| --- Log opened Mon Aug 19 00:00:21 2013 | ||
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| shogun-buildbot | build #439 of nightly_none is complete: Failure [failed compile] Build details are at http://www.shogun-toolbox.org/buildbot/builders/nightly_none/builds/439 | 03:46 |
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| shogun-notifier- | shogun: Soeren Sonnenburg :develop * e8f9ea7 / examples/undocumented/libshogun/classifier_svmlight_string_features_precomputed_kernel.cpp: https://github.com/shogun-toolbox/shogun/commit/e8f9ea73f5309f4927af26bf6b40c6ff6cfbb710 | 08:34 |
| shogun-notifier- | shogun: ifdef svmlight example to not fail when svmlight is not available | 08:34 |
| shogun-buildbot | build #930 of rpm1 - libshogun is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/rpm1%20-%20libshogun/builds/930 | 08:44 |
| shogun-notifier- | shogun: Soeren Sonnenburg :develop * 64e4618 / CMakeLists.txt: https://github.com/shogun-toolbox/shogun/commit/64e46187b7c9a91dcf362d93dae8907dd6dacf31 | 08:46 |
| shogun-notifier- | shogun: disable warning on cygwing | 08:46 |
| shogun-buildbot | build #440 of nightly_none is complete: Success [build successful] Build details are at http://www.shogun-toolbox.org/buildbot/builders/nightly_none/builds/440 | 08:50 |
| shogun-buildbot | build #931 of rpm1 - libshogun is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/rpm1%20-%20libshogun/builds/931 | 08:53 |
| shogun-buildbot | build #1436 of deb2 - static_interfaces is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/1436 blamelist: Soeren Sonnenburg <sonne@debian.org> | 08:54 |
| shogun-buildbot | build #932 of rpm1 - libshogun is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/rpm1%20-%20libshogun/builds/932 blamelist: Soeren Sonnenburg <sonne@debian.org> | 08:56 |
| shogun-buildbot | build #1467 of bsd1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1467 blamelist: Soeren Sonnenburg <sonne@debian.org> | 08:58 |
| shogun-buildbot | build #933 of rpm1 - libshogun is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/rpm1%20-%20libshogun/builds/933 | 09:02 |
| @wiking | mornin' | 09:18 |
| shogun-buildbot | build #1437 of deb2 - static_interfaces is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/1437 blamelist: Soeren Sonnenburg <sonne@debian.org> | 09:20 |
| shogun-buildbot | build #1555 of deb3 - modular_interfaces is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/1555 blamelist: Soeren Sonnenburg <sonne@debian.org> | 09:21 |
| shogun-buildbot | build #1468 of bsd1 - libshogun is complete: Failure [failed compile] Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1468 blamelist: Soeren Sonnenburg <sonne@debian.org> | 09:21 |
| shogun-buildbot | build #934 of rpm1 - libshogun is complete: Success [build successful] Build details are at http://www.shogun-toolbox.org/buildbot/builders/rpm1%20-%20libshogun/builds/934 | 09:26 |
| shogun-buildbot | build #1554 of deb3 - modular_interfaces is complete: Success [build successful] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/1554 | 09:29 |
| shogun-notifier- | shogun: Viktor Gal :develop * 13837fe / tests/unit/latent/LatentSVM_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/13837fe32615d16c627e7c1be9105da73954e755 | 09:36 |
| shogun-notifier- | shogun: Fix mocking warning in LatentSVM unit test | 09:36 |
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| shogun-buildbot | build #0 of osx1 - libshogun is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/osx1%20-%20libshogun/builds/0 | 10:23 |
| shogun-buildbot | build #1556 of deb3 - modular_interfaces is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/1556 blamelist: Viktor Gal <viktor.gal@maeth.com> | 10:25 |
| shogun-buildbot | build #1438 of deb2 - static_interfaces is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/1438 blamelist: Viktor Gal <viktor.gal@maeth.com> | 10:26 |
| shogun-buildbot | build #1469 of bsd1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1469 blamelist: Viktor Gal <viktor.gal@maeth.com> | 10:28 |
| shogun-buildbot | build #1 of osx1 - libshogun is complete: Success [build successful] Build details are at http://www.shogun-toolbox.org/buildbot/builders/osx1%20-%20libshogun/builds/1 | 10:37 |
| @wiking | oh woah we have osx bot!!! sonney2k coool! | 11:03 |
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| shogun-buildbot_ | build #1260 of cyg1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/1260 blamelist: Viktor Gal <viktor.gal@maeth.com> | 11:07 |
| @wiking | shogun-buildbot_: force build --branch=develop 'osx1 - libshogun' | 11:08 |
| shogun-buildbot_ | The build has been queued, I'll give a shout when it starts | 11:08 |
| shogun-buildbot_ | build #2 forced | 11:10 |
| shogun-buildbot_ | I'll give a shout when the build finishes | 11:10 |
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| @wiking | shogun-buildbot: force build --branch=develop 'rpm1 - libshogun' | 11:13 |
