format the code
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 3e494ba..209e5e2 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
@@ -10,7 +10,7 @@
import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeInputFormat;
import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.TwoStepLogAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.LogAlgorithmForPathMergeVertex;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -27,7 +27,7 @@
job.setDynamicVertexValueSize(true);
job.setOutputKeyClass(KmerBytesWritable.class);
job.setOutputValueClass(ValueStateWritable.class);
- job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 55);
+ job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 5);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
}
@@ -35,20 +35,20 @@
generateNaiveAlgorithmForMergeGraphJob("NaiveAlgorithmForMergeGraph", outputBase + "NaiveAlgorithmForMergeGraph.xml");
}
- private static void generateTwoStepLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
+ private static void generateLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
PregelixJob job = new PregelixJob(jobName);
- job.setVertexClass(TwoStepLogAlgorithmForPathMergeVertex.class);
+ job.setVertexClass(LogAlgorithmForPathMergeVertex.class);
job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class);
job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class);
job.setDynamicVertexValueSize(true);
job.setOutputKeyClass(KmerBytesWritable.class);
job.setOutputValueClass(ValueStateWritable.class);
- job.getConfiguration().setInt(TwoStepLogAlgorithmForPathMergeVertex.KMER_SIZE, 5);
+ job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, 5);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
}
- private static void genTwoStepLogAlgorithmForMergeGraph() throws IOException {
- generateTwoStepLogAlgorithmForMergeGraphJob("TwoStepLogAlgorithmForMergeGraph", outputBase + "TwoStepLogAlgorithmForMergeGraph.xml");
+ private static void genLogAlgorithmForMergeGraph() throws IOException {
+ generateLogAlgorithmForMergeGraphJob("LogAlgorithmForMergeGraph", outputBase + "LogAlgorithmForMergeGraph.xml");
}
/**
@@ -57,7 +57,7 @@
*/
public static void main(String[] args) throws IOException {
genNaiveAlgorithmForMergeGraph();
- genTwoStepLogAlgorithmForMergeGraph();
+ genLogAlgorithmForMergeGraph();
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestCase.java
new file mode 100644
index 0000000..1acf79b
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestCase.java
@@ -0,0 +1,89 @@
+/*
+ * Copyright 2009-2010 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.pregelix.JobRun;
+
+import junit.framework.TestCase;
+
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
+import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
+import org.junit.Test;
+
+import edu.uci.ics.genomix.pregelix.sequencefile.GenerateTextFile;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+import edu.uci.ics.pregelix.core.base.IDriver.Plan;
+import edu.uci.ics.pregelix.core.driver.Driver;
+import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
+
+public class PathMergeSmallTestCase extends TestCase {
+ private final PregelixJob job;
+ private final String resultFileDir;
+ private final String textFileDir;
+ private final String jobFile;
+ private final Driver driver = new Driver(this.getClass());
+ private final FileSystem dfs;
+
+ public PathMergeSmallTestCase(String hadoopConfPath, String jobName,
+ String jobFile, FileSystem dfs, String hdfsInput, String resultFile, String textFile)
+ throws Exception {
+ super("test");
+ this.jobFile = jobFile;
+ this.job = new PregelixJob("test");
+ this.job.getConfiguration().addResource(new Path(jobFile));
+ this.job.getConfiguration().addResource(new Path(hadoopConfPath));
+ FileInputFormat.setInputPaths(job, hdfsInput);
+ FileOutputFormat.setOutputPath(job, new Path(hdfsInput + "_result"));
+ this.textFileDir = textFile;
+ job.setJobName(jobName);
+ this.resultFileDir = resultFile;
+
+ this.dfs = dfs;
+ }
+
+ private void waitawhile() throws InterruptedException {
+ synchronized (this) {
+ this.wait(20);
+ }
+ }
+
+ @Test
+ public void test() throws Exception {
+ setUp();
+ Plan[] plans = new Plan[] { Plan.OUTER_JOIN };
+ for (Plan plan : plans) {
+ driver.runJob(job, plan, PregelixHyracksIntegrationUtil.CC_HOST,
+ PregelixHyracksIntegrationUtil.TEST_HYRACKS_CC_CLIENT_PORT,
+ false);
+ }
+ compareResults();
+ tearDown();
