[SciPy-dev] numpy/scipy some remarks
Arnd Baecker
arnd.baecker at web.de
Wed Jan 18 02:49:18 CST 2006
Hi,
I just successfully installed a recent numpy/scipy using MKL as math
library on Itanium2.
I have few minor comments, which might cause confusion
to new-comers (and me as well;-) to the numpy/scipy combo:
1.) What does the overwriting stuff mean?
In [1]: import scipy
In [2]: scipy.pkgload()
Overwriting lib=<module 'scipy.lib' from
'/home/baecker/python2/scipy_icc_lintst_n_mkl/lib/python2.4/site-packages/scipy/lib/__init__.pyc'>
from
/home/baecker/python2/scipy_icc_lintst_n_mkl/lib/python2.4/site-packages/scipy/lib/__init__.pyc
(was <module 'numpy.lib' from
'/home/baecker/python2/scipy_icc_lintst_n_mkl/lib/python2.4/site-packages/numpy/lib/__init__.pyc'>
from
/home/baecker/python2/scipy_icc_lintst_n_mkl/lib/python2.4/site-packages/numpy/lib/__init__.pyc)
2.) Because I did not use ATLAS, I get the following warnings
during testing (scipy.test(10): Ran 1038 tests in 21.509:
****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
then scipy uses flapack instead of clapack.
****************************************************************
****************************************************************
WARNING: cblas module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
then scipy uses fblas instead of cblas.
****************************************************************
I am not sure, if it is clear (even after reading scipy/INSTALL.txt),
what one has to do with this warning.
Should one in addition also install atlas for the clapack/cblas
part?
(Personally I think that for MKL one should just go for the fortran
wrappers, and don't think about the clapack/cblas stuff.
Isn't this only of importance, if the arrays have the wrong
orderering in memory to avoid a copy?)
3.) There was one of those statistical failures again:
======================================================================
FAIL: check_normal (scipy.stats.morestats.test_morestats.test_anderson)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/baecker/python2/scipy_icc_lintst_n_mkl/lib/python2.4/site-packages/scipy/stats/tests/test_morestats.py",
line 47, in check_normal
assert_array_less(A, crit[-2:])
File
"/home/baecker/python2//scipy_icc_lintst_n_mkl/lib/python2.4/site-packages/numpy/testing/utils.py",
line 207, in assert_array_less
assert cond,\
AssertionError:
Arrays are not less-ordered (mismatch 50.0%):
Array 1: 0.86583024233101469
Array 2: [ 0.858 1.0210000000000001]
((Of course, the more often one builds, the more events of this
type will happen ;-))
Would it make sense to run these statistical tests eg. up to 5 times,
and only if they fail all the time, to issue a FAILURE?
4.) help(scipy)
Contents
--------
numpy name space
[[ looks quite empty here -
is any more contents (eg. a short example?) planned ]]
Available subpackages
---------------------
stats --- Statistical Functions [*]
sparse --- Sparse matrix [*]
lib --- Python wrappers to external libraries [*]
linalg --- Linear algebra routines [*]
signal --- Signal Processing Tools [*]
misc --- Various utilities that don't have another home.
interpolate --- Interpolation Tools [*]
optimize --- Optimization Tools [*]
cluster --- Vector Quantization / Kmeans [*]
fftpack --- Discrete Fourier Transform algorithms [*]
io --- Data input and output [*]
integrate --- Integration routines [*]
lib.lapack --- Wrappers to LAPACK library [*]
special --- Special Functions [*]
lib.blas --- Wrappers to BLAS library [*]
[*] - using a package requires explicit import (see pkgload)
[[ couldn't one get rid of all these [*]? They don't look nice.
Only `misc` is different ]]
Global symbols from subpackages
-------------------------------
stats --> find_repeats
misc --> info, factorial, factorial2, factorialk, comb, who, lena,
central_diff_weights, derivative, pade, source
fftpack --> fft, fftn, fft2, ifft, ifft2, ifftn, fftshift, ifftshift,
fftfreq
Utility tools
-------------
test --- Run scipy unittests
pkgload --- Load scipy packages
show_config --- Show scipy build configuration
show_numpy_config --- Show numpy build configuration
[[ this is directly mapped to `numpy`s show - is it really needed here
as well? ]]
__version__ --- Scipy version string
__numpy_version__ --- Numpy version string
[[ same with this one, why not just have it in numpy?]]
Environment variables
---------------------
SCIPY_IMPORT_VERBOSE --- pkgload verbose flag, default is 0.
Best, Arnd
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