAS' to activate ATLAS.

 * Your C BLAS profile is not set to the ATLAS implementation,
 * Which is required by scipy to compile and run properly.
 * Use: 'blas-config -c ATLAS' to activate ATLAS.

 * Checking active LAPACK implementation for ATLAS.

Current profile:
F77 LAPACK: /usr/lib/lapack/f77-ATLAS


!!! ERROR: sci-libs/scipy-0.4.8-r1 failed.
Call stack:
  ebuild.sh, line 1541:   Called dyn_setup
  ebuild.sh, line 657:   Called pkg_setup
  scipy-0.4.8-r1.ebuild, line 72:   Called die

!!! Active BLAS/LAPACK implementations are not ATLAS.
!!! If you need support, post the topmost build error, and the call stack if
relevant.

When I change the profile to 'ATLAS', it builds without error. Does this mean
my version of scipy is not using the threaded libs, or is this just a problem
with the ATLAS check in the ebuild?

-stephen

You could try changing each instance like f77-ATLAS to 'f77.*ATLAS' and that
might fix it up. Not sure whether scipy will handle adding -lpthread, however.

Also find it very very strange that it only works w/ atlas.

I've reverted this because it seems to work OK with other implems as long as
you're consistent about it, and it breaks in an annoying way with newer eselect
modules (see bug #136023 e.g.)