| --- Log opened Fri Sep 12 00:00:38 2014 | ||
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| sonne|osx | flaxter ccache... | 01:43 |
|---|---|---|
| sonne|osx | broken on 12.04 | 01:43 |
| sonne|osx | so remove it or disable it | 01:43 |
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| -!- flaxter [43520460@gateway/web/freenode/ip.67.82.4.96] has joined #shogun | 02:24 | |
| flaxter | back...still here sonne? | 02:25 |
| flaxter | ok, general question for anyone... | 02:30 |
| flaxter | since I can't get shogun installed on various machines I have ready access to, it seems like terminal.com is a good option (if you've never used it but want to play with it, ask me and I'll give you a referral code...) | 02:31 |
| flaxter | they have ubuntu 13.10 and 14.04 and debian 7.0 | 02:31 |
| flaxter | but I didn't have luck with those...if someone has the time to either help me get one of these working or do it themselves, you can share a snapshot for others to use, which would be very helpful I think | 02:32 |
| flaxter | e.g., right now I see snapshots people have shared preconfigured with PyPy, Rstudio server, Coursera ML, Julia, EulerPy, Octave, pandas, etc... | 02:33 |
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| @wiking | flaxter: it works on ubuntu 12.04 as well: just do cmake -DENABLE_CCACHE=OFF .. | 04:07 |
| flaxter | ok, will try that now | 04:12 |
| flaxter | ok, I've tried a bunch of things so I might have lost track of what the problem was/is or whether I was supposed to do something else | 04:16 |
| flaxter | but I just ran: | 04:16 |
| flaxter | cmake -DENABLE_CCACHE=OFF -DPythonModular=ON .. | 04:16 |
| flaxter | that worked | 04:16 |
| flaxter | then | 04:16 |
| flaxter | make | 04:16 |
| flaxter | which gave: | 04:16 |
| flaxter | /home/ubuntu/shogun-3.2.0/src/shogun/statistics/TestStatistic.cpp:1:0: error: CPU you selected does not support x86-64 instruction set | 04:17 |
| @wiking | mmmm | 04:23 |
| @wiking | r u running like this in a virtual machine enviroment? | 04:23 |
| @wiking | flaxter: btw i suggest to checkout the latest development code of shogun, i.e.: git clone https://github.com/shogun-toolbox/shogun.git | 04:24 |
| flaxter | yep, I'm trying on opensciencedatacloud.org | 04:29 |
| flaxter | ok, will checkout the latest | 04:29 |
| flaxter | same error exactly | 04:31 |
| @wiking | mmm | 04:32 |
| @wiking | what's thie site? :) | 04:32 |
| flaxter | they provide unix VMs for science research | 04:33 |
| @wiking | mmm | 04:33 |
| @wiking | lemme check | 04:33 |
| @wiking | mmm it only works if u have affiliation with a us academic institution? | 04:34 |
| flaxter | somtehing like that, plus they'll make you fill something out | 04:34 |
| flaxter | but I'd be happy to get this going on terminal.com | 04:34 |
| flaxter | I think if I refer you you get $10 free which lets you try it for awhile | 04:35 |
| @wiking | flaxter: have u tried: http://cloud.shogun-toolbox.org/ ? | 04:35 |
| @wiking | althought it's quite outdated | 04:35 |
| @wiking | go ahead drop me an invite for terminal | 04:36 |
| flaxter | yes! great for playing with...but I've got something with gigs of data I want to try | 04:36 |
| flaxter | https://www.terminal.com/signup?ref_u=flaxter&ref_c=9f83804ab0b784a | 04:38 |
| @wiking | ok just trying | 04:38 |
| @wiking | flaxter: why don't u run it on your own machine? | 04:38 |
| @wiking | flaxter: have u been trying to use this with 'Official Ubuntu 14.04 '/? | 04:39 |
| @wiking | i cannot believe that somebody made a service of this :) | 04:40 |
| flaxter | good question. I am currently trying to install the latest from github on my machine. | 04:40 |
| flaxter | yes, 14.04. I also tried Debian and 13.10 | 04:40 |
| @wiking | ok, testing | 04:40 |
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| travis-ci | [travis-ci] it's lisitsyn'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/34651994 | 04:41 |
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| @wiking | btw this is a simple site wrapped around docker :P | 04:41 |
