[SciPy-User] Three scipy.test() errors
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[SciPy-User] Three scipy.test() errors
![McCully, Dwayne (NIH/NLM/LHC) [C]](/images/avatar100.png "McCully, Dwayne (NIH/NLM/LHC) [C]"){kind=avatar} 
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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'. _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
[SciPy-User] Three scipy.test() errors
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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'. _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
Re: Three scipy.test() errors
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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'. _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
[SciPy-User] Three scipy.test() errors
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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'. _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
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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:
Ralf
_______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
Re: Three scipy.test() errors
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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'. _______________________________________________ SciPy-User mailing list [hidden email]<mailto:[hidden email]> http://mail.scipy.org/mailman/listinfo/scipy-user _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
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On Tue, Jul 22, 2014 at 3:26 AM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]> wrote: Hi Ralf, 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
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Re: Three scipy.test() errors
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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]]
On Tue, Jul 22, 2014 at 3:26 AM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]> wrote: Hi Ralf, 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,
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On Tue, Jul 22, 2014 at 10:32 PM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]> wrote:
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
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