rebalance the partition
git-svn-id: https://hyracks.googlecode.com/svn/branches/fullstack_genomix@3082 123451ca-8445-de46-9d55-352943316053
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
index 95078f8..0f8b4a9 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
@@ -37,7 +37,7 @@
int part = hashBytes(buf.array(), startOffset + fieldOffset + slotLength, fieldLength) % nParts;
if (part < 0){
- part = -(part+1);
+ part = -part;
}
return part;
}
diff --git a/genomix/genomix-hyracks/src/main/resources/conf/cluster.properties b/genomix/genomix-hyracks/src/main/resources/conf/cluster.properties
index eabd81b..2d0eb26 100644
--- a/genomix/genomix-hyracks/src/main/resources/conf/cluster.properties
+++ b/genomix/genomix-hyracks/src/main/resources/conf/cluster.properties
@@ -7,11 +7,12 @@
#The directory of hyracks binaries
HYRACKS_HOME="../../../../hyracks"
+WORKPATH="/mnt/data/sda/space/jjia/hyracks"
#The tmp directory for cc to install jars
-CCTMP_DIR=/tmp/t1
+CCTMP_DIR=${WORKPATH}/tmp/t1
#The tmp directory for nc to install jars
-NCTMP_DIR=/tmp/t2
+NCTMP_DIR=${WORKPATH}/tmp/t2
#The directory to put cc logs
CCLOGS_DIR=$CCTMP_DIR/logs
@@ -20,7 +21,7 @@
NCLOGS_DIR=$NCTMP_DIR/logs
#Comma separated I/O directories for the spilling of external sort
-IO_DIRS="/tmp/t3,/tmp/t4"
+IO_DIRS="/mnt/data/sda/space/jjia/hyracks/tmp/t3,/mnt/data/sdb/space/jjia/hyracks/tmp/t3,/mnt/data/sdc/space/jjia/hyracks/tmp/t3,/mnt/data/sdd/space/jjia/hyracks/tmp/t3"
#The JAVA_HOME
JAVA_HOME=$JAVA_HOME
diff --git a/genomix/genomix-hyracks/src/main/resources/conf/master b/genomix/genomix-hyracks/src/main/resources/conf/master
index 2fbb50c..d71f20c 100644
--- a/genomix/genomix-hyracks/src/main/resources/conf/master
+++ b/genomix/genomix-hyracks/src/main/resources/conf/master
@@ -1 +1 @@
-localhost
+asterix-master
diff --git a/genomix/genomix-hyracks/src/main/resources/conf/slaves b/genomix/genomix-hyracks/src/main/resources/conf/slaves
index 2fbb50c..d5272bc 100644
--- a/genomix/genomix-hyracks/src/main/resources/conf/slaves
+++ b/genomix/genomix-hyracks/src/main/resources/conf/slaves
@@ -1 +1,4 @@
-localhost
+asterix-001
+asterix-003
+asterix-002
+asterix-004
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/genomix b/genomix/genomix-hyracks/src/main/resources/scripts/genomix
index bdd7f20..239a46c 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/genomix
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/genomix
@@ -91,7 +91,7 @@
REPO="$BASEDIR"/lib
fi
