| --- Log opened Tue Apr 02 00:00:18 2013 | ||
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| shogun-buildbot_ | build #341 of nightly_default is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/nightly_default/builds/341 | 03:38 |
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| shogun-notifier- | shogun: Soeren Sonnenburg :master * 2234df4 / src/shogun/kernel/string/OligoStringKernel.cpp: https://github.com/shogun-toolbox/shogun/commit/2234df4636c1e6061fcc19209fe279850efa7354 | 08:34 |
| shogun-notifier- | shogun: likely fix oligokernel bug | 08:34 |
| shogun-buildbot_ | build #850 of deb2 - static_interfaces is complete: Failure [failed test python_static] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/850 blamelist: Soeren Sonnenburg <sonne@debian.org> | 08:41 |
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| @sonney2k | x | 08:51 |
| sonne|work | y | 08:51 |
| @sonney2k | z | 08:51 |
| sonne|work | haha! | 08:51 |
| shogun-buildbot_ | build #977 of deb3 - modular_interfaces is complete: Failure [failed test python_modular] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/977 blamelist: Soeren Sonnenburg <sonne@debian.org> | 09:17 |
| blackburn1 | sonne|work: what is going on :D | 10:00 |
| sonne|work | blackburn1: I checked some old version of oligo and that was still giving reasonable results | 10:08 |
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| @sonney2k | blackburn, I am making massive progress on oligo | 19:47 |
| blackburn | sonney2k: nice | 19:47 |
| @sonney2k | now I have a matrix with NaNs instead of 1's | 19:47 |
| @sonney2k | :D | 19:47 |
| @sonney2k | :``-( | 19:47 |
| blackburn | haha | 19:47 |
| blackburn | NaNs for the win | 19:47 |
| * sonney2k eats tons of chocolate for peace of mind | 19:48 | |
| @sonney2k | blackburn, btw similar to SparseUtils we should probably have a LabelFactory class for the casting business | 19:49 |
| @sonney2k | create_from_* | 19:49 |
| blackburn | sonney2k: I was thinking about one thing | 19:50 |
| blackburn | sonney2k: why do we have labels and features (separately)? | 19:50 |
| @sonney2k | blackburn, because labels might be anything, real numbers, ints, strucutres | 19:50 |
| @sonney2k | and features might be strings, etc | 19:51 |
| blackburn | sonney2k: yes but what is the reason to keep them that separate? | 19:51 |
| @sonney2k | if they were same type no need then | 19:51 |
| @sonney2k | I see so some Label entry inside Features | 19:51 |
| blackburn | yes | 19:51 |
| blackburn | I do not suggest it yet but am just trying to understand if there is a special capability | 19:52 |
| @sonney2k | blackburn, there is one CON - for unsupervised methods or dim red etc you have no labels | 19:58 |
| blackburn | sonney2k: yes | 19:58 |
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| @sonney2k | blackburn, haha it gets worse and wors | 20:10 |
| @sonney2k | e | 20:10 |
| blackburn | sonney2k: crashed your kernel? | 20:10 |
| @sonney2k | no but parameters are all crap now | 20:12 |
| blackburn | sonney2k: in linux mean of kernel :) | 20:12 |
| @sonney2k | blackburn, got it to work :D | 20:13 |
| blackburn | cool | 20:13 |
| @sonney2k | there is some oddity when you use it from python | 20:14 |
| @sonney2k | if you do | 20:14 |
| @sonney2k | kernel = OligoStringKernel(size_cache=10, k=3, width=60) | 20:14 |
| @sonney2k | it will accept this | 20:14 |
| @sonney2k | but the parameters for k, width etc are crap | 20:14 |
| blackburn | sonney2k: wait so we do support keywords? | 20:14 |
| @sonney2k | no but this is what n4nd0 wrote in his test script | 20:15 |
| @sonney2k | and python didn't complain | 20:15 |
| @sonney2k | it just called the default constructor (taking no args) | 20:15 |
| @sonney2k | I have no idea why how this can happen | 20:15 |
| blackburn | sonney2k: I expect so | 20:15 |
| @sonney2k | why does it not give an error? | 20:15 |
| blackburn | sonney2k: empty list and kwargs** | 20:15 |
| @sonney2k | blackburn, so argument list is empty but keyword args exist? | 20:16 |
| blackburn | sonney2k: yes | 20:16 |
| @sonney2k | but why does swig allow that? | 20:16 |
