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237 Commits

Author SHA1 Message Date
Pedro Martinez Mediano e11218631e Added myself as author of KSG mixed calculator. 2017-08-29 23:56:28 +01:00
Pedro Martinez Mediano 49afa343fc Removed old variables and functions from KSG mixed, added docs. 2017-08-29 23:55:10 +01:00
Pedro Martinez Mediano bfe8156584 Add KDTrees to computeLocalUsingObservations in KSG mixed calc. 2017-08-16 19:28:24 +01:00
Pedro Martinez Mediano 641d17ec24 Fix bug with normalisation in KSG mixed and change unittest accordingly. 2017-08-16 19:18:51 +01:00
Pedro Martinez Mediano 7635cf8689 Added computeLocalOfPreviousObservations to KSG mixed. 
It follows the same pattern as the continuous MI: there is a
computeFromObservations method that returns either locals or average
based on a flag.
 2017-08-16 14:52:54 +01:00
Pedro Martinez Mediano 2d42e6ebad Removed unused function from KSG mixed. 2017-08-16 14:39:53 +01:00
Pedro Martinez Mediano 23bb573bb1 Replace computeSignificance method in KSG mixed with new one based on clone(). 2017-08-16 14:33:47 +01:00
Pedro Martinez Mediano 8251bdc1cb Removed unused variables from KSG mixed. 2017-08-16 13:35:03 +01:00
Pedro Martinez Mediano f55a7bd961 Add KdTrees to main compute() method in KSG mixed. 2017-08-16 13:31:18 +01:00
Pedro Martinez Mediano bad50ce663 KSG mixed now ignores batches of data shorter than timeDiff. 2017-08-16 13:27:05 +01:00
Pedro Martinez Mediano b5d2b7e367 KSG mixed now throws error if discrete data is out of range. 2017-08-16 13:25:44 +01:00
Pedro Martinez Mediano 437e606233 getNumObservations in KSG mixed now returns totalObservations. 
Before it returned continuousData.length, which more more prone
to null pointer errors, and therefore riskier.
 2017-08-16 00:07:51 +01:00
Pedro Martinez Mediano 39ad14d855 Added function to set timeDiff property. 2017-08-15 21:41:52 +01:00
Pedro Martinez Mediano abeb15cd6e Added standard start/finaliseAddObservations to mixed KSG calc. 2017-08-15 21:25:03 +01:00
Pedro Martinez Mediano 26137d12b1 Added precomputed digammas in KSG mixed calculator, fixed bug in locals. 2017-08-15 20:46:07 +01:00
Pedro Martinez Mediano 6af0e22030 Merge branch 'master' into gpu 2017-05-25 02:44:59 +10:00
Pedro Martinez Mediano a642c0a8c8 Fix prints in digamma timers. 2017-05-25 02:29:07 +10:00
Pedro Martinez Mediano 79859e0832 Add warm-up period to benchmarking script. 2017-05-25 02:15:21 +10:00
Pedro Martinez Mediano c8ceec9f71 Added more timers and unified format a bit. 2017-05-25 01:41:53 +10:00
Pedro Martinez Mediano cce345b0ed Removed comments and prints from perftest.cpp 2017-05-25 01:09:34 +10:00
Pedro Martinez Mediano 3fb9632439 Improved ctimer to align printf outputs. 2017-05-25 01:06:04 +10:00
Pedro Martinez Mediano 82c06abbeb Added C unit tests for GPU digamma reduction. 2017-05-25 00:20:52 +10:00
Pedro Martinez Mediano 715050d4e6 Added GPU chunk digamma reduction to main workflow. 2017-05-25 00:20:06 +10:00
Pedro Martinez Mediano 2d8d0271ca Added first version of GPU chunk digamma reduction function. 
For now the calculation of the digammas is fully parallel but sums are
done in CPU.
