IRC logs of #shogun for Sunday, 2014-05-04

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--- Log opened Sun May 04 00:00:33 2014
shogun-buildbot_build #291 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/291  blamelist: Viktor Gal <viktor.gal@maeth.com>00:08
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shogun-notifier-shogun: Viktor Gal :develop * a0c1fe0 / configs/Dockerfile: https://github.com/shogun-toolbox/shogun/commit/a0c1fe0ef91aca25cc796655ef0c7673bf02a6fc00:54
shogun-notifier-shogun: add shogun repo to /shogun from context in docker [ci skip]00:54
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shogun-buildbot_build #292 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/292  blamelist: Viktor Gal <viktor.gal@maeth.com>02:26
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shogun-buildbot_build #293 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/293  blamelist: Viktor Gal <viktor.gal@maeth.com>05:54
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Beginner1212hi..10:21
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Beginner1212which OS should I use? windows or ubuntu?10:29
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@wikingsonney2k_: ping12:40
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@wikingbesser82: ping13:09
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@besser82wiking, pong? 'sup?13:22
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@wikingbesser82: i'd need nightly builds of shogun packages13:37
@wikingbesser82: would it be possible to do that with fedora?13:37
@wikingbesser82: i mean one of the fedora buildbots could do that13:37
@besser82wiking, either that way or with the opensuse-buildservice13:37
@wikingbesser82: is there currently such thing?13:37
@besser82wiking, yes13:38
@besser82wiking, on fedora we have copr13:38
@wikingbesser82: anything would be good for me... i want to create nightly updated docker images13:38
@besser82wiking, on fedora we have copr, so we can "misuse" that13:38
@wikingbesser82: and there's this trusted build story of docker that finally started to work13:38
@wikingbesser82: but i dont want to compile and add the src to docker13:38
@wikingbesser82: i rather just have a fedora docker image and install the right packages13:39
@wikingbut would like to have them generated nightly13:39
@besser82wiking, that's how copr works  ;)13:39
@besser82wiking, you give link to SRPM and get build-pkg13:39
@wikingbesser82: ok so which version of fedora should i use?13:39
@besser82wiking, currently I'd use FC2013:39
@wikinghttps://index.docker.io/_/fedora/13:40
@wikingi have 20 there13:40
@besser82wiking, +113:40
@wikingbut even rawhide if that's necessary13:40
@wikingok i would need13:40
@besser82wiking, not really13:40
@besser82wiking, rawhide breaks too much13:40
@wikingshogun with python modular interface13:40
@wikingand colpack + arprec13:40
@wikingnlopt13:40
@wikingetc13:40
@besser82all in F20  ;)13:40
@wikingok good13:41
@wikingbut how do i get the nightly built shogun package?13:41
@besser82I just need to setup some rpm-spec magick with cmake && boom13:41
@wikingok cool i'll start preparing the new Dockerfile for this13:41
@besser82so you can just do sth like `cmake && make srpm13:41
@wikingwhat's the ipython version in fedora 20?13:41
@besser82...moment...13:41
@wikingbesser82: that should be done on a buildbot right? :)13:42
@wikingi mean cmake && make srpm13:42
@wikingbut ok i'm waiting13:42
@wikingand preparing the Dockerfile in the meanwhile13:42
@wikingbtw will the package fetch all the necessary dependencies as well for shogun?13:42
@wikingas currently i'm installing all these packages: make gcc g++ libc6-dev libbz2-dev libarpack2-dev libatlas-base-dev libblas-dev libglpk-dev libhdf5-serial-dev zlib1g-dev liblapack-dev cmake libnlopt-dev liblpsolve55-dev libxml2-dev libsnappy-dev liblzo2-dev liblzma-dev swig2.0 python-dev python-numpy python-scipy python-matplotlib python-pandas python-setuptools python-networkx python-tornado python-pip python-zmq python-jinja2 git-core wget13:43
