| --- Log opened Fri Mar 14 00:00:08 2014 | ||
| --- Day changed Fri Mar 14 2014 | ||
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| shogun-buildbot_ | build #501 of precise - libshogun is complete: Success [build successful] Build details are at http://buildbot.shogun-toolbox.org/builders/precise%20-%20libshogun/builds/501 | 00:09 |
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| PirosB3 | hey wiking did you have a look at my answer on the ML? | 00:33 |
| PirosB3 | did you hear from Mark at all? | 00:33 |
| shogun-buildbot_ | build #221 of clang34 - undefined behaviour analysis is complete: Failure [failed compile test] Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20undefined%20behaviour%20analysis/builds/221 blamelist: Thoralf Klein <thoralf.klein@zib.de>, Thoralf Klein <thoralf@fischlustig.de> | 01:06 |
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| shogun-buildbot_ | build #221 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/221 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Thoralf Klein <thoralf.klein@zib.de>, Thoralf Klein <thoralf@fischlustig.de> | 03:40 |
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| travis-ci | [travis-ci] it's Thoralf Klein'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/20726314 | 10:43 |
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| HeikoS1 | [paladin]: hey there | 12:10 |
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| Guest64937 | hey everyone.. I am a beginner.. I have setup shogun with DCMAKE_BUILD_TYPE=Debug -DENABLE_TESTING=ON flags. whenever i make any changes to library class say KernelPCA , do I have to rebuild the project for the changes to reflect..? | 12:25 |
| @wiking | Guest64937: obviously as any other cpp project | 12:26 |
| lambday | Guest64937: yeah | 12:26 |
| Guest64937 | wiking: ok thanks.. | 12:27 |
| PirosB3 | hi guys, do I need a specific flag on cmake to compile with OpenMP? | 12:27 |
| lambday | PirosB3: I think cmake detects it automatically and compiles it with it whenever present | 12:28 |
| lambday | wiking: ^ ? | 12:28 |
| PirosB3 | lambday: is there any way I can make sure it has been compiled? | 12:29 |
| PirosB3 | other than recompiling :) | 12:29 |
| lambday | PirosB3: umm... | 12:29 |
| lambday | PirosB3: I just did a grep -rin openmp in my build directory - it shows a lot of results | 12:31 |
| PirosB3 | ok | 12:31 |
| PirosB3 | I will do that now | 12:31 |
| lambday | you should grep for "-fopenmp" :P | 12:31 |
| lambday | PirosB3: I guess ./src/shogun/CMakeFiles/shogun.dir/link.txt should contain -fopenmp | 12:32 |
| lambday | where . is you build dir | 12:32 |
| PirosB3 | thanks lambday | 12:32 |
| PirosB3 | also, are Python binding necessary for most of the Shogun development? I am STILL having issues in compiling the modular binding.. | 12:33 |
| PirosB3 | it's really giving me a hard time. And I cannot upgrade mac just now (10.7.5 currently) | 12:33 |
| lambday | PirosB3: well, for GSoC its sort of necessary | 12:33 |
| PirosB3 | especially for my project. I really do not know what to do.. | 12:34 |
| lambday | PirosB3: can you get hold of any linux box? (bad solution I agree) | 12:34 |
| PirosB3 | I tried installing latest clang from homebrew, but there are other incompatibility issues over there | 12:34 |
| PirosB3 | lambday: I can, but the emulated environment is tooo slow | 12:34 |
| lambday | PirosB3: ought to be... | 12:34 |
| lambday | no I mean dedicated linux box... not virtual box | 12:35 |
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| PirosB3 | lambday: unfortunately not really. I can when I am working on GSoC because I will be at home | 12:35 |
| lambday | PirosB3: no worries then | 12:35 |
| lambday | :) | 12:35 |
| PirosB3 | really, I should just upgrade my mac | 12:35 |
| PirosB3 | the big mess is that ALL my coruseworks are in when GSoC closes! | 12:36 |
| PirosB3 | I have thought of this, and it's too risky to update now | 12:36 |
| PirosB3 | I am trying to find workarounds | 12:36 |
| jiaolong | Hi, one question about the shogun compiling, after updating the code, it seems the python module still compiles with the old data | 12:36 |
| jiaolong | make[2]: *** [src/interfaces/python_modular/CMakeFiles/_python_modular.dir/modshogunPYTHON_wrap.cxx.o] Error 1 | 12:36 |
| lambday | PirosB3: no worries | 12:36 |