 2017-05-25 00:19:07 +10:00
Pedro Martinez Mediano afcfb61260 Added C unit test for GPU digamma calculation without reduction. 2017-05-24 23:28:41 +10:00
Pedro Martinez Mediano 20c019267c Added full C function for parallel digamma calculation without reduction. 2017-05-24 23:27:41 +10:00
Pedro Martinez Mediano ada9128389 Added kernel for gpu digamma calculation without reduction. 2017-05-24 23:26:33 +10:00
Pedro Martinez Mediano 7fe8bf47cc Added GPU digamma reduction to main workflow for single-chunk cases. 2017-05-24 22:19:36 +10:00
Pedro Martinez Mediano e39afcd5b4 Fixed bug related to manual casting in digamma reduction kernel. 2017-05-24 22:19:07 +10:00
Pedro Martinez Mediano 3a68e27af8 Fixed bugs in single-chunk digamma reduction GPU code. 2017-05-24 22:18:04 +10:00
Pedro Martinez Mediano 3dd4f6b224 Added C unit tests for single-chunk GPU digamma reduction. 2017-05-24 22:16:18 +10:00
Pedro Martinez Mediano 09548028e0 Merge remote-tracking branch 'ghub/master'. This merges Joe's v1.3.1 master into Pedro's master. 2017-05-24 20:24:32 +10:00
Pedro Martinez Mediano 3054461f7a Add note for potential further optimisation. 2017-05-24 19:45:01 +10:00
Pedro Martinez Mediano d17d8cad03 Add small utility script to profile parts of GPU code. 2017-05-24 19:20:54 +10:00
Pedro Martinez Mediano 8da0bfc17b Fixed bugs in pointset arrangement. Inefficient but functional. 2017-05-24 18:52:37 +10:00
Pedro Martinez Mediano 39a5cadf06 RS functions now receive pointers to source/dest within pointset. 
This helps with surrogate calculation and is convenient for later memory
optimisation.
 2017-05-24 18:04:11 +10:00
Pedro Martinez Mediano 4cb9a9bb16 Fixed bug with surrogate digamma calculation. 2017-05-24 18:02:38 +10:00
Pedro Martinez Mediano 3c0ae81505 Added timers to kraskovCuda.c. 2017-05-24 17:28:20 +10:00
Pedro Martinez Mediano 1b1f4f9922 Added timers to gpuMILibrary. 2017-05-24 17:23:50 +10:00
Pedro Martinez Mediano bb241ae415 Added timers to gpuKnnLibrary. 2017-05-24 17:13:26 +10:00
Pedro Martinez Mediano ff868bf79f Added gpuWarmUp function to shorten latency in first GPU call. 2017-05-24 17:02:52 +10:00
Pedro Martinez Mediano cced321abb Renamed unit test source file. 2017-05-24 17:01:16 +10:00
Pedro Martinez Mediano 169c35e990 Makefile revamped. See comments: 
- Added CUSTOMFLAGS to define flags from Make CLI.
- Separated and re-arranged C object targets.
- Added targets for test binaries.
 2017-05-24 16:57:42 +10:00
Pedro Martinez Mediano 7d9d7ad135 Added MI calculation script for benchmarking purposes. 2017-05-24 15:48:19 +10:00
Pedro Martinez Mediano 3a64f2b926 Added lightweight inline timer for C functions. 2017-05-24 15:46:55 +10:00
Pedro Martinez Mediano 492cfe8b53 Added Java+JNI support for surrogate reorderings. 2017-05-23 16:19:33 +10:00
Pedro Martinez Mediano 4a31d3d7f1 Added C unit tests for surrogate reorderings. 2017-05-23 16:19:09 +10:00
Pedro Martinez Mediano 0b66c3a3f8 Added C support for arbitrary reordering of surrogates. 2017-05-23 16:18:16 +10:00
Pedro Martinez Mediano f2d6674a4f Added a few debug mode prints. 2017-05-23 05:13:57 +10:00
Pedro Martinez Mediano a7cef7f87f Added a few tests to check surrogate and pointset handling (more needed). 2017-05-23 02:11:02 +10:00