seperate MessageFlag and State
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
index f3383f4..25eac62 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
@@ -21,14 +21,11 @@
@SuppressWarnings("deprecation")
public class GraphBuildingTestSuite extends TestSuite{
- private static int SIZE_KMER = 3;
+ private static int SIZE_KMER = 5;
private static int LINES_PERMAP = 4 * 100000;
- public static final String PreFix = "data/webmap/PathMerge_TestSet";
+ public static final String PreFix = "data/webmap/RandomWalk_TestSet";
public static final String[] TestDir = { PreFix + File.separator
- + "P2_3", PreFix + File.separator
- + "P2_5", PreFix + File.separator
- + "P2_7", PreFix + File.separator
- + "P2_8"
+ + "SmallGenome"
};
// + "SimpleRectangle", PreFix + File.separator
// + "MediumRectangle", PreFix + File.separator
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/01-BUILD_HADOOP/_logs/history/compute-2-10_1378345383525_job_201309041843_0020_anbangx_Genomix+Graph+Building b/genomix/genomix-pregelix/data/TestSet/PathMerge/01-BUILD_HADOOP/_logs/history/compute-2-10_1378345383525_job_201309041843_0020_anbangx_Genomix+Graph+Building
new file mode 100644
index 0000000..e98f313
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/01-BUILD_HADOOP/_logs/history/compute-2-10_1378345383525_job_201309041843_0020_anbangx_Genomix+Graph+Building
@@ -0,0 +1,82 @@
+Meta VERSION="1" .
+Job JOBID="job_201309041843_0020" JOBNAME="Genomix Graph Building" USER="anbangx" SUBMIT_TIME="1378441653191" JOBCONF="hdfs://compute-2-10:54310/scratch/hadoop-wbiesing/hadoop-tmp-dir/mapred/system/job_201309041843_0020/job\.xml" .
+Job JOBID="job_201309041843_0020" JOB_PRIORITY="NORMAL" .
+Job JOBID="job_201309041843_0020" LAUNCH_TIME="1378441653275" TOTAL_MAPS="1" TOTAL_REDUCES="16" JOB_STATUS="PREP" .
+Task TASKID="task_201309041843_0020_m_000002" TASK_TYPE="SETUP" START_TIME="1378441653304" SPLITS="" .
+MapAttempt TASK_TYPE="SETUP" TASKID="task_201309041843_0020_m_000002" TASK_ATTEMPT_ID="attempt_201309041843_0020_m_000002_0" START_TIME="1378441653414" TRACKER_NAME="tracker_compute-5-3\.local:localhost\.localdomain/127\.0\.0\.1:48745" HTTP_PORT="50060" .
+MapAttempt TASK_TYPE="SETUP" TASKID="task_201309041843_0020_m_000002" TASK_ATTEMPT_ID="attempt_201309041843_0020_m_000002_0" TASK_STATUS="SUCCESS" FINISH_TIME="1378441656651" HOSTNAME="/default-rack/compute-5-3\.local" STATE_STRING="setup" COUNTERS="{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(SPILLED_RECORDS)(Spilled Records)(0)]}" .
+Task TASKID="task_201309041843_0020_m_000002" TASK_TYPE="SETUP" TASK_STATUS="SUCCESS" FINISH_TIME="1378441659310" COUNTERS="{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(SPILLED_RECORDS)(Spilled Records)(0)]}" .
+Job JOBID="job_201309041843_0020" JOB_STATUS="RUNNING" .
+Task TASKID="task_201309041843_0020_m_000000" TASK_TYPE="MAP" START_TIME="1378441659311" SPLITS="" .
+MapAttempt TASK_TYPE="MAP" TASKID="task_201309041843_0020_m_000000" TASK_ATTEMPT_ID="attempt_201309041843_0020_m_000000_0" START_TIME="1378441659326" TRACKER_NAME="tracker_compute-5-3\.local:localhost\.localdomain/127\.0\.0\.1:48745" HTTP_PORT="50060" .
+MapAttempt TASK_TYPE="MAP" TASKID="task_201309041843_0020_m_000000" TASK_ATTEMPT_ID="attempt_201309041843_0020_m_000000_0" TASK_STATUS="SUCCESS" FINISH_TIME="1378441661759" HOSTNAME="/default-rack/compute-5-3\.local" STATE_STRING="hdfs://compute-2-10:54310/user/anbangx/genomix_out/00-initial-input-from-genomix-driver/small\.test\.reads:0+1392" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(HDFS_BYTES_READ)(HDFS_BYTES_READ)(1392)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(43288)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(MAP_INPUT_RECORDS)(Map input records)(100)][(SPILLED_RECORDS)(Spilled Records)(600)][(MAP_OUTPUT_BYTES)(Map output bytes)(41600)][(MAP_INPUT_BYTES)(Map input bytes)(1392)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(MAP_OUTPUT_RECORDS)(Map output records)(600)]}" .
+Task TASKID="task_201309041843_0020_m_000000" TASK_TYPE="MAP" TASK_STATUS="SUCCESS" FINISH_TIME="1378441662316" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(HDFS_BYTES_READ)(HDFS_BYTES_READ)(1392)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(43288)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(MAP_INPUT_RECORDS)(Map input records)(100)][(SPILLED_RECORDS)(Spilled Records)(600)][(MAP_OUTPUT_BYTES)(Map output bytes)(41600)][(MAP_INPUT_BYTES)(Map input bytes)(1392)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(MAP_OUTPUT_RECORDS)(Map output records)(600)]}" .
+Task TASKID="task_201309041843_0020_r_000000" TASK_TYPE="REDUCE" START_TIME="1378441662317" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000001" TASK_TYPE="REDUCE" START_TIME="1378441663460" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000002" TASK_TYPE="REDUCE" START_TIME="1378441663794" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000003" TASK_TYPE="REDUCE" START_TIME="1378441664704" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000004" TASK_TYPE="REDUCE" START_TIME="1378441664823" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000005" TASK_TYPE="REDUCE" START_TIME="1378441665319" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000006" TASK_TYPE="REDUCE" START_TIME="1378441666464" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000007" TASK_TYPE="REDUCE" START_TIME="1378441666801" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000008" TASK_TYPE="REDUCE" START_TIME="1378441667707" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000009" TASK_TYPE="REDUCE" START_TIME="1378441667824" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000010" TASK_TYPE="REDUCE" START_TIME="1378441668322" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000011" TASK_TYPE="REDUCE" START_TIME="1378441669467" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000012" TASK_TYPE="REDUCE" START_TIME="1378441669820" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000013" TASK_TYPE="REDUCE" START_TIME="1378441670710" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000014" TASK_TYPE="REDUCE" START_TIME="1378441670825" SPLITS="" .
+Task TASKID="task_201309041843_0020_r_000015" TASK_TYPE="REDUCE" START_TIME="1378441671327" SPLITS="" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000000" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000000_0" START_TIME="1378441662329" TRACKER_NAME="tracker_compute-5-3\.local:localhost\.localdomain/127\.0\.0\.1:48745" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000000" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000000_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441670111" SORT_FINISHED="1378441670166" FINISH_TIME="1378441671512" HOSTNAME="/default-rack/compute-5-3\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(3852)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(3852)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1350)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(7)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(7)][(SPILLED_RECORDS)(Spilled Records)(54)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(54)]}" .
+Task TASKID="task_201309041843_0020_r_000000" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441674332" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(3852)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(3852)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1350)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(7)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(7)][(SPILLED_RECORDS)(Spilled Records)(54)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(54)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000004" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000004_0" START_TIME="1378441664875" TRACKER_NAME="tracker_compute-2-10\.local:localhost\.localdomain/127\.0\.0\.1:60748" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000004" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000004_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441672876" SORT_FINISHED="1378441672910" FINISH_TIME="1378441674050" HOSTNAME="/default-rack/compute-2-10\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2546)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2546)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1014)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(6)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(6)][(SPILLED_RECORDS)(Spilled Records)(36)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(36)]}" .
+Task TASKID="task_201309041843_0020_r_000004" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441676828" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2546)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2546)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1014)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(6)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(6)][(SPILLED_RECORDS)(Spilled Records)(36)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(36)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000005" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000005_0" START_TIME="1378441665331" TRACKER_NAME="tracker_compute-5-3\.local:localhost\.localdomain/127\.0\.0\.1:48745" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000005" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000005_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441673303" SORT_FINISHED="1378441673357" FINISH_TIME="1378441674603" HOSTNAME="/default-rack/compute-5-3\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2050)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2050)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(862)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(5)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(2050)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(5)][(SPILLED_RECORDS)(Spilled Records)(29)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(29)]}" .
