[SciPy-User] Three scipy.test() errors

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[SciPy-User] Three scipy.test() errors

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

Trying to install scipy 0.14.0 under Python 3.3.4 but got test errors on three modules with the configuration listed below.

Using LAPACK, ATLAS, and BLAS rpm’s that comes with Red Hat 6.

 

Any help would be appreciated.  

 

Dwayne

 

 

======================================================================

FAIL: test_basic.test_xlogy

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_basic.py", line 2878, in test_xlogy

    assert_func_equal(special.xlogy, w2, z2, rtol=1e-13, atol=1e-13)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 87, in assert_func_equal

    fdata.check()

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 292, in check

    assert_(False, "\n".join(msg))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 44, in assert_

    raise AssertionError(msg)

AssertionError:

Max |adiff|: 712.561

Max |rdiff|: 1028.01

Bad results (3 out of 6) for the following points (in output 0):

                            0j                        (nan+0j) =>                        (-0+0j) !=                     (nan+nanj)  (rdiff                                                      0.0)

                        (1+0j)                          (2+0j) => (-711.8665072622568+1.5707963267948752j) !=        (0.6931471805599453+0j)                            (rdiff             1028.0087776302707)

                        (1+0j)                              1j => (-711.8665072622568+1.5707963267948752j) !=            1.5707963267948966j                            (rdiff             453.18829380940315)

 

======================================================================

FAIL: test_lambertw.test_values

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 21, in test_values

    assert_equal(lambertw(inf,1).real, inf)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 304, in assert_equal

    raise AssertionError(msg)

AssertionError:

Items are not equal:

ACTUAL: nan

DESIRED: inf

 

======================================================================

FAIL: test_lambertw.test_ufunc

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 581, in chk_same_position

    assert_array_equal(x_id, y_id)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 718, in assert_array_equal

    verbose=verbose, header='Arrays are not equal')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare

    raise AssertionError(msg)

AssertionError:

Arrays are not equal

 

(mismatch 66.66666666666666%)

x: array([False,  True,  True], dtype=bool)

y: array([False, False, False], dtype=bool)

 

During handling of the above exception, another exception occurred:

 

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 93, in test_ufunc

    lambertw(r_[0., e, 1.]), r_[0., 1., 0.567143290409783873])

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal

    header=('Arrays are not almost equal to %d decimals' % decimal))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 607, in assert_array_compare

    chk_same_position(x_isnan, y_isnan, hasval='nan')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 587, in chk_same_position

    raise AssertionError(msg)

AssertionError:

Arrays are not almost equal to 6 decimals

 

x and y nan location mismatch:

x: array([  0.+0.j,  nan+0.j,  nan+0.j])

y: array([ 0.        ,  1.        ,  0.56714329])

 

----------------------------------------------------------------------

Ran 16420 tests in 223.156s

 

FAILED (KNOWNFAIL=277, SKIP=1178, failures=3)

<nose.result.TextTestResult run=16420 errors=0 failures=3>

 

 

[root ~]# python -c 'from numpy.f2py.diagnose import run; run()'

------

os.name='posix'

------

sys.platform='linux'

------

sys.version:

3.3.4 (default, Feb 27 2014, 17:05:47)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

------

sys.prefix:

/cm/shared/apps/python/3.3.4

------

sys.path=':/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/setuptools-2.2-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/snakemake-2.5-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python33.zip:/cm/shared/apps/python/3.3.4/lib/python3.3:/cm/shared/apps/python/3.3.4/lib/python3.3/plat-linux:/cm/shared/apps/python/3.3.4/lib/python3.3/lib-dynload:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages'

------

Found new numpy version '1.8.1' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/__init__.py

Found f2py2e version '2' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/f2py/f2py2e.py

Found numpy.distutils version '0.4.0' in '/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/distutils/__init__.py'

------

Importing numpy.distutils.fcompiler ... ok

------

Checking availability of supported Fortran compilers:

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 ('4.4.7')

  version_cmd     = ['/usr/bin/gfortran', '--version']

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']

Fortran compilers found:

  --fcompiler=gnu    GNU Fortran 77 compiler (3.4.6)

  --fcompiler=gnu95  GNU Fortran 95 compiler (4.4.7)

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 ------

 

[root@niamsirpapp01 ~]#  gcc -v

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)

[root@niamsirpapp01 ~]# g77 --version

GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6)

Copyright (C) 2006 Free Software Foundation, Inc.

 

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.

You may redistribute copies of GNU Fortran

under the terms of the GNU General Public License.

For more information about these matters, see the file named COPYING

or type the command `info -f g77 Copying'.


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[SciPy-User] Three scipy.test() errors

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

Trying to install scipy 0.14.0 under Python 3.3.4 but got test errors on three modules with the configuration listed below.

Using LAPACK, ATLAS, and BLAS rpm’s that comes with Red Hat 6.

 

Any help would be appreciated.  

