| --- Log opened Mon Nov 12 00:00:17 2012 | ||
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| shogun-buildbot | build #167 of nightly_default is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/nightly_default/builds/167 | 03:52 |
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| -!- nickp_ [836fb85a@gateway/web/freenode/ip.131.111.184.90] has joined #shogun | 15:53 | |
| nickp_ | Hello | 16:00 |
| 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 GaussianARDKernel | 16:05 |
| nickp_ | I pretty much copies the code from GaussianKernel::obtain_from_generic | 16:05 |
| nickp_ | *copied | 16:05 |
| nickp_ | Getting this error from python | 16:06 |
| nickp_ | Traceback (most recent call last): File "main.py", line 23, in <module> from shogun.Features import * File "/path/local/lib/python2.7/dist-packages/shogun/Features/__init__.py", line 1, in <module> from modshogun import * File "/path/local/lib/python2.7/dist-packages/modshogun.py", line 30, in <module> _modshogun = swig_import_helper() File "/path/local/lib/python2.7/dist-packages/modshogun.py", line 26, in swig_i | 16:06 |
| nickp_ | module('_modshogun', fp, pathname, description) ImportError: /path/local/lib/python2.7/dist-packages/_modshogun.so: undefined symbol: _ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE | 16:07 |
| nickp_ | Anyone know what is wrong? | 16:07 |
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| wiking | mmmm | 18:06 |
| wiking | nickp_: 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 |
| wiking | but what is interesting | 18:21 |
| nickp_ | yeah I'm here | 18:21 |
| wiking | ah shit | 18:21 |
| wiking | sorry i've mixed up | 18:21 |
| wiking | ok | 18:21 |
| wiking | have you defined K_GAUSSIANARD in Kernel.h? | 18:21 |
| wiking | but i guess | 18:22 |
| wiking | there must be some other problem.... if u managed to recompile shogun library with that new code | 18:22 |
| wiking | have u for sure (110%) overwritten the library with the new .so and .a? | 18:23 |
| wiking | since if u have this new function in the code | 18:23 |
| wiking | then it should be able to find it | 18:23 |
| nickp_ | Yeah I've defined it: K_GAUSSIANARD = 510, | 18:23 |
| wiking | ok | 18:23 |
| nickp_ | Yeah I'm pretty sure I've over written it. | 18:24 |
| wiking | u use linux? | 18:24 |
| nickp_ | I manually deleted the shogun .so I previously had | 18:24 |
| nickp_ | Yeah I'm on ubuntu | 18:24 |
| wiking | ok | 18:24 |
| nickp_ | I was working with virtualenv for the python environment | 18:26 |
| nickp_ | so I'm trying deleting the whole virtualevn directory | 18:26 |
| nickp_ | and trying again | 18:26 |
| nickp_ | to see if that works | 18:26 |
| wiking | mmm | 18:26 |
| wiking | you should be able to find the symbol in libshogun.13.so | 18:27 |
| wiking | _ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE | 18:27 |
| wiking | but i just cannot remember atm what is the disasm command in linux | 18:28 |
| wiking | ah ok | 18:30 |
| wiking | objdump -d <the path to your shogun>/libshogun.13.so|grep _ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE | 18:31 |
| wiking | this should have an ouptut ; | 18:31 |
| wiking | output | 18:31 |
| wiking | if not then you should try first | 18:31 |
| wiking | objdump -d src/shogun/libshogun.13.so|grep _ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE | 18:31 |
| wiking | that should have an output for sure | 18:31 |
| wiking | nickp_: let me know what are your ouptuts :D | 18:33 |
| nickp_ | ok will try that now | 18:34 |
| nickp_ | just wainting for compilation | 18:34 |
| wiking | no worries | 18:35 |
| nickp_ | Ouput is: | 18:48 |
| nickp_ | $ objdump -d libshogun.so.13.0 |grep _ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE 0000000000b28b60 <_ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE>: b28b72:74 29 je b28b9d <_ZN6shogun18CGaussianARDKernel19obtain_from_genericEPNS_7CKernelE+0x3d> | 18:48 |
| wiking | ok | 18:52 |
| wiking | so it's there | 18:52 |
| wiking | make install | 18:53 |
| wiking | and then try the python code | 18:53 |
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| nickp_ | hmm | 19:14 |
