Open in new window / Try shogun cloud
--- Log opened Fri Sep 12 00:00:38 2014
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sonne|osxflaxter ccache...01:43
sonne|osxbroken on 12.0401:43
sonne|osxso remove it or disable it01:43
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flaxterback...still here sonne?02:25
flaxterok, general question for anyone...02:30
flaxtersince 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
flaxterthey have ubuntu 13.10 and 14.04 and debian 7.002:31
flaxterbut 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 think02:32
flaxtere.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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@wikingflaxter: it works on ubuntu 12.04 as well: just do cmake -DENABLE_CCACHE=OFF ..04:07
flaxterok, will try that now04:12
flaxterok, 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 else04:16
flaxterbut I just ran:04:16
flaxtercmake -DENABLE_CCACHE=OFF -DPythonModular=ON ..04:16
flaxterthat worked04:16
flaxterthen04:16
flaxtermake04:16
flaxterwhich 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 set04:17
@wikingmmmm04:23
@wikingr u running like this in a virtual machine enviroment?04:23
@wikingflaxter: btw i suggest to checkout the latest development code of shogun, i.e.: git clone https://github.com/shogun-toolbox/shogun.git04:24
flaxteryep, I'm trying on opensciencedatacloud.org04:29
flaxterok, will checkout the latest04:29
flaxtersame error exactly04:31
@wikingmmm04:32
@wikingwhat's thie site? :)04:32
flaxterthey provide unix VMs for science research04:33
@wikingmmm04:33
@wikinglemme check04:33
@wikingmmm it only works if u have affiliation with a us academic institution?04:34
flaxtersomtehing like that, plus they'll make you fill something out04:34
flaxterbut I'd be happy to get this going on terminal.com04:34
flaxterI think if I refer you you get $10 free which lets you try it for awhile04:35
@wikingflaxter: have u tried: http://cloud.shogun-toolbox.org/ ?04:35
@wikingalthought it's quite outdated04:35
@wikinggo ahead drop me an invite for terminal04:36
flaxteryes! great for playing with...but I've got something with gigs of data I want to try04:36
flaxterhttps://www.terminal.com/signup?ref_u=flaxter&ref_c=9f83804ab0b784a04:38
@wikingok just trying04:38
@wikingflaxter: why don't u run it on your own machine?04:38
@wikingflaxter: have u been trying to use this with 'Official Ubuntu 14.04 '/?04:39
@wikingi cannot believe that somebody made a service of this :)04:40
flaxtergood question. I am currently trying to install the latest from github on my machine.04:40
flaxteryes, 14.04. I also tried Debian and 13.1004:40
@wikingok, testing04:40
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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/3465199404:41
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@wikingbtw this is a simple site wrapped around docker :P04:41
flaxterinteresting, I hadn't heard of docker04:42
@wikingnevemrind :)04:43
@wikingmmm there is something very wrong with this ubuntu distro on terminal.com :)04:50
flaxterreally? weird...04:50
@wikingyeah because cmake is erroring like never before04:51
@wikingflaxter: we have a machine testing each changes in shogun with ubuntu 14.0404:51
@wikingand never had such problems :S04:51
flaxterI've seen your buildbots...very cool04:52
@wikingwhy cannot i copy paste from terminal.com's termnal...04:53
@wiking:S04:53
flaxterI'm also trying on linode, which is 14.04...totally different error, but I can get the latest from github and try again04:53
@wikinghave u tried to compile python modular?04:54
flaxterpastebin.com/22q6dPcn04:54
@wikingyeah04:54
flaxterI have been trying modular...should I try static?04:54
@wikingit's because linode doesn't have enough memory by default to compile python modular interface04:54
@wikingit requires 4G+ free memory04:55
@wikingunfortunately04:55
flaxterwait, did you look at the pastebin? that error means out of memory?  because it got pretty far04:55
@wikingyes04:55
@wikingthats the momemnt when it's trying to build the python modular interface04:56
