Open in new window / Try shogun cloud
--- Log opened Thu Jun 26 00:00:48 2014
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shogun-buildbotbuild #353 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/353  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>00:10
thoralfHeikoS1: http://buildbot.shogun-toolbox.org/memcheck/20140625-2038.html00:14
thoralfHeikoS1: You know who worked on LDA?00:14
HeikoS1yes00:14
HeikoS1kislay00:14
HeikoS1ill mail him00:14
thoralfThanks :)00:15
thoralfHeikoS1: I tried to write a small example for the workshop, but I just realized this guy is still open: https://github.com/shogun-toolbox/shogun/issues/199100:34
HeikoS1thoralf: does this block you?00:35
thoralfHeikoS1: Not really, I can use smaller examples.00:35
thoralfHeikoS1: Bug if someone comes with a bigger file and we need to tell him "sorry, it's broken for months - please use files < 10 MB"00:36
thoralfBut00:36
thoralfIMO this is a show stopper.00:36
shogun-notifier-shogun: Heiko Strathmann :develop * e3fa634 / src/shogun/machine/gp/InferenceMethod.h: https://github.com/shogun-toolbox/shogun/commit/e3fa63443905e8b8dcb4619a4668287e3d7c32bc00:41
shogun-notifier-shogun: Update InferenceMethod.h00:41
shogun-notifier-shogun:00:41
shogun-notifier-shogun: correct statement about marginal likelihood estimates00:41
shogun-buildbotbuild forced [ETA 9m18s]00:46
shogun-buildbotI'll give a shout when the build finishes00:46
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HeikoS1thoralf: yeah totally00:51
HeikoS1thoralf: maybe we should have a list of bugs that should be fixed until workshop ;)00:52
thoralfhttps://github.com/shogun-toolbox/shogun/issues?milestone=5&state=open00:54
thoralfThat was easy. ;)00:54
thoralfNow we need somebody to fix this. ;)00:54
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shogun-buildbotbuild #732 of nightly_all is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_all/builds/73201:12
shogun-buildbotbuild forced [ETA 2h09m04s]01:12
shogun-buildbotI'll give a shout when the build finishes01:12
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shogun-buildbotbuild #836 of nightly_default is complete: Failure [failed doc]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/83601:38
shogun-buildbotbuild #2401 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2401  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>01:43
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travis-ci[travis-ci] it's khalednasr's turn to pay the next round of drinks for the massacre he caused in khalednasr/shogun: http://travis-ci.org/khalednasr/shogun/builds/2845592401:55
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jiaolongHi, Shell03:14
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jiaolonghushell: Hello03:14
hushelljiaolong: hey man03:14
jiaolongI have found the memory leak is from https://github.com/Jiaolong/shogun/blob/develop/src/shogun/structure/GraphCut.cpp#L6603:15
jiaolongWe should remove REF(fac)03:16
hushellok, try it03:16
jiaolongNow, I have run valgrind to the unit-test again03:16
jiaolong==5337== Memcheck, a memory error detector ==5337== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al. ==5337== Using Valgrind-3.10.0.SVN and LibVEX; rerun with -h for copyright info ==5337== Command: ./shogun-unit-test --gtest_filter=Graph* ==5337==  Note: Google Test filter = Graph* [==========] Running 4 tests from 1 test case. [----------] Global test environment set-up. [----------] 4 tests from GraphCut [ RUN    03:17
hushelljiaolong: sounds great! send a PR when you tested it03:17
jiaolonghushell: Sorry, I juts pasted the output03:17
jiaolonghushell: It looks urgly :(03:17
jiaolonghushell: But the unit-test should be fixed03:18
jiaolonghushell: However, I still have a dout03:18
hushellseems still an error out there03:18
hushellpaste the output of valgrind or send me an email03:18
jiaolongAll heap blocks were freed -- no leaks are possible03:19
jiaolonghushell: OK03:19
jiaolonghushell:  sent you email03:20
jiaolonghushell: Is it OK?03:21
jiaolonghushell: I sent you another email which is from coverity scan report several days ago03:23
jiaolonghushell: It reports >>>     CID 68404:  Unchecked dynamic_cast  (FORWARD_NULL)03:24
jiaolonghushell: >>>     Assigning: "fac" = "dynamic_cast <shogun::CFactor *>(facs->get_element(i))".03:24
jiaolonghushell: So I added REF(fac) to solve this issue03:25
hushelljiaolong: hold on a sec03:26
