IRC logs of #shogun for Tuesday, 2013-05-07

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--- Log opened Tue May 07 00:00:34 2013
pickle27this is what I get now: http://pastebin.com/LHqAyAUv01:30
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@wikingsonney2k: yo11:52
@sonney2kwiking, what?12:33
@wikingsonney2k: ok so i didn't get it the last day12:34
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@wikingsonney2k: about unit testing random12:34
@wikingsonney2k: can i have a test in unit tests where i read a data from data submodule?12:34
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@wikingsonney2k: or that should rather be the part of integration test?12:34
@sonney2kwiking, don't you think generating say 10 numbers and keeping them in ascii as unit test is sufficient?12:37
@sonney2kor even generate 2x 10000 numbers with same seed12:37
@sonney2kcompare that they are the same12:37
@sonney2kand check if the 10000th number is the same12:37
@wikingsonney2k: ah nono12:40
@wikingsonney2k:  i mean what i do now is this12:40
@wikinghttp://pastebin.com/xL6S0Lpc12:40
@wikingthis will generate the same numbers12:40
@wikingthe only 'problem' is that this does not test the arch/os independency12:41
@wikingas for sure these 2 vectors are going to be the same12:41
@wikingbut they are not testing whether they are the same when it's on a different machine ;P12:41
@wikingi mean different os/arch12:41
@wikingshould be of course ... :P12:42
@wikingas the implementation is the same :)12:42
@wikingbut then again we should have a test for this12:42
@wikingbut we can do that then in the integration test12:42
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@sonney2kwiking, yeah but if you just store the 10000th number - in some const then you have your test12:53
@wikingsonney2k: well that's another option as well12:56
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thoralfWhatever I do, shogun never stops throwing "*** glibc detected ***", "double free or corruption (!prev)".13:27
thoralfgdb tells me the pointer - is there a way to find out, where this pointer has been allocated?13:27
thoralfUsing valgrind, gdb, etc.?13:27
@wikingthoralf: valgrind it13:33
thoralfwiking: It's a heisenbug. ;)13:35
thoralfwiking: Valgrind does not tell me - instead it says "Address 0xb092b68 is 0 bytes after a block of size 8,184 alloc'd" (in foreign code)13:36
@wikingwell13:37
@wikingwith gdb and valgrind you pretty much can find any such bug13:37
@wiking;)13:37
thoralfwiking: This claim needs proof... ;)13:41
@sonney2kthoralf, compile w/o optimizations enabled then you will see :D13:43
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thoralfsonney2k: I already compiled with --disable-optimization --enable-debug -O0 -g, etc. ;)13:44
@sonney2kthoralf, then you are running multithreaded Iguess13:44
@wikingthoralf: this claim has been proven by u running an OS13:45
@wiking;)13:45
@wikingthat has mouse, keyboard, screen, gpu etc13:45
thoralfsonney2k: Yes, looks like.13:47
thoralfHow to turn threading off?13:47
thoralfWill mkl->parallel->set_num_threads(1) be enough?13:49
thoralfOkay, seems so.  But at lease it did not change errors.13:50
@sonney2kthoralf, how/when are you getting these double frees?14:04
@sonney2kwith streaming features?14:04
thoralfYes.14:06
@sonney2kargh14:06
@sonney2kyes that's all multi threaded14:06
@sonney2kthere is one thread reading in data14:06
@sonney2ktrying to keep some buffer full14:06
@sonney2kand another doing the learning14:07
thoralfsonney2k: It seems that "anyone" frees the .features in sparsevectors.14:07
thoralfsonney2k: Copying all vectors seems to fix the double-frees, but introduces bigger leaks...14:08
