[SciPy-User] Three scipy.test() errors
McCully, Dwayne (NIH/NIAMS) [C]
dmccully at mail.nih.gov
Tue Jul 15 14:07:27 EDT 2014
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 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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