Merge branch 'nanzhang/hyracks_genomix' of https://code.google.com/p/hyracks into nanzhang/hyracks_genomix
* 'nanzhang/hyracks_genomix' of https://code.google.com/p/hyracks:
add sinlgelongread test set
frameSize pressure test coding complete
add getclassloader() log for hyracks' driver
change the stat package name in graph building of hyracks
add graphviz mac version for graph building of hyracks
add frame size pressure test package in driver
Conflicts:
genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/graph/test/ParameteredTestCaseForSet.java
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixClusterManager.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixClusterManager.java
index 5d41ae2..8ffe16f 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixClusterManager.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixClusterManager.java
@@ -265,6 +265,8 @@
Process p = Runtime.getRuntime().exec(startNCCmd);
p.waitFor(); // wait for ssh
Thread.sleep(sleepms); // wait for NC -> CC registration
+ System.out.println("\nstdout: " + IOUtils.toString(p.getInputStream()) + "\nstderr: "
+ + IOUtils.toString(p.getErrorStream()));
if (p.exitValue() != 0)
throw new RuntimeException("Failed to start the" + type + " NC's! Script returned exit code: "
+ p.exitValue() + "\nstdout: " + IOUtils.toString(p.getInputStream()) + "\nstderr: "
diff --git a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java b/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
index 8da514c..8402da0 100644
--- a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
+++ b/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
@@ -268,7 +268,7 @@
// Patterns.TIP_REMOVE, Patterns.MERGE,
// Patterns.BUBBLE, Patterns.MERGE,
// GenomixJobConf conf = GenomixJobConf.fromArguments(args);
- GenomixJobConf conf = GenomixJobConf.fromArguments(myArgs);
+ GenomixJobConf conf = GenomixJobConf.fromArguments(args);
GenomixDriver driver = new GenomixDriver();
driver.runGenomix(conf);
}
diff --git a/genomix/genomix-driver/src/main/resources/conf/cluster.properties b/genomix/genomix-driver/src/main/resources/conf/cluster.properties
index a083848..57aa1fa 100644
--- a/genomix/genomix-driver/src/main/resources/conf/cluster.properties
+++ b/genomix/genomix-driver/src/main/resources/conf/cluster.properties
@@ -42,9 +42,9 @@
JOB_HISTORY_SIZE=50
#CC JAVA_OPTS
-CCJAVA_OPTS="-Xrunjdwp:transport=dt_socket,address=7001,server=y,suspend=n -Xmx5g -Djava.util.logging.config.file=logging.properties"
+CCJAVA_OPTS="-Xrunjdwp:transport=dt_socket,address=7001,server=y,suspend=n -Xmx5g -Djava.util.logging.config.file=conf/logging.properties"
# Yourkit option: -agentpath:/grid/0/dev/vborkar/tools/yjp-10.0.4/bin/linux-x86-64/libyjpagent.so=port=20001"
#NC JAVA_OPTS
-NCJAVA_OPTS="-Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx10g -Djava.util.logging.config.file=logging.properties"
+NCJAVA_OPTS="-Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx10g -Djava.util.logging.config.file=conf/logging.properties"
diff --git a/genomix/genomix-driver/src/main/resources/conf/logging.properties b/genomix/genomix-driver/src/main/resources/conf/logging.properties
new file mode 100644
index 0000000..a0f9d77
--- /dev/null
+++ b/genomix/genomix-driver/src/main/resources/conf/logging.properties
@@ -0,0 +1,68 @@
+############################################################
+# Default Logging Configuration File
+#
+# You can use a different file by specifying a filename
+# with the java.util.logging.config.file system property.
+# For example java -Djava.util.logging.config.file=myfile
+############################################################
+
+############################################################
+# Global properties
+############################################################
+
+# "handlers" specifies a comma separated list of log Handler
+# classes. These handlers will be installed during VM startup.
+# Note that these classes must be on the system classpath.
+# By default we only configure a ConsoleHandler, which will only
+# show messages at the INFO and above levels.
+
+handlers= java.util.logging.ConsoleHandler
+
+# To also add the FileHandler, use the following line instead.
+
+#handlers= java.util.logging.FileHandler, java.util.logging.ConsoleHandler
+
+# Default global logging level.
+# This specifies which kinds of events are logged across
+# all loggers. For any given facility this global level
+# can be overriden by a facility specific level
+# Note that the ConsoleHandler also has a separate level
+# setting to limit messages printed to the console.
+
+#.level= SEVERE
+ .level= INFO
+# .level= FINE
+# .level = FINEST
+
+############################################################
+# Handler specific properties.
+# Describes specific configuration info for Handlers.
+############################################################
+
+# default file output is in user's home directory.
+
+# java.util.logging.FileHandler.pattern = %h/java%u.log
+# java.util.logging.FileHandler.limit = 50000
+# java.util.logging.FileHandler.count = 1
+# java.util.logging.FileHandler.formatter = java.util.logging.XMLFormatter
+# java.util.logging.FileHandler.formatter = java.util.logging.SimpleFormatter
+
+# Limit the message that are printed on the console to FINE and above.
