[SciPy-User] Three scipy.test() errors
Ralf Gommers
ralf.gommers at gmail.com
Tue Jul 22 16:24:57 EDT 2014
On Tue, Jul 22, 2014 at 3:26 AM, McCully, Dwayne (NIH/NIAMS) [C] <
dmccully at mail.nih.gov> 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 [ralf.gommers at gmail.com]
> 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] <
> dmccully at mail.nih.gov<mailto:dmccully at mail.nih.gov>> 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 at 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 at 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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