+Task TASKID="task_201309041843_0020_r_000005" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441677335" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2050)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2050)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(862)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(5)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(2050)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(5)][(SPILLED_RECORDS)(Spilled Records)(29)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(29)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000001" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000001_0" START_TIME="1378441663549" TRACKER_NAME="tracker_compute-7-15\.local:localhost\.localdomain/127\.0\.0\.1:37666" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000001" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000001_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441672451" SORT_FINISHED="1378441672503" FINISH_TIME="1378441675734" HOSTNAME="/default-rack/compute-7-15\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(4338)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(4338)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1528)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(8)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(8)][(SPILLED_RECORDS)(Spilled Records)(60)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(60)]}" .
+Task TASKID="task_201309041843_0020_r_000001" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441678476" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(4338)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(4338)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1528)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(8)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(8)][(SPILLED_RECORDS)(Spilled Records)(60)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(60)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000006" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000006_0" START_TIME="1378441666474" TRACKER_NAME="tracker_compute-7-15\.local:localhost\.localdomain/127\.0\.0\.1:37666" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000006" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000006_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441673996" SORT_FINISHED="1378441674048" FINISH_TIME="1378441676251" HOSTNAME="/default-rack/compute-7-15\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(3162)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(3162)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1160)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(6)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(6)][(SPILLED_RECORDS)(Spilled Records)(44)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(44)]}" .
+Task TASKID="task_201309041843_0020_r_000006" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441678477" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(3162)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(3162)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1160)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(6)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(6)][(SPILLED_RECORDS)(Spilled Records)(44)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(44)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000002" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000002_0" START_TIME="1378441663946" TRACKER_NAME="tracker_compute-5-2\.local:localhost\.localdomain/127\.0\.0\.1:42328" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000002" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000002_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441675139" SORT_FINISHED="1378441675212" FINISH_TIME="1378441676500" HOSTNAME="/default-rack/compute-5-2\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(1880)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(1880)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(652)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(3)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(1880)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(3)][(SPILLED_RECORDS)(Spilled Records)(26)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(26)]}" .
+Task TASKID="task_201309041843_0020_r_000002" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441678832" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(1880)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(1880)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(652)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(3)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(1880)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(3)][(SPILLED_RECORDS)(Spilled Records)(26)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(26)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000007" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000007_0" START_TIME="1378441666821" TRACKER_NAME="tracker_compute-5-2\.local:localhost\.localdomain/127\.0\.0\.1:42328" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000007" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000007_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441674649" SORT_FINISHED="1378441674740" FINISH_TIME="1378441676138" HOSTNAME="/default-rack/compute-5-2\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2366)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2366)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(852)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(4)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(2366)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(4)][(SPILLED_RECORDS)(Spilled Records)(33)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(33)]}" .
+Task TASKID="task_201309041843_0020_r_000007" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441678832" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2366)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2366)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(852)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(4)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(2366)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(4)][(SPILLED_RECORDS)(Spilled Records)(33)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(33)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000003" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000003_0" START_TIME="1378441664803" TRACKER_NAME="tracker_compute-5-1\.local:localhost\.localdomain/127\.0\.0\.1:55127" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000003" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000003_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441673716" SORT_FINISHED="1378441673765" FINISH_TIME="1378441676993" HOSTNAME="/default-rack/compute-5-1\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(1642)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(1642)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(708)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(4)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(4)][(SPILLED_RECORDS)(Spilled Records)(23)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(23)]}" .
+Task TASKID="task_201309041843_0020_r_000003" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441679721" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(1642)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(1642)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(708)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(4)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(4)][(SPILLED_RECORDS)(Spilled Records)(23)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(23)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000008" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000008_0" START_TIME="1378441667718" TRACKER_NAME="tracker_compute-5-1\.local:localhost\.localdomain/127\.0\.0\.1:55127" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000008" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000008_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441675407" SORT_FINISHED="1378441675457" FINISH_TIME="1378441677677" HOSTNAME="/default-rack/compute-5-1\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2394)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2394)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(886)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(5)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(2394)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(5)][(SPILLED_RECORDS)(Spilled Records)(34)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(34)]}" .
+Task TASKID="task_201309041843_0020_r_000008" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441679721" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2394)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2394)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(886)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(5)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(2394)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(5)][(SPILLED_RECORDS)(Spilled Records)(34)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(34)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000009" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000009_0" START_TIME="1378441667832" TRACKER_NAME="tracker_compute-2-10\.local:localhost\.localdomain/127\.0\.0\.1:60748" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000009" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000009_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441674837" SORT_FINISHED="1378441674868" FINISH_TIME="1378441677074" HOSTNAME="/default-rack/compute-2-10\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(1006)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(1006)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(506)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(3)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(3)][(SPILLED_RECORDS)(Spilled Records)(14)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(14)]}" .
+Task TASKID="task_201309041843_0020_r_000009" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441679830" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(1006)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(1006)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(506)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(3)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(3)][(SPILLED_RECORDS)(Spilled Records)(14)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(14)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000010" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000010_0" START_TIME="1378441668335" TRACKER_NAME="tracker_compute-5-3\.local:localhost\.localdomain/127\.0\.0\.1:48745" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000010" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000010_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441676298" SORT_FINISHED="1378441676354" FINISH_TIME="1378441677594" HOSTNAME="/default-rack/compute-5-3\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(1726)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(1726)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(666)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(3)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(1726)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(3)][(SPILLED_RECORDS)(Spilled Records)(24)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(24)]}" .
+Task TASKID="task_201309041843_0020_r_000010" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441680338" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(1726)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(1726)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(666)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(3)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(1726)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(3)][(SPILLED_RECORDS)(Spilled Records)(24)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(24)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000011" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000011_0" START_TIME="1378441669478" TRACKER_NAME="tracker_compute-7-15\.local:localhost\.localdomain/127\.0\.0\.1:37666" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000011" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000011_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441677040" SORT_FINISHED="1378441677090" FINISH_TIME="1378441679299" HOSTNAME="/default-rack/compute-7-15\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2176)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2176)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(878)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(5)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(5)][(SPILLED_RECORDS)(Spilled Records)(31)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(31)]}" .
+Task TASKID="task_201309041843_0020_r_000011" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441681479" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2176)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2176)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(878)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(5)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(5)][(SPILLED_RECORDS)(Spilled Records)(31)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(31)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000013" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000013_0" START_TIME="1378441670723" TRACKER_NAME="tracker_compute-5-1\.local:localhost\.localdomain/127\.0\.0\.1:55127" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000013" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000013_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441678492" SORT_FINISHED="1378441678547" FINISH_TIME="1378441679809" HOSTNAME="/default-rack/compute-5-1\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(3380)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(3380)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1274)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(7)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(7)][(SPILLED_RECORDS)(Spilled Records)(47)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(47)]}" .
+Task TASKID="task_201309041843_0020_r_000013" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441682723" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(3380)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(3380)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1274)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(7)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(7)][(SPILLED_RECORDS)(Spilled Records)(47)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(47)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000014" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000014_0" START_TIME="1378441670834" TRACKER_NAME="tracker_compute-2-10\.local:localhost\.localdomain/127\.0\.0\.1:60748" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000014" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000014_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441677775" SORT_FINISHED="1378441677808" FINISH_TIME="1378441679939" HOSTNAME="/default-rack/compute-2-10\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(3366)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(3366)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1250)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(7)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(7)][(SPILLED_RECORDS)(Spilled Records)(47)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(47)]}" .
+Task TASKID="task_201309041843_0020_r_000014" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441682831" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(3366)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(3366)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1250)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(7)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(0)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(7)][(SPILLED_RECORDS)(Spilled Records)(47)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(47)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000015" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000015_0" START_TIME="1378441671339" TRACKER_NAME="tracker_compute-5-3\.local:localhost\.localdomain/127\.0\.0\.1:48745" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000015" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000015_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441679348" SORT_FINISHED="1378441679404" FINISH_TIME="1378441680660" HOSTNAME="/default-rack/compute-5-3\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2398)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2398)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(950)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(5)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(2398)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(5)][(SPILLED_RECORDS)(Spilled Records)(33)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(33)]}" .
+Task TASKID="task_201309041843_0020_r_000015" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441683341" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(2398)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(2398)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(950)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(5)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(2398)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(5)][(SPILLED_RECORDS)(Spilled Records)(33)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(33)]}" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000012" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000012_0" START_TIME="1378441669853" TRACKER_NAME="tracker_compute-5-2\.local:localhost\.localdomain/127\.0\.0\.1:42328" HTTP_PORT="50060" .