 

Dwayne

 

 

======================================================================

FAIL: test_basic.test_xlogy

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_basic.py", line 2878, in test_xlogy

    assert_func_equal(special.xlogy, w2, z2, rtol=1e-13, atol=1e-13)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 87, in assert_func_equal

    fdata.check()

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 292, in check

    assert_(False, "\n".join(msg))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 44, in assert_

    raise AssertionError(msg)

AssertionError:

Max |adiff|: 712.561

Max |rdiff|: 1028.01

Bad results (3 out of 6) for the following points (in output 0):

                            0j                        (nan+0j) =>                        (-0+0j) !=                     (nan+nanj)  (rdiff                                                      0.0)

                        (1+0j)                          (2+0j) => (-711.8665072622568+1.5707963267948752j) !=        (0.6931471805599453+0j)                            (rdiff             1028.0087776302707)

                        (1+0j)                              1j => (-711.8665072622568+1.5707963267948752j) !=            1.5707963267948966j                            (rdiff             453.18829380940315)

 

======================================================================

FAIL: test_lambertw.test_values

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 21, in test_values

    assert_equal(lambertw(inf,1).real, inf)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 304, in assert_equal

    raise AssertionError(msg)

AssertionError:

Items are not equal:

ACTUAL: nan

DESIRED: inf

 

======================================================================

FAIL: test_lambertw.test_ufunc

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 581, in chk_same_position

    assert_array_equal(x_id, y_id)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 718, in assert_array_equal

    verbose=verbose, header='Arrays are not equal')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare

    raise AssertionError(msg)

AssertionError:

Arrays are not equal

 

(mismatch 66.66666666666666%)

x: array([False,  True,  True], dtype=bool)

y: array([False, False, False], dtype=bool)

 

During handling of the above exception, another exception occurred:

 

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 93, in test_ufunc

    lambertw(r_[0., e, 1.]), r_[0., 1., 0.567143290409783873])

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal

    header=('Arrays are not almost equal to %d decimals' % decimal))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 607, in assert_array_compare

    chk_same_position(x_isnan, y_isnan, hasval='nan')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 587, in chk_same_position

    raise AssertionError(msg)

AssertionError:

Arrays are not almost equal to 6 decimals

 

x and y nan location mismatch:

x: array([  0.+0.j,  nan+0.j,  nan+0.j])

y: array([ 0.        ,  1.        ,  0.56714329])

 

----------------------------------------------------------------------

Ran 16420 tests in 223.156s

 

FAILED (KNOWNFAIL=277, SKIP=1178, failures=3)

<nose.result.TextTestResult run=16420 errors=0 failures=3>

 

 

[root ~]# python -c 'from numpy.f2py.diagnose import run; run()'

------

os.name='posix'

------

sys.platform='linux'

------

sys.version:

3.3.4 (default, Feb 27 2014, 17:05:47)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

------

sys.prefix:

/cm/shared/apps/python/3.3.4

------

sys.path=':/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/setuptools-2.2-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/snakemake-2.5-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python33.zip:/cm/shared/apps/python/3.3.4/lib/python3.3:/cm/shared/apps/python/3.3.4/lib/python3.3/plat-linux:/cm/shared/apps/python/3.3.4/lib/python3.3/lib-dynload:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages'

------

Found new numpy version '1.8.1' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/__init__.py

Found f2py2e version '2' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/f2py/f2py2e.py

Found numpy.distutils version '0.4.0' in '/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/distutils/__init__.py'

------

Importing numpy.distutils.fcompiler ... ok

------

Checking availability of supported Fortran compilers:

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 ('4.4.7')

  version_cmd     = ['/usr/bin/gfortran', '--version']

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']

Fortran compilers found:

  --fcompiler=gnu    GNU Fortran 77 compiler (3.4.6)

  --fcompiler=gnu95  GNU Fortran 95 compiler (4.4.7)

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 ------

 

[root@niamsirpapp01 ~]#  gcc -v

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)

[root@niamsirpapp01 ~]# g77 --version

GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6)

Copyright (C) 2006 Free Software Foundation, Inc.

 

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.

You may redistribute copies of GNU Fortran

under the terms of the GNU General Public License.

For more information about these matters, see the file named COPYING

or type the command `info -f g77 Copying'.


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Reply | Threaded
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Re: Three scipy.test() errors

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

 

Trying to install scipy 0.14.0 under Python 3.3.4 but got test errors on three modules with the configuration listed below.

Using LAPACK, ATLAS, and BLAS rpm’s that comes with Red Hat 6.

 

Any help would be appreciated.  

