Open in new window / Try shogun cloud
--- Log opened Wed Oct 03 00:00:17 2012
shogun-buildbotbuild #121 of nightly_default is complete: Failure [failed test]  Build details are at
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blackburnhey n4nd016:55
blackburnmanaged to get this linking thing to disappear?16:55
n4nd0blackburn: no :(16:56
n4nd0I have no idea how to fix that kind of problem16:56
n4nd0I saw a similar one today16:56
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adoniscikgreetings! Does Shogun work compile with EPD?22:09
blackburnadoniscik: hey22:10
adoniscikhey blackburn. That's the Enthought Python distribution.22:10
blackburnyeah, thanks22:10
blackburnwell it should work with it since it works with basic python22:10
blackburnadoniscik: I didn't hear anything about compilation of shogun with EPD actually22:12
blackburnadoniscik: just try and let us know if there are any problems22:12
adoniscikthere are. what does it mean if compilation of the Python test fails like
blackburnadoniscik: okay lets try to get rid of it.. when does that happen?22:14
adoniscikduring configure's python/numpy stage22:15
blackburnadoniscik: do you have a configure.log saved?22:16
adoniscikthat's an extract i gave you; the important part22:16
blackburnadoniscik: so it happens when it checks for numpy?22:18
adoniscikcorrect. this is the error returned by running gcc on the code snippet shogun uses to test numpy22:18
blackburnadoniscik: numpy developer files, right?22:19
adoniscikyes. I don't know if I have it though. How can I check manually?22:19
adoniscikI assume it comes with EPD but I don't know22:19
blackburnadoniscik: well the error you've got tells me you have headers22:20
blackburnbut some linking error22:20
blackburnto be honest I do not know what is so different in EPD's python22:20
adoniscikthat's what I thought. Is it some path problem?22:20
blackburnI googled a little and it could be caused by static linking - let me check for more information22:21
blackburnadoniscik: I don't think it is a path problem - rather something wrong with linking flags22:27
blackburnadoniscik: I found that there was a similar problem and we already have a  workaround in configure that adds -ldl flag22:30
adoniscikI think you're getting close.22:30
adonisciklet me try22:30
blackburnadoniscik: I mean it is already here and should work..22:30
blackburnthat's pretty bad it doesn't22:31
blackburnadoniscik: can you paste few lines more that are before these ones?22:32
blackburnwhat is compiler call there?22:32
blackburnadoniscik: I believe that's an enthought's gap btw22:34
adoniscikit's long because I managed to install all the "extras" shogun supports: cc -I. -I..   -I/usr/include/atlas -isystem /usr/include/eigen3   -fPIC -g -Wall -O9 -fexpensive-optimizations -frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2 -fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops -mfpmath=sse -march=native -mtune=native -pthread ./configure-21993-27344.c -o ./configure-17354-27344.o  -Xlinke22:34
adoniscikr --no-undefined -fno-strict-aliasing -fPIC -I/opt/enthought/include/python2.7 -I/opt/enthought/lib/python2.7/site-packages/numpy/core/include -shared -L/opt/enthought/lib/python2.7/config -lpython2.7 -lm -pthread -lhdf5 -llapack -lcblas -llapack_atlas -lsuperlu -lnlopt -lglpk -lm -llzo2 -lz -lbz2 -llzma22:34
blackburnit looks like python was built without dl out there22:34
blackburnI miss -ldl there22:36
blackburnokay no ldl right?22:36
blackburnadoniscik: lets try to hack it then22:37
blackburnadoniscik: easiest way is to add '-ldl' in the string on the line 159 of src/configure22:38
blackburnI'll report an issue meanwhile to not forget about that later22:40
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blackburnheiko: hey there22:45
adoniscikI added it to end and I got a shorter error22:45
heikoblackburn, h22:45
heikohow are you doing?22:45
blackburnworking on a test task for that job I am applying for22:45
blackburnpretty fun - I had to gimp a little:
heikogimp sketches for a job? :)22:46
blackburnheh okay okay22:46
blackburnthey asked me to kinda reverse engineer22:46
blackburnthat thing22:47
blackburnthat's where crazy pictures came from22:47
blackburnI also have an inverted earth that looks like and is categorized like an oyster :D22:47
heikoreverse engeneer?22:47
adoniscikblackburn: adding ldl gave
blackburnadoniscik: closer!22:48
adoniscikyes, indeed, thank you! now we have to deal with libpython?22:48
blackburnadoniscik: -lutil please then too22:48
blackburnheiko: well like to describe how could it work22:48
adoniscikyou da man!22:48
heikoblackburn, alright22:48
heikoimage classification that is ight?22:48
blackburnheiko: yes, multi-label22:49
blackburnheiko: I've made a 5 page long report already and keeping on22:49
blackburnhave two days more to think and write22:49
heikowhat are you describing?22:50
adonisciksorry to butt in... so which lines in the configuration script should I amend?22:50
blackburnadoniscik: right next to -ldl I think22:50
blackburnheiko: well I believe it is the thing that won ILSVRC 2011 (xerox guys again)22:51