flaxteraha04:56
@wikingso you can compile it on a linode machine of course04:57
@wikingbut not with the cheapest version04:57
@wiking...04:57
@wikingok04:57
@wikingi see it's the very same problem i think on terminal.com04:58
flaxteraha, out of memory04:58
@wikingyeah the default terminal has like 250 megs of ram04:58
flaxterso wait, terminal.com has an option to have more memory...did you get cmake to work?04:58
@wikingok no wait now that i don't run the build in parallel it managed to go on04:58
@wikingdunno about what are the options of terminal.com04:59
@wikingi'm just saying that with the one i have now... it's not possible04:59
flaxterooh, how do you disable parallel?04:59
@wikingsince 250 megs of ram is really not enough to compile it04:59
@wikingbut if u change the instance type04:59
@wikingok wait ai'll try taht05:00
@wikingflaxter: apt-get install cmake build-essential git libeigen3-dev05:00
@wikingthese are the minimum set of packages you'll need to build shogun05:01
@wikingok now i've switch to the small instance (1.6 gigs ram) now it continues to build05:01
flaxtercool; after the apt-get you're building from source from git?05:02
@wikingyep05:03
@wikingnow i'm at 12%05:03
@wikingseems to be working05:03
@wikingbut as i said before... you'll need much more ram if u want to compile python modular as well05:03
@wikingi reckon the xlarge instance might do it (6400 megs of ram)05:04
flaxterhow restrictive is the static interface? I'd like to reproduce what's in the Gaussian Processes python notebook...05:07
@wikingmmm05:10
@wikingi doubt that you'll be able to do that05:11
flaxterok, well let's see if small does it, and if not I'll try it on xlarge =)05:12
flaxterok, new error on my home computer....maybe I didn't install libnlopt correctly?05:13
@wikingmmm why what's the error?05:14
flaxterhttp://pastebin.com/WL2jWy0J05:14
@wikinguuu yeah05:14
@wikinghave u installed nlopt from source?05:14
flaxteryes05:16
flaxteris there an ubuntu package?05:16
@wikingflaxter: yeah... depends of course which ubuntu u r using05:20
@wikingfor 12.04 there's no package05:21
flaxterhome computer is 14.0405:21
@wikingbtw: i've just compiled shogun on small05:21
@wikingapt-get install libnlopt-dev05:21
flaxteroh, sweet05:23
flaxtercan you save a snapshot and share it?05:25
@wikingmmmm just a sec the unit test part is still compiling05:27
@wikingin 2 mins i think it's fully ready05:27
flaxtergreat05:28
@wikingflaxter: https://www.terminal.com/tiny/peImyFXuxK05:34
flaxterawesome. thank you!05:35
flaxteroh no, gaussian process binary classification failed ;)05:36
flaxtershogun/data is empty05:36
@wikingflaxter: that's just because i haven't checked out the data submodule05:37
@wikingyeah05:37
@wikinggit submodule init && git submodule update05:37
flaxteryou didn't do make install either, right?05:37
@wikingnoup05:38
flaxterok, just did that05:38
@wikingand there's not python modular interface either05:38
flaxterah ok, so how much ram should I try it with?05:38
@wikingyoull need more than 4gigs free05:38
@wikingso as i said i'd try with xlarge05:39
flaxterok, trying it05:39
flaxterI need swig I guess?05:40
@wikingyeps05:40
flaxtershould I do -DENABLE_CCACHE=OFF?05:40
@wikingnoup since i haven't installed ccache05:40
flaxteralso installing python-dev05:41
@wikingand that is a problem only with ubuntu 12.0405:41
flaxterok05:41
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flaxter(still downloading and installing python-dev....)05:46
flaxterfor anyone who finds this by google search, I now need to install numpy05:49
flaxterwiking, 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
@wikingshould be good05:51
@wikingsame with scipy05:51
flaxterok05:52
flaxteralso need libblas-dev06:09
@wikingyeah well you'll need a lot of packages06:09
flaxterlibatlas-base-dev?06:09
@wikingif u want to have all the features of shogun06:09
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flaxterlibnlopt-dev06:10
flaxterwhat else? :)06:10
@wikingmmmm06:11
@wikingwhen u run cmake06:11
@wikingon the end it shows what libraries has been detected06:12
