diff --git a/genomix/genomix-hadoop/actual/conf.xml b/genomix/genomix-hadoop/actual/conf.xml
index 1ca97f3..d544e83 100755
--- a/genomix/genomix-hadoop/actual/conf.xml
+++ b/genomix/genomix-hadoop/actual/conf.xml
@@ -12,7 +12,7 @@
 <property><name>dfs.namenode.logging.level</name><value>info</value></property>
 <property><name>dfs.datanode.address</name><value>127.0.0.1:0</value></property>
 <property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>fs.default.name</name><value>hdfs://localhost:63103</value></property>
+<property><name>fs.default.name</name><value>hdfs://localhost:58914</value></property>
 <property><name>mapred.child.tmp</name><value>./tmp</value></property>
 <property><name>fs.har.impl.disable.cache</name><value>true</value></property>
 <property><name>dfs.safemode.threshold.pct</name><value>0.999f</value></property>
@@ -125,7 +125,7 @@
 <property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
 <property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
 <property><name>dfs.namenode.decommission.interval</name><value>3</value></property>
-<property><name>dfs.http.address</name><value>localhost:63104</value></property>
+<property><name>dfs.http.address</name><value>localhost:58915</value></property>
 <property><name>dfs.heartbeat.interval</name><value>3</value></property>
 <property><name>mapred.job.tracker</name><value>local</value></property>
 <property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
diff --git a/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs/dataflow/ConfFactory.java b/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs/dataflow/ConfFactory.java
index aa75019..4fa0164 100644
--- a/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs/dataflow/ConfFactory.java
+++ b/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs/dataflow/ConfFactory.java
@@ -11,7 +11,7 @@
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 
 @SuppressWarnings("deprecation")
-class ConfFactory implements Serializable {
+public class ConfFactory implements Serializable {
     private static final long serialVersionUID = 1L;
     private byte[] confBytes;
 
diff --git a/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs/dataflow/InputSplitsFactory.java b/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs/dataflow/InputSplitsFactory.java
index e7227d2..9cc9ebc 100644
--- a/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs/dataflow/InputSplitsFactory.java
+++ b/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs/dataflow/InputSplitsFactory.java
@@ -28,7 +28,7 @@
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 
 @SuppressWarnings({ "deprecation", "rawtypes" })
-class InputSplitsFactory implements Serializable {
+public class InputSplitsFactory implements Serializable {
 
     private static final long serialVersionUID = 1L;
     private byte[] splitBytes;
diff --git a/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs2/dataflow/FileSplitsFactory.java b/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs2/dataflow/FileSplitsFactory.java
index 01fc2f3..14dc70c 100644
--- a/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs2/dataflow/FileSplitsFactory.java
+++ b/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs2/dataflow/FileSplitsFactory.java
@@ -30,7 +30,7 @@
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 
 @SuppressWarnings("rawtypes")
-class FileSplitsFactory implements Serializable {
+public class FileSplitsFactory implements Serializable {
 
     private static final long serialVersionUID = 1L;
     private byte[] splitBytes;
diff --git a/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs2/dataflow/HDFSReadOperatorDescriptor.java b/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs2/dataflow/HDFSReadOperatorDescriptor.java
index 22559e6..8a1ba6d 100644
--- a/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs2/dataflow/HDFSReadOperatorDescriptor.java
+++ b/hyracks/hyracks-hdfs/src/main/java/edu/uci/ics/hyracks/hdfs2/dataflow/HDFSReadOperatorDescriptor.java
@@ -125,7 +125,6 @@
                             synchronized (executed) {
                                 if (executed[i] == false) {
                                     executed[i] = true;
-                                    System.out.println("thread " + Thread.currentThread().getId() + " setting " + i);
                                 } else {
                                     continue;
                                 }
diff --git a/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/io/BasicGenInputSplit.java b/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/io/BasicGenInputSplit.java
index 7179737..ea33691 100644
--- a/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/io/BasicGenInputSplit.java
+++ b/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/io/BasicGenInputSplit.java
@@ -21,60 +21,64 @@
 import java.io.Serializable;
 
 import org.apache.hadoop.io.Writable;
-import org.apache.hadoop.mapreduce.InputSplit;
+import org.apache.hadoop.mapreduce.lib.input.FileSplit;
 