@besser82Name       : python-ipython13:43
@besser82Architektur : noarch13:43
@besser82Version    : 0.13.213:43
@besser82Ausgabe    : 3.fc2013:43
@besser82wiking, ^^13:43
@wikingbut obviously these are for building shogun not just running13:43
@wikingbesser82: ok i guess there's pip on fedora as well so i'll install ipython with pip to get 2.013:43
@besser82wiking, the srpm will be build maxed out and pull all neded deps by automagic13:44
@wikingok cool13:44
@besser82wiking, the only thing is `svm^shit`13:44
@wikingbesser82: that's not included?13:44
@besser82wiking, I'm not sure we can ship that13:44
@besser82wiking, I can include it sure13:44
@wikingthen it's great13:44
@besser82wiking, at least for the cmake-srpm13:45
@wikinggood good13:45
@wikingi guess i should setup a fedora 20 bot then13:45
@wikingdo you maybe have a chroot img for that?13:45
@besser82wiking, sure;  just need to bootstrap  ;)13:45
@wikingor can we use fedora's infra for generating those nightlies? :D)13:46
@besser82wiking, the rpms?13:46
@besser82wiking, sure13:46
@wikingyeah13:46
@besser82wiking, we can use copr13:46
@wikingthat'd be awesome13:46
@besser82wiking, just need an srpm on some $webserver13:46
@wikingi can provide space where you can upload the generated rpms13:46
@besser82wiking, pass that url to copr && go go13:46
@wikingok13:46
@besser82wiking, and copr will give us a custom repo with these build13:47
@wikingdo you need ftp or what sorts of protocol to upload the rpms13:47
@wiking?13:47
@besser82wiking, you can build the srpm on buildbot?13:47
@besser82wiking, and then just upload somewhere13:47
@besser82wiking, copr can fetch from http(s) && ftp(s)13:47
@wikingi could, but would be great if we could do it somewhere else13:47
@wikingas our infra is getting a bit too stuffed13:48
@besser82wiking, building srpm isn't that cpu-intese13:48
@besser82wiking, will do within ~ 2 minutes13:48
@wikingbesser82: it's an extra shogun build from src13:48
@besser82wiking, we just need a checkout and then run cmake && make srpm13:49
@besser82wiking, that's isn't that much13:49
@wikingok i can do that13:49
@wikingi just need the rule file or whatever to generate those rpms13:49
@besser82wiking, and then we need the srpm to fetchable by copr, curl an http and copr does the rest  ;)13:49
@wikingok no worries13:50
@wikingthen just give me the stuff i need to run on the buildbot13:50
@besser82wiking, lemme setup the cmake magic  ;)  I have all we need13:50
@besser82wiking, and generating the rpm-spec for sg is quite tricky13:50
@wikingokey13:50
@wikingw8ing and setting up a new fedora 20 buildbot13:51
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@besser82wiking, fc20-chroot --->  http://besser82.fedorapeople.org/fc20-x86_64.tar.xz14:08
@besser82wiking, just the minimal stuff14:09
@besser82wiking, deps and stuff need to be installed seperatedly14:09
@besser82wiking, will give you needed pkgs in a minute14:10
@wikingcool thnx14:11
@besser82As root:14:18
@besser82yum makecache14:18
@besser82yum install @buildsys-build14:18
@besser82yum install arpack-devel arprec-devel atlas-devel blas-devel bzip2-devel chrpath ColPack-devel glpk-devel hdf5-devel iputils json-c-devel libcurl-devel libxml2-devel lpsolve-devel lzo-devel NLopt-devel protobuf-devel qd-devel snappy-devel tapkee-devel xz-devel zlib-devel cmake eigen3-devel swig gdb valgrind doxygen-latex fdupes graphviz texlive-appendix texlive-lastpage texlive-todonotes java-1.7.0-openjdk-devel jblas lua-devel mono-devel octave-devel n14:18
@besser82umpy python-docutils python-jinja2 python2-devel scipy python3-devel python3-docutils python3-jinja2 python3-numpy python3-scipy ruby-devel rubygem-narray-devel14:18
@besser82wiking:  ^^14:18
@besser82wiking, you're welcome  :D14:18
@wikingbesser82: ok so this is for the bot right?14:19
@wikingbtw: why do we need python3*?14:19
@wikingbesser82: that chroot is amd64?14:20
@besser82wiking, yes chrot is amd6414:20