| shogun-buildbot | build forced [ETA 20m10s] | 11:13 |
| shogun-buildbot | I'll give a shout when the build finishes | 11:13 |
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| thoralf | Hello everybody. | 11:23 |
| shogun-buildbot | Hey! build rpm1 - libshogun #938 is complete: Success [build successful] | 11:28 |
| shogun-buildbot | Build details are at http://www.shogun-toolbox.org/buildbot/builders/rpm1%20-%20libshogun/builds/938 | 11:28 |
| @wiking | \o/ | 11:30 |
| @wiking | mmm we've lost osx | 11:39 |
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| @wiking | HeikoS: back? :) | 12:51 |
| @wiking | btw do we have a simple function for SGMatrix to set a column vector? | 12:51 |
| @wiking | i.e SGMatrix.set_column(index, SGVector) | 12:51 |
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| @HeikoS | wiking: yes, but kicked out my office so currently moving things | 13:25 |
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| @HeikoS | wiking: we should have full slicing and view support on matrices btw :) like numpy | 13:34 |
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| lisitsyn | HeikoS: looks like somebody is reinventing eigen ;) | 13:47 |
| @iglesiasg | lisitsyn, does it support slicing already? | 13:47 |
| lisitsyn | iglesiasg: block | 13:47 |
| @iglesiasg | lisitsyn, aah true | 13:48 |
| @iglesiasg | I have seen it in this cheatsheet for Matlab users | 13:48 |
| thoralf | wiking: Im sometimes getting "/usr/bin/ld: can not read symbols: File truncated" when building shogun. | 13:53 |
| thoralf | wiking: Seems that ld isn't finished when it tries to build the examples or tests. | 13:53 |
| @wiking | HeikoS: yes indeed | 13:54 |
| thoralf | wiking: Does not happen all the time, but when setting high number with -j. | 13:54 |
| @wiking | thoralf: mmmm i wonder... this should be handled by cmake | 13:54 |
| @wiking | thoralf: as i added a dependency to libshogun for building examples and unit tests | 13:54 |
| @wiking | btw is Stack thread safe ? :) | 13:55 |
| thoralf | wiking: Strange. | 13:55 |
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| @wiking | thoralf: yeah i think this is something do with cmake unfortunately | 13:56 |
| @wiking | thoralf: it should wait until the building of libshogun is finished | 13:56 |
| thoralf | wiking: But it works when re-running make in the build dir, so the hotfix is easy. ;) | 13:57 |
| thoralf | wiking: What I did before: I changed a class, ran "make" in a clean build dir, but c++ found out there is a (trivial) syntax error. I fixed it without deleting the build dir an reran make, then the ld error appeared. Running make a second time fixed it. | 13:59 |
| thoralf | wiking: Maybe that helps? | 13:59 |
| @wiking | where should we implement these (or where should it be placed in the shogun struct): http://www.scholarpedia.org/article/Ensemble_learning#Ensemble_combination_rules | 14:00 |
| @wiking | HeikoS: lisitsyn iglesiasg ^ | 14:00 |
| @wiking | thoralf: no idea :( | 14:00 |
| @iglesiasg | wiking, classifier? | 14:02 |
| @iglesiasg | wiking, LPBoost is there at least | 14:03 |
| thoralf | wiking: Oh, it apparently happened in the unit tests: make[1]: *** [tests/unit/CMakeFiles/shogun-unit-test.dir/all] Error 2 | 14:03 |
| @wiking | iglesiasg: well it'd really just a class that takes a set of labels or a matrix and runs the voting on it | 14:03 |
| @wiking | i mean it wouldn't be actually a classifier :) | 14:04 |
| @wiking | in the classical sense | 14:04 |
| thoralf | wiking: It failed shortly after printing that it now links: libgtest_main.a, libgmock_main.a, libgtest.a, libgmock.a (and some other tests) | 14:04 |
| thoralf | wiking: Some dependencies between them? | 14:04 |
| @wiking | thoralf: tests/unit/cmakelists.txt | 14:05 |
| @wiking | add_dependencies(shogun-unit-test gmock gtest) | 14:05 |
| @wiking | target_link_libraries(shogun-unit-test shogun gmock gtest) | 14:05 |
| @wiking | afaik target_link_libraries does define a dependency | 14:05 |
| @wiking | but try adding shogun to add_dependencies as well | 14:05 |
| thoralf | wiking: FYI: Digging in the make output I found that "Linking CXX executable shogun-unit-test" never returned. And that make tried to link gmock/gtest *after* shogun-unit-test. | 14:17 |
| thoralf | wiking: libshogun has already been finished then. | 14:18 |
| lisitsyn | wiking: ensemble! :) | 14:18 |
| @wiking | lisitsyn: okey! :) currently BaggingMachine is about to be added to machine... should we change that as well/ :P | 14:19 |
| lisitsyn | begging machine | 14:22 |
| lisitsyn | :D | 14:22 |
| @wiking | :> | 14:22 |
| @wiking | indeed | 14:22 |
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| shogun-buildbot | build #4 of osx1 - libshogun is complete: Failure [failed test shell] Build details are at http://www.shogun-toolbox.org/buildbot/builders/osx1%20-%20libshogun/builds/4 | 15:17 |
| @wiking | yey almost :) | 15:19 |
| @wiking | sonney2k: what is the osx version on that machine 10.8 or 10.7? | 15:19 |