 /**
  * This InputSplit will not give any ordering or location data. It is used
  * internally by BspInputFormat (which determines how many tasks to run the
  * application on). Users should not use this directly.
  */
-public class BasicGenInputSplit extends InputSplit implements Writable, Serializable {
-    private static final long serialVersionUID = 1L;
-    /** Number of splits */
-    private int numSplits = -1;
-    /** Split index */
-    private int splitIndex = -1;
+public class BasicGenInputSplit extends FileSplit implements Writable,
+		Serializable {
+	private static final long serialVersionUID = 1L;
+	/** Number of splits */
+	private int numSplits = -1;
+	/** Split index */
+	private int splitIndex = -1;
 
-    public BasicGenInputSplit() {
-    }
+	public BasicGenInputSplit() {
+		super(null, 0, 0, null);
+	}
 
-    public BasicGenInputSplit(int splitIndex, int numSplits) {
-        this.splitIndex = splitIndex;
-        this.numSplits = numSplits;
-    }
+	public BasicGenInputSplit(int splitIndex, int numSplits) {
+		super(null, 0, 0, null);
+		this.splitIndex = splitIndex;
+		this.numSplits = numSplits;
+	}
 
-    @Override
-    public long getLength() throws IOException, InterruptedException {
-        return 0;
-    }
+	@Override
+	public long getLength() {
+		return 0;
+	}
 
-    @Override
-    public String[] getLocations() throws IOException, InterruptedException {
-        return new String[] {};
-    }
+	@Override
+	public String[] getLocations() throws IOException {
+		return new String[] {};
+	}
 
-    @Override
-    public void readFields(DataInput in) throws IOException {
-        splitIndex = in.readInt();
-        numSplits = in.readInt();
-    }
+	@Override
+	public void readFields(DataInput in) throws IOException {
+		splitIndex = in.readInt();
+		numSplits = in.readInt();
+	}
 
-    @Override
-    public void write(DataOutput out) throws IOException {
-        out.writeInt(splitIndex);
-        out.writeInt(numSplits);
-    }
+	@Override
+	public void write(DataOutput out) throws IOException {
+		out.writeInt(splitIndex);
+		out.writeInt(numSplits);
+	}
 
-    public int getSplitIndex() {
-        return splitIndex;
-    }
+	public int getSplitIndex() {
+		return splitIndex;
+	}
 
-    public int getNumSplits() {
-        return numSplits;
-    }
+	public int getNumSplits() {
+		return numSplits;
+	}
 