@besser82wiking, for building python3-tests?14:20
@wikingbesser82: naaah i just need python2* atm14:21
@besser82wiking, kk, then just ignore the py3-stuff14:21
@wikingbesser82: ok14:21
@besser82wiking, pkgs were taken from me setup for building the fc rpms14:22
@besser82wiking, will be afk for the next ~30 min. ---> lunch14:23
@wikingbesser82: ok i'm setting up the buildbot in the meanwhile14:23
@besser82wiking, allrighty!  til then  ;)14:23
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@wikingbesser82: ok nightly_fedora bot is up and running14:38
@wikinghttp://buildbot.shogun-toolbox.org/builders/nightly_fedora14:38
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@besser82wiking, nice!  :D14:55
@wikingbesser82: i'm planning to add these packages to the docker container: yum install python-pip scipy numpy python-pandas python-networkx python-matplotlib14:55
@wikingis there others i need to specify that won't be automatically fetched via dependency for shogun?14:56
@besser82wiking, nope14:56
@besser82wiking, everything needed by sg itself will be fetched by explicit deps from it's rpm14:56
@wikingokey14:57
@wikingnow i will need the the cmake flags + the package generator command :)14:57
@wiking-DPythonModular=ON -DUSE_SWIG_DIRECTORS=ON -DCMAKE_INSTALL_PREFIX=`pwd`/../build_install14:57
@wikingi have these specified already14:58
@besser82wiking, those aren't neccessary for generating the srpm15:00
@wikingmmm just tell me then what are the flags i need for running cmake15:00
@besser82wiking, I'm currently thinking about how to make the srpm the most senseful...15:01
@wikingokey15:01
@besser82wiking, `cmake ..` should be enough15:01
@besser82wiking, this basically is just needed to generate some shogun.spec from shogun.spec.templ15:01
@wikingbesser82: but then how will we have python modular interface?15:01
@wikingoh i see15:02
@besser82wiking, the real build-conf is done during docker build then  ;)15:02
@wikingno15:02
@wikingthat's the thing15:02
@besser82wiking, s!docker!copr!15:02
@wikingah ok15:02
@wikingsince i really dont want to build the packages with docker15:02
@wikingi mean within docker container15:02
@wikingin docker container i just want to do15:02
@wikingyum -y install ...15:03
@wikingthat will use the nightly build packages15:03
@wikings/build/built/15:03
@besser82wiking, that ain't the prob with copr  ;)15:15
@wikingok i'll just do what u need me to do on the buildbot15:15
@besser82wiking, allrighty!  I think we need some rpm-dev pkgs on it:  yum groups install "RPM Development Tools"15:16
@besser82wiking, so we can use `spectool` and rpmbuild -bs15:17
@wikingdone15:19
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@besser82wiking, many thx!15:39
@besser82wiking, will start working on the cmake-magic then  ;)15:39
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@wikingbesser82: ping?18:31
@besser82wiking, pong!18:31
@wikingbesser82: ok so another question unrelated18:33
@besser82wiking, shoot it out  ;)18:33
@wikingcurrently in cmake we try to find the python lib that corresponds to the found interpreter's version18:33
@wikingset(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})18:33
@wikingFIND_PACKAGE(PythonLibs REQUIRED)18:34
@wikingi though that this should assure it18:34
@wikingbut now i see on travis the following18:34
@besser82wiking, simple solution  ;)18:34
@wiking-- Found PythonInterp: /home/travis/virtualenv/python3.3.5/bin/python (found version "3.3.5")18:34
@wiking-- Found PythonLibs: /usr/lib/libpython3.2mu.so (found version "3.2.3")18:34
@wikingthis is obviously not right :(18:34
@wikinghence the whole build fails18:35
@wikingi mean it doesn't fail just the tests fails18:35
@besser82wiking, which one get looked up firt?18:35
@wikingwith Fatal Python error: Inconsistent interned string state.18:35
@besser82wiking, lib or interp?18:35
@wikinginterp18:35
@besser82damn!18:35
@wikingas we always need interp18:35
@wikingbut not always need lib18:35
@wikingfor building18:35
@besser82travis is using some crappy cmake...18:35
