| --- Log opened Mon Sep 16 00:00:01 2013 | ||
| wiking | i wonder what is the equivalent of FILE* in python | 00:00 |
|---|---|---|
| @iglesiasg | yep | 00:00 |
| wiking | iglesiasg: maybe you need to implement | 00:00 |
| wiking | CSVFile(int fd) | 00:00 |
| wiking | ctor | 00:00 |
| wiking | and that'll solve your problem | 00:00 |
| @iglesiasg | gsomix, what do you think? ^ | 00:01 |
| wiking | yeah i think that's the problem | 00:01 |
| wiking | that u need a file descriptor ctor | 00:01 |
| wiking | and not a FILE* | 00:01 |
| gsomix | iglesiasg, I'm ok with it. | 00:01 |
| wiking | for this | 00:01 |
| wiking | iglesiasg: just create such a ctor | 00:01 |
| wiking | and just convert fd -> FILE* | 00:01 |
| wiking | in the ctor | 00:02 |
| wiking | ( FILE * | 00:02 |
| wiking | fdopen(int fildes, const char *mode); | 00:02 |
| wiking | ^ is the standard c funct for this | 00:02 |
| @iglesiasg | wiking, and from python the int fd will be the output from gzip.open, right? | 00:02 |
| wiking | mmmm | 00:02 |
| wiking | hope so | 00:02 |
| @iglesiasg | isn't it a bit weird since then the file would be like opened twice? | 00:03 |
| wiking | why? | 00:03 |
| wiking | no | 00:03 |
| wiking | you are passing an FD | 00:03 |
| @iglesiasg | gzip.open | 00:03 |
| @iglesiasg | and then in the constructor | 00:03 |
| wiking | and? | 00:03 |
| @iglesiasg | open(fd) | 00:03 |
| wiking | no | 00:03 |
| wiking | in ctor you open an fd | 00:03 |
| wiking | i mean you pass an fd | 00:03 |
| wiking | hence it's open | 00:03 |
| @iglesiasg | all right | 00:03 |
| wiking | you just ready from the fd starting from that moment in CSVFile | 00:03 |
| wiking | u just need | 00:03 |
| wiking | fdopen(int fildes, const char *mode); | 00:04 |
| wiking | to convert from fd -> FILE* | 00:04 |
| wiking | as CSVFile is writter for using FILE* | 00:04 |
| gsomix | hm, are you sure that gzip.open returns fd? | 00:04 |
| wiking | gsomix: most probably.... | 00:04 |
| gsomix | >> This is a shorthand for GzipFile(filename, mode, compresslevel). | 00:04 |
| gsomix | >> class gzip.GzipFile([filename[, mode[, compresslevel[, fileobj[, mtime]]]]]) | 00:04 |
| gsomix | but class GzipFile class have def fileno(self): method. | 00:07 |
| * gsomix hates python's doc | 00:08 | |
| @iglesiasg | gsomix, any hack required to make a CSVFile constructor visible from interfaces? | 00:11 |
| @iglesiasg | I just compiled and installed and the same error persists | 00:12 |
| @iglesiasg | but in the list of CSVFile constructors printed in the error the CSVFile(int) constructor I created does not appear | 00:12 |
| @iglesiasg | all right, cleaning and re-compiling... | 00:14 |
| gsomix | iglesiasg, I'd like to help, but... z-z-z | 00:20 |
| @iglesiasg | gsomix, no worries | 00:20 |
| gsomix | nite | 00:20 |
| gsomix | iglesiasg, so if ctor works you can use fileno method of GzipFile for getting fd | 00:23 |
| @iglesiasg | gsomix, nice, thanks! | 00:23 |
| @iglesiasg | that can be indeed useful | 00:23 |
| wiking | lol | 00:27 |
| wiking | gta v is out | 00:27 |
| wiking | :d | 00:27 |
| @iglesiasg | good bye guys, see you in three months again :P | 00:29 |
| wiking | indeed | 00:30 |
| wiking | :D | 00:30 |
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| wiking | ah ok | 00:30 |
| wiking | i dont have neither ps3 nor xbox | 00:30 |
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| @iglesiasg | wiking, one of my friends got a ps3 a couple of days ago for this lol | 00:51 |
| @iglesiasg | wiking, btw it seems that gzip.open doesn't return an int | 00:51 |
| @iglesiasg | or a fd for that matter | 00:51 |
| wiking | 00:22 < gsomix> iglesiasg, so if ctor works you can use fileno method of GzipFile for getting fd | 00:52 |
| @iglesiasg | wiking, bah it didn't work for some reason | 00:53 |
| wiking | ? | 00:53 |
| @iglesiasg | wiking, I can call the constructor with CSVFile(gzipfile.fileno()) | 00:53 |
| wiking | how so? | 00:53 |
| @iglesiasg | but the features object has 0 features and vectors | 00:53 |
| wiking | mmm iglesiasg test then first the ctor | 00:54 |
| wiking | i.e. write a small c++ code | 00:54 |
| @iglesiasg | wiking, this is the constructor | 00:54 |
| @iglesiasg | +CCSVFile::CCSVFile(int fd) : | 00:54 |
| @iglesiasg | + CFile(fdopen(fd, "r"), NULL) | 00:54 |
| @iglesiasg | +{ | 00:54 |
| @iglesiasg | + init(); | 00:54 |
| wiking | that open a csv file with int fd = open('filename', 'r') | 00:54 |
| @iglesiasg | + init_with_defaults(); | 00:54 |
| @iglesiasg | +} | 00:54 |
| @iglesiasg | I might have very well screwed | 00:54 |
| wiking | and then pass that fd to the new ctor | 00:55 |
| @iglesiasg | just looked up what the other constructors do | 00:55 |
| wiking | yeah | 00:56 |
| wiking | CFile(fdopen(fd, "r"), NULL) -> CFile(fdopen(fd, rw), name) | 00:57 |
| wiking | and he ctor shouuld be | 00:57 |
| @iglesiasg | wiking, rw is "rw"? | 00:58 |
| @iglesiasg | I just didn't add the arguments for name and permissions at first | 00:59 |
| wiking | CSVFile(int fd, const char* name) | 00:59 |
| wiking | CSVFile(int fd, char rw, const char* name) | 00:59 |
| wiking | .. | 00:59 |
| wiking | but yeah | 00:59 |
| wiking | other than that that should work | 00:59 |
| wiking | The mode of the stream must be compatible with the mode of the file descriptor. | 01:00 |
| wiking | maybe it has different modes? | 01:00 |
| wiking | u should really first test this ctor from c++ code | 01:00 |
| @iglesiasg | wiking, how do you suggest me to try it? | 01:05 |
| wiking | 00:54 < wiking> that open a csv file with int fd = open('filename', 'r') | 01:07 |
| @iglesiasg | wiking, all right, let's do that | 01:07 |
| @iglesiasg | sorry for making you repeat stuff :S | 01:08 |
| @iglesiasg | wiking, so I think the problem is that opening the file with gzip is not doing anything about uncompressing it | 01:20 |
| @iglesiasg | the gzip.GzipFile.read() method does it | 01:20 |
| @iglesiasg | but if we just open it and give it to CSVFile, then it is not uncompressed | 01:20 |
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| besser82 | sonne|osx: Der neue build f?r rubygem-narray f?r FC19 ist unterwegs, sollte im laufe des heutigen Tages in den Repos sein :) | 08:01 |
| sonne|osx | besser82: very good | 08:01 |
| sonne|osx | err sehr sch?n :) | 08:01 |
| besser82 | sonne|osx: F?r FCRH m?sste das update schon da sein :) | 08:01 |
| besser82 | sonne|osx: uuups, was confused. This is an English channel :) | 08:02 |
| lisitsyn | besser82: na ja das ist ok | 08:02 |
| lisitsyn | :D | 08:02 |
| besser82 | OK. :D | 08:02 |
| besser82 | Ihr seid fast alles deutsche, oder? | 08:02 |
| lisitsyn | besser82: well I am very basic with deutsch ;) | 08:03 |
| besser82 | lisitsyn: I see :) | 08:05 |
| lisitsyn | besser82: but HeikoS is native and wiking speaks it ok IIRC | 08:06 |
| besser82 | lisitsyn: HeikoS, I know about :) Had a 1:1 with him when I intially joined this channel. But it's good to know wiking has knowledge in German, too. This may come in handy on squashig problem eith CMake :) | 08:07 |
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| shogun-notifier- | shogun: Soeren Sonnenburg :develop * f56e63e / examples/undocumented/r_modular/classifier_svmocas_modular.R: https://github.com/shogun-toolbox/shogun/commit/f56e63e62ca6a3f6f252e50543ec5b21bd676e8a | 08:08 |
| shogun-notifier- | shogun: fix ocas R example | 08:08 |
| lisitsyn | besser82: and I cover russian side :) | 08:09 |
| besser82 | lisitsyn: Good to know. Some russian buddy of mine possibly wanted to comaintain SHOGUN on FC :) | 08:09 |
| besser82 | lisitsyn: so we have very good lang-covering here ;) | 08:10 |
| lisitsyn | besser82: yeah | 08:11 |
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| shogun-buildbot | build #1742 of bsd1 - libshogun is complete: Failure [failed compile] Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/1742 blamelist: Soeren Sonnenburg <sonne@debian.org> | 08:17 |
