IRC logs of #shogun for Monday, 2016-11-14

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--- Log opened Mon Nov 14 00:00:15 2016
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@sukeyPull Request #3282 "cookbook - CARTree -  classification tree"  synchronized by OXPHOS - https://github.com/shogun-toolbox/shogun/pull/328205:46
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HieronymousHow do I run unit-tests in SHOGUN ?14:31
HieronymousAlso, I am unable to install GoogleMock.14:34
@wikingHieronymous, so15:25
@wikingjust15:25
@wikingcmake -DENABLE_TESTING=ON ..15:25
@wikingand then run15:25
@wikingmake unit-tests15:26
@wikingthat should build googlemock + unit tests15:26
@wikingand as well to run the tests15:26
Hieronymouswiking: Yeah, I did that, read the wiki.15:29
HieronymousI am unable to install GoogleMock. Should I raise an issue ?15:29
@wikingwhat do yo umean15:29
@wikingby unable to install GoogleMock15:29
@wiking?15:29
HieronymousTest suite for meta examples does not exist!15:31
HieronymousWhen I run cmake -DENABLE_TESTING=ON ..15:31
HieronymousIt doesn't successfully complete. I have an error log on Cmake, should I pastebin ?15:31
Hieronymousis OpenCL required for this ?15:34
Hieronymousmake: *** No rule to make target `unit-tests'.  Stop., I get this btw when I do make unit-tests, wiking.15:36
@wikingok15:36
@wikingit's the same problem i had on my mac15:36
HieronymousCould you point me to how you solved it ?15:36
@wikingyou can fix this temporarily15:36
@wikingadding one line15:36
@wikingto tests/unit/CMakeLists.txt15:36
@wikingadd_dependencies(shogun-unit-test GoogleMock)15:37
HieronymousAt the end of the file , wiking ?15:37
@wikingadd it under this line15:38
@wikingADD_EXECUTABLE(shogun-unit-test ${UNITTEST_SRC} ${TEMPLATE_GENERATED_UNITTEST})15:38
Hieronymouswiking: Doesn't fix it :(15:40
@wikingyou have to15:40
@wikingdelete build15:40
@wikingand rerun cmake15:40
@wikingand then do the make unit-tests15:40
@wikingbut now i have to go15:40
@wikingttyl15:40
Hieronymouswiking: Thanks. Sure. Its running now :)15:41
Hieronymouswiking: btw, still the same. ttyl then.15:42
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@HeikoSwiking: jo16:43
HieronymousHeikoS: I am unable to install GoogleMock, could you help ?16:52
@HeikoSHieronymous:  hi!16:52
@HeikoSI guess it is because it was deleted from the servers16:52
HieronymousI also wrote some tests and would like to test them.16:53
@HeikoSyes I understand16:53
@HeikoSwhich version of shogun?16:53
HieronymousI am reading the instruction from the wiki.16:53
@HeikoSI see16:53
@HeikoScan you sen dme a link?16:53
HieronymousI have the "bleeding edge", cloned directly from GitHub16:53
HieronymousSure16:53
Hieronymoushttps://github.com/shogun-toolbox/shogun/wiki/README_developer16:53
HieronymousIts at the end.16:53
Hieronymouswiking was helping me out, but had to leave.16:54
@HeikoSThat file is outdated a bit I guess16:54
@HeikoSI think googlemock is bundled these days16:54
@HeikoSyou can run the unit tests locally?16:54
@HeikoSmake test16:54
@HeikoSthe cmake switches are16:54
@HeikoS-DENABLE_TESTING=ON16:54
Hieronymousmake: *** No rule to make target `test'.  Stop.16:55
HieronymousDo I need to run it in build ?16:55
@HeikoSyes16:55
@HeikoSdo make first16:55
@HeikoSjust make16:55
@HeikoSand then cancel it16:55
@HeikoSthen try make test again16:55
@HeikoSIll be afk for a few mins now, but back later16:56
