Open in new window / Try shogun cloud
--- Log opened Sat Mar 01 00:00:19 2014
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bluenotebookhello, I had a doubt regarding the "Shogun Missionary & Shogun in Education" project idea07:19
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dhruv13I have a question...10:01
dhruv13in Math.h, the values for MIN_REAL_VALUE and MACHINE EPSILON are defined explicitly, rather than use the IEEE 754 values defined in float.h10:02
dhruv13this is causing some unit tests which test float comparison to fail...10:02
dhruv13Is it recommended that I use the values directly from float.h, or change/add CMath::* equivalents?10:03
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kislayI am getting difficulty in building the shogun using python interface. while running make I get : shogun/src/shogun/mathematics/lapack.h:37:19: fatal error: cblas.h: No such file or directory12:19
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@sonney2kdhruv13, well we simply didn't know back then so send a patch that defines these things in Math.h and use them!12:42
@sonney2kkislay, install libatlas-dev12:43
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thoralfHey!12:43
thoralfWhere does HeikoS find all this cool things? -> http://osrc.dfm.io/tklein2312:44
kislaythanks a lot sonney2k   :)12:46
@sonney2kthoralf, lisitsyn did send this around a year or so ago12:50
@sonney2kbesser82, please send me the kill_svmlight script!12:51
dhruv13okay12:51
thoralfsonney2k: Didn't know that.12:51
thoralflisitsyn: You're so cool as well, because you found it first! :S12:52
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@besser82sonney2k: http://pkgs.fedoraproject.org/cgit/shogun.git/plain/light-scrubber.sh  :D13:08
@sonney2kbesser82, that does work on the extracted source or where?13:08
@besser82sonney2k: yes, it's for the extracted 3.2.0-release.tar.bz213:09
@sonney2kbesser82, perfect! Then I can add some debian magic that downloads the 3.2.0 runs the script and generates a debian.orig.tar.gz13:09
@sonney2kbesser82, btw I have some weird build failures on powerpc now13:10
@besser82sonney2k: yes, sir, I can boogie  ;)13:10
@sonney2khttps://buildd.debian.org/status/package.php?p=python-shogun&suite=sid13:10
@besser82sonney2k: I can haz logz, plz?13:10
@besser82sonney2k: you've been faster ;)13:10
@sonney2kbesser82, I managed to build even on mips and mipsel btw :)13:10
@sonney2kusing clang!13:10
kislayah! got another error at 85% : Linking CXX executable balanced_conditional_probability_tree13:10
kislay../../../src/shogun/libshogun.so.16.1: undefined reference to `shogun::CPCA::CPCA(bool, shogun::EPCAMode, double, shogun::EPCAMemoryMode)'13:10
@sonney2kit needs a lot less memory!13:10
@besser82sonney2k: is clang allowed for debian?!?  No gcc-only policy around?!?13:11
@sonney2ksure I can use clang when I want - and I do need it just for these archs13:11
@sonney2kbesser82, and note the error on ppc - it seems gcc is generating invalid assembly code13:12
@besser82sonney2k: nope, for me it looks like some weird stuff with numpy13:12
@sonney2kbesser82, ?13:13
@sonney2k/tmp/cchNjNvK.s ...13:13
@besser82sonney2k: iirc that was the reason for RHEL not to ship Numpy / Scipy for the ppc releases...13:13
@sonney2kseems like a src file13:13
@sonney2kasm src I mean13:13
@besser82sonney2k: that's gcc trying to compile the numpy header...13:14
@besser82sonney2k: within SWIG-context...13:14
@besser82sonney2k: and that goes ***BOOM-BANG!!!*** even on RHEL 5 && 6 PPC{64}13:14
@sonney2kkislay, indeed that is a bug - PCA should not be available when EIGEN3 is not13:14
@sonney2kkislay, workaround for now is to install eigen3 !13:15
kislaysure!!13:15
@besser82sonney2k: that was the reason for RH not to ship / support that for RHEL PPC-releases...13:15