| shogun-buildbot | build #80 of precise - libshogun is complete: Success [build successful] Build details are at http://buildbot.shogun-toolbox.org/builders/precise%20-%20libshogun/builds/80 | 08:25 |
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| gsomix | sonney2k, hey | 08:30 |
| shogun-buildbot | build #96 of FC19 - modular_interfaces is complete: Failure [failed configure] Build details are at http://buildbot.shogun-toolbox.org/builders/FC19%20-%20modular_interfaces/builds/96 blamelist: Soeren Sonnenburg <sonne@debian.org> | 08:31 |
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| shogun-buildbot | build #1477 of cyg1 - libshogun is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1477 blamelist: Soeren Sonnenburg <sonne@debian.org> | 08:49 |
| shogun-buildbot | build #1824 of deb3 - modular_interfaces is complete: Failure [failed test python_modular test r_modular] Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1824 blamelist: Soeren Sonnenburg <sonne@debian.org> | 08:55 |
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| travis-ci | [travis-ci] it's Soeren Sonnenburg'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/11403552 | 09:09 |
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| sonne|work | wiking: awake? | 09:27 |
| wiking | yep yep | 09:28 |
| wiking | what'sup | 09:28 |
| sonne|work | wiking: could you enable running examples and tests for the static interfaces? | 09:29 |
| sonne|work | wiking: you currently enabled for cmdline only | 09:29 |
| wiking | hahah | 09:29 |
| sonne|work | and no tests | 09:29 |
| wiking | it's not about enabling them | 09:29 |
| wiking | it's about implementing them.. | 09:29 |
| wiking | and that's more time | 09:29 |
| sonne|work | errm what changed? | 09:30 |
| wiking | nothing but it was never implemented | 09:30 |
| sonne|work | I mean how do you run *_modular examples? | 09:30 |
| wiking | it has nothing to do with it | 09:30 |
| wiking | i mean cmake needs to be created | 09:31 |
| wiking | the files that actually will run the examples | 09:31 |
| sonne|work | ok | 09:32 |
| sonne|work | so I guess later then :/ | 09:32 |
| sonne|work | wiking: and what did you find out about the R dispatcher? | 09:32 |
| sonne|work | wiking: not sure if you have seen but we now have only 2 examples failing | 09:32 |
| sonne|work | and it seems like real bugs / memory corruption | 09:33 |
| lisitsyn | sonne|work: is thursday 18:00 ok for you? | 09:33 |
| lisitsyn | (meeting) | 09:33 |
| sonne|work | timezone? | 09:33 |
| lisitsyn | sonne|work: your | 09:33 |
| sonne|work | no time | 09:34 |
| lisitsyn | http://doodle.com/4ctd4cwr588nwe52 | 09:34 |
| lisitsyn | I am having hard time with that doodle | 09:34 |
| lisitsyn | sonne|work: do you see anything that fits your timespans? | 09:34 |
| besser82 | sonne|work: with the recent git-checkout build fails again, when no .git-dir is present: src/shogun/base/Version.cpp:20:43: Fehler: too many decimal points in number: const int32_t Version::version_revision = VERSION_REVISION; | 09:34 |
| besser82 | sonne|osx: src/shogun/base/Version.cpp: In statischer Elementfunktion >>static int32_t shogun::Version::get_version_revision()<<: | 09:35 |
| besser82 | sonne|osx: src/shogun/base/Version.cpp:70:1: Warnung: Kontrollfluss erreicht Ende von Nicht-void-Funktion [-Wreturn-type] | 09:35 |
| sonne|work | besser82: I didn't change a thing though, please paste the generated src/shogun/lib/versionstring.h | 09:35 |
| sonne|work | lisitsyn: looking | 09:36 |
| wiking | sonne|work: yeah i'll do the things... | 09:36 |
| wiking | sonne|work: but now i'm working on something else :) | 09:36 |
| wiking | for the first time | 09:36 |
| sonne|work | wiking: what did you find out about R? | 09:36 |
| sonne|work | lisitsyn: times are in UTC? | 09:36 |
| lisitsyn | sonne|work: berlin tz | 09:36 |
| lisitsyn | hmm | 09:37 |
| lisitsyn | sonne|work: argh | 09:37 |
| sonne|work | lisitsyn: so when I click 11PM then it is local time right? | 09:37 |
| lisitsyn | sonne|work: at the top of the table | 09:37 |
| sonne|work | ? | 09:37 |
| lisitsyn | sonne|work: there is timezone thing | 09:37 |
| sonne|work | yes it says berlin | 09:37 |
| lisitsyn | sonne|work: yeah then what you see is berlin tz | 09:38 |
| besser82 | sonne|work: here you go: http://ur1.ca/fk9m5 | 09:38 |
| lisitsyn | sonne|work: because it shows me moscow tz for a reason :D | 09:38 |
| sonne|work | besser82: #define VERSION_REVISION 0x3.0.0 | 09:38 |
| sonne|work | so yes indeed wrong | 09:38 |
| besser82 | sonne|work: how should it be supposed to look like? 3.0.0? | 09:39 |
| sonne|work | I guess I will have to strip the dots and fill in some 0's | 09:39 |
| sonne|work | maybe 0x300000 | 09:40 |
| besser82 | sonne|work: looks better, meanwhile I'll use some sed-magic on it.... | 09:41 |
| sonne|work | lisitsyn: ok filled in | 09:42 |
| besser82 | sonne|work: sed-magick doesn't work file get's regenerated on `make` | 09:43 |
| sonne|work | besser82: sure I will fix it relax | 09:45 |
| besser82 | sonne|work: thanks :) | 09:45 |
| lisitsyn | sonne|work: ohh the best case is w/o pickle27 lambday hushell patrick and fernando | 09:46 |
| sonne|work | lisitsyn: what shall I say... | 09:47 |
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| sonne|work | besser82: any idea how to generate a regexp that adds a trailing 0 ? Or some cmake way to do the job 1 -> 01 ? | 09:57 |
| besser82 | sonne|work: you are talking about PREpending a "0"? | 09:58 |
| sonne|work | besser82: yeah that is what I meant | 09:58 |
| besser82 | sonne|work: SET (var "0${var}") should do :) | 09:58 |
| sonne|work | besser82: well but var needs to be 0...9 then | 09:59 |
| besser82 | sonne|work: or you can SET(var "0") .... SET( var "${var}${new-value}") ;) | 10:00 |
| besser82 | sonne|work: if you need some more elaborated way, please point me to the code/script in question | 10:01 |
| sonne|work | besser82: well version.cmake in cmake dir | 10:02 |
| sonne|work | besser82: I am extracting a VERSION_MAJOR / MINOR now | 10:02 |
| sonne|work | for getting the | 10:02 |
| sonne|work | 0x030000 | 10:02 |
| sonne|work | I need to prepend a 0 if the MAJOR/MINOR is <10 | 10:03 |
| besser82 | if (${var} <= 9) | 10:04 |
| besser82 | set(var "0${var}") | 10:04 |
| besser82 | endif | 10:04 |
| besser82 | sonne|work: ^^^ | 10:05 |
| lisitsyn | damn | 10:06 |
| lisitsyn | I am the worst manager | 10:09 |
| lisitsyn | :D | 10:09 |
| besser82 | sonne|work: build of testsuit fails, too: Linking CXX executable shogun-unit-test | 10:09 |
| besser82 | CMakeFiles/shogun-unit-test.dir/SerializationAscii_unittest.cc.o: In function `Dummy_dummy_Test::TestBody()': | 10:09 |
| besser82 | /home/besser82/shared/github/shogun/third_party/GoogleMock/gtest/include/gtest/internal/gtest-internal.h:443: multiple definition of `Dummy_dummy_Test::TestBody()' | 10:09 |
| besser82 | CMakeFiles/shogun-unit-test.dir/clone_unittest.cc.o:/home/besser82/shared/github/shogun/third_party/GoogleMock/gtest/include/gtest/internal/gtest-internal.h:425: first defined here | 10:09 |
| besser82 | CMakeFiles/shogun-unit-test.dir/SerializationAscii_unittest.cc.o: In function `Dummy_dummy_Test::TestBody()': | 10:09 |
| besser82 | /home/besser82/shared/github/shogun/third_party/GoogleMock/gtest/include/gtest/internal/gtest-internal.h:443: multiple definition of `Dummy_dummy_Test::test_info_' | 10:09 |
| besser82 | CMakeFiles/shogun-unit-test.dir/clone_unittest.cc.o:/home/besser82/shared/github/shogun/third_party/GoogleMock/gtest/include/gtest/internal/gtest-internal.h:425: first defined here | 10:09 |
| besser82 | CMakeFiles/shogun-unit-test.dir/SerializationHDF5_unittest.cc.o: In function `Dummy_dummy_Test::TestBody()': | 10:09 |
