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asterix-gerrit.ics.uci.edu / hyracks / b4a494e422a9bb7699794d44fa69e477f39bb64b / genomix / genomix-data / src
  1. 3274eac try to have 2 local stes of CCs and NCs (-runLocal not working) by Jake Biesinger · 12 years ago
  2. d688f36 don't use a max number of readids on edges by Jake Biesinger · 12 years ago
  3. da9eeaf hadoop uses |IO_DIRS| * #slaves reducers by Jake Biesinger · 12 years ago
  4. a9f475d use $IO_DIRS, not -coresPerMachine for hyracks partitions + hadoop #reducers by Jake Biesinger · 12 years ago
  5. 6dfc4bb Hadoop graphbuild works! by Jake Biesinger · 12 years ago
  6. b0aed82 hadoop dist cache must be an absolute path by Jake Biesinger · 12 years ago
  7. 7294ef7 hadoop jar deployment fix by Jake Biesinger · 12 years ago
  8. d21026a shut down previous clusters again by Jake Biesinger · 12 years ago
  9. f173509 tweak cluster shutdown by Jake Biesinger · 12 years ago
  10. a56a98a read FRAME_SIZE and FRAME_LIMIT from cluster.properties by Jake Biesinger · 12 years ago
  11. bb0540c fix shutdown bug when -runLocal=false by Jake Biesinger · 12 years ago
  12. 2d358c6 runLocal is working but doesn't shut down properly by Jake Biesinger · 12 years ago
  13. db95a42 only shut down pregelix cluster if it's running by Jake Biesinger · 12 years ago
  14. 0734cd2 STATS is a separate option and DUMP_FASTA can happen after any step by Jake Biesinger · 12 years ago
  15. 16a94ca WIP: partial support for local/nonlocal for hadoop, hyracks and pregelix by Jake Biesinger · 12 years ago
  16. b8ec304 fix framesize: 256MB buffer, 64k page by Jake Biesinger · 12 years ago
  17. ed5a065 less aggressive and adjustable cluster wait times by Jake Biesinger · 12 years ago
  18. f389e7e tweak framesize by Jake Biesinger · 12 years ago
  19. eecb337 increase wait time and add a shutdown hook that stops the clusters by Jake Biesinger · 12 years ago
  20. 2d72d3e add -followsGraphBuild for those inputs proceeding build by Jake Biesinger · 12 years ago
  21. 56af037 remove framesize from command-line parameters by Jake Biesinger · 12 years ago
  22. b6ca725 add the option of frame size by Nan Zhang · 12 years ago
  23. 15b6f47 add MAX_READ_IDS_PER_EDGE in opts parser and jobs by Jake Biesinger · 12 years ago
  24. d169c54 auto-discover CC port and IP settings (broke runLocal) by Jake Biesinger · 12 years ago
  25. 6a6ff67 modify the option of NlinesPerMap to false by Nan Zhang · 12 years ago
  26. 558ea60 Merge aggregator with main branch by Anbang Xu · 12 years ago
  27. 50b28b6 Adpat hadoop testsuite to have linespermap arg by Anbang Xu · 12 years ago
  28. 4da15b2 add many similar bubbles in one pattern test case and BubbleMerge pass test by Anbang Xu · 12 years ago
  29. a9c60b3 The aggregator for all the patterns are completed by Anbang Xu · 12 years ago
  30. 1aed014 add statistics counters to removeTip, pathMerge, removeBridge by Anbang Xu · 12 years ago
  31. 4e63417 fix location of stores.properties by Jake Biesinger · 12 years ago
  32. dd63616 add stores.properties (deleted by?) by Jake Biesinger · 12 years ago
  33. 476760d Add timed logging to genomix-driver jobs by Jake Biesinger · 12 years ago
  34. affc0b4 toString's on edgeList and positionList are sorted by Jake Biesinger · 12 years ago
  35. 65ee367 add STATS and DUMP_FASTA steps to the graph (run locally) by Jake Biesinger · 12 years ago
  36. 5be5c46 fix coresPerMachine's default values by Jake Biesinger · 12 years ago
  37. 28cbeae save intermediate results by default (found a bug in pregelix-core?) by Jake Biesinger · 12 years ago
  38. 8b79c57 don't save intermediate results by default; add option to do so by Jake Biesinger · 12 years ago
  39. f9e6e5f add hadoop building to the driver by Jake Biesinger · 12 years ago
  40. 1e03787 Merge branch 'anbangx/backupMergingWithMaster_errorcase' into wbiesing/merge_fs_backup by Jake Biesinger · 12 years ago
  41. d75565c add option for corespermachine in jobconf by Nan Zhang · 12 years ago
  42. 96eab83 Merge branch 'anbangx/backupMergingWithMaster' into wbiesing/driver_backup_merge by Jake Biesinger · 12 years ago
  43. 26e7332 BubbleMerge test is almost finished except grid test case by Anbang Xu · 12 years ago
  44. 0d6afba remove minidfs cluster (so writing directly to lcoal disk now) by Jake Biesinger · 12 years ago
  45. 34c19fd refactoring local mode by Jake Biesinger · 12 years ago
  46. febbaf1 add EdgeListWritable.addUnion(edge) by Jake Biesinger · 12 years ago
  47. 85dfedf Add broadcaseKillselfAndNoticeToUpdateEdges and responseToDeadVertexAndUpdateEdges by Anbang Xu · 12 years ago
