Open in new window / Try shogun cloud
--- Log opened Mon Jan 05 00:00:22 2015
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nszcetagreetings all03:57
nszcetaI have encountered a linker error
nszcetaon CentOS 703:57
@wikingi'm currently building shogun on centos7 w/o problems04:10
@wikingthis is how i run cmake: mkdir build && cd build && cmake -DENABLE_TESTING=ON ..04:11
@wikingand then i compile simpley with: make -j404:11
@wikingand then i just run the tests: ctest --output-on-failure -j204:11
@wikingnszceta: so i'm wondering what could b wrong on your side04:12
@wikingcould u tell me how u run cmake?04:12
nszcetasure thing04:12
nszcetamkdir build && cd build && cmake -DPythonModular=ON .. && make04:13
@wikingthat ran fine right?04:14
nszcetajust rm -rf'd build and I am doing it again to get output04:14
nszcetahere's what cmake has so far
@wikingok cool04:15
@wikingrun make now04:15
@wikingbtw you'll need to install some more packages on your distribution04:15
@wikingotherwise you'll miss most of the new features of shogun04:15
nszcetawhat would you recommend04:16
nszcetaI got atlas blas-devel... can't remember what else04:16
nszcetathat is EPEL04:16
@wikingi mean sorry i'm just suggesting04:16
@wikingu do what you really need to do04:17
nszcetawhat does Eigen bring to the table04:17
@wikingwe use eigen in most of our new implementations04:17
@wikingbasically anything that is deep learning, GP and some more04:17
nszcetawill install04:17
nszcetaI'm going to CTRL-C this make and get Eigen from EPEL before I go further04:17
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nszceta@wiking it's still not working04:48
nszcetawhat package do I need to compile from source?05:00
nszcetaweirdly enough I have double cblas_dnrm2(const int N, const double *X, const int incX); in /usr/include/cblas.h05:02
nszcetaso it seems like I already have the functions that error out during make05:02
nszcetanot sure what is going on here...05:03
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@wikingnszceta: ping?15:25
nszcetaI've been up since a few hours compiling ATLAS and LAPACK15:26
nszcetaeverything is still all ate up15:26
@wikingcompiling atlas?15:27
@wikingwhy didn't u install it with yum?15:27
nszcetadidn't work15:28
nszcetaI had it installed15:28
@wikingoh no15:28
nszcetashogun complained of missing symbols15:28
@wikingyeah but that could have fixed15:28
nszcetaanyway shogun cmake never ever detected ATLAS15:28
@wikinganother wahy15:28
nszcetao ok, I can remove the libraries I compiled15:29
nszcetawhat do you recommend15:29
@wikingso i have these package installed under centos715:31
* nszceta takes note15:31
@wikinglapack.x86_64                                3.4.2-4.el7                @base15:31
@wikinglapack-devel.x86_64                          3.4.2-4.el7                @base15:31
@wikingatlas.x86_64                                 3.10.1-7.el7               @base15:31
@wikingatlas-devel.x86_64                           3.10.1-7.el7               @base15:31
@wikingblas.x86_64                                  3.4.2-4.el7                @base15:31
@wikingblas-devel.x86_64                            3.4.2-4.el7                @base15:31
@wikingeigen3-devel.noarch                          3.2.2-1.el7                @epel15:32
@wikingbut of course if u want i can give you the full list of packages installed on that instance15:35
nszcetawiking thanks a lot for helping me out. I'll give you an update in a minute15:39
nszcetajust ran a $ sudo yum -y install lapack lapack-devel atlas atlas-devel blas blas-devel eigen3-devel15:40
nszcetaatlas is still not detected15:42
nszceta-- Could NOT find ATLAS (missing:  ATLAS_LIBRARIES)15:43
@wikingnszceta: what version of shogun r u trying to use15:43
nszcetaI do have /usr/lib64/atlas/
nszcetaand libsatlas and libtatlas15:43
@wikinghere's the cmake output:
nszcetaweird, it doesn't find ATLAS either15:44
@wikingnszceta: oh so you are saying that you are trying to use the src downloaded from the website15:44
nszcetaI downloaded shogun source15:44
nszcetawhat do you mean15:44
@wikingok so15:45
@besser82nszceta, add `-DATLAS_LIBRARIES=/usr/lib64/atlas/ -DATLAS_LAPACK=/usr/lib64/atlas/` to your cmake-command  ;)15:45
@wikingnszceta: use the latest version15:46
nszcetawhat do you mean latest version?15:46
nszcetagit master?15:46
nszcetabesser82 trying that out15:46
@wikingnszceta: git clone
@besser82nszceta, checkout from github15:46
@besser82nszceta, yes15:46
