Dear Scipy Users- I am trying to compile from source scipy (with lapack and blas) and numpy - but when executing scipy.test() I receive "undefined symbol: s_stop" errors on fblas.so: Could someone please advise if I have an incompatibility with a compiler or software version? I am stuck using "Red Hat Enterprise Linux Server release 6.3". Once I have this working on one system, my next task is to roll this out to 600 more servers. Your help would be GREATLY appreciated with helping me overcome this error. *ERROR*: Failure: ImportError (/usr/lib64/python2.6/site-packages/scipy/lib/blas/fblas.so: undefined symbol: s_stop) *SOFTWARE VERSIONS*: numpy-1.6.2 scipy-0.11.0 blas lapack-3.4.2 scikit-learn-0.12 *SYSTEM ENVIRONMENT*: # python -c 'from numpy.f2py.diagnose import run; run()' ------ os.name='posix' ------ sys.platform='linux2' ------ sys.version: 2.6.6 (r266:84292, May 1 2012, 13:52:17) [GCC 4.4.6 20110731 (Red Hat 4.4.6-3)] ------ sys.prefix: /usr ------ sys.path=':/usr/lib64/python26.zip:/usr/lib64/python2.6:/usr/lib64/python2.6/plat-linux2:/usr/lib64/python2.6/lib-tk:/usr/lib64/python2.6/lib-old:/usr/lib64/python2.6/lib-dynload:/usr/lib64/python2.6/site-packages:/usr/lib64/python2.6/site-packages/gtk-2.0:/usr/lib/python2.6/site-packages' ------ Found new numpy version '1.6.2' in /usr/lib64/python2.6/site-packages/numpy/__init__.pyc Found f2py2e version '2' in /usr/lib64/python2.6/site-packages/numpy/f2py/f2py2e.pyc Found numpy.distutils version '0.4.0' in '/usr/lib64/python2.6/site-packages/numpy/distutils/__init__.pyc' ------ Importing numpy.distutils.fcompiler ... ok ------ Checking availability of supported Fortran compilers: GnuFCompiler instance properties: archiver = ['/usr/bin/g77', '-cr'] compile_switch = '-c' compiler_f77 = ['/usr/bin/g77', '-g', '-Wall', '-fno-second- underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_f90 = None compiler_fix = None libraries = ['g2c'] library_dirs = [] linker_exe = ['/usr/bin/g77', '-g', '-Wall', '-g', '-Wall'] linker_so = ['/usr/bin/g77', '-g', '-Wall', '-g', '-Wall', '- shared'] object_switch = '-o ' ranlib = ['/usr/bin/g77'] version = LooseVersion ('3.4.6') version_cmd = ['/usr/bin/g77', '--version'] Gnu95FCompiler instance properties: archiver = ['/usr/bin/gfortran', '-cr'] compile_switch = '-c' compiler_f77 = ['/usr/bin/gfortran', '-Wall', '-ffixed-form', '-fno- second-underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_f90 = ['/usr/bin/gfortran', '-Wall', '-fno-second-underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_fix = ['/usr/bin/gfortran', '-Wall', '-ffixed-form', '-fno- second-underscore', '-Wall', '-fno-second-underscore', '- fPIC', '-O3', '-funroll-loops'] libraries = ['gfortran'] library_dirs = [] linker_exe = ['/usr/bin/gfortran', '-Wall', '-Wall'] linker_so = ['/usr/bin/gfortran', '-Wall', '-Wall', '-shared'] object_switch = '-o ' ranlib = ['/usr/bin/gfortran'] version = LooseVersion ('4.4.6') version_cmd = ['/usr/bin/gfortran', '--version'] Fortran compilers found: --fcompiler=gnu GNU Fortran 77 compiler (3.4.6) --fcompiler=gnu95 GNU Fortran 95 compiler (4.4.6) Compilers available for this platform, but not found: --fcompiler=absoft Absoft Corp Fortran Compiler --fcompiler=compaq Compaq Fortran Compiler --fcompiler=g95 G95 Fortran Compiler --fcompiler=intel Intel Fortran Compiler for 32-bit apps --fcompiler=intele Intel Fortran Compiler for Itanium apps --fcompiler=intelem Intel Fortran Compiler for 64-bit apps --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler --fcompiler=nag NAGWare Fortran 95 Compiler --fcompiler=pathf95 PathScale Fortran Compiler --fcompiler=pg Portland Group Fortran Compiler --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler Compilers not available on this platform: --fcompiler=hpux HP Fortran 90 Compiler --fcompiler=ibm IBM XL Fortran Compiler --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps --fcompiler=intelvem Intel Visual Fortran Compiler for 64-bit apps --fcompiler=mips MIPSpro Fortran Compiler --fcompiler=none Fake Fortran compiler --fcompiler=sun Sun or Forte Fortran 95 Compiler For compiler details, run 'config_fc --verbose' setup command. ------ Importing numpy.distutils.cpuinfo ... ok ------ CPU information: CPUInfoBase__get_nbits getNCPUs has_mmx has_sse has_sse2 has_sse3 has_ssse3 is_64bit is_Intel is_XEON is_Xeon is_i686 ------ Sincerely, Ed Sexton / PayPal *ERROR*: python Python 2.6.6 (r266:84292, May 1 2012, 13:52:17) [GCC 4.4.6 20110731 (Red Hat 4.4.6-3)] on linux2 Type "help", "copyright", "credits" or "license" for more information.