+ReduceAttempt TASK_TYPE="REDUCE" TASKID="task_201309041843_0020_r_000012" TASK_ATTEMPT_ID="attempt_201309041843_0020_r_000012_0" TASK_STATUS="SUCCESS" SHUFFLE_FINISHED="1378441678426" SORT_FINISHED="1378441678497" FINISH_TIME="1378441681926" HOSTNAME="/default-rack/compute-5-2\.local" STATE_STRING="reduce > reduce" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(4614)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(4614)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1736)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(10)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(4614)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(10)][(SPILLED_RECORDS)(Spilled Records)(65)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(65)]}" .
+Task TASKID="task_201309041843_0020_r_000012" TASK_TYPE="REDUCE" TASK_STATUS="SUCCESS" FINISH_TIME="1378441684841" COUNTERS="{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(4614)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(4614)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(1736)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(10)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(4614)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(10)][(SPILLED_RECORDS)(Spilled Records)(65)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(65)]}" .
+Task TASKID="task_201309041843_0020_m_000001" TASK_TYPE="CLEANUP" START_TIME="1378441684842" SPLITS="" .
+MapAttempt TASK_TYPE="CLEANUP" TASKID="task_201309041843_0020_m_000001" TASK_ATTEMPT_ID="attempt_201309041843_0020_m_000001_0" START_TIME="1378441684866" TRACKER_NAME="tracker_compute-5-2\.local:localhost\.localdomain/127\.0\.0\.1:42328" HTTP_PORT="50060" .
+MapAttempt TASK_TYPE="CLEANUP" TASKID="task_201309041843_0020_m_000001" TASK_ATTEMPT_ID="attempt_201309041843_0020_m_000001_0" TASK_STATUS="SUCCESS" FINISH_TIME="1378441687525" HOSTNAME="/default-rack/compute-5-2\.local" STATE_STRING="cleanup" COUNTERS="{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(SPILLED_RECORDS)(Spilled Records)(0)]}" .
+Task TASKID="task_201309041843_0020_m_000001" TASK_TYPE="CLEANUP" TASK_STATUS="SUCCESS" FINISH_TIME="1378441687847" COUNTERS="{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(SPILLED_RECORDS)(Spilled Records)(0)]}" .
+Job JOBID="job_201309041843_0020" FINISH_TIME="1378441687847" JOB_STATUS="SUCCESS" FINISHED_MAPS="1" FINISHED_REDUCES="16" FAILED_MAPS="0" FAILED_REDUCES="0" COUNTERS="{(org\.apache\.hadoop\.mapred\.JobInProgress$Counter)(Job Counters )[(TOTAL_LAUNCHED_REDUCES)(Launched reduce tasks)(16)][(TOTAL_LAUNCHED_MAPS)(Launched map tasks)(1)]}{(FileSystemCounters)(FileSystemCounters)[(FILE_BYTES_READ)(FILE_BYTES_READ)(42896)][(HDFS_BYTES_READ)(HDFS_BYTES_READ)(1392)][(FILE_BYTES_WRITTEN)(FILE_BYTES_WRITTEN)(86184)][(HDFS_BYTES_WRITTEN)(HDFS_BYTES_WRITTEN)(16272)]}{(org\.apache\.hadoop\.mapred\.Task$Counter)(Map-Reduce Framework)[(REDUCE_INPUT_GROUPS)(Reduce input groups)(88)][(COMBINE_OUTPUT_RECORDS)(Combine output records)(0)][(MAP_INPUT_RECORDS)(Map input records)(100)][(REDUCE_SHUFFLE_BYTES)(Reduce shuffle bytes)(17428)][(REDUCE_OUTPUT_RECORDS)(Reduce output records)(88)][(SPILLED_RECORDS)(Spilled Records)(1200)][(MAP_OUTPUT_BYTES)(Map output bytes)(41600)][(MAP_INPUT_BYTES)(Map input bytes)(1392)][(MAP_OUTPUT_RECORDS)(Map output records)(600)][(COMBINE_INPUT_RECORDS)(Combine input records)(0)][(REDUCE_INPUT_RECORDS)(Reduce input records)(600)]}" .
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/01-BUILD_HADOOP/_logs/history/compute-2-10_1378345383525_job_201309041843_0020_conf.xml b/genomix/genomix-pregelix/data/TestSet/PathMerge/01-BUILD_HADOOP/_logs/history/compute-2-10_1378345383525_job_201309041843_0020_conf.xml
new file mode 100644
index 0000000..ad0e61b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/01-BUILD_HADOOP/_logs/history/compute-2-10_1378345383525_job_201309041843_0020_conf.xml
@@ -0,0 +1,228 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
+<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
+<property><name>mapred.task.cache.levels</name><value>2</value></property>
+<property><name>hadoop.tmp.dir</name><value>/scratch/hadoop-wbiesing/hadoop-tmp-dir</value></property>
+<property><name>hadoop.native.lib</name><value>true</value></property>
+<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
+<property><name>dfs.namenode.decommission.nodes.per.interval</name><value>5</value></property>
+<property><name>dfs.https.need.client.auth</name><value>false</value></property>
+<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
+<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
+<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
+<property><name>dfs.namenode.logging.level</name><value>info</value></property>
+<property><name>dfs.datanode.address</name><value>0.0.0.0:50010</value></property>
+<property><name>io.skip.checksum.errors</name><value>false</value></property>
+<property><name>fs.default.name</name><value>hdfs://compute-2-10:54310</value></property>
+<property><name>mapred.child.tmp</name><value>./tmp</value></property>
+<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
+<property><name>dfs.safemode.threshold.pct</name><value>0.999f</value></property>
+<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
+<property><name>dfs.namenode.handler.count</name><value>10</value></property>
+<property><name>dfs.blockreport.initialDelay</name><value>0</value></property>
+<property><name>genomix.hyracks.slaves.list</name><value>compute-2-10
+compute-5-1
+compute-5-2
+compute-5-3
+</value></property>
+<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
+<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
+<property><name>io.sort.factor</name><value>10</value></property>
+<property><name>genomix.hyracks.IO_DIRS</name><value>"${WORKPATH}/tmp/t3,${WORKPATH}/tmp/t4,${WORKPATH}/tmp/t5,${WORKPATH}/tmp/t6"</value></property>
+<property><name>mapred.task.timeout</name><value>600000</value></property>
+<property><name>genomix.tipRemove.maxLength</name><value>6</value></property>
+<property><name>mapred.max.tracker.failures</name><value>4</value></property>
+<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
+<property><name>mapred.mapoutput.key.class</name><value>edu.uci.ics.genomix.type.VKmerBytesWritable</value></property>
+<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
+<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
+<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
+<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.VKmerBytesWritable</value></property>
+<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
+<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
+<property><name>genomix.initial.input.dir</name><value>genomix_out/00-initial-input-from-genomix-driver</value></property>
+<property><name>dfs.safemode.extension</name><value>30000</value></property>
+<property><name>tasktracker.http.threads</name><value>40</value></property>
+<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
+<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
+<property><name>user.name</name><value>anbangx</value></property>
+<property><name>mapred.output.compress</name><value>false</value></property>
+<property><name>io.bytes.per.checksum</name><value>512</value></property>
+<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
+<property><name>dfs.https.server.keystore.resource</name><value>ssl-server.xml</value></property>
+<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
+<property><name>genomix.bubbleMerge.maxDissimilarity</name><value>0.5</value></property>
+<property><name>genomix.framelimit</name><value>2048</value></property>
+<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
+<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
