Open in new window / Try shogun cloud
--- Log opened Tue Feb 11 00:00:53 2014
shogun-buildbotbuild #197 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/197  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>00:04
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shogun-buildbotbuild #192 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/192  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>00:29
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mattNSomeone PLEASE help me install shogun on mac osx 10.802:13
mattNI cannot compile the .tar file contents02:14
mattNwhen I type "./configure" it says "no such file or directory"02:14
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shogun-buildbotbuild #709 of nightly_default is complete: Failure [failed]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/70903:32
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shogun-buildbotbuild #710 of nightly_default is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/71008:53
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sonne|workwiking: in case you are alive - we have the dmg's finally uploaded to the website - now the question is how why it does not contain the python files http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/5809:52
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besser82sonne|work:  Hey there!  I'm back from Brno and still feel like having some blood left in the alcohol!  :-P10:32
sonne|workbesser82: it is good that you practised before going there :D10:34
sonne|workbesser82: I am in the process of trying to get nightly snapshots going10:36
sonne|workbesser82: any idea how we could do that with *.rpm's ?10:36
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shogun-notifier-shogun: Roman Votyakov :develop * 752c0d1 / tests/unit/machine/gp/InferenceMethod_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/752c0d13f6e5f848a228e5404c1725f589d69cb410:36
shogun-notifier-shogun: add unit test with marginal likelihood estimate with EP10:36
shogun-notifier-shogun: Heiko Strathmann :develop * 8d98aab / tests/unit/machine/gp/InferenceMethod_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/8d98aab328c649e90e5300b7a698f25de5a8296a10:36
shogun-notifier-shogun: Merge pull request #1833 from votjakovr/feature/gp_refactoring10:36
shogun-notifier-shogun:10:36
shogun-notifier-shogun: Add unit test with marginal likelihood estimate with EP10:36
besser82sonne|work:  Yes, we can do this with COPR  :D10:41
besser82sonne|work:  We just need some SRPM on some http-location and curl a small hook10:42
besser82sonne|work:  that will trigger a build on COPR and provide a public repo for them  ;)10:42
sonne|workbesser82: what do you need for that - my plan would be in the nightly_default when all tests went fine to build the stuff10:43
sonne|workor to trigger some build and I can give you the sha10:43
besser82I can try to implement some auto-rpm-spec into cmake and then we just need `rpmbuild -bs shogun.spec` && upload to some http-location && curl that copr-hook10:46
besser82sonne|work:  ^^^ i can setup a copr-account for that  ;)10:47
sonne|workbesser82: please do :)10:47
sonne|workyou are the rpm king anyways10:47
besser82sonne|work:  will do so  ;)  Thanks!  :D10:48
sonne|workno thank YOU!10:48
besser82sonne|work:  btw. there will be some real good nifty thing for our cloud-plans  :D10:52
besser82sonne|work:  there will be docker.io integration for openShift && openStack  && oVirt!!!!10:53
besser82sonne|work:  I talked to some devs of these @Brno10:54
besser82sonne|work:  and openShift will get a scaling mechanism based on Mem/CPU-Usage to scale over different workers (like Bare metal or different VMs)10:55
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sonne|workbesser82: sounds excellent10:59
besser82sonne|work:  and there is more stuff for awesome features upcoming, too!11:03
besser82sonne|work:  like kdebus11:03
besser82sonne|work:  which will provide us with stuff to parallelize some more tasks inside shogun11:04
besser82sonne|work:  and new version of fedmsg  (avail in debian, too) for doing communication between different instances on different containers / VMs and such11:05
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sonne|worklambday: any idea why the SSK kernel is gone?11:54
lambdaysonne|work: I never sent a PR for ssk kernel :(11:54
shogun-buildbotbuild #189 of clang34 - undefined behaviour analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20undefined%20behaviour%20analysis/builds/189  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>11:55
sonne|workrahul <rahul@localhost.localdomain added a new kernel SSKStringKernel which implements the subsequence kernel11:59
sonne|worklambday: now I am mixing up everyone11:59
lambdaysonne|work: no no this is me only :) but that time heiko said its not in shogun style...12:00
lambdayso we decided to add this later..12:00
lambdayI removed the code12:00
lambdayI didn't originally intend to send any PR for that - but it was already pushed to my fork so it got added (fighting with git)12:01
sonne|workyou removed it in ac917f29ab1ad60b4933f130d352e7aeab487b9012:01
sonne|workobviously people want to use it: http://stackoverflow.com/questions/21675240/string-subsequence-kernel-and-svm-using-python12:02
sonne|worklambday: so just get it back :D12:02
lambdaysonne|work: alright :) will polish the code a bit12:03
lambdaysonne|work: whic DS I should use for 3d array? NDARRAY?12:03