| besser82 | /home/besser82/shared/github/shogun/third_party/GoogleMock/gtest/include/gtest/internal/gtest-internal.h:443: multiple definition of `Dummy_dummy_Test::TestBody()' | 10:09 |
| besser82 | CMakeFiles/shogun-unit-test.dir/clone_unittest.cc.o:/home/besser82/shared/github/shogun/third_party/GoogleMock/gtest/include/gtest/internal/gtest-internal.h:425: first defined here | 10:09 |
| besser82 | CMakeFiles/shogun-unit-test.dir/SerializationHDF5_unittest.cc.o: In function `Dummy_dummy_Test::TestBody()': | 10:09 |
| besser82 | /home/besser82/shared/github/shogun/third_party/GoogleMock/gtest/include/gtest/internal/gtest-internal.h:443: multiple definition of `Dummy_dummy_Test::test_info_' | 10:09 |
| besser82 | CMakeFiles/shogun-unit-test.dir/clone_unittest.cc.o:/home/besser82/shared/github/shogun/third_party/GoogleMock/gtest/include/gtest/internal/gtest-internal.h:425: first defined here | 10:09 |
| besser82 | CMakeFiles/shogun-unit-test.dir/SerializationJSON_unittest.cc.o: In function `Dummy_dummy_Test::TestBody()': | 10:09 |
| besser82 | /home/besser82/shared/github/shogun/th | 10:10 |
| besser82 | sonne|work: ^^^ | 10:10 |
| sonne|work | besser82: no idea about that one - that is sth for wiking... | 10:10 |
| besser82 | sonne|work: kk, will ping him about ;) | 10:11 |
| besser82 | wiking: can you have a look, please. ^^^^ | 10:11 |
| wiking | mmm will do | 10:11 |
| wiking | later | 10:11 |
| wiking | besser82: send me an email | 10:11 |
| besser82 | wiking: your adress? | 10:12 |
| wiking | wiking@maeth.com | 10:12 |
| besser82 | wiking: thx! | 10:13 |
| besser82 | wiking: should be there in a sec ;) | 10:14 |
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| wiking | gotitwillreplysoon | 10:16 |
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| sonne|work | excellent https://www.djangoproject.com/weblog/2013/sep/15/security/ | 11:12 |
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| @HeikoS | lambday: hi! | 12:17 |
| lambday | HeikoS: hi | 12:17 |
| lambday | hehe I pinged at the same time | 12:17 |
| @HeikoS | just checked your PR, still building in travis | 12:17 |
| @HeikoS | haha :) | 12:17 |
| lambday | HeikoS: with 10 log-det samples, I get pretty good accuracy | 12:17 |
| @HeikoS | so how are things? | 12:17 |
| lambday | >>> print sum(probing_estimates)/len(probing_estimates) 1422.85679236 >>> print actual 1422.84404724 | 12:17 |
| lambday | working with python now | 12:17 |
| @HeikoS | this is the sparse matrix we had? | 12:18 |
| lambday | west0479 | 12:18 |
| lambday | I took A'*A+eye | 12:18 |
| @HeikoS | ok cool | 12:18 |
| @HeikoS | is this dataset public open? | 12:18 |
| lambday | HeikoS: I guess so | 12:19 |
| @HeikoS | http://math.nist.gov/MatrixMarket/data/Harwell-Boeing/chemwest/west0479.html | 12:19 |
| lambday | scipy is an angel | 12:19 |
| @HeikoS | lambday: yep its very cool | 12:19 |
| lambday | great! So I can use this for all the examples, right? | 12:19 |
| @HeikoS | yeah, we just have to find the license | 12:20 |
| @HeikoS | I dont know whether we can just copy it into our gpl repo | 12:20 |
| lambday | HeikoS: how about I store the A'A+I one in the repo, that too would be causing license issues? | 12:21 |
| @HeikoS | mmmh | 12:21 |
| @HeikoS | I dont know | 12:21 |
| @HeikoS | better check | 12:21 |
| @HeikoS | If it is one, we can download it from the python example or so | 12:21 |
| @HeikoS | The original data sets and descriptions are from the NIST web site and were not covered by an explicit copyright. Modifications for R data sets are covered by GPL (>= 2). | 12:22 |
| @HeikoS | so thats the way we should do it | 12:22 |
| @HeikoS | should add some comment stating where the data is from and that its not under gpl, but the changes are | 12:23 |
| lambday | alrighty | 12:23 |
| @HeikoS | https://svn.r-project.org/R-packages/trunk/NISTnls/DESCRIPTION | 12:23 |
| @HeikoS | thats how R does it | 12:23 |
| @HeikoS | lambday: your latest patch, does that work with python modular? | 12:23 |
| lambday | HeikoS: locally it works | 12:23 |
| @HeikoS | ok cool, | 12:24 |
| @HeikoS | there were other problems too | 12:24 |
| @HeikoS | did you rebase recently? | 12:24 |
| lambday | but on travis some examples/tests fail | 12:24 |
| lambday | yep | 12:24 |
| @HeikoS | ok I will have a look once they are done | 12:24 |
| lambday | HeikoS: got an weird swig related error for JobResultAggregator, left that one for the time being from adding to modular interface... | 12:24 |
| lambday | the java modular failure was being caused by that | 12:25 |
| lambday | oh btw I converted this to ascii for libshogune examples as well, but some changes in the load_svmlight_file in SGSparseMatrix lately and it can't read | 12:25 |
| lambday | HeikoS: weirdly enough, I just set the max iteration limit to 10000 and it converges properly | 12:26 |
| lambday | for CG-M | 12:26 |
| lambday | max/min eigs are similar to the one you had for your ipython | 12:26 |
| lambday | not same but of similar range | 12:27 |
| @HeikoS | lambday: ah annyoing with the changes | 12:27 |
| @HeikoS | ok | 12:27 |
| @HeikoS | lanczos might converge to different things in different runs | 12:27 |
| @HeikoS | make sure the examples do not take too long to run | 12:27 |
| @HeikoS | the python ones are part of the test-suite, so should be in less than say 2-3seconds | 12:28 |
| @HeikoS | the ipython can take slightly longer (maybe 30s max) | 12:28 |
| @HeikoS | but shorter is better | 12:28 |
| @HeikoS | rather add a comment for the users that they can increase this or that to get "proper" results | 12:28 |
| lambday | 2-3 secs! | 12:29 |
| lambday | I have to do with just 1 log-det sample then | 12:29 |
| lambday | yeah that sounds good | 12:29 |
| lambday | so, the matrix (mat and ascii) of A'A+I, where would it go? | 12:30 |
| @HeikoS | ok thats ok | 12:30 |
| lambday | shogun/data? | 12:30 |
| @HeikoS | into the data repository, in fact put the original dataset there | 12:30 |
| @HeikoS | have a look at the other files | 12:30 |
| @HeikoS | and add some comment with the readme | 12:30 |
| lambday | shogun-data? | 12:30 |
| lambday | alright checking | 12:30 |
| @HeikoS | you can compute A^T A yourself then | 12:30 |
| lambday | ummm... yeah, but for the libshogun ones, it would be easier if we have the final matrix too, otherwise again gotta use eigen3 | 12:31 |
| lambday | but for the time being only adding python examples | 12:32 |
| @HeikoS | lambday: thats fine isnt it? | 12:32 |
| lambday | will add libshogun ones when load_from_svmlight works | 12:32 |
| lambday | yeah, should be fine | 12:32 |
| @HeikoS | I mean eigen needs to be there anyway | 12:32 |
| @HeikoS | lambday: yep ok | 12:32 |
| @HeikoS | let me know how it goes | 12:32 |
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| lambday | HeikoS: alright | 12:33 |
| @HeikoS | lambday: I told some people about this stuff and they liked it a lot. In particular that you did this c-implementation | 12:33 |
| lambday | :D | 12:33 |
| lambday | I hope this becomes useful... but we sure need to add preconditioners | 12:34 |
| @HeikoS | lambday: yep we need those | 12:34 |
| lambday | feels good that things work properly | 12:36 |
| lambday | cocg too works now | 12:36 |
| @HeikoS | lambday: yep very good! | 12:36 |
| @HeikoS | probably takes much longer right? | 12:36 |
| lambday | I checked up to rational approximation of log(A) using unit basis vectors - they work as good as triangular solvers | 12:37 |
| lambday | for that test, they don't take long, converges within a few iterations | 12:38 |
| besser82 | sonne|work, wiking: /home/besser82/rpmbuild/BUILD/shogun-f56e63e62ca6a3f6f252e50543ec5b21bd676e8a/examples/undocumented/csharp_modular/regression_svrlight_modular.cs(23,17): error CS0246: The type or namespace name `SVRLight' could not be found. Are you missing a using directive or an assembly reference? | 12:40 |