@besser82sonney2k: I can ask ausil / dgilmore on monday for details about that...13:16
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shogun-notifier-shogun: Soeren Sonnenburg :develop * 0801359 / src/shogun/preprocessor/PCA.cpp,src/shogun/preprocessor/PCA.h: https://github.com/shogun-toolbox/shogun/commit/0801359be7f056b74b8e4be8532d11f4f756d32313:18
shogun-notifier-shogun: ifdef with EIGEN3 in PCA too13:18
@besser82sonney2k: I'm sure he knows what was going on there && details to get some direction to hunt down that....13:19
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kislayHave installed libeigen3-dev, but the same error persists.13:38
kislayIs there is some problem regarding linking libshogun.a, libshogun.so ?13:43
@besser82kislay: did you erase the build-folder && recreated / rerun cmake after install of Eigen3?13:47
@besser82kislay: which version of Eigen3, btw, did you install?13:47
@besser82kislay: shogun need eigen3 >= 3.1.213:47
kislayI installed the one available in the ubuntu repo i.e libeigen3-dev (3.0.5-1)13:48
@besser82kislay: 3.0.5 is much too old13:49
@besser82kislay: which version of ubuntu do you use?13:49
kislayubuntu 12.04.2 precise13:50
@besser82kislay: is there any specific reason for you using ubuntu (lts)?13:50
kislaynaah!! Here most people use it , just that!13:51
kislayIs eigen3 > 3.1.2 not available for ubuntu 12.0413:52
@besser82kislay: possibly in backports or some ppa, perhaps... I dunno...13:52
* besser82 uses Fedora 2013:52
kislayokay , let me try a bit.13:52
@besser82kislay: otherwise I can just recommend using Fedora 2013:53
@besser82kislay: There are pre-build rpm for shogun avail there, which are frequently maintained by me13:53
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kislayGot eigen3 3.1.2-1 at precise-backports. Then after erasing the previous build and re running make, cmake  in python interface the same problem persists :(14:18
@besser82kislay: delete the build-folder, recreate, re-run cmake and try again, plz...14:19
@besser82kislay: It basically should build fine...14:20
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lisitsynoh guys we are going to have some war I guess :D15:11
kislaybesser82: thanks a lot for bearing me, it's finally completely  build. :)15:17
kislaythe problem was due to various ppa's of eigen3 untill I found the correct one15:18
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@sonney2kkislay, heh! excellent!16:06
@sonney2klisitsyn, what kind of war? You jbossing?16:06
lisitsynsonney2k: you will see in the news soon16:06
@besser82kislay: thx! nice to hear!  :D16:10
@besser82lisitsyn: c'mon, tell us now!!!1111one-eleven-one16:10
lisitsynbesser82: russian forces is entering ukraine :)16:11
@besser82lisitsyn: oh, sh*t, man!  CCCP 2.016:11
lisitsynbesser82: yeah fck that16:11
kislaysonney2k, one thing which is intriguing me a lot is -  I googled a lot on the error : "ImportError: libshogun.so.16: cannot open shared object file: No such file or directory", and got various answers in this channels log. I managed to overcome it. but why don't you document it?16:12
* besser82 wonders if there now some chances to get "Schlesien" back??? :-P16:12
@besser82kislay: that depends on the location you have libshogun.so* installed16:13
lisitsynbesser82: just take that - you see how easy it is16:13
@besser82kislay: e.g. if you place that in system's /usr/lib/ you won't get that error;  it is mostly due to custom locations16:14
@besser82kislay: and if someone uses custom locations, I think the one knows what he does and know how to correctly use the linker-flags, when linking against *.so in custom location16:15
@besser82lisitsyn: can you lend me some tanks?!?16:15
lisitsynbesser82: I have seen some (~18) tanks moving on the road yesterday actually :D16:16
@besser82lisitsyn: what are you w8ing for?  Conquer them and give them to me!!! :-P16:16