@besser82nszceta, and those additional switches for cmake  ;)15:47
nszcetaoh boy15:47
nszcetanothing like bleeding edge :D15:47
@wikingbesser82: no that should't be required for the git develop cmake anymore15:47
@wikingbesser82: it works out of box15:47
@wikingbesser82: on centos7 ;) see buildbot output15:47
shogun-buildbotbuild #2620 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at  blamelist: sanuj <>, Fernando Iglesias <>, Bj?rn Esser <>15:47
@besser82wiking, allrighty, ic  ;)15:47
nszcetaI thought you just showed me that wiking and it clearly says it doesn't see ATLAS15:48
nszceta-- Could NOT find ATLAS (missing:  ATLAS_LIBRARIES)15:48
nszcetain the build bot output15:48
@wikingnszceta: :D15:48
nszcetawhat's going on15:48
@wikingtrue :DDD15:48
@wikingbut still15:48
@wikingit works15:48
nszcetawtf lol15:48
@wikingok let's just try with the latest github15:49
@wikinggit version15:49
@wikingi think the errors you have is do to missing safeguards (macros) in the examples15:49
nszcetaok but we need to sort out ATLAS somehow also later15:49
@wikingnszceta: why? :)15:50
@wikingi mean yeah we need a fix for cmake15:50
@wikingbut trust me15:50
@wikingyou rather want eigen15:50
@wikingbecause we are slowly switching everything to eigen15:50
nszcetaI get that but how much is in eigen15:51
nszcetahow much in atlas15:51
nszcetaand also why eigen?15:51
@wikingmost of it is in eigen15:51
nszcetaisn't atlas really old and tried and true?15:51
@wikingnszceta: since it's a header only library15:51
@wikingyeah and it is requiring fortran15:51
@wikingand binary compiled libraries15:51
nszcetawhat's wrong with fortran lol15:51
nszcetaif it works...15:52
@wikingwhile eigen doesn't need anything15:52
nszcetaalright fair enough15:52
@wikingand that works for not only on x86 arch15:52
nszcetaATLAS only works on x86?15:52
@wikingi dont know if it has for example NEON optimization15:52
nszcetaalright I am building shogun with -j16 lets see how this works :D15:52
@wiking(see arm)15:52
@wikingi know that atlas has MMX, SSE2 optimization15:53
@wikingi assue they haven't done arm optimization15:53
@wikingso yeah eigen is lightweight but a bit more updated with current technologies15:54
@wikinglapack blas and all that is great15:54
@wikingbut it's a bit ancient....15:55
@wikingwhich is not bad... just sometimes having the zxcqy as a function name15:55
@wikingis driving u crazy15:56
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marinahappy new year everyone!16:04
marinaI want to execute the following code16:05
marinapm = PerformanceMeasures(labels_test, output); acc = pm.get_accuracy();16:05
marinathe problem is, that python could not find the method PerformanceMeasures...16:05
marinaI have already imported shogun.Evaluation16:06
marinaanyone who can help?16:06
@besser82guess who  :P16:06
nszcetaok it failed16:10
nszcetawiking same error16:10
@wikingnszceta: whooooooo whooo16:11
@wikingwe got to the impossible16:11
@wikingas the exact same thing works on my centos716:11
@wikingbesser82: care to elaborate here?16:12
nszcetasuggestions are welcome :D16:12
@besser82wiking, sure  :D16:12
@besser82nszceta, did you try my additional cmake-switches, yet?16:13
nszcetaabout to :D16:13
nszcetait found atlas with -DATLAS_LIBRARIES=/usr/lib64/atlas/ -DATLAS_LAPACK=/usr/lib64/atlas/libtatlas.so16:14
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shogun-notifier-shogun: Viktor Gal :develop * 276dd31 / src/shogun/lib/GPUMatrix.cpp,src/shogun/lib/GPUMatrix.h:
shogun-notifier-shogun: Fix a lot of indenting error and include <memory>16:21
shogun-notifier-shogun: we need to include <memory> for std::shared_ptr16:21
shogun-buildbotbuild #183 of trusty - libshogun - viennacl is complete: Failure [failed compile]  Build details are at  blamelist: Viktor Gal <>16:23
@besser82nszceta, allrighty then  ;)16:23
nszceta60% :D16:23
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travis-ciit's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun:
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@wikingoh motherfuckers16:24
nszcetaviktor breaking the builds......16:25
@besser82wiking, there is ladies inside the chan...  ;(16:27
shogun-notifier-shogun: Viktor Gal :develop * f59e2cf / src/shogun/lib/GPUVector.cpp,src/shogun/lib/GPUVector.h:
shogun-notifier-shogun: yet another indent fixing and memory include movearound commit16:28
shogun-notifier-shogun: in order to fix std::shared_ptr16:28
@wikingit'll be still motherfuckers16:28
nszcetaoh crap it might be working now16:28