@sonney2kthoralf, when we did the conversion from e.g. double* vec, int vec_len -> SGVector14:08
@sonney2kwe didn't manage to finish this for everything yet14:08
@sonney2kIIRC SparseFeatures still uses no SGSparseMatrix14:09
@sonney2kwhich it should14:09
thoralfsonney2k: I've been filling SGSparseMatrix by myself - with vectors from get_vector() ;)14:10
@sonney2kno wonder then14:10
thoralfsonney2k: So what's the intended use of the sparse vectors from get_vectors()?14:13
thoralfAm I supposed to copy them?14:13
thoralfcopy as-in deep copy14:13
@sonney2kthoralf, *intended* is that you create / get a sparse vector and use it / pass it around14:17
@sonney2kfreeing is done automagically14:17
thoralfsonney2k: Okay, that's what I did.14:18
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thoralfExcept that freeing is done automagically by someone else. ;)14:18
@sonney2kthoralf, yeah streaming features I guess14:19
thoralfsonney2k: Yes, maybe it's related to this example buffer?14:19
thoralfsonney2k: I initialized the example buffer to 1024 examples - are they freed or reused?14:20
@sonney2kthoralf, well each example is a separately allocated14:21
@sonney2kso it is just a list with 1k examples14:21
@sonney2kand for sure they will be freed once you are done with them14:21
@sonney2kthoralf, let me explain in detail how it is supposed to work once transitioned to the SG* structures:14:23
@sonney2kthe SGVector (or SGSparseVector etc) structures keep an internal reference count14:24
@sonney2kso whenever you do SGVector x = y;14:24
@sonney2kand y is some SGVector too14:24
@sonney2kthen we only copy references and size of the vector14:24
@sonney2kto decrease refcount one needs to do14:25
@sonney2kx=SGVector()14:25
@sonney2kwhich will then assign an empty vector to x14:25
@sonney2kdecreasing the refcount for y again14:25
@sonney2kand if y is no longer used14:26
@sonney2kit will be destroyed too14:26
@sonney2know I guess you are seeing things like someone manually SG_FREE'ing the vector14:27
@sonney2kand then it will later be destroyed -> boom14:27
thoralfsonney2k: Yeah, thats what I'm thinking.14:27
@sonney2kthe correct fix is difficult :/14:28
@sonney2kmaybe you can put NULL to the sgvector after the SG_FREE14:28
@sonney2kas workaround14:29
@sonney2kbut you might suffer from an even more subtle situation:14:29
@sonney2kconsider you want to have an array of SGVectors14:30
@sonney2kSGVector x[17];14:30
@sonney2kthat is all good14:30
@sonney2kbut SGVector* x = malloc (...);14:31
@sonney2kyou get a kaboom14:31
@sonney2kb'cause it needs the inplace new[]()  - otherwise the constructor of sgvector is not called14:31
@sonney2kand some stuff like refcount is not initialized14:31
@sonney2kI tried to make this automatic by using SG_MALLOC - and for that malloc for SGVector is overloaded to call new[]14:32
@sonney2kit is not ideal but I don't see a better way14:33
lisitsynsonney2k: it doesn't look normal to have SGVector*14:40
thoralfsonney2k: shogun/io/streaming/ParseBuffer.h, finalize_example(), SG_FREE is called on ex_ring[i].fv.vector; the same fv.vector, has been passed to InputParser.h, which passes CStreamingSparseFeatures<T>::get_next_example() and current_vector.14:42
thoralfsonney2k: The same reference then gets into SGSparseVector... q.e.d. ;)14:42
@sonney2kthoralf, yeah14:42
@sonney2kthoralf, if we would rewrite this to use14:43
thoralfsonney2k: But I don't know how to fix ;)14:43
@sonney2ksome SGSpareseVector buf[1024]14:43
@sonney2kthen no more free is needed14:43
@sonney2kbut just a buf[10]=SGSparseVector()14:43
@sonney2kto decrease the refcount of vector 1014:44
thoralfsonney2k: current_vector is SGSparseVectorEntry<T>*14:44
@sonney2kthat has to be refactored14:44