+<property><name>mapred.job.classpath.files</name><value>/user/anbangx/genomix_out/jar-dependencies/hyracks-hdfs-0.20.2-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/junit-4.8.1.jar:/user/anbangx/genomix_out/jar-dependencies/genomix-data-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/args4j-maven-plugin-2.0.25.jar:/user/anbangx/genomix_out/jar-dependencies/args4j-tools-2.0.25-all.jar:/user/anbangx/genomix_out/jar-dependencies/maven-project-2.0.4.jar:/user/anbangx/genomix_out/jar-dependencies/maven-settings-2.0.4.jar:/user/anbangx/genomix_out/jar-dependencies/maven-profile-2.0.4.jar:/user/anbangx/genomix_out/jar-dependencies/maven-model-2.0.4.jar:/user/anbangx/genomix_out/jar-dependencies/maven-artifact-manager-2.0.4.jar:/user/anbangx/genomix_out/jar-dependencies/maven-repository-metadata-2.0.4.jar:/user/anbangx/genomix_out/jar-dependencies/wagon-provider-api-1.0-alpha-6.jar:/user/anbangx/genomix_out/jar-dependencies/plexus-utils-1.1.jar:/user/anbangx/genomix_out/jar-dependencies/maven-artifact-2.0.4.jar:/user/anbangx/genomix_out/jar-dependencies/plexus-container-default-1.0-alpha-9.jar:/user/anbangx/genomix_out/jar-dependencies/classworlds-1.1-alpha-2.jar:/user/anbangx/genomix_out/jar-dependencies/maven-plugin-api-2.0.jar:/user/anbangx/genomix_out/jar-dependencies/commons-lang3-3.1.jar:/user/anbangx/genomix_out/jar-dependencies/pregelix-core-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/pregelix-api-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/pregelix-dataflow-std-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/pregelix-dataflow-std-base-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/pregelix-dataflow-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/pregelix-runtime-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-common-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/javax.servlet-api-3.0.1.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-dataflow-std-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/commons-io-2.4.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-api-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/json-20090211.jar:/user/anbangx/genomix_out/jar-dependencies/httpclient-4.1-alpha2.jar:/user/anbangx/genomix_out/jar-dependencies/httpcore-4.1-beta1.jar:/user/anbangx/genomix_out/jar-dependencies/commons-logging-1.1.1.jar:/user/anbangx/genomix_out/jar-dependencies/args4j-2.0.12.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-dataflow-common-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/genomix-hadoop-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/slf4j-jcl-1.6.3.jar:/user/anbangx/genomix_out/jar-dependencies/slf4j-api-1.6.3.jar:/user/anbangx/genomix_out/jar-dependencies/mrunit-1.0.0-hadoop1.jar:/user/anbangx/genomix_out/jar-dependencies/mockito-all-1.8.5.jar:/user/anbangx/genomix_out/jar-dependencies/genomix-hyracks-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/genomix-pregelix-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-hdfs-core-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-data-std-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-control-cc-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-control-common-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-server-8.0.0.RC0.jar:/user/anbangx/genomix_out/jar-dependencies/servlet-api-3.0.20100224.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-continuation-8.0.0.RC0.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-http-8.0.0.RC0.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-io-8.0.0.RC0.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-webapp-8.0.0.RC0.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-xml-8.0.0.RC0.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-util-8.0.0.RC0.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-servlet-8.0.0.RC0.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-security-8.0.0.RC0.jar:/user/anbangx/genomix_out/jar-dependencies/wicket-core-1.5.2.jar:/user/anbangx/genomix_out/jar-dependencies/wicket-util-1.5.2.jar:/user/anbangx/genomix_out/jar-dependencies/wicket-request-1.5.2.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-control-nc-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-net-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-comm-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-btree-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-common-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-lsm-btree-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-bloomfilter-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-lsm-common-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hyracks-ipc-0.2.10-SNAPSHOT.jar:/user/anbangx/genomix_out/jar-dependencies/hadoop-core-0.20.2.jar:/user/anbangx/genomix_out/jar-dependencies/commons-cli-1.2.jar:/user/anbangx/genomix_out/jar-dependencies/xmlenc-0.52.jar:/user/anbangx/genomix_out/jar-dependencies/commons-httpclient-3.0.1.jar:/user/anbangx/genomix_out/jar-dependencies/commons-codec-1.3.jar:/user/anbangx/genomix_out/jar-dependencies/commons-net-1.4.1.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-6.1.14.jar:/user/anbangx/genomix_out/jar-dependencies/jetty-util-6.1.14.jar:/user/anbangx/genomix_out/jar-dependencies/jasper-runtime-5.5.12.jar:/user/anbangx/genomix_out/jar-dependencies/jasper-compiler-5.5.12.jar:/user/anbangx/genomix_out/jar-dependencies/jsp-api-2.1-6.1.14.jar:/user/anbangx/genomix_out/jar-dependencies/jsp-2.1-6.1.14.jar:/user/anbangx/genomix_out/jar-dependencies/ant-1.6.5.jar:/user/anbangx/genomix_out/jar-dependencies/commons-el-1.0.jar:/user/anbangx/genomix_out/jar-dependencies/jets3t-0.7.1.jar:/user/anbangx/genomix_out/jar-dependencies/servlet-api-2.5-6.1.14.jar:/user/anbangx/genomix_out/jar-dependencies/kfs-0.3.jar:/user/anbangx/genomix_out/jar-dependencies/hsqldb-1.8.0.10.jar:/user/anbangx/genomix_out/jar-dependencies/oro-2.0.8.jar:/user/anbangx/genomix_out/jar-dependencies/core-3.1.1.jar:/user/anbangx/genomix_out/jar-dependencies/hadoop-test-0.20.2.jar:/user/anbangx/genomix_out/jar-dependencies/ftplet-api-1.0.0.jar:/user/anbangx/genomix_out/jar-dependencies/mina-core-2.0.0-M5.jar:/user/anbangx/genomix_out/jar-dependencies/ftpserver-core-1.0.0.jar:/user/anbangx/genomix_out/jar-dependencies/ftpserver-deprecated-1.0.0-M2.jar:/user/anbangx/genomix_out/jar-dependencies/jfreechart-1.0.13.jar:/user/anbangx/genomix_out/jar-dependencies/jcommon-1.0.16.jar:/user/anbangx/genomix_out/jar-dependencies/genomix-driver-0.2.10-SNAPSHOT.jar</value></property>
+<property><name>dfs.name.edits.dir</name><value>${dfs.name.dir}</value></property>
+<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
+<property><name>genomix.kmerlength</name><value>5</value></property>
+<property><name>hadoop.job.ugi</name><value>anbangx,cbcl</value></property>
+<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
+<property><name>mapred.jar</name><value>/scratch/hadoop-wbiesing/hadoop-tmp-dir/mapred/local/jobTracker/job_201309041843_0020.jar</value></property>
+<property><name>dfs.block.size</name><value>67108864</value></property>
+<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
+<property><name>job.end.retry.attempts</name><value>0</value></property>
+<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
+<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
+<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
+<property><name>dfs.datanode.ipc.address</name><value>0.0.0.0:50020</value></property>
+<property><name>dfs.permissions</name><value>true</value></property>
+<property><name>genomix.ipAddress</name><value>10.1.255.112</value></property>
+<property><name>topology.script.number.args</name><value>100</value></property>
+<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
+<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
+<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
+<property><name>dfs.datanode.https.address</name><value>0.0.0.0:50475</value></property>
+<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
+<property><name>dfs.secondary.http.address</name><value>0.0.0.0:50090</value></property>
+<property><name>dfs.replication.max</name><value>512</value></property>
+<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
+<property><name>hadoop.security.authorization</name><value>false</value></property>
+<property><name>local.cache.size</name><value>10737418240</value></property>
+<property><name>mapred.min.split.size</name><value>0</value></property>
+<property><name>mapred.map.tasks</name><value>1</value></property>
+<property><name>mapred.child.java.opts</name><value>-Xmx2096m</value></property>
+<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.type.NodeWritable</value></property>
+<property><name>genomix.cluster.wait.time</name><value>6000</value></property>
+<property><name>dfs.https.client.keystore.resource</name><value>ssl-client.xml</value></property>
+<property><name>mapred.job.queue.name</name><value>default</value></property>
+<property><name>dfs.https.address</name><value>0.0.0.0:50470</value></property>
+<property><name>dfs.balance.bandwidthPerSec</name><value>1048576</value></property>
+<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
+<property><name>group.name</name><value>cbcl</value></property>
