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15 Commits (5a1e01e5f15302cd3aa33905645ce97954028be8)

Author SHA1 Message Date
Jennifer Liu 9d6ed9def3 Merge fastCover into DictBuilder (#1274) 
* Minor fix

* Run non-optimize FASTCOVER 5 times in benchmark

* Merge fastCover into dictBuilder

* Fix mixed declaration issue

* Add fastcover to symbol.c

* Add fastCover.c and cover.h to build

* Change fastCover.c to fastcover.c

* Update benchmark to run FASTCOVER in dictBuilder

* Undo spliting fastcover_param into cover_param and f

* Remove convert param functions

* Assign f to parameter

* Add zdict.h to Makefile in lib

* Add cover.h to BUCK

* Cast 1 to U64 before shifting

* Remove trimming of zero freq head and tail in selectSegment and rebenchmark

* Remove f as a separate parameter of tryParam

* Read 8 bytes when d is 6

* Add trimming off zero frequency head and tail

* Use best functions from COVER and remove trimming part(which leads to worse compression ratio after previous bugs were fixed)

* Add finalize= argument to FASTCOVER to specify percentage of training samples passed to ZDICT_finalizeDictionary

* Change nbDmer to always read 8 bytes even when d=6

* Add skip=# argument to allow skipping dmers in computeFrequency in FASTCOVER

* Update comments and benchmarking result

* Change default method of ZDICT_trainFromBuffer to ZDICT_optimizeTrainFromBuffer_fastCover

* Add dictType enum and fix bug about passing zParam when converting to coverParam

* Combine finalize and skip into a single parameter

* Update acceleration parameters and benchmark on 3 sample sets

* Change default splitPoint of FASTCOVER to 0.75 and benchmark first 3 sample sets

* Initialize variables outside of for loop in benchmark.c

* Update benchmark result for hg-manifest

* Remove cover.h from install-includes

* Add explanation of f

* Set default compression level for trainFromBuffer to 3

* Add assertion of fastCoverParams in DiB_trainFromFiles

* Add checkTotalCompressedSize function + some minor fixes

* Add test for multithreading fastCovr

* Initialize segmentFreqs in every FASTCOVER_selectSegment and move mutex_unnlock to end of COVER_best_finish

* Free segmentFreqs

* Initialize segmentFreqs before calling FASTCOVER_buildDictionary instead of in FASTCOVER_selectSegment

* Add FASTCOVER_MEMMULT

* Minor fix

* Update benchmarking result
 2018-08-23 12:06:20 -07:00
Jennifer Liu 0acb0abd1e Add non-optimize FASTCOVER (#1260) 
* Add non-optimize FASTCOVER

* Minor fix

* Pass param as value instead of pointer
 2018-08-01 11:06:16 -07:00
Jennifer Liu 4e29bc2469 Use CDict instead of CCtx in analyzeEntropy 2018-07-31 10:36:45 -07:00
Jennifer Liu 31229e527b Increment frequency for every dmer occurence within same sample instead of at most once per sample 2018-07-30 12:54:22 -07:00
Jennifer Liu 51b109c1b5 Delete old benchmarking result 2018-07-27 17:31:33 -07:00
Jennifer Liu 96d84ee235 Revert test.sh 2018-07-27 16:54:05 -07:00
Jennifer Liu 61262f6c0d Save segmentFreqs in ctx instead of malloc and memset in SelectSegment 2018-07-27 16:51:38 -07:00
Jennifer Liu 49b398e93f Use same param after optimizing cover and fastCover and record k and d for benchmarking 2018-07-27 13:39:19 -07:00
Jennifer Liu 759c543312 Rerun cover and fastCover with optimized values 2018-07-26 19:03:01 -07:00
Jennifer Liu 3d7941ce41 Benchmark different f values 2018-07-26 16:24:13 -07:00
Jennifer Liu 3b163e0b5b Add array to keep track of frequency within active segment, fix malloc bug, update benchmarking result 2018-07-26 13:53:13 -07:00
Jennifer Liu 1e85f314d8 Benchmark fast cover optimize vs k=200 2018-07-25 17:53:38 -07:00
Jennifer Liu d1fc507ef9 Initial benchmarking result for fastCover 2018-07-25 17:05:54 -07:00
Jennifer Liu b6c5d4982c Minor fix 2018-07-20 17:41:22 -07:00
Jennifer Liu 71e767ac09 Refactoring and benchmark without dictionary 2018-07-20 17:03:47 -07:00