+ waitawhile();
+ }
+
+ private void compareResults() throws Exception {
+ dfs.copyToLocalFile(FileOutputFormat.getOutputPath(job), new Path(
+ resultFileDir));
+ GenerateTextFile.generateFromPathmergeResult(5, resultFileDir, textFileDir);
+ // TestUtils.compareWithResultDir(new File(expectedFileDir), new
+ // File(resultFileDir));
+ }
+
+ public String toString() {
+ return jobFile;
+ }
+
+}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
new file mode 100644
index 0000000..956a646
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
@@ -0,0 +1,234 @@
+/*
+ * Copyright 2009-2010 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.genomix.pregelix.JobRun;
+
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import junit.framework.Test;
+import junit.framework.TestResult;
+import junit.framework.TestSuite;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hdfs.MiniDFSCluster;
+import org.apache.hadoop.mapred.JobConf;
+
+import edu.uci.ics.pregelix.core.jobgen.clusterconfig.ClusterConfig;
+import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
+
+@SuppressWarnings("deprecation")
+public class PathMergeSmallTestSuite extends TestSuite {
+ private static final Logger LOGGER = Logger
+ .getLogger(PathMergeSmallTestSuite.class.getName());
+
+ public static final String PreFix = "data/PathTestSet"; //"graphbuildresult";
+ public static final String[] TestDir = { PreFix + File.separator
+ //+ "split.aa"};
+ ///+ "split.aa"};/*, PreFix + File.separator
+ /*+ "CyclePath", PreFix + File.separator
+ + "SimplePath", PreFix + File.separator
+ + "SinglePath", PreFix + File.separator
+ + "TreePath"};*/
+ + "2", PreFix + File.separator
+ + "3", PreFix + File.separator
+ + "4", PreFix + File.separator
+ + "5", PreFix + File.separator
+ + "6", PreFix + File.separator
+ + "7", PreFix + File.separator
+ + "8", PreFix + File.separator
+ + "9", PreFix + File.separator
+ + "TwoKmer", PreFix + File.separator
+ + "ThreeKmer", PreFix + File.separator
+ + "SinglePath", PreFix + File.separator
+ + "SimplePath", PreFix + File.separator
+ + "Path", PreFix + File.separator
+ + "BridgePath", PreFix + File.separator
+ + "CyclePath", PreFix + File.separator
+ + "RingPath", PreFix + File.separator
+ + "LongPath", PreFix + File.separator
+ + "TreePath"};
+ private static final String ACTUAL_RESULT_DIR = "actual";
+ private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
+ private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
+ private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
+ private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
+ private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
+
+ public static final String HDFS_INPUTPATH = "/PathTestSet";
+
+ private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR
+ + File.separator + "conf.xml";
+ private MiniDFSCluster dfsCluster;
+
+ private JobConf conf = new JobConf();
+ private int numberOfNC = 2;
+
+ public void setUp() throws Exception {
+ ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
+ ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
+ cleanupStores();
+ PregelixHyracksIntegrationUtil.init("src/test/resources/topology.xml");
+ LOGGER.info("Hyracks mini-cluster started");
+ FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+ FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+ startHDFS();
+ }
+
+ private void startHDFS() throws IOException {
+ conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
+ conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
+ conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
+ FileSystem lfs = FileSystem.getLocal(new Configuration());
+ lfs.delete(new Path("build"), true);
+ System.setProperty("hadoop.log.dir", "logs");
+ dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
+ FileSystem dfs = FileSystem.get(conf);
+
+ for (String testDir : TestDir) {
+ File src = new File(testDir);
+ Path dest = new Path(HDFS_INPUTPATH + File.separator + src.getName());
+ dfs.mkdirs(dest);
+ //src.listFiles()
+ //src.listFiles((FilenameFilter)(new WildcardFileFilter("part*")))
+ for (File f : src.listFiles()){
+ dfs.copyFromLocalFile(new Path(f.getAbsolutePath()), dest);
+ }
+ }
+
+ DataOutputStream confOutput = new DataOutputStream(
+ new FileOutputStream(new File(HADOOP_CONF_PATH)));
+ conf.writeXml(confOutput);
+ confOutput.flush();
+ confOutput.close();
+ }
+
+ private void cleanupStores() throws IOException {
