[SciPy-User] Scipy Test failures

McCully, Dwayne (NIH/NLM/LHC) [C] dmccully@mail.nih....
Sun Aug 16 20:27:04 CDT 2009


Hello Everyone,

This is my first time sending e-mail to the scipy user community.   I have a small problem and I would like some help from anyone:

Why does the scipy.test() fail to find omp_set_lock when its compiled into ATLAS?  My ATLAS variable is set correctly.  See below

Dwayne

[root@niamssolexa lib]# env | grep ATLAS
ATLAS=/usr/local/atlas/lib

[root@niamssolexa lib]# ls
libatlas.a  libatlas.so  libcblas.a  libcblas.so  libf77blas.a  libf77blas.so  liblapack.a  liblapack.so  libptcblas.a  libptcblas.so  libptf77blas.a  libptf77blas.so
[root@niamssolexa lib]# strings libatlas.a | grep omp_set_lock
omp_set_lock
omp_set_lock
omp_set_lock
omp_set_lock
omp_set_lock
[root@niamssolexa lib]# strings libatlas.so | grep omp_set_lock
omp_set_lock


[root@niamssolexa ~]# python
Python 2.5.2 (r252:60911, Mar  5 2008, 20:59:51)
[GCC 4.1.2 20070626 (Red Hat 4.1.2-14)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.2.1
NumPy is installed in /usr/local/lib/python2.5/site-packages/numpy
SciPy version 0.7.1
SciPy is installed in /usr/local/lib/python2.5/site-packages/scipy
Python version 2.5.2 (r252:60911, Mar  5 2008, 20:59:51) [GCC 4.1.2 20070626 (Red Hat 4.1.2-14)]
nose version 0.11.0
/usr/local/lib/python2.5/site-packages/scipy/linsolve/__init__.py:4: DeprecationWarning: scipy.linsolve has moved to scipy.sparse.linalg.dsolve
  warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve', DeprecationWarning)
............................................................................................................................................................................................................EE......................../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:111: Warning: Unreadable variable "testfunc", because "Cannot read matlab functions"
  matfile_dict = MR.get_variables()
........../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:165: FutureWarning: Using oned_as default value ('column') This will change to 'row' in future versions
  oned_as=oned_as)
........................./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:438: FutureWarning: Using oned_as default value ('column') This will change to 'row' in future versions
  mfw = MatFile5Writer(StringIO())
......../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:84: FutureWarning: Using struct_as_record default value (False) This will change to True in future versions
  return MatFile5Reader(byte_stream, **kwargs)
...............................Warning: 1000000 bytes requested, 20 bytes read.
./usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:110: DeprecationWarning: write_array is deprecated
  warnings.warn(str1, DeprecationWarning)
/usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:110: DeprecationWarning: read_array is deprecated
  warnings.warn(str1, DeprecationWarning)
..E..................../usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:110: DeprecationWarning: npfile is deprecated
  warnings.warn(str1, DeprecationWarning)
.........EEEEE.................................................................................................................................................................................................................................................................................................................................................................................................................................EEEEE............................................................................................................................................................................................................................................................................................................................................K.K................................................................................................................................................................................................................................................................................................................E...warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations
.....warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations
...............................building extensions here: /root/.python25_compiled/m15
................................................................................................
======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/integrate/__init__.py", line 10, in <module>
    from odepack import *
  File "/usr/local/lib/python2.5/site-packages/scipy/integrate/odepack.py", line 7, in <module>
    import _odepack
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/interpolate/__init__.py", line 13, in <module>
    from rbf import Rbf
  File "/usr/local/lib/python2.5/site-packages/scipy/interpolate/rbf.py", line 47, in <module>
    from scipy import linalg
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in <module>
    from basic import *
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in <module>
    from scipy.linalg import flapack
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: test_integer (test_array_import.TestReadArray)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/scipy/io/tests/test_array_import.py", line 52, in test_integer
    from scipy import stats
  File "/usr/local/lib/python2.5/site-packages/scipy/stats/__init__.py", line 7, in <module>
    from stats import *
  File "/usr/local/lib/python2.5/site-packages/scipy/stats/stats.py", line 199, in <module>
    import scipy.linalg as linalg
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in <module>
    from basic import *
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in <module>
    from scipy.linalg import flapack
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/lib/blas/__init__.py", line 9, in <module>
    import fblas
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/lib/lapack/__init__.py", line 9, in <module>
    import calc_lwork
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in <module>
    from basic import *
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in <module>
    from scipy.linalg import flapack
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/linsolve/__init__.py", line 6, in <module>
    from scipy.sparse.linalg.dsolve import *
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/__init__.py", line 5, in <module>
    from isolve import *
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 4, in <module>
    from iterative import *
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 5, in <module>
    import _iterative
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/maxentropy/__init__.py", line 9, in <module>
    from maxentropy import *
  File "/usr/local/lib/python2.5/site-packages/scipy/maxentropy/maxentropy.py", line 74, in <module>
    from scipy import optimize
  File "/usr/local/lib/python2.5/site-packages/scipy/optimize/__init__.py", line 11, in <module>
    from lbfgsb import fmin_l_bfgs_b
  File "/usr/local/lib/python2.5/site-packages/scipy/optimize/lbfgsb.py", line 30, in <module>
    import _lbfgsb
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/odr/__init__.py", line 11, in <module>
    import odrpack
  File "/usr/local/lib/python2.5/site-packages/scipy/odr/odrpack.py", line 103, in <module>
    from scipy.odr import __odrpack
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/optimize/__init__.py", line 11, in <module>
    from lbfgsb import fmin_l_bfgs_b
  File "/usr/local/lib/python2.5/site-packages/scipy/optimize/lbfgsb.py", line 30, in <module>
    import _lbfgsb
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/signal/__init__.py", line 10, in <module>
    from filter_design import *
  File "/usr/local/lib/python2.5/site-packages/scipy/signal/filter_design.py", line 12, in <module>
    from scipy import special, optimize
  File "/usr/local/lib/python2.5/site-packages/scipy/optimize/__init__.py", line 11, in <module>
    from lbfgsb import fmin_l_bfgs_b
  File "/usr/local/lib/python2.5/site-packages/scipy/optimize/lbfgsb.py", line 30, in <module>
    import _lbfgsb
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/__init__.py", line 5, in <module>
    from isolve import *
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 4, in <module>
    from iterative import *
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 5, in <module>
    import _iterative
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/tests/test_base.py", line 31, in <module>
    from scipy.sparse.linalg import splu
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/__init__.py", line 5, in <module>
    from isolve import *
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 4, in <module>
    from iterative import *
  File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 5, in <module>
    import _iterative
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

======================================================================
ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib/python2.5/site-packages/scipy/stats/__init__.py", line 7, in <module>
    from stats import *
  File "/usr/local/lib/python2.5/site-packages/scipy/stats/stats.py", line 199, in <module>
    import scipy.linalg as linalg
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in <module>
    from basic import *
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/local/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in <module>
    from scipy.linalg import flapack
ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock

----------------------------------------------------------------------
Ran 1539 tests in 27.082s

FAILED (KNOWNFAIL=2, errors=14)
<nose.result.TextTestResult run=1539 errors=14 failures=0>
>>>
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