--- Log opened Mon Jun 08 00:00:00 2015 | ||
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@wiking | besser82: hey | 10:15 |
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@besser82 | wiking, ho! =) | 10:16 |
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@besser82 | HeikoS, hey =) | 11:43 |
@HeikoS | besser82: hey man! | 11:44 |
@HeikoS | how are things? :) | 11:44 |
@besser82 | depends on POV... ;( | 11:44 |
@besser82 | and yourself | 11:45 |
@besser82 | ? | 11:45 |
@besser82 | caught NIPS deadline? | 11:46 |
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@besser82 | HeikoS, ^ | 11:48 |
guiniol | Hello all. I'm trying to learn how to use shogun, but I can't get the examples to work | 11:49 |
guiniol | specifically, I'm using python3 and trying the hmm example | 11:49 |
guiniol | the 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 |
guiniol | could anyone give me some pointers? | 11:50 |
@HeikoS | guiniol: hi there | 11:54 |
@HeikoS | besser82: NIPS is submitted (phew!) | 11:54 |
@HeikoS | besser82: now catching up with all the stuff I left for the weeks ;) | 11:54 |
@HeikoS | guiniol: use python modular, not static | 11:54 |
@HeikoS | do the other examples work? | 11:54 |
guiniol | HeikoS: trying out a few now | 11:55 |
guiniol | I got 2 segafaults and 2 eigen3 missing | 11:55 |
guiniol | but I didn't even read them, just tried to execute them | 11:56 |
guiniol | BTW, this is on the 4.0.0 release | 11:56 |
@HeikoS | guiniol: this can be due to many reasons | 11:57 |
@HeikoS | guiniol: did you compile from source? | 11:57 |
guiniol | maybe there's a problem with my install | 11:57 |
@HeikoS | guiniol: if so, try the latest versionn, if you still get an error, post it on github issues | 11:57 |
guiniol | HeikoS: will do | 11:57 |
@HeikoS | segfaults usually happen when your python version used to compile shogun are different to those used to run it | 11:57 |
@HeikoS | guiniol: so double check your python setup | 11:58 |
guiniol | I installed it from the AUR (archlinux) which should just be compiled from source | 11:58 |
guiniol | I'll check | 11:58 |
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CaBa | hi | 13:47 |
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CaBa | are the installation instructions on the website outdated? the docs look like autotools, but there is not configure script in the tarball... | 14:53 |
guiniol | HeikoS: 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 |
CaBa | seems to be cmake now... okay | 14:59 |
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CaBa | hm. 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 |
CaBa | any known issues there? | 16:24 |
@wiking | mmmm | 16:25 |
@wiking | ooooh | 16:25 |
@wiking | that is a nice story | 16:25 |
@wiking | ok so you have like brew or macports? | 16:25 |
guiniol | CaBa: not on macosx, but I get a segfault on most python examples, the other ones I get an "eigen3 missing" error | 16:29 |
CaBa | wiking: i built from the source tarball, also tried brew | 16:29 |
@wiking | ok do this | 16:30 |
@wiking | rm -rf build | 16:30 |
@wiking | and redo the whole, mkdir build && cd build && cmake ... stuff | 16:31 |
@wiking | and send the cmake output via pastebin | 16:31 |
CaBa | wiking: https://photomics.org/ucah7aS8_cmakeout.txt | 16:33 |
@wiking | mmm this is interesting | 16:34 |
CaBa | in what respect? | 16:34 |
@wiking | that the reason for the segfault is something else :( | 16:35 |
@wiking | not the thing i thought it is | 16:35 |
CaBa | is there a on-liner to invoce the library somehow? so i dont have to try with an example script all the time... | 16:35 |
CaBa | just to keep my testbed minimal | 16:35 |
CaBa | *oneliner | 16:36 |
@wiking | yeah | 16:36 |
@wiking | when does it segfault btw? | 16:36 |
@wiking | already at the import of modshogun? | 16:36 |
@wiking | or when u try an operation? | 16:36 |
CaBa | nope | 16:36 |
