change script of starting hyracks
diff --git a/genomix/genomix-hyracks/pom.xml b/genomix/genomix-hyracks/pom.xml
index b8dc757..b246a0e 100644
--- a/genomix/genomix-hyracks/pom.xml
+++ b/genomix/genomix-hyracks/pom.xml
@@ -38,7 +38,15 @@
<mainClass>edu.uci.ics.genomix.driver.Driver</mainClass>
<name>genomix</name>
</program>
- </programs>
+ <program>
+ <mainClass>edu.uci.ics.hyracks.control.cc.CCDriver</mainClass>
+ <name>genomixcc</name>
+ </program>
+ <program>
+ <mainClass>edu.uci.ics.hyracks.control.nc.NCDriver</mainClass>
+ <name>genomixnc</name>
+ </program>
+ </programs>
<repositoryLayout>flat</repositoryLayout>
<repositoryName>lib</repositoryName>
</configuration>
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startCluster.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startCluster.sh
index 4727764..843a6b1 100755
--- a/genomix/genomix-hyracks/src/main/resources/scripts/startCluster.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startCluster.sh
@@ -2,18 +2,3 @@
sleep 5
bin/startAllNCs.sh
-. conf/cluster.properties
-# do we need to specify the version somewhere?
-hyrackcmd=`ls ${HYRACKS_HOME}/hyracks-cli/target/hyracks-cli-*-binary-assembly/bin/hyrackscli`
-# find zip file
-appzip=`ls $PWD/../genomix-*-binary-assembly.zip`
-
-[ -f $hyrackcmd ] || { echo "Hyracks commandline is missing"; exit -1;}
-[ -f $appzip ] || { echo "Genomix binary-assembly.zip is missing"; exit -1;}
-
-CCHOST_NAME=`cat conf/master`
-
-IPADDR=`bin/getip.sh`
-echo "connect to \"${IPADDR}:${CC_CLIENTPORT}\"; create application genomix \"$appzip\";" | $hyrackcmd
-echo ""
-
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
index 63b1aca..67023c1 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
@@ -20,6 +20,7 @@
export JAVA_HOME=$JAVA_HOME
export JAVA_OPTS=$CCJAVA_OPTS
+GENOMIX_HOME=`pwd`
+cd $CCTMP_DIR
#Launch hyracks cc script
-chmod -R 755 $HYRACKS_HOME
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyrackscc -client-net-ip-address $CCHOST -cluster-net-ip-address $CCHOST -client-net-port $CC_CLIENTPORT -cluster-net-port $CC_CLUSTERPORT -max-heartbeat-lapse-periods 999999 -default-max-job-attempts 0 -job-history-size 3 &> $CCLOGS_DIR/cc.log &
+${GENOMIX_HOME}/bin/genomixcc -client-net-ip-address $CCHOST -cluster-net-ip-address $CCHOST -client-net-port $CC_CLIENTPORT -cluster-net-port $CC_CLUSTERPORT -max-heartbeat-lapse-periods 999999 -default-max-job-attempts 0 -job-history-size 3 &> $CCLOGS_DIR/cc.log &
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
index 1a45521..bfcc1d4 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
@@ -39,11 +39,10 @@
#Set JAVA_OPTS
export JAVA_OPTS=$NCJAVA_OPTS
-cd $HYRACKS_HOME
-HYRACKS_HOME=`pwd`
+GENOMIX_HOME=`pwd`
#Enter the temp dir
cd $NCTMP_DIR
#Launch hyracks nc
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyracksnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}" &> $NCLOGS_DIR/$NODEID.log &
+${GENOMIX_HOME}/bin/genomixnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}" &> $NCLOGS_DIR/$NODEID.log &
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/stopcc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/stopcc.sh
index 1865054..6d1b2d2 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/stopcc.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/stopcc.sh
@@ -2,9 +2,19 @@
. conf/cluster.properties
#Kill process
-PID=`ps -ef|grep ${USER}|grep java|grep hyracks|awk '{print $2}'`
+PID=`ps -ef|grep ${USER}|grep java|grep 'Dapp.name=genomixcc'|awk '{print $2}'`
+
+if [ "$PID" == "" ]; then
+ PID=`ps -ef|grep ${USER}|grep java|grep 'hyracks'|awk '{print $2}'`
+fi
+
+if [ "$PID" == "" ]; then
+ USERID=`id | sed 's/^uid=//;s/(.*$//'`
+ PID=`ps -ef|grep ${USERID}|grep java|grep 'Dapp.name=genomixcc'|awk '{print $2}'`
+fi
+
echo $PID
-[ "$PID" != "" ] && kill -9 $PID
+kill -9 $PID
#Clean up CC temp dir
rm -rf $CCTMP_DIR/*
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/stopnc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/stopnc.sh
index 3928bb7..092e232 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/stopnc.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/stopnc.sh
@@ -2,15 +2,23 @@
. conf/cluster.properties
#Kill process
-PID=`ps -ef|grep ${USER}|grep java|grep 'Dapp.name=hyracksnc'|awk '{print $2}'`
+PID=`ps -ef|grep ${USER}|grep java|grep 'Dapp.name=genomixnc'|awk '{print $2}'`
+
+if [ "$PID" == "" ]; then
+ PID=`ps -ef|grep ${USER}|grep java|grep 'hyracks'|awk '{print $2}'`
+fi
+
+if [ "$PID" == "" ]; then
+ PID=`ps -ef|grep ${USER}|grep java|grep 'hyracks'|awk '{print $2}'`
+fi
if [ "$PID" == "" ]; then
USERID=`id | sed 's/^uid=//;s/(.*$//'`
- PID=`ps -ef|grep ${USERID}|grep java|grep 'Dapp.name=hyracksnc'|awk '{print $2}'`
+ PID=`ps -ef|grep ${USERID}|grep java|grep 'Dapp.name=genomixnc'|awk '{print $2}'`
fi
echo $PID
-[ "$PID" != "" ] && kill -9 $PID
+kill -9 $PID
#Clean up I/O working dir
io_dirs=$(echo $IO_DIRS | tr "," "\n")