| --- Log opened Wed Feb 20 00:00:47 2013 | ||
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| lambday | hi... this is soumyajit again.. I tried to run the java modular example [http://www.shogun-toolbox.org/doc/en/current/modular_tutorial.html] but got some errors... | 05:00 |
|---|---|---|
| lambday | cannot find symbol symbol : constructor RealFeatures(org.jblas.DoubleMatrix) location: class org.shogun.RealFeatures RealFeatures feats_train = new RealFeatures(traindata_real); | 05:00 |
| lambday | same with BinaryLabels class... | 05:01 |
| lambday | and another type mismatch | 05:03 |
| lambday | incompatible types found : org.shogun.RealVector required: org.jblas.DoubleMatrix DoubleMatrix out = obtain_from_generic(svm.apply(feats_test)).get_labels(); | 05:03 |
| lambday | is that a bug or I am doing something wrong? :( | 05:03 |
| lambday | shall I take a look at src/interfaces/java_modular/swig_typemaps.i ? | 05:12 |
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| sonne|work | lambday: the java examples just compile fine? | 09:24 |
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| shogun-notifier- | shogun: Soeren Sonnenburg :master * 2998970 / src/shogun/lib/SGMatrix.cpp: https://github.com/shogun-toolbox/shogun/commit/299897031ea438bbe18044d162cf4e9be4186885 | 09:26 |
| shogun-notifier- | shogun: include SGMatrixList.h instead of .cpp (Closes: #855) | 09:26 |
| shogun-notifier- | shogun: | 09:26 |
| shogun-notifier- | shogun: Thanks bianjiang for the fix! | 09:26 |
| sonne|work | lambday: http://shogun-toolbox.org/doc/en/current/java_modular_examples.html | 09:27 |
| sonne|work | lambday: if you compile for java and run make check-examples these work... | 09:28 |
| blackburn | sonne|work: surprising bug | 09:32 |
| blackburn | with include.cpp | 09:32 |
| shogun-buildbot_ | build #850 of deb1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb1%20-%20libshogun/builds/850 blamelist: Sergey Lisitsyn <lisitsyn.s.o@gmail.com> | 09:33 |
| sonne|work | yeah stupid typo? | 09:34 |
| shogun-buildbot_ | build #849 of deb1 - libshogun is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb1%20-%20libshogun/builds/849 blamelist: Soeren Sonnenburg <sonne@debian.org> | 09:35 |
| n4nd0 | sonne|work: my bad | 09:39 |
| n4nd0 | I got probably confused for using a templated class separated in cpp and header | 09:39 |
| shogun-notifier- | shogun: Sergey Lisitsyn :master * 35a512f / src/NEWS: https://github.com/shogun-toolbox/shogun/commit/35a512f25737b36f835a2613127e23f39a9a2d74 | 09:42 |
| shogun-notifier- | shogun: Mention of include fix in NEWS. Related to #855 | 09:42 |
| lambday | sonne|work: hi... I tried with the make check-examples but its not working.. | 10:42 |
| lambday | make -C interfaces/java_modular check-examples-java_modular && true make[1]: Entering directory `/usr/home3/rahul/shogun/shogun/src/interfaces/java_modular' cd ../../../examples/undocumented/java_modular && \ ( LD_LIBRARY_PATH=//usr/home3/rahul/shogun/shogun_java/lib ./check.sh ) Load.java:2: package org.jblas does not exist import org.jblas.*; ^ Load.java:7: cannot find symbol symbol : class DoubleMatrix location: class Load pu | 10:42 |
| lambday | i have jblas-1.2.3.jar in /usr/share/java/jblas | 10:43 |
| sonne|work | lambday: seems not to be in CLASSPATH ... | 10:44 |
| lambday | sonne|work: while compiling with javac, I mentioned both jars (shogun.jar and jblas.jar) with -cp but even then its giving similar error :( | 10:44 |
| n4nd0 | sonne|work: hey | 10:46 |
| n4nd0 | sonne|work: is there any Username/password valid for the shogun-web in github? | 10:46 |
| sonne|work | n4nd0: errm for what? | 10:46 |
| sonne|work | n4nd0: you should be able to fork/checkout / just do a pull request as usual | 10:47 |
| n4nd0 | n4nd0: I think we are not talking about the same thing | 10:47 |
| n4nd0 | I mean | 10:47 |
| n4nd0 | if I run locally my shogun-web | 10:47 |
| sonne|work | lambday: please try to create some minimal jblas example and try to get that work first | 10:47 |
| n4nd0 | in 127.0.0.1:8000 for example | 10:47 |
| n4nd0 | and I want to access 127.0.0.1:8000/admin/ | 10:48 |