CaBa | that works | 16:37 |
CaBa | running classifier_averaged_perceptron_modular.py is what i tried next | 16:37 |
CaBa | that segfaulted | 16:37 |
@wiking | btw | 16:37 |
@wiking | if you are in build | 16:37 |
@wiking | you could type | 16:37 |
@wiking | ctest -R python* | 16:37 |
guiniol | CaBa: 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 Debian | 16:38 |
CaBa | wiking: just a sec. have to build again first | 16:39 |
CaBa | maybe i should try a gcc build, too... | 16:39 |
CaBa | why is there an openmp dependency? should i use gcc for parallelization? | 16:40 |
@wiking | nono | 16:41 |
@wiking | it's ok | 16:41 |
CaBa | wiking: hm. nothing in the build directory matches 'python*' | 16:42 |
CaBa | wiking: actually i cant find anything ctest-ish anywhere | 16:48 |
CaBa | wiking: http://pastebin.com/raw.php?i=RQUCEiQd <- this works | 16:51 |
guiniol | wiking: 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 ago | 16:51 |
CaBa | wiking: http://pastebin.com/raw.php?i=1Ag68Mj8 <- this doesn't | 16:51 |
CaBa | wiking: the segfault occurs at the perceptron.apply() invokation | 16:53 |
CaBa | not even sure about that... | 16:58 |
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@HeikoS | guiniol: hi | 17:05 |
@HeikoS | try the development version | 17:05 |
@HeikoS | and check the python library that CMake detects and compare it to the one that is in your PYTHONPATH when you execute Shogun | 17:06 |
guiniol | HeikoS: what do you mean by the dev version? I tried with master | 17:09 |
@HeikoS | try using the develop branch | 17:10 |
@HeikoS | but the problem is not the version | 17:10 |
@HeikoS | I guess it is the Python | 17:10 |
@HeikoS | unless you are on ma | 17:10 |
@HeikoS | mac | 17:10 |
@HeikoS | then, try the develop as we recently fixed a problem in osx | 17:11 |
guiniol | not on mac ( CaBa is though, might want to take a look), but I'll try the develop branch | 17:11 |
guiniol | HeikoS: how do I see what version of python cmake is seeing? | 17:12 |
guiniol | my default version is 3.4 I think | 17:12 |
@HeikoS | guiniol: cat CMakeCache.txt | grep ython | 17:15 |
@HeikoS | and then see whats in your environment | 17:15 |
CaBa | git/develop doesn't even build on my mac, at least not with clang. will try gcc-5.1 | 17:15 |
@HeikoS | python3 on mac was segaulting until a while ago | 17:15 |
@HeikoS | CaBa: yes outdated, check the readmes instead | 17:15 |
guiniol | HeikoS: the version matches my default version: 3.4 I' | 17:16 |
guiniol | m on archlinux, so usually their python is rather vanilla | 17:16 |
CaBa | HeikoS: hm? yes outdated? | 17:17 |
@HeikoS | CaBa: the docs on the website | 17:17 |
@wiking | CaBa: sorry was away | 17:18 |
@HeikoS | guiniol: that is weird | 17:18 |
@HeikoS | guiniol: could you post your exact system specs and the error on github issues? | 17:18 |
@HeikoS | wiking: hexy there! | 17:18 |
@wiking | CaBa: ok the problem is actually | 17:18 |
guiniol | HeikoS: I'm installing all the optional packages that cmake didn't find to see if that helps | 17:18 |
@wiking | that you are mixing python libraries | 17:18 |
guiniol | HeikoS: will do, but probably tomorrow | 17:18 |
@wiking | HeikoS: alohaaa! | 17:18 |
CaBa | wiking: that means? | 17:18 |
@HeikoS | wiking: hows life? | 17:19 |
@HeikoS | guiniol: no that is not the problem | 17:19 |
@HeikoS | guiniol: ususally there are config problems if this happens, | 17:19 |
@HeikoS | guiniol: especially on linux | 17:19 |
@HeikoS | wiking: any other reason python examples segfault=? | 17:19 |
@wiking | HeikoS: back to europe for couple of weeks | 17:19 |
@wiking | CaBa: means that you have your system python library and that's what you are using for compiling the shogun modulare interface | 17:20 |
@wiking | ok so what's in here | 17:21 |
@wiking | PYTHONPATH=~/local/lib/python2.7/site-packages | 17:21 |
@wiking | ? | 17:21 |
