Open in new window / Try shogun cloud
--- Log opened Mon Nov 12 00:00:17 2012
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shogun-buildbotbuild #167 of nightly_default is complete: Failure [failed test]  Build details are at
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nickp_Is this the right place to ask dev questions about Shogun?16:00
nickp_I'm trying to add the obtain_from_generic method to the GaussianARDKernel16:05
nickp_I pretty much copies the code from GaussianKernel::obtain_from_generic16:05
nickp_Getting this error from python16:06
nickp_Traceback (most recent call last):   File "", line 23, in <module>     from shogun.Features import *   File "/path/local/lib/python2.7/dist-packages/shogun/Features/", line 1, in <module>     from modshogun import *   File "/path/local/lib/python2.7/dist-packages/", line 30, in <module>     _modshogun = swig_import_helper()   File "/path/local/lib/python2.7/dist-packages/", line 26, in swig_i16:06
nickp_module('_modshogun', fp, pathname, description) ImportError: /path/local/lib/python2.7/dist-packages/ undefined symbol: _ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE16:07
nickp_Anyone know what is wrong?16:07
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wikingnickp_: if u are still here: that's what actually happen... it should typecast the kernel to gaussianARDkernel as in python you cannot do this...18:20
wikingbut what is interesting18:21
nickp_yeah I'm here18:21
wikingah shit18:21
wikingsorry i've mixed up18:21
wikinghave you defined K_GAUSSIANARD in Kernel.h?18:21
wikingbut i guess18:22
wikingthere must be some other problem.... if u managed to recompile shogun library with that new code18:22
wikinghave u for sure (110%) overwritten the library with the new .so and .a?18:23
wikingsince if u have this new function in the code18:23
wikingthen it should be able to find it18:23
nickp_Yeah I've defined it: K_GAUSSIANARD = 510,18:23
nickp_Yeah I'm pretty sure I've over written it.18:24
wikingu use linux?18:24
nickp_I manually deleted the shogun .so I previously had18:24
nickp_Yeah I'm on ubuntu18:24
nickp_I was working with virtualenv for the python environment18:26
nickp_so I'm trying deleting the whole virtualevn directory18:26
nickp_and trying again18:26
nickp_to see if that works18:26
wikingyou should be able to find the symbol in libshogun.13.so18:27
wikingbut i just cannot remember atm what is the disasm command in linux18:28
wikingah ok18:30
wikingobjdump -d <the path to your shogun>/|grep _ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE18:31
wikingthis should have an ouptut ;18:31
wikingif not then you should try first18:31
wikingobjdump -d src/shogun/|grep _ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE18:31
wikingthat should have an output for sure18:31
wikingnickp_: let me know what are your ouptuts :D18:33
nickp_ok will try that now18:34
nickp_just wainting for compilation18:34
wikingno worries18:35
nickp_Ouput is:18:48
nickp_$ objdump -d |grep _ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE 0000000000b28b60 <_ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE>:   b28b72:74 29                je     b28b9d <_ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE+0x3d>18:48
wikingso it's there18:52
wikingmake install18:53
wikingand then try the python code18:53
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nickp_so I tried the same command and get the same output19:14
nickp_but then from a python console19:14
nickp_>>> import shogun >>> from shogun.Kernel import GaussianKernel Traceback (most recent call last):   File "<stdin>", line 1, in <module>   File "/home/nickp/Dropbox/Repos/mkl/mklenv/local/lib/python2.7/dist-packages/shogun/Kernel/", line 1, in <module>     from modshogun import *   File "/home/nickp/Dropbox/Repos/mkl/mklenv/local/lib/python2.7/dist-packages/", line 30, in <module>     _modshogun = swig_import_he19:14
nickp_>>> from shogun.Kernel import GaussianARDKernel Segmentation fault19:14
nickp_So gives unresolved import for GaussianARDKernel when importing GaussianKernel19:14
nickp_and then a segfault when importing GaussianARDKernel19:14
blackburn1nickp_: I just read your mail19:15
blackburn1and I thinkyou missed static word in .cpp19:15
blackburn1I do not remember if it is relevant here19:15
blackburn1probably not19:15
nickp_I have static CGaussianARDKernel* obtain_from_generic(CKernel* kernel); in GaussianARDKernel.h19:16
nickp_Is that correct ^19:16
nickp_It's the same as for GaussianKernel19:17
wikingthat should be alright19:19
wikingdo you use the latest commit of the shogun repo19:20
wikingbecause it looks like as if you dont have that interfaces patch i've done the other time19:23
blackburn1wiking: did you get your paper done?19:24
wikingran out of time19:25
wikingyeah shit happens19:25
nickp_Yeah I've got those changes:19:26
nickp_%rename(LinearARDKernel) CLinearARDKernel; %rename(GaussianARDKernel) CGaussianARDKernel;19:26
nickp_in Kernel.i and Kernel_includes.i19:26
wikingnickp_: i'll try your patch on my machine19:26
wikingjust to be safe19:26
wikingbut i'm 100% that that should work alright19:26
nickp_ok cool thanks so much19:30
nickp_If you're works, I'll just grab that instead.19:30
nickp_No idea what I'm doing wrong.19:30
wikingme neither19:30
wikingbut i'm defenetly sure that somewhere it tries to use a wrong library19:31
wikingand older version of it19:31
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@sonney2knickp_, what does ldd  /path/local/lib/python2.7/dist-packages/ say?20:51
@sonney2kI second wiking - you have the wrong lib lying around somewhere20:52
nickp_I'll check20:52
nickp_sec20:52 => /usr/local/lib/ (0x00007fdb15dc4000)20:54
nickp_so that's the problem ^ ?20:55
nickp_because I thought I had shogun installed in a virtualenv20:55
@sonney2kis that the correct one?20:55
nickp_but seems to be linking to system wide one I installed earlier.20:55
@sonney2kor do you expect the lib somewhere else?20:55
nickp_I expect it to be in /path/ ...20:55
nickp_not /usr/local20:55
nickp_When I ran ./configure20:55
@sonney2kyeah then it is clear20:56
nickp_I passed --interfaces=python_modular --prefix=/home/nickp/path/...20:56
@sonney2kwhat were your configure options?20:56
@sonney2kthen it will install into /home/nickp/path/20:56
nickp_Won't  it put everything in that directory when I run make install20:56
nickp_Yeah that's what I want20:56
@sonney2kbut you need to give it LD_LIBRARY_PATH=/home/nickp/path/... too20:56
@sonney2kwhen running python etc20:56
@sonney2kand PYTHON_PATH etc etc20:56
nickp_to why does _modshogun link to /usr/local/lib/...20:57
nickp_cool thats20:57
nickp_Will recompile now and give it a try, but that sounds like it should fix things.20:57
nickp_are ld_library_path and python_path the only other args I need to add.20:58
@sonney2kI am not 100% sure but I think so20:58
nickp_thanks chaps!22:07
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--- Log closed Tue Nov 13 00:00:17 2012