@HeikoSI can help you sort that out then16:56
HieronymousSure HeikoS. Thanks. Also I wrote some Notebook examples for Manifold Learning (real world).16:57
HieronymousCheck that out, I have tagged you. I haven't submitted a PR, need your input for it.16:58
Hieronymousreal world - > real dataset I meant.16:58
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HieronymousHey HeikoS17:37
@HeikoSHieronymous:  jo!17:37
HieronymousRunning this cmake -DENABLE_TESTING=on .. on a fresh build doesn't do anything.17:38
HieronymousTest suite for meta examples does not exist!17:38
Hieronymous^Get this.17:38
HieronymousHeikoS: Could you tell me how you installed GoogleMock on your machine ?17:47
@HeikoSI didnt17:57
@HeikoSHieronymous: let me check17:57
HieronymousHeikoS: Sure.17:57
@HeikoSso it downloads it17:58
@HeikoSScanning dependencies of target GoogleMock17:58
@HeikoS[  0%] Creating directories for 'GoogleMock'17:58
@HeikoS[  1%] Performing download step (download, verify and extract) for 'GoogleMock'17:58
@HeikoS-- verifying file...17:58
@HeikoS     file='/home/heiko/git/shogun/shogun_develop/shogun/third_party/GoogleMock/release-1.8.0.tar.gz'17:58
@HeikoSversion 1.8.017:58
HieronymousMine doesn't.17:58
@HeikoStest suite for meta examples doesnt exist comes since you forgot17:59
@HeikoSgit submodule init17:59
@HeikoSgit submodule update17:59
@HeikoSbtw17:59
@HeikoSso whats the log thelling after this17:59
@HeikoS[  1%] Performing build step for 'GoogleMock'17:59
HieronymousI will pastebin. Hold on.17:59
Hieronymoushttp://pastebin.com/yQXbN8N218:00
HieronymousI do the git submodule init/update in the root folder, shogun right ?18:01
@HeikoSyes18:03
@HeikoSoh yeah this error is from git submodule18:04
HieronymousHold on. I am doing the update now.18:04
HieronymousHeikoS: I also added the KNN_KDTREE comparison, take a look when you can.18:05
@sukeyIssue #3535 "Propper error message when meta-testsuite doesnt exist" karlnapf added label: "entrance" - https://github.com/shogun-toolbox/shogun/issues/353518:05
@sukeyIssue #3535 "Propper error message when meta-testsuite doesnt exist" karlnapf added label: "cmake" - https://github.com/shogun-toolbox/shogun/issues/353518:05
@sukeyIssue #3535 "Propper error message when meta-testsuite doesnt exist" opened by karlnapf - https://github.com/shogun-toolbox/shogun/issues/353518:05
@sukeyIssue #3535 "Propper error message when meta-testsuite doesnt exist" karlnapf added label: "Cleanups" - https://github.com/shogun-toolbox/shogun/issues/353518:05
@sukeyIssue #3535 "Propper error message when meta-testsuite doesnt exist"- https://github.com/shogun-toolbox/shogun/issues/353518:05
@HeikoSHieronymous: https://github.com/shogun-toolbox/shogun/issues/353518:05
@HeikoSfeel free to send a fix :)18:05
@HeikoSIt should say: "Please initialize or update the 'data' git submodule"18:06
@HeikoSHieronymous: cool will do soon18:06
HieronymousHeikoS: Great, Also I wrote a notebook on Manifold Learning on real world dataset.18:07
HieronymousLots to review, take your time :)18:07
Hieronymoushttps://github.com/shogun-toolbox/shogun/issues/267418:07
@HeikoSHieronymous: hey that is great18:07
@HeikoSfor the tapkee notebook?18:07
HieronymousYep. USPS datset18:08
@HeikoSnice one18:08
@HeikoSshould add it, we like such things18:08
Hieronymouson, hold on.18:08
HieronymousThere is a caveat.18:08
HieronymousI don't know if what I've done is "accurate" or not.18:08