| blackburn | sounds legit to me | 20:16 |
| blackburn | sonney2k: I think kws are always allowed | 20:16 |
| blackburn | it is just a matter if you handle them or not | 20:17 |
| @sonney2k | I mean then it should set kws properly | 20:17 |
| @sonney2k | but it doesn't | 20:17 |
| @sonney2k | anyway results look very sane to me now | 20:22 |
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| @sonney2k | blackburn, OK I've thoroughly checked local alignment, oligo and locality improved kernel | 20:53 |
| @sonney2k | they are ok | 20:53 |
| @sonney2k | the simple locality improved kernel is not | 20:54 |
| blackburn | sonney2k: I see | 20:54 |
| @sonney2k | gunnars code is pretty hard to digest | 20:55 |
| @sonney2k | problem is that the kernel sometimes gives OK results | 20:55 |
| @sonney2k | sometimes not | 20:55 |
| @sonney2k | I don't understand why | 20:55 |
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| @sonney2k | and of course valgrind is happy too... | 20:58 |
| @sonney2k | blackburn, while we are at it - we should get rid of all the bool init() functions | 20:59 |
| @sonney2k | but use void() instead | 20:59 |
| blackburn | sonney2k: why? | 20:59 |
| @sonney2k | there are very few functions where we actually return anything | 21:00 |
| @sonney2k | we usually SG_ERROR if something goes wrong | 21:00 |
| @sonney2k | so the code looks like | 21:00 |
| @sonney2k | SG_ERROR / ASSERT | 21:00 |
| @sonney2k | and then return true; | 21:00 |
| @sonney2k | so return values are stupid | 21:00 |
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| shogun-notifier- | shogun: Soeren Sonnenburg :master * de9a300 / src/shogun/kernel/string/ (5 files): https://github.com/shogun-toolbox/shogun/commit/de9a3005ebd65c53c16a24f40e75a2662a46c45d | 21:11 |
| shogun-notifier- | shogun: String kernel fixes | 21:11 |
| shogun-notifier- | shogun: | 21:11 |
| shogun-notifier- | shogun: - add reasonable sqrtdiag normalizer to LI kernel | 21:11 |
| shogun-notifier- | shogun: - add convenience constructor to the oligo kernel | 21:11 |
| shogun-notifier- | shogun: - add slow compute function back to oligo kernel | 21:11 |
| shogun-buildbot_ | build #851 of deb2 - static_interfaces is complete: Failure [failed test python_static] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/851 blamelist: Soeren Sonnenburg <sonne@debian.org> | 21:16 |
| @sonney2k | blackburn, found it | 21:19 |
| @sonney2k | blackburn, the SLIK kernel is not thread safe | 21:19 |
| @sonney2k | so when we call get_kernel_matrix | 21:19 |
| @sonney2k | it is done w/ multiple threads | 21:19 |
| @sonney2k | -> kaboom | 21:19 |
| blackburn | sonney2k: hah | 21:19 |
| @sonney2k | blackburn, it would be actually but it contains the init code in the compute function again - wtf!? | 21:25 |
| @sonney2k | just some left over code | 21:25 |
| @sonney2k | so it will be quicker once removed and work too.. | 21:25 |
| blackburn | sonney2k: that's why we should call all the things as generic as possible | 21:26 |
| blackburn | I mean in kernel we should only define init | 21:26 |
| @sonney2k | blackburn, well it is some left over code obviously sb. optimized the code but forgot to remove it from comput() | 21:28 |
| @sonney2k | btw oligokernel looks like it gives best results here | 21:30 |
| @sonney2k | blackburn, what do you mean w/ only define init? | 21:31 |
| blackburn | sonney2k: it should be called in CKernel | 21:31 |
| shogun-notifier- | shogun: Soeren Sonnenburg :master * cf38f2c / src/shogun/kernel/string/SimpleLocalityImprovedStringKernel.cpp: https://github.com/shogun-toolbox/shogun/commit/cf38f2c9f2c6a2737b76e9fb95d0e7c2cdfaf37d | 21:32 |
| shogun-notifier- | shogun: Bugfix for SLIK kernel | 21:32 |
| shogun-notifier- | shogun: | 21:32 |
| shogun-notifier- | shogun: - remove left over init code in compute function of SLIK kernel | 21:32 |
| shogun-notifier- | shogun: - this init code caused an unstable pyramid array, making | 21:32 |
| shogun-notifier- | shogun: the kernel fail when #threads > 1 | 21:32 |
| @sonney2k | blackburn, in constructor you mean? | 21:32 |
| blackburn | sonney2k: yeah probably | 21:33 |