blackburnheiko: horse with skates is recognized as winter sports, hockey and donkey22:51
heikoI see22:51
blackburnso I kinda state that it is a local patch based22:51
heikothats pretty good isnt it22:51
heikowhich means?22:51
blackburnSIFT/SURF, etc22:52
blackburnso it basically counts visual words22:52
blackburnskates, some white areas22:52
blackburnso the approach in a nutshell is local patches + BoW (bag of words) or Fisher vectors22:52
blackburnand then SVM22:52
blackburnmay be some improvements along but I believe it works like that22:53
blackburna few evidences already22:53
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blackburnheiko: the system works pretty well, yes22:53
blackburnit fails terribly with cats though22:53
blackburnI can't stand that22:54
heikowe did something similar in our MV class22:54
heikothese visual words are pretty cool I think22:54
blackburnheiko: xerox owns a few patents about visual words22:54
blackburncontext-dependent is of some interest I think22:55
blackburnI am unsure it works well already though - in the end it recognizes paris+london in the same pic22:55
blackburnor donkey+hockey22:55
heikosounds like you will get the job :D22:56
blackburnheh why?22:56
adoniscikthe python_static compiled! do you need SWIG to compile python_modular22:56
blackburnadoniscik: yeah, swig is required only for python_modular22:56
blackburnstatic does not require swig at all22:57
adoniscikokay so that's why it failed that part; will fix quickly22:57
blackburnheiko: alex helped me quite a lot too - I asked him22:57
blackburnhe is the expert in this field you know22:57
heikoblackburn, because you sound competent22:57
heikoI see22:57
blackburnbtw may be you have ideas too - feel free to share :)22:58
blackburnheiko: that job would mean I won't be gsoc student next summer but rather mentor22:59
heikoblackburn, I am not really fit in MV, sorry :)22:59
heikowell I think that would be better anyway :D22:59
heikomore mentore=more students22:59
heiko= more SHOGUN :)22:59
blackburnand I feel like a ship captain sometimes so it would not be hard for me23:00
blackburnheiko: that company is like the only one having consistent salaries around there23:01
blackburnwell I am now having less than 1/10 of gsoc per month23:02
blackburnnot really reasonable23:03
adoniscikblackburn: I got both python interfaces to compile. I added the two flags to LINKFLAGS_PYTHON in the configure script. Perhaps it should detect EPD and take care of it automatically in a future release?23:03
blackburnadoniscik: exactly23:03
heikoblackburn, wow23:03
heikomaybe come to london and earn 50k punds a year :)23:04
heikowith your skills, you could easily do that23:04
adoniscikIs there anything I can do to help or will you take care of it?23:04
blackburnadoniscik: I issued an issue :) we shouldn't lost that23:04
heikoand thats the wages for machine learners here23:04
blackburnadoniscik: well I'll test if it would work without any bugs/warnings when we forcely add -ldl and -lutil there23:05
blackburnon usual python23:05
blackburnand then add that to the master thing23:05
blackburnI will do that now23:06
blackburnheiko: I have runglish23:06
heikoblackburn, youll pick that up quickly - also some of the people here speak such a bad english, you are probably better23:06
blackburnheiko: I do not have speaking practice at all..23:07
blackburnheiko: btw is that true in germany people care about pronunciation?23:07
blackburnI rather meant accent23:08
heikohow do you  mean that?23:08
blackburnI heard like it is hard to get job if you speak like russian invader :D23:08
heikothat depends on the place23:09
heikobut that might be true23:09
heikoLondon --since much more international-- is less strict about that23:09
blackburnheh I see23:09
heikoyou could also do a 2 week course or so23:10
heikoI bet you would pick up things quickly23:10
blackburnyeah I hope so23:10
heikoblackburn, I visited the Google offices in London today23:13
heikothat is an *awesome* place23:13
blackburnyeah, I've seen photos23:13
blackburnI am acknowledged with one guy23:14
blackburnwho works there23:14
blackburnformer netcracker job and SSAU university (just like me)23:14
blackburnmay be I will be able to get on that lane too :)23:15
heikoyeah :)23:15
heikounfortunately no data analysis or software engineering in London23:15
heikoonly business23:15
blackburnI thought he is a software developer23:15
heikoa friend of mine applied to Mountain View, CA and is going for an interview next week23:15
heikowell, only minor23:15
heikoI did only see well-dressed women,    no nerds :)23:16
blackburnheiko: google interview is a hell23:16
heikoblackburn, dont know. what is it like?23:16
blackburnheiko: one guy from St. petersburg who were applying for GSoC 2011 tried23:17
blackburn(I talk to him sometimes)23:17
blackburnit was like 6 hours of questions, questions, questions23:17
blackburntasks and more tasks23:17
blackburnso in the end there were like two accept and one reject23:18
blackburnand he was unfortunately rejected23:18
blackburnsoftware engineering position that was23:18
heikooh wow23:18
blackburnheiko: well didn't you heard of their crazy questions like what is a cost of washing all windows in seattle?23:19
