Open in new window / Try shogun cloud
--- Log opened Wed Feb 20 00:00:47 2013
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lambdayhi... 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
lambdaysame with BinaryLabels class...05:01
lambdayand another type mismatch05:03
lambdayincompatible types found   : org.shogun.RealVector required: org.jblas.DoubleMatrix DoubleMatrix out = obtain_from_generic(svm.apply(feats_test)).get_labels();05:03
lambdayis that a bug or I am doing something wrong? :(05:03
lambdayshall I take a look at src/interfaces/java_modular/swig_typemaps.i ?05:12
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sonne|worklambday: 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/299897031ea438bbe18044d162cf4e9be418688509:26
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|worklambday: http://shogun-toolbox.org/doc/en/current/java_modular_examples.html09:27
sonne|worklambday: if you compile for java and run make check-examples these work...09:28
blackburnsonne|work: surprising bug09:32
blackburnwith include.cpp09:32
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|workyeah 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
n4nd0sonne|work: my bad09:39
n4nd0I got probably confused for using a templated class separated in cpp and header09:39
shogun-notifier-shogun: Sergey Lisitsyn :master * 35a512f / src/NEWS: https://github.com/shogun-toolbox/shogun/commit/35a512f25737b36f835a2613127e23f39a9a2d7409:42
shogun-notifier-shogun: Mention of include fix in NEWS. Related to #85509:42
lambdaysonne|work: hi... I tried with the make check-examples but its not working..10:42
lambdaymake -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 pu10:42
lambdayi have jblas-1.2.3.jar in /usr/share/java/jblas10:43
sonne|worklambday: seems not to be in CLASSPATH ...10:44
lambdaysonne|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
n4nd0sonne|work: hey10:46
n4nd0sonne|work: is there any Username/password valid for the shogun-web in github?10:46
sonne|workn4nd0: errm for what?10:46
sonne|workn4nd0: you should be able to fork/checkout / just do a pull request as usual10:47
n4nd0n4nd0: I think we are not talking about the same thing10:47
n4nd0I mean10:47
n4nd0if I run locally my shogun-web10:47
sonne|worklambday: please try to create some minimal jblas example and try to get that work first10:47
n4nd0in 127.0.0.1:8000 for example10:47
n4nd0and I want to access 127.0.0.1:8000/admin/10:48
sonne|workn4nd0: ohh - ask your friend - I forgot the password10:48
n4nd0sonne|work: hehe ok - I think he is sleeping now or sth10:48
lambdaysonne|work: okay... thanks10:48
sonne|workn4nd0: if you can figure out how to reset the passphrase - that would be good10:49
sonne|workI would also like to have access to that stuff again :D10:49
n4nd0sonne|work: I will ask him10:49
n4nd0sonne|work: it seems that he doesn't remember...10:55
n4nd0the credentials10:55
n4nd0sonne|work: lol I got in10:56
lambdaysonne|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
n4nd0lambday: hey11:01
lambdayn4nd0: hello :)11:01
n4nd0can you paste the line you use to compile for the jblas example that works11:01
n4nd0and for the shogun example that doesn't11:01
lambdayjavac -cp ".:/usr/home3/rahul/jblas/jblas-1.2.3.jar" jblas_test.java11:02
lambdaythis works11:02
lambdayjavac -cp ".:/usr/home3/rahul/jblas/jblas-1.2.3.jar:/usr/home3/rahul/shogun/shogun_java/share/java/shogun.jar" classifier_domainadaptationsvm_modular.java11:02
lambdaythis doesn't :(11:02
n4nd0lambday: what does the error say?11:02
lambdayclassifier_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_gene11:03
n4nd0lambday: mm alright11:03
lambdaywhat am I missing here :(11:04
n4nd0so you could compile and run a minimal shogun java example?11:04
lambdayn4nd0: no.. minimal jblas example compiles... but I couldn't get shogun java example compiled with the commands I mentioned11:05
n4nd0lambday: so no shogun example can be run?11:06
n4nd0I am interested in finding out if the problem is due to java_modular interface not properly setup in your system11:06
