mlpack IRC logs, 2018-02-07

Logs for the day 2018-02-07 (starts at 0:00 UTC) are shown below.

February 2018
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--- Log opened Wed Feb 07 00:00:01 2018
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16:23 < travis-ci> mlpack/mlpack#3877 (master - 8403b92 : Ryan Curtin): The build has errored.
16:23 < travis-ci> Change view : https://github.com/mlpack/mlpack/compare/4f664d208d32...8403b92d17fb
16:23 < travis-ci> Build details : https://travis-ci.org/mlpack/mlpack/builds/338556219
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17:17 < rcurtin> ok, I will try rebooting masterblaster now...
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17:29 < zoq> looks like everything works
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17:31 < travis-ci> ShikharJ/mlpack#60 (Test - dae4106 : Shikhar Jaiswal): The build has errored.
17:31 < travis-ci> Change view : https://github.com/ShikharJ/mlpack/compare/64d7a8961da3...dae4106803f8
17:31 < travis-ci> Build details : https://travis-ci.org/ShikharJ/mlpack/builds/338587686
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17:58 < rcurtin> yep, good to see :)
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18:32 < travis-ci> ShikharJ/mlpack#61 (Test - a6e4443 : Shikhar Jaiswal): The build has errored.
18:32 < travis-ci> Change view : https://github.com/ShikharJ/mlpack/compare/dae4106803f8...a6e44437ac61
18:32 < travis-ci> Build details : https://travis-ci.org/ShikharJ/mlpack/builds/338609762
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18:52 < ShikharJ> rcurtin: I am still getting the build errors, inspite of removing CmakeCache.txt file and also the build/ directory. I'm practically unable to test my code locally, and am pushing blindly to Travis. What else can be done?
18:52 < ShikharJ> The same log: Building CXX object src/mlpack/methods/sparse_coding/CMakeFiles/mlpack_sparse_coding.dir/sparse_coding_main.cpp.o [ 45%] Linking CXX executable ../../../../bin/mlpack_sparse_coding [ 45%] Built target mlpack_sparse_coding [ 45%] Generating CXX prefix source src/mlpack/tests/cotire/mlpack_test_CXX_prefix.cxx [ 45%] Generating CXX prefix header src/mlpack/tests/cotire/mlpack_test_CXX_prefix.hxx make[2]: *** No rule to ma
18:52 < rcurtin> the message was cut off, is it still about cli_deleter.hpp?
18:52 < ShikharJ> make[2]: *** No rule to make target 'src/mlpack/core/util/cli_deleter.hpp', needed by 'src/mlpack/tests/cotire/mlpack_test_CXX_prefix.hxx.gch'. Stop. CMakeFiles/Makefile2:4371: recipe for target 'src/mlpack/tests/CMakeFiles/mlpack_test.dir/all' failed make[1]: *** [src/mlpack/tests/CMakeFiles/mlpack_test.dir/all] Error 2 Makefile:140: recipe for target 'all' failed make: *** [all] Error 2
18:52 < ShikharJ> Yes
18:54 < rcurtin> so you have entirely new build directory and you are still getting this problem?
18:55 < ShikharJ> Yep. I tried first by just removing the CmakeCache.txt file, didn't work, then removed the build directory as well.
18:55 < rcurtin> are you working in a branch? is the branch synced to upstream master?
18:56 < rcurtin> and does the phrase 'cli_deleter' show up anywhere in the repository src/ directory?
18:56 < rcurtin> i.e. 'grep -r cli_deleter src/'
18:56 < ShikharJ> It is rebased to the latest master, yes.
18:57 < daivik_> I was facing the same problem as ShikharJ, but deleting and recreating the build directory, reconfiguring and running make solved the issue
18:58 < ShikharJ> It gives a vast log. Something like this: grep -r cli_deleter src/ src/mlpack/bindings/python/tests/CMakeFiles/generate_pyx_test_python_binding.dir/depend.make:src/mlpack/bindings/python/tests/CMakeFiles/generate_pyx_test_python_binding.dir/__/generate_pyx_test_python_binding.cpp.o: src/mlpack/core/util/cli_deleter.hpp src/mlpack/bindings/python/tests/CMakeFiles/generate_pyx_test_python_binding.dir/depend.make:src/mlpack/bindings/p
19:00 < rcurtin> no, run the grep in the source directory, not the build/src/ directory
19:08 < ShikharJ> I ran it in the main folder, but now it doesn't show anything.