 

Dwayne

 

 

======================================================================

FAIL: test_basic.test_xlogy

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_basic.py", line 2878, in test_xlogy

    assert_func_equal(special.xlogy, w2, z2, rtol=1e-13, atol=1e-13)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 87, in assert_func_equal

    fdata.check()

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 292, in check

    assert_(False, "\n".join(msg))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 44, in assert_

    raise AssertionError(msg)

AssertionError:

Max |adiff|: 712.561

Max |rdiff|: 1028.01

Bad results (3 out of 6) for the following points (in output 0):

                            0j                        (nan+0j) =>                        (-0+0j) !=                     (nan+nanj)  (rdiff                                                      0.0)

                        (1+0j)                          (2+0j) => (-711.8665072622568+1.5707963267948752j) !=        (0.6931471805599453+0j)                            (rdiff             1028.0087776302707)

                        (1+0j)                              1j => (-711.8665072622568+1.5707963267948752j) !=            1.5707963267948966j                            (rdiff             453.18829380940315)

 

======================================================================

FAIL: test_lambertw.test_values

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 21, in test_values

    assert_equal(lambertw(inf,1).real, inf)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 304, in assert_equal

    raise AssertionError(msg)

AssertionError:

Items are not equal:

ACTUAL: nan

DESIRED: inf

 

======================================================================

FAIL: test_lambertw.test_ufunc

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 581, in chk_same_position

    assert_array_equal(x_id, y_id)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 718, in assert_array_equal

    verbose=verbose, header='Arrays are not equal')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare

    raise AssertionError(msg)

AssertionError:

Arrays are not equal

 

(mismatch 66.66666666666666%)

x: array([False,  True,  True], dtype=bool)

y: array([False, False, False], dtype=bool)

 

During handling of the above exception, another exception occurred:

 

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 93, in test_ufunc

    lambertw(r_[0., e, 1.]), r_[0., 1., 0.567143290409783873])

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal

    header=('Arrays are not almost equal to %d decimals' % decimal))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 607, in assert_array_compare

    chk_same_position(x_isnan, y_isnan, hasval='nan')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 587, in chk_same_position

    raise AssertionError(msg)

AssertionError:

Arrays are not almost equal to 6 decimals

 

x and y nan location mismatch:

x: array([  0.+0.j,  nan+0.j,  nan+0.j])

y: array([ 0.        ,  1.        ,  0.56714329])

 

----------------------------------------------------------------------

Ran 16420 tests in 223.156s

 

FAILED (KNOWNFAIL=277, SKIP=1178, failures=3)

<nose.result.TextTestResult run=16420 errors=0 failures=3>

 

 

[root ~]# python -c 'from numpy.f2py.diagnose import run; run()'

------

os.name='posix'

------

sys.platform='linux'

------

sys.version:

3.3.4 (default, Feb 27 2014, 17:05:47)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

------

sys.prefix:

/cm/shared/apps/python/3.3.4

------

sys.path=':/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/setuptools-2.2-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/snakemake-2.5-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python33.zip:/cm/shared/apps/python/3.3.4/lib/python3.3:/cm/shared/apps/python/3.3.4/lib/python3.3/plat-linux:/cm/shared/apps/python/3.3.4/lib/python3.3/lib-dynload:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages'

------

Found new numpy version '1.8.1' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/__init__.py

Found f2py2e version '2' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/f2py/f2py2e.py

Found numpy.distutils version '0.4.0' in '/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/distutils/__init__.py'

------

Importing numpy.distutils.fcompiler ... ok

------

Checking availability of supported Fortran compilers:

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 ('4.4.7')

  version_cmd     = ['/usr/bin/gfortran', '--version']

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']

Fortran compilers found:

  --fcompiler=gnu    GNU Fortran 77 compiler (3.4.6)

  --fcompiler=gnu95  GNU Fortran 95 compiler (4.4.7)

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 ------

 

[root@niamsirpapp01 ~]#  gcc -v

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)

[root@niamsirpapp01 ~]# g77 --version

GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6)

Copyright (C) 2006 Free Software Foundation, Inc.

 

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.

You may redistribute copies of GNU Fortran

under the terms of the GNU General Public License.

For more information about these matters, see the file named COPYING

or type the command `info -f g77 Copying'.


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[SciPy-User] Three scipy.test() errors

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

Trying to install scipy 0.14.0 under Python 3.3.4 but got test errors on three modules with the configuration listed below.

Using LAPACK, ATLAS, and BLAS rpm’s that comes with Red Hat 6.

 

Any help would be appreciated.  

 

Dwayne

 

 

======================================================================

FAIL: test_basic.test_xlogy

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_basic.py", line 2878, in test_xlogy

    assert_func_equal(special.xlogy, w2, z2, rtol=1e-13, atol=1e-13)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 87, in assert_func_equal

    fdata.check()

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 292, in check

    assert_(False, "\n".join(msg))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 44, in assert_

    raise AssertionError(msg)

AssertionError:

Max |adiff|: 712.561

Max |rdiff|: 1028.01

Bad results (3 out of 6) for the following points (in output 0):

                            0j                        (nan+0j) =>                        (-0+0j) !=                     (nan+nanj)  (rdiff                                                      0.0)

                        (1+0j)                          (2+0j) => (-711.8665072622568+1.5707963267948752j) !=        (0.6931471805599453+0j)                            (rdiff             1028.0087776302707)

                        (1+0j)                              1j => (-711.8665072622568+1.5707963267948752j) !=            1.5707963267948966j                            (rdiff             453.18829380940315)

 

======================================================================

FAIL: test_lambertw.test_values

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 21, in test_values

    assert_equal(lambertw(inf,1).real, inf)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 304, in assert_equal

    raise AssertionError(msg)

