IRC logs of #shogun for Friday, 2016-05-13

« Thursday, 2016-05-12 Index Saturday, 2016-05-14 »
--- Log opened Fri May 13 00:00:53 2016
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@HeikoSwiking: jo07:43
@HeikoSSaurabh7: jo07:44
@HeikoSarianepaola: jo07:44
@HeikoSlisitsyn: hi07:44
@wikinghelo08:04
@wikingwtf r u doing up at 6:42am :>08:04
@HeikoShehe08:25
@HeikoSI was up 5am08:25
@HeikoStravelling for work08:26
@HeikoSnorth england08:26
@HeikoSmeeting time 1030 gnaaa08:26
@HeikoSwiking: whats the time for you atm?08:26
@wikingHeikoS: i'm still in eu08:37
@wikingfor another 3 weeks08:37
@wikingthen i'm back to sg08:37
@HeikoSI see08:37
@HeikoSwhy were you up so early08:37
@wikingi wake up with the sun08:38
@wiking:)08:38
@HeikoSwiking: hehe08:38
@wikingno joek :)08:38
@wikingit's a shit here in eu08:38
@wikingbecause the sun comes up at 5am08:38
@HeikoSI like that08:38
@wikingsg it's a stable 7am08:38
@wikingso that's ok08:38
@HeikoSI need light in my face for at least an hour before my body can start ;)08:38
@wikinghahahah08:38
@wikingyeah you live in england08:38
@wiking:))))))))))08:38
@wikingbtw when you come to sg visit ? :)08:38
@HeikoShehe08:38
@wikingdo this08:39
@HeikoScool08:39
@HeikoSwould love to08:39
@HeikoSwhen is good?08:39
@wikinganytime08:39
@wikingjust not this xmas08:39
@HeikoShehe08:39
@wikingbeause then we are off to nz08:39
@wikinghttps://fellowships.data.gov.sg/08:39
@HeikoSand not before 7am08:39
@HeikoShaha08:39
@wiking^ HeikoS do this08:39
@HeikoSwhat is that?08:39
@wikingit's a 3+ month08:40
@wikingfellowship in sg08:40
@HeikoSay cool08:40
@wiking"Expertise in computer and social sciences, software development, data science, UI/UX design, or technology (wireless and sensor networks, ICT and cybersecurity, Internet of Things)"08:40
@wikingthey'll pay you everything08:40
@HeikoScool idea in fact08:40
@wikingso come over for 3 months :P08:40
@wikingwhile i'm tehre08:40
@HeikoShow are you there fore?08:41
@HeikoSand what is nz?08:41
@wikinghttps://scontent-vie1-1.xx.fbcdn.net/t31.0-8/12314291_1027579657265195_2268379013512691573_o.jpg08:41
@wikingif you come in time we can go with my boat a ride :P08:41
@wikingnz = new zealand08:41
@wikingi'm there because my partner is doing her phd ther08:42
@wiking*there08:42
@HeikoSah man amazing the boat08:43
@HeikoSah cool, heard it is a nice place08:43
@wikingso i'm off for xmas there08:44
@HeikoSok08:44
@wikingbut i'm back in jan08:44
@wikingso you can come any other time basically08:44
@HeikoSso autumn it has to be08:44
@wikingwe have a guest room as well08:44
@wikingyou can come next spring as well08:44
@wiking:)08:44
@HeikoSmaybe I'll come for a visit trip fist08:44
@HeikoScool man, appreciated! :)08:44
@wikingHeikoS: ideas where to place the cluster?09:20
@wikingi was thinking to have it in the ireland centre of aws09:20
@HeikoSmmmh09:21
@HeikoSrationale?09:21
@wikingwell it is still eu09:21
@HeikoSmaybe the one that people like most?09:21
@wikingbut has good connectivity to the us09:21
@wikingi dont wanna host the thing in usa :)09:21
@HeikoSyeah I see that09:21
@HeikoSso yes fine then09:21
@HeikoSgermany also ok09:21
@HeikoSstrong privacy there09:21
@wikingwe can move it there as well09:22
@wikinganyhow09:22
@wikingfirst i need to figure out09:22
@wikingwhy we cannot have instances atm in ireland09:22
@wikingor german09:22
@wikingy09:22
@wiking:)09:22
@HeikoShehe I see09:22
@HeikoShey btw, what is the state of the file io stuff09:23
@HeikoSjust asking, not pushing :)09:23
@HeikoSbtw sonney has got the ltter from foundation09:23
@HeikoShe needs to go to notar and sign it with him09:23
@HeikoSwe need to push him09:23
@wikingcool09:23
@wikingyeah i have a local commit09:23
@wikingbut that needs fixing09:23
@wikingstill09:23
@wikingi refactored the whole thing09:23
@HeikoSwiking: serious fixing or just glitches?09:23
@wikingnono it's a full refactor09:24