19:10 < rcurtin> ok, are you sure that you deleted your build folder and reconfigured?
19:10 < rcurtin> because this looks to me like there are still old configuration artifacts in your build folder
19:11 < ShikharJ> I deleted the build folder for sure, I'll try again and update it here.
19:14 < rcurtin> ok, I think that should fix it if you remove the build folder entirely and start over
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19:22 < travis-ci> mlpack/mlpack#3880 (master - 01eae23 : Ryan Curtin): The build has errored.
19:22 < travis-ci> Change view : https://github.com/mlpack/mlpack/compare/8403b92d17fb...01eae230e621
19:22 < travis-ci> Build details : https://travis-ci.org/mlpack/mlpack/builds/338623551
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19:27 < daivik_> rcurtin: I am trying some of the HMM command line tools. I was able to train an HMM (using hmm_train) and store the model in an output model file (xml). However, when I input the same model file to hmm_loglik, it gives the following error "DiscreteDistribution::Probability(): received observation 0; observation must be in [0, 0] for this distributi
19:27 < daivik_> on." I have double checked that the sequence I'm trying to compute the loglikelihood for has only those labels that are present in the training file. Any clue on what I'm doing wrong?
19:30 < rcurtin> hmm, maybe you have found a bug, but before we are sure, can you tell me what the sequence you are passing to hmm_loglik is?
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19:30 < rcurtin> and the data you are passing to hmm_train also?
19:32 < daivik_> https://thepasteb.in/p/lOhOKAvXW66FB --> training data to hmm_train
19:32 < daivik_> 0
19:32 < daivik_> 2
19:32 < daivik_> 1
19:32 < daivik_> to hmm_loglik
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19:32 < travis-ci> ShikharJ/mlpack#61 (Test - a6e4443 : Shikhar Jaiswal): The build has errored.
19:32 < travis-ci> Change view : https://github.com/ShikharJ/mlpack/compare/dae4106803f8...a6e44437ac61
19:32 < travis-ci> Build details : https://travis-ci.org/ShikharJ/mlpack/builds/338609762
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19:34 < rcurtin> if you saved the HMM as an XML, can you paste that too?
19:34 < rcurtin> the data is looking correct to me
19:35 < daivik_> https://thepasteb.in/p/O7h5X0ywPPZiq --> model file in xml format
19:36 < rcurtin> perfect, thank you
19:36 < rcurtin> so what I am looking for here is the emission probabilities for each hidden state
19:36 < rcurtin> "<probabilities ...>"
19:36 < rcurtin> each of those should be a single-dimension distribution with 12 elements in them
19:36 < rcurtin> 12 or 13, not sure of the exact number, but anyway something like that
19:36 < daivik_> 12
19:37 < rcurtin> right
19:37 < daivik_> I can confirm that the model file is correct -- and is being written (by hmm_train) and read (by hmm_loglik) correctly
19:38 < rcurtin> yeah, it seems correct, so the question is why DiscreteDistribution::Probability() is having problems
19:38 < rcurtin> are you willing to pull out the debugger and trace what is going on? I can help point you in the right direction
19:38 < daivik_> yeah sure
19:39 < daivik_> you'll have to tell me the steps though (sorry for being a noob)
19:39 < rcurtin> it's no problem; honestly printf-style debugging can get us most of what we need here
19:39 < rcurtin> the file I'm interested in is discrete_distribution.cpp in src/mlpack/core/dists/
19:39 < rcurtin> our failure is on line 85
19:40 < rcurtin> I would say, inside of that if statement, add the following output:
19:40 < rcurtin> std::cout << "number of dimensions in DiscreteDistribution: " << probabilities.size();
19:41 < rcurtin> std::cout << "; input observation:\n" << observation;
19:41 < rcurtin> ack, that should be "<< observations;"
19:41 < rcurtin> std::cout << "probabilities for dimension " << i << ": " << probabilities[i].t();
19:41 < rcurtin> std::cout << "obs: " << obs << "\n";
19:41 < rcurtin> and I think that should give some interesting output that will help figure out what is going on
19:42 < daivik_> okay .. let me try that and I'll get back to you here in a few minutes
19:44 < rcurtin> sure, I hope there are no errors in what I wrote :)
19:44 < rcurtin> but ideally that should give us some output on what is actually going on inside the DiscreteDistribution
19:49 < daivik_> no output, a similar error is printed by line 144 -- should i add the cout statements there as well
19:53 < daivik_> I think the correct place to put the cout is in discrete_distribution.hpp line 146 .. rather than where we did
19:53 < daivik_> because that is the function mentioned in the error message
19:56 < rcurtin> ah yeah, sorry
19:56 < rcurtin> my mistake
19:57 < rcurtin> yeah, I was thinking line 144 but for some reason gave the wrong line number
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19:58 < travis-ci> mlpack/mlpack#3882 (master - eae2453 : Ryan Curtin): The build has errored.
