Open in new window / Try shogun cloud
--- Log opened Tue May 07 00:00:34 2013
pickle27this is what I get now:
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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
@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
@wikingwith gdb and valgrind you pretty much can find any such bug13:37
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
@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
@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
@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
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:
ZhengAn entrance issue15:40
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pickle27iglesiasg: hey I re-ran after building with no optimization and got this
@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
votjakovrHi guys :) Has anyone run integration tests on local machine? Is failed?19:49
@sonney2kvotjakovr, seems it works:
@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
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
@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
@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
@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
@lisitsynno, I am here for two years I think20:44
@sonney2klisitsyn, true20:45
@sonney2kheiko dates back to 201020:46
@lisitsynwiking: good!20:56
@wikingyes keyboard works!20:56
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@sonney2kwiking, get the ubuntu buildbot back to work!20:56
@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
@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):
shogun-notifier-shogun: Updated tapkee library20:58
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  blamelist: Sergey Lisitsyn <>21:03
@sonney2kguys punish him!21:03
@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:
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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?
@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:
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
@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
@wikingand all those 10 are tops?21:21
@wikingi mean super great applications?21:21
shogun-buildbotbuild #925 of bsd1 - libshogun is complete: Success [build successful]  Build details are at
@wikingwell if u cannot really prioritize21:21
@wikingthen let's kick out 3 and 721:22
@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
@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
@wikinglet's start gathering money for those 221:24
@wikinggo to kaggle21:24
@wikingwin a competition21:24
@wikingand then we can support them21:24
@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
@wikingi bet we can measure there a very nice objective way21:26
@wikingbtw who's not here out of those 10 ppl? :)21:27
@sonney2kwiking, a couple :D21:27
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@wikingtheeere you gooooo21:27
@wikingno IRC no GSOC21:27
@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:
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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,
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
@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