@HeikoSnot sure I know what you mean18:09
@HeikoSbut let me look at a PR if you send it18:09
HieronymousI will link the prelim code, take a look, if thats what you want, a PR will be ready.18:09
@HeikoSthats easiest18:09
@HeikoSyeah cool, give a gist18:09
HieronymousHeikoS: PR it is then.18:09
@HeikoSHieronymous: so what about your error?=18:17
HieronymousThe download just finished now.18:18
HieronymousHeikoS: et voila!18:19
@HeikoSworks?18:19
@HeikoSyeah so not sure why you were after googlemock?18:19
Hieronymousmake GoogleMock succeeded18:20
@HeikoScool18:20
@HeikoSso a few tips18:20
@HeikoSyou want to try your unit test right?18:20
Hieronymousmake[3]: *** [Eigen3/src/Eigen3-stamp/Eigen3-download] Error 118:20
HieronymousHold on HeikoS18:20
@HeikoSk18:20
HieronymousThis is what I got after make unit-tests18:20
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@HeikoSfull error pls18:20
Hieronymousfile DOWNLOAD HASH mismatch18:21
@HeikoSmaybe download failed?18:21
@HeikoSdo you have eigen3 installed?18:21
@HeikoSon your machine I mean?18:21
@HeikoSbecause if you had, shogun would use that rather than downloading18:21
HieronymousYes, I do have eigen3, its in usr/include18:21
Hieronymousin fact, I have played around with eigen a bit.18:22
@HeikoSdoesnt cmake detect it?18:22
HieronymousIt does actually. Its in the list of packages which it found.18:22
HieronymousAlthough make was downloading the latest one I guess 3.2.818:23
HieronymousI don't know my version.18:23
HieronymousI ran make unit-tests with sudo, it works!18:24
HieronymousI guess it needed permissions for writing stuff.18:24
HieronymousHeikoS: Can I run unit-tests submodule wise ?18:24
HieronymousI don't need to run all the tests just tests from SGSparseMatrix thats it.18:25
HieronymousHeikoS: The HessianLLE notebook (Tapkee) - https://gist.github.com/sudk1896/2b79f983e838e57a2d2cfc4f392edca918:33
HieronymousIts an Ipython Notebook, let me know if thats something you want.18:33
@HeikoSno sudo please18:40
@HeikoSyeah you might have screwed up your directory rights at some point18:41
@HeikoSHieronymous: running tests submodule wise doenst make sense18:41
@HeikoSwe only have one src module18:41
@HeikoSso a few tips for runing tests18:41
@HeikoSyou only want to run the tests you are after, right?18:41
@HeikoSso if that is unit18:42
@HeikoSyou can disable the others in the build18:42
HieronymousYep, HeikoS18:42
@HeikoS-DTRAVIS_DISABLE_*18:42
@HeikoScheck this switch18:42
@HeikoSthere is one for meta and one for libshogun examples18:42
@HeikoSthen make test just runs the unit tests18:42
@HeikoSthen second, you can filter out tests18:43
@HeikoSfor that, you go to the build/tests/unit folder18:43
@HeikoSit contains the unit test binary18:43
@HeikoSyou can run that by hand18:43
@HeikoS./shogun-unit-tests --getest_filter=YourTestName18:43
@HeikoSalso accepts wildcards in the test name18:43
@HeikoSHieronymous: BTW, we would welcome a patch with a readme on this :)18:43
HieronymousGreat, HeikoS. A README on the entire process I went through ? :)18:44
@HeikoSHieronymous: not the entire18:44
@HeikoSjust little bits and pieces, tips that are useful18:44
@HeikoSlike the ones I sent above18:44
@HeikoSit is always about small improvements to an existing readme18:44
@HeikoSrather than re-writing the whole thing from scratch :)18:44
HieronymousSure, I will add them in the README then :)18:44
@HeikoSin the developer I guess18:45