+
+java.util.logging.ConsoleHandler.level = FINEST
+java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
+
+
+############################################################
+# Facility specific properties.
+# Provides extra control for each logger.
+############################################################
+
+# For example, set the com.xyz.foo logger to only log SEVERE
+# messages:
+
+#edu.uci.ics.genomix.pregelix = INFO
+#edu.uci.ics.asterix.level = FINE
+#edu.uci.ics.algebricks.level = FINE
+#edu.uci.ics.hyracks.level = SEVERE
+#edu.uci.ics.hyracks.control.nc.net.level = FINE
diff --git a/genomix/genomix-driver/src/main/resources/scripts/startcc.sh b/genomix/genomix-driver/src/main/resources/scripts/startcc.sh
index 8f160b9..b6aaee2 100755
--- a/genomix/genomix-driver/src/main/resources/scripts/startcc.sh
+++ b/genomix/genomix-driver/src/main/resources/scripts/startcc.sh
@@ -1,6 +1,7 @@
#!/bin/bash
set -e
set -o pipefail
+set -x
GENOMIX_HOME="$( dirname "$( cd "$(dirname "$0")" ; pwd -P )" )" # script's parent dir's parent
cd "$GENOMIX_HOME"
@@ -50,7 +51,7 @@
#Launch cc script
printf "\n\n\n********************************************\nStarting CC with command %s\n\n" "$CMD" >> "$CCLOGS_DIR"/cc.log
-eval "$CMD &>> \"$CCLOGS_DIR\"/cc.log &"
+eval "$CMD >>\"$CCLOGS_DIR/cc.log\" 2>&1 &"
# save the PID of the process we just launched
PID=$!
diff --git a/genomix/genomix-driver/src/main/resources/scripts/startnc.sh b/genomix/genomix-driver/src/main/resources/scripts/startnc.sh
index ea926e5..02d8f97 100755
--- a/genomix/genomix-driver/src/main/resources/scripts/startnc.sh
+++ b/genomix/genomix-driver/src/main/resources/scripts/startnc.sh
@@ -62,7 +62,7 @@
printf "\n\n\n********************************************\nStarting NC with command %s\n\n" "$CMD" >> "$NCLOGS_DIR"/$NODEID.log
#Launch nc
-eval "$CMD &>> \"$NCLOGS_DIR\"/$NODEID.log &"
+eval "$CMD >> \"$NCLOGS_DIR/$NODEID.log\" 2>&1 &"
echo $! # write PID of bg'ed script
diff --git a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/realtests/FrameSizePressureTest.java b/genomix/genomix-driver/src/test/java/edu/uci/ics/genomix/driver/realtests/FrameSizePressureTest.java
similarity index 78%
rename from genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/realtests/FrameSizePressureTest.java
rename to genomix/genomix-driver/src/test/java/edu/uci/ics/genomix/driver/realtests/FrameSizePressureTest.java
index 8044792..67c0360 100644
--- a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/realtests/FrameSizePressureTest.java
+++ b/genomix/genomix-driver/src/test/java/edu/uci/ics/genomix/driver/realtests/FrameSizePressureTest.java
@@ -25,8 +25,12 @@
test.cleanDiskFile();
test.generateString();
test.writeToDisk();
- String[] fsPressureArgs = { "-kmerLength", String.valueOf(options.kmerLength), "-coresPerMachine",
- String.valueOf(options.coresPerMachine), "-saveIntermediateResults", "true", "-localInput",
+ System.out.println(System.getProperty("java.class.path"));
+ System.out.println(System.getenv("HADOOP_HOME"));
+ System.out.println(System.getenv("JAVA_HOME"));
+ String[] fsPressureArgs = { "-kmerLength", String.valueOf(options.kmerLength),
+// "-coresPerMachine", String.valueOf(options.coresPerMachine),
+ "-saveIntermediateResults", "true", "-localInput",
test.getTestDir(), "-pipelineOrder", "BUILD_HYRACKS,MERGE" };
GenomixDriver.main(fsPressureArgs);
}
diff --git a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/realtests/SingleLongReadCreateTool.java b/genomix/genomix-driver/src/test/java/edu/uci/ics/genomix/driver/realtests/SingleLongReadCreateTool.java
similarity index 100%
rename from genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/realtests/SingleLongReadCreateTool.java
rename to genomix/genomix-driver/src/test/java/edu/uci/ics/genomix/driver/realtests/SingleLongReadCreateTool.java
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/graph/test/ParameteredTestCaseForSet.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/graph/test/ParameteredTestCaseForSet.java
index 5391a8d..beb41f3 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/graph/test/ParameteredTestCaseForSet.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/graph/test/ParameteredTestCaseForSet.java
@@ -47,8 +47,7 @@
@SuppressWarnings("deprecation")
@RunWith(value = Parameterized.class)
public class ParameteredTestCaseForSet {
- public static final DirType testSetType = DirType.SPLITREPEAT;
-
+ public static final DirType testSetType = DirType.SINGLEREAD;
public String dataPath;
public int KmerSize;