IRC logs of #shogun for Wednesday, 2017-08-16

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--- Log opened Wed Aug 16 00:00:41 2017
-!- olinguyen [81615ad9@gateway/web/freenode/ip.129.97.90.217] has quit [Quit: Page closed]00:34
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/3960 synchronized by MikeLing07:00
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/8613c5be1cb8e15965dfe369f611d6b164a5fccf by vigsterkr09:19
@wikingmikeling, ping09:20
mikelingwiking: pong09:20
@wikingmikeling, so i removed src/shogun/statistical_testing/internals/FeaturesUtil.cpp from feature/BigInput09:20
@wikingwhat i will do is to restart the CI09:20
@wikingon your latest commit09:20
@wikingmmm but wait :)09:20
@wikinghttps://github.com/shogun-toolbox/shogun/pull/396009:20
@wiking:(09:20
@wikingi dont know why there's again a conflict :(09:21
@wikingi didn't change anything :((((09:21
@wikingjust removed the https://github.com/shogun-toolbox/shogun/pull/396009:21
@wikingi mean i removed src/shogun/statistical_testing/internals/FeaturesUtil.cpp09:21
@wikingbut anyhow if you could somehow resolve the merge conflict09:21
@wikingthen i guess we could get some meaningful output09:22
@wikingfrom travis09:22
mikelingsure, I will take care of it09:22
@wikingthnx09:22
mikelingjust wait a moment , let me check where these conflict comes from.09:22
@wikingyeah i'm wondering as well :<09:22
@wikingah yeah09:23
@wikingi know where09:23
@wikingyou have the [wip] 2nd round09:23
@wikingin the branch it seems09:23
mikelingbecause in my cached web page of that pr, the changes only have  https://usercontent.irccloud-cdn.com/file/MGol76s1/Screen%20Shot%202017-08-16%20at%203.20.32%20PM.png09:23
@wiking5563a7882ca92d49ad949d12e8fabbe57940ae5509:23
@wikingyou have this commit in your branch09:23
@wikingright?09:23
@wikingin MikeLing:BiggerInput09:23
mikelingso I have no idea why it suddenly comes to 6,072, so I need to check it09:24
@wikingcheck your MikeLing:BiggerInput branch09:24
@wikingand what is before 31cc2eb93c61b675e7a5071e4de76cc63f42ede109:24
@wikingi.e. the 3nd round commit09:24
@wikingif it's my [wip] 2nd round09:24
@wikingthen it's that09:24
@wiking:)09:24
@wikingbecause i changed that commit09:24
@wikingin shogun-toolbox:feature/BigInput09:24
mikelingit 5563a7882ca92d49ad949d12e8fabbe57940ae5509:25
mikelingit's09:25
@wikingas that contained src/shogun/statistical_testing/internals/FeaturesUtil.cpp09:25
@wikingwhich was wrong09:25
@wikingand caused the compilation problem09:25
mikelingyes, so before 3nd round it's 5563a7882ca92d49ad949d12e8fabbe57940ae5509:26
@wikingyeah that is the old feature/BigInput HEAD :)09:26
mikelingso it's even to the latest commit of feature/BigInput right09:26
mikelingok09:26
@wiking8613c5be1cb8e15965dfe369f611d6b164a5fccf is not the HEAD of feature/BigInput09:26
@wikingbasically i amended09:26
@wiking09:26
@wiking[wip] 2nd round09:27
mikelingso I need to rebase it and solver those conflicts09:27
@wikingwell there's multiple ways to do it :)09:27
mikelingi see09:27
@wikingi mean what you can do is09:27
@wikingthat you do an interactive rebase in your MikeLing:BiggerInput09:28
@wikingdelete 5563a7882ca92d49ad949d12e8fabbe57940ae5509:28
@wikingno09:28
@wikingthat will not work09:28
@wiking:))09:28
@wikingok so the easiest is actually - maybe this is not the best way to do this09:28
@wikingthat you create a new branch09:28
@wikingfrom the latest feature/BigInput09:28
@wikingthen cherry-pick all your (that are after 5563a7882ca92d49ad949d12e8fabbe57940ae55) commits from MikeLing:BiggerInput to the new branch :)09:29
@wikingthat for sure works09:29
@wikingand minimal amount of work09:29
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travis-ciit's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/26503924509:30
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mikelingok, I will do it. Thank you!09:30
@wikingnw09:30
@wikingand then finally we can see some real errors in the PR :P09:30
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@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/3960 synchronized by MikeLing11:30
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@wikingmikeling, hey12:41
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/3954 merged by karlnapf12:42
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/b537cc865416f58f7c88ca8fff45ed8a62c4f19c by karlnapf12:42