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| @HeikoS | lisitsyn, wiking eigen does not do proper slicing and views | 15:32 |
| @HeikoS | its all copies and writing | 15:33 |
| @HeikoS | but not views on the same memory like in numpy | 15:33 |
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| shogun-notifier- | shogun: Roman Votyakov :develop * 9e829cb / src/shogun/machine/gp/LaplacianInferenceMethod.cpp: https://github.com/shogun-toolbox/shogun/commit/9e829cb4fcc95101a7e5168893dc34c3b3760bae | 15:34 |
| shogun-notifier- | shogun: compute covariance matrix more efficiently | 15:34 |
| shogun-notifier- | shogun: Heiko Strathmann :develop * bb39545 / src/shogun/machine/gp/LaplacianInferenceMethod.cpp: https://github.com/shogun-toolbox/shogun/commit/bb39545f4c1d93b1648c301ee0ca7e86ac14745c | 15:34 |
| shogun-notifier- | shogun: Merge pull request #1440 from votjakovr/feature/gp_refactoring | 15:34 |
| shogun-notifier- | shogun: | 15:34 |
| shogun-notifier- | shogun: Compute covariance matrix more efficiently | 15:34 |
| lisitsyn | HeikoS: ?? block doesn't copy things | 15:35 |
| lisitsyn | A.block(1,1,5,5).array() = 3; | 15:35 |
| @HeikoS | lisitsyn: yes that is fine | 15:35 |
| @HeikoS | but A=B(3:4,5:7) doesnt work | 15:35 |
| @HeikoS | such that modifying A changes B | 15:35 |
| lisitsyn | why? | 15:36 |
| lisitsyn | A.noalign() = B.block(3,5,1,2); | 15:36 |
| lisitsyn | sth like that | 15:36 |
| @HeikoS | but in my case, A and B point to the same memory | 15:37 |
| @HeikoS | just different elements | 15:37 |
| @HeikoS | lisitsyn: but doesnt really matter for now, and also eigen is a better place for this than shogun | 15:37 |
| thoralf | wiking: I built shogun with -DENABLE_TESTING=ON, but when calling "make test" I'm getting warnings for each example. | 15:38 |
| thoralf | Could not find executable ./shogun-github/build/examples/undocumented/libshogun/so_factorgraph | 15:39 |
| thoralf | And "Looked in the following places:" followed by a long list of directories | 15:39 |
| thoralf | wiking: My cmake call was: cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_TESTING=ON -DTRACE_MEMORY_ALLOCS=OFF .. | 15:39 |
| thoralf | wiking: Oh. I was typing "make shogun" instead of "make all" - give me a second, trying this first. | 15:41 |
| shogun-buildbot | build #1830 of deb1 - libshogun is complete: Failure [failed compile] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb1%20-%20libshogun/builds/1830 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com> | 15:41 |
| thoralf | wiking: Sorry. Works now. ;) | 15:42 |
| thoralf | HeikoS: I fixed one of your unit tests (among others): https://github.com/shogun-toolbox/shogun/pull/1443 | 15:58 |
| @HeikoS | thoralf: cool, thanks! | 16:00 |
| @HeikoS | just waiting for travis to give ok | 16:00 |
| thoralf | HeikoS: My sanity checks are breaking tests for interfaces I didn't test locally. Grep for "matrix features" in the build output. | 16:24 |
| shogun-buildbot | build #1557 of deb3 - modular_interfaces is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/1557 blamelist: Roman Votyakov <votjakovr@gmail.com> | 16:24 |
| shogun-buildbot | build #1439 of deb2 - static_interfaces is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/1439 blamelist: Roman Votyakov <votjakovr@gmail.com> | 16:25 |
| shogun-buildbot | build #1470 of bsd1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1470 blamelist: Roman Votyakov <votjakovr@gmail.com> | 16:28 |
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| @sonney2k | thoralf, the thing with the bias term and liblinear is that it used to use a w vector of size dim+1 | 16:32 |
| thoralf | sonney2k: I know. | 16:32 |
| @sonney2k | thoralf, when the bias is enabled - so one dim in w is b | 16:32 |
| @sonney2k | thoralf, however we changed all of liblinear to explicitly work with a separate b | 16:33 |
| @sonney2k | well we == I | 16:33 |
| thoralf | sonney2k: Anyway, there is an off-by-one in streaming/sparse_features which only happens when learning without bias. | 16:33 |
| thoralf | sonney2k: When learning with bias, then the +1 saves you from segfaults. ;) | 16:33 |
| @sonney2k | wiking, 10.8 | 16:34 |
| shogun-buildbot | build #5 of osx1 - libshogun is complete: Failure [failed test shell] Build details are at http://www.shogun-toolbox.org/buildbot/builders/osx1%20-%20libshogun/builds/5 blamelist: Roman Votyakov <votjakovr@gmail.com> | 16:36 |
| thoralf | sonney2k: liblinear allocates weights with dim/dim+1 depending on the bias setting. When computing dense_dot() with streaming/sparse_features returns, then sparse_features telling dimensionality is $n$, but the max feature index is also $n$, which leads dense_dot to read excess w's last element. | 16:37 |
| @wiking | sonney2k: ok i'll give u a link for the dmg | 16:37 |
| thoralf | wiking: I cannot run tests for python_modular on my machine. It's always complaining about "ImportError: No module named shogun.XXX" | 16:54 |