@wiking | and here DYLD_FALLBACK_LIBRARY_PATH=~/local/lib | 17:21 |
CaBa | wiking: ~/local is the prefix i gave cmake as an install target | 17:22 |
CaBa | wiking: ~/local was created right before the build / install | 17:22 |
CaBa | wiking: i.e. it only contains what 'make install' put there | 17:22 |
@HeikoS | wiking: cool, where are you based right now? | 17:23 |
@wiking | HeikoS: temp or perm? | 17:25 |
@wiking | :D | 17:25 |
@HeikoS | both? :) | 17:25 |
@wiking | HeikoS: i'm at home atm, but flying back to singapore in 2 weeks | 17:25 |
@wiking | home = serbia,hungary :) | 17:26 |
CaBa | wiking: don't really see where i'm mixing anything here yet... | 17:28 |
@HeikoS | wiking: cool, how come? | 17:28 |
@HeikoS | when are you visiting me in London? :D | 17:28 |
@wiking | CaBa: doh, so only shogun stuff is there, right? | 17:29 |
@wiking | HeikoS: eheheh god knows | 17:29 |
@wiking | HeikoS: well now it's holidays etc | 17:29 |
@wiking | came home to see the family | 17:29 |
CaBa | wiking: yep | 17:29 |
CaBa | wiking: http://pastebin.com/raw.php?i=et4svkgY | 17:31 |
@wiking | dman | 17:33 |
@wiking | i'll have to test this myself then | 17:33 |
@wiking | had some segfaults | 17:34 |
@wiking | before | 17:34 |
CaBa | wiking: in principle install targets other than /usr/local are supported, right? i really want to avoid messing up my /usr/local... ;) | 17:34 |
@wiking | yes of course :> | 17:34 |
@wiking | the segfault previously we've seen was because | 17:34 |
@wiking | cmake used the system's python interpreter but macport's headers/library | 17:35 |
@wiking | i.e. different python was used | 17:35 |
@wiking | but in your case you consistently use the system's python itsel | 17:36 |
@wiking | *itself | 17:36 |
CaBa | i have a homebrew python (2.7.10), too, but that's not what i use | 17:36 |
CaBa | if i use that one, i get the segfault already on 'import modshogun' ;) | 17:36 |
@wiking | mmmm | 17:36 |
@wiking | how did u make that to be used? | 17:37 |
@wiking | what cmake parameter have u used to do that? | 17:37 |
CaBa | to do what? | 17:37 |
CaBa | cmake -DPythonModular=ON -DCMAKE_INSTALL_PREFIX=~/local | 17:37 |
CaBa | this is my cmake call | 17:37 |
@wiking | ok and for using homebrew's python? | 17:37 |
CaBa | oh I meant when i use *that* build with brews python | 17:38 |
CaBa | i.e. | 17:38 |
CaBa | DYLD_FALLBACK_LIBRARY_PATH=~/local/lib/ PYTHONPATH=~/local/lib/python2.7/site-packages/ /usr/local/bin/python | 17:38 |
@wiking | heheh | 17:38 |
@wiking | try to use this | 17:38 |
@wiking | just a sec | 17:38 |
@wiking | -DCMAKE_PREFIX_PATH=/usr/local | 17:44 |
@wiking | and paste the cmake output | 17:44 |
CaBa | as long as you don't make me 'make install'... ;) | 17:45 |
@wiking | prefix path is not install path | 17:46 |
CaBa | ah, right | 17:48 |
CaBa | wiking: http://pastebin.com/raw.php?i=aYfBfKuf | 17:49 |
@wiking | -- Could NOT find CCache (missing: CCACHE) | 17:49 |
@wiking | install ccache | 17:50 |
CaBa | oops | 17:50 |
@wiking | will save you a lot of time in the future ;) | 17:50 |
CaBa | thats with gcc-5 anyway | 17:50 |
@wiking | uuuuu | 17:50 |
@wiking | dont do this | 17:50 |
@wiking | -- The C compiler identification is AppleClang 6.0.0.6000057 | 17:50 |
@wiking | -- The CXX compiler identification is GNU 5.1.0 | 17:50 |
@wiking | :< | 17:50 |
@wiking | as this'll be hardcore segfault :) | 17:51 |
@wiking | make it use the same compiler | 17:51 |
@wiking | whether it is gnu or clang | 17:51 |
@wiking | i dont care | 17:51 |
@wiking | but be consistent | 17:51 |
CaBa | yeah was just a try... and i didn't expect any C code ;) | 17:51 |
@wiking | ther eis | 17:52 |
CaBa | wiking: http://pastebin.com/raw.php?i=bNKQ5ZWt | 17:52 |
CaBa | wiking: there you go. clang all the way and ccache for more fun :P | 17:52 |
@wiking | mmm | 17:53 |
@wiking | find /usr/local -name 'libpython*dylib' | 17:54 |
CaBa | wiking: brew doesn't link those in order not to collid with systems python | 17:55 |