jiaolonghushell: Now it seems REF(fac) should never be added here. Then I am usurious about what is the solution to  CID 68404:  Unchecked dynamic_cast  (FORWARD_NULL)03:27
jiaolonghushell: OK03:27
hushelljiaolong: mem leak has been solved, isn't it03:28
jiaolonghushell: yeah03:28
hushellwhat's the 2nd issue?03:28
jiaolonghushell: Let's look back the coverity scan report03:28
jiaolonghushell: In fact, in my original PR, I removed REF(fac)03:29
hushelljiaolong: you sent a PR for it, isn't it?03:29
hushelljiaolong: no worry, no need to add ref here03:29
hushellif everything is fine03:30
jiaolonghushell: Since coverity scan reports >>>     Assigning: "fac" = "dynamic_cast <shogun::CFactor *>(facs->get_element(i))".03:30
jiaolonghushell: I added REF(fac) back later, which was wrong03:30
jiaolonghushell: yes03:30
hushellthat issue was because you use m_fg->get_num_factors()03:30
jiaolonghushell: OK03:31
hushellbut in fact, this number may not match to the real numer03:31
jiaolonghushell: Now, it is clear03:31
shogun-buildbotbuild #354 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/354  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com>03:31
jiaolonghushell: So, I will send a PR soon03:31
hushellreference Thoralf or Fernando to merge your PR03:32
jiaolongOK03:32
jiaolonghushell: Thanks!03:32
hushelljiaolong: enjoy your trip!03:33
jiaolonghushell: Thanks!03:34
jiaolonghushell: BTW03:35
jiaolonghushell: I haven't fixed the hinge_loss < 0 issue in the sossvm03:35
jiaolonghushell: I have checked the energy03:36
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jiaolonghushell: The graph cuts and tree max product produces similar energy values03:37
hushelljiaolong: sure? check BeliefPropagation.cpp03:37
jiaolonghushell: I mean, they are negative values03:37
hushelljiaolong: yes, this is why needs -energy03:37
hushelljiaolong: yes, then you need to make them positive03:38
jiaolonghushell: But, tree max product is still exact inference, right?03:38
jiaolonghushell: wait03:38
hushelljiaolong: in fact, in log-scale, it's min-sum03:38
jiaolonghushell: you mean make graph cuts energy value positive?03:38
hushelljiaolong: check what I did in BeliefP...cpp03:39
jiaolonghushell: it is not exactly the same03:39
jiaolonghushell: you computed the energy from MAP03:39
hushellyes, min energy, so you want to get as negative as possible03:39
jiaolonghushell: but I computed the energy directly from the assignment03:40
hushellon the other hand, MAP needs to reverse the sign03:40
jiaolonghushell: yeah, that's why you need - energy03:40
jiaolonghushell: but in my case, it is different03:41
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hushelljiaolong: exp(-E(y,x))03:41
hushelljiaolong: GC is the same as min-sum03:42
jiaolonghushell: well, the bug actually is not related to the energy value return by inference()03:44
hushellMAP is exp(-E()), so need -energy in fact03:44
jiaolonghushell: we never use this value in argmax()03:44
jiaolonghushell: I think the problem is the way we get the assignment03:44
jiaolonghushell: I mean, whether we get the assigment from a max(obj_fun) or min(obj_func)03:46
hushelljiaolong: look at FactorGraphModel.cpp:34203:46
hushelljiaolong: where it's called03:46
hushellI know the energy min and MAP is confusing03:48
hushellI need to clarify a bit more in the code03:48
jiaolonghushell: OK03:50
jiaolonghushell: No worry, it may have other reasons03:50
jiaolonghushell: I have got some hint03:50
hushelljiaolong: I still think in GraphCut.cpp:176, should return -energy03:51
jiaolonghushell: I think energy min and MAP is clear03:51
jiaolonghushell: I need to check "CFactorGraphObservation* y_star = infer_met.get_structured_outputs();"03:51
jiaolonghushell: OK, thanks for your advises03:52
jiaolonghushell: I will check them later03:53
hushelljiaolong: great! Talk u later, have a good night!03:55
jiaolonghushell: see you!03:56
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shogun-buildbotbuild #733 of nightly_all is complete: Failure [failed compile test]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_all/builds/733  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Saurabh <saurabh.mahindre@gmail.com>04:37
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shogun-buildbotbuild #837 of nightly_default is complete: Failure [failed notebooks]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/837  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Saurabh <saurabh.mahindre@gmail.com>08:14