AssertionError:

Items are not equal:

ACTUAL: nan

DESIRED: inf

 

======================================================================

FAIL: test_lambertw.test_ufunc

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 581, in chk_same_position

    assert_array_equal(x_id, y_id)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 718, in assert_array_equal

    verbose=verbose, header='Arrays are not equal')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare

    raise AssertionError(msg)

AssertionError:

Arrays are not equal

 

(mismatch 66.66666666666666%)

x: array([False,  True,  True], dtype=bool)

y: array([False, False, False], dtype=bool)

 

During handling of the above exception, another exception occurred:

 

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 93, in test_ufunc

    lambertw(r_[0., e, 1.]), r_[0., 1., 0.567143290409783873])

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal

    header=('Arrays are not almost equal to %d decimals' % decimal))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 607, in assert_array_compare

    chk_same_position(x_isnan, y_isnan, hasval='nan')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 587, in chk_same_position

    raise AssertionError(msg)

AssertionError:

Arrays are not almost equal to 6 decimals

 

x and y nan location mismatch:

x: array([  0.+0.j,  nan+0.j,  nan+0.j])

y: array([ 0.        ,  1.        ,  0.56714329])

 

----------------------------------------------------------------------

Ran 16420 tests in 223.156s

 

FAILED (KNOWNFAIL=277, SKIP=1178, failures=3)

<nose.result.TextTestResult run=16420 errors=0 failures=3>

 

 

[root ~]# python -c 'from numpy.f2py.diagnose import run; run()'

------

os.name='posix'

------

sys.platform='linux'

------

sys.version:

3.3.4 (default, Feb 27 2014, 17:05:47)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

------

sys.prefix:

/cm/shared/apps/python/3.3.4

------

sys.path=':/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/setuptools-2.2-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/snakemake-2.5-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python33.zip:/cm/shared/apps/python/3.3.4/lib/python3.3:/cm/shared/apps/python/3.3.4/lib/python3.3/plat-linux:/cm/shared/apps/python/3.3.4/lib/python3.3/lib-dynload:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages'

------

Found new numpy version '1.8.1' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/__init__.py

Found f2py2e version '2' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/f2py/f2py2e.py

Found numpy.distutils version '0.4.0' in '/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/distutils/__init__.py'

------

Importing numpy.distutils.fcompiler ... ok

------

Checking availability of supported Fortran compilers:

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 ('4.4.7')

  version_cmd     = ['/usr/bin/gfortran', '--version']

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']

Fortran compilers found:

  --fcompiler=gnu    GNU Fortran 77 compiler (3.4.6)

  --fcompiler=gnu95  GNU Fortran 95 compiler (4.4.7)

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 ------

 

[root@niamsirpapp01 ~]#  gcc -v

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)

[root@niamsirpapp01 ~]# g77 --version

GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6)

Copyright (C) 2006 Free Software Foundation, Inc.

 

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.

You may redistribute copies of GNU Fortran

under the terms of the GNU General Public License.

For more information about these matters, see the file named COPYING

or type the command `info -f g77 Copying'.


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Re: Three scipy.test() errors

ralfgommers
In reply to this post by McCully, Dwayne (NIH/NLM/LHC) [C]



On Mon, Jul 14, 2014 at 3:09 PM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]> wrote:

Trying to install scipy 0.14.0 under Python 3.3.4 but got test errors on three modules with the configuration listed below.

Using LAPACK, ATLAS, and BLAS rpm’s that comes with Red Hat 6.

 

Any help would be appreciated.  


Suggested to change gcc version, see https://github.com/scipy/scipy/issues/3568.

Ralf

 

 

Dwayne

 

 

======================================================================

FAIL: test_basic.test_xlogy

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_basic.py", line 2878, in test_xlogy

    assert_func_equal(special.xlogy, w2, z2, rtol=1e-13, atol=1e-13)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 87, in assert_func_equal

    fdata.check()

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 292, in check

    assert_(False, "\n".join(msg))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 44, in assert_

    raise AssertionError(msg)

AssertionError:

Max |adiff|: 712.561

Max |rdiff|: 1028.01

Bad results (3 out of 6) for the following points (in output 0):

                            0j                        (nan+0j) =>                        (-0+0j) !=                     (nan+nanj)  (rdiff                                                      0.0)

                        (1+0j)                          (2+0j) => (-711.8665072622568+1.5707963267948752j) !=        (0.6931471805599453+0j)                            (rdiff             1028.0087776302707)

                        (1+0j)                              1j => (-711.8665072622568+1.5707963267948752j) !=            1.5707963267948966j                            (rdiff             453.18829380940315)

 

======================================================================

FAIL: test_lambertw.test_values

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 21, in test_values

    assert_equal(lambertw(inf,1).real, inf)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 304, in assert_equal

    raise AssertionError(msg)

AssertionError:

Items are not equal:

ACTUAL: nan

DESIRED: inf

 

======================================================================

FAIL: test_lambertw.test_ufunc

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 581, in chk_same_position

    assert_array_equal(x_id, y_id)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 718, in assert_array_equal

    verbose=verbose, header='Arrays are not equal')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare

    raise AssertionError(msg)