+<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
+<property><name>job.end.retry.interval</name><value>30000</value></property>
+<property><name>genomix.port</name><value>4099</value></property>
+<property><name>genomix.follows.graph.build</name><value>false</value></property>
+<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
+<property><name>fs.checkpoint.dir</name><value>/scratch/hadoop-wbiesing/fs-checkpoint-dir</value></property>
+<property><name>genomix.draw.statistics</name><value>false</value></property>
+<property><name>mapred.reduce.tasks</name><value>16</value></property>
+<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
+<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
+<property><name>genomix.hdfs.work.path</name><value>genomix_out</value></property>
+<property><name>dfs.max.objects</name><value>0</value></property>
+<property><name>webinterface.private.actions</name><value>true</value></property>
+<property><name>io.sort.spill.percent</name><value>0.80</value></property>
+<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
+<property><name>mapred.job.split.file</name><value>hdfs://compute-2-10:54310/scratch/hadoop-wbiesing/hadoop-tmp-dir/mapred/system/job_201309041843_0020/job.split</value></property>
+<property><name>mapred.job.name</name><value>Genomix Graph Building</value></property>
+<property><name>dfs.datanode.dns.nameserver</name><value>default</value></property>
+<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
+<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
+<property><name>dfs.blockreport.intervalMsec</name><value>3600000</value></property>
+<property><name>sizeKmer</name><value>5</value></property>
+<property><name>mapred.map.max.attempts</name><value>4</value></property>
+<property><name>dfs.client.block.write.retries</name><value>3</value></property>
+<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
+<property><name>mapred.input.format.class</name><value>org.apache.hadoop.mapred.lib.NLineInputFormat</value></property>
+<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
+<property><name>genomix.PathMergeRandom.randSeed</name><value>1.37844163E12</value></property>
+<property><name>dfs.https.enable</name><value>false</value></property>
+<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
+<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
+<property><name>keep.failed.task.files</name><value>false</value></property>
+<property><name>mapred.output.format.class</name><value>org.apache.hadoop.mapred.SequenceFileOutputFormat</value></property>
+<property><name>genomix.runLocal</name><value>false</value></property>
+<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
+<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
+<property><name>genomix.bridgeRemove.maxLength</name><value>6</value></property>
+<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
+<property><name>io.map.index.skip</name><value>0</value></property>
+<property><name>genomix.save.intermediate.results</name><value>true</value></property>
+<property><name>mapred.working.dir</name><value>hdfs://compute-2-10:54310/user/anbangx</value></property>
+<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
+<property><name>mapred.reducer.class</name><value>edu.uci.ics.genomix.hadoop.contrailgraphbuilding.GenomixReducer</value></property>
+<property><name>dfs.default.chunk.view.size</name><value>32768</value></property>
+<property><name>mapred.cache.files.timestamps</name><value>1378441644835,1378441644868,1378441644918,1378441644960,1378441645027,1378441645085,1378441645135,1378441645185,1378441645235,1378441645285,1378441645335,1378441645385,1378441645435,1378441645501,1378441645535,1378441645585,1378441645635,1378441645685,1378441645735,1378441645785,1378441645835,1378441645893,1378441645960,1378441646018,1378441646068,1378441646118,1378441646168,1378441646218,1378441646268,1378441646318,1378441646368,1378441646443,1378441646476,1378441646526,1378441646576,1378441646626,1378441646676,1378441646726,1378441646776,1378441646826,1378441646926,1378441646959,1378441646993,1378441647043,1378441647076,1378441647118,1378441647151,1378441647193,1378441647242,1378441647309,1378441647342,1378441647392,1378441647434,1378441647467,1378441647526,1378441647559,1378441647601,1378441647667,1378441647742,1378441647776,1378441647817,1378441647867,1378441647901,1378441647934,1378441647976,1378441648009,1378441648068,1378441648117,1378441648167,1378441649675,1378441649708,1378441649742,1378441649783,1378441649825,1378441649900,1378441649958,1378441650033,1378441650100,1378441650166,1378441650225,1378441650291,1378441650366,1378441650583,1378441650624,1378441650666,1378441650816,1378441650874,1378441650924,1378441651024,1378441652507,1378441652549,1378441652599,1378441652640,1378441652674,1378441652732,1378441652799</value></property>
+<property><name>hadoop.logfile.size</name><value>100000</value></property>
+<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
+<property><name>genomix.profile</name><value>false</value></property>
+<property><name>dfs.datanode.du.reserved</name><value>0</value></property>
+<property><name>fs.checkpoint.period</name><value>3600</value></property>
+<property><name>dfs.web.ugi</name><value>webuser,webgroup</value></property>
+<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
+<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
+<property><name>dfs.df.interval</name><value>60000</value></property>
+<property><name>dfs.data.dir</name><value>/scratch/hadoop-wbiesing/dfs-data-dir</value></property>
+<property><name>fs.s3.maxRetries</name><value>4</value></property>
+<property><name>dfs.datanode.dns.interface</name><value>default</value></property>
+<property><name>mapred.mapoutput.value.class</name><value>edu.uci.ics.genomix.type.NodeWritable</value></property>
+<property><name>dfs.support.append</name><value>false</value></property>
+<property><name>dfs.permissions.supergroup</name><value>supergroup</value></property>
+<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
+<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
+<property><name>mapred.mapper.class</name><value>edu.uci.ics.genomix.hadoop.contrailgraphbuilding.GenomixMapper</value></property>
+<property><name>fs.trash.interval</name><value>0</value></property>
+<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
+<property><name>dfs.replication.min</name><value>1</value></property>
+<property><name>mapred.submit.replication</name><value>10</value></property>
+<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
+<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
+<property><name>genomix.max.readids.per.edge</name><value>250</value></property>
+<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
+<property><name>dfs.namenode.decommission.interval</name><value>30</value></property>
+<property><name>dfs.http.address</name><value>0.0.0.0:50070</value></property>
+<property><name>mapred.cache.files</name><value>hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-hdfs-0.20.2-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/junit-4.8.1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/genomix-data-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/args4j-maven-plugin-2.0.25.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/args4j-tools-2.0.25-all.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/maven-project-2.0.4.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/maven-settings-2.0.4.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/maven-profile-2.0.4.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/maven-model-2.0.4.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/maven-artifact-manager-2.0.4.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/maven-repository-metadata-2.0.4.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/wagon-provider-api-1.0-alpha-6.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/plexus-utils-1.1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/maven-artifact-2.0.4.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/plexus-container-default-1.0-alpha-9.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/classworlds-1.1-alpha-2.