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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>
participants (1)
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McCully, Dwayne (NIH/NLM/LHC) [C]