AssertionError:

Arrays are not equal

 

(mismatch 66.66666666666666%)

x: array([False,  True,  True], dtype=bool)

y: array([False, False, False], dtype=bool)

 

During handling of the above exception, another exception occurred:

 

Traceback (most recent call last):

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest

    self.test(*self.arg)

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 93, in test_ufunc

    lambertw(r_[0., e, 1.]), r_[0., 1., 0.567143290409783873])

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal

    header=('Arrays are not almost equal to %d decimals' % decimal))

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 607, in assert_array_compare

    chk_same_position(x_isnan, y_isnan, hasval='nan')

  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 587, in chk_same_position

    raise AssertionError(msg)

AssertionError:

Arrays are not almost equal to 6 decimals

 

x and y nan location mismatch:

x: array([  0.+0.j,  nan+0.j,  nan+0.j])

y: array([ 0.        ,  1.        ,  0.56714329])

 

----------------------------------------------------------------------

Ran 16420 tests in 223.156s

 

FAILED (KNOWNFAIL=277, SKIP=1178, failures=3)

<nose.result.TextTestResult run=16420 errors=0 failures=3>

 

 

[root ~]# python -c 'from numpy.f2py.diagnose import run; run()'

------

os.name='posix'

------

sys.platform='linux'

------

sys.version:

3.3.4 (default, Feb 27 2014, 17:05:47)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

------

sys.prefix:

/cm/shared/apps/python/3.3.4

------

sys.path=':/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/setuptools-2.2-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/snakemake-2.5-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python33.zip:/cm/shared/apps/python/3.3.4/lib/python3.3:/cm/shared/apps/python/3.3.4/lib/python3.3/plat-linux:/cm/shared/apps/python/3.3.4/lib/python3.3/lib-dynload:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages'

------

Found new numpy version '1.8.1' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/__init__.py

Found f2py2e version '2' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/f2py/f2py2e.py

Found numpy.distutils version '0.4.0' in '/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/distutils/__init__.py'

------

Importing numpy.distutils.fcompiler ... ok

------

Checking availability of supported Fortran compilers:

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 ('4.4.7')

  version_cmd     = ['/usr/bin/gfortran', '--version']

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']

Fortran compilers found:

  --fcompiler=gnu    GNU Fortran 77 compiler (3.4.6)

  --fcompiler=gnu95  GNU Fortran 95 compiler (4.4.7)

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 ------

 

[root@niamsirpapp01 ~]#  gcc -v

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)

[root@niamsirpapp01 ~]# g77 --version

GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6)

Copyright (C) 2006 Free Software Foundation, Inc.

 

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.

You may redistribute copies of GNU Fortran

under the terms of the GNU General Public License.

For more information about these matters, see the file named COPYING

or type the command `info -f g77 Copying'.


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Re: Three scipy.test() errors

McCully, Dwayne (NIH/NLM/LHC) [C]
Hi Ralf,

Ran the install script with "python setup.py config_fc --fcompiler=gnu install".   As always I get a lot of warning messages but now the scipy.test() crashes with a Segmentaion fault. I did see g77 and not gfortran when compiling.

maybe used but uninitialized in fuction
unused variable
etc...


Any suggestions on the command line?

Dwayne



________________________________
From: Ralf Gommers [[hidden email]]
Sent: Monday, July 21, 2014 3:47 PM
To: SciPy Users List
Subject: Re: [SciPy-User] Three scipy.test() errors




On Mon, Jul 14, 2014 at 3:09 PM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]<mailto:[hidden email]>> wrote:
Trying to install scipy 0.14.0 under Python 3.3.4 but got test errors on three modules with the configuration listed below.
Using LAPACK, ATLAS, and BLAS rpm’s that comes with Red Hat 6.

Any help would be appreciated.

Suggested to change gcc version, see https://github.com/scipy/scipy/issues/3568.

Ralf



Dwayne


======================================================================
FAIL: test_basic.test_xlogy
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_basic.py", line 2878, in test_xlogy
    assert_func_equal(special.xlogy, w2, z2, rtol=1e-13, atol=1e-13)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 87, in assert_func_equal
    fdata.check()
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 292, in check
    assert_(False, "\n".join(msg))
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 44, in assert_
    raise AssertionError(msg)
AssertionError:
Max |adiff|: 712.561
Max |rdiff|: 1028.01
Bad results (3 out of 6) for the following points (in output 0):
                            0j                        (nan+0j) =>                        (-0+0j) !=                     (nan+nanj)  (rdiff                                                      0.0)
                        (1+0j)                          (2+0j) => (-711.8665072622568+1.5707963267948752j) !=        (0.6931471805599453+0j)                            (rdiff             1028.0087776302707)
                        (1+0j)                              1j => (-711.8665072622568+1.5707963267948752j) !=            1.5707963267948966j                            (rdiff             453.18829380940315)