| @wiking | PirosB3: autodetected (openmp) | 12:36 |
| PirosB3 | can anyone give me any suggestions regarding this? https://gist.github.com/PirosB3/9546152 | 12:37 |
| lambday | jiaolong: old data?? | 12:37 |
| PirosB3 | jiaolong: oh no you too! what what error do you get? | 12:37 |
| jiaolong | Yes, I mean, I wrote a function in the old file | 12:37 |
| @wiking | PirosB3: not necessary but would be good on the end to have modular interfaces for the stuff you've created... | 12:37 |
| jiaolong | OK | 12:38 |
| jiaolong | I always compile the interfeces | 12:38 |
| @wiking | jiaolong: what's old that? | 12:38 |
| PirosB3 | wiking: to debug the memory issues I need to have modular binding | 12:39 |
| PirosB3 | so I MUST get it solved | 12:39 |
| @wiking | PirosB3: you've already fired this as an issue... so i guess you should get an answer there... | 12:39 |
| @wiking | PirosB3: what? | 12:39 |
| @wiking | PirosB3: why would you need to have modular binding if u wanna resolve a memory issue? | 12:39 |
| PirosB3 | for my ticket, regarding the python script | 12:39 |
| @wiking | PirosB3: unless you want to debug the modular binding itself... | 12:39 |
| PirosB3 | because the issue is related to SWIG I assume | 12:40 |
| @wiking | PirosB3: a virtualbox could help you out until you dont have a solution for your issue on osx | 12:40 |
| jiaolong | I switch to the develop branch and compiling reports an error which points to my old branch | 12:40 |
| lambday | jiaolong: you did do a rm -rf * and fresh cmake, right? | 12:41 |
| @wiking | jiaolong: the best in that case is simple recompile it from scratch.... | 12:41 |
| PirosB3 | ok | 12:41 |
| @wiking | jiaolong: see lambday's comment | 12:41 |
| jiaolong | no | 12:41 |
| lambday | jiaolong: could you please try that? should work :) | 12:41 |
| @wiking | PirosB3: anyways debugging memory with valgrind on osx is not working... | 12:42 |
| jiaolong | how to do that? rm -rf * in build folder? | 12:42 |
| @wiking | jiaolong: yeah or rm -rf build | 12:42 |
| @wiking | ;) | 12:42 |
| lambday | jiaolong: yeah ... delete everything inside build | 12:42 |
| jiaolong | haha, oh my god | 12:42 |
| lambday | lol | 12:42 |
| @wiking | and then mkdir build | 12:42 |
| @wiking | whatever fits you better | 12:42 |
| lambday | lol :D | 12:42 |
| jiaolong | a lot of time, :( | 12:42 |
| @wiking | jiaolong: what? | 12:43 |
| jiaolong | I am sure that would work | 12:43 |
| @wiking | jiaolong: compiling? | 12:43 |
| jiaolong | no better way for re-compiling | 12:43 |
| @wiking | jiaolong: install ccache | 12:43 |
| lambday | +1 | 12:43 |
| PirosB3 | ccache is amazing | 12:43 |
| jiaolong | It seems I have installed ccache | 12:43 |
| @wiking | jiaolong: well then just remove the build directory re-run cmake and do make | 12:44 |
| @wiking | that should be much faster than it was for the first time | 12:44 |
| @wiking | it ccache was used | 12:44 |
| jiaolong | OK, thanks | 12:44 |
| PirosB3 | I just wonder, for hdf5 support on Ubuntu. do I need to install anything? | 12:44 |
| lambday | wiking: you mean, instead doing rm -rf * inside build, if one removes and recreates build then it would be faster? | 12:45 |
| @wiking | lambday: it's the same :) | 12:46 |
| @wiking | PirosB3: yeah the -dev packages | 12:46 |
| lambday | wiking: hmm yeah I thought I was missing something :) | 12:46 |
| lambday | HeikoS1: hi! | 12:47 |
| PirosB3 | libhdf5-dev | 12:48 |
| HeikoS1 | heya | 12:48 |
| HeikoS1 | lambday: how are things? | 12:48 |
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| PirosB3 | do I also need libhdf5-openmpi-dev? | 12:48 |
| lambday | HeikoS1: utterly confused :( | 12:48 |
| HeikoS1 | lambday: I just saw your mail ... | 12:48 |
| lambday | HeikoS1: weird that they say something in the paper but have something else in the implementation :( | 12:48 |
| HeikoS1 | lambday: yeah well | 12:48 |
| HeikoS1 | lambday: it is not *that* important acutally | 12:48 |
| HeikoS1 | lambday: just important to do things right, but there are multiple ways | 12:48 |
| HeikoS1 | lambday: I will actually talk to Dino in a bit (I just got back from Germany) | 12:49 |
| lambday | HeikoS1: but they are not actually computing h(z_a, z_b) | 12:49 |
| HeikoS1 | so we will write a response soon | 12:49 |
| lambday | HeikoS1: oh great! How was it :) | 12:49 |
| HeikoS1 | lambday: very nice! | 12:49 |