@HeikoSthere can be something on unit testing18:45
@HeikoSor I think our wiki also has an (empty) page on unit testing18:45
@HeikoSyou could send a pr against that18:45
HieronymousHeikoS: Yes, unfortunately it was. I had to ask wiking here beacuse of that.18:45
HieronymousThe bug is not reproducible, so it is likely a hardware or OS problem.18:45
HieronymousBtw, I got this while running make unit-tests.18:45
Hieronymoushttp://pastebin.com/xza0R8WP, its a problem with GoogleMock apparently.18:47
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HieronymousHeikoS: Seems like there is an OS/hardware issue, I'm updating to Ubuntu 16.0418:58
@HeikoSsorry I dont understand?18:59
@HeikoSoh that is weird18:59
@HeikoSseems like you have filesystem issues18:59
@HeikoSHieronymous: not sure updating ubuntu is the right way to solve this18:59
@HeikoSjust fix your system :)18:59
Hieronymoushttp://pastebin.com/xza0R8WP18:59
HieronymousGoogling the error doesn't show up any results.19:00
HieronymousGiving it a last try. I'm out of options actually.19:01
@HeikoScheck your filesystem19:01
@HeikoSrun checks19:01
@HeikoSchekc access rights of the folder19:01
HieronymousRunning make unit-tests one last time, lets see.19:03
@HeikoSno19:03
@HeikoSrun filesystem tests19:03
@HeikoStry to pinpoint the error down19:03
@HeikoSit has nothing to do with shogun19:03
HieronymousOkay. How do "run filesystem tests". What should I be looking for ?19:04
@HeikoSgoogle :)19:04
HieronymousHeikoS: Is this behavior normal - 58% tests passed, 185 tests failed out of 43619:20
HieronymousShould all the tests pass ideally >19:20
Hieronymous?19:20
@HeikoSit depends on your setup19:21
HieronymousA lot of them didn't evenr run.19:21
@HeikoSon our test servers, all tests pass19:21
Hieronymous*even19:21
@HeikoSyou can check for the reason a test fails easily19:21
@HeikoSctest -R yourTestName -V19:21
Hieronymous75 FAILED TESTS,  YOU HAVE 113 DISABLED TESTS19:22
HieronymousA lot of GPU related tests fail or don't run.19:22
@HeikoSyeah as I said, can be the case19:23
@HeikoSbut you have to check WHY they fail in order to say something19:23
@HeikoSI can only guess otherwise19:23
HieronymousAlso, I don't think I have ViennaCL installed, those tests fail as well.19:23
@HeikoSHieronymous: as I said19:23
@HeikoSthis is guessing ;)19:23
HieronymousDo I need to run that command in root ?19:24
Hieronymousthe ctest one ?19:24
@HeikoS*never* run anything as root unless your installing software :)19:24
HieronymousNoooo, I meant from which directory ?19:24
@HeikoSah :)19:24
HieronymousI meant the main folder i.e. shogun19:24
@HeikoSin build19:24
@HeikoSit is a cmake command19:24
@HeikoSgoogle it, they have nice docs and tips how to use it19:24
HieronymousAnother thing to add to README then :019:24
Hieronymous:)19:24
@HeikoSyep19:25
@HeikoSdefinitely :)19:25
@HeikoSwe hsould have a whole wiki page on testing19:25
@HeikoSwith all the details19:25
HieronymousI will do that then :) I guess I have learnt a fair bit today.19:25
@HeikoSthats great!19:25
@HeikoSmake sure to share it, really useful for others as well19:25
@HeikoSbasically, whenever your have a problem, somebody else will have it as well :)19:26
@HeikoSso help them, so they can start from where you left19:26
HieronymousI will go through today's logs and see what was worth sharing. Yep, I was a GSoC student this year (with a diff. org).19:26
HieronymousI did this a lot, writing docs/READMEs.19:27