-    @Override
-    public String toString() {
-        return "'" + getClass().getCanonicalName() + ", index=" + getSplitIndex() + ", num=" + getNumSplits();
-    }
+	@Override
+	public String toString() {
+		return "'" + getClass().getCanonicalName() + ", index="
+				+ getSplitIndex() + ", num=" + getNumSplits();
+	}
 }
diff --git a/pregelix/pregelix-core/pom.xml b/pregelix/pregelix-core/pom.xml
index 1618810..34faa82 100644
--- a/pregelix/pregelix-core/pom.xml
+++ b/pregelix/pregelix-core/pom.xml
@@ -1,4 +1,5 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>pregelix-core</artifactId>
 	<packaging>jar</packaging>
@@ -57,20 +58,6 @@
 							</includes>
 						</configuration>
 					</execution>
-					<execution>
-						<id>patch</id>
-						<goals>
-							<goal>jar</goal>
-						</goals>
-						<phase>package</phase>
-						<configuration>
-							<classifier>patch</classifier>
-							<finalName>a-hadoop</finalName>
-							<includes>
-								<include>**/org/apache/**</include>
-							</includes>
-						</configuration>
-					</execution>
 				</executions>
 			</plugin>
 			<plugin>
@@ -158,25 +145,6 @@
 							</resources>
 						</configuration>
 					</execution>
-					<execution>
-						<id>copy-hadoop-patch</id>
-						<!-- here the phase you need -->
-						<phase>package</phase>
-						<goals>
-							<goal>copy-resources</goal>
-						</goals>
-						<configuration>
-							<outputDirectory>target/appassembler/lib</outputDirectory>
-							<resources>
-								<resource>
-									<directory>target</directory>
-									<includes>
-										<include>a-hadoop-patch.jar</include>
-									</includes>
-								</resource>
-							</resources>
-						</configuration>
-					</execution>
 				</executions>
 			</plugin>
 			<plugin>
@@ -185,7 +153,8 @@
 				<version>2.7.2</version>
 				<configuration>
 					<forkMode>pertest</forkMode>
-					<argLine>-enableassertions -Xmx512m -XX:MaxPermSize=300m -Dfile.encoding=UTF-8
+					<argLine>-enableassertions -Xmx512m -XX:MaxPermSize=300m
+						-Dfile.encoding=UTF-8
 						-Djava.util.logging.config.file=src/test/resources/logging.properties</argLine>
 					<includes>
 						<include>**/*TestSuite.java</include>
diff --git a/pregelix/pregelix-core/src/main/java/org/apache/hadoop/fs/Path.java b/pregelix/pregelix-core/src/main/java/org/apache/hadoop/fs/Path.java
deleted file mode 100644
index 5efdde8..0000000
--- a/pregelix/pregelix-core/src/main/java/org/apache/hadoop/fs/Path.java
+++ /dev/null
@@ -1,355 +0,0 @@
-/*
- * 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 org.apache.hadoop.fs;
-
-import java.io.IOException;
-import java.io.Serializable;
-import java.net.URI;
-import java.net.URISyntaxException;
-
-import org.apache.hadoop.conf.Configuration;
-
-/**
- * Names a file or directory in a {@link FileSystem}. Path strings use slash as
- * the directory separator. A path string is absolute if it begins with a slash.
- */
-@SuppressWarnings("rawtypes")
-public class Path implements Comparable, Serializable {
-    private static final long serialVersionUID = 1L;
-    /** The directory separator, a slash. */
-    public static final String SEPARATOR = "/";
-    public static final char SEPARATOR_CHAR = '/';
-
-    public static final String CUR_DIR = ".";
-
-    static final boolean WINDOWS = System.getProperty("os.name").startsWith("Windows");
-
-    private URI uri; // a hierarchical uri
-
-    /** Resolve a child path against a parent path. */
-    public Path(String parent, String child) {
-        this(new Path(parent), new Path(child));
-    }
-
-    /** Resolve a child path against a parent path. */
-    public Path(Path parent, String child) {
-        this(parent, new Path(child));
-    }
-
-    /** Resolve a child path against a parent path. */
-    public Path(String parent, Path child) {
-        this(new Path(parent), child);
-    }
-
-    /** Resolve a child path against a parent path. */
-    public Path(Path parent, Path child) {
-        // Add a slash to parent's path so resolution is compatible with URI's
-        URI parentUri = parent.uri;
-        String parentPath = parentUri.getPath();
-        if (!(parentPath.equals("/") || parentPath.equals("")))
-            try {
-                parentUri = new URI(parentUri.getScheme(), parentUri.getAuthority(), parentUri.getPath() + "/", null,
-                        parentUri.getFragment());
-            } catch (URISyntaxException e) {
-                throw new IllegalArgumentException(e);
-            }
-        URI resolved = parentUri.resolve(child.uri);
-        initialize(resolved.getScheme(), resolved.getAuthority(), normalizePath(resolved.getPath()),
-                resolved.getFragment());
-    }
-
-    private void checkPathArg(String path) {
-        // disallow construction of a Path from an empty string
-        if (path == null) {
-            throw new IllegalArgumentException("Can not create a Path from a null string");
-        }
-        if (path.length() == 0) {
-            throw new IllegalArgumentException("Can not create a Path from an empty string");
-        }
-    }
-
-    /**
-     * Construct a path from a String. Path strings are URIs, but with unescaped
-     * elements and some additional normalization.
-     */
-    public Path(String pathString) {
-        checkPathArg(pathString);
-
-        // We can't use 'new URI(String)' directly, since it assumes things are
-        // escaped, which we don't require of Paths.
-