nszcetacan we please add -DATLAS_LIBRARIES=/usr/lib64/atlas/ -DATLAS_LAPACK=/usr/lib64/atlas/ to the cmake find path16:28
@wikingnszceta: shogun magic :)16:29
@wikingwe should rather fix the cmake script i reckon16:29
@besser82wiking, who wrote it?  :P16:29
* wiking 16:29
@wikingdoes that mean that i have to fix it as well?16:29
@wikingisnt' this supposed to be an OSS project16:29
nszceta* shogun/cmake/FindAtlas.cmake16:30
@wikingnszceta: yep... actualy that is taken from some random oss project16:30
nszcetawtf shogun/src/shogun/lib/SGVector.h:57: Warning 503: Can't wrap 'operator std::complex< double >*' unless renamed to a valid identifier.16:31
@wikingnszceta: so that could be updated :)16:31
@wikingnszceta: dont worry about that16:31
@wikingbut if u worry about it, fix it plz16:31
@besser82wiking, lemme check for some updated version =)16:31
@wikingyou have all u need for it :)16:31
@wikingbesser82: thnx16:32
nszcetajust to recap16:32
nszcetaafter make I just run make install and that's that?16:32
@wikingnszceta: regarding what ?:)16:32
@wikingit all depends what u want16:32
nszcetainstalling shogun16:32
nszcetaI am in my python virtual environment16:32
@wikingthat shoudl do it16:32
nszcetai just need it to work with python16:32
@wikingoh virtual env16:33
@wikingthat's a totally different story16:33
nszcetaof course16:33
@wikingi mean if u want to have shogun within the virtenv16:33
nszcetaof course16:33
@wikingok if u know how to fix that16:33
@wikingsince then u need to ship the .so within the virtualenv16:35
@wikingnszceta: might i ask what's the usecase in your case for shogun/16:35
nszcetamachine learning systems for SemanticMD16:36
nszcetain particular we are interested in LMNN16:36
@wikingfor that it's not lmnn what u want16:37
@wikingbut that's my 2 cents16:37
@wiking(i did my phd recently on this topic)16:37
@wikingmost of the stuff i was doing within shogun was regarding that16:38
nszcetawe have been investigating using LMNN stacked with opencv16:38
nszcetaVery nice. I'm not experienced with ML but my team is.16:38
@wikingthat's only my 2 cents16:38
nszcetawhat is it about LMNN that makes you think it is not the best choice16:39
@wikingi've used it16:39
@wikingi mean i don't know what's your dataset size16:39
nszcetaalso for the record this worked: $ cmake -DPythonModular=ON -DATLAS_LIBRARIES=/usr/lib64/atlas/ -DATLAS_LAPACK=/usr/lib64/atlas/ ..16:39
@wikingbut lmnn will blow up your qp quite fast16:40
@wikingbut anyhow we'd be happy to hear if you are using shogun itself16:41
@wikingnote that it's still gplv316:41
shogun-buildbotbuild #184 of trusty - libshogun - viennacl is complete: Success [build successful]  Build details are at
@wikingthere was an initiative to switch to 3 clause bsd but that's still an ongoing operation16:43
nszcetait shouldn't be an issue at all16:43
@wikingwell it is for a lot of companies16:43
nszcetawe are strictly SaaS16:43
@wikingthat's why actually a lot of times it is not being used16:43
@wikingu dont see how that solves the licensing issue16:44
nszcetathe software is not being distributed16:45
@wikingyes but still you'll have to opensource the whole module that is linked to shogun16:45
@wikingor for that matter whatever gplvX code is being used..16:47
@wikingin an ideal case16:47
nszcetashogun will be linked to another module which produces output that is served by a web server and in such a case it does not matter what license is used16:48
@wikingit does16:49
@wikinga good read
@besser82wiking, not by meanings of "offer sources"16:49
@besser82wiking, since there are no binaries offered16:49
shogun-buildbotbuild #2621 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at  blamelist: Viktor Gal <>16:50
nszcetawiking where are you based out of?16:52
@wikingbased out of what?16:52
@wikingyou mean currently based at?16:53
nszcetajust curious which time zone you're working out of16:53
nszcetaUTC + 8 ?16:53
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@wikingnszceta: btw for lmnn u most def need eigen17:03
nszcetaeigen3-devel is installed :D17:03
nszcetaI saw the writing on the wall :P17:03
nszcetanow that there is a big push to eigen17:03
@wikingwell it's easy to depend on it17:04
nszcetathank god for ATLAS though17:04
@wikingas you can see the whole blas is very messed up17:04
@wikingespecially across linux distros17:04
nszcetabesser82 saved my ass on that :P17:04
nszcetacompiling ATLAS is redic17:04
nszcetathanks again17:07