@wiking | as 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.dylib | 17:55 |
CaBa | /usr/local/Cellar/python/2.7.10/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib | 17:55 |
CaBa | /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib | 17:55 |
CaBa | /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib | 17:55 |
@wiking | mmm interesting :S | 17:55 |
CaBa | wiking: i guess building against the system python stuff should be preferred... | 17:57 |
@wiking | mmm yeah | 17:57 |
@wiking | i was just wondering what would it do with brew...? | 17:57 |
@wiking | i'm always using macport's python though :) | 17:58 |
CaBa | wiking: well brews shogun doesnt work, too, fails also already on import | 17:59 |
CaBa | wiking: so maybe the formula just doesn't work | 17:59 |
CaBa | wiking: i also don't see any PREFIX magic in the formula | 17:59 |
CaBa | wiking: it does have a dependency on the brew python though, i guess they intend to build against that | 17:59 |
@wiking | just testing the HEAD of develop now with macports first :) | 18:02 |
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@wiking | heh same here :< | 18:08 |
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@wiking | CaBa: can u fire an issue on github for this and i'll update it when we have a fix for it? | 18:13 |
@wiking | btw | 18:13 |
@wiking | time to fix the notebook generator :) | 18:13 |
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CaBa | wiking: sure. were you able to reproduce this? | 18:14 |
@wiking | CaBa: totally :) | 18:14 |
@wiking | btw we still in outlook for a mac builder :))) | 18:15 |
@wiking | HeikoS: Gunnar once mentioned that he could donate one :) | 18:15 |
CaBa | what fields are you guys actually in? | 18:20 |
@wiking | field? | 18:22 |
@wiking | ah you mean what area of CS? | 18:22 |
@wiking | i was doing image processing but now it's everything that comes around :) | 18:23 |
CaBa | aha :) | 18:26 |
@wiking | u? | 18:27 |
CaBa | bioinformatics, immunogenetics in particular | 18:27 |
@wiking | nice | 18:28 |
@wiking | what brought u to shogun? | 18:28 |
@wiking | what algo u wanna test? | 18:28 |
CaBa | well i want to play around with machine learning a little, string kernels in particular. haven't done anything in that area yet | 18:29 |
CaBa | have to go. thanks for the support, i'll write that ticket :) | 18:30 |
@wiking | thnx | 18:31 |
@HeikoS | wiking: ah | 18:45 |
@HeikoS | wiking: you know we set it up | 18:45 |
@HeikoS | but he never replied anymore | 18:45 |
@HeikoS | Ill cal lhim soon | 18:45 |
@HeikoS | postponed the old meeting as the german bureaucrats are slow in processing our foundation | 18:46 |
@HeikoS | did not hear back yet | 18:46 |
@wiking | :> | 18:58 |
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@wiking | shogun-buildbot: force build --branch=develop 'nightly_default' | 21:51 |
shogun-buildbot | build #1013 forced | 21:51 |
shogun-buildbot | I'll give a shout when the build finishes | 21:51 |
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shogun-buildbot | build #1013 of nightly_default is complete: Failure [failed test notebooks] Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/1013 | 22:10 |
@wiking | shogun-buildbot: force build --branch=develop 'nightly_default' | 22:50 |
shogun-buildbot | build #1014 forced | 22:50 |
shogun-buildbot | I'll give a shout when the build finishes | 22:50 |
shogun-buildbot | build #1014 of nightly_default is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/1014 | 23:05 |
@wiking | shogun-buildbot: force build --branch=develop 'nightly_default' | 23:06 |
shogun-buildbot | build #1015 forced | 23:06 |
shogun-buildbot | I'll give a shout when the build finishes | 23:06 |
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--- Log closed Tue Jun 09 00:00:01 2015 |
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