@wikingbecause the thing was getting out of hand09:24
@HeikoSok09:24
@HeikoSno wait, I mean what fixing does it still need09:24
@wikingah09:24
@HeikoSlike how much work needs to be done on nit?09:24
@wikingin the output format09:24
@wikingi need to fix a buffering mechanism09:24
@wikingbecause currently it can only read with this09:24
@wikingwe dont operate anymore on FILE*09:24
@wikingwe have CFile09:25
@HeikoSok09:25
@wikingthat has write/read09:25
@wikingand we have Codec09:25
@wikingthat is basically the parent of all output formats09:25
@HeikoSso that sounds messy ;)09:25
@HeikoSjust wondering how to manage time wise with OXPHOS09:25
@HeikoSbecause she should look at this stuff soon09:25
@HeikoSmaybe already push into feature branch so that she can read?09:25
@wikingyep yep09:26
@HeikoSwhile you are doing the aws?09:26
@wikingthat was the plan09:26
@wikingbut it's still a messy state09:26
@HeikoShehe09:26
@wikingshe doesn't really need to take care of any IO stuff09:26
@HeikoSdont use swearwords in comments ;)09:26
@HeikoSok then09:26
@HeikoSthen its not important to do that09:26
@wikingwhy? :)09:26
@HeikoShaha ,)09:26
@HeikoSgrep "fuck off" in NEWS09:27
@wikingiss there? :)09:27
@wikingnoup09:27
@wikinggit grep says nothing for "fuck off"09:27
@HeikoSah09:27
@HeikoSnot there anymore?09:27
@HeikoSlet me investigate ;)09:27
@HeikoSnot there anymore indeed09:28
@HeikoSthere used  to be a "fuck off sören" in there09:28
@wiking:DDDDDDDDDDDDDD09:28
@HeikoSby this guy who wrote the serialization stuff09:28
@HeikoSand then somehow turned evil09:28
@wikingwho wrote the serialization stuff?09:29
@HeikoSand threatened shogun leagally to remove some code he wrote in his spare time09:29
@HeikoSyeah09:29
@wikingman we need to prepare so many images for aws09:31
@wikinglike09:31
@wikingfedoraXX, centos6-7, ubuntu..., debian...09:31
@wikinggood that half of that can be automated09:31
lisitsynin the danger of sound stupid09:32
lisitsynwhat's the plan with aws09:32
@wikingmove buildbot there09:32
@wiking+ bring back shogun-cloud09:32
@wikingand then the current machines can run benchmarks09:33
@wikinginstead of builds09:33
@HeikoSlisitsyn: build a spambot to your email ;)09:33
@HeikoScloud will be cool09:33
lisitsynthat's ok I stopped reading mail already09:33
@HeikoSlisitsyn: haha09:34
@wikingbut cloud needs rewamp09:34
@HeikoSlisitsyn: btw when are you coming to london?09:34
@wikingbecause i would start adding support for jupyter09:34
@HeikoSlisitsyn: remember we planned that09:34
@HeikoSwiking: yep !09:34
lisitsynI was reading a self-help book recently and it says it is okay to not answer mails09:34
@HeikoSwiking: you can also come09:34
lisitsynand I was like ooh I am a cool guy09:34
@HeikoSrahul is there09:34
@HeikoSso we can have a hackathoin09:34
@HeikoShe stays 2.5 more months09:34
@HeikoSany time slots for you guys?09:34
lisitsynnot sure now09:34
@wikingnot me09:35
@wikingi'm going back to sg on the end of this month09:35
@wikingasedf fucker aws09:35
@wiking3rd instance09:35
@wikingthat doesn't ping09:35
@wiking\o/09:35
lisitsynI could be coming to nips on my own so not sure I can handle both london and barcelona09:35
@wikingbut an instance for 0.02 usd/hour09:36
@wikingthat 16k will last long09:36
@wikingalthough we can only have it for 1 year09:37
@wikingso lets mine some bitcoin09:37
@wikingany objections?09:37
@HeikoSwiking: hehe :)09:37
@HeikoSlisitsyn: nips?09:37
@HeikoSah yes09:37
@HeikoSbut that in dec man09:37
@HeikoSI am talking July09:37
lisitsynyeah but I am in the poorest oil country :D09:37
@wiking:D09:38
@wikingisn't that iraq?09:38
@HeikoSlisitsyn: you can stay at my place09:38
@HeikoSjust need flight09:38
lisitsynHeikoS: ok I'll think09:39
@HeikoScome over a long weekend or so09:40
@wikingamazing new spams09:42