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/maven-plugin-api-2.0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/commons-lang3-3.1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/pregelix-core-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/pregelix-api-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/pregelix-dataflow-std-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/pregelix-dataflow-std-base-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/pregelix-dataflow-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/pregelix-runtime-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-common-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/javax.servlet-api-3.0.1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-dataflow-std-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/commons-io-2.4.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-api-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/json-20090211.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/httpclient-4.1-alpha2.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/httpcore-4.1-beta1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/commons-logging-1.1.1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/args4j-2.0.12.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-dataflow-common-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/genomix-hadoop-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/slf4j-jcl-1.6.3.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/slf4j-api-1.6.3.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/mrunit-1.0.0-hadoop1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/mockito-all-1.8.5.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/genomix-hyracks-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/genomix-pregelix-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-hdfs-core-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-data-std-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-control-cc-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-control-common-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-server-8.0.0.RC0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/servlet-api-3.0.20100224.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-continuation-8.0.0.RC0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-http-8.0.0.RC0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-io-8.0.0.RC0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-webapp-8.0.0.RC0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-xml-8.0.0.RC0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-util-8.0.0.RC0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-servlet-8.0.0.RC0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-security-8.0.0.RC0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/wicket-core-1.5.2.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/wicket-util-1.5.2.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/wicket-request-1.5.2.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-control-nc-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-net-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-comm-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-btree-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-common-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-lsm-btree-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-bloomfilter-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-storage-am-lsm-common-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hyracks-ipc-0.2.10-SNAPSHOT.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hadoop-core-0.20.2.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/commons-cli-1.2.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/xmlenc-0.52.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/commons-httpclient-3.0.1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/commons-codec-1.3.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/commons-net-1.4.1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-6.1.14.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jetty-util-6.1.14.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jasper-runtime-5.5.12.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jasper-compiler-5.5.12.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jsp-api-2.1-6.1.14.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jsp-2.1-6.1.14.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/ant-1.6.5.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/commons-el-1.0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jets3t-0.7.1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/servlet-api-2.5-6.1.14.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/kfs-0.3.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hsqldb-1.8.0.10.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/oro-2.0.8.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/core-3.1.1.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/hadoop-test-0.20.2.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/ftplet-api-1.0.0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/mina-core-2.0.0-M5.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/ftpserver-core-1.0.0.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/ftpserver-deprecated-1.0.0-M2.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jfreechart-1.0.13.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/jcommon-1.0.16.jar,hdfs://compute-2-10:54310/user/anbangx/genomix_out/jar-dependencies/genomix-driver-0.2.10-SNAPSHOT.jar</value></property>
+<property><name>genomix.pipelineOrder</name><value>BUILD_HADOOP,MERGE_P2</value></property>
+<property><name>dfs.heartbeat.interval</name><value>3</value></property>
+<property><name>mapred.job.tracker</name><value>compute-2-10:54311</value></property>
+<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
+<property><name>dfs.name.dir</name><value>${hadoop.tmp.dir}/dfs/name</value></property>
+<property><name>mapred.line.input.format.linespermap</name><value>400000</value></property>
+<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
+<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
+<property><name>dfs.datanode.http.address</name><value>0.0.0.0:50075</value></property>
+<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
+<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
+<property><name>dfs.replication.interval</name><value>3</value></property>
+<property><name>io.sort.record.percent</name><value>0.05</value></property>
+<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
+<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
+<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>20</value></property>
+<property><name>dfs.replication</name><value>3</value></property>
+<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
+<property><name>genomix.framesize</name><value>65535</value></property>
+<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
+<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
+<property><name>hadoop.logfile.count</name><value>10</value></property>
+<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
+<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
+<property><name>fs.s3.block.size</name><value>67108864</value></property>
+<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
+<property><name>genomix.removeLowCoverage.maxCoverage</name><value>3.0</value></property>
+<property><name>genomix.PathMergeRandom.probBeingRandomHead</name><value>0.5</value></property>
+<property><name>mapred.acls.enabled</name><value>false</value></property>
+<property><name>mapred.queue.names</name><value>default</value></property>
+<property><name>genomix.initial.local.input.dir</name><value>/data/users/anbangx/testdata/SmallGenome/</value></property>
+<property><name>dfs.access.time.precision</name><value>3600000</value></property>
+<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
+<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
+<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
+<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
+<property><name>mapred.output.dir</name><value>hdfs://compute-2-10:54310/user/anbangx/genomix_out/01-BUILD_HADOOP</value></property>
+<property><name>io.sort.mb</name><value>150</value></property>
+<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
+<property><name>mapred.compress.map.output</name><value>false</value></property>
+<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
+<property><name>ipc.client.kill.max</name><value>10</value></property>
+<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
+<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
+<property><name>genomix.graphCleanMaxIterations</name><value>10000000</value></property>