| thoralf | wiking: I'm not supposed to "make install" first? | 16:54 |
| @wiking | thoralf: yes | 16:57 |
| @wiking | thoralf: as .py files are not populated unders <pythonlibpath>/shogun/... | 16:57 |
| thoralf | wiking: Can I set the install path to somewhere relative to build/? ;) | 16:58 |
| @wiking | thoralf: -DCMAKE_INSTALL_PREFIX | 16:59 |
| @wiking | and you put it where u set that whatever you want it to be... | 16:59 |
| @wiking | rtfm cmake | 16:59 |
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| shogun-buildbot | build #1261 of cyg1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/1261 blamelist: Roman Votyakov <votjakovr@gmail.com> | 17:06 |
| thoralf | wiking: Thanks for command line switch and sort for not reading 16k lines of cmake manpage at once. I think someone should update the READMEs - some shortcuts of how to use shogun. | 17:19 |
| thoralf | wiking: Otherwise you eventually will kill us... ;) | 17:19 |
| thoralf | s/sort/sorry/ | 17:20 |
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| thoralf | The example python_modular/features_io_modular.py (line 25) breaks because something is wrong with examples/undocumented/python_modular/fm_train_sparsereal.bin, but I can't tell what exactly. | 17:31 |
| @wiking | thoralf: there's a cmake faq ;) | 17:31 |
| thoralf | It's loaded from SparseRealFeatures(fm_train_real.dat) and then saved back to disk. | 17:31 |
| thoralf | wiking: Grr. | 17:34 |
| thoralf | wiking: It's really too much pain for just fixing a bug and contributing a patch. | 17:35 |
| thoralf | I know it's not your fault, but it's still too complicated. ;) | 17:35 |
| @HeikoS | thoralf: currently using virutalenv | 17:49 |
| @HeikoS | thats soo cool | 17:49 |
| thoralf | HeikoS: Yeah, it's great. | 17:49 |
| @HeikoS | thoralf: best thing is the freeze option | 17:49 |
| @HeikoS | so I can just install my stuff along the cluster | 17:49 |
| thoralf | HeikoS: What's that? | 17:49 |
| thoralf | Oh. | 17:49 |
| thoralf | Really? | 17:50 |
| @HeikoS | you can save the installed packages | 17:50 |
| @HeikoS | and then you get a text file which you can use on other machines to reproduce the env | 17:50 |
| thoralf | wiking: I need some assistance. I'm trying to debug run a python_modular example and get a (c++) stacktrace of what happens there. | 17:51 |
| thoralf | wiking: Usually, I'd just run "gdb python script.py" | 17:51 |
| thoralf | wiking: I see there's something in the ctest file in build/examples/undocumented/python_modular, but I can't get it running | 17:52 |
| thoralf | HeikoS: I'm giving up, because I can't tell how to fix the python examples. I'll send another patch without assertions soon. | 18:00 |
| @HeikoS | thoralf: ok | 18:00 |
| @HeikoS | thoralf: I know debugging python is a pain | 18:00 |
| @HeikoS | what you can do is to run it with valgrind then you at least get the shogun place where things fail | 18:00 |
| thoralf | wiking: It's running, but I don't see a backtrace because python exists normally. | 18:00 |
| thoralf | HeikoS: valgrind won't care about failing "REQUIRE"s ;) | 18:01 |
| @HeikoS | ah | 18:01 |
| @HeikoS | sorry I though something else was wrong | 18:01 |
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| @HeikoS | wiking: around? | 18:33 |
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| @wiking | yes yes | 18:41 |
| @HeikoS | wiking: I want to do the following | 18:42 |
| @HeikoS | cluster here has many computers with different architectures | 18:42 |
| @HeikoS | and I want to use shogun python from all of them | 18:43 |
| @HeikoS | so now I do this virtualenv stuff | 18:43 |
| thoralf | Something is really wrong with python_modular. | 18:43 |
| @HeikoS | and compile shogun against it | 18:43 |
| thoralf | It just started 20000 threads. | 18:43 |
| thoralf | (And growing) | 18:43 |
| @HeikoS | wiking: how would you do that? | 18:43 |
| @HeikoS | wiking: I just wrote a script that installs python locally and then got clones shogun and compiles | 18:43 |
| @HeikoS | wiking: but there is a subtlety: all machines share the same FS, but machines might have different architectures | 18:44 |
| @HeikoS | so each job will have to do/update this local installation on start | 18:44 |
| @HeikoS | any idea how to best do this? | 18:44 |
| @wiking | HeikoS: ? | 18:44 |
| @HeikoS | even worse, there might be multiple jobs on the same machine | 18:44 |
| @wiking | HeikoS: so they share the repo? | 18:44 |
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| @HeikoS | wiking: what? | 18:45 |
| @wiking | HeikoS: share fs -> share the cloned repo of shogun u use for building? | 18:45 |
| @HeikoS | wiking: yes but that is not good | 18:45 |
| @HeikoS | there should be one thing per job | 18:45 |
| thoralf | HeikoS: -DCMAKE_INSTALL_PREFIX | 18:45 |
| @HeikoS | so every job starts with building shogun | 18:45 |
| thoralf | HeikoS: Solved my problem. :) | 18:45 |
| thoralf | HeikoS: Just install locally | 18:46 |
