IRC logs of #shogun for Tuesday, 2016-06-14

« Monday, 2016-06-13 Index Wednesday, 2016-06-15 »
--- Log opened Tue Jun 14 00:00:39 2016
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shogun-notifier-shogun: Ariane Paola Gomes :develop * 2aab17c / examples/meta/generator/generate.py: https://github.com/shogun-toolbox/shogun/commit/2aab17cc7cf099dfa3e8ffbc8d361d3ebd000f2501:04
shogun-notifier-shogun: Fixes #3253 Cookbook generation failure missing responsible file indicator.01:04
shogun-notifier-shogun: Heiko Strathmann :develop * 997e54c / examples/meta/generator/generate.py: https://github.com/shogun-toolbox/shogun/commit/997e54c7a262baf7833454f154593398bb935ff301:04
shogun-notifier-shogun: Merge pull request #3255 from arianepaola/fix_325301:04
shogun-notifier-shogun:01:04
shogun-notifier-shogun: Fixes #3253 Cookbook generation failure missing file indicator01:04
shogun-buildbotbuild #2912 of bsd1 - libshogun is complete: Failure [failed configure]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2912  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Ariane Paola Gomes <arianepaola@users.noreply.github.com>01:12
shogun-buildbotbuild #53 of xenial - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/xenial%20-%20libshogun/builds/53  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Ariane Paola Gomes <arianepaola@users.noreply.github.com>01:13
shogun-buildbotbuild #881 of deb4 - python3 is complete: Failure [failed install test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb4%20-%20python3/builds/881  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Ariane Paola Gomes <arianepaola@users.noreply.github.com>01:40
shogun-buildbotbuild #41 of FC23 - libshogun - aarch64 is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/FC23%20-%20libshogun%20-%20aarch64/builds/41  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Ariane Paola Gomes <arianepaola@users.noreply.github.com>01:49
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shogun-buildbotbuild #1020 of nightly_none is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_none/builds/1020  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Ariane Paola Gomes <arianepaola@users.noreply.github.com>03:04
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shogun-buildbotbuild #19 of memleak - valgrind is complete: Failure [failed memory check]  Build details are at http://buildbot.shogun-toolbox.org/builders/memleak%20-%20valgrind/builds/19  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Ariane Paola Gomes <arianepaola@users.noreply.github.com>05:28
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shogun-buildbotbuild #1150 of nightly_default is complete: Failure [failed test notebooks]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/1150  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Ariane Paola Gomes <arianepaola@users.noreply.github.com>06:10
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shogun-buildbotbuild #470 of deb1 - libshogun - PR is complete: Failure [failed cookbook]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun%20-%20PR/builds/470  blamelist: OXPHOS07:13
shogun-buildbotbuild #471 of deb1 - libshogun - PR is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun%20-%20PR/builds/47107:17
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@wikingSaurabh7: hey here?10:03
Saurabh7wiking: yes, sry was away10:23
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Saurabh7I have updated things, I will ping there10:30
@wikingSaurabh7: yep i saw them10:34
@wikingi was just wondering if you maybe benchmarked it10:35
@wikingafter the final changes10:35
@wiking(lars)10:35
Saurabh7Yes same results not much difference10:36
Saurabh7but I havent changed much that has impact10:36
Saurabh7just chcanged memcpy for 1 column10:37
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Saurabh7wiking: ^10:38
@wikingSaurabh7: perfect10:41
@wikingok let's see the output of travis10:41
@wikingif it's green we merge10:41
@wiking:)10:41
@wikingok10:42
@wikingkmeans is grean10:42
@wiking*green10:43
@wikingmergeoooooo10:43
Saurabh7cool :)10:43
@wikingboom10:44
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shogun-notifier-shogun: Saurabh7 :develop * 802b810 / / (13 files): https://github.com/shogun-toolbox/shogun/commit/802b8100080bd28e1099950176d69c437ad29e0510:44
