Open in new window / Try shogun cloud
--- Log opened Mon Jun 08 00:00:00 2015
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@wikingbesser82: hey10:15
@besser82wiking, ho!  =)10:16
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@besser82HeikoS, hey =)11:43
@HeikoSbesser82: hey man!11:44
@HeikoShow are things? :)11:44
@besser82depends on POV...  ;(11:44
@besser82and yourself11:45
@besser82?11:45
@besser82caught NIPS deadline?11:46
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@besser82HeikoS, ^11:48
guiniolHello all. I'm trying to learn how to use shogun, but I can't get the examples to work11:49
guiniolspecifically, I'm using python3 and trying the hmm example11:49
guiniolthe modular one gives me a segfault, and the static one doesn't find the module 'sg' to import (which I haven't found either)11:50
guiniolcould anyone give me some pointers?11:50
@HeikoSguiniol: hi there11:54
@HeikoSbesser82: NIPS is submitted (phew!)11:54
@HeikoSbesser82: now catching up with all the stuff I left for the weeks ;)11:54
@HeikoSguiniol: use python modular, not static11:54
@HeikoSdo the other examples work?11:54
guiniolHeikoS: trying out a few now11:55
guiniolI got 2 segafaults and 2 eigen3 missing11:55
guiniolbut I didn't even read them, just tried to execute them11:56
guiniolBTW, this is on the 4.0.0 release11:56
@HeikoSguiniol: this can be due to many reasons11:57
@HeikoSguiniol: did you compile from source?11:57
guiniolmaybe there's a problem with my install11:57
@HeikoSguiniol: if so, try the latest versionn, if you still get an error, post it on github issues11:57
guiniolHeikoS: will do11:57
@HeikoSsegfaults usually happen when your python version used to compile shogun are different to those used to run it11:57
@HeikoSguiniol: so double check your python setup11:58
guiniolI installed it from the AUR (archlinux) which should just be compiled from source11:58
guiniolI'll check11:58
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CaBahi13:47
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CaBaare the installation instructions on the website outdated? the docs look like autotools, but there is not configure script in the tarball...14:53
guiniolHeikoS: so, I compiled from the source and both the 4.0.0 release and master give me a segfault. Are there specific versions of some libraries that are required?14:57
CaBaseems to be cmake now... okay14:59
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CaBahm. i built shogun with python bindings from source, unfortunately it segfaults when the library is invoked..16:23
CaBa(mac os 10.9)16:24
CaBaany known issues there?16:24
@wikingmmmm16:25
@wikingooooh16:25
@wikingthat is a nice story16:25
@wikingok so you have like brew or macports?16:25
guiniolCaBa: not on macosx, but I get a segfault on most python examples, the other ones I get an "eigen3 missing" error16:29
CaBawiking: i built from the source tarball, also tried brew16:29
@wikingok do this16:30
@wikingrm -rf build16:30
@wikingand redo the whole, mkdir build && cd  build && cmake ... stuff16:31
@wikingand send the cmake output via pastebin16:31
CaBawiking: https://photomics.org/ucah7aS8_cmakeout.txt16:33
@wikingmmm this is interesting16:34
CaBain what respect?16:34
@wikingthat the reason for the segfault is something else :(16:35
@wikingnot the thing i thought it is16:35
CaBais there a on-liner to invoce the library somehow? so i dont have to try with an example script all the time...16:35
CaBajust to keep my testbed minimal16:35
CaBa*oneliner16:36
@wikingyeah16:36
@wikingwhen does it segfault btw?16:36
@wikingalready at the import of modshogun?16:36
@wikingor when u try an operation?16:36
CaBanope16:36
CaBathat works16:37
CaBarunning classifier_averaged_perceptron_modular.py is what i tried next16:37
CaBathat segfaulted16:37
@wikingbtw16:37
@wikingif you are in build16:37
@wikingyou could type16:37
@wikingctest -R python*16:37
guiniolCaBa: wiking I seem to have exactly the same problem, with 4.0.0 and master installed from source, and the 3.2.0 version packaged in Debian16:38
CaBawiking: just a sec. have to build again first16:39
CaBamaybe i should try a gcc build, too...16:39
CaBawhy is there an openmp dependency? should i use gcc for parallelization?16:40
@wikingnono16:41
@wikingit's ok16:41
CaBawiking: hm. nothing in the build directory matches 'python*'16:42
CaBawiking: actually i cant find anything ctest-ish anywhere16:48
CaBawiking: http://pastebin.com/raw.php?i=RQUCEiQd <- this works16:51
guiniolwiking: is there some kind of dependency or something that we could be missing? or are the examples outdated? from the github repo, it seems all the examples are from 2 years ago16:51
CaBawiking: http://pastebin.com/raw.php?i=1Ag68Mj8 <- this doesn't16:51