======================================================================
FAIL: test_lambertw.test_values
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 21, in test_values
    assert_equal(lambertw(inf,1).real, inf)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 304, in assert_equal
    raise AssertionError(msg)
AssertionError:
Items are not equal:
ACTUAL: nan
DESIRED: inf

======================================================================
FAIL: test_lambertw.test_ufunc
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 581, in chk_same_position
    assert_array_equal(x_id, y_id)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 718, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not equal

(mismatch 66.66666666666666%)
x: array([False,  True,  True], dtype=bool)
y: array([False, False, False], dtype=bool)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 93, in test_ufunc
    lambertw(r_[0., e, 1.]), r_[0., 1., 0.567143290409783873])
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 607, in assert_array_compare
    chk_same_position(x_isnan, y_isnan, hasval='nan')
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 587, in chk_same_position
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

x and y nan location mismatch:
x: array([  0.+0.j,  nan+0.j,  nan+0.j])
y: array([ 0.        ,  1.        ,  0.56714329])

----------------------------------------------------------------------
Ran 16420 tests in 223.156s

FAILED (KNOWNFAIL=277, SKIP=1178, failures=3)
<nose.result.TextTestResult run=16420 errors=0 failures=3>


[root ~]# python -c 'from numpy.f2py.diagnose import run; run()'
------
os.name<http://os.name>='posix'
------
sys.platform='linux'
------
sys.version:
3.3.4 (default, Feb 27 2014, 17:05:47)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]
------
sys.prefix:
/cm/shared/apps/python/3.3.4
------
sys.path=':/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/setuptools-2.2-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/snakemake-2.5-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python33.zip:/cm/shared/apps/python/3.3.4/lib/python3.3:/cm/shared/apps/python/3.3.4/lib/python3.3/plat-linux:/cm/shared/apps/python/3.3.4/lib/python3.3/lib-dynload:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages'
------
Found new numpy version '1.8.1' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/__init__.py
Found f2py2e version '2' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/f2py/f2py2e.py
Found numpy.distutils version '0.4.0' in '/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/distutils/__init__.py'
------
Importing numpy.distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
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 ('4.4.7')
  version_cmd     = ['/usr/bin/gfortran', '--version']
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']
Fortran compilers found:
  --fcompiler=gnu    GNU Fortran 77 compiler (3.4.6)
  --fcompiler=gnu95  GNU Fortran 95 compiler (4.4.7)
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 ------

[root@niamsirpapp01 ~]#  gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)
[root@niamsirpapp01 ~]# g77 --version
GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6)
Copyright (C) 2006 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
or type the command `info -f g77 Copying'.

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Re: Three scipy.test() errors

ralfgommers



On Tue, Jul 22, 2014 at 3:26 AM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]> wrote:
Hi Ralf,

Ran the install script with "python setup.py config_fc --fcompiler=gnu install".   As always I get a lot of warning messages but now the scipy.test() crashes with a Segmentaion fault. I did see g77 and not gfortran when compiling.

If your blas/lapack was built with gfortran and you now build scipy with g77, that won't work. Search for "g77" on http://scipy.org/scipylib/building/linux.html for more details.

Cheers,
Ralf


maybe used but uninitialized in fuction
unused variable
etc...


Any suggestions on the command line?

Dwayne



________________________________
From: Ralf Gommers [[hidden email]]
Sent: Monday, July 21, 2014 3:47 PM
To: SciPy Users List
Subject: Re: [SciPy-User] Three scipy.test() errors




On Mon, Jul 14, 2014 at 3:09 PM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]<mailto:[hidden email]>> wrote:
Trying to install scipy 0.14.0 under Python 3.3.4 but got test errors on three modules with the configuration listed below.
Using LAPACK, ATLAS, and BLAS rpm’s that comes with Red Hat 6.

Any help would be appreciated.

Suggested to change gcc version, see https://github.com/scipy/scipy/issues/3568.

Ralf



Dwayne


======================================================================
FAIL: test_basic.test_xlogy
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_basic.py", line 2878, in test_xlogy
    assert_func_equal(special.xlogy, w2, z2, rtol=1e-13, atol=1e-13)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 87, in assert_func_equal
    fdata.check()
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 292, in check
    assert_(False, "\n".join(msg))
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 44, in assert_
    raise AssertionError(msg)
AssertionError:
Max |adiff|: 712.561
Max |rdiff|: 1028.01
Bad results (3 out of 6) for the following points (in output 0):
                            0j                        (nan+0j) =>                        (-0+0j) !=                     (nan+nanj)  (rdiff                                                      0.0)
                        (1+0j)                          (2+0j) => (-711.8665072622568+1.5707963267948752j) !=        (0.6931471805599453+0j)                            (rdiff             1028.0087776302707)
                        (1+0j)                              1j => (-711.8665072622568+1.5707963267948752j) !=            1.5707963267948966j                            (rdiff             453.18829380940315)

======================================================================
FAIL: test_lambertw.test_values
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 21, in test_values
    assert_equal(lambertw(inf,1).real, inf)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 304, in assert_equal
    raise AssertionError(msg)
AssertionError:
Items are not equal:
ACTUAL: nan
DESIRED: inf