  48. 002533a genomix driver -ip and -runLocal are mutually exclusive by Jake Biesinger · 12 years ago
  49. 3e1eb90 change bubble merge "add" to use boolean `flip` by Jake Biesinger · 12 years ago
  50. 97d97cd add bubble's addReadIDs by Jake Biesinger · 12 years ago
  51. e763a06 add complicated test case for BubbleMerge by Anbang Xu · 12 years ago
  52. 51a0502 separate genomix driver in/out to local/hdfs by Jake Biesinger · 12 years ago
  53. 9071ad4 Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  54. 3aba0f0 SplitRepeat test is completed by Anbang Xu · 12 years ago
  55. 0ca485b Don't use l1 and l2 in VKmerBytesWritable by Anbang Xu · 12 years ago
  56. 41ffd05 Merge with main branch by Anbang Xu · 12 years ago
  57. 4a9e45c Add testcases for SplitRepeat by Anbang Xu · 12 years ago
  58. 6d42a69 add medification on jobconf by Nan Zhang · 12 years ago
  59. d688b5a Add skip tandem repeat to pathmerge. TODO: detect cycle in pathmerge by Anbang Xu · 12 years ago
  60. 87b679f Merge branch 'anbangx/fullstack_genomix' into wbiesing/driver by Jake Biesinger · 12 years ago
  61. c9fe0a9 driver adapts to build output (InitialGraphInputFormat) by Jake Biesinger · 12 years ago
  62. 9c01d09 Fix mergeReadID RF and RR by Jake Biesinger · 12 years ago
  63. 7a75b07 add updateEdges for pathmerge. Issue: mergeWithStartreads by Anbang Xu · 12 years ago
  64. 9ac0dda Modify mergeWithKmer to mergeWithNode by Anbang Xu · 12 years ago
  65. 2e92709 remove bogus reference to com.sun.tools.javac.util.List by Jake Biesinger · 12 years ago
  66. 6fc84f1 Add additional merge info to pathmerge by Anbang Xu · 12 years ago
  67. fea8393 add unrollTandem to driver by Jake Biesinger · 12 years ago
  68. 6eade1d use local test cluster by Jake Biesinger · 12 years ago
  69. 639c806 separate config from driver and pipeline setup by Jake Biesinger · 12 years ago
  70. 56e291f Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  71. ced394a Make pathmerge robost by Anbang Xu · 12 years ago
  72. b37b705 Add UnRollTandemRepeat. TODO: add the corresponding MSG and update edges by Anbang Xu · 12 years ago
  73. fc7d4b8 fix the positionWritable unionUpdate(), and add automatic test case by Nan Zhang · 12 years ago
  74. de3a280 Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  75. c970d65 Adapt BTSTraverseVertex to new graph structure by Anbang Xu · 12 years ago
  76. 000fa26 getReadIDs added to EdgeWritable by Jake Biesinger · 12 years ago
  77. 112cdf7 Adapt MapReduceVertex and P4 to new graph structure by Anbang Xu · 12 years ago
  78. 3786935 hyracks graph building test complete. by Nan Zhang · 12 years ago
  79. b02033e BasicPathMergeVertex is completed by Anbang Xu · 12 years ago
  80. 0d72095 Make generic message class for all patterns by Anbang Xu · 12 years ago
  81. 128eb0e Revert "update hyracks_genomix branch" by Nan Zhang · 12 years ago
  82. 9a664b7 update hyracks_genomix branch by Nan Zhang · 12 years ago
  83. 9296bb6 Add EdgeList.getKeys for iterating over keys by Jake Biesinger · 12 years ago
  84. 6266614 Simplify edgewritable interface by Jake Biesinger · 12 years ago
  85. 2d17c5b Complete the Graph construction(Hadoop) by Anbang Xu · 12 years ago
  86. 60782f4 Add test cases; reinstate compareTo function use Hadoop's version by Jake Biesinger · 12 years ago
  87. 35875ce removed cursed autogen stub that was breaking hadoop by Jake Biesinger · 12 years ago
  88. e73873e merge with new argmented graph by Anbang Xu · 12 years ago
  89. dfd2e0f added shallower interface for readIDs by Jake Biesinger · 12 years ago
  90. ab3d8f4 add interface for edgewritable.appendReadID by Jake Biesinger · 12 years ago
  91. 034979c Partial refactor following edge type changes in NodeWritable by Jake Biesinger · 12 years ago
  92. 82aca33 Refactor merging into NodeWritable and add tests by Jake Biesinger · 12 years ago
  93. 2b9ba78 Starting on NodeWritable merge by Jake Biesinger · 12 years ago
  94. 473c225 Consolidate edges and threads into a single element by Jake Biesinger · 12 years ago
  95. 76f4101 add license header to NodeWritable (can't we just have it in ONE place?) by Jake Biesinger · 12 years ago
  96. 14df82f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  97. 13348bf Graph construcion is completed by Anbang Xu · 12 years ago
  98. bb8e581 Complete NaiveBFSTraverse and make more test cases by Anbang Xu · 12 years ago
  99. d282e07 argumented graph building pass test successfully by Nan Zhang · 12 years ago
  100. f010494 adapt new NodeWritable and extends it in VertexValue by Anbang Xu · 12 years ago