@wikingHello, my name is Miss Jovita Gomez, I saw your profile email at github.com I am interested in having a good friendship with you. I'll tell you more about me and send my pictures to you as soon as you reply to my email.(jovitagomez120@hotmail.com) I'll be waiting for your mail soon. Honestly Jovita.09:42
@wiking:>09:43
@HeikoSwiking: how/where do you do the aws images?09:43
lisitsynHeikoS: is it like anytime now as you all are there?09:43
@HeikoSlisitsyn: more or less09:43
@HeikoSI am away a few days here and there09:43
@HeikoSbut anytime for the next 2.5 months in general09:43
@HeikoSwiking: hahaha09:43
@wikingHeikoS: packer.io09:43
@HeikoSwiking: cool09:43
@wikingit'll get into shogun-infra09:43
@wikingbut now we have some problemos09:43
@HeikoScool, looking forward to see that09:43
@wikingwith the limitations of aws09:44
@wikingi've fired a request09:44
@wikinglets see how long it'll take them to reply09:44
@HeikoSyou already broke it? :D09:44
@wikingnono i mean09:44
@wikingwe had 0 slots09:44
@wikingof running any instance09:44
@wikingin ireland09:44
@wikingfor god knows what reason09:45
@wikingok i give up09:45
@wikingi've tried to bring up a fucking m4.large09:45
@wikingwith ubuntu 16.0409:45
@wikingfor the 4th time09:45
lisitsynwiking: github friendship is magic09:50
@wikinglisitsyn: :d09:51
lisitsynwiking: recvd it as well09:51
@wikinghahahaha09:52
@wikingpworked the first instance09:56
@wikingfuck09:56
@wiking:)09:56
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@HeikoSlisitsyn: btw I have a questions regarding plugin10:01
lisitsynyes10:01
@HeikoSlisitsyn: are there any plans for the "base interface"10:01
@HeikoSthat is which methods are in shogun's swig interface?10:01
lisitsynHeikoS: yes wiking and I asked sanuj just yesterday or so10:01
lisitsynto have a gist10:01
@HeikoSlisitsyn: to draft one10:01
lisitsynHeikoS: https://gist.github.com/sanuj/56f03cd242473137fad851e68fa0f2c110:02
lisitsynyes10:02
lisitsynthis is it10:02
@HeikoSsince it is a chance to re-work our supervised interfaces10:02
@HeikoSbetter structure10:02
lisitsynyeah it would enforce better structure10:02
@HeikoScool10:02
@HeikoSwill comment10:02
@HeikoSthanks10:02
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arianepaolaHi HeikoS15:30
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travis-ciit's lambday's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/13000457116:52
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@HeikoSSaurabh7: around?18:16
Saurabh7HeikoS: hi !18:20
Saurabh7HeikoS: i saw your comment about modelselection18:33
@HeikoShi18:33
@HeikoSyeah18:33
@HeikoSso we need a plan18:33
@HeikoSwith concrete findings18:33
@HeikoSmore than the proposal18:33
@HeikoSmore concrete18:34
Saurabh7I was wondering how much the new plugin thing will affect the framework18:34
@HeikoSmore technical18:34
@HeikoSdoesnt matter for now18:34
@HeikoSmore important is to make it multicore for now18:34
Saurabh7ok18:34
@HeikoSthis requires some thinking about thread safety18:34
@HeikoSmaybe start with a kernel svm?18:34
@HeikoSthis requires the subset on features to be thread safe18:34
@HeikoSi.e. one needs to register a subset and then access via an identifier18:35
Saurabh7sure18:35
Saurabh7but we ned thread safe views18:35
Saurabh7yes18:35
Saurabh7last  discussion i remember there was something like a shallow copy and adding subset18:35
@HeikoSdo you need help with that?18:35
Saurabh7and a method create_view for features18:35
@HeikoSnot yet views (also need those), but let's start with making the thing we have work18:36
@HeikoSthis will teach us a bit on how to do it18:36
@HeikoSand then we can do more sophisticated18:36
@HeikoSthe point is:18:36
@HeikoSdata should not be doubled in memory18:36
@HeikoSand if the kernel matrix is pre-computed, this should also not be duplicated in memory18:36
@HeikoSfurthermore18:36
@HeikoSx-validation should be cache friendly (currently it is not) -- this is even true before we start doing things in parallel18:37