+ FileUtils.forceMkdir(new File("teststore"));
+ FileUtils.forceMkdir(new File("build"));
+ FileUtils.cleanDirectory(new File("teststore"));
+ FileUtils.cleanDirectory(new File("build"));
+ }
+
+ /**
+ * cleanup hdfs cluster
+ */
+ private void cleanupHDFS() throws Exception {
+ dfsCluster.shutdown();
+ }
+
+ public void tearDown() throws Exception {
+ PregelixHyracksIntegrationUtil.deinit();
+ LOGGER.info("Hyracks mini-cluster shut down");
+ cleanupHDFS();
+ }
+
+ public static Test suite() throws Exception {
+ List<String> onlys = getFileList(PATH_TO_ONLY);
+ File testData = new File(PATH_TO_JOBS);
+ File[] queries = testData.listFiles();
+ PathMergeSmallTestSuite testSuite = new PathMergeSmallTestSuite();
+ testSuite.setUp();
+ boolean onlyEnabled = false;
+ FileSystem dfs = FileSystem.get(testSuite.conf);
+
+ if (onlys.size() > 0) {
+ onlyEnabled = true;
+ }
+
+ for (File qFile : queries) {
+ if (qFile.isFile()) {
+ if (onlyEnabled && !isInList(onlys, qFile.getName())) {
+ continue;
+ } else {
+ for (String testPathStr : TestDir) {
+ File testDir = new File(testPathStr);
+ String resultFileName = ACTUAL_RESULT_DIR
+ + File.separator
+ + jobExtToResExt(qFile.getName())
+ + File.separator + "bin"
+ + File.separator + testDir.getName();
+ String textFileName = ACTUAL_RESULT_DIR
+ + File.separator
+ + jobExtToResExt(qFile.getName())
+ + File.separator + "txt"
+ + File.separator + testDir.getName();
+ testSuite.addTest(new PathMergeSmallTestCase(
+ HADOOP_CONF_PATH, qFile.getName(), qFile
+ .getAbsolutePath().toString(),
+ dfs, HDFS_INPUTPATH + File.separator + testDir.getName(),
+ resultFileName, textFileName));
+ }
+ }
+ }
+ }
+ return testSuite;
+ }
+
+ /**
+ * Runs the tests and collects their result in a TestResult.
+ */
+ @Override
+ public void run(TestResult result) {
+ try {
+ int testCount = countTestCases();
+ for (int i = 0; i < testCount; i++) {
+ // cleanupStores();
+ Test each = this.testAt(i);
+ if (result.shouldStop())
+ break;
+ runTest(each, result);
+ }
+ tearDown();
+ } catch (Exception e) {
+ throw new IllegalStateException(e);
+ }
+ }
+
+ protected static List<String> getFileList(String ignorePath)
+ throws FileNotFoundException, IOException {
+ BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
+ String s = null;
+ List<String> ignores = new ArrayList<String>();
+ while ((s = reader.readLine()) != null) {
+ ignores.add(s);
+ }
+ reader.close();
+ return ignores;
+ }
+
+ private static String jobExtToResExt(String fname) {
+ int dot = fname.lastIndexOf('.');
+ return fname.substring(0, dot);
+ }
+
+ private static boolean isInList(List<String> onlys, String name) {
+ for (String only : onlys)
+ if (name.indexOf(only) >= 0)
+ return true;
+ return false;
+ }
+
+}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/ResultGen/ReportGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/ResultGen/ReportGenerator.java
index 3281a3b..00298a3 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/ResultGen/ReportGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/ResultGen/ReportGenerator.java
@@ -10,8 +10,8 @@
import org.apache.commons.io.FileUtils;
public class ReportGenerator {
- public static final String PATH_TO_REPORT = "report/";
- public static final String PATH_TO_LOGINFO = "log/";
+ public static final String PATH_TO_REPORT = "report";
+ public static final String PATH_TO_LOGINFO = "log";
public static void generateReportFromLoginfo(String fileName) throws Exception {
DecimalFormat df = new DecimalFormat("0.00");
@@ -41,10 +41,10 @@
public static void main(String[] args) throws Exception {
FileUtils.forceMkdir(new File(PATH_TO_REPORT));
FileUtils.cleanDirectory(new File(PATH_TO_REPORT));
- generateReportFromLoginfo("naive");
- generateReportFromLoginfo("log");
- generateReportFromLoginfo("log_yourkit");
+ generateReportFromLoginfo("naive_converge");
+ generateReportFromLoginfo("log_converge");
generateReportFromLoginfo("naive_36");
generateReportFromLoginfo("log_13");
+
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
index 5681ae0..6d4e421 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
@@ -30,6 +30,7 @@
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.KmerCountValue;
+@SuppressWarnings("deprecation")
public class GraphBuildTest {
private static final String ACTUAL_RESULT_DIR = "graphbuildresult";
private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
@@ -128,14 +129,12 @@
private boolean checkResults(String expectedPath) throws Exception {