@wikingmikeling, lemme know when you are back12:43
mikelingwiking: hey, I'm having dinner right now. Will back after 30 minutes12:43
mikelingOk12:43
@wikingmikeling, kk anyhow the thing is that now what fails is gpl stuff. so you would need to create a separate PR for this repo https://github.com/shogun-toolbox/shogun-gpl/tree/random-refactor12:43
@wikingi mean the shogun-gpl repo but agains the random-refactor branch :)12:44
Erwan_Hi there, quick question (I'm new to Shogun) : I installed shogun on ubuntu 16.04 from binaries (libshogun16, 17 doesn't show up in repo) and linked it in my project (throught cmake). I only included the GMM header as I only want to use that yet. When compiling, I get an error related to inclusion of clapack.h in lapack.h included from Gaussian.h : File not found ; The file is located in /usr/include/atlas, but shogun seems to be unab13:24
Erwan_... correctly13:24
Erwan_Is it a known bug and should I compile the lib manually ?13:24
Erwan_Or is there some settings to overcome that issue ?13:24
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travis-ciit's Olivier's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/26510026913:32
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mikelingwiking: hi, how could I make find_k_nearest_neighbors here(https://github.com/shogun-toolbox/shogun/blob/d6ba3f4841c0c116de29db5be3e1e9a656164ec0/src/shogun/multiclass/LSHKNNSolver.cpp#L64) can accept vector<index_t>()13:37
mikelingit looks like the 'indices' is a type of std::vector<LSHTableKeyType>*  https://github.com/shogun-toolbox/shogun/blob/270ff9200daeb273bec6c82543d82d5a275b39d3/src/shogun/lib/external/falconn/core/nn_query.h#L8713:39
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mikelingok, I know how to pass index_t to it, just forget it ;)13:53
@wikingno need to pass13:54
@wikingaaah13:55
@wikinglemme see13:55
mikelingactually I need to do something like auto lsh_table = falconn::construct_table<falconn::DenseVector<double>, index_t>(feats, params);13:55
mikelingto make it can use index_t as key type13:55
@wikingNearestNeighborQuery's 3rd template parameter is LSHTableKeyType13:56
mikelingbut we have a warpper for it13:56
mikelingin here https://github.com/shogun-toolbox/shogun/blob/270ff9200daeb273bec6c82543d82d5a275b39d3/src/shogun/lib/external/falconn/wrapper/cpp_wrapper_impl.h#L31813:57
@wikingLSHNNTableWrapper13:57
@wikingok13:57
@wikingso it's second param is KeyType13:57
mikelingyes13:57
@wikingwhich should be indext_13:57
@wikingthat should work i hope13:57
mikelingI'm try to make all the unit and meta tests works before I trun gpl building on13:58
mikeling*trying13:58
@wikingokey13:59
mikelingoh, I have another question about meta test13:59
mikelingjust a second13:59
@wikingsure13:59
@wikingErwan_, mmm sorry havent seen your quesiton just a sec14:03
mikelingFor sparse_gaussian_process_regression meta test, the 'inducing_points' which defined as IntVector in https://github.com/shogun-toolbox/shogun/blob/813575ddc6eba4746caa0893d3cccbe5e839b946/examples/meta/src/gaussian_processes/sparse_gaussian_process_regression.sg#L21 will be been translated to SGVector<int32_t>14:03
@wikingErwan_, ok so you used the ppa repository to install shogun?14:04
@wikingmikeling, mmm i guess we need to define in meta-examples generator14:05
@wikinga new type14:05
@wikingIndexVector14:05
@wikingthat maps to SGVector<index_t>14:05
mikelingok, I see14:06
@wikingmikeling, so in examples/meta/generator14:06
@wikingif you do git grep IntVector14:07
@wikingthen you'll see where IntVector is defined14:07
@wikingyou should introduce14:08
@wikingIndexVector there14:08
@wikingsee what i mean?14:08
mikelingyes, got it14:09
@wikingk14:09
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/3953 merged by vigsterkr14:42
@sukey[https://github.com/shogun-toolbox/shogun] vigsterkr pushed 10 commits:14:42
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/73b21e353e8cae64141357e4a39afcddef702ad114:42
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/f3bb11e42147788540a58e0b63c3d1c0812cea7d14:42
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/ffc882d70e79fe20b5abe2f8beb108954c6a2ace14:42
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/185cd7e148847b15b18679a8cb9f6ee48fb156e714:42
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/1caf8929e6ceb8300546e5043e3b0582a318991614:42
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/6e2a531c45e43b5db0643201f594448e6e3c556914:42