@HeikoSmaybe that is a good start?18:37
@HeikoSto find out how bad it is? :D18:37
Saurabh7ok so the kernel matrix will differ by alogirthm right18:37
Saurabh7i mean different algos will ahve diffrent compuattions that need not be duplicated18:37
Saurabh7ok so you think we should start with one ?18:38
@HeikoSyes18:38
@HeikoSbut it illustrates the issues of doing things multicore18:38
@HeikoSso it is a good one to start with18:38
@HeikoSsee what I mean?18:38
@HeikoSas in: some data structures will be shared along model selection18:39
@HeikoSx-validation18:39
Saurabh7yes and those should be thread safe18:39
@HeikoSstep1: make x-validation on a kernel machine work (without precomputed kernel matrix)18:39
@HeikoSthis involves making the subsets thread safe18:39
@HeikoSstep2: make it work with precomputed kernel matrix18:39
@HeikoSstep3: make bagging machine work with the thread safe subset features18:40
@HeikoSall required for gsoc18:40
@HeikoSbut for the draft: we can start with step 118:40
@HeikoSand find out what we can gain there18:40
@HeikoSstep0: make x-validation cache friendly18:40
@HeikoSthat is first in fact18:40
@HeikoScan you add those points to the doc and fill them with details?18:40
Saurabh7alright18:40
@HeikoSbtw is there a benchmark on x-validation in the mlpack framework18:41
Saurabh7yes i have added points i will ad these details there18:41
@HeikoSrcurtin: ^18:41
@HeikoSSaurabh7: cool18:41
@HeikoSand for the toher algos18:42
@HeikoSit would be good to have some kiund of summary of which algos are slow and what causes it, i.e. profiler information18:42
@HeikoSor benchmarks in mlpacks lib18:42
Saurabh7i might need help with cache i will ask as i come accross18:42
Saurabh7so i have to profile to understand the implications ?18:42
@HeikoSdoesnt need to fix things now, but the WHY is important18:42
@HeikoSSaurabh7: yeah definitely18:42
@HeikoSwhats interesting in profiling:18:42
Saurabh7HeikoS: i dont think there xvalidation in the framework18:43
@HeikoSa) which calls is most time spent on (we are interested in overhead here)18:43
@HeikoSb) what is the fraction of cache misses18:43
@HeikoSSaurabh7: yeah that would be bets18:43
@HeikoSc) where can we parallelise18:43
@HeikoSc) is independent of profiler, can can mostly be answered with looking at implementation18:43
@HeikoS?18:44
@HeikoSah I see18:44
Saurabh7yes i was using callgrind thats how i came across the linalg::dot thing :D  but havent looked at the cache miss thing18:44
@HeikoSSaurabh7: ok then, profiling is needed then18:44
Saurabh7yet18:44
@HeikoSits just another statistic18:44
@HeikoSnbut you need to isolate the particular part of the program18:44
Saurabh7yup wasnt aware of it much18:44
@HeikoSI expect speedups up to one order of magnitude18:44
@HeikoSSaurabh7: ok that also added to plan18:45
@HeikoSSaurabh7: then whats next?18:45
@HeikoSyou were talking about the random forests a while ago18:45
@HeikoSwhat is the matter there ?18:45
Saurabh7hm they require the same thread safe views to parallelize18:46
Saurabh7after that it should be straight forward18:46
@HeikoSi see cool18:46
@HeikoSSaurabh7: also would be good to profile them18:47
@HeikoSdecision trees can be optimized a lot even single core18:47
Saurabh7HeikoS: but other decision tree implementation id3, cart etc did look well in comparison18:47
Saurabh7so that maybe another thing to add to test18:48
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@HeikoSSaurabh7: sorry got disconnected ,)18:49
@HeikoSin train atm18:49
Saurabh7wifi in train, one day i enjoy it too :)18:49
@HeikoShehe18:49
Saurabh7HeikoS: but other decision tree implementation id3, cart etc did look well in comparison18:49
@HeikoSfirst class only18:49
Saurabh7didnt *18:49
@HeikoSSaurabh7: also profile it18:49
@HeikoSthe thing I recently realized is: you should always pass through the data linear in memory18:50