@sonney2kit needs to become14:44
@sonney2kSGSparseVector14:44
thoralfsonney2k: in fact, current_vector is redundant, since it's the same as current_sgvector.features (only after calling get_vector())14:46
@sonney2ksounds like14:46
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thoralfsonney2k: But in any case we need to copy the contents of current_vector, since ParseBuffer seems to take care of it (including deallocation).14:51
@sonney2kthoralf, doesn't hurt - comparing this copy to a read from disk is like 1000 times faster14:51
thoralfsonney2k: where does the disk read come from?14:52
@sonney2kthoralf, streaming features!14:53
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ZhengHi, has anyone tried to handle this issue: https://github.com/shogun-toolbox/shogun/issues/1060?15:39
ZhengAn entrance issue15:40
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gsomixhi17:45
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pickle27iglesiasg: hey I re-ran after building with no optimization and got this http://pastebin.com/LHqAyAUv18:57
@iglesiasgpickle27: hey18:57
@iglesiasgI checked the log you pasted last night18:57
@iglesiasglet me see this one18:57
@iglesiasgpickle27: but it is still the same error I am afraid18:58
@iglesiasgvex amd64->IR: unhandled instruction bytes: 0xC5 0xF9 0x57 0xC0 0xE8 0x73 0x4 0xFF18:58
@iglesiasgpickle27: isn't it?18:58
pickle27iglesiasg: yeah I saw that there in the middle but there was more upfront I thought might help18:58
@iglesiasgpickle27: not really honestly18:59
pickle27iglesiasg: can we re-try the build server and see if it crashes when running the example again18:59
@iglesiasgpickle27: I can try to take a look at it in my computer18:59
pickle27iglesiasg: okay. because I don't know what else I can do to debug if I can't replicate the actual crash on my pc18:59
@iglesiasgpickle27: both the MLDA code and the example has been merged to upstream develop right?19:01
pickle27iglesiasg: yes it was merged yesterday19:01
@iglesiasgpickle27: so I will take a look ASAP and give you and answer in the mailing list19:02
pickle27okay sounds good, thanks!19:02
@iglesiasgprobably by tomorrow midday19:03
@iglesiasgso that is like 15h from now for me19:03
@iglesiasgpickle27: I think we are in different time zones :)19:03
pickle27iglesiasg: yeah I've come to notice haha, Europe?19:04
@iglesiasgpickle27: yep19:04
pickle27iglesiasg: cool, I'm in Canada19:04
@iglesiasgpickle27: nice! I will try to take more care of my English then :P19:06
@iglesiasgwell are you in English or French speaking area?19:06
pickle27iglesiasg: I'm in an English area, I do speak a bit of french though, whereabouts are you in Europe?19:06
@iglesiasgpickle27: right now in Spain, I live in Sweden though19:07
pickle27iglesiasg: neat!19:07
thoralfpickle27: Tried to add --enable-debug --disable-optimization to ./configure?  This should remove the illegal instructions in valgrind.19:24
@iglesiasgthoralf: I think he has already tried compiling with the disabel-optimization option19:27
thoralfiglesiasg: Maybe, but as he didn't mention it in his post, I thought it could save him some trial and error. :)19:31
@iglesiasgsonney2k suggested doing that yesterday19:32
thoralfiglesiasg: It still looks too familiar to me... ;)19:36
thoralfpickle27: We're wondering if you tried (in shogun/src): make clean; ./configure --enable-debug --disable-optimization19:37
@iglesiasg:)19:37
votjakovrHi guys :) Has anyone run integration tests on local machine? Is regression_gaussian_process_modular.py failed?19:49
@sonney2kvotjakovr, seems it works: http://shogun-toolbox.org/buildbot/waterfall19:52
@sonney2kwhy?19:53
@sonney2kwiking, ubu1 - libshogun buildbot is down19:53
thoralfsonney2k: Cool visualization.19:54