- File dumped = null;
String format = conf.get(GenomixJob.OUTPUT_FORMAT);
if ("text".equalsIgnoreCase(format)) {
FileUtil.copyMerge(FileSystem.get(conf),
new Path(HDFS_OUTPUT_PATH), FileSystem
.getLocal(new Configuration()), new Path(
DUMPED_RESULT), false, conf, null);
- dumped = new File(DUMPED_RESULT);
} else {
FileSystem.getLocal(new Configuration()).mkdirs(
@@ -173,7 +172,6 @@
reader.close();
}
bw.close();
- dumped = new File(CONVERT_RESULT);
}
// TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
index 54cecbc..afd2477 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
@@ -20,13 +20,13 @@
public class MergePathTest {
public static final String PATH_TO_TESTSTORE = "testcase/pathmerge/";
//"genomix_result/pathmerge/new_naive";
- public static final String NAIVE_DATA_INPUT = "genomix_result/pathmerge/naive_newest";//"actual/NaiveAlgorithmForMergeGraph/BinaryOutput/test";
+ public static final String NAIVE_DATA_INPUT = "genomix_result/P1_nc8";//"actual/NaiveAlgorithmForMergeGraph/BinaryOutput/test";
//"genomix_result/pathmerge/new_log";
- public static final String LOG_DATA_INPUT = "genomix_result/pathmerge/log_newest";//"actual/TwoStepLogAlgorithmForMergeGraph/BinaryOutput/test";
+ public static final String LOG_DATA_INPUT = "genomix_result/P2_nc8";//"actual/TwoStepLogAlgorithmForMergeGraph/BinaryOutput/test";
public static final String TEXT_OUTPUT = PATH_TO_TESTSTORE + "textfile";
public static final String CHAIN_OUTPUT = PATH_TO_TESTSTORE + "chain";
- private static int nc = 4;
+ private static int nc = 8;
private static int kmerSize = 55;
private static int maxLength = 102;
@@ -58,18 +58,26 @@
if (key == null || value == null){
break;
}
- if(value.getLengthOfMergeChain() != 0
- && value.getLengthOfMergeChain() != -1
- && value.getState() == State.FINAL_VERTEX){
+ //if(value.getState() == State.FINAL_VERTEX){
+ /*bw.write(value.getMergeChain().toString()
+ + "\t" + GeneCode.getSymbolFromBitMap(value.getAdjMap()));
+ bw.newLine();*/
+ bw.write(key.toString()
+ + "\t" + value.toString());
+ bw.newLine();
+ //}
+ //if(value.getLengthOfMergeChain() != 0
+ // && value.getLengthOfMergeChain() != -1
+ // && value.getState() == State.FINAL_VERTEX){
//bw.write(key.toString() + "\t" +
// value.toString());
- bw.write(value.getLengthOfMergeChain() + "\t" +
- value.getMergeChain().toString() + "\t" +
- GeneCode.getSymbolFromBitMap(value.getAdjMap()) + "\t" +
- value.getState());
- //+ "\t" + key.toString());
- bw.newLine();
- }
+ //bw.write(value.getLengthOfMergeChain() + "\t" +
+ // value.getMergeChain().toString() + "\t" +
+ // GeneCode.getSymbolFromBitMap(value.getAdjMap()) + "\t" +
+ // key.toString());
+ //value.getState());
+
+ //}
}
reader.close();
}
diff --git a/genomix/genomix-pregelix/src/test/resources/cluster/cluster.properties b/genomix/genomix-pregelix/src/test/resources/cluster/cluster.properties
index 94eb599..0c6abd1 100644
--- a/genomix/genomix-pregelix/src/test/resources/cluster/cluster.properties
+++ b/genomix/genomix-pregelix/src/test/resources/cluster/cluster.properties
@@ -20,7 +20,7 @@
NCLOGS_DIR=$NCTMP_DIR/logs
#Comma separated I/O directories for the spilling of external sort
-IO_DIRS="/tmp/t3,/tmp/t4"
+IO_DIRS="/tmp/t3,/tmp/t4,/tmp/t5,/tmp/t6"
#The JAVA_HOME
JAVA_HOME=$JAVA_HOME
@@ -33,5 +33,5 @@
# 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="-Xdebug -Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
+NCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx3g -Djava.util.logging.config.file=genomix-pregelix/src/test/resources/logging.properties"
diff --git a/genomix/genomix-pregelix/src/test/resources/cluster/stores.properties b/genomix/genomix-pregelix/src/test/resources/cluster/stores.properties
index 04732be..2daf1ee 100644
--- a/genomix/genomix-pregelix/src/test/resources/cluster/stores.properties
+++ b/genomix/genomix-pregelix/src/test/resources/cluster/stores.properties
@@ -1 +1 @@
-store=teststore1,teststore2
\ No newline at end of file
+store=teststore1,teststore2,teststore3,teststore4,
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/test/resources/logging.properties b/genomix/genomix-pregelix/src/test/resources/logging.properties
index b8f2be9..0ed3dfc 100644
--- a/genomix/genomix-pregelix/src/test/resources/logging.properties
+++ b/genomix/genomix-pregelix/src/test/resources/logging.properties
@@ -60,6 +60,7 @@
# 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