======================================================================
FAIL: test_lambertw.test_ufunc
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 581, in chk_same_position
    assert_array_equal(x_id, y_id)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 718, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not equal

(mismatch 66.66666666666666%)
x: array([False,  True,  True], dtype=bool)
y: array([False, False, False], dtype=bool)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 93, in test_ufunc
    lambertw(r_[0., e, 1.]), r_[0., 1., 0.567143290409783873])
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 607, in assert_array_compare
    chk_same_position(x_isnan, y_isnan, hasval='nan')
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 587, in chk_same_position
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

x and y nan location mismatch:
x: array([  0.+0.j,  nan+0.j,  nan+0.j])
y: array([ 0.        ,  1.        ,  0.56714329])

----------------------------------------------------------------------
Ran 16420 tests in 223.156s

FAILED (KNOWNFAIL=277, SKIP=1178, failures=3)
<nose.result.TextTestResult run=16420 errors=0 failures=3>


[root ~]# python -c 'from numpy.f2py.diagnose import run; run()'
------
os.name<http://os.name>='posix'
------
sys.platform='linux'
------
sys.version:
3.3.4 (default, Feb 27 2014, 17:05:47)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]
------
sys.prefix:
/cm/shared/apps/python/3.3.4
------
sys.path=':/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/setuptools-2.2-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/snakemake-2.5-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python33.zip:/cm/shared/apps/python/3.3.4/lib/python3.3:/cm/shared/apps/python/3.3.4/lib/python3.3/plat-linux:/cm/shared/apps/python/3.3.4/lib/python3.3/lib-dynload:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages'
------
Found new numpy version '1.8.1' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/__init__.py
Found f2py2e version '2' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/f2py/f2py2e.py
Found numpy.distutils version '0.4.0' in '/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/distutils/__init__.py'
------
Importing numpy.distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
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 ('4.4.7')
  version_cmd     = ['/usr/bin/gfortran', '--version']
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']
Fortran compilers found:
  --fcompiler=gnu    GNU Fortran 77 compiler (3.4.6)
  --fcompiler=gnu95  GNU Fortran 95 compiler (4.4.7)
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 ------

[root@niamsirpapp01 ~]#  gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)
[root@niamsirpapp01 ~]# g77 --version
GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6)
Copyright (C) 2006 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
or type the command `info -f g77 Copying'.

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Re: Three scipy.test() errors

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

Hi Ralf,

 

When compiling scipy with g77 or gfortran, why are there so many warning messages?  Do you get them?

 

Dwayne

 

From: Ralf Gommers [mailto:[hidden email]]
Sent: Tuesday, July 22, 2014 4:25 PM
To: SciPy Users List
Subject: Re: [SciPy-User] Three scipy.test() errors

 

 

 

On Tue, Jul 22, 2014 at 3:26 AM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]> wrote:

Hi Ralf,

Ran the install script with "python setup.py config_fc --fcompiler=gnu install".   As always I get a lot of warning messages but now the scipy.test() crashes with a Segmentaion fault. I did see g77 and not gfortran when compiling.

 

If your blas/lapack was built with gfortran and you now build scipy with g77, that won't work. Search for "g77" on http://scipy.org/scipylib/building/linux.html for more details.

Cheers,
Ralf


maybe used but uninitialized in fuction
unused variable
etc...


Any suggestions on the command line?

Dwayne



________________________________
From: Ralf Gommers [[hidden email]]
Sent: Monday, July 21, 2014 3:47 PM
To: SciPy Users List
Subject: Re: [SciPy-User] Three scipy.test() errors




On Mon, Jul 14, 2014 at 3:09 PM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]<mailto:[hidden email]>> wrote:
Trying to install scipy 0.14.0 under Python 3.3.4 but got test errors on three modules with the configuration listed below.
Using LAPACK, ATLAS, and BLAS rpm’s that comes with Red Hat 6.

Any help would be appreciated.

Suggested to change gcc version, see https://github.com/scipy/scipy/issues/3568.

Ralf



Dwayne


======================================================================
FAIL: test_basic.test_xlogy
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_basic.py", line 2878, in test_xlogy
    assert_func_equal(special.xlogy, w2, z2, rtol=1e-13, atol=1e-13)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 87, in assert_func_equal
    fdata.check()
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/_testutils.py", line 292, in check
    assert_(False, "\n".join(msg))
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 44, in assert_
    raise AssertionError(msg)
AssertionError:
Max |adiff|: 712.561
Max |rdiff|: 1028.01
Bad results (3 out of 6) for the following points (in output 0):
                            0j                        (nan+0j) =>                        (-0+0j) !=                     (nan+nanj)  (rdiff                                                      0.0)
                        (1+0j)                          (2+0j) => (-711.8665072622568+1.5707963267948752j) !=        (0.6931471805599453+0j)                            (rdiff             1028.0087776302707)
                        (1+0j)                              1j => (-711.8665072622568+1.5707963267948752j) !=            1.5707963267948966j                            (rdiff             453.18829380940315)