| HeikoS1 | lambday: maybe its even a bug ;) but who knows ..... | 12:49 |
| lambday | HeikoS1: in their code? | 12:50 |
| lambday | nope! | 12:50 |
| HeikoS1 | lambday: are you idling without that thing being clear? then I could discuss this now. otherwise this afternoon | 12:50 |
| lambday | HeikoS1: nono... I am reading papers :D | 12:50 |
| HeikoS1 | lambday: ok! | 12:51 |
| HeikoS1 | lambday: dino also set up some other things that are good for the beginning | 12:51 |
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| HeikoS1 | see his issues | 12:51 |
| HeikoS1 | but yeah, well get back to you later today | 12:52 |
| lambday | HeikoS1: alright... I am checking | 12:52 |
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| [paladin] | HeikoS1: Hey. Sorry for the delay. | 13:22 |
| HeikoS1 | [paladin]: no worries, but lets talk later, I have to go now for a couple of hours, back later today | 13:23 |
| HeikoS1 | see you | 13:23 |
| [paladin] | HeikoS1: okay, I've sent a mail, anyways. | 13:23 |
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| jiaolong | Hi, what is the 'push_back' function in SGVector? Any suggestions to get familiar with libshogun faster? What I am doing is to check the online help document again and again. Sometimes, I have to try different functions for many times. | 14:54 |
| PirosB3 | hi guys | 14:56 |
| fs_ | hi | 15:16 |
| kislay | hey, I was working with the idea on OpenCV integration. Any starting point on how to work on adding an optional dependency for opencv in cmake. | 15:24 |
| kislay | I couldn't comprehend it fully :( | 15:25 |
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| wavelander | 1 | 15:40 |
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| kislay | Hey lambday , could you help me with the issue. | 15:41 |
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| PirosB3 | kislay: what issue do you have | 16:46 |
| PirosB3 | ? | 16:46 |
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| lambday | kislay: hey.. sorry I was away | 17:43 |
| lambday | kislay: I am afraid I won't be of much help regarding cmake stuff :( | 17:43 |
| lambday | kislay: may be try to get how existing things work? | 17:44 |
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| PirosB3 | hey guys, can someone explain to me what the parameter framework is used for? | 17:55 |
| PirosB3 | it's for serialization purposes right? | 17:55 |
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| @sonney2k | PirosB3, yes and for model selection / clone() | 18:00 |
| PirosB3 | why can I see lots of castings to (SGString<float64_t>**) | 18:01 |
| PirosB3 | string of type float64? | 18:01 |
| kislay | lambday, oh. I was away! | 18:06 |
| kislay | no, openCV is not integrated right now with shogun. | 18:07 |
| kislay | I just want to know what its meant by "adding an optional dependency for opencv in cmake" | 18:08 |
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| kislay | PirosB3, hey sorry... I was away | 18:14 |
| kislay | I was trying to work on the issue regarding #1700, where some preliminary steps were listed | 18:15 |
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| PirosB3 | cool | 18:50 |
| PirosB3 | sonney2k: with regards to ticket: https://github.com/shogun-toolbox/shogun/issues/1972 I should: | 18:51 |
| PirosB3 | 1) add a new datatype for vector | 18:51 |
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| PirosB3 | 2) Implement new methods for SGVector | 18:51 |
| PirosB3 | 3) modify the save, load method | 18:52 |
| PirosB3 | is that correct? | 18:52 |
| cameo54321 | HeikoS1: Hi! I looked into how random number generation happens in shogun | 18:55 |
| HeikoS1 | cameo54321: yeah? | 18:56 |
| cameo54321 | HeikoS1: I also looked to random number generation pointed out by wiking | 18:57 |
| cameo54321 | It turns out that shogun uses sfmt | 18:57 |
| cameo54321 | for random number generation | 18:57 |
| cameo54321 | but the link i mentioned above has a lot of implementations | 18:57 |
| cameo54321 | directly from cplusplus | 18:57 |
| cameo54321 | including the mersene twister | 18:58 |
| cameo54321 | aka http://en.cppreference.com/w/cpp/numeric/random | 18:58 |
| HeikoS1 | cameo54321: wow I see | 18:59 |
| HeikoS1 | cameo54321: please open an issue to discuss that and reference me and wiking with some suggestions how to fix that then. Could be a very nice intro task | 18:59 |
