small change on hyracks_genomix
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/resources/scripts/startcc.sh b/genomix/genomix-driver/src/main/resources/scripts/startcc.sh
index e94ad17..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"
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..4912c22 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
@@ -47,7 +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;