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shogun-notifier-shogun: khalednasr :develop * e7962d5 / / (9 files): https://github.com/shogun-toolbox/shogun/commit/e7962d54ad46f280452d17f3c047f4fe180868f508:55
shogun-notifier-shogun: Implemented denoising autoencoders08:55
shogun-notifier-shogun: Sergey Lisitsyn :develop * cb6c042 / / (9 files): https://github.com/shogun-toolbox/shogun/commit/cb6c04296a12c2b4b7d793c29d1bb776ce1333d008:55
shogun-notifier-shogun: Merge pull request #2340 from khalednasr/autoencoders08:55
shogun-notifier-shogun:08:55
shogun-notifier-shogun: Implemented denoising autoencoders08:55
shogun-notifier-shogun: jiaolong :develop * 7c82af7 / src/shogun/structure/GraphCut.cpp: https://github.com/shogun-toolbox/shogun/commit/7c82af796d0050ad4d87c3337e76594dc5efcae809:02
shogun-notifier-shogun: fixed memory leak in graph cut unit test09:02
shogun-notifier-shogun: tklein23 :develop * 243a8a4 / src/shogun/structure/GraphCut.cpp: https://github.com/shogun-toolbox/shogun/commit/243a8a4fc29b98e770a9d8d3a5b9580478e8e5b609:02
shogun-notifier-shogun: Merge pull request #2341 from Jiaolong/graph_cut09:02
shogun-notifier-shogun:09:02
shogun-notifier-shogun: fixed memory leak in graph cut unit test09:02
shogun-notifier-shogun: Abhijeet :develop * c99d14d / tests/unit/classifier/LDA_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/c99d14df9b138f738e1d6a8203b195b4ccafd35109:06
shogun-notifier-shogun: memory leaks fixed.09:06
shogun-notifier-shogun: tklein23 :develop * 49c4cbb / tests/unit/classifier/LDA_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/49c4cbbb55b7c6a2ae9c33f9d866c13b0f5cb49309:06
shogun-notifier-shogun: Merge pull request #2342 from kislayabhi/unittest_old_lda09:06
shogun-notifier-shogun:09:06
shogun-notifier-shogun: memory leaks fixed in LDA unittest09:06
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shogun-buildbotbuild #355 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/355  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>09:53
shogun-buildbotbuild #2402 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2402  blamelist: tklein23 <tklein23@users.noreply.github.com>, jiaolong <jiaolongxu@gmail.com>, Sergey Lisitsyn <lisitsyn.s.o@gmail.com>, khalednasr <k.nasr92@gmail.com>, Abhijeet <abhijeetkislay@gmail.com>10:02
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shogun-buildbotbuild #356 of debian wheezy - memcheck is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/35612:56
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shogun-notifier-shogun: sejDino :feature/mmd * 3af3fd3 / src/shogun/statistics/HSIC.h: https://github.com/shogun-toolbox/shogun/commit/3af3fd33197703846d297ee6a26d048d29fb303016:23
shogun-notifier-shogun: small updates to HSIC documentation16:23
shogun-notifier-shogun: Heiko Strathmann :feature/mmd * 68c3727 / src/shogun/statistics/HSIC.h: https://github.com/shogun-toolbox/shogun/commit/68c372761cb3a412f599f2ebaf71cc5f5bf2eb4516:23
shogun-notifier-shogun: Merge pull request #2345 from sejdino/feature/mmd16:23
shogun-notifier-shogun:16:23
shogun-notifier-shogun: small updates to HSIC documentation16:23
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shogun-notifier-shogun: Saurabh :develop * 50c76b1 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/50c76b1a4adf22a9fefd11be952078f3c59f1e4c18:33
shogun-notifier-shogun: Intro nb added18:33
shogun-notifier-shogun: Saurabh :develop * 45e5879 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/45e587988d1911f16d7617f866c002480fbda25318:33
shogun-notifier-shogun: clean up and regression18:33
shogun-notifier-shogun: Saurabh :develop * c10d217 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/c10d2177bfba8123f8e775fbf66ecf05da6f317518:33
shogun-notifier-shogun: preprocessor example18:33
shogun-notifier-shogun: Saurabh :develop * 712a28c / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/712a28cdba657295d41f6f93f9d9fb8350c0fe8d18:33
shogun-notifier-shogun: some more additions18:33
shogun-notifier-shogun: Saurabh :develop * 28aefd4 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/28aefd482330ecf75ab94e2b1ca3dabc656e137218:33
shogun-notifier-shogun: revamp structure18:33
shogun-notifier-shogun: Saurabh :develop * 2d71eda / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/2d71edaa6402afdfe09cc8ab61d00803626d736a18:33
shogun-notifier-shogun: some cleanups18:33
shogun-notifier-shogun: Saurabh :develop * 6130908 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/6130908fa19d7e47a7cb585c9db7b1289f971bee18:33