| cameo54321 | One way is to keep the legacy way of how random number generation is done in shogun | 18:59 |
| cameo54321 | The other way is to directly take the distributions from random number generation methods already mentioned in the link above | 19:00 |
| cameo54321 | using sfmt and then eigen | 19:00 |
| cameo54321 | A new issue? or discussion on the existing 1929? | 19:00 |
| PirosB3 | HeikoS1: when you have finished with cameo54321, can I ask you a question regarding Parameter framework? | 19:01 |
| HeikoS1 | PirosB3: sure shoot | 19:03 |
| HeikoS1 | cameo54321: yeah, taking some external implementation might be a nice idea, but lets discuss that in the issue, feel free to guide the discussion, point out alternatives, their implementations etc | 19:03 |
| PirosB3 | I am trying to understand more regarding https://github.com/shogun-toolbox/shogun/issues/1972. From what I understand, I should: | 19:03 |
| PirosB3 | add a new datatype for vector (DataType) | 19:03 |
| PirosB3 | implement the add_vector function with type SGVector | 19:04 |
| PirosB3 | (Parameter) | 19:04 |
| PirosB3 | and then, override some methods (save, load) in Parameter | 19:04 |
| PirosB3 | is that correct? | 19:04 |
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| HeikoS1 | mmmh | 19:05 |
| HeikoS1 | I am not so sure there, let me read the issue | 19:05 |
| PirosB3 | thx :) | 19:07 |
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| HeikoS1 | PirosB3: we want a method similar to | 19:13 |
| HeikoS1 | void add_vector(SGSparseVector<bool>** param, index_t* length, | 19:13 |
| HeikoS1 | const char* name, const char* description="") | 19:13 |
| HeikoS1 | just for SGVector<T> | 19:14 |
| HeikoS1 | SGVector<T>** | 19:14 |
| HeikoS1 | a vector of SGVectors | 19:14 |
| HeikoS1 | have a look at the above method to see how its done, should be easy | 19:14 |
| PirosB3 | yep, but that not all of it | 19:14 |
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| PirosB3 | you need to also add the vector to the switch statement | 19:15 |
| HeikoS1 | where? | 19:15 |
| PirosB3 | struct type | 19:15 |
| HeikoS1 | file, line? | 19:15 |
| PirosB3 | 3799 | 19:15 |
| PirosB3 | Parmater.cpp | 19:15 |
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| PirosB3 | also, shouldn't I need to add another EStructType? | 19:16 |
| dhruv13 | HeikoS1: wiking: Is there a clean way to access the idx'th feature's dim'th value cleanly? | 19:18 |
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| HeikoS1 | PirosB3: I see | 19:19 |
| HeikoS1 | yes thats true | 19:19 |
| HeikoS1 | PirosB3: than the task is not that easy in fact | 19:19 |
| HeikoS1 | PirosB3: but first step is being able to register | 19:19 |
| PirosB3 | HeikoS1: I think the best way of approaching this problem is stating with a unit test | 19:19 |
| dhruv13 | HeikoS1: wiking: I've had to assume a CDenseFeature<float64_t> to do it | 19:19 |
| dhruv13 | HeikoS1: wiking: can i be more generic? | 19:20 |
| PirosB3 | but as I have never used the parameter framework before, i would need an example | 19:20 |
| HeikoS1 | afk for 5 mins .... | 19:20 |
| PirosB3 | hey dhruv13 hows it goin | 19:20 |
| PirosB3 | are you doing id3? | 19:20 |
| dhruv13 | PirosB3: okay, a little puzzled by the myriad of Feature type classed | 19:20 |
| dhruv13 | PirosB3: id3? | 19:21 |
| PirosB3 | it's crazy isn't it | 19:21 |
| PirosB3 | decision tree | 19:21 |
| dhruv13 | PirosB3: yeah! i found a way to do what i need to do, but it seems dirty | 19:21 |
| dhruv13 | PirosB3: nope, still on kdtree | 19:21 |
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| dhruv13 | besser82: hey! | 19:21 |
| @besser82 | dhruv13, ho! :D | 19:22 |
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| PirosB3 | yeah, really little progress here too | 19:22 |
| dhruv13 | PirosB3: we need to keep at it! Gambatte!! | 19:23 |
| PirosB3 | ahahah! | 19:23 |
| dhruv13 | i was wondering, is there a reason this project is called shogun? | 19:24 |
| HeikoS1 | PirosB3: yes unit test is the best start | 19:25 |
| PirosB3 | HeikoS1: can you help me formulate a unit test to begin with? | 19:25 |
| HeikoS1 | PirosB3: have a look at the existing unit tests for the ST_SPARSE things | 19:26 |
| HeikoS1 | PirosB3: both implementation and testing should be very similar | 19:27 |