CaBawiking: the segfault occurs at the perceptron.apply() invokation16:53
CaBanot even sure about that...16:58
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@HeikoSguiniol: hi17:05
@HeikoStry the development version17:05
@HeikoSand check the python library that CMake detects and compare it to the one that is in your PYTHONPATH when you execute Shogun17:06
guiniolHeikoS: what do you mean by the dev version? I tried with master17:09
@HeikoStry using the develop branch17:10
@HeikoSbut the problem is not the version17:10
@HeikoSI guess it is the Python17:10
@HeikoSunless you are on ma17:10
@HeikoSmac17:10
@HeikoSthen, try the develop as we recently fixed a problem in osx17:11
guiniolnot on mac ( CaBa is though, might want to take a look), but I'll try the develop branch17:11
guiniolHeikoS: how do I see what version of python cmake is seeing?17:12
guiniolmy default version is 3.4 I think17:12
@HeikoSguiniol: cat CMakeCache.txt | grep ython17:15
@HeikoSand then see whats in your environment17:15
CaBagit/develop doesn't even build on my mac, at least not with clang. will try gcc-5.117:15
@HeikoSpython3 on mac was segaulting until a while ago17:15
@HeikoSCaBa: yes outdated, check the readmes instead17:15
guiniolHeikoS: the version matches my default version: 3.4 I'17:16
guiniolm on archlinux, so usually their python is rather vanilla17:16
CaBaHeikoS: hm? yes outdated?17:17
@HeikoSCaBa: the docs on the website17:17
@wikingCaBa: sorry was away17:18
@HeikoSguiniol: that is weird17:18
@HeikoSguiniol: could you post your exact system specs and the error on github issues?17:18
@HeikoSwiking: hexy there!17:18
@wikingCaBa: ok the problem is actually17:18
guiniolHeikoS: I'm installing all the optional packages that cmake didn't find to see if that helps17:18
@wikingthat you are mixing python libraries17:18
guiniolHeikoS: will do, but probably tomorrow17:18
@wikingHeikoS: alohaaa!17:18
CaBawiking: that means?17:18
@HeikoSwiking: hows life?17:19
@HeikoSguiniol: no that is not the problem17:19
@HeikoSguiniol: ususally there are config problems if this happens,17:19
@HeikoSguiniol: especially on linux17:19
@HeikoSwiking: any other reason python examples segfault=?17:19
@wikingHeikoS: back to europe for couple of weeks17:19
@wikingCaBa: means that you have your system python library and that's what you are using for compiling the shogun modulare interface17:20
@wikingok so what's in here17:21
@wikingPYTHONPATH=~/local/lib/python2.7/site-packages17:21
@wiking?17:21
@wikingand here DYLD_FALLBACK_LIBRARY_PATH=~/local/lib17:21
CaBawiking: ~/local is the prefix i gave cmake as an install target17:22
CaBawiking: ~/local was created right before the build / install17:22
CaBawiking: i.e. it only contains what 'make install' put there17:22
@HeikoSwiking: cool, where are you based right now?17:23
@wikingHeikoS: temp or perm?17:25
@wiking:D17:25
@HeikoSboth? :)17:25
@wikingHeikoS: i'm at home atm, but flying back to singapore in 2 weeks17:25
@wikinghome = serbia,hungary :)17:26
CaBawiking: don't really see where i'm mixing anything here yet...17:28
@HeikoSwiking: cool, how come?17:28
@HeikoSwhen are you visiting me in London? :D17:28
@wikingCaBa: doh, so only shogun stuff is there, right?17:29
@wikingHeikoS: eheheh god knows17:29
@wikingHeikoS: well now it's holidays etc17:29
@wikingcame home to see the family17:29
CaBawiking: yep17:29
CaBawiking: http://pastebin.com/raw.php?i=et4svkgY17:31
@wikingdman17:33
@wikingi'll have to test this myself then17:33
@wikinghad some segfaults17:34
@wikingbefore17:34
CaBawiking: in principle install targets other than /usr/local are supported, right? i really want to avoid messing up my /usr/local... ;)17:34
@wikingyes of course :>17:34
@wikingthe segfault previously we've seen was because17:34
@wikingcmake used the system's python interpreter but macport's headers/library17:35
@wikingi.e. different python was used17:35
@wikingbut in your case you consistently use the system's python itsel17:36
@wiking*itself17:36
CaBai have a homebrew python (2.7.10), too, but that's not what i use17:36
CaBaif i use that one, i get the segfault already on 'import modshogun' ;)17:36
@wikingmmmm17:36
@wikinghow did u make that to be used?17:37
@wikingwhat cmake parameter have u used to do that?17:37
CaBato do what?17:37
CaBacmake -DPythonModular=ON -DCMAKE_INSTALL_PREFIX=~/local17:37
CaBathis is my cmake call17:37
@wikingok and for using homebrew's python?17:37
CaBaoh I meant when i use *that* build with brews python17:38
CaBai.e.17:38
CaBaDYLD_FALLBACK_LIBRARY_PATH=~/local/lib/ PYTHONPATH=~/local/lib/python2.7/site-packages/  /usr/local/bin/python17:38
@wikingheheh17:38
@wikingtry to use this17:38
@wikingjust a sec17:38
@wiking-DCMAKE_PREFIX_PATH=/usr/local17:44