| sonne|work | n4nd0: ohh - ask your friend - I forgot the password | 10:48 |
| n4nd0 | sonne|work: hehe ok - I think he is sleeping now or sth | 10:48 |
| lambday | sonne|work: okay... thanks | 10:48 |
| sonne|work | n4nd0: if you can figure out how to reset the passphrase - that would be good | 10:49 |
| sonne|work | I would also like to have access to that stuff again :D | 10:49 |
| n4nd0 | sonne|work: I will ask him | 10:49 |
| n4nd0 | sonne|work: it seems that he doesn't remember... | 10:55 |
| n4nd0 | the credentials | 10:55 |
| n4nd0 | sonne|work: lol I got in | 10:56 |
| lambday | sonne|work: hi... jblas example working.. [tried this one http://schabby.de/jblas-simple-example/]... used jblas with -cp, but then again tried to run classifier_domainadaptationsvm_modular.java and it doesn't compile... shall I try putting the jblas.jar in shogun installation dir/share/java? | 11:00 |
| n4nd0 | lambday: hey | 11:01 |
| lambday | n4nd0: hello :) | 11:01 |
| n4nd0 | can you paste the line you use to compile for the jblas example that works | 11:01 |
| n4nd0 | and for the shogun example that doesn't | 11:01 |
| lambday | javac -cp ".:/usr/home3/rahul/jblas/jblas-1.2.3.jar" jblas_test.java | 11:02 |
| lambday | this works | 11:02 |
| lambday | javac -cp ".:/usr/home3/rahul/jblas/jblas-1.2.3.jar:/usr/home3/rahul/shogun/shogun_java/share/java/shogun.jar" classifier_domainadaptationsvm_modular.java | 11:02 |
| lambday | this doesn't :( | 11:02 |
| n4nd0 | lambday: what does the error say? | 11:02 |
| lambday | classifier_domainadaptationsvm_modular.java:57: cannot find symbol symbol : constructor BinaryLabels(org.jblas.DoubleMatrix) location: class org.shogun.BinaryLabels BinaryLabels labels = new BinaryLabels(new DoubleMatrix(label_train_dna)); ^ classifier_domainadaptationsvm_modular.java:65: incompatible types found : org.shogun.RealVector required: org.jblas.DoubleMatrix DoubleMatrix out = obtain_from_gene | 11:03 |
| n4nd0 | lambday: mm alright | 11:03 |
| lambday | what am I missing here :( | 11:04 |
| n4nd0 | so you could compile and run a minimal shogun java example? | 11:04 |
| lambday | n4nd0: no.. minimal jblas example compiles... but I couldn't get shogun java example compiled with the commands I mentioned | 11:05 |
| n4nd0 | lambday: so no shogun example can be run? | 11:06 |
| n4nd0 | I am interested in finding out if the problem is due to java_modular interface not properly setup in your system | 11:06 |
| n4nd0 | or jblas not found with shogun examples | 11:07 |
| n4nd0 | lambday: do you see what I mean? | 11:07 |
| lambday | well, i used configure with java_modular interface, | 11:07 |
| lambday | wait let me paste first few lines of make check-examples | 11:08 |
| lambday | http://pastebin.com/c2UBEi99 | 11:10 |
| n4nd0 | lambday: in what dir are you executing that? | 11:11 |
| lambday | shogun/src | 11:11 |
| n4nd0 | lambday: ok in src | 11:11 |
| n4nd0 | what I meant was | 11:11 |
| n4nd0 | if any of the examples in examples/undocumented/java_modular worked for you | 11:12 |
| lambday | I tried with only one though and it didn't compile :( | 11:13 |
| lambday | tried this one "classifier_domainadaptationsvm_modular.java" | 11:13 |
| n4nd0 | lambday: yep, but that one uses jblas | 11:14 |
| n4nd0 | my point is | 11:14 |
| n4nd0 | does your java_modular interface work at all? | 11:14 |
| n4nd0 | or the error arises when jblas comes into play? | 11:14 |
| lambday | ohkay I got your point | 11:14 |
| lambday | I'm trying with a hello world program | 11:15 |
| n4nd0 | yeah do that | 11:15 |
| n4nd0 | sth similar to examples/undocumented/libshogun/basic_minimal.cpp (BUT translated into java!) should be enough | 11:16 |
| lambday | n4nd0: alright.... thanks a ton.. I'm trying :) | 11:17 |
| n4nd0 | no worries :) | 11:17 |
| lambday | n4nd0: well, it compiles fine... I tried this code [http://pastebin.com/0bWfYiYf]... compiled with javac -cp ".:/usr/home3/rahul/shogun/shogun_java/share/java/shogun.jar" helloworld.java | 11:36 |
| lambday | but couldn't run it... with -Djava.library.path | 11:36 |
| n4nd0 | lambday: aham! | 11:36 |