votjakovrsonney2k: Oh, but travis-ci shows an errors.19:54
@sonney2kthoralf, what?19:56
thoralfsonney2k: The buildbot/waterfall19:57
@sonney2kthoralf, ahh ok19:58
@sonney2kwasn't so impressive to me..19:58
@sonney2kvotjakovr, checking19:59
@sonney2kvotjakovr, hmmhh the returned label vector is *slightly* different19:59
@sonney2kany idea why that could be?19:59
@sonney2kany randomness in there?19:59
@sonney2kor different numerical libraries?20:00
@sonney2kiglesiasg, don't you have ubuntu?20:05
@iglesiasgsonney2k: I currently use more arch than ubuntu20:06
@iglesiasgsonney2k: why?20:06
@sonney2kI wish we could reproduce the travis failure20:06
@sonney2ktravis runs on ubuntu20:06
votjakovrsonney2k: Nope, when I changed implementation of ExactInferenceMethod, I regenerated test data. And everything is OK on my machine.20:07
@iglesiasglisitsyn uses ubuntu I think20:07
votjakovrsonney2k: And I use Ubuntu 13.0420:07
@sonney2kvotjakovr, which version of numpy?20:07
@sonney2k1.6.1 or .2?20:07
pickle27thoralf: I will try now20:07
votjakovrsonney2k: 1.7.120:08
@sonney2kvotjakovr, hmm - labels is generated randomly though20:11
@sonney2kvotjakovr, I just checked the diff20:15
@sonney2kfor some reason the 100 dim label vector differs in 3 entries20:15
@sonney2k1.144566753132682 vs 1.14456675313268120:15
@sonney2k1.15097403962122 vs 1.15097403962121920:15
@sonney2k1.447796756701278 vs 1.44779675670127720:16
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@sonney2kwiking, is there any way to specify the numpy version in travis?20:18
votjakovrsonney2k: Yep, I have done the same. But I have no idea why they are different...20:18
votjakovrsonney2k: Maybe some problem with floating point precision20:19
@sonney2kvotjakovr, me neither and I don't understand how the rest of the output can match perfectly20:19
@sonney2kvotjakovr, does the algorithm use threads or anything20:28
@lisitsynwhat's up?20:32
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votjakovrsonney2k: there's just operations with matrices20:33
@lisitsynsonney2k: have you seen? we've got some slots20:34
@sonney2klisitsyn, no I haven't20:34
@lisitsynsonney2k: 820:34
naywhayarenice!  I was hoping for that many but just like I was told to expect we got only two :)20:35
@sonney2kcool20:35
gsomixlisitsyn, sonney2k hey, guys, wuts goin' on?20:35
@sonney2kso we only have to unaccept 2 :D20:35
@lisitsynhah yes currently20:35
@sonney2kwe had 9 last year but used only 8 right?20:36
@lisitsynyes20:36
@sonney2knaywhayare, be grateful it's a lot of work20:38
@iglesiasglisitsyn: oh we already got an answer?20:38
@lisitsyniglesiasg: yeah carols is fast this time20:38
@iglesiasgI thought it was going to be tom!20:38
@lisitsynI guess it may be changed20:38
@sonney2kshe wants to be on vacations soon so :)20:38
@iglesiasghehe20:39
@lisitsynoh! I should ask her about delivering t-shirt to you sonney2k20:39
@lisitsynare you ok with it?20:39
@iglesiasg8 is a nice number anyway20:39
@iglesiasglet's do some vodking20:39
@lisitsyniglesiasg: you know the way20:39
@iglesiasgsonney2k: is it a good idea to tweet about this?20:39
@sonney2kwhy not20:40
naywhayaresonney2k: yeah, you are probably right...20:40
naywhayare(well... more than probably. you've done this before :))20:40
@lisitsyntwice20:40
@lisitsyn:D20:40
@sonney2knaywhayare, it really depends on your students/mentors though. with 8 it already is quite a bit of coordination. and if one student/mentor sucks you can easily cope with that20:41
@sonney2kwhen you have 'just' 2 slots20:41
naywhayareyeah; we got a number of good applications though, so it will be tough to choose which two to accept20:42