@HeikoSHieronymous: ah there you go, you know a bit about open source then19:27
@HeikoSyeah its most important19:27
@HeikoSand we are bad at it :)19:27
@HeikoSHieronymous: so all help really really welcome19:27
@HeikoSHieronymous: so what brings you to shogun?19:27
HieronymousHeikoS: C++ and ML. I am tired of using C++ narrowly for 3 years. Want to learn "real-world" usage.19:28
HieronymousI use C++ for programming competitions.19:28
@HeikoSah cool !19:28
HieronymousAlbeit only STL. NOt much of anything else really.19:28
@HeikoSyeah shogun has a big build process around it due to the many interfaces19:28
@HeikoSand due to its portability and backwards compatibility19:28
@HeikoSso lots of non c++ things to learn, cmake, buildbot, travis, our own stuff, etc19:28
@HeikoSwe do some cool low level c++ stuff atm19:29
HieronymousHence looking for C++ projects to contribute to. Yep, Travis I know :)19:29
@HeikoSor did in gsoc19:29
HieronymousTravisCI is like a good friend :) My previous org was a bit small compared to SHOGUN. not to forget, it was Python based.19:29
HieronymousNot a lot of low level stuff there.19:30
@HeikoSHieronymous: cool yeah so let me know if you need any help19:30
@HeikoSit can be quite overwhealming our framework19:30
@HeikoSwhich project was it?19:30
@HeikoSmaybe I met them at the summit19:30
HieronymousHeikoS: OpenAstronomy is the umbrella.19:30
@HeikoSah cool19:30
HieronymousSunPY was the org i contributed to.19:30
@HeikoSyeah I met these german physicists19:30
@HeikoSfrom munich19:30
HieronymousThe project lead is actually based out of UCL.19:31
@HeikoSI think they might have been part of that19:31
@HeikoSah cool19:31
@HeikoSI should meet up with them19:31
@HeikoSyour know wolfgang kernzendorf?19:31
HieronymousMy mentor is a Researcher in Astrophysics at UCL. HeikoS: I only know them by nicknames.19:31
Hieronymous:)19:31
HieronymousIRC nicks.19:31
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HieronymousHeikoS: Got it! I ran the tests I added, it passed. I know how to run tests now !!19:54
HieronymousHeikoS: When are you usually available here (UTC timings if you will).19:54
@sukeyPull Request #3536 "Adding a test for transposing a Square SGSparseMatrix ."  opened by sudk1896 - https://github.com/shogun-toolbox/shogun/pull/353620:04
@sukeyPull Request #3536 "Test for transposing a Square SGSparseMatrix ." - https://github.com/shogun-toolbox/shogun/pull/353620:05
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@HeikoSHieronymous: jo20:51
@HeikoSHieronymous: usually like midday to evening London time20:52
@HeikoSHieronymous: cool about the tests :)20:52
@HeikoSwiking: jo21:08
@sukeyPull Request #3303 "cookbook - CHAIDTree"  merged by karlnapf - https://github.com/shogun-toolbox/shogun/pull/330321:09
@sukeyNew Commit "Merge pull request #3303 from OXPHOS/cookbook_CHAIDtree21:09
@sukeycookbook - CHAIDTree" to shogun-toolbox/shogun by karlnapf: https://github.com/shogun-toolbox/shogun/commit/4b629269d3cf3c14dd81133fdd95bed8ee97d04321:09
@sukeyPull Request #3532 "Correct the link  doc/readme/INSTALL.md points at"  merged by karlnapf - https://github.com/shogun-toolbox/shogun/pull/353221:09
@sukeyNew Commit "Merge pull request #3532 from mickyaero/Correct-installation-link21:09
@sukeyCorrect the link  doc/readme/INSTALL.md points at" to shogun-toolbox/shogun by karlnapf: https://github.com/shogun-toolbox/shogun/commit/5dc071d1c9428760c794fcf2c83b04d93243ad9221:10