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/12000872db6228214cbf9277c4201f0d7fd7dc3114:42
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/0bbfe369e7ff5e217b8a3d363baccf80fecf259714:43
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/1e4b35eead7f642dddb66315293a641800f9427514:43
@sukeyhttps://github.com/shogun-toolbox/shogun/commit/affb9496b9bf1eecf086461733837f3cb102b02a14:43
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@wikingpoor sukey14:43
@wikingdied :)14:43
Trixislol14:44
geektoniwiking: too many messages at once :P14:44
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@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/396514:46
micmnwiking: could we have a branch for the feature refactor?15:24
Erwan_wiking: yes, installed shogun from ppa15:37
Erwan_(sorry, some student management :) )15:37
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travis-ciit's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/26513602716:02
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@wikingErwan_, which ppa?16:33
@wikingthe stable or the nightly?16:33
@wikingmicmn, most def16:33
Erwan_wiking: the stable one16:34
@wikingmmm yeah that's why it's libshogun1616:34
Erwan_I followed the INSTALL.md for ubuntu16:34
@wikingbut yeah that should16:35
@wikingpull in the lapack16:35
@wikingmmmmm aaaah i guess the problem is that the libshogun-dev package does not pull in the lapack-dev package? :S16:35
@wikinghence you are getting the clapack.h error16:35
@wikingor i mean16:36
@wikingcould you do a find /usr/include -name 'clapack.h'16:36
@wikingand copy here the result?16:36
Erwan_Did it with locate but the result is the same : /usr/include/atlas/clapack.h16:38
mikelingwiking: mmm, so I found GraphColoringInterface can only accept int rather than index_t(int64_t) vector https://github.com/shogun-toolbox/shogun/blob/270ff9200daeb273bec6c82543d82d5a275b39d3/tests/unit/mathematics/linalg/ProbingSampler_unittest.cc#L5616:40
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olinguyenHeikoS: hey16:42
@wikingErwan_, mmm yeah i think libshogun debian package of stable is not having the ShogunConfig.cmake or something16:43
@wikingthat exports the CFLAGS for compilation16:43
@wikingmikeling|brb, GraphColoringInterface is from colpack16:44
@wikingwell if they dont support it16:44
@wikingthen we just have to obey16:44
@wikingand use int16:44
@wikingErwan_, so basically when you compile your thing you should add a -I/usr/include/atlas16:45
@wikingi know it's annoying16:45
@wikingi'm not so sure16:45
@wikingif i install the config cmake stuff in nightly16:45
@wikingi ought to check16:45
@wikingsince in that case if you use cmake and find_package(shogun ...) and then do target_link_libraries(whateverYourTarget shogun ...)16:46
@wikingthen the right cflags will be added to your cmake target16:46
Erwan_wiking: Does the FindShogun.cmake file is available when installed from deb ?16:47
@wikinglemme check16:47
@wikingidk by heart sorry16:47
Erwan_For now I'm using find_library and find_path to fill the corresponding cmake variables16:48
Erwan_(no problem :) )16:48
@wikingjust a sec16:48
@wikingif you would be using the nightly version16:50
@wikingthen16:50
@wikingFIND_PACKAGE(shogun CONFIG)16:50
@wikingshould work16:50
@wikingas libshogun-dev contains /usr/lib/cmake/shogun/.16:50
@wikingcmake configs16:50
@wikingthat helps you with all the detection of shogun etc16:50
Erwan_going to test that16:52
@wikingErwan_, nono16:52
@wikingactually16:52
@wikingstable has that as well16:52
@wiking:))16:52
@wikingbut looking into the .cmake files16:52
@wikingit might be that they are not having what you need16:52
@wikingstill16:52
@wikingif you use cmake16:52
Erwan_Ah, I just removed shogun :(16:52
@wikingthen the proper way to depend on shogun16:52
@wikingapt-get install16:52
@wikingpretty simple16:53
@wiking :)16:53
@wikingso the proper way should be FIND_PACKAGE(shogun CONFIG)16:53
@wikingas the cmake files should be in your path16:53
@wiking:)16:53
Erwan_Hmm, don't find anything like "Findshogun.cmake" or "shogunConfig.cmake" on my system17:02
@wikinghave you installed17:04
@wikinglibshogun-dev?17:04
@wikingit should be under /usr/lib/cmake/shogun/17:04
@wikingit was in this package //launchpad.net/~shogun-toolbox/+archive/ubuntu/stable/+files/libshogun-dev_6.0.0-0_amd64.deb17:04