| besser82 | /home/besser82/rpmbuild/BUILD/shogun-f56e63e62ca6a3f6f252e50543ec5b21bd676e8a/examples/undocumented/csharp_modular/regression_svrlight_modular.cs(24,17): error CS0841: A local variable `svr' cannot be used before it is declared | 12:40 |
| besser82 | /home/besser82/rpmbuild/BUILD/shogun-f56e63e62ca6a3f6f252e50543ec5b21bd676e8a/examples/undocumented/csharp_modular/regression_svrlight_modular.cs(26,17): error CS0841: A local variable `svr' cannot be used before it is declared | 12:40 |
| besser82 | /home/besser82/rpmbuild/BUILD/shogun-f56e63e62ca6a3f6f252e50543ec5b21bd676e8a/examples/undocumented/csharp_modular/regression_svrlight_modular.cs(29,67): error CS0841: A local variable `svr' cannot be used before it is declared | 12:40 |
| besser82 | /home/besser82/rpmbuild/BUILD/shogun-f56e63e62ca6a3f6f252e50543ec5b21bd676e8a/examples/undocumented/csharp_modular/regression_svrlight_modular.cs(29,53): error CS1502: The best overloaded method match for `LabelsFactory.to_regression(Labels)' has some invalid arguments | 12:40 |
| besser82 | /home/besser82/rpmbuild/BUILD/shogun-f56e63e62ca6a3f6f252e50543ec5b21bd676e8a/build/src/interfaces/csharp_modular/modshogun.dll (Location of the symbol related to previous error) | 12:40 |
| besser82 | /home/besser82/rpmbuild/BUILD/shogun-f56e63e62ca6a3f6f252e50543ec5b21bd676e8a/examples/undocumented/csharp_modular/regression_svrlight_modular.cs(29,53): error CS1503: Argument `#1' cannot convert `object' expression to type `Labels' | 12:40 |
| besser82 | Compilation failed: 6 error(s), 0 warnings | 12:40 |
| besser82 | make[2]: *** [examples/undocumented/csharp_modular/csharp-regression_svrlight_modular] Error 1 | 12:41 |
| besser82 | sonne|work, wiking: ^^^ happenes when -DUSE_SVMLIGHT=OFF. | 12:41 |
| @HeikoS | besser82: this looks like forgotten guards for SVMLight | 12:41 |
| besser82 | HeikoS: who in charge for this? | 12:42 |
| @HeikoS | besser82: the one who finds it :D | 12:42 |
| @HeikoS | I think in the example, there just needs to be a check whether USE_SVMLIGHT is defined | 12:42 |
| @HeikoS | and if not, not execute things | 12:43 |
| @HeikoS | or not compile to be more exact | 12:43 |
| besser82 | HeikoS: I'm no official SHOGUN, I'm afraid... Nor do I know about C#.... | 12:43 |
| @HeikoS | like #ifdef HAVE_BLABLALBA ..... #endif | 12:43 |
| @HeikoS | besser82: yeah was just a joke, could you fill in an issue | 12:43 |
| @HeikoS | besser82: I dont know who knows c# here | 12:44 |
| besser82 | HeikoS: kk, will do :D | 12:44 |
| lambday | man shogun-data is *huge* | 12:46 |
| @HeikoS | lambday: yep | 12:46 |
| besser82 | HeikoS: https://github.com/shogun-toolbox/shogun/issues/1600 | 12:47 |
| lambday | HeikoS: still downloading... oh and it doesn't have any README, so should I just add a separate directory for logdet and add a Readme.txt there, where I say that this matrix from this and that and GPL thing | 12:47 |
| besser82 | lambday: what are going to bundle into SHOGUN? | 12:48 |
| besser82 | lambday: s/are /&you | 12:48 |
| @HeikoS | besser82: thanks! | 12:49 |
| lambday | besser82: adding a .mat file basically | 12:49 |
| @HeikoS | lambday: no put it there directly | 12:49 |
| @HeikoS | lambday: dont put a mat file | 12:49 |
| @HeikoS | put a more standard format like csv, like the other files in there | 12:49 |
| @HeikoS | maybe even zipped | 12:49 |
| @HeikoS | lambday: we can ask sonney2k about the license stuff later, just add for now | 12:49 |
| lambday | HeikoS: alright.. so I have it in svmlight format | 12:50 |
| @HeikoS | thats good | 12:50 |
| lambday | HeikoS: but for python, I was planning to use the mat/mtx one | 12:51 |
| @HeikoS | lambday: you can load the thing and convert or? | 12:52 |
| lambday | HeikoS: ya scipy.io.mmread, and then tocsc()... | 12:53 |
| @HeikoS | lambday: yeah thats good | 12:53 |
| @HeikoS | csc_matrix() from scipy.sparse | 12:53 |
| @HeikoS | also does that | 12:53 |
| lambday | yeah | 12:53 |
| lambday | alright | 12:53 |
| besser82 | lambday: I thought I would have been another piece of code ;) | 12:53 |
| besser82 | HeikoS: np. We all want to get that in shape, don't we? | 12:54 |
| lambday | HeikoS: so, shall I add the mtx that I directly downloaded from the website, and then my converted ascii svmlight format one (for libshogun examples), tarzipped | 12:55 |
| lambday | besser82: :D | 12:55 |
| @HeikoS | besser82: yes! | 12:56 |
| @HeikoS | besser82: you could also try to compile with LAPACK not being installed | 12:57 |
| @HeikoS | I fixed like 50 issues around that a few weeks ago | 12:57 |
| @HeikoS | but there are more | 12:57 |
| lambday | HeikoS: shogun-data/testsuite/mathematics/west0479.tar.gz sounds good? | 12:59 |
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| gsomix | sonney2k, sonne|work hey ho | 12:59 |
| lambday | west0479.mtx and west0479.txt inside | 12:59 |
| @HeikoS | lambday: yep! | 12:59 |
| lambday | alright | 13:00 |
| @HeikoS | ls /share/apps/lapack-3-4.1/ | 13:00 |
| @HeikoS | liblapack.a librefblas.a libtmglib.a | 13:00 |
| @HeikoS | this is what I have | 13:00 |
| @HeikoS | ah sorry wrong window | 13:00 |
| lisitsyn | wiking: ping | 13:06 |
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| van51 | sonne|work: ping | 13:17 |
| sonne|work | van51: hey! | 13:21 |
| sonne|work | gsomix: ho! | 13:21 |
| van51 | sonne|work: hey! I've started a comment on github, so I'll finish it there :) | 13:21 |
| gsomix | sonne|work, thnx for comments! | 13:22 |
| sonne|work | gsomix: hope they were useful... | 13:23 |
| sonne|work | van51: ok ping me once done | 13:23 |
| lambday | HeikoS: changed... moved it under logdet/ | 13:23 |
| gsomix | sonne|work, yep, of course. CProtobufFile is a good idea I think. | 13:23 |
| sonne|work | HeikoS: btw have you seen almost all R examples seem to work now... | 13:24 |
| sonne|work | HeikoS: r_modular that is | 13:24 |
| @HeikoS | sonne|work: its R modular | 13:24 |
| @HeikoS | yeah I have seen something | 13:24 |
| @HeikoS | is it wiking? | 13:24 |
| sonne|work | only 2 failing | 13:24 |
| @HeikoS | sonne|work: is this with reference counting? | 13:24 |
| sonne|work | I fixed them... | 13:24 |
| @HeikoS | sonne|work: wow! great job! | 13:25 |
| @HeikoS | many people will love you for that? :) | 13:25 |
| sonne|work | I would wish we could compare if they do the right job... | 13:25 |
| sonne|work | still things are a bit awkward | 13:25 |
| sonne|work | e.g. there are some weird bugs | 13:25 |
| @HeikoS | sonne|work: yeah testing the interfaces somehow would be great | 13:25 |
| sonne|work | like you do kernel.init() for linear kernel | 13:25 |
| @HeikoS | sonne|work: btw a question: where in shogun-data should sparse test matrices for log-det framework go, new folder logdet? | 13:25 |
| sonne|work | and for some reason kernel.init_optimization is attempted to be called | 13:26 |
| @HeikoS | sonne|work: ok ... | 13:26 |
| van51 | sonne|work: done | 13:26 |
| @HeikoS | sonne|work: if we can get it working at least minimally | 13:26 |
| @HeikoS | then people would already use it, find more problems and maybe some people will start fixing them | 13:26 |
| @HeikoS | sonne|work: just have been to a stats workshop and everyone is using R | 13:26 |
| @HeikoS | its so weird | 13:26 |
| sonne|work | HeikoS: well it is it seems http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1824/steps/test%20r_modular/logs/stdio | 13:27 |
| @HeikoS | they dont know anything else, they dont know even what else exists | 13:27 |
| sonne|work | statistics people... | 13:27 |
| sonne|work | van51: ok will have a look | 13:27 |
| @HeikoS | but would be good users ;) | 13:27 |
| @HeikoS | lambday: merged the data | 13:27 |