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import scipy scipy.test() Running unit tests for scipy NumPy version 1.6.2 NumPy is installed in /usr/lib64/python2.6/site-packages/numpy SciPy version 0.11.0 SciPy is installed in /usr/lib64/python2.6/site-packages/scipy Python version 2.6.6 (r266:84292, May 1 2012, 13:52:17) [GCC 4.4.6 20110731 (Red Hat 4.4.6-3)] nose version 1.2.1 ..............................................................................................................................................................................................................................K........................................................................................................K......................E....................................................................................................................................................................................................................................................................................................................................................................................................................................................ESSSSSS...FFFSSSSSS...FFFSSSS....EEE...........SSSSS.K..........S......................................................................................................................................................................................................................................................................................................................................................................................................................................EE........................................................................................EE....................................................................................................................................................................................................................................................................................................................................................................................................K.K.............................................................................................................................................................................................................................................................................................................................................................................................K........K..............SSSSSSS............................E........................................................................................................................................ ====================================================================== ERROR: Failure: ImportError (/usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop)

Traceback (most recent call last): File "nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python2.6/site-packages/scipy/interpolate/__init__.py", line 154, in <module> from rbf import Rbf File "/usr/lib64/python2.6/site-packages/scipy/interpolate/rbf.py", line 49, in <module> from scipy import linalg File "/usr/lib64/python2.6/site-packages/scipy/linalg/__init__.py", line 132, in <module> from misc import * File "/usr/lib64/python2.6/site-packages/scipy/linalg/misc.py", line 3, in <module> import fblas ImportError: /usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop ====================================================================== ERROR: Failure: ImportError (/usr/lib64/python2.6/site-packages/scipy/lib/blas/fblas.so: undefined symbol: s_stop) ---------------------------------------------------------------------- Traceback (most recent call last): File "nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python2.6/site-packages/scipy/lib/blas/__init__.py", line 86, in <module> import fblas ImportError: /usr/lib64/python2.6/site-packages/scipy/lib/blas/fblas.so: undefined symbol: s_stop ====================================================================== ERROR: Failure: ImportError (/usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop) ---------------------------------------------------------------------- Traceback (most recent call last): File "nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python2.6/site-packages/scipy/linalg/__init__.py", line 132, in <module> from misc import * File "/usr/lib64/python2.6/site-packages/scipy/linalg/misc.py", line 3, in <module> import fblas ImportError: /usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop ====================================================================== ERROR: test_common.test_pade_trivial ---------------------------------------------------------------------- Traceback (most recent call last): File "nose/case.py", line 197, in runTest self.test(*self.arg) File "/usr/lib64/python2.6/site-packages/scipy/misc/tests/test_common.py", line 9, in test_pade_trivial nump, denomp = pade([1.0], 0) File "/usr/lib64/python2.6/site-packages/scipy/misc/common.py", line 371, in pade from scipy import linalg File "/usr/lib64/python2.6/site-packages/scipy/linalg/__init__.py", line 132, in <module> from misc import * File "/usr/lib64/python2.6/site-packages/scipy/linalg/misc.py", line 3, in <module> import fblas