@wikingand paste the cmake output17:44
CaBaas long as you don't make me 'make install'... ;)17:45
@wikingprefix path is not install path17:46
CaBaah, right17:48
CaBawiking: http://pastebin.com/raw.php?i=aYfBfKuf17:49
@wiking-- Could NOT find CCache (missing:  CCACHE)17:49
@wikinginstall ccache17:50
CaBaoops17:50
@wikingwill save you a lot of time in the future ;)17:50
CaBathats with gcc-5 anyway17:50
@wikinguuuuu17:50
@wikingdont do this17:50
@wiking-- The C compiler identification is AppleClang 6.0.0.600005717:50
@wiking-- The CXX compiler identification is GNU 5.1.017:50
@wiking:<17:50
@wikingas this'll be hardcore segfault :)17:51
@wikingmake it use the same compiler17:51
@wikingwhether it is gnu or clang17:51
@wikingi dont care17:51
@wikingbut be consistent17:51
CaBayeah was just a try... and i didn't expect any C code ;)17:51
@wikingther eis17:52
CaBawiking: http://pastebin.com/raw.php?i=bNKQ5ZWt17:52
CaBawiking: there you go. clang all the way and ccache for more fun :P17:52
@wikingmmm17:53
@wikingfind /usr/local -name 'libpython*dylib'17:54
CaBawiking: brew doesn't link those in order not to collid with systems python17:55
@wikingas for some reason:17:55
@wiking-- Found PythonLibs: /usr/lib/libpython2.7.dylib (found version "2.7.5")17:55
CaBa$ find /usr/local -name 'libpython*dylib'17:55
CaBa/usr/local/Cellar/python/2.7.10/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib17:55
CaBa/usr/local/Cellar/python/2.7.10/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib17:55
CaBa/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib17:55
CaBa/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib17:55
@wikingmmm interesting :S17:55
CaBawiking: i guess building against the system python stuff should be preferred...17:57
@wikingmmm yeah17:57
@wikingi was just wondering what would it do with brew...?17:57
@wikingi'm always using macport's python though :)17:58
CaBawiking: well brews shogun doesnt work, too, fails also already on import17:59
CaBawiking: so maybe the formula just doesn't work17:59
CaBawiking: i also don't see any PREFIX magic in the formula17:59
CaBawiking: it does have a dependency on the brew python though, i guess they intend to build against that17:59
@wikingjust testing the HEAD of develop now with macports first :)18:02
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@wikingheh same here :<18:08
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@wikingCaBa: can u fire an issue on github for this and i'll update it when we have a fix for it?18:13
@wikingbtw18:13
@wikingtime to fix the notebook generator :)18:13
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CaBawiking: sure. were you able to reproduce this?18:14
@wikingCaBa: totally :)18:14
@wikingbtw we still in outlook for a mac builder :)))18:15
@wikingHeikoS: Gunnar once mentioned that he could donate one :)18:15
CaBawhat fields are you guys actually in?18:20
@wikingfield?18:22
@wikingah you mean what area of CS?18:22
@wikingi was doing image processing but now it's everything that comes around :)18:23
CaBaaha :)18:26
@wikingu?18:27
CaBabioinformatics, immunogenetics in particular18:27
@wikingnice18:28
@wikingwhat brought u to shogun?18:28
@wikingwhat algo u wanna test?18:28
CaBawell i want to play around with machine learning a little, string kernels in particular. haven't done anything in that area yet18:29
CaBahave to go. thanks for the support, i'll write that ticket :)18:30
@wikingthnx18:31
@HeikoSwiking: ah18:45
@HeikoSwiking: you know we set it up18:45
@HeikoSbut he never replied anymore18:45
@HeikoSIll cal lhim soon18:45
@HeikoSpostponed the old meeting as the german bureaucrats are slow in processing our foundation18:46
@HeikoSdid not hear back yet18:46
@wiking:>18:58
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@wikingshogun-buildbot: force build --branch=develop 'nightly_default'21:51
shogun-buildbotbuild #1013 forced21:51
shogun-buildbotI'll give a shout when the build finishes21:51
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shogun-buildbotbuild #1013 of nightly_default is complete: Failure [failed test notebooks]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/101322:10
@wikingshogun-buildbot: force build --branch=develop 'nightly_default'22:50
shogun-buildbotbuild #1014 forced22:50
shogun-buildbotI'll give a shout when the build finishes22:50
shogun-buildbotbuild #1014 of nightly_default is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/101423:05
@wikingshogun-buildbot: force build --branch=develop 'nightly_default'23:06
shogun-buildbotbuild #1015 forced23:06
shogun-buildbotI'll give a shout when the build finishes23:06
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--- Log closed Tue Jun 09 00:00:01 2015