Issue 1:
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'.

Issue 2:
Hello,

I compiled scipy 0.13.3 succesfully on my CentOS laptop on which I run the following kernel:

2.6.32-431.11.2.el6.x86_64

I have a two core proc (0,1) of the following type:

more /proc/cpuinfo

processor : 0

vendor_id : GenuineIntel

cpu family : 6

model : 23

model name : Intel(R) Core(TM)2 Duo CPU U9600 @ 1.60GHz

stepping : 10

cpu MHz : 800.000

cache size : 3072 KB

physical id : 0

siblings : 2

core id : 0

cpu cores : 2

apicid : 0

initial apicid : 0

fpu : yes

fpu_exception : yes

cpuid level : 13

wp : yes

flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm const

ant_tsc arch_perfmon pebs bts rep_good aperfmperf pni dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 xsave lahf_lm ida dts tpr_shadow vnmi

flexpriority

bogomips : 3192.04

clflush size : 64

cache_alignment : 64

address sizes : 36 bits physical, 48 bits virtual

power management:

....

(I omitted the second core)

I used the gcc and gfortran to compile the scipy code

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)

In order to compile scipy I compiled the following packages from source:

a.OpenBlas 0.2.8 (single threaded) (blas, lapack)

b.SuiteSparse suite (amd,umfpack) using the OpenBlas libraries

c. numpy, nose and setuptools

with the same gcc/gfortran compilers.

I ran the full numpy test suite successfully.

python3 -c "import numpy; numpy.test(label='full',verbose=10)" >& np_test.out

tail -9 np_test.out

Ran 5334 tests in 614.631s

OK (KNOWNFAIL=6, SKIP=3)

Running unit tests for numpy

NumPy version 1.8.1

NumPy is installed in /software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy

Python version 3.3.5 (default, Apr 22 2014, 13:31:40) [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

nose version 1.3.1

Besides the Arpack errors I also got three other errors (The errors can be found below)

Please let me know if you need more info.

Thanks in advance,

Wim

FAIL: test_arpack.test_real_nonsymmetric_modes(False, , 'f', 2, 'LM', None, 0.1, <function asarray at 0x7f7bdbc64f80>, 'r')

Traceback (most recent call last):

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py", line 198, in runTest

self.test(*self.arg)

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 259, in eval_evec

assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py", line 1183, in assert_allclose

verbose=verbose, header=header)

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare

raise AssertionError(msg)

AssertionError:

Not equal to tolerance rtol=0.000357628, atol=0.000357628

error for eigs:standard, typ=f, which=LM, sigma=0.1, mattype=asarray, OPpart=r, mode=normal

(mismatch 100.0%)

x: array([[-0.11649324+0.j, -0.05435310+0.j],

[ 0.13801208+0.j, -0.05894032+0.j],

[-0.21229853+0.j, -0.02815625+0.j],...

y: array([[-0.05698580+0.08018474j, -0.05435318+0.j ],

[ 0.06439485-0.09061003j, -0.05894023+0.j ],

[-0.12503998+0.17594382j, -0.02815617+0.j ],...

AIL: test_arpack.test_real_nonsymmetric_modes(False, , 'f', 2, 'LR', None, None, <function aslinearoperator at 0x7f7bcf0c1170>, None)

Traceback (most recent call last):

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py", line 198, in runTest

self.test(*self.arg)

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 259, in eval_evec

assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py", line 1183, in assert_allclose

verbose=verbose, header=header)

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py", line 644, in assert_array_compare

raise AssertionError(msg)

AssertionError:

Not equal to tolerance rtol=0.00178814, atol=0.000357628

error for eigs:standard, typ=f, which=LR, sigma=None, mattype=aslinearoperator, OPpart=None, mode=normal

(mismatch 100.0%)

x: array([[ 0.13884316+0.j, -1.07112074+0.j],

[-0.08962911+0.j, -1.39801252+0.j],

[ 0.21701422+0.j, -0.93968379+0.j],...

y: array([[ 0.06020537+0.08471544j, -1.07112110+0.j ],

[-0.07497437-0.10549703j, -1.39801240+0.j ],

[ 0.13326693+0.18752094j, -0.93968397+0.j ],...

FAIL: test_basic.test_xlogy

Traceback (most recent call last):

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py", line 198, in runTest

self.test(*self.arg)

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/special/tests/test_basic.py", line 2736, in test_xlogy

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

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/special/testutils.py", line 87, in assert_func_equal

fdata.check()

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/special/testutils.py", line 292, in check

assert(False, "\n".join(msg))

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py", line 44, in assert

raise AssertionError(msg)

AssertionError:

Max |adiff|: 712.209

Max |rdiff|: 1027.5

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) => (-711.5156069932148+0.7853981633976757j) != (0.6931471805599453+0j) (rdiff 1027.5006624894627)

(1+0j) 1j => (-711.5156069932148+0.7853981633976757j) != 1.5707963267948966j (rdiff 452.9651797194877)

FAIL: test_lambertw.test_values

Traceback (most recent call last):

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py", line 198, in runTest

self.test(*self.arg)

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py", line 21, in test_values

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

File "/software/pkg/python/3.3.5/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 "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py", line 581, in chk_same_position

assert_array_equal(x_id, y_id)

File "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py", line 718, in assert_array_equal

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

File "/software/pkg/python/3.3.5/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 "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py", line 198, in runTest

self.test(*self.arg)

File "/software/pkg/python/3.3.5/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 "/software/pkg/python/3.3.5/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 "/software/pkg/python/3.3.5/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 "/software/pkg/python/3.3.5/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. , 0.567])

Ran 9532 tests in 698.956s

FAILED (KNOWNFAIL=130, SKIP=324, failures=5)

Running unit tests for scipy

NumPy version 1.8.1

NumPy is installed in /software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy

SciPy version 0.13.3

SciPy is installed in /software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy

Python version 3.3.5 (default, Apr 22 2014, 13:31:40) [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

nose version 1.3.1