| flaxter | interesting, I hadn't heard of docker | 04:42 |
| @wiking | nevemrind :) | 04:43 |
| @wiking | mmm there is something very wrong with this ubuntu distro on terminal.com :) | 04:50 |
| flaxter | really? weird... | 04:50 |
| @wiking | yeah because cmake is erroring like never before | 04:51 |
| @wiking | flaxter: we have a machine testing each changes in shogun with ubuntu 14.04 | 04:51 |
| @wiking | and never had such problems :S | 04:51 |
| flaxter | I've seen your buildbots...very cool | 04:52 |
| @wiking | why cannot i copy paste from terminal.com's termnal... | 04:53 |
| @wiking | :S | 04:53 |
| flaxter | I'm also trying on linode, which is 14.04...totally different error, but I can get the latest from github and try again | 04:53 |
| @wiking | have u tried to compile python modular? | 04:54 |
| flaxter | pastebin.com/22q6dPcn | 04:54 |
| @wiking | yeah | 04:54 |
| flaxter | I have been trying modular...should I try static? | 04:54 |
| @wiking | it's because linode doesn't have enough memory by default to compile python modular interface | 04:54 |
| @wiking | it requires 4G+ free memory | 04:55 |
| @wiking | unfortunately | 04:55 |
| flaxter | wait, did you look at the pastebin? that error means out of memory? because it got pretty far | 04:55 |
| @wiking | yes | 04:55 |
| @wiking | thats the momemnt when it's trying to build the python modular interface | 04:56 |
| flaxter | aha | 04:56 |
| @wiking | so you can compile it on a linode machine of course | 04:57 |
| @wiking | but not with the cheapest version | 04:57 |
| @wiking | ... | 04:57 |
| @wiking | ok | 04:57 |
| @wiking | i see it's the very same problem i think on terminal.com | 04:58 |
| flaxter | aha, out of memory | 04:58 |
| @wiking | yeah the default terminal has like 250 megs of ram | 04:58 |
| flaxter | so wait, terminal.com has an option to have more memory...did you get cmake to work? | 04:58 |
| @wiking | ok no wait now that i don't run the build in parallel it managed to go on | 04:58 |
| @wiking | dunno about what are the options of terminal.com | 04:59 |
| @wiking | i'm just saying that with the one i have now... it's not possible | 04:59 |
| flaxter | ooh, how do you disable parallel? | 04:59 |
| @wiking | since 250 megs of ram is really not enough to compile it | 04:59 |
| @wiking | but if u change the instance type | 04:59 |
| @wiking | ok wait ai'll try taht | 05:00 |
| @wiking | flaxter: apt-get install cmake build-essential git libeigen3-dev | 05:00 |
| @wiking | these are the minimum set of packages you'll need to build shogun | 05:01 |
| @wiking | ok now i've switch to the small instance (1.6 gigs ram) now it continues to build | 05:01 |
| flaxter | cool; after the apt-get you're building from source from git? | 05:02 |
| @wiking | yep | 05:03 |
| @wiking | now i'm at 12% | 05:03 |
| @wiking | seems to be working | 05:03 |
| @wiking | but as i said before... you'll need much more ram if u want to compile python modular as well | 05:03 |
| @wiking | i reckon the xlarge instance might do it (6400 megs of ram) | 05:04 |
| flaxter | how restrictive is the static interface? I'd like to reproduce what's in the Gaussian Processes python notebook... | 05:07 |
| @wiking | mmm | 05:10 |
| @wiking | i doubt that you'll be able to do that | 05:11 |
| flaxter | ok, well let's see if small does it, and if not I'll try it on xlarge =) | 05:12 |
| flaxter | ok, new error on my home computer....maybe I didn't install libnlopt correctly? | 05:13 |
| @wiking | mmm why what's the error? | 05:14 |
| flaxter | http://pastebin.com/WL2jWy0J | 05:14 |
| @wiking | uuu yeah | 05:14 |
| @wiking | have u installed nlopt from source? | 05:14 |
| flaxter | yes | 05:16 |
| flaxter | is there an ubuntu package? | 05:16 |
| @wiking | flaxter: yeah... depends of course which ubuntu u r using | 05:20 |
| @wiking | for 12.04 there's no package | 05:21 |
| flaxter | home computer is 14.04 | 05:21 |
| @wiking | btw: i've just compiled shogun on small | 05:21 |
| @wiking | apt-get install libnlopt-dev | 05:21 |
| flaxter | oh, sweet | 05:23 |