shogun-buildbotbuild #953 of FCRH - libshogun is complete: Failure [failed test]  Build details are at  blamelist: Viktor Gal <>17:10
@wikingbesser82: any idea when this is going to b fixed in FCRH?17:11
@wikingi mean the json thingy17:11
@besser82wiking, working on it ^^17:11
nszcetawhat do you guys use shogun for?17:13
@wikingwell that's a good question17:17
@wikingwe are not aware of any other usage17:17
@wikingother than our own phds17:17
@wikingor masters17:17
@wikingsometimes we saw some ppl from thomsonreuters and yahoo17:18
@wikingbut we have no clue if it's actually being used and if yes on what exactly17:18
@wikinglisitsyn: merry xmas, btw:
@lisitsynwiking: heh17:29
@wikinglisitsyn: check fig 1 ;)17:30
@lisitsynwiking: ohh that's so past17:30
@wikinglisitsyn: :DDDD17:31
@lisitsynwiking: everything has changed17:31
@lisitsynwiking: crimea is taken, support is overwhelming17:31
@lisitsynwiking: I mean17:32
@lisitsynyou don't talk about elections here now17:32
nszceta99% of crimea is pro-russian17:32
@lisitsynit is just not an issue17:32
nszcetajk :P17:32
@wikinglisitsyn: :>17:32
@lisitsynthey found a way to control majority17:33
@wikinglisitsyn: so what' today's usd/rub17:33
@lisitsynI mean really educated and smart people are really like zombie nazis17:33
@lisitsynwiking: ~5917:33
@wikingstable then17:33
@lisitsynwiking: quite17:33
@wikingfor the last 3 weeks no? :)17:33
@lisitsynwiking: holidays till 11th17:33
@wikingyeah new year's is just about to come17:33
@lisitsynyeah russia is dead after new year17:34
@lisitsynjust consider there is no such country as it is totally passive17:34
@wikingwell the bear needs a sleep aswell :)17:35
@lisitsynnszceta: that's actually quite close to true :D17:35
@lisitsynwiking: usd/rub = 3600/(brent)17:35
@wikinglisitsyn: :D17:36
@lisitsynwiking: putin said the more roubles USD cost the more money we have17:36
@wikingmarina: where did u get this PerformanceMeasures(...) from ?17:36
@wikinglisitsyn: he is so true!17:36
@lisitsynwiking: zimbabwe is quite a rich country huh17:37
@lisitsyneverybody is a billionaire17:37
nszcetalisitsyn made my day17:37
nszcetaare you joking?17:37
@lisitsynnope ;)17:37
nszcetazimbabwean billionaires are poor17:37
@lisitsynbut they are billionaires! :D17:37
@wikingbut they are still billionaires :)17:37
nszcetano, look17:37
@wikinglisitsyn: we used to have that though...17:38
@lisitsynyeah I am kidding ;)17:38
nszceta100 trillion dollar bill :D17:38
@wikinglisitsyn: 10E1217:38
@wikingi think i still have a copy somewhere in the attick :)17:38
nszcetathey couldnt fit more zeros on the bill so they threw in the towel17:38
@lisitsynit is quite difficult to pay some tips there I guess17:38
nszcetajust throw down 400 trillion dollars17:39
nszcetashould be enough for a tip17:39
@wikingoh noooo17:39
@wikingwe had 5E11 :)17:39
@lisitsynso you go to some restaurant17:39
@lisitsynorder some stuff17:39
@lisitsynand while you eat it gets another zero17:40
@wikinglisitsyn: yep that was the case17:40
@wikinglisitsyn: till u got from the bank to the black market exchange17:40
@lisitsynactually usd/rub was similar17:40
@wikingyour montly salary went down to be enough to buy 2 bread and some milk17:40
@lisitsynpeople were rushing to local exchanges17:40
@wikingheheh yeah usual shit17:41
@wikingmarina: we dont have PerformanceMeasures anymore... it was deprecated around 200917:41
@lisitsynperformance measure hmm17:41
@lisitsynI think I wrote something about that17:42
@lisitsynhahha zero obama17:42
@wiking420 would have been more classy17:42
@wikingnm :)17:42
@lisitsynhah this pic is fascinating17:43
@lisitsynthis fuel empty :D17:43
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@lisitsynwiking: must end with some anal control system17:46
@lisitsynwiking: may be like that
@wikingok so this commit17:54
@wikingi mean this commit:
@wikingsupposed to be responsible for 2 leaks + uninited memory in shogun :D17:55
@wikinghow :17:55
@wikingah ok no17:56
@wikingit's actually a differnt fail17:56
@wikingso this one17:57
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shogun-buildbotbuild #179 of osx2 - modular_interfaces is complete: Failure [failed csharp modular]  Build details are at  blamelist: Viktor Gal <>18:04
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shogun-buildbotbuild #508 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at  blamelist: Viktor Gal <>20:29
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--- Log closed Tue Jan 06 00:00:23 2015