@wikingas lib only required if you want python modular or static18:35
@besser82there is a patch around for findlibs18:36
@besser82lemme look it up18:36
@besser82so we need a patch FindPyLibs.cmake18:36
@besser82in custom cmake-script-dir  ;)18:36
@wikingit uses the 'Setting up cmake-data (2.8.12.2-0ubuntu1~ubuntu12.04.1~ppa2) ...'18:37
@wikingthat's kind of latest cmake :S18:37
@besser82wiking, which is crappy  ;)18:37
@wikingis it?18:37
@wikingi have that as well on my machine18:37
@besser82wiking, as all cmakes, those don't have the patch applied  ;)18:37
@besser82wiking, since kitware didn't apply it yet18:37
@besser82wiking, but we have it in fedora  ;)18:38
@wikingoh i see so yet another custom cmake script?18:38
@besser82no, the orig one but with applied patch  ;)18:38
@besser82so yes...  kinda "custom"18:38
@wikingoh no i do not want to apply patches on system's cmake script18:38
@wikingso i rather just put it into our cmake/ dir18:38
@wikingdo you have the FindPythonLibs.cmake of fedora somewhere?18:39
@besser82you can use the two patches listed here:  http://pkgs.fedoraproject.org/cgit/cmake.git/commit/?id=cdf5b807274180c3eddc2a89d91b52216e481ad518:39
@besser82wiking, cmake 3.0.0 will have the patch applied...18:40
@besser82on src.tar18:41
@wikingok i'll apply those patches on my original FindPythonLibs.cmake and then add it to our custom cmake scripts18:41
@besser82wiking, allrighty  ;)18:42
@besser82wiking, that should do the trick  ;)18:42
@wikingfor what version of cmake is this patch?18:46
@wikingoh fuck this is a patch of a patch18:49
@wiking....18:49
@wikingso what's the original patch?18:49
@wikingok i've got it18:49
@wikingok actually this way the set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}) is not required18:52
@wikingas PYTHON_VERSION_MAJOR and PYTHON_VERSION_MINOR is defined already18:52
@wikingwtf is this: CMAKE_FIND_FRAMEWORKS(Python)18:54
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@wikingheheh this wont work besser8218:55
@wikinginclude(${CMAKE_CURRENT_LIST_DIR}/CMakeFindFrameworks.cmake)18:56
@wikingand that is shogun's cmake dir18:56
@wiking${CMAKE_CURRENT_LIST_DIR} = <shogun repo>/cmake18:56
@wikingbesser82: would it hurt if i would replace all these includes (as there are 2 of them) from19:03
@wikinginclude(${CMAKE_CURRENT_LIST_DIR}/CMakeFindFrameworks.cmake)19:03
@wikinginto19:03
@wikinginclude(CMakeFindFrameworks)19:03
@wikingi mean i dont understand why is it required to include the CMakeFindFrameworks cmake script from ${CMAKE_CURRENT_LIST_DIR} only19:03
@besser82wiking, if cmake_module_path is set propely, no  ;)19:03
@wikingSET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake")19:04
@wikingi set it in the beginning like this19:04
@besser82wiking, that is fine then  ;)19:04
@wikingok let's test19:04
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shogun-notifier-shogun: Viktor Gal :feature/PythonDetection * 8f7847e / CMakeLists.txt,cmake/FindPythonLibs.cmake: https://github.com/shogun-toolbox/shogun/commit/8f7847e0abd4aa8f8b29d0266d09a5fd79827ac319:07
shogun-notifier-shogun: Fix python interpreter and library version detection19:07
@wikingbesser82: how's the cmake hack going with srpm?19:09
@besser82wiking, on it  ;)19:09
@wikingbesser82: i mean i dont mind if it's not integrated into cmake... it's enough for me if the bot generates it itself19:09
@wikingi really don't need anything fancy here.. just to work19:10
@besser82wiking, I know, but we need to get some stuff from cmake into the spec-file ;)19:10
@besser82wiking, which is used to generate the srpm19:10
@wikingok this doesn't fix the problem :(19:10
@wiking-- Found PythonLibs: /usr/lib/libpython3.2mu.so (found version "3.2.3")19:10
@wiking-- Found PythonInterp: /home/travis/virtualenv/python3.3.5/bin/python (found version "3.3.5")19:10
@besser82wiking, interp was found first?19:16
@wikingyes19:18
@wikingi've pasted in the wrong order19:18
@besser82wiking, :S19:26
@besser82wiking, Then I need to investigate a bit deeper into that...19:26