@wikingsorry i meant to paste: https://launchpad.net/~shogun-toolbox/+archive/ubuntu/stable/+files/libshogun-dev_6.0.0-0_amd64.deb17:04
Erwan_I installed the dev and dbg packages along with the libshogun16 package (stable)17:06
Erwan_no shogun folder in my /usr/lib/cmake folder17:06
@wikingthat is weird17:07
@wikingas if you wget that pkg17:07
Erwan_Dependancy can't be satisfied : libshogun1817:08
@wikingit's in it17:08
@wikinglibshogun18?17:08
@wikingthat's the nightly17:08
Erwan_(I downloaded the deb from your link)17:08
Erwan_Yup17:08
@wikingyou want the stable17:08
@wikingoh wait yeah17:09
Erwan_Let me check the ppa17:09
@wikingthat one wants libshogun1817:09
@wikingbut yeah17:09
@wikingi mean it's there as well17:09
@wikinghttps://launchpad.net/~shogun-toolbox/+archive/ubuntu/stable/+files/libshogun18_6.0.0-0_amd64.deb17:09
@wikingi mean if you have added the ppa17:10
@wikingthe stable ppa17:10
@wikingdeb http://ppa.launchpad.net/shogun-toolbox/stable/ubuntu trusty main17:10
@wikingor sudo add-apt-repository ppa:shogun-toolbox/stable17:10
@wikingthat should have all the stuff u need17:10
@wikingunless the hiccup is due to the fact that you use other version of trusty17:10
@wikingi mean ubuntu17:11
@wikingi..e not trusty but some other verison17:11
@wikingand then it's fetching somethign weird17:11
@wikingbut yeah in that case use the nightly17:11
Erwan_I'm on Xenial17:11
Erwan_Ubuntu 16.0417:11
@wikingmmm afaik there's no xenial package17:11
@wikingof the stable ppa17:11
Erwan_I can only access libshogun16 from ppa17:11
@wikingthere's in nightly tthough17:12
@wikinghttps://launchpad.net/~shogun-toolbox/+archive/ubuntu/nightly17:12
Erwan_XD17:12
@sukey[https://github.com/shogun-toolbox/shogun] New branch feature/features-refactor created17:14
@wikingmicmn, ^17:14
micmnwiking: thx17:14
@wikingnw17:14
Erwan_\o/17:25
Erwan_It's working :)17:25
Erwan_got the shogun cmakefolder17:26
Erwan_find_package(Shogun CONFIG) find it17:26
Erwan_And then I can compile my example without problem17:27
Erwan_wiking: Thanks for your time and help !17:27
@wiking\o/17:29
@wikingperfecto17:30
@wikingno worries17:30
@wikingenjoy17:30
@wikingErwan_, can i ask about your application for shogun?17:42
@wikingjust the eare17:42
@wiking*area17:42
Erwan_Yup17:43
Erwan_Research in robotics17:43
@wikingoh nice :)17:43
@wikingusing GMM? :)17:43
Erwan_For now, GMM and GP, yes17:43
@wikingcool17:44
@wikingplz let us know if u run into bugs17:44
Erwan_we are evaluating several libraries in C++ that provide these implementation17:44
Erwan_Okey :)17:44
@wikingErwan_, GP is quite the most complete17:45
@wikingnot only c++ but any17:45
@wikingWu did a great job there17:46
@wikinghe had even a comparison somewhere17:46
@wikinglemme try to find the PR/issue17:46
@wikingErwan_, maybe that helps u17:46
Erwan_Yep, that can be interesting17:48
@wikingErwan_, it's not the latest info (see dates) but there's a lot of info here https://github.com/shogun-toolbox/shogun/issues/305417:48
@wikinglike https://github.com/shogun-toolbox/shogun/issues/3054#issuecomment-20059842717:48
@wikingok there's even this http://nbviewer.jupyter.org/gist/yorkerlin/b742cfe1669170ec0a6a17:49
@wikingthis notebook is actually more what you wanna see17:49
@wikingi'd guess17:49
Erwan_Thanks17:52
Erwan_I'll have a look to that17:52
Erwan_for now the driving criterion is more about the easy integration that pure performance17:53
Erwan_But that's still interesting to know17:53
@wiking:>17:53
@wikingany feedback is more than welcome17:53
olinguyenwiking: I created a new unit test class file, but it doesn't seem to be included when i'm building/running make18:03
olinguyendo i have to include it somewhere else?18:03
@wikingah18:03
@wikingthe problem is that for recognising18:03
@wikingyou'll have to re-run cmake18:03
olinguyenah i see18:03
@wikingas the list of files18:03
@wikingto compile in the unit tests18:03
@wikingare generated when cmake is being run18:03
olinguyengotcha, thanks!18:04
@wikingnow one would only hope that it isn't cached :S18:04
@wikingif yes you'll have to delete build/tests ;P18:04
@wiking(hope u have ccache installed)18:04
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@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/3961 closed by Shenggang18:40
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--- Log closed Thu Aug 17 00:00:42 2017
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