19:58 < travis-ci> Change view : https://github.com/mlpack/mlpack/compare/01eae230e621...eae2453913b2
19:58 < travis-ci> Build details : https://travis-ci.org/mlpack/mlpack/builds/338652963
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20:27 < daivik_> number of dimensions in DiscreteDistribution: 1; input observation:
20:27 < daivik_> 0
20:27 < daivik_> probabilities for dimension 0: [matrix size: 1x0]
20:27 < daivik_> obs: 0
20:29 < rcurtin> well that is not expected
20:29 < rcurtin> let me see if I can reproduce this
20:29 < rcurtin> or would you like to continue debugging?
20:29 < daivik_> These are the lines I added to discrete_distribution.hpp (rather than discrete_distribution.cpp)
20:29 < daivik_> std::cout << "number of dimensions in DiscreteDistribution: " << probabilities.size();
20:29 < daivik_> std::cout << "; input observation:\n" << observation;
20:29 < daivik_> std::cout << "probabilities for dimension " << dimension << ": " << probabilities[dimension].t();
20:29 < daivik_> std::cout << "obs: " << obs << "\n";
20:30 < rcurtin> basically we now know that there is some DiscreteDistribution that has 0 dimensions
20:30 < daivik_> I think I'd like to work on this a bit more
20:30 < rcurtin> but now the next question is, why is there a DiscreteDistribution with 0 dimensions?
20:30 < rcurtin> sure, I can keep providing pointers if you like :)
20:30 < daivik_> yeah, i had sort of arrived at the same conclusion too
20:30 < daivik_> i'll ask here if I get stuck if thats okay?
20:31 < rcurtin> sure, of course
20:31 < daivik_> thanks a lot for your help
20:31 < rcurtin> I think maybe the next place to look would be to print the HMM emission probabilities in HMM::Serialize()
20:32 < rcurtin> after the HMM is loaded
20:32 < daivik_> okay, I'll have a look at that
20:32 < rcurtin> sorry, HMM::serialize(), hmm_impl.hpp:590
20:32 < rcurtin> after line 603, the emissions should be loaded, and you could print the emission distribution probabilities there
20:36 < daivik_> I was hoping to write tests for the hmm command line bindings -- but I think I'll try and solve this first :)
20:39 < rcurtin> yeah, I think for many binding tests, some bugs in the underlying code get discovered :)
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21:50 < rcurtin> ok, I'll be shutting down all the mlpack build servers in Oregon at 1800 UTC on Friday (masterblaster, gekko, scrooloos, savannah, slake, skyfish, aunty, collector, ironbar) and they should be received in Tucson Arizona on Monday and re-racked shortly thereafter
21:59 < zoq> fingers crossed
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23:05 < travis-ci> ShikharJ/mlpack#63 (RBM - f47f3e7 : Shikhar Jaiswal): The build has errored.
23:05 < travis-ci> Change view : https://github.com/ShikharJ/mlpack/compare/754f3cc293fd...f47f3e771f95
23:05 < travis-ci> Build details : https://travis-ci.org/ShikharJ/mlpack/builds/338743493
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23:20 < travis-ci> ShikharJ/mlpack#62 (master - eae2453 : Ryan Curtin): The build has errored.
23:20 < travis-ci> Change view : https://github.com/ShikharJ/mlpack/compare/8aea1a87050f...eae2453913b2
23:20 < travis-ci> Build details : https://travis-ci.org/ShikharJ/mlpack/builds/338740469
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23:45 < travis-ci> ShikharJ/mlpack#64 (RBM - 92a29c3 : Shikhar Jaiswal): The build has errored.
23:45 < travis-ci> Change view : https://github.com/ShikharJ/mlpack/compare/f47f3e771f95...92a29c33d9ca
23:45 < travis-ci> Build details : https://travis-ci.org/ShikharJ/mlpack/builds/338745780
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--- Log closed Thu Feb 08 00:00:03 2018