Open in new window / Try shogun cloud
--- Log opened Wed Feb 04 00:00:05 2015
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xAndreLopesxAnyone here?02:37
xAndreLopesxIm on Ubuntu03:00
xAndreLopesxim trying to build shogun03:00
xAndreLopesxbut.. im getting a weird error03:01
xAndreLopesxcan you help me ?03:01
@wikingwhats the error?03:01
xAndreLopesxso im on shogun folder03:01
xAndreLopesxand i type :03:01
xAndreLopesxmake install03:02
xAndreLopesxmake: *** No rule to make target 'install'03:05
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xAndreLopesxSo it seems shogun only work on debian distri04:09
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shogun-buildbotbuild #960 of nightly_default is complete: Failure [failed notebooks]  Build details are at  blamelist: sanuj <>, Soumyajit De <>06:03
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@besser82? XD08:12
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chintakhey anyone around?09:30
chintakwhile trying to install shogun on OSX yosemite, I'm getting the following error - GPUMatrix.h:47:2: error: too many template parameters in template redeclaration09:31
chintakThe following OPTIONAL packages have been found:   * CCache  * GDB  * BLAS  * LAPACK  * GLPK  * Eigen3 (required version >= 3.1.2)  * ViennaCL (required version >= 1.5.0)  * OpenCV  * NLopt  * LpSolve  * ColPack  * Doxygen  * LibXml2  * HDF5  * CURL  * ZLIB  * BZip2  * LibLZMA  * SNAPPY  * LZO  * Spinlock  * Threads  * Protobuf09:32
chintakpls help me out09:32
sonne|worklambday: GPUMatrix.h  line 47? that's you?09:34
sonne|workchintak: which viennacl version do you have?09:35
chintaki have the latest one09:35
chintakdownloaded from their site and compiled09:35
sonne|workIIRC they changed the matrix layout internally09:35
sonne|workchintak: so uninstall viennacl until we fixed this09:36
chintak version 1.6.209:36
sonne|workchintak: yeah 1.6 won't work09:36
chintakshould i try and install 1.5 ?09:36
sonne|workchintak: well shogun will work without but if you want viennacl then yes09:37
chintakbetter off without it then09:37
chintakthanks for hte help!09:37
@lisitsynyes yes that's the reason09:39
@lisitsynthanks sonne|work09:39
@lisitsynchintak: you won't get much from viennacl yet anyway09:40
chintakcool, installing without it :D09:40
sonne|worklisitsyn: is the plan to use viennacl for GPU based NNs?09:40
@lisitsynsonne|work: yes09:41
@lisitsynsome kernels like convolution are already here09:41
@lisitsynand rlu and sigm09:41
sonne|worklisitsyn: and I guess you have blas /lapack / etc fallbacks right?09:41
@lisitsynsonne|work: mainly for (int i=0; fallbacks09:42
@lisitsynsome ops are quite specific09:42
@lisitsynsonne|work: but yeah I don't want it to be removed09:43
@lisitsynI still don't have gpu but playing with NNs is interesting sometimes09:43
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@lambdaysonne|work: khaled added that - I already raised an issue here
@lambdaysonne|work: I'll take care of it09:48
sonne|worklambday: ok09:49
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chintaksonne|work: are you there? while building modular python bindings, i get the following error - python_modular/modshogunPYTHON_wrap.cxx:8419:23: error: use of undeclared identifier '_seq'10:10
sonne|workchintak: let me guess swig 3.0.3 ?10:11
sonne|workchintak: or that yes10:11
chintakwon't work?10:11
sonne|workyou need 3.0.5 now - they introduced a bug in some 3.0.X release that causes this issue10:12
chintakso build from source, cool np10:12
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@lisitsynI love such users :D10:33
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@lisitsynlambday: yeah sure I can co-mentor11:04
@lambdaylisitsyn: great!11:11
@lambdaylisitsyn: what's your plans for REST? :P11:12
@lisitsynlambday: world domination11:13
@lambdaylisitsyn: how would it work?11:13
@lambdaylisitsyn: I mean, the data11:13
@lisitsynlambday: but wiking's idea on mesos is also very very cool11:13
@lambdaylisitsyn: works on docker?11:14
@lisitsynlambday: no mesos is a way to go distributed11:14
@lisitsynlambday: as for rest11:15
@lisitsynremember some guys had some specification?11:15
@lisitsynI should read it more but I think they had an idea11:15
@lambdaywhat guys? shogun guys?11:15
@lisitsynlambday: no, that guy from australia hmmm11:15
@lisitsynmark reid!11:15
@lambdaylol you lost me11:16
@lisitsynlet me find that mail11:16
@lambdayah found it11:16
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@lisitsynlambday: ok then11:20
@lisitsynso you see there is a spec11:20