| lambday | java -cp ".:/usr/home3/rahul/shogun/shogun_java/share/java/shogun.jar" -Djava.library.path=".:/usr/home3/rahul/shogun/shogun_java/lib/jni/libmodshogun.so" helloworld | 11:36 |
| n4nd0 | what happens when you run it? | 11:36 |
| lambday | it says | 11:37 |
| lambday | Exception in thread "main" java.lang.UnsatisfiedLinkError: no modshogun in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1681) at java.lang.Runtime.loadLibrary0(Runtime.java:840) at java.lang.System.loadLibrary(System.java:1047) at helloworld.main(helloworld.java:5) | 11:37 |
| lambday | tried with System.load() also but that too failed :-/ | 11:37 |
| n4nd0 | lambday: mmm | 11:41 |
| lambday | n4nd0: when I try with System.load("path/to/libmodshogun.so") it says - | 11:41 |
| lambday | Exception in thread "main" java.lang.UnsatisfiedLinkError: Can't load library: /usr/home3/rahul/shogun/shogun_java/share/java/libmodshogun.so | 11:41 |
| n4nd0 | lambday: when you compiled shogun, what did you exactly? | 11:42 |
| n4nd0 | did you ./configure, make and then sudo make install? | 11:42 |
| n4nd0 | I am just guessing | 11:42 |
| lambday | yeah | 11:42 |
| lambday | not sudo, I installed it into another directory, specified with the configure --prefix option | 11:43 |
| n4nd0 | mmm ok | 11:43 |
| n4nd0 | I guess you should tell java somehow where your library is | 11:44 |
| n4nd0 | it could be the one you specified, I am not sure | 11:44 |
| n4nd0 | lambday: are you in linux? | 11:45 |
| n4nd0 | then try running whereis libshogun | 11:45 |
| lambday | hmm... I thought -Djava.library.path=/path/to/libmodshogun.so" should do :( | 11:45 |
| lambday | n4nd0: yes... fedora 16 | 11:45 |
| lambday | okay | 11:45 |
| n4nd0 | mmm I guess <path/to> should be substituted byt the path to libshogun hehe | 11:46 |
| lambday | [rahul@cfdvs4-2 test]$ whereis libshogun libshogun: /usr/local/lib/libshogun.so /usr/local/lib/libshogun.a | 11:46 |
| lambday | well... I guess whereis is giving the libshogun.so from a previous installation that I did on /usr/local :) | 11:47 |
| lambday | n4nd0: okay I'm trying with libshogun.so path | 11:47 |
| n4nd0 | hehe yeah it can be | 11:47 |
| n4nd0 | I am not sure what kind of path is System.loadLibrary waiting for - I am not a java expert :D | 11:48 |
| blackburn | n4nd0: LD_LIBRARY_PATH I think | 11:50 |
| blackburn | n4nd0: and CLASSPATH should be set too | 11:50 |
| blackburn | just take a look at https://github.com/shogun-toolbox/shogun/blob/master/examples/undocumented/java_modular/check.sh | 11:50 |
| lambday | blackburn: now I am using System.load, which expects direct path to the shared library.. System.loadLibrary() didn't work for me | 11:51 |
| n4nd0 | lambday: ^ | 11:51 |
| lambday | blackburn: thanks... I'm checking :) | 11:51 |
| blackburn | lambday: does ./check.sh work for you? | 11:53 |
| lambday | blackburn: I guess I need to move a few files... according to the LD_LIBRARY_PATH and CLASSPATH... I'm trying.. | 11:56 |
| blackburn | lambday: I don't think you should move anything - check.sh is supposed to run in a typical case | 11:57 |
| n4nd0 | blackburn: maybe < lambday> not sudo, I installed it into another directory, specified with the configure --prefix option | 11:59 |
| n4nd0 | that affects | 11:59 |
| lambday | blackburn: I had jblas.jar in a different directory... I just moved that to /usr/share/java/jblas.jar... and running check.sh | 12:00 |
| blackburn | ah | 12:00 |
| lambday | its running... most of the examples shows ERROR, some showed OK | 12:00 |
| blackburn | okay I see | 12:00 |
| lambday | blackburn: but when I run a simple example like [http://pastebin.com/0bWfYiYf], it compiles fine but doesn't run.. | 12:01 |
| blackburn | lambday: something is wrong with LD_LIBRARY_PATH I guess | 12:07 |
| lambday | blackburn: okay.. I'm trying again :( | 12:08 |
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| lambday | blackburn: thanks a lot... it works now... :) | 12:32 |
| lambday | did a make again, and installed in /usr/local/... | 12:32 |
| blackburn | nice | 12:33 |
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| n4nd0 | lambday: is it working too already for examples using jblas and shogun? | 13:02 |