+<property><name>mapred.input.dir</name><value>hdfs://compute-2-10:54310/user/anbangx/genomix_out/00-initial-input-from-genomix-driver</value></property>
+<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
+<property><name>io.file.buffer.size</name><value>4096</value></property>
+<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
+<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
+<property><name>dfs.datanode.handler.count</name><value>3</value></property>
+<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
+<property><name>mapred.task.profile</name><value>false</value></property>
+<property><name>dfs.replication.considerLoad</name><value>true</value></property>
+<property><name>jobclient.output.filter</name><value>FAILED</value></property>
+<property><name>mapred.tasktracker.map.tasks.maximum</name><value>20</value></property>
+<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
+<property><name>fs.checkpoint.size</name><value>67108864</value></property>
+<property><name>genomix.final.local.output.dir</name><value>/data/users/anbangx/result/SmallGenome_hadoop_P2</value></property>
+</configuration>
\ No newline at end of file
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diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/SmallGenome_5/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/SmallGenome_5/bin/part-00000
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diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/SmallGenome_5/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/SmallGenome_5/data
new file mode 100644
index 0000000..cca8c78
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/SmallGenome_5/data
@@ -0,0 +1,88 @@
+TAAAA {[{AAAAG:[93]}] [] [] [{CTAAA:[93]}] {5':[], ~5':[]} 1.0x}
+GGAAA {[] [{ATTTC:[2,14,49,75,81,94,97]}] [] [{TGGAA:[2,14,49,54,75]}] {5':[(81-0_0)], ~5':[(54-0_0)]} 8.0x}
+TGAAA {[] [{ATTTC:[4,27,30,41,64]}] [] [{GTGAA:[1,4,27,41,67]}] {5':[], ~5':[(1-0_0),(67-0_0)]} 7.0x}
+ATAAA {[] [{CTTTA:[81,83,89,94,97]}] [] [{AATAA:[49,81,83,89,94,97]}] {5':[], ~5':[(49-0_0)]} 6.0x}
+CTAAA {[{TAAAA:[93]}] [] [] [{GCTAA:[93]}] {5':[], ~5':[]} 1.0x}
+GACAA {[{ACAAT:[29,55,79]}] [] [] [{AGACA:[29,79]}] {5':[], ~5':[]} 3.0x}
+CAGAA {[{AGAAG:[8,25,42,46,66,78,80,86]}] [] [] [{TCAGA:[8,25,42,46,66,70,78,80,86]}] {5':[], ~5':[(70-0_0)]} 9.0x}
+ACGAA {[] [{ATTCG:[13,17,33,45,59,77,98]}] [] [{GACGA:[13,17,33,45,59,77,98]}] {5':[], ~5':[]} 7.0x}
+GCGAA {[{CGAAG:[32,47,52,62,71,84]}] [] [] [{AGCGA:[32,38,47,52,62,71,84,91]}] {5':[], ~5':[(38-0_0),(91-0_0)]} 8.0x}
+TGGAA {[{GGAAA:[2,14,49,54,75]}] [] [] [{CTGGA:[2,10,14,54,63,75]}] {5':[], ~5':[(63-0_0)]} 7.0x}
+GTGAA {[{TGAAA:[1,4,27,41,67]}] [] [] [{AGTGA:[1,4,20,27,41,67]}] {5':[], ~5':[]} 6.0x}
+AATAA {[{ATAAA:[49,81,83,89,94,97]}] [] [] [{AAATA:[49,75,81,83,94,97]}] {5':[(89-0_0)], ~5':[(75-0_0)]} 7.0x}
+CCTAA {[{CTAAG:[38,39,88,91]}] [] [] [{GCCTA:[12,39,61,88]}] {5':[], ~5':[(12-0_0)]} 6.0x}
+GCTAA {[{CTAAA:[93]}] [] [] [{CGCTA:[16,82,93]}] {5':[], ~5':[]} 3.0x}
+GGTAA {[] [{ATTAC:[7,11,37,40,56]}] [] [{CGGTA:[7,37,40,56]}] {5':[], ~5':[]} 5.0x}
+AGACA {[{GACAA:[29,79]}] [] [] [{AAGAC:[79,89]}] {5':[(29-0_0)], ~5':[]} 3.0x}
+AGCCA {[{GCCAC:[19,26,31,50,69,92]}] [] [] [{CAGCC:[19,26,31,50,69,90,92]}] {5':[], ~5':[]} 7.0x}
+CGGCA {[] [{ATGCC:[5,15,21,23,48,96]}] [] [{CCGGC:[5,15,21,23,48,96]}] {5':[], ~5':[]} 6.0x}
+GATCA {[{ATCAG:[19,60,72,90,92]}] [] [{GATCA:[60,72,90]}] [] {5':[(19-0_0)], ~5':[(90-0_0)]} 8.0x}
+GCTCA {[{CTCAG:[6,25,46,66,70,80]}] [] [{GAGCC:[6,25,36,46,53,70,80,87]}] [] {5':[(66-0_0)], ~5':[(87-0_0)]} 9.0x}
+AAAGA {[{AAGAC:[89]}] [] [{CTTTA:[83,89]}] [] {5':[], ~5':[(83-0_0)]} 2.0x}
+CCAGA {[{CAGAG:[10,43,54,63,100]}] [] [{CTGGA:[2,10,14,43,54,63]}] [] {5':[], ~5':[(14-0_0)]} 7.0x}
+TCAGA {[{CAGAA:[8,25,42,46,66,70,78,80,86]}] [] [] [{CTCAG:[25,46,66,70,80]}] {5':[(8-0_0),(42-0_0)], ~5':[]} 9.0x}
+GACGA {[{ACGAA:[13,17,33,45,59,77,98]}] [] [{CGTCC:[13,17,18,33,45,74,77,98]}] [] {5':[(59-0_0)], ~5':[]} 9.0x}
+CCCGA {[] [{ATCGG:[28,35,44,73,95]}] [{CGGGA:[3,28,35,44,51,95]}] [] {5':[(73-0_0)], ~5':[(3-0_0),(51-0_0)]} 7.0x}
+TCCGA {[] [{ATCGG:[9,18,30,64,74]}] [{CGGAC:[9,18,33,74]}] [] {5':[(30-0_0),(64-0_0)], ~5':[]} 6.0x}
+AGCGA {[{GCGAA:[32,38,47,52,62,71,84,91]}] [] [] [{AAGCG:[32,38,39,47,52,62,71,84,91]}] {5':[], ~5':[]} 9.0x}
+GCGGA {[] [{ATCCG:[11,16,82,85]}] [] [{AGCGG:[16,82,85]}] {5':[(11-0_0)], ~5':[]} 4.0x}
+CGGGA {[] [{CTCCC:[3,20,35,44,51]}] [{CCCGA:[3,28,35,44,51,95]}] [] {5':[(20-0_0)], ~5':[(28-0_0)]} 7.0x}
+CTGGA {[{TGGAA:[2,10,14,54,63,75]}] [] [{CCAGA:[2,10,14,43,54,63]}] [] {5':[], ~5':[]} 7.0x}
+GCTGA {[] [{ATCAG:[19,26,60,72,90,92]}] [{CAGCC:[19,26,31,50,60,69,72,90,92]}] [] {5':[], ~5':[(31-0_0),(69-0_0)]} 9.0x}
+AGTGA {[{GTGAA:[1,4,20,27,41,67]}] [] [{CACTC:[1,3,4,20,27,41,51,67]}] [] {5':[], ~5':[]} 8.0x}
+AAATA {[{AATAA:[49,75,81,83,94,97]}] [] [{ATTTC:[2,14,49,75,81,83,94,97]}] [] {5':[], ~5':[(2-0_0)]} 8.0x}
+CAATA {[{AATAT:[22,29,34,55,57,68,73,79]}] [] [] [{ACAAT:[22,29,34,55,57,68,79]}] {5':[], ~5':[]} 8.0x}
+CGATA {[] [{ATATC:[22,28,34,55,57,68,73,95]}] [{ATCGG:[22,28,34,35,44,57,68,73,95]}] [] {5':[(55-0_0)], ~5':[(35-0_0),(44-0_0)]} 10.0x}
+GCCTA {[{CCTAA:[12,39,61,88]}] [] [] [{AGCCT:[12,24,61,88]}] {5':[(39-0_0)], ~5':[]} 5.0x}
+AGCTA {[] [{CTAGC:[24,58,65,99,100]}] [{AGCTC:[43,58,65,99,100]}] [] {5':[(24-0_0)], ~5':[(43-0_0)]} 6.0x}
+CGCTA {[{GCTAA:[16,82,93]}] [] [{AGCGG:[16,82,85,93]}] [] {5':[], ~5':[(85-0_0)]} 4.0x}
+GGCTA {[] [{CTAGC:[12,24,58,61,99]}] [{AGCCT:[12,24,58,61,88]}] [] {5':[], ~5':[]} 6.0x}
+CGGTA {[{GGTAA:[7,37,40,56]}] [] [{ACCGG:[5,7,21,37,40]}] [] {5':[(56-0_0)], ~5':[(5-0_0)]} 6.0x}
+GATTA {[{ATTAC:[7,11,37,40,56]}] [] [{AATCC:[11,37,56,85]}] [] {5':[(7-0_0)], ~5':[]} 6.0x}
+GCTTA {[] [{CTAAG:[38,39,71,88,91]}] [{AAGCG:[38,39,47,52,71,91]}] [] {5':[(88-0_0)], ~5':[(47-0_0)]} 7.0x}
+CTTTA {[] [{ATAAA:[81,83,89,94,97]}] [{AAAGA:[83,89]}] [] {5':[(94-0_0),(97-0_0)], ~5':[]} 5.0x}
+GCCAC {[] [{AGTGG:[26,31,50,69]}] [] [{AGCCA:[19,26,31,50,69,92]}] {5':[], ~5':[(92-0_0)]} 6.0x}
+AAGAC {[{AGACA:[79,89]}] [] [] [{AAAGA:[89]}] {5':[], ~5':[]} 2.0x}
+CGGAC {[] [{CGTCC:[18,33,45,74,77]}] [{TCCGA:[9,18,33,74]}] [] {5':[], ~5':[(9-0_0)]} 6.0x}
+ATTAC {[] [{GGTAA:[7,11,37,40,56]}] [] [{GATTA:[7,11,37,40,56]}] {5':[], ~5':[]} 5.0x}
+AGCCC {[] [{AGGGC:[6,36,53,76,87]}] [] [{GAGCC:[6,36,53,70,76,87]}] {5':[], ~5':[]} 6.0x}
+CTCCC {[] [{CGGGA:[3,20,35,44,51]}] [] [{ACTCC:[1,3,20,35,44,51,67]}] {5':[], ~5':[]} 7.0x}
+CAGCC {[{AGCCA:[19,26,31,50,69,90,92]}] [] [{GCTGA:[19,26,31,50,60,69,72,90,92]}] [] {5':[], ~5':[]} 9.0x}
+GAGCC {[{AGCCC:[6,36,53,70,76,87]}] [] [{GCTCA:[6,25,36,46,53,70,80,87]}] [] {5':[], ~5':[]} 9.0x}
+ATGCC {[] [{CGGCA:[5,15,21,23,48,96]}] [] [{AATGC:[5,15,21,23,48,59,96]}] {5':[], ~5':[]} 7.0x}
+AATCC {[{ATCCG:[11,16,56,82,85]}] [] [{GATTA:[11,37,56,85]}] [] {5':[(16-0_0),(82-0_0)], ~5':[(37-0_0)]} 6.0x}
+ACTCC {[{CTCCC:[1,3,20,35,44,51,67]}] [] [] [{CACTC:[1,3,4,20,51,67]}] {5':[], ~5':[(4-0_0)]} 8.0x}
+CGTCC {[] [{CGGAC:[18,33,45,74,77]}] [{GACGA:[13,17,18,33,45,74,77,98]}] [] {5':[], ~5':[(17-0_0)]} 8.0x}
+AGAGC {[] [{AGCTC:[10,43,63,65,99,100]}] [] [{CAGAG:[10,43,54,63,65,100]}] {5':[(99-0_0)], ~5':[]} 7.0x}
+CTAGC {[] [{AGCTA:[24,58,65,99,100]},{GGCTA:[12,24,58,61,99]}] [{CTAGC:[12,24,58,61,65,99]}] [] {5':[(100-0_0)], ~5':[(61-0_0)]} 13.0x}
+CCGGC {[{CGGCA:[5,15,21,23,48,96]}] [] [] [{ACCGG:[5,7,15,21,23,40,48]}] {5':[(96-0_0)], ~5':[(40-0_0)]} 8.0x}
+AGGGC {[] [{AGCCC:[6,36,53,76,87]}] [] [{AAGGG:[6,36,53,76,87]}] {5':[], ~5':[]} 5.0x}
+AATGC {[{ATGCC:[5,15,21,23,48,59,96]}] [] [{CATTC:[13,15,17,23,48,59,96,98]}] [] {5':[(21-0_0)], ~5':[(13-0_0),(98-0_0)]} 10.0x}
+AAATC {[{AATCG:[9,30,64]}] [] [{ATTTC:[9,27,30,41,64]}] [] {5':[], ~5':[]} 5.0x}
+ATATC {[] [{CGATA:[22,28,34,55,57,68,73,95]}] [] [{AATAT:[22,28,29,34,55,57,68,73,95]}] {5':[], ~5':[]} 9.0x}
+CACTC {[{ACTCC:[1,3,4,20,51,67]}] [] [{AGTGA:[1,3,4,20,27,41,51,67]}] [] {5':[], ~5':[(27-0_0),(41-0_0)]} 8.0x}
+AGCTC {[] [{AGAGC:[10,43,63,65,99,100]}] [{AGCTA:[43,58,65,99,100]}] [] {5':[(10-0_0)], ~5':[(58-0_0)]} 7.0x}
+CATTC {[{ATTCG:[13,17,45,59,77,96,98]}] [] [{AATGC:[13,15,17,23,48,59,96,98]}] [] {5':[(45-0_0),(77-0_0)], ~5':[]} 10.0x}
+ACTTC {[] [{AGAAG:[8,42,66,78,86]}] [{AAGTG:[8,42,78,86]}] [] {5':[], ~5':[]} 5.0x}
+CCTTC {[] [{CGAAG:[32,47,52,62,76,84]}] [{AAGGG:[32,36,53,62,76,84,87]}] [] {5':[(52-0_0)], ~5':[(36-0_0),(53-0_0)]} 9.0x}