shogun-notifier-shogun: refactor KMeans10:44
shogun-notifier-shogun: Viktor Gal :develop * e541a92 / / (13 files): https://github.com/shogun-toolbox/shogun/commit/e541a9288a12c2ee1b70f7944feae2246f178bea10:44
shogun-notifier-shogun: Merge pull request #3166 from Saurabh7/kmeans_refactor10:44
shogun-notifier-shogun:10:44
shogun-notifier-shogun: refactor KMeans10:44
Saurabh7aha10:44
Saurabh7oh theres a kmeans cookbook open10:49
Saurabh7guess it needs updating :)10:50
shogun-buildbotbuild #2913 of bsd1 - libshogun is complete: Failure [failed configure]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2913  blamelist: Viktor Gal <vigsterkr@gmail.com>, Saurabh7 <saurabh.mahindre@gmail.com>10:51
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c4goldswwiking ping11:29
shogun-buildbotbuild #882 of deb4 - python3 is complete: Failure [failed install test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb4%20-%20python3/builds/882  blamelist: Viktor Gal <vigsterkr@gmail.com>, Saurabh7 <saurabh.mahindre@gmail.com>11:37
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c4goldswclear12:37
c4goldswoops, meant for bash12:40
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@wikingc4goldsw: pong12:45
c4goldswwiking hey12:46
c4goldswdoing well?12:46
@wikingyep yep12:46
@wikinghow about you?12:46
c4goldswGood - I was at an ML hackathon in Germany this weekend, so I haven't done much on Shogun12:47
c4goldswgetting back to work on it.12:47
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c4goldswafk12:54
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c4goldswwiking question: I started off by making EuclideanDistance generic, which would also involve making it's parent class generic (which would then involve making all descendents of the base class generic).  So, at this point, it seems as if I'd have to do this for all distance classes (I count  + 15).  I should try to find something with fewer depende13:42
c4goldswncies and start over, right?13:42
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c4goldswUnless you wouldn't mind going through all those files.13:49
c4goldswIn which case I'd keep going13:49
@wikingc4goldsw: mmmm13:51
@wikinglemme checkin13:51
@wikingah yeah that's nasty13:52
@wikinglemme find you an easier13:53
@wikingcheck LARS13:53
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shogun-notifier-shogun: Saurabh7 :develop * 5aa89b7 / / (3 files): https://github.com/shogun-toolbox/shogun/commit/5aa89b7d1b3f59de03bb98b0f5ea90ea114f12d913:53
shogun-notifier-shogun: Update LARS13:53
shogun-notifier-shogun: Viktor Gal :develop * 3618469 / / (3 files): https://github.com/shogun-toolbox/shogun/commit/3618469f489698e6ac15d6e3a6938d3210be7b8013:53
shogun-notifier-shogun: Merge pull request #3243 from Saurabh7/lars13:53
shogun-notifier-shogun:13:53
shogun-notifier-shogun: Lars update13:53
@wikingjust merged some updates there13:53
@wikingbut that thing prettey much assumes the same thing13:54
@wikingthat the features is actually DenseFeatures<float64_t>13:54
@wiking(only13:54
@wikingwhich is for no reason :P13:54
c4goldswHaha, ok, I'll pull that then.  I have a git question too13:55
c4goldswI have PR on my develop branch that is still  open - if I want to start working on new work, should I make a new branch?13:55
c4goldswAnd work from there?13:56
@wikingeither that or just recreate the branch13:58
@wikingdelete and create13:58
@wiking:)13:58
c4goldswWhich would also delete the PR, right?13:58
@wikingnoup13:59
@wikingbut no reason to delete the pr13:59
@wikingthe pr will just monitor that branch13:59
c4goldswGreat, thanks for the info.13:59
@wikingwhich i suppose u wanna have13:59
@wikingif not13:59
@wikingthen just close the pr via github13:59
c4goldswI'll keep it open, just want to make sure it isn't affected.14:00
@wikingmmm buildbot is sick :(14:10
c4goldswwiking: Since LARS inherits from CLinearMachine, which inherits from CMachine, should I just make the methods in LARs generic rather than the whole class?14:10
@wikingwhat exactly do you mean14:12
@wikingi mean the problem in lars is this exactly14:12
@wikingaaaaaaaaaaaaaaaaaaah14:13
@wikingSaurabh7: still here?14:13
@wikingc4goldsw: https://github.com/shogun-toolbox/shogun/blob/develop/src/shogun/regression/LeastAngleRegression.cpp#L11814:13