| lambday | n4nd0: tried running classifier_domainadaptationsvm_modular.class and it worked :) | 13:04 |
| n4nd0 | lambday: cool | 13:05 |
| n4nd0 | then you are ready to play :) | 13:05 |
| lambday | n4nd0: hope so.. can't wait to get my hands dirty :) | 13:05 |
| lambday | need to do an assignment this week... will be using shogun :) | 13:06 |
| n4nd0 | lambday: cool, what is the assignment about? | 13:06 |
| lambday | I gotta implement a string kernel... | 13:07 |
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| alexlovesdata | @sonney2k: I still have the CDOT feature extension of the random fourier preproc in my mind ... it is not forgotten | 17:08 |
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| blackburn | http://care.diabetesjournals.org/content/17/2/152.full.pdf+html hahahhah | 18:01 |
| alexlovesdata | blackburn? Tai's formula? What is that person doing there?explicit integration?? | 18:05 |
| blackburn | alexlovesdata: hhahaha yeeeeeees | 18:05 |
| blackburn | alexlovesdata: biologists reinvented integration | 18:05 |
| alexlovesdata | who reviewed that?? A monkey? A Donkey? | 18:06 |
| blackburn | alexlovesdata: it is even listed in wikipedia page 'Peer-review fail' | 18:06 |
| blackburn | alexlovesdata: wait wait | 18:07 |
| blackburn | this one would kill you | 18:07 |
| alexlovesdata | Thats the joke of the day :D :D :D | 18:07 |
| blackburn | http://scholar.google.ru/scholar?hl=ru&q=http%3A%2F%2Fcare.diabetesjournals.org%2Fcontent%2F17%2F2%2F152.full.pdf%2Bhtml&btnG= | 18:07 |
| blackburn | alexlovesdata: see # of citations | 18:07 |
| alexlovesdata | zitirueyetsa 176 ??? | 18:08 |
| alexlovesdata | sorry ... I cant type kyrillian or the proper english replacement | 18:08 |
| alexlovesdata | 176 cites??? | 18:08 |
| blackburn | alexlovesdata: oops my url is bad for you | 18:09 |
| alexlovesdata | O-M-G | 18:09 |
| blackburn | yes | 18:09 |
| blackburn | 176 cites | 18:09 |
| alexlovesdata | life is sooo unfair :'( | 18:09 |
| alexlovesdata | somebody cites this wheel reinvention 176 | 18:09 |
| alexlovesdata | my papers :'( :D | 18:09 |
| alexlovesdata | bookmarked that! :D | 18:10 |
| blackburn | alexlovesdata: next time you use integration cite it | 18:10 |
| alexlovesdata | hahaha, the risk is that some reviewers would not get the irony | 18:12 |
| alexlovesdata | 7 months review time for THAT | 18:12 |
| alexlovesdata | I guess they used an ant colony to rate that paper or so\ | 18:13 |
| alexlovesdata | unfortunately Ms. Tai has no webpage | 18:17 |
| blackburn | alexlovesdata: yeah it is pretty old | 18:18 |
| alexlovesdata | I still cant believe that reviewing these two pages took 7 months. Monty pythons happens every day | 18:21 |
| blackburn | alexlovesdata: there are a lot of things to reinvent still | 18:22 |
| blackburn | we should take it | 18:22 |
| alexlovesdata | blackburn: there was a time when I thought about a career in mathematical physics, took courses in differential geometry about fiber bundles and classifications of lie groups and stuff like that | 18:24 |
| blackburn | alexlovesdata: I guess it is nearly impossible to get such fake in math. physics | 18:25 |
| alexlovesdata | how about astrology :D ? | 18:26 |
| blackburn | alexlovesdata: I had to take a few courses on that actually (especially on numeric) | 18:26 |
| blackburn | yeah astrology is a great field | 18:26 |
| blackburn | everything is possible | 18:26 |
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| blackburn | n4nd0: http://care.diabetesjournals.org/content/17/2/152.full.pdf+html | 19:36 |
| blackburn | n4nd0: new gsoc idea | 19:36 |
| alexlovesdata | I am not sure whether anybody has the qualifications to mentor it :D | 19:36 |
| blackburn | alexlovesdata: we should contact DOCTOR mary tai | 19:37 |
| n4nd0 | blackburn: hehe | 19:47 |
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| n4nd0 | sonney2k, sonne|work : is it possible to open the option of issues in shogun-web? | 22:42 |
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| --- Log closed Thu Feb 21 00:00:48 2013 | ||
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