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@sonney2klisitsyn, yeah I also want a tank for x-mas18:43
@sonney2klisitsyn, and some MIG's too!18:43
lisitsynsonney2k: I am afraid all these I have seen yesterday are already moving to kharkiv18:44
lisitsynsonney2k: MiGs are in voronezh ;)18:45
lisitsyngo take it18:45
lisitsynif you need some helicopters - torzhok18:47
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@sonney2kHeikoS, I am now going to package shogun 3.2.0 for debian20:51
@sonney2kthanks to besser82 light-scrubber.sh it becomes automagic and in future very  easy :)20:51
@HeikoSnice!20:51
@HeikoSsonney2k, besser82 great work! Very important for us since many unis use ubuntu20:52
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@HeikoSsonney2k, wiking I have a request: Would it be possible to let travis generate the rendered ipython notebooks? Otherwise its so hard and annoying to review pull requests with them.21:03
@HeikoSsonney2k, wiking it would be great if it generated a temporary link with all of them in a list for checking. This way we can also detect if some of them fail. Thats very hard to do from the diff in the PR itself21:04
@sonney2kHeikoS, no idea if travis can keep files? generating stuff yes but this here needs some file upload...21:10
@HeikoSsonney2k: yeah upload to a temp dir on our webserver21:17
@sonney2kHeikoS, well - that would mean *anyone* could upload there21:17
@HeikoSsonney2k:  no way around this somehow?21:18
@HeikoSsonney2k: ah21:18
@HeikoSsonney2k: gist!21:18
@HeikoSsonney2k: and then print the links in the output21:19
@HeikoSsonney2k: intro task?21:19
@HeikoSwiking: ^ thoughts on this?21:20
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@sonney2kHeikoS, found a way21:23
@sonney2kHeikoS, http://sleepycoders.blogspot.de/2013/03/sharing-travis-ci-generated-files.html21:23
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lambdayHeikoS1: there??21:30
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lambdayHeikoS1: I edited the test statistic code! although not too sure!21:31
HeikoS1lambday: hi!21:32
HeikoS1lambday: nice! show me :)21:32
lambdayHeikoS1: I am not too sure! this is first edit21:32
lambdayHeikoS1: :-/ shall I send a PR?? :-/21:32
HeikoS1lambday:  donty worry! send a PR21:32
HeikoS1lambday: well have to think of a way of testing this, but for now I can just have a look21:33
lambdayHeikoS1: few things are really ugly21:33
lambdayplease bear with these21:33
lambdaybut I need to understand one thing21:33
lambdayfor independece test, we only need to permute sample from one distribution and not from the other, right21:34
lambdayHeikoS1: pardon my ugly PR21:34
lambdayHeikoS1: 180x2 = 360 ml down actually :D21:34
HeikoS1lambday: yes only fro one21:35
HeikoS1180x2? :)21:35
lambdayyeah two quarters! :D21:35
HeikoS1ehm what?21:36
lambdayHeikoS1: (ssshhh! alcohol :-s)21:36
lambdayHeikoS1: please have a look at indepence test statistic21:37
lambdayHeikoS1: HSIC::sample_null falls back to this... but the PR is not quite ready I think!21:38
@sonney2kHeikoS1, so you are on shogun planet now :D21:38
@sonney2khttp://shogun-toolbox.org/page/planet/shogun21:38
@sonney2klisitsyn, vodking you too21:38
HeikoS1sonney2k: yeah :) but why does it ignore the formatting?21:39
lisitsynsonney2k: I am vodker21:39
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@iglesiasgHeikoS1, lisitsyn cool interview :)21:39
lisitsyniglesiasg: haha thanks that's HeikoS121:39
HeikoS1lambday: reading21:40
lambdayHeikoS1: I don't think its merable yet! but still sent the PR for your comments.... specially for the independence test21:41
HeikoS1lambday: oh I just realised, another intro task is to allow different numbers of points for p and q21:42
HeikoS1lambday: no thats fine, I will just read to get the idea21:42