@sukeyPull Request #3528 "Fixed memory leak in LDA unit test"  merged by karlnapf - https://github.com/shogun-toolbox/shogun/pull/352821:16
@sukeyNew Commit "Merge pull request #3528 from c4goldsw/lda_fix21:16
@sukeyFixed memory leak in LDA unit test" to shogun-toolbox/shogun by karlnapf: https://github.com/shogun-toolbox/shogun/commit/230625440b7cfcfd0b53aad432b07fb8e9d6532121:16
@sukeyIssue #3537 "Systematically test serialization of trained models" opened by karlnapf - https://github.com/shogun-toolbox/shogun/issues/353721:18
@sukeyIssue #3537 "Systematically test serialization of trained models"- https://github.com/shogun-toolbox/shogun/issues/353721:18
@sukeyIssue #3537 "Systematically test serialization of trained models" karlnapf added label: "testing" - https://github.com/shogun-toolbox/shogun/issues/353721:18
@sukeyIssue #3537 "Systematically test serialization of trained models" karlnapf added label: "entrance" - https://github.com/shogun-toolbox/shogun/issues/353721:18
shogun-buildbotbuild #54 of bsd1 - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/54  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, mickyaero <mickydroch@gmail.com>, OXPHOS <engelzora@gmail.com>21:20
@HeikoSshogun-buildbot: force build 'bsd1 - libshogun' -branch=develop21:25
shogun-buildbotbuild forced [ETA 2m15s]21:25
shogun-buildbotI'll give a shout when the build finishes21:25
shogun-buildbotbuild #55 of bsd1 - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/5521:26
@sukeyIssue #3460 "Rmodular cannot be built " karlnapf added label: "BUG" - https://github.com/shogun-toolbox/shogun/issues/346021:31
@sukeyIssue #3460 "Rmodular cannot be built " karlnapf added label: "SWIG" - https://github.com/shogun-toolbox/shogun/issues/346021:31
@sukeyIssue #3460 "Rmodular cannot be built "- https://github.com/shogun-toolbox/shogun/issues/346021:31
@wikingHeikoS, what?21:48
@sukeyIssue #3460 "Rmodular cannot be built " closed by karlnapf - https://github.com/shogun-toolbox/shogun/issues/346021:50
@sukeyIssue #3460 "Rmodular cannot be built " reopened by karlnapf - https://github.com/shogun-toolbox/shogun/issues/346021:50
@HeikoSwiking: ah cool greeting to the same country :)21:59
@HeikoSwiking: looking into issues21:59
@HeikoShad a few quetsions21:59
@HeikoSah yeah21:59
@HeikoSthe cookbook21:59
@HeikoSpreview link21:59
@HeikoSisnt there anymore21:59
@wikingyeah we have couple21:59
@HeikoSalso did some stuff for the numfocus22:00
@wikingfix it :)22:00
@wikingyou have access22:00
@HeikoSyeah might do22:00
@HeikoSthis R error also is annoying22:00
@HeikoSthe list for 5.1 is growing so fast :)22:00
@wikingi'm looking into osx related issues22:01
@wikingsince GaussianARDKernel is failing for some reason22:01
@wikinghence the osx unit tests are faiing22:01
@wikingand because of that we cannot have the homebrew updated to 5.0.0 :(22:01
@HeikoSkk22:01
@HeikoSwiking: oh and the ppa failed I think22:01
@wikingyep22:02
@wikingi'm gonna fix some of them this week22:02
@wikingyes22:03
@wikingsomething broke it22:03
@wikingin develop22:03
@wiking:(22:03
@sukeyPull Request #3538 "temporary workaround for #3460"  opened by karlnapf - https://github.com/shogun-toolbox/shogun/pull/353822:32
-!- HeikoS [~heiko@untrust-out.swc.ucl.ac.uk] has quit [Ping timeout: 248 seconds]22:54
--- Log closed Tue Nov 15 00:00:16 2016
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