c4goldswSure, I have the line open in front of me.14:14
@wikingSaurabh7: you've forgot this here: https://github.com/shogun-toolbox/shogun/blob/develop/src/shogun/regression/LeastAngleRegression.cpp#L1314:14
@wikingSaurabh7: you've removed all the lapack dependencies no?14:14
@wikingbecause then i reckon we should remove https://github.com/shogun-toolbox/shogun/blob/develop/src/shogun/regression/LeastAngleRegression.cpp#L13 and https://github.com/shogun-toolbox/shogun/blob/develop/src/shogun/regression/LeastAngleRegression.cpp#L40614:14
c4goldswwiking you know what, never mind.  I just realised that there shouldn't be a problem with making the whole class generic.14:18
c4goldsw(or so I think)14:18
@wikingc4goldsw: hehe cool :)14:19
arianepaolahello everyone :-)14:33
c4goldswwiking sorry to keep bother you, but I merged the main repo with my fork and it isn't compiling.  It fails at "Generating examples from meta-language (I couldn't think of any solutions).  Here's the output: https://gist.github.com/c4goldsw/2b7d1597d13472f7dd3bd92b014ed6ea14:34
c4goldswarianepaola: Hello14:34
arianepaolahi c4goldsw14:34
@wikingmmm good question14:35
@wikinglol14:35
@wikingtry to remove the build directory14:35
@wikingand recompile14:35
@wikingbtw14:36
@wikinginstall ccache if you dont have it yet14:36
c4goldswDoes it just keep track of what bytecode has / hasn't changed?14:36
arianepaolahi wiking14:36
@wikinghihi114:36
@wikingc4goldsw: yep should14:36
c4goldswSounds useful.  Let's hope rebuilding works lol.14:37
arianepaolawiking: the PR for setup.py is squashed14:37
@wikingarianepaola: i'll try debugging now14:37
@wikingbut if i cannot find it in the next 1-1.5 hours14:37
@wikingi'll just merge it14:37
arianepaolaok, thanks14:37
c4goldswwiking still getting the same error after rebuilding from scratch - are there any issues on your end?15:08
@wikingnoup :)15:14
c4goldswIn that case, I'll dig around myself15:16
c4goldswwiking ^15:16
Saurabh7back15:41
Saurabh7wiking: there is an optional routine I had not touched, since no implciations15:42
Saurabh7it has some lapack i think15:42
Saurabh7If i replace it , then can remvoe the guards15:43
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@wikingSaurabh7: aaaah15:51
@wikingwould be difficult to replace that optional routine?15:51
@wikingor just put that safeguard around the optional routine?15:52
@wikingnot on the whole class implementtion?15:52
Saurabh7I can replace I think15:53
Saurabh7yeah no point in guarding whole thing just for it15:54
@wikingyeah so basically woudl be at least put the guard around the optional thingy15:57
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Saurabh7hm whats this with python 3    except Exception, err:16:28
Saurabh7                    ^16:28
Saurabh7SyntaxError: invalid syntax16:28
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Saurabh7wiking: ok I removed the guards https://github.com/shogun-toolbox/shogun/pull/328816:36
@wikingmmm where do u get this?16:37
Saurabh7develop16:37
Saurabh7building with meta on16:37
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shogun-notifier-shogun: OXPHOS :develop * 02d277b / / (3 files): https://github.com/shogun-toolbox/shogun/commit/02d277b053fdd0ed0f30c15f47ca2adfa730583716:42
shogun-notifier-shogun: cookbook - final16:42
shogun-notifier-shogun: Heiko Strathmann :develop * f8155b1 / / (3 files): https://github.com/shogun-toolbox/shogun/commit/f8155b157f485bdbafa12cfaaabe4f2aedcce4bc16:42
shogun-notifier-shogun: Merge pull request #3244 from OXPHOS/cookbook_mclr16:42
shogun-notifier-shogun:16:42
shogun-notifier-shogun: cookbook: multiclass logistic regression16:42
shogun-notifier-shogun-data: OXPHOS :master * 81a6441 / testsuite/meta/clustering/kmeans.dat: https://github.com/shogun-toolbox/shogun-data/commit/81a64416c3f91d2f5aa333c8dac9667d4a4db54c16:53
shogun-notifier-shogun-data: dataset16:53
shogun-notifier-shogun-data: Heiko Strathmann :master * e316fd6 / testsuite/meta/clustering/kmeans.dat: https://github.com/shogun-toolbox/shogun-data/commit/e316fd67f45cb6e1b8b799369bf50878ddb0c56016:54
shogun-notifier-shogun-data: Merge pull request #101 from OXPHOS/temp16:54
shogun-notifier-shogun-data:16:54
shogun-notifier-shogun-data: update kmeans test dataset16:54