@sonney2kHeikoS1, there is no formatting in there <span>H</span>21:42
HeikoS1sonney2k: the questions are boldface on my page21:42
@sonney2kHeikoS1, yeah but you did some weird stuff there21:43
lambdayHeikoS1: lisitsyn: sonney2k: can I read it??? :D21:43
@sonney2kHeikoS1, <span style="font-size: 12px; font-family: Arial; color: #222222; background-color: #ffffff; font-weight: bold; font-style: italic; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">21:43
HeikoS1sonney2k: ah, just copy pasted from googledoc21:43
@sonney2klambday, http://shogun-toolbox.org/page/planet/shogun21:43
@sonney2klambday, the most funny thing I ever read :D21:43
lambdayHeikoS1: yes! right now, its only possible with equal number of samples :-/21:43
@sonney2kHeikoS1, ahh ok :(21:43
lambdayHeikoS1: I need to change a few things then :-/21:43
@sonney2kHeikoS1, a normal <b> would have worked21:43
@sonney2kor <strong>21:44
HeikoS1sonney2k: I did this WYSIWYG21:45
HeikoS1with googledoc21:45
HeikoS1why the hell is the exporter so bad?21:45
@sonney2kHeikoS1, I submitted my first patch to swig :)21:46
@sonney2kHeikoS1, github PR heh21:46
HeikoS1lambday: can do this later21:46
HeikoS1lambday: otherwise its too much21:46
HeikoS1sonney2k:  nice! :)21:46
HeikoS1haha21:46
@sonney2kHeikoS1, and for swig-R Dr Joe (swig R maintainer) said he will look at the issue :)21:46
HeikoS1after all those years21:47
HeikoS1sonney2k: nice21:47
HeikoS1sonney2k: I will write the R project soon21:47
HeikoS1sonney2k:although maybe the meta language guy can do that21:47
lisitsynsonney2k: so you can participate in gsoc as a student of swig!21:48
@sonney2klisitsyn, no not allowed by the rules! I cannot be mentor/admin *and* student21:49
lisitsynreally? this sucks21:49
@sonney2kmight be a world record attempt21:49
@sonney2klisitsyn, yeah you cannot be student and mentor...21:49
lisitsynand select yourself21:49
lisitsyn:D21:49
@sonney2kheh21:49
@sonney2kman21:49
@sonney2kmy internet is too slow21:50
@sonney2kuploading new shogun release and updating the tomtom map takes just too long21:50
@wikinghre21:50
@wikingwhat?21:50
@sonney2kwhy can't we have BROADband21:50
lambdayHeikoS1: yeah better do it later....21:50
@sonney2kwiking, debian pkg...21:50
@wikingHeikoS1: can u repeat taht? as i've just dropped in the internetz in tallin21:51
@sonney2kuploading with 50kb/s21:51
lambdayHeikoS1: reading your interview :D21:51
@wikingsonney2k: mmm from where to wherE?21:51
HeikoS1wiking: travis should upload the rendered notebooks to gist and put the link in the output so that its easier to review ipython notebook, can you magic that?21:51
@sonney2kwiking, he wants github to upload travis notebooks21:51
@wikingHeikoS1: too slow job...21:51
@sonney2kwiking, so we would need some travis account on sgtb21:51
@wikingHeikoS1: i mean travis job has a soft limit of 30 mins21:52
@wikingHeikoS1: i reckon having travis compile python modular + compile the notebooks would be too slow21:52
@wikingi.e. over 30 mins21:52
HeikoS1wiking: but wait21:52
@sonney2kalready notebooks themself have a timeout of 20 mins IIRC21:52
HeikoS1running the notebook just takes not so much time21:53
* sonney2k remembers increasing it for iglesiasg and hushell21:53
HeikoS1and we are compiling python already21:53
@sonney2kHeikoS1, it does21:53
@sonney2ksome are *slow*21:53
@wikingok so 10 min 14 sec21:53
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@wikingthis is the python modular job's build time21:53
* lambday (without any sense) love you guys! - the interview is just awesome!21:53
@wikingso that'd mean that we can have around 15-18 mins time for building the notebooks... (to be on a 'safe side')21:54
@wikingHeikoS1: so yeah building notebooks is quite time consuming in some of the cases...21:55
HeikoS1wiking: mmh, I dont know21:55
HeikoS1wiking: can we trigger a buildbot to do this?21:55