ImportError: /usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop ====================================================================== ERROR: test_common.test_pade_4term_exp ---------------------------------------------------------------------- Traceback (most recent call last): File "nose/case.py", line 197, in runTest self.test(*self.arg) File "/usr/lib64/python2.6/site-packages/scipy/misc/tests/test_common.py", line 18, in test_pade_4term_exp nump, denomp = pade(an, 0) File "/usr/lib64/python2.6/site-packages/scipy/misc/common.py", line 371, in pade from scipy import linalg File "/usr/lib64/python2.6/site-packages/scipy/linalg/__init__.py", line 132, in <module> from misc import * File "/usr/lib64/python2.6/site-packages/scipy/linalg/misc.py", line 3, in <module> import fblas ImportError: /usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop ====================================================================== ERROR: Failure: ImportError (/usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop) ---------------------------------------------------------------------- Traceback (most recent call last): File "nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python2.6/site-packages/scipy/optimize/__init__.py", line 146, in <module> from _root import * File "/usr/lib64/python2.6/site-packages/scipy/optimize/_root.py", line 17, in <module> import nonlin File "/usr/lib64/python2.6/site-packages/scipy/optimize/nonlin.py", line 116, in <module> from scipy.linalg import norm, solve, inv, qr, svd, lstsq, LinAlgError File "/usr/lib64/python2.6/site-packages/scipy/linalg/__init__.py", line 132, in <module> from misc import * File "/usr/lib64/python2.6/site-packages/scipy/linalg/misc.py", line 3, in <module> import fblas ImportError: /usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop ====================================================================== ERROR: Failure: ImportError (/usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop) ---------------------------------------------------------------------- Traceback (most recent call last): File "nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python2.6/site-packages/scipy/signal/__init__.py", line 218, in <module> from cont2discrete import * File "/usr/lib64/python2.6/site-packages/scipy/signal/cont2discrete.py", line 9, in <module> from scipy import linalg File "/usr/lib64/python2.6/site-packages/scipy/linalg/__init__.py", line 132, in <module> from misc import * File "/usr/lib64/python2.6/site-packages/scipy/linalg/misc.py", line 3, in <module> import fblas ImportError: /usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop ====================================================================== ERROR: Failure: ImportError (/usr/lib64/python2.6/site-packages/scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: s_stop) ---------------------------------------------------------------------- Traceback (most recent call last): File "nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python2.6/site-packages/scipy/sparse/linalg/__init__.py", line 90, in <module> from isolve import * File "/usr/lib64/python2.6/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 4, in <module> from iterative import * File "/usr/lib64/python2.6/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 5, in <module> import _iterative ImportError: /usr/lib64/python2.6/site-packages/scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: s_stop ====================================================================== ERROR: Failure: ImportError (/usr/lib64/python2.6/site-packages/scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: s_stop) ---------------------------------------------------------------------- Traceback (most recent call last): File "nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python2.6/site-packages/scipy/sparse/tests/test_base.py", line 34, in <module> from scipy.sparse.linalg import splu File "/usr/lib64/python2.6/site-packages/scipy/sparse/linalg/__init__.py", line 90, in <module> from isolve import * File "/usr/lib64/python2.6/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 4, in <module> from iterative import * File "/usr/lib64/python2.6/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 5, in <module> import _iterative ImportError: /usr/lib64/python2.6/site-packages/scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: s_stop ====================================================================== ERROR: Failure: ImportError (/usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop) ---------------------------------------------------------------------- Traceback (most recent call last): File "nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib64/python2.6/site-packages/scipy/stats/__init__.py", line 321, in <module> from stats import * File "/usr/lib64/python2.6/site-packages/scipy/stats/stats.py", line 194, in <module> import scipy.linalg as linalg