blackburnthis way they check how one thinks23:19
heikohow many ping pong balls do fit into a Swimming Pool?23:19
heikothese are easy23:19
heikoyou just have to structure the answer a bit23:20
blackburnwell yes, not hard23:20
heikoI would be more afraid of technical questions23:20
blackburnheiko: that company I am applying to gave me a brainbench C++ test23:20
blackburnon the interview23:20
blackburnthey are lazy to check whether one knows C++ I guess :)23:21
blackburnsonney2k's STL hate played a bad role there, I've got sth like 74% percentile23:21
heikowhat is that?23:21
heikoah stl23:21
heikowhat did you have to do?23:22
blackburn that is the site23:22
blackburnwell just some test like23:22
blackburnwhat is wrong there23:22
blackburnand some code with algorithms and STD23:22
blackburnor what will be outputted after the running of the following code23:22
heikoah I see23:23
heikoyeah I only know the containers of the STL :)23:23
blackburnheiko: it is not that ugly I think23:23
heikoI actually like them23:23
heikoI mean23:23
heikowhat else to use? :)23:23
heikothere is nothing23:23
heikoin shogun we got the base-class so things are different23:24
heikoand we want to serialise23:24
heikobtw any new ideas for the SGReferenced problem and serialization?23:24
blackburnI do not like things without alternative (we have president here for 12 years already :D)23:24
blackburnnot really, last days were pretty busy and I failed to even think about that23:25
blackburnbtw we broke things a little23:25
heikoI worked a bit more on the streaming framwork for my part23:25
blackburnI disabled Lua string tests for now23:25
blackburnbut streaming features fail in python23:25
blackburnwith segmentation fault23:26
heikojep probably my fault23:26
blackburnprobably I caused that somehow23:26
heikowill catch up with that this week23:26
heikowas in germany over the weekend23:26
blackburni changed something out there too23:26
heikoI made some streaming features run again in libshogun23:26
heikothis code btw23:26
heikois not really well written23:26
blackburnwe just need to bisect a problem23:26
blackburnvalgrind error appears to be strange23:26
blackburnheiko: *tss* shogun is not really well written in general :D23:27
heikoblackburn, LOL :)23:28
blackburnhowever proprietary business things are much worse23:28
heikoyeah we are at least open-source so people find problems23:28
blackburnheiko: did you ever work with some proprietary code for say java or sth like that?23:28
heikoI once tried to use a commercial software for graph visualization in java23:28
heikothat was the worst library I ever came across with :D23:29
blackburnheiko: I support that kind of code at job day by day23:29
heikofinally, we decided to re-implement it ourselves23:29
blackburnI thank all gods that we are migrated to SVN instead of clearcase23:29
heikoI think its dangerous if one doesnt pay enough attention to well written code which is hack-free23:29
heikobecause all the errors come back and steal your time23:29
blackburnyeah that's our mistake as well23:30
heikotoo many quick changes23:31
heikoand stopping at 95%23:32
heikothats bad on the long run23:32
blackburnadoniscik: still around?23:32
heikoI  should write unit-tests instead complaining :D23:32
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blackburnI am thinking where to put these -ldl -lutil things23:33
blackburnheiko: btw about these 50k pounds - isn't that near to sum one spends living in london?23:35
blackburnyou told me and I heard that it is crazy expensive23:35
adoniscikyes, sorry to overhear! there's a slight problem with nlopt which I'll write about in a sec23:35
adoniscikit fails with /usr/bin/ld: /usr/local/lib/libnlopt.a(optimize.o): relocation R_X86_64_32S against `.text' can not be used when making a shared object; recompile with -fPIC23:36
adoniscik/usr/local/lib/libnlopt.a: could not read symbols: Bad value23:36
adoniscikI found a mention of this error in
blackburnright right23:36
blackburnadoniscik: did you compile nlopt by yourself?23:36
heikoblackburn, me and my girlfriend, we live on about 1800 pounds a month23:37
adoniscikerr, no. Should I?23:37
heikoso much less23:37
blackburnadoniscik: where it comes from?23:37
blackburnEPD too?23:37
blackburnif you don't mind compilation of another package (pretty simple for nlopt) you could do that23:39
blackburnit requires -fPIC to be linked properly but for some reason nlopt ignores that in binary and source (by default)23:40
adoniscikyes EPD23:40
adoniscikI mean wait no23:40
adoniscikI downloaded it myself I think.23:41
adoniscikand stuffed it in /usr/lib23:41
adoniscikright. so what should I compile?23:42
blackburnjust download nlopt sources, set -fPIC option, recompile and install23:42
blackburnI am currently trying to find how to set -fPIC there23:42
adoniscikokay. I only downloaded it manually because I couldn't find an nlopt package for Ubuntu23:43
adoniscikin the software center23:43
blackburnyeah, there is no yet23:43
blackburnadoniscik: just do23:44
blackburn./configure --enable-shared23:44
blackburnsudo make install23:45
--- Log closed Thu Oct 04 00:00:17 2012