@lambdayMLAAS :/11:20
@lisitsynlambday: well we can get support on that11:20
@lambdaylisitsyn: just from a quick glance - they already wrote some wrapper for scikit learn and they wanted to write one for shogun as well11:21
@lambdayso yeah11:21
@lisitsynlambday: we can improve that11:23
@lisitsynanyway much easier to start with that11:23
@lisitsynlambday: aaS is good11:24
@lisitsynnot just showcase but say in some companies like I am working in11:24
@lisitsynI'd setup some rest to do some experiments I think11:24
@lambdaylisitsyn: yeah that's true11:24
@lisitsynmuch easier11:25
@lambdaylisitsyn: I'm working on REST here as well11:25
sonne|worklambday & lisitsyn +111:25
sonne|workwe wanted that in for last year's gsoc11:26
@lisitsynlets just do it11:26
sonne|workbut didn't find a student for that11:26
@lisitsyndocker + mesos + rest11:26
@lisitsynthat's like when you install shogun in one second11:27
@lisitsynand you have distributed core with rest interface11:27
@lambdaysonne|work: lisitsyn: I'm wondering how would it work - say we have data - we specify classification method, params and their values in http req param and get json/xml result11:29
@lambdayhow to send the data via http? which format?11:29
@lisitsyna few possible formats I think11:29
@lisitsynbinary + sth like svmlight11:30
@lambdaylisitsyn: what about binary data?11:30
@lisitsynI think it would be necessary to support storages11:30
@lisitsynlike S3 or whatever11:30
@lisitsynso I just say11:30
@lisitsyntrain on s3://mydataset11:30
@lisitsynnot just push all the data through http11:30
@lisitsynas its inefficient11:30
@lambdayok gotcha provide the uri11:31
sonne|workyeah or file://11:31
@lisitsynyeah anything11:31
@lisitsynhdfs is important11:31
@lisitsynso you just say train on that thing11:32
@lisitsynwith all the details11:32
@lisitsynlambday: what's very important is to have very compact core11:33
@lisitsynthat can apply your trained model11:33
@lambdaylisitsyn: what do you mean by compact core?11:34
@lisitsynnot 100mb .so11:34
@lisitsynbut very very small thing11:34
@lambdaylisitsyn: yeah11:34
@lisitsynit has to be crazy fast11:34
@lambdaylisitsyn: so it goes back to plugin thingi11:35
@lambdaylisitsyn: without plugin framework it would be impossible to manage the size of shogun11:35
@lisitsynso that one can really rely on shogun in production env11:35
@lisitsynyeah but that's other thing11:35
@lambdaylisitsyn: so about rest, we specify the data - where does the processing occurs?11:37
@lisitsynlambday: what kind of processing?11:37
@lambdaylisitsyn: train/test - user's local system or some shogun server?11:38
@lisitsynlambday: to be discussed I guess11:39
@lisitsynsome basic preproc can be done by shogun11:39
@lisitsynbut not much of it11:39
@lambdaylisitsyn: okay11:40
@lambdaysounds great :D let's do this11:40
@lisitsynphew oil prices raise11:42
@lisitsynsonne|work: my salary vanished with these prices :D11:46
sonne|worklisitsyn: maybe the evil strategist behind this is running out of money?11:47
@lisitsynsonne|work: yes and russia already ran out of money11:47
sonne|workthe proxy war stuff is really running well! europe is suffering too :)11:48
@lisitsynsonne|work: I doubt that's serious, ain't it marginal?11:49
@lisitsynwe have inflation like 30% I think11:49
sonne|workyeah compared to that it is marginal11:50
@lambdaysonne|work: shall we add shogun's name in the ML section here ? :D11:52
sonne|workfeel free!11:53
@lisitsynwe really need to get rid of pointers11:54
@lisitsynI write modern C++ and there are no pointers, really cumbersome to use shogun11:54
sonne|worklisitsyn: do it :)12:00
@lisitsynsonne|work: waiting to be merged12:00
sonne|worklisitsyn: what would it do?12:01
@lisitsynsonne|work: Some<CClassifier> classifier = some<CSVM>();12:01
@lisitsynI believe it is very linguistic12:02
sonne|worklisitsyn: so classifier is refcounted internally then or what?12:03
@lisitsynsonne|work: just another name for shared_ptr12:03
@lisitsynso yes12:03
@lisitsynsonne|work: but now it just SG_REF/UNREF it12:03
@lisitsynon copy and delete12:04
sonne|worklisitsyn: I see - so the biggest issue is then to convert all the code to use that right?12:05
sonne|work(a nightmare so to say)12:05
@lisitsynnot really that hard12:06
sonne|workbut certainly possible withing one GSOC12:06
@lisitsynjust remove all sg_ref and sg_unref and convert [a-b]*\* to Some<..>12:06
@lisitsynshould instantly work12:06
@lisitsynor not12:06
chintaksonne|work: i tried installing modular python interface with SWIG 3.05 but same error - _seq undeclared identifier12:18