lambdayor vector of sg matrices? :-/12:04
sonne|worklambday: don't you just need that as temp buffer?12:07
sonne|workso anything is fine...12:07
lambdaysonne|work: yeah!12:07
lambdaysonne|work: alright then!12:07
sonne|workmaybe SGVector is easiest12:07
lambdayokay12:08
sonne|worknah just keep it like you did it before12:08
sonne|workjust use SG_MALLOC for the thing and good12:08
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sonne|work^ lambday12:08
lambdaysonne|work: okay12:09
sonne|worklambday: just make sure you have an example & some test12:09
lambdaysonne|work: I already have a test on a real dataset - can add that12:10
shogun-buildbotbuild #183 of clang34 - thread analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20thread%20analysis/builds/183  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>12:11
lambdaysonne|work: btw the clone bug is creepy - still couldn't figure out what it is - but despite calloc being a temp hack - I think we should use calloc for ptype SGObject - here we use calloc for it already https://github.com/shogun-toolbox/shogun/blob/develop/src/shogun/base/Parameter.cpp#L208212:15
lambdayI will run some more tests12:15
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shogun-buildbotbuild #198 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/198  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>12:52
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siddharth_sharmahello all, i wanted to know that will shogun participate in gsoc 201413:17
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shogun-buildbotbuild #193 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/193  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>13:34
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sonne|worksiddharth_sharma: yes that is the plan13:39
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huskaI'd like to use a spectrum kernel with some DNA sequences that contain unknown/masked nucleotides (=N characters). Is there any reason not to convert these to 0 and use the SNP alphabet? The IUPAC alphabet includes 'N' but it's a large alphabet and I don't use any of the other symbols.16:47
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@sonney2khuska, sure you can use that but then not too such high order20:42
@sonney2khuska, you could however use the ngram features or preprocessor and then a linear svm for example20:43
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@sonney2kshogun-buildbot, force build --branch=develop 'clang34 - static analysis'20:53
shogun-buildbotbuild #199 forced20:53
shogun-buildbotI'll give a shout when the build finishes20:53
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@sonney2klambday, any news on the SSK patch?20:57
lambdaysonney2k: working on the example... will send the patch by tonight or tomorrow :)20:57
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mattNhello. can someone help with an installation problem?20:58
mattNi used cmake to compile and attempt to compile the python modular and I get a error related to SWIG20:59
mattNit says "unable to find python.swig"20:59
mattNand is unable to build properly20:59
mattNthis is odd becuase I already have swig installed21:01
mattNany suggestions?21:01
@iglesiasgmattN, what version of swig do you have installed?21:03
mattNI have swig 2.0.421:04
mattNit came packaged with enthought python21:04
@iglesiasgthat version of swig should be ok21:04
mattNmore specifically, I have use Canopy. This is a distribution by Enthought that includes a lot of scientific libraries21:05
mattNany idea why I get the "cannot find python.swig" error when trying to build?21:06
@iglesiasgmattN, I have no real idea what Canopy, but could you try to find that file in your system?21:06
@iglesiasgmattN, is it .swg or .swig btw?21:06
mattN.swg21:07
@iglesiasgmattN, if this canopy is some sort of linux, or at least similar, check if you have the directory /swig21:07
mattNhere is the exact error I get if it helps21:08
mattN[ 86%] copying SWIG files [ 86%] Built target python_modular_src [ 86%] Swig source :3: Error: Unable to find 'python.swg' SGBase.i:317: Error: Unable to find 'std_vector.i' make[2]: *** [src/interfaces/python_modular/modshogunPYTHON_wrap.cxx] Error 1 make[1]: *** [src/interfaces/python_modular/CMakeFiles/_python_modular.dir/all] Error 2 make: *** [all] Error 221:08
@sonney2klambday, http://stackoverflow.com/questions/21675240/string-subsequence-kernel-and-svm-using-python/21675241#2167524121:08
@sonney2klambday, ^ pretty good example :D21:08
lambdaysonney2k: :P should I just steal it ;)21:09
@sonney2klambday, let me ask him21:09
@sonney2klambday, I cannot so use it and we give him credit and mention this in the comment asking if he is ok21:11
@sonney2kwith it21:11
@sonney2kmattN, your swig version is too old21:11
@sonney2kmattN, I don't remember when but I think you need at least swig 2.0.7 nowadays21:11
lambdaysonney2k: I can mail him21:12
mattNso i found the python.swg file that it says it can't find21:12
@iglesiasgmattN, where is it21:13
lambdaysonney2k: I was thinking of attaching a real dataset example that I used for my project21:13
lambdaybut this one is simple and pretty cool :)21:13
@sonney2klambday, add the data set but then start a notebook rather than an example with that21:13
@sonney2klambday, our policy now is examples are minimal usage examples21:13
mattNsonny2k, the shogun i am using only requires 2.0.421:13
@sonney2klambday, notebooks really give cool explanations21:14