+ATTTC {[] [{GGAAA:[2,14,49,75,81,94,97]},{TGAAA:[4,27,30,41,64]}] [{AAATA:[2,14,49,75,81,83,94,97]},{AAATC:[9,27,30,41,64]}] [] {5':[], ~5':[]} 14.0x}
+AAAAG {[] [] [] [{TAAAA:[93]}] {5':[], ~5':[]} 1.0x}
+AGAAG {[] [{ACTTC:[8,42,66,78,86]}] [] [{CAGAA:[8,25,42,46,66,78,80,86]}] {5':[], ~5':[(25-0_0),(46-0_0),(80-0_0)]} 8.0x}
+CGAAG {[] [{CCTTC:[32,47,52,62,76,84]}] [] [{GCGAA:[32,47,52,62,71,84]}] {5':[(76-0_0)], ~5':[(71-0_0)]} 7.0x}
+CTAAG {[] [{GCTTA:[38,39,71,88,91]}] [] [{CCTAA:[38,39,88,91]}] {5':[], ~5':[]} 5.0x}
+ATCAG {[] [{GCTGA:[19,26,60,72,90,92]}] [] [{GATCA:[19,60,72,90,92]}] {5':[], ~5':[(60-0_0),(72-0_0)]} 8.0x}
+CTCAG {[{TCAGA:[25,46,66,70,80]}] [] [] [{GCTCA:[6,25,46,66,70,80]}] {5':[], ~5':[]} 6.0x}
+CAGAG {[{AGAGC:[10,43,54,63,65,100]}] [] [] [{CCAGA:[10,43,54,63,100]}] {5':[(65-0_0)], ~5':[]} 6.0x}
+ATCCG {[] [{GCGGA:[11,16,82,85]}] [] [{AATCC:[11,16,56,82,85]}] {5':[], ~5':[]} 5.0x}
+AAGCG {[{AGCGA:[32,38,39,47,52,62,71,84,91]}] [] [{GCTTA:[38,39,47,52,71,91]}] [] {5':[(62-0_0)], ~5':[]} 9.0x}
+AATCG {[{ATCGG:[9,18,30,64,74]}] [] [] [{AAATC:[9,30,64]}] {5':[(18-0_0),(74-0_0)], ~5':[]} 5.0x}
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diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index b90aed3..303d9b7 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -18,44 +18,70 @@
private static final long serialVersionUID = 1L;
- public static class State extends VertexStateFlag{
+// public static class State extends VertexStateFlag{
+// public static final byte HEAD_SHOULD_MERGEWITHPREV = 0b0 << 2; //use for initiating head
+// public static final byte HEAD_SHOULD_MERGEWITHNEXT = 0b1 << 2;
+// public static final byte HEAD_SHOULD_MERGE_MASK = 0b1 << 2;
+// public static final byte HEAD_SHOULD_MERGE_CLEAR = (byte) 11001011;
+//
+// public static final byte NO_MERGE = 0b00 << 3;
+// public static final byte SHOULD_MERGEWITHNEXT = 0b01 << 3;
+// public static final byte SHOULD_MERGEWITHPREV = 0b10 << 3;
+// public static final byte SHOULD_MERGE_MASK = 0b11 << 3;
+// public static final byte SHOULD_MERGE_CLEAR = 0b1100111;
+//
+// public static final byte UNCHANGE = 0b0 << 3;
+// public static final byte KILL = 0b1 << 3;
+// public static final byte KILL_MASK = 0b1 << 3;
+//
+// public static final byte DIR_FROM_DEADVERTEX = 0b10 << 3;
+// public static final byte DEAD_MASK = 0b10 << 3;
+// }
+//
+// public static class VertexStateFlag extends FakeFlag {
+// public static final byte IS_NON = 0b00 << 5;
+// public static final byte IS_HEAD = 0b01 << 5;
+// public static final byte IS_FINAL = 0b10 << 5;
+//
+// public static final byte IS_OLDHEAD = 0b11 << 5;
+//
+// public static final byte IS_HALT = 0b1111110;
+// public static final byte IS_DEAD = 0b0111110;
+// public static final byte VERTEX_MASK = 0b11 << 5;
+// public static final byte VERTEX_CLEAR = (byte) 11001111;
+// }
+ public static class HeadMergeDir{
public static final byte HEAD_SHOULD_MERGEWITHPREV = 0b0 << 2; //use for initiating head
public static final byte HEAD_SHOULD_MERGEWITHNEXT = 0b1 << 2;
public static final byte HEAD_SHOULD_MERGE_MASK = 0b1 << 2;
- public static final byte HEAD_SHOULD_MERGE_CLEAR = (byte) 11001011;
-
- public static final byte NO_MERGE = 0b00 << 3;
- public static final byte SHOULD_MERGEWITHNEXT = 0b01 << 3;
- public static final byte SHOULD_MERGEWITHPREV = 0b10 << 3;
- public static final byte SHOULD_MERGE_MASK = 0b11 << 3;
- public static final byte SHOULD_MERGE_CLEAR = 0b1100111;
-
- public static final byte UNCHANGE = 0b0 << 3;
- public static final byte KILL = 0b1 << 3;
- public static final byte KILL_MASK = 0b1 << 3;
-
- public static final byte DIR_FROM_DEADVERTEX = 0b10 << 3;
- public static final byte DEAD_MASK = 0b10 << 3;
+ public static final byte HEAD_SHOULD_MERGE_CLEAR = (byte)1000011;
}
- public static class VertexStateFlag extends FakeFlag {
- public static final byte IS_NON = 0b00 << 5;
- public static final byte IS_HEAD = 0b01 << 5;
- public static final byte IS_FINAL = 0b10 << 5;
+ public static class VertexStateFlag extends HeadMergeDir{
+ public static final byte IS_NON = 0b000 << 3;
+ public static final byte IS_HEAD = 0b001 << 3;
+ public static final byte IS_FINAL = 0b010 << 3;
- public static final byte IS_OLDHEAD = 0b11 << 5;
+ public static final byte IS_OLDHEAD = 0b011 << 3;
- public static final byte IS_HALT = 0b1111110;
- public static final byte IS_DEAD = 0b0111110;
- public static final byte VERTEX_MASK = 0b11 << 5;
- public static final byte VERTEX_CLEAR = (byte) 11001111;
+ public static final byte IS_HALT = 0b100 << 3;
+ public static final byte IS_DEAD = 0b101 << 3;
+
+ public static final byte VERTEX_MASK = 0b111 << 3;
+ public static final byte VERTEX_CLEAR = (byte)1000111;
}
- public static class FakeFlag{
- public static final byte IS_NONFAKE = 0 << 0;
- public static final byte IS_FAKE = 1 << 0;
+ public static class State extends VertexStateFlag{
+ public static final byte NO_MERGE = 0b00 << 0;
+ public static final byte SHOULD_MERGEWITHNEXT = 0b01 << 0;
+ public static final byte SHOULD_MERGEWITHPREV = 0b10 << 0;
+ public static final byte SHOULD_MERGE_MASK = 0b11 << 0;
+ public static final byte SHOULD_MERGE_CLEAR = 0b1111100;
- public static final byte FAKEFLAG_MASK = (byte) 1 << 0;
+ public static final byte IS_NONFAKE = 0 << 6;
+ public static final byte IS_FAKE = 1 << 6;
+
+ public static final byte FAKEFLAG_MASK = (byte) 1 << 6;
}
private byte state;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
index 0ac8dbc..8354b27 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
@@ -126,7 +126,7 @@
else if (getSuperstep() % 4 == 3){
outFlag |= headFlag;
- outFlag |= MessageFlag.NO_MERGE;
+ outFlag |= State.NO_MERGE;
setStateAsNoMerge();
// only PATH vertices are present. Find the ID's for my neighbors
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirFlag.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirFlag.java
deleted file mode 100644
index 451810a..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirFlag.java
+++ /dev/null
@@ -1,12 +0,0 @@
-package edu.uci.ics.genomix.pregelix.type;
-
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
-
-public class DirFlag extends State{
- public static final byte DIR_FF = 0b00 << 0;
- public static final byte DIR_FR = 0b01 << 0;
- public static final byte DIR_RF = 0b10 << 0;
- public static final byte DIR_RR = 0b11 << 0;
- public static final byte DIR_MASK = 0b11 << 0;
- public static final byte DIR_CLEAR = 0b1111100 << 0;
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
index 59a5937..a09aa7e 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
@@ -1,12 +1,29 @@
package edu.uci.ics.genomix.pregelix.type;
-public class MessageFlag extends DirFlag {
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.VertexStateFlag;
+
+public class MessageFlag extends VertexStateFlag {
+ public static final byte DIR_FF = 0b00 << 0;
+ public static final byte DIR_FR = 0b01 << 0;
+ public static final byte DIR_RF = 0b10 << 0;
+ public static final byte DIR_RR = 0b11 << 0;
+ public static final byte DIR_MASK = 0b11 << 0;
+ public static final byte DIR_CLEAR = 0b1111100 << 0;
+
+ public static final byte[] values = { DIR_FF, DIR_FR, DIR_RF, DIR_RR };
+
+ public static final byte UNCHANGE = 0b0 << 6;
+ public static final byte KILL = 0b1 << 6;
+ public static final byte KILL_MASK = 0b1 << 6;
+
+ public static final byte DIR_FROM_DEADVERTEX = 0b1 << 5;
+ public static final byte DEAD_MASK = 0b1 << 5;
+
public static final byte STOP = 0b1 << 2;
public static final byte STOP_MASK = 0b1 << 2;
public static String getFlagAsString(byte code) {
- // TODO: allow multiple flags to be set
return "ERROR_BAD_MESSAGE";
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index ee45ed5..b6e9841 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -83,7 +83,7 @@
}
private static void generateP2ForMergeGraphJob(String jobName, String outputPath) throws IOException {
- PregelixJob job = new PregelixJob(new GenomixJobConf(3), jobName);
+ PregelixJob job = new PregelixJob(new GenomixJobConf(5), jobName);
job.setVertexClass(P2ForPathMergeVertex.class);
job.setGlobalAggregatorClass(StatisticsAggregator.class);
job.setVertexInputFormatClass(P2InitialGraphCleanInputFormat.class);
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
index 191f502..211fd8d 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
@@ -19,7 +19,7 @@
"SimpleTreePath", "ComplexTreePath",
"Triangle", "Rectangle",
"synthetic",
- "SmallGenome"
+// "SmallGenome_5"
};
init(pattern, testSet);
BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();