| HeikoS1 | PirosB3: but careful, this is involved stuff, not sure whether this is a good entrance task | 19:27 |
| PirosB3 | do you think I should document the ticket with some steps? | 19:27 |
| PirosB3 | in this way, if I am doing something dumb, people could tell me so | 19:28 |
| HeikoS1 | PirosB3: nobody except me really knows this stuff unfortunately, so you wont get a lot of feedback | 19:28 |
| PirosB3 | good to know! | 19:28 |
| PirosB3 | anyways thanks for your help HeikoS1 | 19:28 |
| HeikoS1 | PirosB3: I in fact suggest to try something else. If you still want to do it, read code first to get a feeling for what is to do | 19:28 |
| HeikoS1 | PirosB3: once you understand that, it should not be too hard. | 19:29 |
| PirosB3 | HeikoS1: do you suggest any task related to the Shogun SaaS? | 19:29 |
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| HeikoS1 | PirosB3: you need to do it very systematically, increasing step by step with unit tests, thats the best way to go in my experience for those things | 19:29 |
| dhruv13 | HeikoS1: Hey! can you help me out with something? | 19:29 |
| HeikoS1 | PirosB3: I cant really say something about SaaS, dont know that | 19:29 |
| HeikoS1 | dhruv13: yes, sorry | 19:29 |
| dhruv13 | HeikoS1: Please take a look at this: https://gist.github.com/dhruv13J/9553753 | 19:30 |
| HeikoS1 | dhruv13: accessing individual features is hard for non CDenseFeatures (I think) | 19:30 |
| dhruv13 | HeikoS1: could the kdtree_get_pt() be any cleaner? | 19:30 |
| HeikoS1 | dont reaturn NaN, throw an error, people should only askig for valid features | 19:31 |
| HeikoS1 | why do you cast to float64_t | 19:31 |
| HeikoS1 | I think this can be done for any dense features | 19:31 |
| HeikoS1 | Oh and please use the get_feature_vector() method which returns SGVector | 19:32 |
| HeikoS1 | cleaner to read | 19:32 |
| HeikoS1 | dhruv13: String features also support get_feature_vector btw | 19:33 |
| HeikoS1 | but its all discrete | 19:33 |
| HeikoS1 | dhruv13: does that help? | 19:34 |
| dhruv13 | HeikoS1: umm... a lot of questions... | 19:34 |
| HeikoS1 | dhruv13: ok go | 19:34 |
| HeikoS1 | dhruv13: dont have loads of time but a little bit :) | 19:34 |
| dhruv13 | HeikoS1: 1) Since KDTrees make sense with number type features only, do i keep the CDenseFeatures assumption? | 19:35 |
| HeikoS1 | dhruv13: yeah, but maybe do a generalisation to any type? | 19:35 |
| HeikoS1 | dhruv13: or do you only want to be float64? | 19:35 |
| dhruv13 | HeikoS1: 2) Since I will integrate this with KNN.cpp, I think I can get away with the nan | 19:35 |
| HeikoS1 | dhruv13: but why do you want to do that? | 19:36 |
| dhruv13 | HeikoS1: the same assumption was made in EuclideanDistance::distance() | 19:36 |
| HeikoS1 | dhruv13: well, ok then | 19:36 |
| HeikoS1 | although I dont like it | 19:36 |
| HeikoS1 | since its easy to check before | 19:36 |
| HeikoS1 | calling | 19:37 |
| dhruv13 | HeikoS1: oh, the nan i can change | 19:37 |
| HeikoS1 | Thats the same as checking for NaN | 19:37 |
| HeikoS1 | dhruv13: ok then, stay 64 bit | 19:37 |
| dhruv13 | I meant the float64_t assumption | 19:37 |
| HeikoS1 | otherwise its also annoying for the modular interfaces | 19:37 |
| HeikoS1 | RealEuclideanDistance, ShortEuclideanDistance, thats ugly | 19:37 |
| dhruv13 | so i will change the nan to throwing errors, and keep the CDenseFeatures<float64_t> | 19:38 |
| dhruv13 | is that fine? | 19:38 |
| HeikoS1 | yeah, thats good I think | 19:38 |
| dhruv13 | cool! I was worried that i was not being generic enough | 19:38 |
| HeikoS1 | dhruv13: maybe talk to somebody else about this, to get a second opinion | 19:38 |
| dhruv13 | was stuck with that for a couple of days :-( | 19:38 |
| dhruv13 | HeikoS1: okay... I' mostly looking at iglesiasg's implementation for Covertrees for inspiration | 19:39 |
| dhruv13 | HeikoS1: most of my interface assumptions come from there... I will test this and get a PR ready soon | 19:40 |
| dhruv13 | HeikoS1: Thanks a lot!! | 19:40 |
| PirosB3 | hey guys how do I run the unit test framework=? | 19:43 |
| PirosB3 | I do make test, but says "no target found"! | 19:43 |
| dhruv13 | PirosB3: go to $BUILD_DIR/tests/unit/ | 19:44 |
| dhruv13 | PirosB3: and run ./shogun_unit_test | 19:44 |
| PirosB3 | oh nice thx | 19:44 |