| flaxter | can you save a snapshot and share it? | 05:25 |
| @wiking | mmmm just a sec the unit test part is still compiling | 05:27 |
| @wiking | in 2 mins i think it's fully ready | 05:27 |
| flaxter | great | 05:28 |
| @wiking | flaxter: https://www.terminal.com/tiny/peImyFXuxK | 05:34 |
| flaxter | awesome. thank you! | 05:35 |
| flaxter | oh no, gaussian process binary classification failed ;) | 05:36 |
| flaxter | shogun/data is empty | 05:36 |
| @wiking | flaxter: that's just because i haven't checked out the data submodule | 05:37 |
| @wiking | yeah | 05:37 |
| @wiking | git submodule init && git submodule update | 05:37 |
| flaxter | you didn't do make install either, right? | 05:37 |
| @wiking | noup | 05:38 |
| flaxter | ok, just did that | 05:38 |
| @wiking | and there's not python modular interface either | 05:38 |
| flaxter | ah ok, so how much ram should I try it with? | 05:38 |
| @wiking | youll need more than 4gigs free | 05:38 |
| @wiking | so as i said i'd try with xlarge | 05:39 |
| flaxter | ok, trying it | 05:39 |
| flaxter | I need swig I guess? | 05:40 |
| @wiking | yeps | 05:40 |
| flaxter | should I do -DENABLE_CCACHE=OFF? | 05:40 |
| @wiking | noup since i haven't installed ccache | 05:40 |
| flaxter | also installing python-dev | 05:41 |
| @wiking | and that is a problem only with ubuntu 12.04 | 05:41 |
| flaxter | ok | 05:41 |
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| flaxter | (still downloading and installing python-dev....) | 05:46 |
| flaxter | for anyone who finds this by google search, I now need to install numpy | 05:49 |
| flaxter | wiking, if you're still here, do you know if the ubuntu package for 14.04 is good or should I install it with pip? | 05:49 |
| @wiking | should be good | 05:51 |
| @wiking | same with scipy | 05:51 |
| flaxter | ok | 05:52 |
| flaxter | also need libblas-dev | 06:09 |
| @wiking | yeah well you'll need a lot of packages | 06:09 |
| flaxter | libatlas-base-dev? | 06:09 |
| @wiking | if u want to have all the features of shogun | 06:09 |
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| flaxter | libnlopt-dev | 06:10 |
| flaxter | what else? :) | 06:10 |
| @wiking | mmmm | 06:11 |
| @wiking | when u run cmake | 06:11 |
| @wiking | on the end it shows what libraries has been detected | 06:12 |
| @wiking | and which not | 06:12 |
| flaxter | opencl is the only required one not found | 06:13 |
| @wiking | mmm well that u won't have in a virtualenv like this anwyas | 06:13 |
| @wiking | *anyways | 06:13 |
| flaxter | do you know which package I need? | 06:14 |
| @wiking | for? | 06:14 |
| flaxter | sorry, didnt see you say I won't need it | 06:14 |
| flaxter | so I shouldn't take the *REQUIRED* packages part too seriously? | 06:15 |
| @wiking | mmm is it in required section... wonder why it ended up there:S | 06:15 |
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| flaxter | anyone know about "NameError: name 'GradientEvaluation' is not defined"? | 14:55 |
| flaxter | I have nlopt; maybe I also need one of these optional packages which were not found? * CCache * GDB * Mosek * OpenMP * Atlas * GLPK * CPLEX * ARPACK * ViennaCL (required version >= 1.5.0) * LpSolve * ColPack * ARPREC * Doxygen * LibXml2 * HDF5 * CURL * ZLIB * LibLZMA * SNAPPY * LZO * Protobuf * Jinja2 -- The follo | 14:59 |
| @wiking | mmm | 15:13 |
| @wiking | flaxter: src/shogun/evaluation/GradientEvaluation.h doesn't need any special library | 15:14 |
| flaxter | I am also missing GaussianProcessBinaryClassification | 15:14 |
| flaxter | ImportError: cannot import name GaussianProcessBinaryClassification | 15:15 |
| flaxter | oh wait, GradientEvaluation is there. it's GradientModelSelection that's missing | 15:15 |
| @wiking | flaxter: it GradientModelSelection needs nlopt | 15:17 |
| @wiking | and there's no more GaussianProcessBinaryClassification | 15:17 |
| @wiking | it's GaussianProcessClassification | 15:18 |
| flaxter | (ok, I have been collecting issues with the GP python notebook--when I fix it up I should probably do a pull request or something?) | 15:18 |