shogun-notifier-shogun: more cleanups18:33
shogun-notifier-shogun: Saurabh :develop * 9ea64ca / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/9ea64cadf913ccd03edebb0f9f2da4e4f7e1a8f918:33
shogun-notifier-shogun: update krr example18:33
shogun-notifier-shogun: Heiko Strathmann :develop * 8a30213 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/8a302139039c5665ed65bf0b55f92a3190377af118:33
shogun-notifier-shogun: Merge pull request #2244 from Saurabh7/intronb18:33
shogun-buildbotbuild #2403 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2403  blamelist: Saurabh <saurabh.mahindre@gmail.com>18:47
shogun-buildbotbuild #2404 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2404  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com>18:52
shogun-buildbotbuild #751 of FCRH - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/FCRH%20-%20libshogun/builds/751  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com>19:02
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HeikoS1yorkerlin: hi19:22
HeikoS1yorkerlin: I talked to emt and we think you should go ahead with the KL methods for multiclass, but please send him an email with the details of your plan19:23
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yorkerlinok19:27
HeikoS1yorkerlin: did you already write some notebook stuff? just asking in case I can already read somethings19:28
yorkerlinnot too much. I will try to get it done at the end of this week.19:29
yorkerlinI will email emt once I finish the notebook stuff. I guess next Monday or Tuesday19:30
HeikoS1yorkerlin: please share notebook drafts as early as possible19:30
yorkerlinok. I will let you know ASAP19:31
yorkerlinplease take a look at the lbfgs stuff19:32
yorkerlinso that I can send the dual likelihood19:32
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HeikoS1yorkerlin: could you send the PR?19:48
yorkerlinok then.19:50
yorkerlinI need to create a new git branch.19:50
HeikoS1yorkerlin:  I mena the link for the bfgs19:50
yorkerlinhttps://github.com/shogun-toolbox/shogun/pull/233719:52
HeikoS1yorkerlin: did you run these tests locally already? did you check memory leak?19:55
yorkerlinyes. I run all KL methods locally19:56
HeikoS1any idea why the CMath unit test fails?19:56
HeikoS1[  FAILED  ] CMath.get_abs_tolorance19:56
HeikoS1yorkerlin: ^19:56
HeikoS1your CMath changes broke something19:57
yorkerlinlet me take a loot19:57
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yorkerlinI think I correct a bug but forget to change in unit test.20:02
yorkerlinEXPECT_EQ(CMath::get_abs_tolorance(0.0, 0.01), 0.01);    should be right20:03
yorkerlinabs_tolorance = true_value * rel_tolorance usually.20:03
yorkerlinbut when true_value equals to 0, abs_tolorance should be the same as rel_tolorance20:04
HeikoS1yorkerlin: ok, please update and tell me that test passes locally - then I will merge20:04
yorkerlinbtw do travis fix the bug in python modual now. I usually take a look at the flag of travis but once the python modual issue. I forget to check the result. sorry about that20:05
yorkerlinI usually take a look at the flag of travis. Since the python code issue leads to the red flag, I forget to check the detailed information of building failure20:07
HeikoS1yorkerlin: thats what we have travis for :)20:15
HeikoS1yorkerlin: I gotta go now, will check back tomorrow how things are going20:15
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yorkerlinok20:18
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shogun-buildbotbuild #154 of osx2 - python is complete: Failure [failed examples and unit tests]  Build details are at http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/154  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com>22:29
shogun-buildbotbuild #155 of osx2 - python is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/155  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, jiaolong <jiaolongxu@gmail.com>, Sergey Lisitsyn <lisitsyn.s.o@gmail.com>, khalednasr <k.nasr92@gmail.com>22:55
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shogun-buildbotbuild #156 of osx2 - python is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/156  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com>, Abhijeet <abhijeetkislay@gmail.com>, tklein23 <tklein23@users.noreply.github.com>23:13
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--- Log closed Fri Jun 27 00:00:50 2014