======================================================================
FAIL: test_lambertw.test_values
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 21, in test_values
    assert_equal(lambertw(inf,1).real, inf)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 304, in assert_equal
    raise AssertionError(msg)
AssertionError:
Items are not equal:
ACTUAL: nan
DESIRED: inf

======================================================================
FAIL: test_lambertw.test_ufunc
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 581, in chk_same_position
    assert_array_equal(x_id, y_id)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 718, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not equal

(mismatch 66.66666666666666%)
x: array([False,  True,  True], dtype=bool)
y: array([False, False, False], dtype=bool)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 93, in test_ufunc
    lambertw(r_[0., e, 1.]), r_[0., 1., 0.567143290409783873])
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 811, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 607, in assert_array_compare
    chk_same_position(x_isnan, y_isnan, hasval='nan')
  File "/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/testing/utils.py", line 587, in chk_same_position
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 6 decimals

x and y nan location mismatch:
x: array([  0.+0.j,  nan+0.j,  nan+0.j])
y: array([ 0.        ,  1.        ,  0.56714329])

----------------------------------------------------------------------
Ran 16420 tests in 223.156s

FAILED (KNOWNFAIL=277, SKIP=1178, failures=3)
<nose.result.TextTestResult run=16420 errors=0 failures=3>


[root ~]# python -c 'from numpy.f2py.diagnose import run; run()'
------
os.name<http://os.name>='posix'
------
sys.platform='linux'
------
sys.version:
3.3.4 (default, Feb 27 2014, 17:05:47)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]
------
sys.prefix:
/cm/shared/apps/python/3.3.4
------
sys.path=':/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/setuptools-2.2-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/snakemake-2.5-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/nose-1.3.0-py3.3.egg:/cm/shared/apps/python/3.3.4/lib/python33.zip:/cm/shared/apps/python/3.3.4/lib/python3.3:/cm/shared/apps/python/3.3.4/lib/python3.3/plat-linux:/cm/shared/apps/python/3.3.4/lib/python3.3/lib-dynload:/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages'
------
Found new numpy version '1.8.1' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/__init__.py
Found f2py2e version '2' in /cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/f2py/f2py2e.py
Found numpy.distutils version '0.4.0' in '/cm/shared/apps/python/3.3.4/lib/python3.3/site-packages/numpy/distutils/__init__.py'
------
Importing numpy.distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
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 ('4.4.7')
  version_cmd     = ['/usr/bin/gfortran', '--version']
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']
Fortran compilers found:
  --fcompiler=gnu    GNU Fortran 77 compiler (3.4.6)
  --fcompiler=gnu95  GNU Fortran 95 compiler (4.4.7)
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 ------

[root@niamsirpapp01 ~]#  gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)
[root@niamsirpapp01 ~]# g77 --version
GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6)
Copyright (C) 2006 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
or type the command `info -f g77 Copying'.

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Re: Three scipy.test() errors

ralfgommers



On Tue, Jul 22, 2014 at 10:32 PM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]> wrote:

Hi Ralf,

 

When compiling scipy with g77 or gfortran, why are there so many warning messages?  Do you get them?


Yeah, everyone who compiles with distutils gets those. There is a lot of Fortran 77 code in scipy that is very old and was only wrapped by the scipy developers. We don't want to modify that code just to fix the build warnings, because that would make it quite hard to later apply patches from upstream (packages like Arpack are still developed). And of course it would be a lot of work as well.

Modifying the default distutils build flags is not easy, because they come from Python distutils.

Ralf


 

Dwayne

 

From: Ralf Gommers [mailto:[hidden email]]
Sent: Tuesday, July 22, 2014 4:25 PM


To: SciPy Users List
Subject: Re: [SciPy-User] Three scipy.test() errors

 

 

 

On Tue, Jul 22, 2014 at 3:26 AM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]> wrote:

Hi Ralf,

Ran the install script with "python setup.py config_fc --fcompiler=gnu install".   As always I get a lot of warning messages but now the scipy.test() crashes with a Segmentaion fault. I did see g77 and not gfortran when compiling.

 

If your blas/lapack was built with gfortran and you now build scipy with g77, that won't work. Search for "g77" on http://scipy.org/scipylib/building/linux.html for more details.

Cheers,
Ralf


maybe used but uninitialized in fuction
unused variable
etc...


Any suggestions on the command line?

Dwayne



________________________________
From: Ralf Gommers [[hidden email]]
Sent: Monday, July 21, 2014 3:47 PM
To: SciPy Users List
Subject: Re: [SciPy-User] Three scipy.test() errors




On Mon, Jul 14, 2014 at 3:09 PM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]<mailto:[hidden email]>> wrote:
Trying to install scipy 0.14.0 under Python 3.3.4 but got test errors on three modules with the configuration listed below.
Using LAPACK, ATLAS, and BLAS rpm’s that comes with Red Hat 6.

Any help would be appreciated.

Suggested to change gcc version, see https://github.com/scipy/scipy/issues/3568.

Ralf



Dwayne


======================================================================
FAIL: test_basic.test_xlogy
----------------------------------------------------------------------



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