naywhayareeven so, with how busy I tend to be, it's probably a good thing in terms of "work/life balance" (not that I get to know what that is as a grad student...)20:42
@sonney2knaywhayare, what we did was ask our top candidates all for patches20:42
@sonney2keven already for their project20:42
@sonney2kthen you select the most engaged20:43
@sonney2kand that obviously wasn't the wrong decision20:43
naywhayarethat is probably a good idea; a few of our candidates have already taken the initiative and started doing that20:43
@sonney2klisitsyn and heiko are still around :D20:43
@sonney2k3 years later now20:43
@lisitsynyeah I am a gsoc child20:43
@lisitsyn:D20:43
@lisitsynno, I am here for two years I think20:44
@sonney2klisitsyn, true20:45
@sonney2k201120:45
@sonney2kheiko dates back to 201020:46
@wiking123420:55
@lisitsynwiking: good!20:56
@wikingyes keyboard works!20:56
@wiking:>20:56
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@sonney2kwiking, get the ubuntu buildbot back to work!20:56
@wikingoh20:56
@wikingsonney2k: i would if i would access to that machine20:56
@wikingit's down and i really have no clue when it's going to be back20:56
@sonney2kwiking, hmm!?20:57
@wikingthe machine20:57
@wikingit's down20:57
@wikingor somebody took out the utp cable20:57
@wikingor i have no clue20:57
@wikinganyhow i have no physical access to that machine20:57
@wikingso i cannot do anything about it20:57
@sonney2kwiking, ohh and could you merge from develop -> master the configure change for swig2.0 or what do we do about master failing?20:57
@sonney2kon bsd1?20:57
@wikingmmmm20:57
@wikingnoclue :)20:58
@wikingi'll check tonight20:58
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shogun-notifier-shogun: Sergey Lisitsyn :develop * b466c0d / src/shogun/lib/tapkee/ (11 files): https://github.com/shogun-toolbox/shogun/commit/b466c0dcca4467d7c219619367488b104fc88e1b20:58
shogun-notifier-shogun: Updated tapkee library20:58
shogun-notifier-shogun:20:58
shogun-notifier-shogun: - Proper non-negativity checks in parameters20:58
shogun-notifier-shogun: - VP-tree neighbors method20:58
shogun-notifier-shogun: - Some minor fixes20:58
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shogun-buildbotbuild #1110 of deb1 - libshogun is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb1%20-%20libshogun/builds/1110  blamelist: Sergey Lisitsyn <lisitsyn.s.o@gmail.com>21:03
@lisitsynoops!21:03
@lisitsynsorry21:03
@sonney2kguys punish him!21:03
@lisitsynfixing21:04
@lisitsynmy script for auto-conversion of includes failed here21:04
@iglesiasghehe shit happens21:05
@lisitsyniglesiasg: bad you are not in sweden, ice hockey event there21:06
@lisitsynrus-usa right now21:06
@sonney2klisitsyn, ohh cold war!21:07
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travis-ci[travis-ci] it's Sergey Lisitsyn'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/696675121:07
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* sonney2k sigh21:07
@sonney2kwe have to kick out 2 students now21:07
@sonney2kif anyone has a better idea than throwing a dice... say so21:08
thoralfsonney2k: Random numbers needed? http://xkcd.com/221/21:09
thoralf(off-topic)21:10
@sonney2kthoralf, I choose the seed :P21:10
@sonney2kand wiking provides the prng21:10
shogun-notifier-shogun: Sergey Lisitsyn :develop * 542609f / src/shogun/lib/tapkee/neighbors/vptree.hpp: https://github.com/shogun-toolbox/shogun/commit/542609f99d210296a9a9fed81a657914548b29af21:11
shogun-notifier-shogun: Fixed include in vptree21:11
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shogun-buildbotbuild #1111 of deb1 - libshogun is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb1%20-%20libshogun/builds/111121:14
@wikingsonney2k: why so?21:20
@wikingsonney2k: u think we wont' get enough slots?21:20
