Open in new window / Try shogun cloud
--- Log opened Sat Nov 19 00:00:27 2011
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CIA-37shogun: Sergey Lisitsyn master * ra41c477 / (2 files): Added MKL memleak test -
shogun-buildbotbuild #336 of r_static is complete: Failure [failed test_1]  Build details are at  blamelist: blackburn91@gmail.com17:44
shogun-buildbotbuild #353 of cmdline_static is complete: Failure [failed test_1]  Build details are at  blamelist: blackburn91@gmail.com17:44
shogun-buildbotbuild #336 of octave_static is complete: Failure [failed test_1]  Build details are at  blamelist: blackburn91@gmail.com17:46
shogun-buildbotbuild #328 of python_static is complete: Failure [failed test_1]  Build details are at  blamelist: blackburn91@gmail.com17:47
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blackburnLina: guess who20:35
Linai downloaded and compiled everything from blank20:36
blackburnLina: and it still is not working?20:37
Linablackburn: no20:37
blackburnbad bad20:37
Linayes, same error20:38
Linamake[1]: *** No rule to make target `.depend', needed by `'.  Stop.20:38
blackburnlet me check again20:39
blackburnLina: did you download it with git?20:39
blackburni.e. not as archive but git clone?20:40
Linano, i downloaded it directly from
blackburnLina: could you please git clone it?20:41
Linayes, i will try20:43
blackburnLina: it could help us to find out which commit caused your error20:44
Linaok, that seems to work20:53
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Linait is compiling20:53
blackburnLina: hmm I don't know the cause but let it go away at least for now20:53
blackburnif you have time (I have) we could discuss how to fix your issue20:54
blackburnLina: could you please try to run your script without System.gc and check memory usage with top20:54
Linayes, if the compilation is done, i will test it20:56
Linai'll let you know20:56
blackburnheh yes20:56
blackburnit is pretty slow20:56
blackburnLina: btw you can use --disable-optimization to speed up your compilation20:56
blackburnin configure20:56
blackburnLina: how soon you need to get these results?20:57
blackburnI can help you with rewriting it into more stable python or even C++20:57
blackburndon't afraid python it is easy :)20:57
Linathanks :-)20:57
blackburnso what should I do?20:58
blackburnalthough my real work is heavily engaged with java ee I really don't like it :D20:59
Linai need the results soon, since i am collaborating with somone20:59
blackburnand java interface is result of this gsoc20:59
blackburnwe have some issues already so it is pretty fresh20:59
Linaif there are still memory leaks when running the script, then i have no other choice..21:00
blackburnLina: it would be really better to use python, you will like it21:00
blackburnoh it doesn't looks like I'm talking about python if we remove 'python'21:00
blackburnLina: pros is you don't have to loadlibrary, set paths, etc21:01
blackburnLina: did it compile already?21:01
Linayes, but i have to do the confgure again and set "prefix" since i am not able to do make install otherwise21:03
Linai have no root access on this computer21:03
blackburnLina: oh don't you use your notebook now?21:03
blackburnLina: ok21:04
blackburnLina: what is os on that machine?21:06
shogun-buildbotbuild #52 of nightly_default is complete: Failure [failed test_1]  Build details are at
blackburnsurprise haha21:08
blackburnoh did I broke kernelpca21:08
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LinaLinux 2.6.32-5-amd6421:11
blackburnLina: and distrib?21:13
LinaDebian 2.6.32-35squeeze221:14
Linasorry, setting the prefix in ./configure does not help either21:18
Linawhen i make install, i get install: cannot remove `//usr/local/lib/R/site-library/sg/libs/': Permission denied21:18
blackburnLina: hmm do you configure it with R?21:19
Linaso, i try it without R21:20
blackburnLina: why? do you need all of them?21:25
blackburnit takes \infty time to compile all of them :)21:25
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Linano, there was no reason for it ;-) in case i need another module...21:26
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Linaok, done21:30
Linai am running the script now21:30
blackburnLina: hooray :)21:30
blackburnLina: what is memory usage?21:31
Linabut it keeps increasing21:36
blackburnLina: oh21:37
blackburnLina: do you have valgrind on that machine?21:37
Linayes, seems to be installed21:37
blackburnvalgrind --leak-check=full --log-file=log.log ./mkl_memleak_test21:38
Linahmm,  c++ -O3 -g -I/usr/include  basic_minimal.cpp   -lshogun -L/usr/lib  -o basic_minimal basic_minimal.cpp:1:30: error: shogun/base/init.h: No such file or directory basic_minimal.cpp:3: error: 'shogun' is not a namespace-name basic_minimal.cpp:3: error: expected namespace-name before ';' token basic_minimal.cpp: In function 'int main(int, char**)': basic_minimal.cpp:7: error: 'init_shogun' was not declared in this sc21:39
Linawhen doing make21:39
blackburnwhere is shogun installed?21:40
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Linain my home directory21:40
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blackburnLina: pidgin is buggy :)21:41
Linai see :-)21:41
blackburnLina: you need to specify paths I guess21:42
Linawhich ones?21:44
blackburnLina: is shogun headers in /usr/include?21:45
blackburnLina: where is it?21:46
blackburnthen change it in examples/undocumented/libshogun/Makefile21:47
blackburnline 2 or so21:47
Linahm, it seems like valgrind is not installed; /usr/lib/valgrind and /usr/lib64/valgrind only contain the file python.supp21:59
blackburnLina: so you can't do valgrind?22:04
blackburnLina: bad.. okay should I rewrite your example into python?22:07
blackburnor do you want try it more? :)22:07
Linai am not sure if it makes sense to try it more22:07
Linawhat do you think?22:07
blackburnLina: it would be at least faster22:09
blackburnLina: what if I send it tomorrow?22:09
Linato write it in python you mean?22:09
blackburnLina: yes22:12
blackburnI guess it should take less than hour22:12
blackburnLina: deal? :)22:12
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--- Log closed Sun Nov 20 00:00:32 2011