n4nd0or jblas not found with shogun examples11:07
n4nd0lambday: do you see what I mean?11:07
lambdaywell, i used configure with java_modular interface,11:07
lambdaywait let me paste first few lines of make check-examples11:08
lambdayhttp://pastebin.com/c2UBEi9911:10
n4nd0lambday: in what dir are you executing that?11:11
lambdayshogun/src11:11
n4nd0lambday: ok in src11:11
n4nd0what I meant was11:11
n4nd0if any of the examples in examples/undocumented/java_modular worked for you11:12
lambdayI tried with only one though and it didn't compile :(11:13
lambdaytried this one "classifier_domainadaptationsvm_modular.java"11:13
n4nd0lambday: yep, but that one uses jblas11:14
n4nd0my point is11:14
n4nd0does your java_modular interface work at all?11:14
n4nd0or the error arises when jblas comes into play?11:14
lambdayohkay I got your point11:14
lambdayI'm trying with a hello world program11:15
n4nd0yeah do that11:15
n4nd0sth similar to examples/undocumented/libshogun/basic_minimal.cpp (BUT translated into java!) should be enough11:16
lambdayn4nd0: alright.... thanks a ton.. I'm trying :)11:17
n4nd0no worries :)11:17
lambdayn4nd0: 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.java11:36
lambdaybut couldn't run it... with -Djava.library.path11:36
n4nd0lambday: aham!11:36
lambdayjava -cp ".:/usr/home3/rahul/shogun/shogun_java/share/java/shogun.jar" -Djava.library.path=".:/usr/home3/rahul/shogun/shogun_java/lib/jni/libmodshogun.so" helloworld11:36
n4nd0what happens when you run it?11:36
lambdayit says11:37
lambdayException 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
lambdaytried with System.load() also but that too failed :-/11:37
n4nd0lambday: mmm11:41
lambdayn4nd0: when I try with System.load("path/to/libmodshogun.so") it says -11:41
lambdayException in thread "main" java.lang.UnsatisfiedLinkError: Can't load library: /usr/home3/rahul/shogun/shogun_java/share/java/libmodshogun.so11:41
n4nd0lambday: when you compiled shogun, what did you exactly?11:42
n4nd0did you ./configure, make and then sudo make install?11:42
n4nd0I am just guessing11:42
lambdayyeah11:42
lambdaynot sudo, I installed it into another directory, specified with the configure --prefix option11:43
n4nd0mmm ok11:43
n4nd0I guess you should tell java somehow where your library is11:44
n4nd0it could be the one you specified, I am not sure11:44
n4nd0lambday: are you in linux?11:45
n4nd0then try running whereis libshogun11:45
lambdayhmm... I thought -Djava.library.path=/path/to/libmodshogun.so" should do :(11:45
lambdayn4nd0: yes... fedora 1611:45
lambdayokay11:45
n4nd0mmm I guess <path/to> should be substituted byt the path to libshogun hehe11:46
lambday[rahul@cfdvs4-2 test]$ whereis libshogun libshogun: /usr/local/lib/libshogun.so /usr/local/lib/libshogun.a11:46
lambdaywell... I guess whereis is giving the libshogun.so from a previous installation that I did on /usr/local :)11:47
lambdayn4nd0: okay I'm trying with libshogun.so path11:47
n4nd0hehe yeah it can be11:47
n4nd0I am not sure what kind of path is System.loadLibrary waiting for - I am not a java expert :D11:48
blackburnn4nd0: LD_LIBRARY_PATH I think11:50
blackburnn4nd0: and CLASSPATH should be set too11:50
blackburnjust take a look at https://github.com/shogun-toolbox/shogun/blob/master/examples/undocumented/java_modular/check.sh11:50
lambdayblackburn: now I am using System.load, which expects direct path to the shared library.. System.loadLibrary() didn't work for me11:51
n4nd0lambday: ^11:51
lambdayblackburn: thanks... I'm checking :)11:51
blackburnlambday: does ./check.sh work for you?11:53
lambdayblackburn: I guess I need to move a few files... according to the LD_LIBRARY_PATH and CLASSPATH... I'm trying..11:56
blackburnlambday: I don't think you should move anything - check.sh is supposed to run in a typical case11:57
n4nd0blackburn: maybe < lambday> not sudo, I installed it into another directory, specified with the configure --prefix option11:59