| blackburn | sonney2k: I know it can't be virtual but we should find a way to avoid such errors | 21:33 |
| @sonney2k | blackburn, that is not possible... we dont' know the kernels' features yet and we need to construct some array based on these features (to speed up compute) | 21:33 |
| @sonney2k | this here was really just some stupid bug | 21:34 |
| @sonney2k | so let me regenerate data for these kernels to get tests to pass | 21:34 |
| blackburn | alrigh | 21:35 |
| @sonney2k | no idea how to do that though for static hmmm | 21:35 |
| @sonney2k | hmmhh probably generate_testdata.py | 21:36 |
| @sonney2k | kaboomn | 21:37 |
| @sonney2k | this old test generator is just so obsolete... | 21:39 |
| @sonney2k | blackburn, however it is our only chance for testing what we have in static interfaces :/ | 21:40 |
| blackburn | yeah | 21:40 |
| shogun-buildbot_ | build #852 of deb2 - static_interfaces is complete: Failure [failed test python_static] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/852 blamelist: Soeren Sonnenburg <sonne@debian.org> | 21:41 |
| shogun-notifier- | shogun: Soeren Sonnenburg :master * 73f200d / tests/integration/generator/dataop.py: https://github.com/shogun-toolbox/shogun/commit/73f200df9b88813c5740feaae2e43c833180a4a2 | 21:49 |
| shogun-notifier- | shogun: fix data generator for kernel integration tests | 21:49 |
| shogun-notifier- | shogun: Soeren Sonnenburg :master * 06939d9 / data: https://github.com/shogun-toolbox/shogun/commit/06939d951d1aa1efc592034373dbb2493ceaf947 | 21:49 |
| shogun-notifier- | shogun: suck in new integration test data | 21:49 |
| @sonney2k | blackburn, I looked at all the HMM related stuff | 21:49 |
| @sonney2k | results are really crap | 21:49 |
| @sonney2k | some inf's in there | 21:50 |
| blackburn | sonney2k: whoops | 21:50 |
| @sonney2k | so it is only HMM_1en10_60_4_1_0_6_3_False_CUBE | 21:51 |
| @sonney2k | failing in tests now AFAIK | 21:51 |
| shogun-buildbot_ | build #978 of deb3 - modular_interfaces is complete: Failure [failed test python_modular] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/978 blamelist: Soeren Sonnenburg <sonne@debian.org> | 21:52 |
| @sonney2k | that shouldn't be too hard to fix - I mean it worked at some point :D | 21:52 |
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| shogun-buildbot_ | build #853 of deb2 - static_interfaces is complete: Failure [failed test python_static] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/853 blamelist: Soeren Sonnenburg <sonne@debian.org> | 22:19 |
| shogun-buildbot_ | build #979 of deb3 - modular_interfaces is complete: Failure [failed test python_modular] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/979 blamelist: Soeren Sonnenburg <sonne@debian.org> | 22:22 |
| shogun-notifier- | shogun: Soeren Sonnenburg :master * 8ffd610 / data,tests/integration/generator/kernel.py: https://github.com/shogun-toolbox/shogun/commit/8ffd610d0fc72be7e1ce93db147dab98fe234074 | 22:23 |
| shogun-notifier- | shogun: 1e-9 accuracy for LA kernel | 22:23 |
| shogun-buildbot_ | build #854 of deb2 - static_interfaces is complete: Failure [failed test python_static] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/854 blamelist: Soeren Sonnenburg <sonne@debian.org> | 22:25 |
| shogun-buildbot_ | build #855 of deb2 - static_interfaces is complete: Failure [failed test python_static] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/855 blamelist: Soeren Sonnenburg <sonne@debian.org> | 22:31 |
| shogun-buildbot_ | build #980 of deb3 - modular_interfaces is complete: Failure [failed test python_modular] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/980 blamelist: Soeren Sonnenburg <sonne@debian.org> | 22:58 |
| shogun-buildbot_ | build #981 of deb3 - modular_interfaces is complete: Failure [failed test python_modular] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/981 blamelist: Soeren Sonnenburg <sonne@debian.org> | 23:00 |
| @sonney2k | blackburn, you don't happen to recall when the tests worked last time for HMM? | 23:20 |
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| --- Log closed Wed Apr 03 00:00:18 2013 | ||
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