chintakthe C++ code is nicely compiled12:21
chintak*SWIG 3.0.512:21
@lambdaysonne|work: done! :D12:25
@lambdaylisitsyn: shall we use a c++ sdk for rest?12:26
@lambdaylisitsyn: or java/jersey-jackson12:27
@lisitsynlambday: no idea12:27
@lisitsynshould not matter a lot actually12:27
@lisitsynbut I'd avoid java :D12:27
@lisitsynfor religious reasons12:27
@lambdaylisitsyn: me too :D
@lisitsynlambday: beta ;)12:29
@lambdaylisitsyn: microsoft has one12:30
@lambdaybut that doesn't support xml12:30
@lisitsynwe don't need xml I think12:30
@lisitsynchintak: is there a chance wrong swig is used?12:32
@lisitsynlike if you have a few of them installed12:32
chintaki removed the earlier version12:32
chintakhad brew installed it earlier12:33
chintakjust 3.0.5 now12:33
@lambdayApache License 2.0 (Apache)12:34
@lisitsynchintak: I am on yosemite let me try to reproduce12:35
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chintaklisitsyn: were you able to reproduce it?12:55
@lisitsynchintak: compiling12:56
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@lisitsynchintak: yeah it failed13:01
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chintakwhich swig version had you built it with last?13:02
@lisitsynI don't remember whether I built it on mac recently13:03
@lisitsynwith swig13:03
@lisitsynshould be possible to fix13:03
@lisitsynlet me check13:03
@lisitsynchintak: I think I know what's going on13:06
@lisitsynit is clang issue13:07
chintakis it about the default std lib changing from libc++ to stdlibc++ ?13:10
@lisitsynchintak: looks like apple's compiler is not really good at compiling static member functions13:11
@lisitsynchintak: I am now trying to fix the source code of generated wrapper13:14
@lisitsynonce done you could do the same and get it working13:14
chintaklisitsyn: I'm trying to compile using gcc-4.9/g++-4.9 instead of the default clang13:18
@lisitsynchintak: good idea just to try13:18
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@lisitsynchintak: hah that's really cryptic what swig generates nowadays13:25
chintakno problems13:26
chintak60% done13:26
chintakhopefully this goes through, else I'll stick to C++ only13:26
chintakfor some reason this compilation is way slower, in spite of using the usual -j813:26
@lisitsynchintak: gcc is slower13:27
@lisitsynchintak: much more complex inside13:27
chintaklisitsyn: nope, it breaks at 84%13:31
chintakApplications/ file: libshogun.a(PrimalMosekSOSVM.cpp.o) has no symbol13:31
@lisitsynain't it a warning?13:32
chintakoh right13:34
chintaksymbol(s) not found for architecture x86_6413:34
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@lisitsynchintak: I think I am quite close to solve this thing13:37
@lisitsynchintak: it caused by 'check' word13:37
chintaklisitsyn: how are you doing it?13:37
@lisitsynthey named a few functions 'check'13:37
@lisitsynit conflicts with something13:37
@lisitsynwell I just edit the generated .cxx and try things13:37
@lisitsynyeah I did that13:39
@lisitsynchintak: it takes like 6-7 replaces13:40
sonne|worklisitsyn: what happened?13:40
@lisitsynsonne|work: gonna patch swig now13:41
sonne|worklisitsyn: I am tempted to let some version of shogun to always compile against latest swig13:41
chintaksonne|work: error with the latest swig13:41
* sonne|work sighs13:42
sonne|workchintak: I meant so we can find swig bugs before they release13:43
chintakoops my bad13:43
@lisitsynchintak: ok the workflow is13:43
@lisitsynyou make13:43
@lisitsynand get some error right near to the 'check' function13:44
@lisitsynrename it to check_13:44
chintakI get errors regarding undeclared identifier _seq13:46
@lisitsynchintak: yeah13:47
@lisitsynfind the error about 'check'13:47
@lisitsynthis would solve it13:47
chintaklisitsyn: i dont seem to get any error mentioning `check`13:51
@lisitsynchintak: could you please paste errors somewhere?13:52
@lisitsyn1.error: expected member name or ';' after declaration specifiers13:53
@lisitsyn2.    static bool {13:53
@lisitsynuhmm tihs error is quite strange13:54
@lisitsynhow did that happen to have static bool {13:54
chintakstatic bool check(PyObject *obj) {13:55
chintakshould i replace this to `check_`?13:56
chintakthe line corresponding to one of the "error: expected member name or ';' after declaration specifiers "13:56
@lisitsynstatic bool check_(PyObject* obj) {13:57
@lisitsynchintak: any help needed?14:02
chintak4 matches?14:10
@lisitsynchintak: yeah probably14:10
@lisitsynand two calls iirc14:10
chintakim sorry, iirc?14:11
chintakbool check(bool set_err = true) const?14:11