@wikingand which not06:12
flaxteropencl is the only required one not found06:13
@wikingmmm well that u won't have in a virtualenv like this anwyas06:13
@wiking*anyways06:13
flaxterdo you know which package I need?06:14
@wikingfor?06:14
flaxtersorry, didnt see you say I won't need it06:14
flaxterso I shouldn't take the *REQUIRED* packages part too seriously?06:15
@wikingmmm is it in required section... wonder why it ended up there:S06:15
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flaxteranyone know about "NameError: name 'GradientEvaluation' is not defined"?14:55
flaxterI 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 follo14:59
@wikingmmm15:13
@wikingflaxter: src/shogun/evaluation/GradientEvaluation.h doesn't need any special library15:14
flaxterI am also missing GaussianProcessBinaryClassification15:14
flaxterImportError: cannot import name GaussianProcessBinaryClassification15:15
flaxteroh wait, GradientEvaluation is there. it's GradientModelSelection that's missing15:15
@wikingflaxter: it GradientModelSelection needs nlopt15:17
@wikingand there's no more GaussianProcessBinaryClassification15:17
@wikingit's GaussianProcessClassification15:18
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
flaxterI installed nlopt...double-checking15:18
@wikingyeah15:19
flaxteryes, libnlopt-dev is installed from apt15:19
flaxter-- The following OPTIONAL packages have been found: includes NLopt15:20
@wikingmmm15:23
@wikingthen u should have GradientModelSelection15:23
flaxterrecompiling, just in case15:25
flaxterbbiab15:25
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flaxterback, 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
flaxterbuild complete16:28
flaxter>>> from modshogun import GradientModelSelection Traceback (most recent call last):   File "<stdin>", line 1, in <module> ImportError: cannot import name GradientModelSelection16:28
flaxterno luck...16:28
sonne|workflaxter: have a look at the GradientModelSelection.{h,cpp} files and look for the ifdefs there16:29
sonne|workI guess you still don't have some dep installed16:29
flaxteronly one that's there is HAVE_NLOPT...16:30
sonne|workflaxter:  and did NLOPT get detected?16:31
sonne|work(HAVE_NLOPT should be in lib/config.h)16:31
flaxterit got detected, yeah, see here: http://pastebin.com/Jtxx4Bk416:32
flaxterok, just looked there as well-- #define HAVE_NLOPT 116:33
flaxterwait! I might have done just make and not make install for this one16:34
sonne|worksounds like :)16:35
flaxterfixed! ok, cool16:35
sonne|workheh16:35
flaxterbtw, 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|workwhat is terminal.com?16:37
flaxterI 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 research16:41
flaxterlet 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|workflaxter: I am currently scarce in time but hey why  not won't hurt16:46
flaxtertry this link? http://www.terminal.com/signup?ref_u=flaxter&ref_c=9f83804ab0b784a16:46
sonne|workok registered - I am sonne - where is that terminal?16:48
flaxtersharing, hold on16:49
flaxterhttps://www.terminal.com/tiny/yAzDIQeZpq16:50
flaxterbbiab16:50
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flaxterback17:02
flaxterare there any dependencies for StringFeatures?17:19
flaxterNameError: name 'SimpleFeatures' is not defined17:19
flaxterNameError: name 'StringFeatures' is not defined17:19
flaxterdoxygen?17:19
flaxterno wait, that seems unlikely17:21
flaxtermaybe I should just be using StringCharFeatures instead.17:28
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flaxterok, I am using StringCharFeatures, perhaps incorrectly. the model fits but gp.apply crashes18:27
flaxterhere is a minimum working example...18:27
flaxterhttp://pastebin.com/iAE3771h18:27
flaxterjust tried the same kernel with an svm and everything is fine18:53
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flaxtertotally unrelated...I'm looking at the TensorProductPairKernel19:20
flaxteris 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
flaxterbut 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