-CLASSPATH=$CLASSPATH_PREFIX:"$BASEDIR"/etc:"$REPO"/hyracks-dataflow-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-api-0.2.3-SNAPSHOT.jar:"$REPO"/json-20090211.jar:"$REPO"/httpclient-4.1-alpha2.jar:"$REPO"/httpcore-4.1-beta1.jar:"$REPO"/commons-logging-1.1.1.jar:"$REPO"/commons-codec-1.4.jar:"$REPO"/args4j-2.0.12.jar:"$REPO"/commons-lang3-3.1.jar:"$REPO"/hyracks-dataflow-common-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-data-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-cc-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-common-0.2.3-SNAPSHOT.jar:"$REPO"/jetty-server-8.0.0.RC0.jar:"$REPO"/servlet-api-3.0.20100224.jar:"$REPO"/jetty-continuation-8.0.0.RC0.jar:"$REPO"/jetty-http-8.0.0.RC0.jar:"$REPO"/jetty-io-8.0.0.RC0.jar:"$REPO"/jetty-webapp-8.0.0.RC0.jar:"$REPO"/jetty-xml-8.0.0.RC0.jar:"$REPO"/jetty-util-8.0.0.RC0.jar:"$REPO"/jetty-servlet-8.0.0.RC0.jar:"$REPO"/jetty-security-8.0.0.RC0.jar:"$REPO"/wicket-core-1.5.2.jar:"$REPO"/wicket-util-1.5.2.jar:"$REPO"/wicket-request-1.5.2.jar:"$REPO"/slf4j-api-1.6.1.jar:"$REPO"/slf4j-jcl-1.6.3.jar:"$REPO"/hyracks-control-nc-0.2.3-SNAPSHOT.jar:"$REPO"/dcache-client-0.0.1.jar:"$REPO"/jetty-client-8.0.0.M0.jar:"$REPO"/hyracks-net-0.2.3-SNAPSHOT.jar:"$REPO"/commons-io-1.3.1.jar:"$REPO"/hyracks-ipc-0.2.3-SNAPSHOT.jar:"$REPO"/genomix-0.2.3-SNAPSHOT.pom
+CLASSPATH=$CLASSPATH_PREFIX:"$BASEDIR"/etc:"$REPO"/hyracks-dataflow-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-api-0.2.3-SNAPSHOT.jar:"$REPO"/json-20090211.jar:"$REPO"/httpclient-4.1-alpha2.jar:"$REPO"/httpcore-4.1-beta1.jar:"$REPO"/commons-logging-1.1.1.jar:"$REPO"/args4j-2.0.12.jar:"$REPO"/commons-lang3-3.1.jar:"$REPO"/hyracks-dataflow-common-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-data-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-cc-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-common-0.2.3-SNAPSHOT.jar:"$REPO"/jetty-server-8.0.0.RC0.jar:"$REPO"/servlet-api-3.0.20100224.jar:"$REPO"/jetty-continuation-8.0.0.RC0.jar:"$REPO"/jetty-http-8.0.0.RC0.jar:"$REPO"/jetty-io-8.0.0.RC0.jar:"$REPO"/jetty-webapp-8.0.0.RC0.jar:"$REPO"/jetty-xml-8.0.0.RC0.jar:"$REPO"/jetty-util-8.0.0.RC0.jar:"$REPO"/jetty-servlet-8.0.0.RC0.jar:"$REPO"/jetty-security-8.0.0.RC0.jar:"$REPO"/wicket-core-1.5.2.jar:"$REPO"/wicket-util-1.5.2.jar:"$REPO"/wicket-request-1.5.2.jar:"$REPO"/slf4j-api-1.6.1.jar:"$REPO"/slf4j-jcl-1.6.3.jar:"$REPO"/hyracks-control-nc-0.2.3-SNAPSHOT.jar:"$REPO"/dcache-client-0.0.1.jar:"$REPO"/jetty-client-8.0.0.M0.jar:"$REPO"/hyracks-net-0.2.3-SNAPSHOT.jar:"$REPO"/commons-io-1.3.1.jar:"$REPO"/hyracks-ipc-0.2.3-SNAPSHOT.jar:"$REPO"/hadoop-core-0.20.2.jar:"$REPO"/commons-cli-1.2.jar:"$REPO"/xmlenc-0.52.jar:"$REPO"/commons-httpclient-3.0.1.jar:"$REPO"/commons-codec-1.3.jar:"$REPO"/commons-net-1.4.1.jar:"$REPO"/jetty-6.1.14.jar:"$REPO"/jetty-util-6.1.14.jar:"$REPO"/jasper-runtime-5.5.12.jar:"$REPO"/jasper-compiler-5.5.12.jar:"$REPO"/jsp-api-2.1-6.1.14.jar:"$REPO"/jsp-2.1-6.1.14.jar:"$REPO"/ant-1.6.5.jar:"$REPO"/commons-el-1.0.jar:"$REPO"/jets3t-0.7.1.jar:"$REPO"/servlet-api-2.5-6.1.14.jar:"$REPO"/kfs-0.3.jar:"$REPO"/hsqldb-1.8.0.10.jar:"$REPO"/oro-2.0.8.jar:"$REPO"/core-3.1.1.jar:"$REPO"/hadoop-test-0.20.2.jar:"$REPO"/ftplet-api-1.0.0.jar:"$REPO"/mina-core-2.0.0-M5.jar:"$REPO"/ftpserver-core-1.0.0.jar:"$REPO"/ftpserver-deprecated-1.0.0-M2.jar:"$REPO"/hyracks-hdfs-core-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-hdfs-0.20.2-0.2.3-SNAPSHOT.jar:"$REPO"/genomix-data-0.2.3-SNAPSHOT.jar:"$REPO"/genomix-hyracks-0.2.3-SNAPSHOT.jar
# For Cygwin, switch paths to Windows format before running java
if $cygwin; then
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat b/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat
index 1bd2098..abcafaf 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat
@@ -71,7 +71,7 @@
if "%REPO%"=="" set REPO=%BASEDIR%\lib
-set CLASSPATH="%BASEDIR%"\etc;"%REPO%"\hyracks-dataflow-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-api-0.2.3-SNAPSHOT.jar;"%REPO%"\json-20090211.jar;"%REPO%"\httpclient-4.1-alpha2.jar;"%REPO%"\httpcore-4.1-beta1.jar;"%REPO%"\commons-logging-1.1.1.jar;"%REPO%"\commons-codec-1.4.jar;"%REPO%"\args4j-2.0.12.jar;"%REPO%"\commons-lang3-3.1.jar;"%REPO%"\hyracks-dataflow-common-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-data-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-cc-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-common-0.2.3-SNAPSHOT.jar;"%REPO%"\jetty-server-8.0.0.RC0.jar;"%REPO%"\servlet-api-3.0.20100224.jar;"%REPO%"\jetty-continuation-8.0.0.RC0.jar;"%REPO%"\jetty-http-8.0.0.RC0.jar;"%REPO%"\jetty-io-8.0.0.RC0.jar;"%REPO%"\jetty-webapp-8.0.0.RC0.jar;"%REPO%"\jetty-xml-8.0.0.RC0.jar;"%REPO%"\jetty-util-8.0.0.RC0.jar;"%REPO%"\jetty-servlet-8.0.0.RC0.jar;"%REPO%"\jetty-security-8.0.0.RC0.jar;"%REPO%"\wicket-core-1.5.2.jar;"%REPO%"\wicket-util-1.5.2.jar;"%REPO%"\wicket-request-1.5.2.jar;"%REPO%"\slf4j-api-1.6.1.jar;"%REPO%"\slf4j-jcl-1.6.3.jar;"%REPO%"\hyracks-control-nc-0.2.3-SNAPSHOT.jar;"%REPO%"\dcache-client-0.0.1.jar;"%REPO%"\jetty-client-8.0.0.M0.jar;"%REPO%"\hyracks-net-0.2.3-SNAPSHOT.jar;"%REPO%"\commons-io-1.3.1.jar;"%REPO%"\hyracks-ipc-0.2.3-SNAPSHOT.jar;"%REPO%"\genomix-0.2.3-SNAPSHOT.pom
+set CLASSPATH="%BASEDIR%"\etc;"%REPO%"\hyracks-dataflow-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-api-0.2.3-SNAPSHOT.jar;"%REPO%"\json-20090211.jar;"%REPO%"\httpclient-4.1-alpha2.jar;"%REPO%"\httpcore-4.1-beta1.jar;"%REPO%"\commons-logging-1.1.1.jar;"%REPO%"\args4j-2.0.12.jar;"%REPO%"\commons-lang3-3.1.jar;"%REPO%"\hyracks-dataflow-common-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-data-