| @HeikoS | thoralf: so depending on the job id the prefix changes you mean? | 18:46 |
| @wiking | HeikoS: install it to a specific dir.... | 18:46 |
| thoralf | HeikoS: Yes, | 18:46 |
| thoralf | HeikoS: Same problem here. | 18:46 |
| @HeikoS | thoralf: do you use this distributed stuff with shogun? | 18:46 |
| thoralf | HeikoS: Got harded with cmake, but is possible. ;) | 18:46 |
| thoralf | HeikoS: What do you mean? | 18:47 |
| @HeikoS | it would be cool to offer a script for this | 18:47 |
| @wiking | thoralf: harded? | 18:47 |
| @HeikoS | thoralf, wiking it would be good to have a script that locally installs shogun to a dir, including a local python install | 18:47 |
| @HeikoS | with virtualenv and pip | 18:47 |
| thoralf | s/harded/harder/ | 18:47 |
| @HeikoS | so that I just need to give a path and the rest is done automagically | 18:47 |
| @wiking | thoralf: how? | 18:48 |
| @wiking | thoralf: -DCMAKE_INSTALL_PREFIX | 18:48 |
| @wiking | i mean | 18:48 |
| thoralf | PYTHON=/usr/bin/python PYTHONPATH=xxx/python2.7/dist-packages:. LD_LIBRARY_PATH=xxx/lib:. python script | 18:48 |
| @wiking | HeikoS: -DCMAKE_INSTALL_PREFIX= | 18:48 |
| @HeikoS | wiking: ok, I will play a bit and share the script then | 18:49 |
| @wiking | HeikoS: that'll install u the shogun stuff whereever you want it to | 18:49 |
| @HeikoS | wiking: yeah but to use python there is more involved | 18:49 |
| @HeikoS | if I dont have root rights | 18:49 |
| @HeikoS | which is why I want to use virtualenv | 18:49 |
| @wiking | HeikoS: ? | 18:49 |
| @wiking | i dont get it | 18:49 |
| @wiking | the whole shogun thing will be installed under | 18:49 |
| @wiking | <prefix> | 18:49 |
| @HeikoS | wiking: yes, but now imagine python is not installed | 18:50 |
| @wiking | <prefix>/lib <prefix>/include <prefix>/lib/python... | 18:50 |
| @wiking | HeikoS: install it to <prefix> | 18:50 |
| @HeikoS | wiking: exact, and now there are multiple architectures for the same FS | 18:50 |
| @wiking | HeikoS: and? u create different <prefix> for different arch | 18:50 |
| @HeikoS | wiking: yes | 18:51 |
| @HeikoS | thats what I want | 18:51 |
| @HeikoS | with 1 click ;) | 18:51 |
| @wiking | HeikoS: what do u mean 1 click? | 18:51 |
| @HeikoS | wiking: a one liner | 18:51 |
| @wiking | HeikoS: create a script for it and that's all | 18:51 |
| @HeikoS | wiking: yes thats what I want, but not that experienced with this stuff | 18:51 |
| @wiking | i mean seriously it's not shogun's job to do this | 18:51 |
| @HeikoS | wiking: you are right | 18:51 |
| @HeikoS | but still I want it, dont want to add it to shogun, just asking for advice | 18:52 |
| @wiking | ah i see | 18:52 |
| @wiking | sorry then i misunderstood | 18:52 |
| @HeikoS | wiking: could you help me a bit with that? | 18:53 |
| @HeikoS | Ill share a google doc for live editing | 18:53 |
| @HeikoS | sent | 18:53 |
| @wiking | HeikoS: better share a gist ;) | 18:53 |
| @HeikoS | wiking: yeah once its more mature | 18:54 |
| @HeikoS | because now I want to edit it a lot | 18:54 |
| thoralf | Anyone knows what this tester.py does? | 19:03 |
| @HeikoS | thoralf: yes | 19:03 |
| @HeikoS | it runs the integration tests | 19:03 |
| @HeikoS | which means that it runs all python examples, and compares their output to the stored file | 19:03 |
| thoralf | HeikoS: It starts 1000 threads per second... ;) | 19:03 |
| @HeikoS | thoralf: really? thats not nice :) | 19:04 |
| thoralf | HeikoS: My system is unresponsible for about 5-10 seconds. | 19:04 |
| thoralf | No mouse movement. | 19:04 |
| @HeikoS | thoralf: oh man, thats not good | 19:04 |
| @HeikoS | any idea why it does that? | 19:04 |
| thoralf | No:( | 19:04 |
| @HeikoS | thoralf: it didnt before (on my machine=) | 19:05 |
| thoralf | libshogun-evaluation_cross_validation_locked_comparison starts about 10000 threads at once (?) | 19:06 |
| thoralf | libshogun-modelselection_grid_search_kernel started 19000 threads | 19:08 |
| @HeikoS | thoralf: did someone parallelize the cross-validation maybe? | 19:08 |
| thoralf | Something is wrong here. | 19:08 |
| @HeikoS | because these examples did not do that when I wrote them | 19:08 |
| @HeikoS | all 1 threaded | 19:08 |
| thoralf | I only have 8 cores on my workstation... I would expect that nobody tries to start more than 16 at once. ;) | 19:09 |
| thoralf | HeikoS: Btw. another PR which should be merged before 1443, because it fixes the tests: https://github.com/shogun-toolbox/shogun/pull/1444 | 19:10 |
| @HeikoS | thoralf: why is this needed? | 19:11 |
| @HeikoS | the maximum? | 19:11 |
| thoralf | HeikoS: Because the overhead is bigger than running 1 thread per core :) | 19:11 |
| @HeikoS | ok, waiting fo travis | 19:12 |
| @HeikoS | oh it did not trigger yet | 19:12 |
| shogun-buildbot | build #6 of osx1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/osx1%20-%20libshogun/builds/6 | 19:15 |
| thoralf | wiking: I happened again that cmake started building gtest/gmock while Linking CXX executable shogun-unit-test | 19:28 |