n4nd0that affects11:59
lambdayblackburn: I had jblas.jar in a different directory... I just moved that to /usr/share/java/jblas.jar... and running check.sh12:00
blackburnah12:00
lambdayits running... most of the examples shows ERROR, some showed OK12:00
blackburnokay I see12:00
lambdayblackburn: but when I run a simple example like [http://pastebin.com/0bWfYiYf], it compiles fine but doesn't run..12:01
blackburnlambday: something is wrong with LD_LIBRARY_PATH I guess12:07
lambdayblackburn: okay.. I'm trying again :(12:08
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lambdayblackburn: thanks a lot... it works now... :)12:32
lambdaydid a make again, and installed in /usr/local/...12:32
blackburnnice12:33
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n4nd0lambday: is it working too already for examples using jblas and shogun?13:02
lambdayn4nd0: tried running classifier_domainadaptationsvm_modular.class and it worked :)13:04
n4nd0lambday: cool13:05
n4nd0then you are ready to play :)13:05
lambdayn4nd0: hope so.. can't wait to get my hands dirty :)13:05
lambdayneed to do an assignment this week... will be using shogun :)13:06
n4nd0lambday: cool, what is the assignment about?13:06
lambdayI 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 forgotten17:08
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blackburnhttp://care.diabetesjournals.org/content/17/2/152.full.pdf+html hahahhah18:01
alexlovesdatablackburn? Tai's formula? What is that person doing there?explicit integration??18:05
blackburnalexlovesdata: hhahaha yeeeeeees18:05
blackburnalexlovesdata: biologists reinvented integration18:05
alexlovesdatawho reviewed that?? A monkey? A Donkey?18:06
blackburnalexlovesdata: it is even listed in wikipedia page 'Peer-review fail'18:06
blackburnalexlovesdata: wait wait18:07
blackburnthis one would kill you18:07
alexlovesdataThats the joke of the day :D :D :D18:07
blackburnhttp://scholar.google.ru/scholar?hl=ru&q=http%3A%2F%2Fcare.diabetesjournals.org%2Fcontent%2F17%2F2%2F152.full.pdf%2Bhtml&btnG=18:07
blackburnalexlovesdata: see # of citations18:07
alexlovesdatazitirueyetsa 176 ???18:08
alexlovesdatasorry ... I cant type kyrillian or the proper english replacement18:08
alexlovesdata176 cites???18:08
blackburnalexlovesdata: oops my url is bad for you18:09
alexlovesdataO-M-G18:09
blackburnyes18:09
blackburn176 cites18:09
alexlovesdatalife is sooo unfair :'(18:09
alexlovesdatasomebody cites this wheel reinvention 17618:09
alexlovesdatamy papers :'( :D18:09
alexlovesdatabookmarked that! :D18:10
blackburnalexlovesdata: next time you use integration cite it18:10
alexlovesdatahahaha, the risk is that some reviewers would not get the irony18:12
alexlovesdata7 months review time for THAT18:12
alexlovesdataI guess they used an ant colony to rate that paper or so\18:13
alexlovesdataunfortunately Ms. Tai has no webpage18:17
blackburnalexlovesdata: yeah it is pretty old18:18
alexlovesdataI still cant believe that reviewing these two pages took 7 months. Monty pythons happens every day18:21
blackburnalexlovesdata: there are a lot of things to reinvent still18:22
blackburnwe should take it18:22
alexlovesdatablackburn: 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 that18:24
blackburnalexlovesdata: I guess it is nearly impossible to get such fake in math. physics18:25
alexlovesdatahow about astrology :D ?18:26
blackburnalexlovesdata: I had to take a few courses on that actually (especially on numeric)18:26
blackburnyeah astrology is a great field18:26
blackburneverything is possible18:26
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blackburnn4nd0: http://care.diabetesjournals.org/content/17/2/152.full.pdf+html19:36
blackburnn4nd0: new gsoc idea19:36
alexlovesdataI am not sure whether anybody has the qualifications to mentor it :D19:36
blackburnalexlovesdata: we should contact DOCTOR mary tai19:37
n4nd0blackburn: hehe19:47
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n4nd0sonney2k, 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