-        // add a slash in front of paths with Windows drive letters
-        if (hasWindowsDrive(pathString, false))
-            pathString = "/" + pathString;
-
-        // parse uri components
-        String scheme = null;
-        String authority = null;
-
-        int start = 0;
-
-        // parse uri scheme, if any
-        int colon = pathString.indexOf(':');
-        int slash = pathString.indexOf('/');
-        if ((colon != -1) && ((slash == -1) || (colon < slash))) { // has a
-                                                                   // scheme
-            scheme = pathString.substring(0, colon);
-            start = colon + 1;
-        }
-
-        // parse uri authority, if any
-        if (pathString.startsWith("//", start) && (pathString.length() - start > 2)) { // has
-                                                                                       // authority
-            int nextSlash = pathString.indexOf('/', start + 2);
-            int authEnd = nextSlash > 0 ? nextSlash : pathString.length();
-            authority = pathString.substring(start + 2, authEnd);
-            start = authEnd;
-        }
-
-        // uri path is the rest of the string -- query & fragment not supported
-        String path = pathString.substring(start, pathString.length());
-
-        initialize(scheme, authority, path, null);
-    }
-
-    /** Construct a Path from components. */
-    public Path(String scheme, String authority, String path) {
-        checkPathArg(path);
-        initialize(scheme, authority, path, null);
-    }
-
-    /**
-     * Construct a path from a URI
-     */
-    public Path(URI aUri) {
-        uri = aUri;
-    }
-
-    private void initialize(String scheme, String authority, String path, String fragment) {
-        try {
-            this.uri = new URI(scheme, authority, normalizePath(path), null, fragment).normalize();
-        } catch (URISyntaxException e) {
-            throw new IllegalArgumentException(e);
-        }
-    }
-
-    private String normalizePath(String path) {
-        // remove double slashes & backslashes
-        if (path.indexOf("//") != -1) {
-            path = path.replace("//", "/");
-        }
-        if (path.indexOf("\\") != -1) {
-            path = path.replace("\\", "/");
-        }
-
-        // trim trailing slash from non-root path (ignoring windows drive)
-        int minLength = hasWindowsDrive(path, true) ? 4 : 1;
-        if (path.length() > minLength && path.endsWith("/")) {
-            path = path.substring(0, path.length() - 1);
-        }
-
-        return path;
-    }
-
-    private boolean hasWindowsDrive(String path, boolean slashed) {
-        if (!WINDOWS)
-            return false;
-        int start = slashed ? 1 : 0;
-        return path.length() >= start + 2
-                && (slashed ? path.charAt(0) == '/' : true)
-                && path.charAt(start + 1) == ':'
-                && ((path.charAt(start) >= 'A' && path.charAt(start) <= 'Z') || (path.charAt(start) >= 'a' && path
-                        .charAt(start) <= 'z'));
-    }
-
-    /** Convert this to a URI. */
-    public URI toUri() {
-        return uri;
-    }
-
-    /** Return the FileSystem that owns this Path. */
-    public FileSystem getFileSystem(Configuration conf) throws IOException {
-        return FileSystem.get(this.toUri(), conf);
-    }
-
-    /** True if the directory of this path is absolute. */
-    public boolean isAbsolute() {
-        int start = hasWindowsDrive(uri.getPath(), true) ? 3 : 0;
-        return uri.getPath().startsWith(SEPARATOR, start);
-    }
-
-    /** Returns the final component of this path. */
-    public String getName() {
-        String path = uri.getPath();
-        int slash = path.lastIndexOf(SEPARATOR);
-        return path.substring(slash + 1);
-    }
-
-    /** Returns the parent of a path or null if at root. */
-    public Path getParent() {
-        String path = uri.getPath();
-        int lastSlash = path.lastIndexOf('/');
-        int start = hasWindowsDrive(path, true) ? 3 : 0;
-        if ((path.length() == start) || // empty path
-                (lastSlash == start && path.length() == start + 1)) { // at root
-            return null;
-        }
-        String parent;
-        if (lastSlash == -1) {
-            parent = CUR_DIR;
-        } else {
-            int end = hasWindowsDrive(path, true) ? 3 : 0;
-            parent = path.substring(0, lastSlash == end ? end + 1 : lastSlash);
-        }
-        return new Path(uri.getScheme(), uri.getAuthority(), parent);
-    }
-
-    /** Adds a suffix to the final name in the path. */
-    public Path suffix(String suffix) {
-        return new Path(getParent(), getName() + suffix);
-    }
-
-    public String toString() {
-        // we can't use uri.toString(), which escapes everything, because we
-        // want
-        // illegal characters unescaped in the string, for glob processing, etc.
-        StringBuffer buffer = new StringBuffer();
-        if (uri.getScheme() != null) {
-            buffer.append(uri.getScheme());
-            buffer.append(":");
-        }
-        if (uri.getAuthority() != null) {
-            buffer.append("//");
-            buffer.append(uri.getAuthority());
-        }
-        if (uri.getPath() != null) {
-            String path = uri.getPath();
-            if (path.indexOf('/') == 0 && hasWindowsDrive(path, true) && // has
-                                                                         // windows