OXPHOSlambday: hey!16:57
OXPHOSHeikoS: thx for the merge16:57
@lambdayOXPHOS: hey16:57
@HeikoSOXPHOS: thanks for da patch!16:57
OXPHOSHeikoS: np!16:58
OXPHOSlambday: I was thinking, there will always be a CPUVector, and the transfertoGPU only makes a copy to GPU16:59
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OXPHOSlambday: and actually the GPU vector is never changed. all the operations (now) return CPU type17:00
@lambdayOXPHOS: umm not sure I fully understand17:00
@lambdayOXPHOS: can you please elaborate a bit?17:00
OXPHOSlambday: so GPUVec is just an add-on to the Vector once users call transfertoGPU. and transfertoGPU doesn't change CPUVector at all17:01
OXPHOSSo it won't happen that there's no CPUVector17:02
@lambdayOXPHOS: no it doesn't change the cpu vector17:02
shogun-notifier-shogun: OXPHOS :develop * 36cf05c / / (5 files): https://github.com/shogun-toolbox/shogun/commit/36cf05c6e15c93b661167f606fee88a8f7aa14a217:02
shogun-notifier-shogun: cookbook - final17:02
shogun-notifier-shogun: Heiko Strathmann :develop * da02a92 / / (5 files): https://github.com/shogun-toolbox/shogun/commit/da02a9280aa2fea485be2fe670aaeff34232496217:02
shogun-notifier-shogun: Merge pull request #3280 from OXPHOS/cookbook_ecoc_random17:02
shogun-notifier-shogun:17:02
@lambdayOXPHOS: oh so you wanted to understand why we need to transfer the gpu memory back to cpu ?17:02
shogun-notifier-shogun: Cookbook ecoc random17:02
OXPHOSlambday: actually yeah17:02
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HeikoS1big improvement that was17:03
@lambdayOXPHOS: so let's imagine this scenario: you transfer the memory to gpu..17:03
@lambdaynow you perform some operation on the vector in-place..17:03
@lambdayas in, say, all the elements are squared.. or something like that17:04
@lambdaysince the data was on gpu, the gpubackend then changed the data on gpu as per the operation specifies it17:04
@lambdaybut it didn't touch cpu data at all17:04
@lambdayso, at the end of all your calls, if you want to return your vector, then the content of the cpu memory is different (obsolete) than that of gpu mem array17:05
@lambdayso if you don't copy the gpu memory to cpu then, the result is incorrect!17:05
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@lambdaybecause the user would expect that all he did in between should be reflected in the result, no?17:06
@lambdayas in, in-place element-wise square, etc etc17:06
@lambdayOXPHOS: am I making sense?17:06
OXPHOSlambday: yes but i am thinking17:06
OXPHOSonly a few operations require in-place change17:07
@lambdayOXPHOS: would it be safe to assume that?17:07
OXPHOSshould we just return the cpu type from the operation?17:07
@lambdayOXPHOS: return from where?17:08
OXPHOSlambday: I might have confused sth. - so say T dot()17:09
OXPHOSthe T is on GPU if ViennaCL is called? or doesn't matter17:09
@lambdayOXPHOS: dot is easy.. dot returns a single scalar value..17:09
@lambdayOXPHOS: what about element-wise square/sin/cos/log/exp/pow(N) ?17:10
@lambdayI mean, in-place operations would be there sometimes I think17:10
OXPHOSlambday: yeah u'r right..17:10
@lambdayyou don't want to create a new memory every-time you do a small operation.. sometimes it is better to be done in-place17:10
@lambdayOXPHOS: say, you want to add two vectors, a and b, and want to store the result in a itself..17:11
@lambdaythis is another example17:11
OXPHOSlambday: sure! and for the transfer to CPU - if onGPU=false, we throw SG_SINFO?17:14
@lambdayso, in the end, when all is said and done, you transfer your gpu data to cpu and return that17:14
@lambdayOXPHOS: yeah, should not be an error..17:14
OXPHOSlambday: and the threadsafe, should it be sth. like mutex? how sure how to accomplish that?17:18
@lambdayOXPHOS: yeah something like mutex or atomic or so.. just wanted that you thought about this a bit17:19
@lambdayOXPHOS: doesn't have to be in this patch.. but maybe in next patch you can add that17:19
OXPHOSlambday: cool thx!17:19
@lambdayOXPHOS: issues like, say, two threads want to transfer the data to gpu.. and such and such17:19
OXPHOSI see17:21
arianepaolaHeikoS would it be possible to add the content from the wiki, containing the description to README.md?17:22
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@HeikoSSaurabh7: hi!18:21