| @wiking | thoralf: /j #cmake | 19:29 |
| @wiking | thoralf: and start asking around | 19:29 |
| thoralf | wiking: Sorry, I can't start debugging something else yet. I just you might be interested in bug reports related to cmake. | 19:31 |
| @wiking | thoralf: this kind of stuff i cannot help with as they are really cmake related bugs | 19:33 |
| @wiking | so you are better of talking with cmake developers | 19:33 |
| thoralf | wiking: I understand. But in this case I won't do anything because this exceeds what I can do in my time. | 19:34 |
| thoralf | wiking: I'd really like to. | 19:34 |
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| @sonney2k | wiking, so what is missing wrt cmake now - static interfaces, detection of ruby narray and well all the failing tests of course then we are back | 19:40 |
| @sonney2k | wiking, which of these things can you still do? | 19:40 |
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| @sonney2k | wiking, ohh and any news on the video upload? | 19:42 |
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| @sonney2k | wiking, any ideas about http://shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/1261/steps/test/logs/stdio ? | 19:47 |
| @wiking | sonney2k: narray i'll check becuase that's really weird... but i'll do it | 19:47 |
| @sonney2k | HeikoS, looks like you broke the tests? http://shogun-toolbox.org/buildbot/builders/deb1%20-%20libshogun/builds/1830/steps/compile/logs/stdio | 19:48 |
| @sonney2k | HeikoS, MMDKernelSelectionMedian_unittest.cc | 19:48 |
| @wiking | sonney2k: for cygwin maybe a make install would help... but i'm not so sure, basically it just cannot find the shared lib, but i'll try setting an env variable or something | 19:48 |
| @HeikoS | sonney2k: I did not even commit anything | 19:49 |
| @sonney2k | wiking, Re cygwin didn't this work? | 19:49 |
| @wiking | sonney2k: i never seen cygwin running examples... | 19:49 |
| @HeikoS | wiking, sonney2k is there a way to statically link certain parts of shogun? | 19:50 |
| @wiking | sonney2k: http://shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/900 | 19:50 |
| @sonney2k | CMakeFiles/shogun-unit-test.dir/statistics/MMDKernelSelectionMedian_unittest.cc.o: In function `CmpHelperEQ<double, double>': | 19:50 |
| @sonney2k | /usr/include/gtest/gtest.h:1328: undefined reference to `testing::internal::EqFailure(char const*, char const*, testing::internal::String const&, testing::internal::String const&, bool)' | 19:50 |
| @sonney2k | so it is w/ linking already | 19:50 |
| @wiking | sonney2k: this is like the old ./configure stuff... it never ran examples | 19:50 |
| @iglesiasg | time for the weekly report! | 19:50 |
| @HeikoS | sonney2k: yes I saw that, but no idea whats the problem there | 19:50 |
| @sonney2k | wiking, seems like LD_LIBRARY_PATH can be set withing cygwin | 19:51 |
| @sonney2k | wiking, so that would fix it | 19:51 |
| @sonney2k | HeikoS, no | 19:51 |
| @wiking | sonney2k: i'll do that soonish | 19:51 |
| @sonney2k | wiking, and whats up with the workshop videos? | 19:52 |
| @wiking | sonney2k: b/w problem here | 19:52 |
| @sonney2k | wiking, so now what? | 19:52 |
| @wiking | sonney2k: i'll be on a good net this week | 19:52 |
| @wiking | i'll try to upload as mcuh as i can then | 19:53 |
| @sonney2k | wiking, ok | 19:53 |
| @wiking | btw: any ideas how i can find fast unique values in an SGVector? | 19:53 |
| @HeikoS | wiking: best you can do is linear I guess | 19:53 |
| @wiking | HeikoS: and creating a histogram of an SGVector elements? i mean w/o using some funky std::map shit? | 19:54 |
| @HeikoS | wiking: why not using map? | 19:55 |
| @wiking | HeikoS: well i didn't want it | 19:55 |
| @wiking | but seems i have to | 19:55 |
| @HeikoS | wiking: best way | 19:56 |
| @HeikoS | and almost no effort | 19:56 |
| @HeikoS | haha use boost ;) | 19:56 |
| @wiking | HeikoS: heheh it's going to be part of shogun | 19:56 |
| @wiking | ;) | 19:56 |
| @HeikoS | or add a unique method to vector then its also easy | 19:56 |
| foulwall | sonney2k , I've checked applications/arts, and got error "[ERROR] ALPHABET too small to contain all symbols in histogram", don't know why | 19:57 |
| thoralf | wiking: unique values? What about hashing? | 19:58 |
| @wiking | thoralf: std::map will then do that for me ;P | 19:58 |
| thoralf | wiking: Sorry, I was lagging. Python tests are still sucking :( | 19:59 |
| thoralf | sonney2k: Any idea? I have 3 tests which are dying after generating tons of threads: integration-python_modular-tester, libshogun-modelselection_grid_search_kernel, python_modular-modelselection_grid_search_libsvr_modular | 20:00 |
| @HeikoS | wiking: what do I do if my installed swig version is 1.3 | 20:07 |
| @HeikoS | thoralf, sonney2k ^ | 20:07 |
| @HeikoS | ah sorry | 20:08 |
| @HeikoS | install swig2.0 does it | 20:08 |
| @HeikoS | swig points to 1.3 | 20:08 |