-                                                                         // drive
-                    uri.getScheme() == null && // but no scheme
-                    uri.getAuthority() == null) // or authority
-                path = path.substring(1); // remove slash before drive
-            buffer.append(path);
-        }
-        if (uri.getFragment() != null) {
-            buffer.append("#");
-            buffer.append(uri.getFragment());
-        }
-        return buffer.toString();
-    }
-
-    public boolean equals(Object o) {
-        if (!(o instanceof Path)) {
-            return false;
-        }
-        Path that = (Path) o;
-        return this.uri.equals(that.uri);
-    }
-
-    public int hashCode() {
-        return uri.hashCode();
-    }
-
-    public int compareTo(Object o) {
-        Path that = (Path) o;
-        return this.uri.compareTo(that.uri);
-    }
-
-    /** Return the number of elements in this path. */
-    public int depth() {
-        String path = uri.getPath();
-        int depth = 0;
-        int slash = path.length() == 1 && path.charAt(0) == '/' ? -1 : 0;
-        while (slash != -1) {
-            depth++;
-            slash = path.indexOf(SEPARATOR, slash + 1);
-        }
-        return depth;
-    }
-
-    /** Returns a qualified path object. */
-    public Path makeQualified(FileSystem fs) {
-        Path path = this;
-        if (!isAbsolute()) {
-            path = new Path(fs.getWorkingDirectory(), this);
-        }
-
-        URI pathUri = path.toUri();
-        URI fsUri = fs.getUri();
-
-        String scheme = pathUri.getScheme();
-        String authority = pathUri.getAuthority();
-        String fragment = pathUri.getFragment();
-        if (scheme != null && (authority != null || fsUri.getAuthority() == null))
-            return path;
-
-        if (scheme == null) {
-            scheme = fsUri.getScheme();
-        }
-
-        if (authority == null) {
-            authority = fsUri.getAuthority();
-            if (authority == null) {
-                authority = "";
-            }
-        }
-
-        URI newUri = null;
-        try {
-            newUri = new URI(scheme, authority, normalizePath(pathUri.getPath()), null, fragment);
-        } catch (URISyntaxException e) {
-            throw new IllegalArgumentException(e);
-        }
-        return new Path(newUri);
-    }
-
-    /** Returns a qualified path object. */
-    public Path makeQualified(URI defaultUri, Path workingDir) {
-        Path path = this;
-        if (!isAbsolute()) {
-            path = new Path(workingDir, this);
-        }
-
-        URI pathUri = path.toUri();
-
-        String scheme = pathUri.getScheme();
-        String authority = pathUri.getAuthority();
-        String fragment = pathUri.getFragment();
-
-        if (scheme != null && (authority != null || defaultUri.getAuthority() == null))
-            return path;
-
-        if (scheme == null) {
-            scheme = defaultUri.getScheme();
-        }
-
-        if (authority == null) {
-            authority = defaultUri.getAuthority();
-            if (authority == null) {
-                authority = "";
-            }
-        }
-
-        URI newUri = null;
-        try {
-            newUri = new URI(scheme, authority, normalizePath(pathUri.getPath()), null, fragment);
-        } catch (URISyntaxException e) {
-            throw new IllegalArgumentException(e);
-        }
-        return new Path(newUri);
-    }
-}
\ No newline at end of file
diff --git a/pregelix/pregelix-core/src/main/java/org/apache/hadoop/mapreduce/InputSplit.java b/pregelix/pregelix-core/src/main/java/org/apache/hadoop/mapreduce/InputSplit.java
deleted file mode 100644
index ac72160..0000000
--- a/pregelix/pregelix-core/src/main/java/org/apache/hadoop/mapreduce/InputSplit.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * 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 org.apache.hadoop.mapreduce;
-
-import java.io.IOException;
-import java.io.Serializable;
-
-/**
- * <code>InputSplit</code> represents the data to be processed by an individual {@link Mapper}.
- * <p>
- * Typically, it presents a byte-oriented view on the input and is the responsibility of {@link RecordReader} of the job to process this and present a record-oriented view.
- * 
- * @see InputFormat
- * @see RecordReader
- */
-public abstract class InputSplit implements Serializable {
-    private static final long serialVersionUID = 1L;
-
-    /**
-     * Get the size of the split, so that the input splits can be sorted by
-     * size.
-     * 
-     * @return the number of bytes in the split
-     * @throws IOException
-     * @throws InterruptedException
-     */
-    public abstract long getLength() throws IOException, InterruptedException;
-
-    /**
-     * Get the list of nodes by name where the data for the split would be
-     * local. The locations do not need to be serialized.
-     * 
-     * @return a new array of the node nodes.
-     * @throws IOException
-     * @throws InterruptedException
-     */
-    public abstract String[] getLocations() throws IOException, InterruptedException;
-}
\ No newline at end of file
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/pregelix b/pregelix/pregelix-core/src/main/resources/scripts/pregelix
index c3fd27b..6997078 100644
--- a/pregelix/pregelix-core/src/main/resources/scripts/pregelix
+++ b/pregelix/pregelix-core/src/main/resources/scripts/pregelix
@@ -91,7 +91,7 @@
   REPO="$BASEDIR"/lib
 fi
 