| flaxter | I installed nlopt...double-checking | 15:18 |
| @wiking | yeah | 15:19 |
| flaxter | yes, libnlopt-dev is installed from apt | 15:19 |
| flaxter | -- The following OPTIONAL packages have been found: includes NLopt | 15:20 |
| @wiking | mmm | 15:23 |
| @wiking | then u should have GradientModelSelection | 15:23 |
| flaxter | recompiling, just in case | 15:25 |
| flaxter | bbiab | 15:25 |
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| flaxter | back, in case you've had any ideas about GradientModelSelection...still recompiling (it crashed because not enough memory, reconfigured (on the fly!) to have more memory, now waiting.) | 16:21 |
| flaxter | build complete | 16:28 |
| flaxter | >>> from modshogun import GradientModelSelection Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: cannot import name GradientModelSelection | 16:28 |
| flaxter | no luck... | 16:28 |
| sonne|work | flaxter: have a look at the GradientModelSelection.{h,cpp} files and look for the ifdefs there | 16:29 |
| sonne|work | I guess you still don't have some dep installed | 16:29 |
| flaxter | only one that's there is HAVE_NLOPT... | 16:30 |
| sonne|work | flaxter: and did NLOPT get detected? | 16:31 |
| sonne|work | (HAVE_NLOPT should be in lib/config.h) | 16:31 |
| flaxter | it got detected, yeah, see here: http://pastebin.com/Jtxx4Bk4 | 16:32 |
| flaxter | ok, just looked there as well-- #define HAVE_NLOPT 1 | 16:33 |
| flaxter | wait! I might have done just make and not make install for this one | 16:34 |
| sonne|work | sounds like :) | 16:35 |
| flaxter | fixed! ok, cool | 16:35 |
| sonne|work | heh | 16:35 |
| flaxter | btw, I now think I have a pretty much working version of python modular on terminal.com...which I'd be happy to share for others (it took lots of ram to compile, but once it's compiled you can reduce the amount of ram allocated to save money) | 16:36 |
| sonne|work | what is terminal.com? | 16:37 |
| flaxter | I pretty much know what it says on www.terminal.com but I've had fun playing with it so far ... I was referred by a friend who does systems / ML research | 16:41 |
| flaxter | let me know if you want an invite to try it out (not sure if this is necessary, but I get some kind credit for referring) | 16:41 |
| sonne|work | flaxter: I am currently scarce in time but hey why not won't hurt | 16:46 |
| flaxter | try this link? http://www.terminal.com/signup?ref_u=flaxter&ref_c=9f83804ab0b784a | 16:46 |
| sonne|work | ok registered - I am sonne - where is that terminal? | 16:48 |
| flaxter | sharing, hold on | 16:49 |
| flaxter | https://www.terminal.com/tiny/yAzDIQeZpq | 16:50 |
| flaxter | bbiab | 16:50 |
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| flaxter | back | 17:02 |
| flaxter | are there any dependencies for StringFeatures? | 17:19 |
| flaxter | NameError: name 'SimpleFeatures' is not defined | 17:19 |
| flaxter | NameError: name 'StringFeatures' is not defined | 17:19 |
| flaxter | doxygen? | 17:19 |
| flaxter | no wait, that seems unlikely | 17:21 |
| flaxter | maybe I should just be using StringCharFeatures instead. | 17:28 |
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| flaxter | ok, I am using StringCharFeatures, perhaps incorrectly. the model fits but gp.apply crashes | 18:27 |
| flaxter | here is a minimum working example... | 18:27 |
| flaxter | http://pastebin.com/iAE3771h | 18:27 |
| flaxter | just tried the same kernel with an svm and everything is fine | 18:53 |
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| flaxter | totally unrelated...I'm looking at the TensorProductPairKernel | 19:20 |
| flaxter | is the documentation wrong or the code? I think it should be Kp ((A,B),(C,D)) = K(A,C)K(B,D)+K(A,D)K(B,C), following http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275314/ | 19:21 |
| flaxter | but the docs say it calculates k(a,c)k(b,c) + k(a,d)k(b,c) | 19:21 |
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| --- Log closed Sat Sep 13 00:00:40 2014 | ||
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