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-cc-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-common-0.2.3-SNAPSHOT.jar;"%REPO%"\jetty-server-8.0.0.RC0.jar;"%REPO%"\servlet-api-3.0.20100224.jar;"%REPO%"\jetty-continuation-8.0.0.RC0.jar;"%REPO%"\jetty-http-8.0.0.RC0.jar;"%REPO%"\jetty-io-8.0.0.RC0.jar;"%REPO%"\jetty-webapp-8.0.0.RC0.jar;"%REPO%"\jetty-xml-8.0.0.RC0.jar;"%REPO%"\jetty-util-8.0.0.RC0.jar;"%REPO%"\jetty-servlet-8.0.0.RC0.jar;"%REPO%"\jetty-security-8.0.0.RC0.jar;"%REPO%"\wicket-core-1.5.2.jar;"%REPO%"\wicket-util-1.5.2.jar;"%REPO%"\wicket-request-1.5.2.jar;"%REPO%"\slf4j-api-1.6.1.jar;"%REPO%"\slf4j-jcl-1.6.3.jar;"%REPO%"\hyracks-control-nc-0.2.3-SNAPSHOT.jar;"%REPO%"\dcache-client-0.0.1.jar;"%REPO%"\jetty-client-8.0.0.M0.jar;"%REPO%"\hyracks-net-0.2.3-SNAPSHOT.jar;"%REPO%"\commons-io-1.3.1.jar;"%REPO%"\hyracks-ipc-0.2.3-SNAPSHOT.jar;"%REPO%"\hadoop-core-0.20.2.jar;"%REPO%"\commons-cli-1.2.jar;"%REPO%"\xmlenc-0.52.jar;"%REPO%"\commons-httpclient-3.0.1.jar;"%REPO%"\commons-codec-1.3.jar;"%REPO%"\commons-net-1.4.1.jar;"%REPO%"\jetty-6.1.14.jar;"%REPO%"\jetty-util-6.1.14.jar;"%REPO%"\jasper-runtime-5.5.12.jar;"%REPO%"\jasper-compiler-5.5.12.jar;"%REPO%"\jsp-api-2.1-6.1.14.jar;"%REPO%"\jsp-2.1-6.1.14.jar;"%REPO%"\ant-1.6.5.jar;"%REPO%"\commons-el-1.0.jar;"%REPO%"\jets3t-0.7.1.jar;"%REPO%"\servlet-api-2.5-6.1.14.jar;"%REPO%"\kfs-0.3.jar;"%REPO%"\hsqldb-1.8.0.10.jar;"%REPO%"\oro-2.0.8.jar;"%REPO%"\core-3.1.1.jar;"%REPO%"\hadoop-test-0.20.2.jar;"%REPO%"\ftplet-api-1.0.0.jar;"%REPO%"\mina-core-2.0.0-M5.jar;"%REPO%"\ftpserver-core-1.0.0.jar;"%REPO%"\ftpserver-deprecated-1.0.0-M2.jar;"%REPO%"\hyracks-hdfs-core-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-hdfs-0.20.2-0.2.3-SNAPSHOT.jar;"%REPO%"\genomix-data-0.2.3-SNAPSHOT.jar;"%REPO%"\genomix-hyracks-0.2.3-SNAPSHOT.jar
goto endInit
@REM Reaching here means variables are defined and arguments have been captured
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
index 93967e7..63b1aca 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
@@ -10,11 +10,11 @@
#Remove the temp dir
#rm -rf $CCTMP_DIR
-mkdir $CCTMP_DIR
+mkdir -p $CCTMP_DIR
#Remove the logs dir
#rm -rf $CCLOGS_DIR
-mkdir $CCLOGS_DIR
+mkdir -p $CCLOGS_DIR
#Export JAVA_HOME and JAVA_OPTS
export JAVA_HOME=$JAVA_HOME
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
index ceaa7bc..5397244 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
@@ -12,11 +12,11 @@
#Clean up temp dir
#rm -rf $NCTMP_DIR
-mkdir $NCTMP_DIR
+mkdir -p $NCTMP_DIR
#Clean up log dir
#rm -rf $NCLOGS_DIR
-mkdir $NCLOGS_DIR
+mkdir -p $NCLOGS_DIR
#Clean up I/O working dir
@@ -24,7 +24,7 @@
for io_dir in $io_dirs
do
#rm -rf $io_dir
- mkdir $io_dir
+ mkdir -p $io_dir
done
#Set JAVA_HOME