@HeikoSarianepaola: ping!18:21
Saurabh7HeikoS: hihi18:23
shogun-notifier-shogun-data: OXPHOS :master * 8bc728a / testsuite/meta/classifier/relaxed_tree.dat: https://github.com/shogun-toolbox/shogun-data/commit/8bc728a585c3457cd3480b81ef63d80974fb97ea18:23
shogun-notifier-shogun-data: data18:23
shogun-notifier-shogun-data: Heiko Strathmann :master * d4c420b / testsuite/meta/classifier/relaxed_tree.dat: https://github.com/shogun-toolbox/shogun-data/commit/d4c420b6c93f16b3c3439f45de7245d7f432ff0418:23
shogun-notifier-shogun-data: Merge pull request #100 from OXPHOS/master18:23
shogun-notifier-shogun-data:18:23
shogun-notifier-shogun-data: integration test dataset - relaxed tree classifier18:23
@HeikoSSaurabh7: happy about the merge?18:23
@HeikoSSaurabh7: lets discuss next steps18:23
@HeikoSSaurabh7: I have a little side thing:18:23
Saurabh7HeikoS:  yes ofc :018:23
Saurabh7:)18:23
@HeikoSso xvalidation18:23
@HeikoSwe have that parfor thing18:23
@HeikoSwhat happens if I use parfor in an algorithm?18:24
@HeikoSwhat happens?18:24
@HeikoShow is speed affected?18:24
Saurabh7hmm18:24
Saurabh7I need to check , havent run any parallel algo yet18:25
@HeikoSok18:25
@HeikoSmight be a nice little side thing18:25
@HeikoSI think first step is to read up on this case18:25
@HeikoSlambday seemed to remember that doing this is actually strongly discouraged18:26
@HeikoSso we need to protect ourselves against that18:26
@HeikoSapart from that, what algo do you wanna do next?18:26
Saurabh7really, must look into then18:26
Saurabh7HeikoS: I had a look at KNN and CART18:26
Saurabh7CART is really huge,18:27
@HeikoSKNN has something in it already hasnt it=18:27
@HeikoSI know18:27
arianepaolaHeikoS would it be possible to add the content from the wiki, containing the description to http://readme.md/?18:28
@HeikoSwe will do both anyways18:28
@HeikoSarianepaola: yes, actually the readme.md should contain the description from the wiki18:28
@HeikoSI did that a while ago but it got reverted by an accident I think18:28
@HeikoSfeel free to send a patch18:28
arianepaolaok18:28
@HeikoSarianepaola: how is the setup.py going?18:29
@HeikoSalmost done?18:29
arianepaolayes18:30
arianepaolawiking will be merging it18:30
@HeikoSarianepaola: cool18:32
@HeikoSarianepaola: whats the next steps from there?18:32
arianepaolathe debian package18:32
@HeikoSarianepaola: btw, also ping me here if you updated the cookbooks or need help18:32
@HeikoSarianepaola: ah yes cool..18:32
@HeikoSarianepaola: and I guess some testing of the setup.py on our buildbot?18:33
arianepaolayes18:33
@HeikoSarianepaola: ok, looking good18:34
@HeikoSkeep on pushing it :)18:34
arianepaola:-)18:35
Saurabh7HeikoS: then I will be profiling CART now, since its very cluttered , I can then find something to begin with18:36
@HeikoSSaurabh7: ok18:36
@HeikoScool18:36
@HeikoSSaurabh7: yeah profile it, and benchmark it18:36
@HeikoSuse datasets with different N, D, and number of relevant features18:36
@HeikoSa bit like lasso, but the irrelevant features just contain noise18:37
@HeikoSand not sparse18:37
Saurabh7ok cool18:38
@HeikoSOXPHOS: hoi18:46
@HeikoSOXPHOS: can you give me a brief update ?18:47
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OXPHOSHeikoS: sure. I refactored (again) the Linalg Vector class by merging CPU/GPU vector into one vector class and added memory align19:35
OXPHOSHeikoS: also started two cookbooks - sharedboost and relaxed tree19:35
@HeikoSOXPHOS: cool19:36
@HeikoSwas mostly after the linalg19:36
OXPHOSyep19:36
@HeikoSOXPHOS: and next steps for the linalgVector are?19:37
OXPHOStransfer data from GPU back to CPU - add test case - (maybe merge Vector to SGVector) - modify linalg class to be compatible with new Vector class19:39
OXPHOSHeikoS ^19:39
@HeikoSok coo19:39
@HeikoSI discussed a bit with lambday, I think SGVector should not be merged with linalgVector19:40
@HeikoSbut wiking is of different opinion, I dont know how strong though19:40
@HeikoSbut I guess transferring is first19:40
@HeikoScool19:40
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arianepaolabye everyone, see you all tomorrow22:04
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--- Log opened Tue Jun 14 23:09:47 2016
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