| @sonney2k | thoralf, yeah libsvm's parallelization might be slow | 20:08 |
| thoralf | sonney2k: But 20000 threads? | 20:08 |
| @HeikoS | wiking: Error at cmake/FindSuperLU.cmake:67 (include) | 20:09 |
| @HeikoS | include could not find load file | 20:09 |
| @wiking | HeikoS: it's there in the repo | 20:09 |
| @wiking | so i wonder how's that possible at all | 20:10 |
| @sonney2k | thoralf, sure kernel rows computed in parallel | 20:10 |
| @HeikoS | wiking: whats the name? | 20:10 |
| @wiking | cmake/FindSuperLU.cmake | 20:10 |
| @HeikoS | wiking: how to install it? | 20:11 |
| @sonney2k | wiking, do we have an option w/ cmake to specify a swig executable / python executable? | 20:11 |
| @wiking | HeikoS: ? | 20:11 |
| @HeikoS | cmake outputs an error and dies | 20:11 |
| @HeikoS | with this superlu message, what to do? | 20:12 |
| @wiking | HeikoS: dunno man... cmake/FindSuperLU.cmake is in the repository | 20:12 |
| @wiking | it's impossible it cannot find it | 20:12 |
| @wiking | sonney2k: yes | 20:12 |
| @wiking | sonney2k: one way is to set -DCMAKE_PREFIX_PATH | 20:13 |
| @wiking | where the python/swig resides u want | 20:13 |
| @wiking | other way is to set the exact path | 20:13 |
| @wiking | but this are all standard cmake stuff | 20:13 |
| @wiking | i'm not the manual of cmake :( | 20:13 |
| @sonney2k | wiking, we really need a cmake documentation. you are repeating things too often :/ | 20:13 |
| @sonney2k | wiking, no but this would only look for swig right? if my swig executable is named swig2.2 then what? | 20:14 |
| @wiking | check your FindSWIG.cmake | 20:14 |
| @wiking | sonney2k: the cmake documentation is pretty fucking great | 20:14 |
| @wiking | just need to google it | 20:14 |
| @wiking | sonney2k: and yes i agree that we need cmake related info about shogun | 20:15 |
| @wiking | but not about the things you are asking now | 20:15 |
| @wiking | because those are really cmake related FAQs | 20:15 |
| thoralf | sonney2k: Mind if I add a limit to simultaneous sg_parallel->get_num_threads(); threads? ;) | 20:15 |
| @sonney2k | thoralf, these are *not* parallel threads | 20:15 |
| @sonney2k | thoralf, just #cpu | 20:15 |
| thoralf | sonney2k: It looks like it's creating all threads at a time. | 20:16 |
| @sonney2k | foulwall, I guess you used an example file that contains not just 'ACGT' characters | 20:17 |
| @sonney2k | thoralf, then it would be a bug - why do you think so? | 20:17 |
| @HeikoS | wiking: I found the problem: cmake_push_check_state() Unknown cmake command | 20:18 |
| @HeikoS | cmake 2.8.5 | 20:18 |
| thoralf | sonney2k: It calls pthread_create in a loop. | 20:18 |
| thoralf | sonney2k: My fault. | 20:19 |
| thoralf | Sorry. | 20:19 |
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| foulwall | sonney2k: I did ` python arts.py data/ARTS.dat.bz2 ` in applications/arts , is it correct? | 20:19 |
| thoralf | sonney2k: Okay, it's no problem in there. | 20:19 |
| thoralf | sonney2k: But then it doesn't explain 20000 threads when running libshogun-modelselection_grid_search_kernel or python_modular-modelselection_grid_search_libsvr_modular | 20:20 |
| @sonney2k | foulwall, no | 20:21 |
| foulwall | sonney2k: argh, do I need to extract ARTS.data.bz2? | 20:21 |
| @sonney2k | foulwall, let me find a file for you | 20:21 |
| @sonney2k | foulwall, no | 20:21 |
| @sonney2k | sec | 20:21 |
| thoralf | sonney2k: gtg, can wait until tomorrow. | 20:23 |
| @sonney2k | foulwall, https://dl.dropboxusercontent.com/u/31480471/dna.fa | 20:23 |
| @sonney2k | thoralf, well does threads=1 help? | 20:24 |
| foulwall | ok sonney2k , let me have a try | 20:24 |
| @sonney2k | thoralf, IIRC modsel is not done in parallel | 20:24 |
| @sonney2k | foulwall, it will take ~600MB CPU | 20:24 |
| @sonney2k | foulwall, and at least 5mins | 20:24 |
| thoralf | sonney2k: I'm just running "make tests", so it should work like everywhere else. | 20:25 |
| @sonney2k | foulwall, did it work? | 20:28 |
| foulwall | sonney2k: finished , only got -1, -42 , how do I demostrate them on web? | 20:29 |
| foulwall | finished in 134 secs:) | 20:30 |
| @HeikoS | wiking: shogun needs cmake>2.8.5 | 20:33 |
| @HeikoS | thats a bit annoying | 20:33 |
| @wiking | HeikoS: life's cruel | 20:33 |
| @sonney2k | foulwall, you have an old version of shogun installed then | 20:33 |
| @wiking | HeikoS: you can replace cmake_push_check_state | 20:33 |
| @wiking | in FindSuperLu | 20:34 |
| foulwall | than I'll recompile the newest one | 20:34 |
| @wiking | and then it won't need that | 20:34 |
| @HeikoS | wiking: yeah, will try some other things | 20:34 |
| foulwall | sonney2k: and retry | 20:34 |
| @HeikoS | I need things to work automatically thats the problem | 20:34 |
| @sonney2k | foulwall, you should have gotton -42 and some real valued numbers. so just plot the numbers in a curve | 20:34 |
| @wiking | HeikoS: well it's only that Find* stuff... so i really think that there's a way around.. look in other Find.cmake script | 20:34 |