File "/usr/lib64/python2.6/site-packages/scipy/linalg/__init__.py", line 132, in <module> from misc import * File "/usr/lib64/python2.6/site-packages/scipy/linalg/misc.py", line 3, in <module> import fblas ImportError: /usr/lib64/python2.6/site-packages/scipy/linalg/fblas.so: undefined symbol: s_stop ====================================================================== FAIL: test_ssyev (test_esv.TestEsv) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.6/site-packages/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_esv.py", line 84, in test_ssyev self._test_base('ssyev', 'F') File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_esv.py", line 26, in _test_base assert_array_almost_equal(w, SYEV_REF, decimal=PREC[tp]) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 800, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 5 decimals (mismatch 100.0%) x: array([-1.1349628 , 2.38857079, 7.74639225], dtype=float32) y: array([-0.66992434, 0.48769389, 9.18223045]) ====================================================================== FAIL: test_ssyevr (test_esv.TestEsv) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.6/site-packages/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_esv.py", line 92, in test_ssyevr self._test_base('ssyevr', 'F') File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_esv.py", line 26, in _test_base assert_array_almost_equal(w, SYEV_REF, decimal=PREC[tp]) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 800, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 5 decimals (mismatch 100.0%) x: array([-1.13496113, 2.38857222, 7.74639177], dtype=float32) y: array([-0.66992434, 0.48769389, 9.18223045]) ====================================================================== FAIL: test_ssyevr_ranges (test_esv.TestEsv) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.6/site-packages/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_esv.py", line 100, in test_ssyevr_ranges self._test_syevr_ranges('ssyevr', 'F') File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_esv.py", line 76, in _test_syevr_ranges self._test_base_irange(func, irange, lang) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_esv.py", line 47, in _test_base_irange assert_array_almost_equal(w, SYEV_REF[rslice], decimal=PREC[tp]) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 800, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 5 decimals (mismatch 100.0%) x: array([-1.13496113, 2.38857222, 7.74639177], dtype=float32) y: array([-0.66992434, 0.48769389, 9.18223045]) ====================================================================== FAIL: test_ssygv_1 (test_gesv.TestSygv) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.6/site-packages/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_gesv.py", line 41, in test_ssygv_1 self._test_base('ssygv', 'F', 1) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_gesv.py", line 29, in _test_base decimal=PREC[tp]) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 800, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 5 decimals (mismatch 100.0%) x: array([ 0.98113459, 0.95912313, 1.87169743], dtype=float32) y: array([ -0.00000000e+00, 2.52944849e+17, -5.80304557e+19], dtype=float32) ====================================================================== FAIL: test_ssygv_2 (test_gesv.TestSygv) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.6/site-packages/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_gesv.py", line 45, in test_ssygv_2 self._test_base('ssygv', 'F', 2) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_gesv.py", line 32, in _test_base decimal=PREC[tp]) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 800, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 5 decimals (mismatch 100.0%) x: array([ 0.58952832, 2.39465809, 5.379776 ], dtype=float32) y: array([-0.60370338, 1.07345402, -0.36409575], dtype=float32) ====================================================================== FAIL: test_ssygv_3 (test_gesv.TestSygv) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.6/site-packages/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_gesv.py", line 49, in test_ssygv_3 self._test_base('ssygv', 'F', 3) File "/usr/lib64/python2.6/site-packages/scipy/lib/lapack/tests/test_gesv.py", line 35, in _test_base w[i]*v[:,i], decimal=PREC[tp] - 1) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 800, in assert_array_almost_equal header=('Arrays are not almost equal to %d decimals' % decimal)) File "/usr/lib64/python2.6/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 4 decimals (mismatch 100.0%) x: array([ 9.9355526 , 8.03703594, 29.26363754], dtype=float32) y: array([ -7.47458363, 10.02687263, -5.13589382], dtype=float32) ---------------------------------------------------------------------- Ran 2334 tests in 27.363s FAILED (KNOWNFAIL=7, SKIP=29, errors=10, failures=6) <nose.result.TextTestResult run=2334 errors=10 failures=6>