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| dhruv13 | PirosB3: do ./shogun_unit_test --help to check options | 19:44 |
| dhruv13 | PirosB3: you can filter the tests you want to run | 19:45 |
| PirosB3 | thx | 19:47 |
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| cameo54321 | HeikoS1: https://github.com/shogun-toolbox/shogun/issues/1998 | 20:18 |
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| dhruv13__ | wiking: are you there? | 20:37 |
| dhruv13__ | HeikoS1: are you free to answer something? | 20:39 |
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| thoralf | Hey everybody. | 20:46 |
| thoralf | PirosB3: Hey! | 20:47 |
| PirosB3 | hey thoralf :) | 20:47 |
| thoralf | PirosB3: I'll be here for appox. 30 minutes. If you want me to help, then now would be a good time. ;) | 20:47 |
| PirosB3 | thx | 20:49 |
| PirosB3 | so basically I was looking at the Parameters ticket | 20:49 |
| PirosB3 | i'll link it | 20:49 |
| PirosB3 | https://github.com/shogun-toolbox/shogun/issues/1972 | 20:49 |
| PirosB3 | and I was trying to understand the best way to handle this | 20:50 |
| PirosB3 | I would need to add a DataType | 20:50 |
| PirosB3 | I would also need to modify Parameters add_vector to be compatible with SGVector | 20:51 |
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| PirosB3 | and then do some changes in copy() | 20:52 |
| PirosB3 | and save | 20:52 |
| PirosB3 | is that the correct way of doing it? | 20:52 |
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| dhruv13__ | thoralf: can you help me out with something? | 20:54 |
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| thoralf | PirosB3: Don't you want to debug the memory issues in the other ticket first? ;) | 20:57 |
| thoralf | dhruv13__: Depends. | 20:57 |
| thoralf | dhruv13__: Just ask. ;) | 20:57 |
| PirosB3 | oh sure! thoralf did you pull down my branch | 20:57 |
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| PirosB3 | git remote add pirosb3 http://github.com/PirosB3/shogun.git | 20:58 |
| PirosB3 | git fetch pirosb3 feature/1868 | 20:59 |
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| PirosB3 | git checkout pirosb3/feature/1868 | 20:59 |
| thoralf | PirosB3: No, I will not pull your branch. Can you simply just try to run gdb or valgrind on your script and tell, if you can gather more information? | 20:59 |
| thoralf | No time to pull and compile everything, sorry. | 21:00 |
| PirosB3 | thoralf: I am having some issues with valgrind and mac | 21:00 |
| PirosB3 | I will try to virtualize it | 21:01 |
| PirosB3 | that's the only thing I can do | 21:01 |
| thoralf | PirosB3: Having proper tooling is important... isn't there a package for valgrind? | 21:01 |
| PirosB3 | yes, but it's full of issues on mac 10.7 unfortunately | 21:01 |
| PirosB3 | the idea is that I will virtualize everything | 21:02 |
| PirosB3 | thoralf: in get_confusion_matrix | 21:04 |
| PirosB3 | there is a memset | 21:04 |
| PirosB3 | memset(confusion_matrix.matrix,0,sizeof(int32_t)*num_classes*num_classes); | 21:04 |
| PirosB3 | where is that freed? is it up to us to free it? | 21:05 |
| thoralf | The freeing happens automatically. | 21:06 |
| lisitsyn | what memset has to do with free'ing ;) | 21:06 |
| PirosB3 | in fact | 21:07 |
| thoralf | We have a framework for this - it's done by SGRefObject. | 21:07 |
| PirosB3 | lol :) | 21:07 |
| thoralf | lisitsyn: :) | 21:07 |
| PirosB3 | shogun has it's own memory management correct? | 21:07 |
| thoralf | PirosB3: Calling SG_REF/SG_UNREF when we want to in-/decrement usage counters | 21:07 |
| PirosB3 | could that interfere with SWIG? | 21:07 |
| thoralf | When it's 0, then it will be freed automatically. | 21:07 |
| thoralf | PirosB3: I think SWIG handles this. | 21:08 |
| lisitsyn | yes | 21:09 |
| lisitsyn | well we tell swig to call our ref/unref | 21:09 |
| PirosB3 | thoralf: well then there is free called twice | 21:10 |
| PirosB3 | lol | 21:10 |
| PirosB3 | where is it! | 21:10 |
| lisitsyn | 5 %feature("ref") shogun::SGRefObject "SG_REF($this);" | 21:12 |
| lisitsyn | 6 %feature("unref") shogun::SGRefObject "SG_UNREF($this);" | 21:12 |
| thoralf | that't why we need this stacktrace. ;) | 21:12 |
| lisitsyn | PirosB3: src/interfaces/modular/SGBase.i | 21:12 |
| PirosB3 | you know what's funny lisitsyn, if I put a breakpoint just before get_confusion_matrix | 21:13 |