| nickp_ | so I tried the same command and get the same output | 19:14 |
| nickp_ | but then from a python console | 19:14 |
| 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/__init__.py", line 1, in <module> from modshogun import * File "/home/nickp/Dropbox/Repos/mkl/mklenv/local/lib/python2.7/dist-packages/modshogun.py", line 30, in <module> _modshogun = swig_import_he | 19:14 |
| nickp_ | >>> from shogun.Kernel import GaussianARDKernel Segmentation fault | 19:14 |
| nickp_ | So gives unresolved import for GaussianARDKernel when importing GaussianKernel | 19:14 |
| wiking | lol | 19:14 |
| nickp_ | and then a segfault when importing GaussianARDKernel | 19:14 |
| blackburn1 | nickp_: I just read your mail | 19:15 |
| blackburn1 | and I thinkyou missed static word in .cpp | 19:15 |
| blackburn1 | I do not remember if it is relevant here | 19:15 |
| blackburn1 | probably not | 19:15 |
| nickp_ | I have static CGaussianARDKernel* obtain_from_generic(CKernel* kernel); in GaussianARDKernel.h | 19:16 |
| nickp_ | Is that correct ^ | 19:16 |
| nickp_ | It's the same as for GaussianKernel | 19:17 |
| wiking | that should be alright | 19:19 |
| wiking | do you use the latest commit of the shogun repo | 19:20 |
| wiking | ? | 19:20 |
| wiking | because it looks like as if you dont have that interfaces patch i've done the other time | 19:23 |
| blackburn1 | wiking: did you get your paper done? | 19:24 |
| wiking | lol | 19:25 |
| wiking | no | 19:25 |
| wiking | :) | 19:25 |
| wiking | ran out of time | 19:25 |
| blackburn1 | argh | 19:25 |
| wiking | yeah shit happens | 19:25 |
| 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.i | 19:26 |
| wiking | nickp_: i'll try your patch on my machine | 19:26 |
| wiking | just to be safe | 19:26 |
| wiking | but i'm 100% that that should work alright | 19:26 |
| nickp_ | ok cool thanks so much | 19:30 |
| nickp_ | If you're works, I'll just grab that instead. | 19:30 |
| nickp_ | No idea what I'm doing wrong. | 19:30 |
| wiking | me neither | 19:30 |
| wiking | but i'm defenetly sure that somewhere it tries to use a wrong library | 19:31 |
| wiking | and older version of it | 19:31 |
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| @sonney2k | nickp_, what does ldd /path/local/lib/python2.7/dist-packages/_modshogun.so say? | 20:51 |
| @sonney2k | I second wiking - you have the wrong lib lying around somewhere | 20:52 |
| nickp_ | I'll check | 20:52 |
| nickp_ | sec | 20:52 |
| nickp_ | libshogun.so.13 => /usr/local/lib/libshogun.so.13 (0x00007fdb15dc4000) | 20:54 |
| nickp_ | so that's the problem ^ ? | 20:55 |
| nickp_ | because I thought I had shogun installed in a virtualenv | 20:55 |
| @sonney2k | is that the correct one? | 20:55 |
| nickp_ | but seems to be linking to system wide one I installed earlier. | 20:55 |
| @sonney2k | or do you expect the lib somewhere else? | 20:55 |
| nickp_ | I expect it to be in /path/ ... | 20:55 |
| nickp_ | not /usr/local | 20:55 |
| nickp_ | When I ran ./configure | 20:55 |
| @sonney2k | yeah then it is clear | 20:56 |
| nickp_ | I passed --interfaces=python_modular --prefix=/home/nickp/path/... | 20:56 |
| @sonney2k | what were your configure options? | 20:56 |
| @sonney2k | then it will install into /home/nickp/path/ | 20:56 |
| nickp_ | Won't it put everything in that directory when I run make install | 20:56 |
| nickp_ | Yeah that's what I want | 20:56 |
| @sonney2k | but you need to give it LD_LIBRARY_PATH=/home/nickp/path/... too | 20:56 |
| @sonney2k | when running python etc | 20:56 |
| @sonney2k | and PYTHON_PATH etc etc | 20:56 |
| nickp_ | to why does _modshogun link to /usr/local/lib/... | 20:57 |
| nickp_ | ooooh | 20:57 |
| nickp_ | ok | 20:57 |
| nickp_ | cool thats | 20:57 |
| nickp_ | *thanks | 20:57 |
| 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 |
| @sonney2k | I am not 100% sure but I think so | 20:58 |
| nickp_ | Working | 22:07 |
| nickp_ | thanks chaps! | 22:07 |
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| --- Log closed Tue Nov 13 00:00:17 2012 | ||
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