@HeikoSand then check what to do with it18:50
@HeikoSrather than letting the algorithm decide the order in which you pass18:50
@HeikoSso that should be made sure18:50
@HeikoSand it will reduce the cache misses18:50
@HeikoSyou should also check this for the kmeans we have18:50
@HeikoSSaurabh7: what is great about all this is: it cannot really be done in Python18:51
Saurabh7yup i was thinking about it18:51
@HeikoSso we can win big time18:51
Saurabh7but how to ensure it passes linearlly ?18:51
Saurabh7that would depend i guess18:52
@HeikoSfor (auto i=0 ..... )18:52
@HeikoS   do something with X[i]18:52
@HeikoSyou will need to precompute something for that18:52
@HeikoSfor kmeans, e.g. that would be in which cluster X[i] currently is18:52
@HeikoSand then do the corresponding thing18:52
@HeikoSanother idea is to always sort indices so that they ressemble the data structure in memory18:53
@HeikoSSaurabh7: do you see what I mean?18:54
@HeikoSsay you need to touch all data (as e.g. in x-validation)18:54
@HeikoSand you have some vector of indices18:54
@HeikoScall it perm18:54
@HeikoSthen you can do18:54
Saurabh7HeikoS: yup i get the idea18:54
@HeikoSfor (auto i=0 .....)18:55
@HeikoS    do something with X[perm[i]]18:55
@HeikoSfor18:55
@HeikoSor18:55
@HeikoSfor (auto i=0 .....)18:55
@HeikoS    do something with X[i]18:55
@HeikoSsuch that the second is equal to the first18:55
@HeikoSin x-validation, sorting the combined folds is e.g. an idea18:56
Saurabh7ah so whatever you have in that fold its good to have them in an order18:57
@HeikoSyes exactly18:57
@HeikoSSaurabh7: BUT18:58
@HeikoSthat has to be benchmarked18:58
@HeikoSand compared18:58
@HeikoSand that needs to be in the plan before GSoC start18:58
@HeikoSs18:58
@HeikoSthen optimizing it is part after the 22nd18:58
@HeikoSthis is what I mean by spelling out the details18:58
Saurabh7HeikoS: right , i will try a minimal example with kernel svm then18:59
@HeikoSgreat19:00
@HeikoSthis is much about exploring the problem and learning what we can do19:00
@HeikoSbecause after GSoC we want it to be as close as possible to  being optimal19:00
@HeikoSso that we are faster than python implementations19:01
@HeikoSand its a useful skill ;)19:01
Saurabh7we deifnelty want that :)19:01
@HeikoSI mean you saw the table in the slides I sent19:02
@HeikoSlots to gain19:02
@wikinggimem table19:02
@wikingHeikoS: ^19:02
@HeikoSwiking: qualitative, but will send it19:03
@wikingk19:03
@HeikoSinternal talk at gatsby I did19:03
@HeikoSon this sequential stuff19:03
@HeikoSdid some benchmark on my laptop19:03
@HeikoSthe cache actually killed one of my supervisors nips paper ;D19:05
rcurtinHeikoS: no cross-validation in mlpack19:05
rcurtinwould be cool but nobody has done it19:05
@wikingHeikoS: :D19:05
@HeikoSrcurtin: ok Saurabh7 might help there if we find time19:05
@HeikoSwiking: rahul pulled that, pretty cool19:05
@wikingcool19:06
@HeikoSreduced mem from D^2 to D and is 10 times faster than my old c code19:06
@HeikoSstarted with this idea of only visiting data once and do the rest from there19:06
@HeikoSonly possible in that algo though19:06
@HeikoSbut good example19:06
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@wikingshogun-buildbot: force build --branch=develop 'CentOS7 - libshogun'22:05
shogun-buildbotThe build has been queued, I'll give a shout when it starts22:05
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@wikingshogun-buildbot: force build --branch=develop 'CentOS7 - libshogun'22:07
shogun-buildbotThe build has been queued, I'll give a shout when it starts22:07
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@wiking\o/22:26
@wikingfirst aws spot instance based build is on its way22:26
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-!- mode/#shogun [+o HeikoS] by ChanServ23:21
--- Log closed Sat May 14 00:00:55 2016
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