lambdaysonney2k: alrighty - yeah that would be better...21:14
lambdaysonney2k: may be a notebook using a number of string kernels21:14
lambdayfisher's dataset is a good one21:15
@sonney2klambday, so just do a minimal example maybe even with dna features21:16
@sonney2klambday, and in the notebook use this guys example21:16
@sonney2klambday, and then we can extend the notebook with other string kernels21:16
@sonney2kwe have soo damn many21:16
@sonney2kiglesiasg, we have a problem21:17
@iglesiasgwhat is it21:17
@sonney2kiglesiasg, stuff doesn't work with python 3.3.4rc because your name in the .h's leads to unicode errors21:17
lambdaysonney2k: okay sounds good - currently adding unit-test... one for the values computed and another for psd checking21:18
lambdaythen will add a python example21:18
@iglesiasgsonney2k, aaargh yeah.. I stopped using the accent in the vowels when I realized that might bring problems21:18
mattNiglesiasg, swig in /Users/matthewnorton/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages21:23
@sonney2kiglesiasg, found a workaround lines=open(fname, encoding='utf-8', errors='ignore').readlines()21:23
@iglesiasgsonney2k, great!21:23
@iglesiasghope it doesn't bring other problems21:23
@iglesiasgmattN, swig is there or the python.swg file?21:24
@iglesiasgmattN, I think you should copy the python.swg file inside the directory where swig is installed21:25
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shogun-notifier-shogun: Parijat Mazumdar :develop * 28f0753 / tests/unit/clustering/kmeans_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/28f07533c5fcad87a29558fb5e9f80765ffb881d21:29
shogun-notifier-shogun: KMeans unit test memory leak fix21:29
shogun-notifier-shogun: Fernando Iglesias :develop * 1cf1954 / tests/unit/clustering/kmeans_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/1cf1954a57031be998efb9c2a8b0e8fa7b8a804b21:29
shogun-notifier-shogun: Merge pull request #1860 from mazumdarparijat/KMeans_notebook21:29
shogun-notifier-shogun:21:29
shogun-notifier-shogun: KMeans unit test memory leak fix21:29
votjakovrsonney2k: hi! i've just sent a PR, if you have some time, please have a look at it.21:35
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@sonney2kmattN, there seems to be a workaround - locate the directory where the python.swg is in21:37
@sonney2kthen do ln -s /the/dir/to/swig /usr/local/share21:37
@sonney2kmattN, then it should find it21:37
mattNok, i will try, thanks21:38
@sonney2kHeikoS, maybe you have time - please look at votjakovr's patch21:38
votjakovrit is very small :)21:39
shogun-notifier-shogun: Roman Votyakov :develop * f5dcc16 / src/shogun/kernel/Kernel.cpp: https://github.com/shogun-toolbox/shogun/commit/f5dcc164bb447d8f26c85359358bb0496c989a6221:41
shogun-notifier-shogun: fix data types in K_THREAD_PARAM struct21:41
shogun-notifier-shogun: Soeren Sonnenburg :develop * 68cf95f / src/shogun/kernel/Kernel.cpp: https://github.com/shogun-toolbox/shogun/commit/68cf95f3c43c4fe77ebfc52ca035220c9585866621:41
shogun-notifier-shogun: Merge pull request #1861 from votjakovr/develop21:41
shogun-notifier-shogun:21:41
shogun-notifier-shogun: Fix data types in K_THREAD_PARAM struct21:41
@sonney2kvotjakovr, indeed correct :)21:41
votjakovrsonney2k: cool :)21:42
@sonney2kvotjakovr, this reminds me that we should encapsulate all the pthread based stuff into some CThread class - java style!21:48
@sonney2kiglesiasg, I just reconfigured the buildbot to only send emails when stuff is failing21:49
@sonney2kiglesiasg, ignoring the 3 thread analysis things21:49
@sonney2kiglesiasg, so now all we need to get working is the http://buildbot.shogun-toolbox.org/memcheck/20140211-1052.html21:49
@sonney2kso if anyone here is up to fixing some memory leaks / uninited memory reads go for it!21:50
shogun-notifier-shogun: Soeren Sonnenburg :develop * 1629671 / src/shogun/base/class_list.cpp.py: https://github.com/shogun-toolbox/shogun/commit/162967130fac10d5cac68b7b7cbb5b403cb5a7f221:58
shogun-notifier-shogun: python3 compile fix21:58
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@sonney2klisitsyn, please fix malsar!~22:06
lisitsynsonney2k: yeah ok22:06
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@sonney2kwiking, you alive? I dont' understand why cpack doesn't include the python files in its dmg....22:24
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@HeikoSsonney2k: just sent you the updated billl22:28
shogun-buildbot_build #96 of deb4 - python3 is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb4%20-%20python3/builds/96  blamelist: Parijat Mazumdar <mazumdarparijat@gmail.com>22:31
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shogun-buildbot_build #97 of deb4 - python3 is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb4%20-%20python3/builds/9723:24
shogun-notifier-shogun: Sergey Lisitsyn :develop * d4df44b / / (2 files): https://github.com/shogun-toolbox/shogun/commit/d4df44bc3ff501f9c579cdf650f307f0c3ddce6c23:28
shogun-notifier-shogun: A fix for malsar clustered logistic regression (closes #1360)23:28
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travis-ci[travis-ci] it's Soeren Sonnenburg's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1868065523:32
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shogun-buildbot_build #59 of osx2 - python is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/59  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>23:48
--- Log closed Wed Feb 12 00:00:55 2014