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| shogun-notifier- | shogun-data: lambday :master * a12a28c / logdet/west0479.tar.gz: https://github.com/shogun-toolbox/shogun-data/commit/a12a28c93767c9c265295232cade3c490a7a3710 | 13:27 |
| shogun-notifier- | shogun-data: Added matrix-data in mtx (original) and ascii (converted) (log-det) | 13:27 |
| shogun-notifier- | shogun-data: Heiko Strathmann :master * 7d37a77 / logdet/west0479.tar.gz: https://github.com/shogun-toolbox/shogun-data/commit/7d37a7713c407618bb5b790811040e6c71027922 | 13:27 |
| shogun-notifier- | shogun-data: Merge pull request #19 from lambday/master | 13:27 |
| shogun-notifier- | shogun-data: | 13:27 |
| sonne|work | gsomix: have you seen the <size> <protobufmsg> format suggestion? | 13:27 |
| shogun-notifier- | shogun-data: Added matrix-data in mtx (original) and ascii (converted) (log-det) | 13:27 |
| lambday | HeikoS: thanks :) | 13:28 |
| gsomix | sonne|work, yep, I'm using this format for now. | 13:28 |
| lambday | HeikoS: my PR gives green except python modular, that fails for a few tests | 13:28 |
| lambday | 3 tests basically | 13:28 |
| sonne|work | gsomix: just make sure that the <size> thing is endian save | 13:29 |
| shogun-notifier- | shogun: lambday :develop * bc17983 / / (163 files): https://github.com/shogun-toolbox/shogun/commit/bc179839b8f4b051a09c9c7f22529a962155ade9 | 13:30 |
| shogun-notifier- | shogun: refactored log-det and computation framework | 13:30 |
| shogun-notifier- | shogun: lambday :develop * d49c048 / / (16 files): https://github.com/shogun-toolbox/shogun/commit/d49c048a5f0b26fd0985afb16d6f61311f6fcb62 | 13:30 |
| shogun-notifier- | shogun: COCG linear solver fixed, unit-test modified (log-det) | 13:30 |
| shogun-notifier- | shogun: lambday :develop * 050f2a2 / src/ (5 files): https://github.com/shogun-toolbox/shogun/commit/050f2a2935c219b1a80ddcfd5f4a54e42e7cb1ee | 13:30 |
| shogun-notifier- | shogun: modular interface updated (log-det) | 13:30 |
| shogun-notifier- | shogun: Heiko Strathmann :develop * af2d9dc / / (175 files): https://github.com/shogun-toolbox/shogun/commit/af2d9dcbdc27cff4553f41ebce910251809f0120 | 13:30 |
| shogun-notifier- | shogun: Merge pull request #1586 from lambday/feature/log_determinant | 13:30 |
| shogun-notifier- | shogun: | 13:30 |
| shogun-notifier- | shogun: Refactored log-det and computation framework | 13:30 |
| @HeikoS | lambday: yep thats not your fault, merged :) | 13:30 |
| lambday | HeikoS: silly question - how shall I use this data for examples? | 13:30 |
| lambday | :) | 13:30 |
| @HeikoS | lambday: well, import it | 13:31 |
| @HeikoS | look at the other examples :) | 13:31 |
| @HeikoS | very easy | 13:31 |
| lambday | alright checking | 13:31 |
| sonne|work | van51: can I reply here? | 13:31 |
| sonne|work | van51: you can do w/o function pointers - I mean this is C++ so just an interface class would do | 13:32 |
| sonne|work | van51: and you could add the abstraction to do the dot into this function | 13:32 |
| shogun-buildbot | build #2160 of deb1 - libshogun is complete: Failure [failed compile] Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2160 blamelist: lambday <heavensdevil6909@gmail.com> | 13:32 |
| sonne|work | van51: so some can call dense_dot some can do it better | 13:32 |
| shogun-buildbot | build #2162 of deb1 - libshogun is complete: Failure [failed compile] Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2162 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com> | 13:34 |
| van51 | sonne|work: ok sounds reasonable. I'll do it this way then :) | 13:35 |
| van51 | I'll go grab a bite and get started | 13:36 |
| sonne|work | van51: cool! | 13:36 |
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| travis-ci | [travis-ci] it's Heiko Strathmann'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/11412622 | 14:27 |
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| @HeikoS | votjakovr: hi! | 14:28 |
| @HeikoS | votjakovr: hope you are fine! | 14:29 |
| @HeikoS | votjakovr: I thought that maybe for the notebook, one example could be on string data | 14:30 |
| @HeikoS | what do you think? | 14:30 |
| votjakovr | HeikoS: hi! yeah it will be cool, do you have any particular suggestions on dataset or i could choose the data by myself? | 14:37 |
| @HeikoS | votjakovr: if you want, you can choose yourself, if not, I am just about to look something up | 14:38 |
| @HeikoS | http://www.retrovirology.com/content/5/1/110 | 14:38 |
| @HeikoS | this one here is good | 14:38 |
| @HeikoS | I tried that before with an SVM | 14:38 |
| @HeikoS | the string kernel they use is implemented in shogun | 14:38 |
| @HeikoS | votjakovr: would be really cool to have a string example since most toolboxes dont have that | 14:39 |
| votjakovr | HeikoS: ok, cool, i'll add one :) | 14:40 |
| @HeikoS | votjakovr: maybe you can also compare to an SVM in the notebook? (not in the examples) | 14:40 |
| @HeikoS | this way, we could illustrate the certainties etc | 14:40 |
| votjakovr | HeikoS: yeah, great idea | 14:41 |
| @HeikoS | votjakovr: if the dataset is too hard to import or so, you can choose another one, let me know ... | 14:42 |
| @HeikoS | actually, I think I might still have the plain sequence files somewhere | 14:42 |
| @HeikoS | Ill look it up at home | 14:42 |
| @HeikoS | votjakovr: and as a standard numerical dataset, just pick something from UCI | 14:43 |
| @HeikoS | http://archive.ics.uci.edu/ml/datasets/Glass+Identification | 14:43 |
| @HeikoS | votjakovr: like this one ^ | 14:43 |
| @HeikoS | there you can do window-glass against non-window-glass | 14:43 |
| @HeikoS | that is very popular | 14:43 |
| @HeikoS | and no missing values etc | 14:44 |
| @HeikoS | just import, normalise (remove mean and whiten or scale features to unit variance) and then it directly should work | 14:44 |
| @HeikoS | I tried it before with your binary logit classifier | 14:44 |
| @HeikoS | ok going for lunch, see you! | 14:44 |
| votjakovr | HeikoS: Ok, thank you very much on datasets :) BTW Could you please look at some draft on gradients here: http://github.com/votjakovr/shogun/blob/feature/gp_refactoring/src/shogun/machine/gp/InferenceMethod.cpp#L142 | 14:45 |
| @HeikoS | ok, will do after lunch if thats ok? | 14:45 |
| votjakovr | HeikoS: ok :) | 14:45 |
| @HeikoS | cool! :) | 14:45 |
| @HeikoS | ah cool you pthreaded it? | 14:45 |
| votjakovr | HeikoS: yeah | 14:46 |
| @HeikoS | awesome! | 14:46 |
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| @HeikoS | votjakovr: I like the derivative method! | 15:57 |
| @HeikoS | votjakovr: any reason why you used pthread rather than openmp (which makes the code more readable, although thats not a problem here) | 15:57 |
| @HeikoS | wiking: ping | 15:58 |
| votjakovr | HeikoS: huh, good :) currently i'm using clang as a main compiler and clang doesn't support openmp yet, but we can change implementation in future, since it's pretty simple :-) | 16:03 |
| @HeikoS | votjakovr: yeah no problem, just asking whether it was a conscious decision | 16:04 |
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| shogun-notifier- | shogun: Soeren Sonnenburg :develop * 20a7eb6 / cmake/version.cmake: https://github.com/shogun-toolbox/shogun/commit/20a7eb64cbd3a73ff66f986902d9f7637752df5d | 17:05 |
| shogun-notifier- | shogun: wip commit | 17:05 |
| shogun-buildbot | build #2163 of deb1 - libshogun is complete: Failure [failed compile] Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2163 blamelist: Soeren Sonnenburg <sonne@debian.org> | 17:19 |
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| shogun-buildbot | build #152 of osx1 - libshogun is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/osx1%20-%20libshogun/builds/152 blamelist: Soeren Sonnenburg <sonne@debian.org> | 17:39 |
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| lambday | HeikoS: I added two examples, one for CG and another for log-det | 17:49 |
