Yaroslav Halchenko wrote:
On Mon, 08 Mar 2010, Fabian Pedregosa wrote:
test_basic_clf_train_predict
(mvpa.tests.test_svmkernels.SVMKernelTests) ... Segmentation fault
Can any mac user reproduce this ?
tried to reproduce on one of the systems we have access to (see details
below, not running Snow Leopard! still known I believe to have problems with
Python):
But what I know is that our libsvm bindings or libsvm itself does have some
issues which can lead to segfaults (and/or memory leaks) -- I hadn't luck yet
to localize it. You can valgrind your script (if it is available on your box)
to see if there are related warnings.
Thanks for looking at this. I solved the problem by uninstalling shogun.
It seems the problem was due to name clashing between libsvm & shogun.
The stack trace is interesting:
0 libshogun.4.dylib 0x03f87656 SVC_Q::get_Q(int, int)
const + 54
1 libsvm.dylib 0x0425ecd9
Solver::select_working_set(int&, int&) + 777
2 libsvm.dylib 0x0426109a Solver::Solve(int, QMatrix
const&, double const*, signed char const*, double*, double, double,
double, Solver::SolutionInfo*, int) + 778
which means it 'jumps' from libsvm to shogun (I have no clue why this
happens)
Thanks,
P.S. I had to add 'from mvpa.datasets.miscfx import *' to your script
so we get .summmary available for the dataset.
In [1]: run t.py
Dataset: 2...@int32, <sa: targets>
stats: mean=1.5 std=1.11803 var=1.25 min=0 max=3
No per targets/chunks due to KeyError('chunks',)Sequence statistics for 2
entries from set [0, 1]
Counter-balance table for orders up to 2:
Targets/Order O1 | O2 |
0: 0 1 | 0 0 |
1: 0 0 | 0 0 |
Correlations: min=-1 max=-1 mean=-1 sum(abs)=1
[1.0]
In [2]: import mvpa
In [3]: print mvpa.wtf()
Current date: 2010-03-08 13:37
PyMVPA:
Version: 0.5.0.dev
Path: /Users/yoh/proj/pymvpa/mvpa/__init__.pyc
Version control (GIT):
Status:
# On branch master
nothing to commit (working directory clean)
Reference:
d32bba93da5f02d0ef986e4cb40c4cdbed723455 HEAD
d32bba93da5f02d0ef986e4cb40c4cdbed723455 refs/remotes/origin/HEAD
Difference from last release 0.5.0.dev:
332 files changed, 46592 insertions(+), 10344 deletions(-)
SYSTEM:
OS: posix Darwin 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386
Distribution: 10.5.8/i386
EXTERNALS:
Present: cPickle, ctypes, good scipy.stats.rv_discrete.ppf, griddata,
gzip, hcluster, libsvm, libsvm verbosity control, nose, numpy, reportlab, rpy2,
running ipython env, scipy, weave
Absent: atlas_fsl, atlas_pymvpa, elasticnet, glmnet, good
scipy.stats.rdist, h5py, lars, lxml, matplotlib, mdp, mdp ge 2.4, nibabel,
nifti, nifti ge 0.20090205.1, nipy, openopt, pprocess, pylab, pylab plottable,
pywt, pywt wp reconstruct, pywt wp reconstruct fixed, rpy, sg ge 0.6.4, sg ge
0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.lightsvm, shogun.mpd,
shogun.svrlight
Versions of critical externals:
ipython : 0.8.1
reportlab : 2.1
scipy : 0.7.0
numpy : 1.3.0
rpy2 : 2.0.3
ctypes : 1.0.3
numpy : 1.3.0
RUNTIME:
PyMVPA Environment Variables:
PYTHONPATH : "/Users/yoh/proj/pymvpa"
....
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