Lapack import error from scipy in virtualenv

[jazzvibes]

Hi Ubuntu forums,


I have installed numpy and scipy into a virtualenv using pip but I have import errors in the linalg libraries that prevent me from continuing to make SimpleCV work. Does anyone know where I can start to try and resolve this issue?


running numpy.test() prints out no big messages like this.

running scipy.test() prints out the following. Importantly, some of the clapack and flapack routines are missing.



I am using Ubuntu 12.10 64-bit on my laptop, and I prepared for this installation by using "sudo apt-get build-dep numpy scipy".


Thanks in advance

Regards,
Jonathan

================================================== ====================
ERROR: Failure: ImportError (/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/clapack.so: undefined symbol: clapack_sgesv)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/interpolate/__init__.py", line 154, in <module>
from rbf import Rbf
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/interpolate/rbf.py", line 49, in <module>
from scipy import linalg
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in <module>
from basic import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in <module>
from lapack import get_lapack_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 15, in <module>
from scipy.linalg import clapack
ImportError: /home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/clapack.so: undefined symbol: clapack_sgesv

================================================== ====================
ERROR: Failure: ImportError (/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/lib/lapack/clapack.so: undefined symbol: clapack_sgesv)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/lib/lapack/__init__.py", line 148, in <module>
import clapack
ImportError: /home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/lib/lapack/clapack.so: undefined symbol: clapack_sgesv

================================================== ====================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in <module>
from basic import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in <module>
from lapack import get_lapack_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 14, in <module>
from scipy.linalg import flapack
ImportError: cannot import name flapack

================================================== ====================
ERROR: test_common.test_pade_trivial
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_common.py", line 9, in test_pade_trivial
nump, denomp = pade([1.0], 0)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/common.py", line 371, in pade
from scipy import linalg
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in <module>
from basic import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in <module>
from lapack import get_lapack_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 14, in <module>
from scipy.linalg import flapack
ImportError: cannot import name flapack

================================================== ====================
ERROR: test_common.test_pade_4term_exp
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_common.py", line 18, in test_pade_4term_exp
nump, denomp = pade(an, 0)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/common.py", line 371, in pade
from scipy import linalg
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in <module>
from basic import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in <module>
from lapack import get_lapack_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 14, in <module>
from scipy.linalg import flapack
ImportError: cannot import name flapack

================================================== ====================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/optimize/__init__.py", line 146, in <module>
from _root import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/optimize/_root.py", line 17, in <module>
import nonlin
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/optimize/nonlin.py", line 116, in <module>
from scipy.linalg import norm, solve, inv, qr, svd, lstsq, LinAlgError
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in <module>
from basic import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in <module>
from lapack import get_lapack_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 14, in <module>
from scipy.linalg import flapack
ImportError: cannot import name flapack

================================================== ====================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/signal/__init__.py", line 218, in <module>
from cont2discrete import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/signal/cont2discrete.py", line 9, in <module>
from scipy import linalg
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in <module>
from basic import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in <module>
from lapack import get_lapack_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 14, in <module>
from scipy.linalg import flapack
ImportError: cannot import name flapack

================================================== ====================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/__init__.py", line 90, in <module>
from isolve import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 6, in <module>
from lgmres import lgmres
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/lgmres.py", line 5, in <module>
from scipy.linalg import get_blas_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in <module>
from basic import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in <module>
from lapack import get_lapack_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 14, in <module>
from scipy.linalg import flapack
ImportError: cannot import name flapack

================================================== ====================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/tests/test_base.py", line 34, in <module>
from scipy.sparse.linalg import splu
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/__init__.py", line 90, in <module>
from isolve import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 6, in <module>
from lgmres import lgmres
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/lgmres.py", line 5, in <module>
from scipy.linalg import get_blas_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in <module>
from basic import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in <module>
from lapack import get_lapack_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 14, in <module>
from scipy.linalg import flapack
ImportError: cannot import name flapack

================================================== ====================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/stats/__init__.py", line 321, in <module>
from stats import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/stats/stats.py", line 194, in <module>
import scipy.linalg as linalg
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in <module>
from basic import *
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in <module>
from lapack import get_lapack_funcs
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 14, in <module>
from scipy.linalg import flapack
ImportError: cannot import name flapack

================================================== ====================
FAIL: Test generator for parametric tests
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_pilutil.py", line 52, in tst_fromimage
assert_(img.min() >= imin)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 34, in assert_
raise AssertionError(msg)
AssertionError

================================================== ====================
FAIL: Test generator for parametric tests
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_pilutil.py", line 52, in tst_fromimage
assert_(img.min() >= imin)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 34, in assert_
raise AssertionError(msg)
AssertionError

================================================== ====================
FAIL: Test generator for parametric tests
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_pilutil.py", line 52, in tst_fromimage
assert_(img.min() >= imin)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 34, in assert_
raise AssertionError(msg)
AssertionError

================================================== ====================
FAIL: test_io.test_imread
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/decorators.py", line 146, in skipper_func
return f(*args, **kwargs)
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/ndimage/tests/test_io.py", line 16, in test_imread
assert_array_equal(img.shape, (300, 420, 3))
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal
verbose=verbose, header='Arrays are not equal')
File "/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 600, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not equal

(shapes (0,), (3,) mismatch)
x: array([], dtype=float64)
y: array([300, 420, 3])

----------------------------------------------------------------------
Ran 2446 tests in 24.397s

FAILED (KNOWNFAIL=7, SKIP=7, errors=10, failures=4)
Out[2]: <nose.result.TextTestResult run=2446 errors=10 failures=4>

[MadCow108]

can you show the output of this:

ldd /home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/clapack.so

my guess is that you have a libatlas-base-dev or libopenblas-base-dev package installed, so it linked against these

in debian/ubuntu these libraries are installed in subfolders and pulled in via the alternatives mechanism setting libblas.so.3 to the right place

either remove all -dev packages besides libblas-dev or export BLAS=/usr/lib/libblas/libblas.so.3 before building

or set LD_LIBRARY_PATH to the right path (e.g. /usr/lib/atlas-base/atlas/ or /usr/lib/openblas-base/) at runtime

[jazzvibes]

ldd /home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/clapack.so
linux-vdso.so.1 => (0x00007fffbb7ff000)
liblapack.so.3 => /usr/lib/liblapack.so.3 (0x00007f2a807c5000)
libatlas.so.3 => /usr/lib/libatlas.so.3 (0x00007f2a7ffa1000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2a7fbe1000)
libblas.so.3 => /usr/lib/libblas.so.3 (0x00007f2a7f38b000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007f2a7f077000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2a7ed7a000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f2a7eb64000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f2a7e947000)
/lib64/ld-linux-x86-64.so.2 (0x00007f2a816f5000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f2a7e710000)


so I tried "export BLAS=/usr/lib/libblas.so.3" and "export LD_LIBRARY_PATH=/usr/lib" which didn't work unfortunately.

Specifically which packages would be conflicting ... ?
I don't have openblas at all
I have these which i think may be relevant
libblas3
libblas-dev
libatlas3-base
libatlas-base-dev
libatlas-dev

Does this help?

[MadCow108]

have you done a custom install of atlas?
/usr/lib/libatlas.so.3 clapack.so finds does not exist in the package archive
what does /usr/lib/libblas.so.3 link to?

try building without libatlas-base-dev and libatlas-dev installed