| @HeikoS | cool, where? | 17:50 |
| @HeikoS | is there a PR? | 17:50 |
| lambday | HeikoS: but the data I put there is in tar.gz, so | 17:50 |
| lambday | HeikoS: yeah just sending | 17:50 |
| lambday | HeikoS: currently I loaded the matrix from the data as if its extracted in the same dir :-/ | 17:51 |
| @HeikoS | lambday: are you working in python? | 17:51 |
| @HeikoS | since in there you can easily extract compressed files | 17:52 |
| lambday | HeikoS: two more python modular examples I thought of, one for COCG, and another is CG-M (because the rest of the solvers are pretty much common but I haven't seen these two anywhere) | 17:52 |
| lambday | HeikoS: yes | 17:52 |
| @HeikoS | and the file reader fraction of shogun is working on zipped formats, too | 17:52 |
| lambday | HeikoS: oh cool! | 17:52 |
| @HeikoS | lambday: ok cool | 17:52 |
| @HeikoS | send the PR, Ill grab a coffee now but will look later | 17:52 |
| lambday | HeikoS: but then I should modify to use the zipped one | 17:53 |
| @HeikoS | lambday: yeah with python thats easy | 17:53 |
| lambday | checking | 17:53 |
| @HeikoS | lambday: getting coffee :) | 17:56 |
| lambday | alright | 17:56 |
| lambday | :) | 17:56 |
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| shogun-notifier- | shogun: Soeren Sonnenburg :develop * 97d3a04 / cmake/version.cmake: https://github.com/shogun-toolbox/shogun/commit/97d3a04a392502e6d7c53948f27bc46c60b0ce69 | 18:04 |
| shogun-notifier- | shogun: fix version | 18:04 |
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| travis-ci | [travis-ci] it's Soeren Sonnenburg'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/11421263 | 18:05 |
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| besser82 | sonne|osx: still fails with new commit: /home/besser82/shared/github/shogun-test/src/shogun/base/Version.cpp:20:43: Fehler: numerischer literaler Operator >>operator"" x<< konnte nicht gefunden werden | 18:09 |
| besser82 | const int32_t Version::version_revision = VERSION_REVISION; | 18:09 |
| besser82 | ^ | 18:09 |
| besser82 | /home/besser82/shared/github/shogun-test/src/shogun/base/Version.cpp: In statischer Elementfunktion >>static int32_t shogun::Version::get_version_revision()<<: | 18:09 |
| besser82 | /home/besser82/shared/github/shogun-test/src/shogun/base/Version.cpp:70:1: Warnung: Kontrollfluss erreicht Ende von Nicht-void-Funktion [-Wreturn-type] | 18:09 |
| besser82 | } | 18:10 |
| besser82 | ^ | 18:10 |
| besser82 | make[2]: *** [src/shogun/CMakeFiles/shogun.dir/base/Version.cpp.o] Fehler 1 | 18:10 |
| besser82 | sonne|osx: ^^^ | 18:10 |
| besser82 | sonne|osx: http://ur1.ca/fkfs4 ---> paste of versionstring.h | 18:11 |
| besser82 | sonne|work: ^^^^ | 18:12 |
| lambday | HeikoS: sending PR | 18:20 |
| shogun-buildbot | build #2164 of deb1 - libshogun is complete: Failure [failed compile] Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2164 blamelist: Soeren Sonnenburg <sonne@debian.org> | 18:20 |
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| lambday | HeikoS: please have a look | 18:23 |
| lambday | HeikoS: I am going for dinner.. will be back in an hour or so | 18:23 |
| lambday | HeikoS: regarding plots, I am thinking of these 1) CG-M convergence for the log-det (residuals over the iterations), 2) Probing/Normal sampler estimates 3) matrix-power vs log-det-estimates (was trying with matrix power 2 and I think it can make a difference) | 18:26 |
| lambday | oh and 4) number of shifts vs log-det accuracy | 18:27 |
| lambday | HeikoS: with diagrams explaining sparsity, fill-in | 18:28 |
| lambday | HeikoS: brb after dinner :) | 18:29 |
| @HeikoS | lambday: that sounds very nice! | 18:52 |
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| travis-ci | [travis-ci] it's Soeren Sonnenburg'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/11423486 | 19:26 |
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| @HeikoS | wiking: hi! | 19:44 |
| wiking | hey hey | 19:44 |
| wiking | i'm still not online actually | 19:44 |
| wiking | bbl | 19:44 |
| @HeikoS | ok | 19:44 |
| @HeikoS | then nevermind :D | 19:44 |
| @HeikoS | I need a break anyways | 19:44 |
| @HeikoS | be back in 10 | 19:44 |
| @HeikoS | wiking: now? | 19:57 |
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| @HeikoS | lisitsyn: hi! | 20:00 |
| lisitsyn | HeikoS: hey | 20:00 |
| @HeikoS | lisitsyn: I have more questions | 20:00 |
| lisitsyn | oh | 20:00 |
| lisitsyn | shoot | 20:00 |
| @HeikoS | lisitsyn: so the cluster guy now installed lapack for me | 20:00 |
| lisitsyn | HeikoS: .so? | 20:00 |
| @HeikoS | but I still have problems | 20:00 |
| @HeikoS | yes | 20:00 |
| lisitsyn | alright | 20:00 |
| lisitsyn | HeikoS: what's the problem? | 20:01 |
| @HeikoS | so first of all, cmake did not detect them even though they were in /usr/lib64 | 20:01 |
| @HeikoS | however -DBLAS_LIBRARIES=/usr/lib64 -DLAPACK_LIBRARIES=/usr/lib64 did that | 20:01 |
| @HeikoS | but now unit tests dont compile | 20:01 |
| lisitsyn | HeikoS: sorry will get back in ten minutes | 20:01 |
| @HeikoS | ok | 20:01 |
| @HeikoS | https://gist.github.com/karlnapf/6584235 | 20:06 |
| lisitsyn | HeikoS: re | 20:11 |
| lisitsyn | HeikoS: did you revert your changes in cmakelists? | 20:12 |
| @HeikoS | lisitsyn: hi | 20:12 |
| @HeikoS | yes I did | 20:12 |
| @HeikoS | git reset --hard should do it right? | 20:12 |
| lisitsyn | HeikoS: heh yeah | 20:12 |
| lisitsyn | HeikoS: alright | 20:13 |
| @HeikoS | so any idea? | 20:13 |
| @HeikoS | first weird thing: why doesnt cmake detect my files? | 20:13 |
| lisitsyn | HeikoS: so the problem is that it doesn't work when you don't do /usr/lib64 | 20:15 |
| lisitsyn | right? | 20:15 |
| @HeikoS | yes | 20:15 |
| @HeikoS | -- A library with BLAS API not found. Please specify library location. | 20:15 |
| @HeikoS | -- LAPACK requires BLAS | 20:15 |
| @HeikoS | -- A library with LAPACK API not found. Please specify library location. | 20:15 |
| @HeikoS | I did not touch LD_LIBRARY_PATH | 20:15 |
| @HeikoS | (for those things) | 20:15 |
| @HeikoS | since it is /usr/lib64 | 20:15 |
| @HeikoS | that should not be the problem right? | 20:15 |
| lisitsyn | HeikoS: I think we use default lapack finder | 20:15 |
| @HeikoS | yes | 20:16 |
| @HeikoS | but ok | 20:16 |
| @HeikoS | I can specify the path and then it works | 20:16 |
| lisitsyn | so that's out-of-box bug | 20:16 |
| @HeikoS | also, I checked my files, they contain that symbol | 20:16 |
| lisitsyn | HeikoS: so the main problem is that unit-tests do not compile I guess | 20:17 |
| lisitsyn | that's more interesting | 20:17 |
| @HeikoS | yes | 20:17 |
| @HeikoS | no other problem compiling libshogun | 20:17 |
| @HeikoS | they should also fail if lapack is not there right? | 20:17 |
| lisitsyn | HeikoS: I don't know if it is still needed | 20:19 |
| @HeikoS | ah wait | 20:19 |
| @HeikoS | -- A library with BLAS API found. | 20:19 |
| @HeikoS | -- A library with LAPACK API found. | 20:19 |
| @HeikoS | -- Looking for clapack_dpotrf in /usr/lib64/atlas/liblapack.so.3 | 20:19 |
| @HeikoS | WARNING: Target "cmTryCompileExec2276832605" requests linking to directory "/usr/lib64". Targets may link only to libraries. CMake is dropping the item. | 20:19 |
| @HeikoS | -- Looking for clapack_dpotrf in /usr/lib64/atlas/liblapack.so.3 - found | 20:19 |
| @HeikoS | -- Found ATLAS: /usr/lib64/atlas/liblapack.so.3;/usr/lib64/atlas/libcblas.so.3;/usr/lib64/atlas/libf77blas.so.3;/usr/lib64/atlas/libatlas.so.3;/usr/lib64/liblapack.so.3 | 20:19 |
| @HeikoS | there is this warning | 20:19 |
| lisitsyn | HeikoS: that sounds like cmake glitch | 20:19 |
| lisitsyn | no idea what to do about it | 20:19 |
| @HeikoS | ok | 20:20 |
| @HeikoS | so any idea whether maybe the lib order in the build command causes this? | 20:20 |
| lisitsyn | HeikoS: yeah may be | 20:21 |
