preamble: the bug here seems to be due to incorrect
np.asarray(ctypes.cdouble array)
ok -- I tried with a debug build of python and -O0 build of numpy, and
the same old valgrind... this time valgrind is silent BUT then python itself
says
test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests) ... XXX
undetected error
ERROR
and nose failure (now I see it) has nothing actually to do with the operation
on the object but just get reported to the first line after the function call
where I guess a problematic object was created...
======================================================================
ERROR: test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/testing/sweepargs.py", line 67, in
do_sweep
method(*args_, **kwargs_)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/testing/sweepargs.py", line 67, in
do_sweep
method(*args_, **kwargs_)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/testing/tools.py", line 179, in
newfunc
return func(*arg, **kwargs)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/tests/test_procrust.py", line 67, in
test_simple
pm.train(ds)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/base/learner.py", line 119, in train
result = self._train(ds)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/mappers/procrustean.py", line 161,
in _train
print "------------"
TypeError: object of type 'float' has no len()
that function is fancy only in that it uses ctypes to call a function
from the cdll.LoadLibrary('liblapack.so'):
https://github.com/PyMVPA/PyMVPA/blob/HEAD/mvpa2/support/lapack_svd.py but even
if I comment out that call to lapacklib. it still screws up the same way -- so
it has to do with those variable definitions before then I guess...
ok -- it boils down to numpy.asarray(s) in return statement... I improved it
with a printout now where I assigned constructed array to a variable first
NB if I swap print lines, it would lead me to crash above, but with this order
-- it manages to continue without crashing BUT showing incorrect values.
s_arr = numpy.asarray(s)
print "s_arr", s_arr
print "s:", s
return vt, s_arr, u
so it gives me
$> MVPA_SEED=1928295852 `which nosetests` -s -v mvpa2/tests/test_procrust.py
T: MVPA_SEED=1928295852
test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests) ... VERSION
1.7.0rc1.dev-ea23de8
s_arr [[ 6.90689888e-310 1.83759219e-316]
[ -3.16388621e+134 -3.16388621e+134]]
s: <mvpa2.support.lapack_svd.c_double_Array_2 object at 0x28c4ae0>
FAIL
======================================================================
FAIL: test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/testing/tools.py", line 179, in
newfunc
return func(*arg, **kwargs)
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/tests/test_procrust.py", line
93, in test_simple
"perfectly. Now got d scale*R=%g" % dsR)
AssertionError:
Single scenario lead to failures of unittest test_simple:
on
oblique=False :
Single scenario lead to failures of unittest test_simple:
on
svd=dgesvd :
We should have got reconstructed rotation+scaling perfectly. Now got d
scale*R=1.34232e+134
----------------------------------------------------------------------
Ran 1 test in 0.222s
FAILED (failures=1)
[161643 refs]
when with 1.6.2 (using the same seed, so if numpy's RNG didn't change -- data
should be the same):
$> MVPA_SEED=1928295852 nosetests -s -v mvpa2/tests/test_procrust.py
T: MVPA_SEED=1928295852
test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests) ... VERSION
1.6.2
s_arr [0.775771814652 0.224228185348]
s: <mvpa2.support.lapack_svd.c_double_Array_2 object at 0xad65d40>
s_arr [0.775771814652 0.224228185348]
s: <mvpa2.support.lapack_svd.c_double_Array_2 object at 0xad65c20>
s_arr [0.365993114976 0.101324191354 0.0959100894799 0.0861936270658
0.0712098129231 0.0694159685405 0.0636016740376 0.056058975141
0.0481853714064 0.042107175076]
s: <mvpa2.support.lapack_svd.c_double_Array_10 object at 0xad65d40>
s_arr [0.365993114976 0.101324191354 0.0959100894799 0.0861936270658
0.0712098129231 0.0694159685405 0.0636016740376 0.056058975141
0.0481853714064 0.042107175076]
s: <mvpa2.support.lapack_svd.c_double_Array_10 object at 0xad65c20>
s_arr [0.775771814652 0.224228185348 0.0]
s: <mvpa2.support.lapack_svd.c_double_Array_3 object at 0xad65d40>
s_arr [0.775771814652 0.224228185348 0.0]
s: <mvpa2.support.lapack_svd.c_double_Array_3 object at 0xad65c20>
s_arr [0.703907195999 0.200251541932 0.0]
s: <mvpa2.support.lapack_svd.c_double_Array_3 object at 0xad65d40>
s_arr [0.703907195999 0.200251541932 0.0]
s: <mvpa2.support.lapack_svd.c_double_Array_3 object at 0xad65c20>
ok
----------------------------------------------------------------------
Ran 1 test in 7.031s
OK
MVPA_SEED=1928295852 nosetests -s -v mvpa2/tests/test_procrust.py 7,14s
user 0,79s system 96% cpu 8,219 total
which immediately shows that np.asarray created a 2d array whenever it
should have been a 1d (original definition of s is s=(c_double*min(x,y))())
ok -- added printing of dtype of that array -- with 1.6.2 it is reported as
object while with 1.7.0b1 -- float64...
from here I pass it onto experts! ;)
On Thu, 06 Sep 2012, Yaroslav Halchenko wrote:
> On Thu, 06 Sep 2012, Aron Ahmadia wrote:
> > Are you running the valgrind test with the Python suppression
> >
> > file:�[1]http://svn.python.org/projects/python/trunk/Misc/valgrind-python.supp
> yes -- on Debian there is /usr/lib/valgrind/python.supp which comes
> with python package and I believe enabled by default, and it is
> identical to above (just dynamic library versions different) but it
> still produces lots of false positives -- IIRC it needs additional tune
> ups per architecture etc... I just ignored those messages
> "manually" and listed the relevant one which comes from numpy
> functionality.
--
Yaroslav O. Halchenko
Postdoctoral Fellow, Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik
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