@besser82wiking, w819:27
@besser82wiking, is the custom py3 libs dir in searchpath?!?19:27
@wikingbesser82: ok another question19:36
@besser82wiking, yes19:36
@wikingbesser82: as i just saw a fucking amazing solution for travis + ccache19:36
@besser82wiking, go on  ;)19:37
@wikingso these guys are using iron.io to store 7ziped ccache directories19:37
@wikingbut travis actually supports directory caching as well19:37
@wikingnow the only question is that whether it's possible to define for ccache which directory to use19:37
@wikingfor storing the ccache files19:38
@wikingCCACHE_BASEDIR19:38
@wikingnice19:38
@wiking:)19:38
@wikingsince ccache would be obsolete otherwise right?19:38
@wikingi mean if i ccache everything in the same directory across all the builds19:39
@wiking(all the modular interface and gcc and clang builds)19:39
@wikingthat way a lot of caches would be invalidated19:39
@wikinghence ccache wouldn't really work19:39
@wikingbut if i define for each job a separate CCACHE_BASEDIR19:39
@wikingthen that would be good i guess19:39
shogun-notifier-shogun: Viktor Gal :feature/PythonDetection * 704010f / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/704010f5533b8f3a92d1c1668e8cfb09f333375819:58
shogun-notifier-shogun: Enable ccache and caching the output of it on travis19:58
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travis-ci[travis-ci] it's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/2439612820:00
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jd89Hi, I'm trying to set max_train_time for LibSVM classifier training using the python swig interface, but it appears to have no effect. I found some previous posts in the mailing list archive that reported the same issue, with static builds: http://comments.gmane.org/gmane.comp.ai.machine-learning.shogun/1118, but those were apparently addressed a long time back.20:38
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travis-ci[travis-ci] it's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/2439904120:45
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shogun-notifier-shogun: Viktor Gal :feature/PythonDetection * e2dfa74 / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/e2dfa74b9446e9d73aaf001a4e10812e5e6fca6922:07
shogun-notifier-shogun: Switch to anaconda when building python3.322:07
shogun-notifier-shogun: remove caching in travis as it is only available for private repositories22:07
shogun-notifier-shogun: Viktor Gal :feature/PythonDetection * a0ed9b2 / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/a0ed9b2a21c43b021f19562dffbb429dde7a161322:14
shogun-notifier-shogun: travis: add fast_finish option and fix anaconda path22:14
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travis-ci[travis-ci] it's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/2440569822:28
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shogun-notifier-shogun: Viktor Gal :feature/PythonDetection * 7012034 / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/7012034969c7346f2a22e490ce5a98fd0da7e0b423:09
shogun-notifier-shogun: travis: upgrade miniconda version and activate conda environment23:09
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shogun-notifier-shogun: Viktor Gal :feature/PythonDetection * 93fec06 / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/93fec060f8645a91e91f601e3aab34478805e42b23:18
shogun-notifier-shogun: travis specify PYTHON_LIBRARY for cmake when using miniconda23:18
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travis-ci[travis-ci] it's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/2440885523:32
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shogun-notifier-shogun: Viktor Gal :feature/PythonDetection * 3466b62 / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/3466b622383826f8bb2b5084edb668d3e07f91f323:38
shogun-notifier-shogun: travis: set CMAKE_PREFIX_PATH to miniconda virtualenv path23:38
--- Log closed Mon May 05 00:00:35 2014
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