| lisitsyn | as your library files are here in the command line | 20:21 |
| @HeikoS | yeah and all those files exist | 20:24 |
| @HeikoS | lisitsyn: updated the issue | 20:26 |
| @HeikoS | the files also contain the symbol that is needed | 20:26 |
| @HeikoS | so it *has* to be some homemade problem | 20:26 |
| lisitsyn | HeikoS: weird | 20:27 |
| @HeikoS | ah and annoying since I need that for work | 20:27 |
| @HeikoS | lisitsyn: so libshogun.so.14.0 is first in the list | 20:28 |
| @HeikoS | maybe it should be last? | 20:28 |
| @HeikoS | but I dont really believe that | 20:28 |
| lisitsyn | HeikoS: just try to rearrange them in the command | 20:28 |
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| @HeikoS | trying | 20:30 |
| @HeikoS | nope | 20:30 |
| @HeikoS | lisitsyn: I asked wiking to add a bundle lapack option, that might help here | 20:33 |
| wiking | HeikoS: bundle lapack is impossible | 20:34 |
| @HeikoS | wiking: why? | 20:34 |
| wiking | HeikoS: if u can do it | 20:34 |
| wiking | go for it | 20:34 |
| @HeikoS | I managed to compile it locally and create a shared library | 20:35 |
| wiking | it's just crazy shit | 20:35 |
| @HeikoS | mmh ok | 20:35 |
| @HeikoS | there is this tool that helps creating the dynamic stuff | 20:35 |
| @HeikoS | http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=2&t=1895 | 20:35 |
| @HeikoS | wiking: do you have any idea about this problem I have? | 20:35 |
| @HeikoS | https://github.com/shogun-toolbox/shogun/issues/1604 | 20:35 |
| wiking | mmm not yet | 20:36 |
| wiking | HeikoS: what's this distro? | 20:36 |
| @HeikoS | mmh, dont know, let me find out | 20:36 |
| @HeikoS | wiking: centos | 20:37 |
| wiking | HeikoS: which version? | 20:37 |
| shogun-notifier- | shogun: Soeren Sonnenburg :develop * dd41296 / cmake/version.cmake: https://github.com/shogun-toolbox/shogun/commit/dd412963294d6350b1e3ef05776e59e7a31daa6b | 20:37 |
| shogun-notifier- | shogun: fix version (for real) | 20:37 |
| @sonney2k | besser82, ok now! | 20:37 |
| @HeikoS | cat /proc/version | 20:37 |
| @HeikoS | Linux version 2.6.18-308.13.1.el5 (mockbuild@builder10.centos.org) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-52)) #1 SMP Tue Aug 21 17:10:18 EDT 2012 | 20:37 |
| @HeikoS | cat /etc/issue | 20:37 |
| @HeikoS | CentOS release 5.4 (Final) | 20:37 |
| @HeikoS | wiking: ^ | 20:38 |
| wiking | ok | 20:38 |
| wiking | i'll check it | 20:38 |
| @HeikoS | cool man thanks! | 20:38 |
| @HeikoS | wiking: oh and btw, cmake doesnt detect the installed lapack | 20:38 |
| @HeikoS | I have to give the path by hand | 20:38 |
| @sonney2k | HeikoS, errm so it compiles or what? | 20:45 |
| @HeikoS | sonney2k: nope | 20:45 |
| @sonney2k | HeikoS, it fails compiling doing what? | 20:45 |
| @HeikoS | ../../src/shogun/libshogun.so.14.0: undefined reference to `dstemr_' | 20:45 |
| @HeikoS | but this symbol is there | 20:46 |
| @HeikoS | nm /usr/lib64/liblapack.so.3 | grep dstemr_ | 20:46 |
| @HeikoS | 00000000001e46d0 T dstemr_ | 20:46 |
| shogun-buildbot | build #2165 of deb1 - libshogun is complete: Failure [failed compile] Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2165 blamelist: Soeren Sonnenburg <sonne@debian.org> | 20:46 |
| @HeikoS | and this file is also in the library list of the compile command | 20:46 |
| wiking | HeikoS: ldd ../../src/shogun/libshogun.so.14.0 | 20:46 |
| wiking | ? | 20:46 |
| @HeikoS | wiking: | 20:47 |
| @HeikoS | ldd ../../src/shogun/libshogun.so.14.0 | 20:47 |
| @HeikoS | linux-vdso.so.1 => (0x00007fff8b7fd000) | 20:47 |
| @HeikoS | libpthread.so.0 => /lib64/libpthread.so.0 (0x00002abdaf792000) | 20:47 |
| @HeikoS | liblapack.so.3 => /usr/lib64/atlas/liblapack.so.3 (0x00002abdaf9ae000) | 20:47 |
| @HeikoS | libcblas.so.3 => /usr/lib64/atlas/libcblas.so.3 (0x00002abdb00ab000) | 20:47 |
| @HeikoS | libf77blas.so.3 => /usr/lib64/atlas/libf77blas.so.3 (0x00002abdb02ca000) | 20:47 |
| @HeikoS | libatlas.so.3 => /usr/lib64/atlas/libatlas.so.3 (0x00002abdb04e8000) | 20:47 |
| @HeikoS | libz.so.1 => /usr/lib64/libz.so.1 (0x00002abdb0ddd000) | 20:47 |
| @HeikoS | libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002abdb0ff1000) | 20:47 |
| @HeikoS | libm.so.6 => /lib64/libm.so.6 (0x00002abdb12f2000) | 20:47 |
| @HeikoS | libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00002abdb1575000) | 20:47 |
| @HeikoS | libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002abdb1782000) | 20:47 |
| @HeikoS | libc.so.6 => /lib64/libc.so.6 (0x00002abdb1991000) | 20:47 |
| @HeikoS | /lib64/ld-linux-x86-64.so.2 (0x000000315fe00000) | 20:47 |
| @HeikoS | libgfortran.so.1 => /usr/lib64/libgfortran.so.1 (0x00002abdb1ce8000) | 20:47 |
| @HeikoS | librt.so.1 => /lib64/librt.so.1 (0x00002abdb1f80000) | 20:47 |
| @HeikoS | ah sorry | 20:47 |
| @sonney2k | HeikoS, so it compiled! | 20:47 |
| @sonney2k | so what is missing is a proper LD_LIBRARY_PATH= | 20:47 |
| @sonney2k | when running things | 20:47 |
| wiking | HeikoS: Iliblapack.so.3 => /usr/lib64/atlas/liblapack.so.3 | 20:48 |
| wiking | this does not have dstemr_ i guess | 20:48 |
| wiking | right? | 20:48 |
| @HeikoS | nm says "no symbols" | 20:48 |
| wiking | HeikoS: ok so your problem is that the wrong lapack.so is being used | 20:49 |
| besser82 | wiking: It should have that symbol, since it's a rewritten lapack in c ;) | 20:49 |
| @HeikoS | sonney2k: shogun conmpiled, but its the unit tests ... | 20:49 |
| @HeikoS | wiking: ah ok | 20:49 |
| @HeikoS | so the one in lib64/atlas/ rather thanlib64 | 20:49 |
| @HeikoS | how to change that? | 20:49 |
| wiking | as sonney2k said | 20:49 |
| wiking | LD_LIBRARY_PATH | 20:49 |
| @HeikoS | really that easy? let me try | 20:50 |
| @HeikoS | export LD_LIBRARY_PATH=/usr/lib64/:$LD_LIBRARY_PATH ? | 20:50 |
| wiking | yeah | 20:50 |
| wiking | try that | 20:51 |
| @HeikoS | nope | 20:51 |
| @HeikoS | doesnt work | 20:51 |
| @HeikoS | what about this list of .so files in the make command of the unit tests? | 20:51 |
| @HeikoS | in the gist | 20:51 |
| @HeikoS | sonney2k: to what do I have to set the LD_LIBRARY_PATH? | 20:51 |
| besser82 | HeikoS, wiking: nm -D /usr/lib64/liblapack.so | grep dstemr ---> shows the symbol is there | 20:52 |
| @HeikoS | besser82 yes it does, but liblapack.so.3 => /usr/lib64/atlas/liblapack.so.3 | 20:52 |
| @HeikoS | and in there, it is not | 20:52 |
| @sonney2k | HeikoS, to /usr/lib64/atlas if it is there | 20:53 |
| @HeikoS | sonney2k: doesnt work either | 20:54 |
| @HeikoS | wiking, sonney2k cant I tell the compiler somehow to reference the right library somehow else? | 20:55 |
| lisitsyn | I just wanted to note it is dstemr_ that is missed | 21:11 |
| lisitsyn | may be it is important here | 21:11 |
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| @HeikoS | lisitsyn: ? | 21:12 |
| lisitsyn | HeikoS: dstemr_ dstemr | 21:12 |
| lisitsyn | HeikoS: do you have dstemr_ or dstemr? | 21:13 |
| @HeikoS | dstemr_ | 21:13 |
| @HeikoS | lisitsyn: I think it is as sonney2k and wiking said, libshogun.so references the wrong file, which is lib64/atlas/liblapack.so, but the file doesnt contain the symbol. However, lib64/liblapack.so contains it, I just dont know how to make libshogun reference to it | 21:14 |
| lisitsyn | HeikoS: ah | 21:14 |
| lisitsyn | I see | 21:14 |
| @HeikoS | I tried prepending its path to LD_LIBRARY_PATH, the (re)-linking libshogun, but I still get the same error | 21:14 |
| besser82 | HeikoS: lib64/atlas/liblapack.so contains dstemr_ ---> nm -D /usr/lib64/atlas/liblapack.so | grep dstemr | 21:15 |
| lambday | HeikoS: back | 21:17 |
| lambday | HeikoS: what's wrong with dstemr? | 21:18 |
| @HeikoS | lambday: hi! ah, dont worry about that | 21:18 |
| @HeikoS | trying to install things on weird machines | 21:18 |
| @HeikoS | lambday: I had some comments in the PR, minor things | 21:18 |
| lambday | I added/used dstemr.. :-/ | 21:18 |