| PirosB3 | I can call it once (from debugger) | 21:13 |
| lisitsyn | what's going on? | 21:13 |
| PirosB3 | then I call it again, at I have the issue | 21:13 |
| lisitsyn | :D | 21:13 |
| lisitsyn | I do not understand the issue | 21:13 |
| PirosB3 | lisitsyn: the issue is that there is a double free | 21:14 |
| lisitsyn | where? | 21:15 |
| PirosB3 | when using the Python binding | 21:15 |
| PirosB3 | https://github.com/shogun-toolbox/shogun/issues/1999 | 21:15 |
| lisitsyn | PirosB3: uhm interesting | 21:18 |
| PirosB3 | also, is there no way to init_shogun in the modular bindings? it would be good to redirect the output | 21:18 |
| lisitsyn | PirosB3: not sure about that | 21:18 |
| lisitsyn | PirosB3: okay to resolve that please compile with debug and run valgrind over it | 21:19 |
| lisitsyn | it will be pretty clear | 21:19 |
| lisitsyn | I glanced over this method and can't see the error | 21:20 |
| lisitsyn | I wouldn't expect it is something with typemaps | 21:21 |
| lisitsyn | they are pretty good already so the error is somewhere else | 21:21 |
| PirosB3 | whoa... | 21:21 |
| PirosB3 | now it works | 21:21 |
| lisitsyn | haha | 21:21 |
| thoralf | Heisenbugs :) | 21:21 |
| PirosB3 | yeah but it's not stable | 21:21 |
| PirosB3 | how can this be stable | 21:22 |
| lisitsyn | race condition or whatever like that | 21:22 |
| PirosB3 | woohooo confusioon matrix works! | 21:22 |
| thoralf | Bebugging has side effects. | 21:22 |
| PirosB3 | lisitsyn: py is single threaded tho | 21:22 |
| PirosB3 | thats what I thought | 21:22 |
| lisitsyn | python is but not shogun | 21:23 |
| PirosB3 | do you want to see my confusion matrix! | 21:23 |
| PirosB3 | [[ 34 21 1 0 0] | 21:23 |
| PirosB3 | [ 28 438 159 0 0] | 21:23 |
| PirosB3 | [ 3 253 844 58 0] | 21:23 |
| PirosB3 | [ 0 0 3 63 9] | 21:23 |
| PirosB3 | [ 0 0 0 6 2]] | 21:23 |
| PirosB3 | :) sorry | 21:23 |
| lisitsyn | 5th class is pretty bad :D | 21:23 |
| PirosB3 | anyways, lisitsyn is shogun all OpenMP? | 21:23 |
| lisitsyn | no | 21:23 |
| lisitsyn | mostly pthread | 21:24 |
| PirosB3 | can I ask you a question regarding a task? | 21:24 |
| PirosB3 | i'll just ask | 21:24 |
| thoralf | Can I answer my questions myself? ;) | 21:24 |
| thoralf | Yes! | 21:24 |
| lisitsyn | hah | 21:25 |
| PirosB3 | https://github.com/shogun-toolbox/shogun/issues/1942 | 21:25 |
| PirosB3 | what is Q | 21:27 |
| PirosB3 | compute_statistic_and_Q | 21:27 |
| PirosB3 | (q statistic) | 21:27 |
| PirosB3 | (q test?) | 21:28 |
| lisitsyn | I guess that's some estimate on variance | 21:28 |
| PirosB3 | I think I really need to pick up a couple of books | 21:29 |
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| thoralf | PirosB3: Okay, since the memory problem is away now, please rename `test_multiclass_svm.py` to `predict_multiclass_svm.py` (or `multiclass_svm_predict.py`). And it should be done. But in order to try it myself, you can make a small comment on how to invoke and which shogun-data files to use as an example. | 21:29 |
| thoralf | Then it should be done. | 21:29 |
| PirosB3 | sure | 21:29 |
| PirosB3 | I'll add it into the ticket | 21:30 |
| lisitsyn | PirosB3: that's pretty narrow thing on these MMD deals | 21:30 |
| thoralf | PirosB3: If the memory issue comes back, I'll visit you at home and force you to fix it. :D | 21:30 |
| lisitsyn | so you probably should not care that much ;) | 21:30 |
| PirosB3 | ahaha, are you sure? it's cold over here! | 21:31 |
| thoralf | PirosB3: Where are you? | 21:31 |
| PirosB3 | Berlin is so much better | 21:31 |
| PirosB3 | UK | 21:31 |
| lisitsyn | what do you know about cold | 21:31 |
| thoralf | lol | 21:31 |
| thoralf | lisitsyn: +10 degree is pretty cold! :) | 21:32 |
| PirosB3 | lisitsyn: you probably know more about cold, but I know more about rain + cold + sudden change in temperature + humidity (all together) | 21:32 |
| thoralf | Haha. Rainman. :) | 21:32 |
| lisitsyn | yeah that's true | 21:32 |
| lisitsyn | here I just have it from -30 to +30 | 21:32 |
| dhruv13_ | india at this time of the year is +34... and don't get me started on humidity :-P | 21:34 |
| dhruv13_ | i really don't know cold :-( | 21:35 |
| PirosB3 | thoralf: pushed | 21:35 |
| PirosB3 | dhruv13_: I want to go to india so much | 21:36 |
| dhruv13_ | PirosB3: what parts? | 21:36 |