@lisitsynchintak: yes this thing as well14:19
@lisitsynchintak: I am now going to commit these changes14:19
chintakyep fixed14:19
@lisitsynand do a pull request14:19
@lisitsynfor swig14:19
@lisitsynbut for now we can use patched swig from my branch14:19
chintakcool! thanks a lot! :D14:19
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@lisitsynsonne|work: so fix comes in
sonne|worklisitsyn: woah! you are running under full steam again!14:53
@lisitsynI am curious whether they assume this 'check' thing comes from somewhere else14:54
@lisitsynuntil we have that patch in latest swig macosx shogun is impossible :D14:54
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chintaklisitsyn: can you check if the python interface is working?15:57
@lisitsynchintak: oh you're back15:57
@lisitsynif you compile swig from that branch15:58
@lisitsynyou should get it working15:58
chintakit makes correctly, but I get a seg fault on running `from modshogun import Classifier`15:58
chintakcool, ill try it out15:58
sonne|workchintak: make sure you use the same python version you compiled with15:58
sonne|workchintak: not that you have 2 different ones installed - you might get mixups and crashes15:59
@lisitsynI didn't check to be honest15:59
chintakjust 1 version15:59
@lisitsynlet me check15:59
sonne|workchintak: not one from e.g. brew and one system python?15:59
chintakbrew installed one15:59
sonne|workchintak: so there you have it15:59
sonne|workso you have 2 different ones15:59
sonne|workone in /usr/local/bin/python15:59
sonne|workand one on /usr/bin16:00
sonne|workchintak: well try to do the import modshogun16:00
sonne|workfrom both python versions16:00
chintakno module for system python, seg fault in brew version16:01
chintaklisitsyn: same for you?16:03
@lisitsynchintak: yeah16:04
@lisitsynok debugging part 216:04
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@lisitsynchintak: seems it is not caused by that fix16:07
@lisitsynswig unit tests pass16:07
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shogun-notifier-shogun: Sergey :develop * 8079fb0 / / (7 files):
shogun-notifier-shogun: Added ifdef for the fdopen function that is absent in cygwin16:50
shogun-notifier-shogun: Sergey Lisitsyn :develop * e7362af / CMakeLists.txt:
shogun-notifier-shogun: Use AppendToDefines instead of list append16:50
shogun-notifier-shogun: Sergey Lisitsyn :develop * c7efa3a / / (7 files):
shogun-notifier-shogun: Merge pull request #2684 from lisitsyn/bugfix/cygwin_fdopen16:50
shogun-notifier-shogun: Optional fdopen calls16:50
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travis-ciit's Sergey Lisitsyn's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun:
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shogun-buildbotbuild #2639 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at  blamelist: Sergey <>, Sergey Lisitsyn <>17:11
xAndreLopesxfatal error: cblas.h : No such file or directory #include <cblas.h>17:14
xAndreLopesxCan anyone help me please?17:14
shogun-buildbotbuild #971 of FCRH - libshogun is complete: Failure [failed test]  Build details are at  blamelist: Sergey <>, Sergey Lisitsyn <>17:25
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xAndreLopesx[14:52] <xAndreLopesx> [90%] Generating Classifier_lda_modular.class [14:52] <xAndreLopesx> Cannot find Symbol [14:53] <xAndreLopesx> LDA lda = new LDA(gamma, feats_train,labels);17:53
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shogun-buildbotbuild #209 of osx2 - modular_interfaces is complete: Failure [failed csharp modular]  Build details are at  blamelist: Sergey <>18:12
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shogun-buildbotbuild #210 of osx2 - modular_interfaces is complete: Failure [failed csharp modular]  Build details are at  blamelist: Sergey Lisitsyn <>18:32
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shogun-buildbotbuild #525 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at  blamelist: Sergey <>, Sergey Lisitsyn <>20:47
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xAndreLopesxException in thread "main" java.lang.UnsatisfiedLinkError: no modshogun in java.library.path21:37
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@sonney2kxAndreLopesx, put it in the path then :)22:19
@sonney2kxAndreLopesx, java -cp <youknowwhattoputhere>  -Djava.library.path=".:/path/to/"22:23
xAndreLopesxim using netbeans...22:23
@sonney2kxAndreLopesx, I am just using vi and bash22:23
xAndreLopesxwheres the ?22:24
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--- Log closed Thu Feb 05 00:00:06 2015