| lambday | HeikoS: yeah checking | 21:18 |
| @HeikoS | lambday: I cannot drop lapack unfortunately since I need the Lanczos on the cluster | 21:19 |
| @HeikoS | if only eigen could do that little thing ;) | 21:19 |
| @HeikoS | then I wouldnt have these stupid problems with stupid lapack | 21:19 |
| lambday | HeikoS: at times, I feel like adding that to eigen :-/ | 21:20 |
| lambday | HeikoS: lapack API is horrible.. I only succeded because lisitsyn explain each and every params to me one by one :D | 21:20 |
| lambday | explained* | 21:20 |
| @HeikoS | yeah I know that, he did that for me too a while ago | 21:20 |
| lambday | lisitsyn: kudos, master yoda! | 21:21 |
| @HeikoS | we should just get rid of lapack as soon as possible | 21:22 |
| @HeikoS | almost all things can be replaced by eigen | 21:22 |
| lambday | HeikoS: does lapack work faster than eigen3? | 21:22 |
| @HeikoS | it just burned 3 working days of mine, so no | 21:23 |
| @HeikoS | cannot be that fast ;) | 21:23 |
| lambday | :D | 21:24 |
| @sonney2k | HeikoS, well you suffer from bad ass ubuntu not lapack | 21:24 |
| @sonney2k | on debian you wouldn't have such trouble | 21:24 |
| @HeikoS | sonney2k: no its not ubuntu | 21:24 |
| @sonney2k | then FC* | 21:24 |
| @HeikoS | well I cannot do anything about this since its not my machine | 21:24 |
| @sonney2k | :) | 21:24 |
| @HeikoS | sonney2k: how to change this reference? | 21:24 |
| lambday | sonney2k: you support lapack? :( | 21:25 |
| @sonney2k | HeikoS, what I would do is run make with verbose | 21:25 |
| @sonney2k | so you see the cmdline of linking libshogun | 21:25 |
| lambday | using it is so hard | 21:25 |
| @sonney2k | then copy that line | 21:25 |
| @HeikoS | yes, its in the issue I made | 21:25 |
| @HeikoS | sonney2k: https://github.com/shogun-toolbox/shogun/issues/1604 | 21:25 |
| @sonney2k | and then make sure it links to the libs you want by specifying -L/path | 21:25 |
| @sonney2k | and have *the same* libs in LD_LIBRARY_PATH | 21:26 |
| @sonney2k | then it works | 21:26 |
| @sonney2k | HeikoS, where is the line? | 21:27 |
| @sonney2k | I only see attempts to link the example | 21:27 |
| @HeikoS | ah sorry, will post | 21:27 |
| @sonney2k | HeikoS, and of course LD_LIBRARY_PATH won't help with *linking* an example | 21:28 |
| @sonney2k | you need the proper -L / -l | 21:28 |
| lambday | HeikoS: I have two files there, one mtx and another is libsvm.. I should add these individually zipped you meant | 21:28 |
| @HeikoS | lambday: why have two? why not one? | 21:29 |
| lambday | HeikoS: the mtx one is for python modular examples, I intended to use the libsvm ones for libshogun examples | 21:29 |
| @sonney2k | HeikoS, try to add -/usr/lib64 -llapack to the end of the line | 21:29 |
| @HeikoS | sonney2k: ok thanks will try | 21:30 |
| @HeikoS | sonney2k: besser82 had another suggestion, comment out find_atlas in cmake, that in fact made cmake realize the proper .so file, currently compiling this way ... | 21:31 |
| @sonney2k | you have most likely a clash between /usr/lib64/atlas/liblapack.so.3 and /usr/lib64/liblapack.so.3 | 21:31 |
| @sonney2k | HeikoS, that can work too | 21:31 |
| @HeikoS | /usr/lib64/atlas/liblapack.so.3 doesnt contain the symbol thats the problem | 21:31 |
| @sonney2k | HeikoS, then just don't link against it | 21:31 |
| besser82 | sonney2k: the problem is CMakeLists.txt preferes ATLAS over FORTRAN-LAPACK | 21:32 |
| @HeikoS | sonney2k: besser82, doesnt work with disabling atlas, got even more undefined symbols | 21:32 |
| @HeikoS | sonney2k: I dont know how to not link against it | 21:32 |
| besser82 | HeikoS: export LDFLAGS="-Wl,-l/usr/lib64/lapack.so" | 21:33 |
| besser82 | and try rebuilding with ATLAS re-enabled | 21:33 |
| @HeikoS | besser82: what does that do? | 21:33 |
| besser82 | adds original LAPACK to the linker-flags | 21:34 |
| @HeikoS | so before building I need to export right? | 21:34 |
| @HeikoS | before linking I mean | 21:34 |
| besser82 | right, before configuring with comake ;) | 21:34 |
| besser82 | cmake hardcodes ldflags to Makefile | 21:35 |
| @HeikoS | besser that screws up the cmake totally | 21:36 |
| besser82 | really? What's the output? | 21:36 |
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| besser82 | wb, HeikoS | 21:41 |
| @HeikoS | sorry connection dropped | 21:42 |
| @HeikoS | now compiling with verbose to see the link command of libshogun | 21:42 |
| besser82 | kk | 21:42 |
| * HeikoS is dreaming of shogun in the cloud without installation | 21:44 | |
| * besser82 would say let's get started on openShift :) | 21:45 | |
| @HeikoS | openshift? | 21:45 |
| wiking | HeikoS: well it needs to be installed once on the cloud as well | 21:45 |
| besser82 | HeikoS: and will allow Software-as-a-Service ;) | 21:46 |
| besser82 | HeikoS: easy deployment with containers and cartirdges ;) | 21:46 |
| @HeikoS | besser82: yeah something like that | 21:46 |
| besser82 | HeikoS: imageine a container as a vm | 21:46 |
| @HeikoS | an ipython server would actually be enough | 21:46 |
| wiking | besser82: is it free? :D | 21:47 |
| @HeikoS | can write code in my browser then | 21:47 |
| besser82 | wiking: openShift-community is free ;) | 21:47 |
| wiking | besser82: yeah but not the service itself | 21:47 |
| besser82 | wiking: and that's the EXACT codebase redhat uses ;) | 21:47 |
| besser82 | wiking: a limited use is free as well | 21:48 |
| wiking | besser82: i mean what we need is actually a machine where we can run it | 21:48 |
| wiking | because then we already have like virtualenv | 21:48 |
| besser82 | amazon EC2? | 21:48 |
| wiking | besser82: money? :) | 21:48 |
| lisitsyn | wiking: CV help needed ;) | 21:49 |
| lisitsyn | anyone else having a clue please comment too | 21:49 |
| wiking | lisitsyn: shoot although i'm like only 10% here | 21:49 |
| besser82 | wiking: try creditcard, doesn't cost money, will be collect automatically ;) | 21:49 |
| lisitsyn | my problem is quite silly | 21:49 |
| lisitsyn | I have bounding box where object is probably is | 21:49 |
| @HeikoS | sonney2k, wiking so the linking command of shogun contains /usr/lib64/atlas/libatlas.so.3 /usr/lib64/liblapack.so.3 in this order | 21:50 |
| lisitsyn | but I need to generate some candidates you know | 21:50 |
| lisitsyn | how not-brain-damaged-people-like-me do it? | 21:50 |
| wiking | how do u assign probabilities? | 21:51 |
| lisitsyn | wiking: no probabilities I just learned svm and have background model | 21:51 |
| lisitsyn | so I just track background changes | 21:51 |
| wiking | ok so u have the bo | 21:51 |
| wiking | x | 21:51 |
| lisitsyn | yeah some box and I need candidates around it | 21:52 |
| wiking | what's candidates aroudn it? | 21:52 |
| lisitsyn | wiking: well these regions I'll apply svm to | 21:52 |
| lambday | HeikoS: there is a bug reagarding reading gzipped mtx file in python mmread : https://github.com/scipy/scipy/issues/2152 | 21:58 |
| lambday | HeikoS: I am adding the ImportErrors though, but not sure how to work with individual gzipped mtx files | 21:59 |
| @HeikoS | can you just only have libsvm format? | 21:59 |
| lambday | HeikoS: yes, if I can read it from python, which I can I guess | 22:00 |
| @HeikoS | lambday: I am sure you can | 22:02 |
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| lisitsyn | HeikoS: is that lambday poweroff time? | 22:06 |
| @HeikoS | lisitsyn: maybe :) | 22:06 |
| lisitsyn | HeikoS: ain't it insane? | 22:07 |
| @HeikoS | sonney2k: https://gist.github.com/karlnapf/6584235 | 22:07 |
| @HeikoS | here is the output of the linking of shogun | 22:07 |
| @HeikoS | lisitsyn: it is insane | 22:09 |
| @HeikoS | but it really is like that oer there | 22:09 |
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| --- Log closed Tue Sep 17 00:00:02 2013 | ||
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