| dhruv13_ | PirosB3: india is huge! | 21:36 |
| PirosB3 | I have a really good friend in Punjab | 21:36 |
| lisitsyn | what do you know about huge | 21:36 |
| lisitsyn | :D | 21:36 |
| PirosB3 | I have an ex colleague from Kerela | 21:36 |
| dhruv13_ | lisitsyn: ha ha | 21:36 |
| PirosB3 | and I want to go to Ladakh | 21:36 |
| dhruv13_ | PirosB3: cool places! I want to go to ladakh too :-P | 21:37 |
| PirosB3 | it must be amazing.. | 21:37 |
| dhruv13_ | lisitsyn: where are you from? | 21:37 |
| PirosB3 | thoralf: do you want the instructions on a gist, or shall i just add them to the ticket? | 21:37 |
| lisitsyn | dhruv13_: from really huge country ;) | 21:38 |
| dhruv13_ | lisitsyn: Russia? | 21:38 |
| lisitsyn | exactly | 21:38 |
| dhruv13_ | cool! | 21:38 |
| lisitsyn | no idea who needs that huge area though :D | 21:38 |
| dhruv13_ | :D | 21:39 |
| dhruv13_ | we seem to need every inch of ours :-P | 21:39 |
| PirosB3 | ooh I did NYE with 3 russians | 21:39 |
| PirosB3 | that was cool | 21:39 |
| PirosB3 | actually 1 from belarus | 21:40 |
| lisitsyn | well he still could be russian | 21:41 |
| dhruv13_ | CDistance::get_lhs() should really be CDistance::get_lhs() const | 21:41 |
| lisitsyn | dhruv13_: actually yes | 21:41 |
| lisitsyn | we have this issue for well a long :) | 21:41 |
| PirosB3 | actually | 21:42 |
| PirosB3 | what I do not get | 21:42 |
| PirosB3 | is that these structures should be immutable | 21:42 |
| dhruv13_ | lisitsyn: causing a lot of problems for my adaptor... | 21:42 |
| PirosB3 | but then you have methods like Distance::init(CFeatures* l, CFeatures* r) | 21:43 |
| PirosB3 | remove_lhs_and_rhs(); | 21:43 |
| PirosB3 | shouldn't it return a new copy? | 21:43 |
| lisitsyn | they are not immutable | 21:43 |
| dhruv13_ | lisitsyn: is there a clean way to access feature vectors from distance objects? right now i have to assume i'm dealing with EuclideanDistance | 21:44 |
| PirosB3 | lisitsyn: shouldn't they be? | 21:44 |
| lisitsyn | PirosB3: they never intended to be ;) | 21:44 |
| lisitsyn | dhruv13_: you may get features from distance | 21:44 |
| lisitsyn | then get feature vector from features | 21:45 |
| dhruv13_ | lisitsyn: i mean feature idx's dim'th element | 21:45 |
| lisitsyn | PirosB3: immutability would be like a great change for whole library | 21:46 |
| lisitsyn | a bit too much :D | 21:46 |
| dhruv13_ | i'm doing distance->get_lhs()->get_feature_vector() in an inline function | 21:46 |
| lisitsyn | dhruv13_: oh I see | 21:46 |
| dhruv13_ | oh, do i have to unref the sgvector? | 21:46 |
| lisitsyn | why do you need to access some feature vector element? | 21:46 |
| lisitsyn | dhruv13_: on | 21:46 |
| lisitsyn | no | 21:46 |
| dhruv13_ | nanoflann integration, trying to crate an adaptor | 21:47 |
| lisitsyn | sgvector acts like a shared_ptr | 21:47 |
| dhruv13_ | okay | 21:47 |
| lisitsyn | sorry I am off for today ;) | 21:48 |
| lisitsyn | dhruv13_: what I can suggest is to try to avoid accessing that frequently | 21:48 |
| PirosB3 | ok see you | 21:48 |
| lisitsyn | so that you just get whole vector instead of accessing this vector in a loop | 21:49 |
| dhruv13_ | lisitsyn: bye! but I can't seem to find a work around | 21:49 |
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| dhruv13_ | lisitsyn: yeah, it's really bad right now... | 21:50 |
| thoralf | PirosB3: Just put the instruction on the ticket. | 21:50 |
| thoralf | PirosB3: Should be only 3 lines, right? | 21:51 |
| PirosB3 | 3 | 21:52 |
| PirosB3 | train, predict, evaluate | 21:52 |
| thoralf | Is there a suitable example multilabel file in data? | 21:54 |
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| dhruv13 | lisitsyn: hey! went offline for a while... can you think of a workaround? nanoflann calls this function quite often | 21:55 |
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| dhruv13 | thoralf: any ideas? | 21:58 |
| thoralf | dhruv13: Don't even know what this is about, sorry. | 22:00 |
| dhruv13 | thoralf: oh, sorry; i'm trying to access individual feature vectors from a distance object in an inline function | 22:01 |
| thoralf | dhruv13: No, not my domain, sorry. | 22:01 |
| dhruv13 | thoralf: okay :-) | 22:01 |
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| --- Log closed Sat Mar 15 00:00:25 2014 | ||
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