@sonney2kwiking, we got 821:20
@wikingaaah it's already decided?21:20
@wikingi mean the slots?21:20
@sonney2kliving behind the moon aren't ya?21:20
@wikingi missed that21:21
@wikingsorry man21:21
@wikingtoo busy in the last 1 month21:21
@sonney2kwiking, yeah we have to kick out 2 students21:21
@wikingmmmm21:21
@wikingand all those 10 are tops?21:21
@wikingi mean super great applications?21:21
@sonney2kyes21:21
shogun-buildbotbuild #925 of bsd1 - libshogun is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/92521:21
@wikingmmmm21:21
@wikingwell if u cannot really prioritize21:21
@wikingthen let's kick out 3 and 721:22
@wiking:)21:22
@wikingi mean i was just your random machine21:22
@sonney2kno prime numbers have to stay :D21:22
@wikingand i'm totally objective as i dont even know21:22
thoralfGood choice. ;)21:22
@wikingthe applications21:22
@wikingsonney2k: hehehe well u can assign any of the applications to be 3 and 721:22
@wiking:P21:22
@wikinghaven't defined the order of the applications21:22
@wikingbut then again21:23
@wikingother option is a very stupid one21:23
@wikingorder them by submission date21:23
@wikingand remove the last 221:23
@wikingi mean it's really stupid21:23
@wikingbut it's another option21:23
@wikingoooooor21:23
@wikinglet's start gathering money for those 221:24
@wiking\o/21:24
@wikinggo to kaggle21:24
@wikingwin a competition21:24
@wikingand then we can support them21:24
@wiking:D21:24
@wikingsonney2k: or give me the list and i'll review them for ya ;)21:24
@wikingi bet i can find you 2 not so good ones :DDD21:24
@wikingeven 3 :P21:24
* wiking is accepting bribes :DDD21:25
@wikingsonney2k: or why not to somehow prio them by the entrance21:25
@wikingPRs21:25
@wikingi bet we can measure there a very nice objective way21:26
@wikingok21:26
@wikingretweeted21:26
@wikingbtw who's not here out of those 10 ppl? :)21:27
@sonney2kwiking, a couple :D21:27
@wikingheh21:27
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@wikingtheeere you gooooo21:27
@wiking:))))21:27
@wikingno IRC no GSOC21:27
@wiking:DDD21:27
@wikingpretty standard measure :P21:28
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pickle27haha good thing I'm on IRC right now lol21:30
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travis-ci[travis-ci] it's Sergey Lisitsyn'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/696709121:35
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pickle27the people involved in this left but I just re-ran the valgrind after compiling shogun with debugging symbols and got the same result, http://pastebin.com/00rU2vcU21:45
pickle27iglesias is going to try on his machine and see if he can reproduce the error because I can not - the classifier_lda example still runs fine on my system21:47
@sonney2kpickle27, what is the issue?22:06
gsomixwiking, hey, you're awesome.22:10
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@sonney2khmmhh I would wish we could have sprint meetings like scikits https://github.com/scikit-learn/scikit-learn/wiki/Past-sprints22:30
@sonney2klike meet once / year in berlin or so22:30
@sonney2kand then do a week of coding vodking :D22:30
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@wikinggsomix: :D23:05
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iglesiasgpickle27: hey, I just checked logs23:38
iglesiasgpickle27: for some reason the last pastebin link doesn't open find23:39
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iglesiasgoh fine*23:39
iglesiasgpickle27: anyway, if valgrind complains about it, it is a sign that it doesn't run fine in your system ;)23:39
--- Log closed Wed May 08 00:00:35 2013
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