| foulwall | ok sonney2k | 20:34 |
| @sonney2k | foulwall, the -42 is sth that you should maybe move to 0 in the curve | 20:35 |
| @HeikoS | ah we should have a binary shogun release with static stuff this eats my nerves ;) | 20:36 |
| foulwall | sonney2k: ok | 20:36 |
| @HeikoS | btw how is the .deb coming along? | 20:37 |
| @sonney2k | HeikoS, we don't even have cmake replacing all of configure so far so far far away | 20:43 |
| @HeikoS | wiking, sonney2k please see my latest push | 20:55 |
| @HeikoS | and let me know if oyu agree | 20:55 |
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| shogun-notifier- | shogun: Heiko Strathmann :develop * fbddd15 / cmake/CMakePushCheckState.cmake: https://github.com/shogun-toolbox/shogun/commit/fbddd15d9bb6f1a4ff706d60b4a1c3d7c3f8db7e | 20:55 |
| shogun-notifier- | shogun: added push check state file to make superlu check work for cmake 2.8.4 | 20:55 |
| @sonney2k | HeikoS, why do we need that? It is already in cmake? | 20:57 |
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| @HeikoS | sonney2k: yes but not in the old version I have here on the institute cluster | 20:58 |
| @HeikoS | so adding it makes things work | 20:58 |
| @sonney2k | HeikoS, I would rather require a new version then | 20:58 |
| @HeikoS | sonney2k: this would deny cmake for me, but this mini fix makes it work so I thought it is easier this way | 20:58 |
| @sonney2k | HeikoS, no you could easily download http://www.cmake.org/files/v2.8/cmake-2.8.11.2-Linux-i386.tar.gz and be happy | 20:59 |
| @HeikoS | sonney2k: you mean install locally? | 21:00 |
| @sonney2k | HeikoS, sure. | 21:00 |
| @sonney2k | I did this on many buildbots | 21:00 |
| @HeikoS | ok then, we can remove the thing again, | 21:00 |
| @HeikoS | I gotta go now though, will do it tomorrow | 21:00 |
| @HeikoS | see you! | 21:01 |
| @sonney2k | HeikoS, do you know which version | 21:01 |
| @sonney2k | HeikoS, has that file? | 21:01 |
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| @sonney2k | lambday, hey. Looks like HeikoS is about to leave so be fast ... | 21:01 |
| lambday | sonney2k: oh | 21:02 |
| lambday | HeikoS: hi | 21:02 |
| lambday | HeikoS: I will check out colpack (its the same one that Krylstat uses) for graph coloring thing | 21:02 |
| lambday | and check out how our sparse matrix things fit into that | 21:03 |
| lambday | HeikoS: but I am kinda worried about CG solvers.... | 21:03 |
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| lambday | without preconditioners, for some data they don't seem to converge | 21:03 |
| lambday | HeikoS: but I will check on real data (the ozone matrix) and then will see... the thing is, I don't have a reference value to check it with (our CStatistics::log_det fails for that huge matrix) | 21:04 |
| lambday | HeikoS: I will try if I can use Krylstat to generate that | 21:04 |
| lambday | sonney2k: do we have logistic regression? | 21:05 |
| @sonney2k | lambday, yes with liblinear | 21:05 |
| lambday | sonney2k: alright.. great! one of my friends was asking about it, I said I'll check out... will tell him | 21:06 |
| lambday | :D | 21:06 |
| @sonney2k | lambday, you have to use L2R_LR_DUAL or L1R_LR (or see LIBLINEAR_SOLVER_TYPE in Liblinear.h) | 21:06 |
| lambday | sonney2k: okay.. thanks :) | 21:07 |
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| shogun-buildbot | build #1831 of deb1 - libshogun is complete: Success [build successful] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb1%20-%20libshogun/builds/1831 | 21:46 |
| shogun-buildbot | build #1440 of deb2 - static_interfaces is complete: Failure [failed configure] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb2%20-%20static_interfaces/builds/1440 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com> | 21:46 |
| shogun-buildbot | build #1471 of bsd1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1471 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com> | 21:50 |
| -!- hushell [~hushell@8-92.ptpg.oregonstate.edu] has joined #shogun | 21:56 | |
| shogun-buildbot | build #7 of osx1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/osx1%20-%20libshogun/builds/7 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com> | 21:58 |
| -!- lambday [67157e37@gateway/web/freenode/ip.103.21.126.55] has quit [Ping timeout: 250 seconds] | 22:03 | |
| shogun-buildbot | build #1558 of deb3 - modular_interfaces is complete: Success [build successful] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/1558 | 22:21 |
| shogun-buildbot | build #1262 of cyg1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/1262 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com> | 22:27 |
| -!- pickle27 [~kevin@d67-193-243-174.home3.cgocable.net] has joined #shogun | 22:39 | |
| @wiking | HeikoS: yo | 23:13 |
| -!- shogun-notifier- [~irker@7nn.de] has quit [Quit: transmission timeout] | 23:55 | |
| --- Log closed Tue Aug 20 00:00:23 2013 | ||
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