@wikingsonney2k: is there a way to extend the command timeout on buildbot: "command timed out: 1200 seconds without output, attempting to kill"21:56
@wikingthat's for memcheck job21:56
@wikingHeikoS1: it's possible of course21:56
@wikingHeikoS1: by using github hooks one can setup a bot that build stuff21:57
@wikingafter a commit21:57
@wikingor pr21:57
@wikingiglesiasg: seems the fundamental task is quite popular: ))21:58
HeikoS1wiking: indeed :)21:58
HeikoS1wiking: would be *great* to have21:58
HeikoS1in partoicular for people working on notebooks during gsoc21:58
@wikingHeikoS1: mmm yeah i can set that up21:58
@wikingbut just after monday21:59
HeikoS1wiking: cool!21:59
@wikingwhen i finally arrive to my final destination21:59
HeikoS1yeah its not too urgent, but please do it next :)21:59
HeikoS1where are you going?21:59
@wiking(currently doing a 2200km roadtrip)21:59
HeikoS1wow! nice!21:59
@wikingyeah i left serbia to finland21:59
HeikoS1whereabout?21:59
@wikingi'm in tallinn atm21:59
@wikingsonney2k: i'll b in berlin around 5th of may :)21:59
HeikoS1ha, so cool!21:59
@wikingHeikoS1: yeah it's insanely cold here....22:00
@wikingi left spring for winter :S22:00
@wikingnevermind... as soon as i'm settled22:00
@wikingi can get that bot to work22:00
@wikingHeikoS1: btw as an outcome where do u want to have the generated notebooks?22:00
lisitsynI am going to have 1000 km airtrip just this morning22:01
lisitsyn:)22:01
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@wikinglisitsyn: moscow?22:01
lisitsynwiking: yeah22:02
@wikinglisitsyn: glhf!22:02
lisitsynwiking: haha thanks22:02
@wikingand say hi to putin ;)22:02
HeikoS1wiking: if you run them on the buildbot, put them on our webserver maybe22:02
HeikoS1wiking: otherwise, put in gist?22:02
@wiking"Russia approves the deployment of troops in Ukraine, prompting Kiev to put its army on full alert as international leaders express alarm."22:03
@wiking:>>.22:03
HeikoS1wiking: on webserver, keep them for 7 days or so with the option to re-generate22:03
@wikingseems there's heaps of fun approaching :)))22:03
lisitsynwiking: I have no idea where this is going to22:03
lisitsynwiking: I absolutely against anything that would hurt my ability to leave this country :D22:03
@wikinglisitsyn: i was tooootally newsless for 3 days now... today i've read this on bbc :D22:03
@wikinglisitsyn: :DDDDD22:03
lisitsynwiking: that's just happening today22:03
@wikinglisitsyn: seems putin is on acid again :D22:03
@wikingHeikoS1: webserver is easier... ;)22:04
lisitsynwiking: I tend to think it is a matter of bargain22:04
HeikoS1wiking: ok then :)22:04
lisitsynwiking: but if there is going to be a war - he is seriously out of his mind22:05
@wikinglisitsyn: lol man i'm on the wrong place atm22:06
lisitsynwiking: why?22:06
@wikinglisitsyn: if russians start rolling i should get the fuck out of finland22:06
@wiking:)22:06
lisitsynhahah22:06
lisitsynwiking: yah molotov-ribbentrop22:06
@wikinglisitsyn: yeah man this is getting on the not funny side22:07
@wiking:)22:07
lisitsynwiking: it would be much worse if you were in crimea22:07
lisitsynmuch much worse haha22:07
@wikingseems sochi was just a good time to rest22:07
@wiking:)22:07
HeikoS1ok guys, I will go out now, see you later, have a good evening! :)22:08
lambdayHeikoS1: I will change the code according to your comments! :)22:14
lambdayHeikoS1: have a good night!22:14
lambdaysee you guys!22:14
lambdaysonney2k: I have the string kernel notebook 20% ready.. will send a PR soon! :022:15
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kislaythere's a issue #1878 regarding "writing a proper (k)PCA notebook", that i am interested for now. Some ideas other than given there that may facilitate me?..22:28
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--- Log closed Sun Mar 02 00:00:20 2014