-CLASSPATH=$CLASSPATH_PREFIX:"$HADOOP_HOME"/conf:"$BASEDIR"/etc:$(echo ${REPO}/*.jar | tr ' ' ':'):$1
+CLASSPATH=$CLASSPATH_PREFIX:"$HADOOP_HOME"/conf:"$BASEDIR"/etc:$1
 
 # For Cygwin, switch paths to Windows format before running java
 if $cygwin; then
diff --git a/pregelix/pregelix-dataflow/pom.xml b/pregelix/pregelix-dataflow/pom.xml
index 9454ece..31b6adc 100644
--- a/pregelix/pregelix-dataflow/pom.xml
+++ b/pregelix/pregelix-dataflow/pom.xml
@@ -144,5 +144,12 @@
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-hdfs</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
 	</dependencies>
 </project>
diff --git a/pregelix/pregelix-dataflow/src/main/java/edu/uci/ics/pregelix/dataflow/VertexFileScanOperatorDescriptor.java b/pregelix/pregelix-dataflow/src/main/java/edu/uci/ics/pregelix/dataflow/VertexFileScanOperatorDescriptor.java
index 0736e1d..cb0e339 100644
--- a/pregelix/pregelix-dataflow/src/main/java/edu/uci/ics/pregelix/dataflow/VertexFileScanOperatorDescriptor.java
+++ b/pregelix/pregelix-dataflow/src/main/java/edu/uci/ics/pregelix/dataflow/VertexFileScanOperatorDescriptor.java
@@ -17,9 +17,9 @@
 import java.io.DataOutput;
 import java.io.IOException;
 import java.nio.ByteBuffer;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.logging.Logger;
 
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.io.Writable;
@@ -43,6 +43,7 @@
 import edu.uci.ics.hyracks.dataflow.common.comm.util.FrameUtils;
 import edu.uci.ics.hyracks.dataflow.std.base.AbstractSingleActivityOperatorDescriptor;
 import edu.uci.ics.hyracks.dataflow.std.base.AbstractUnaryOutputSourceOperatorNodePushable;
+import edu.uci.ics.hyracks.hdfs2.dataflow.FileSplitsFactory;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.io.VertexInputFormat;
 import edu.uci.ics.pregelix.api.io.VertexReader;
@@ -51,9 +52,8 @@
 
 @SuppressWarnings("rawtypes")
 public class VertexFileScanOperatorDescriptor extends AbstractSingleActivityOperatorDescriptor {
-    private static final Logger LOGGER = Logger.getLogger(VertexFileScanOperatorDescriptor.class.getName());
     private static final long serialVersionUID = 1L;
-    private final List<InputSplit> splits;
+    private final FileSplitsFactory splitsFactory;
     private final IConfigurationFactory confFactory;
     private final int fieldSize = 2;
     private final String[] scheduledLocations;
@@ -65,7 +65,11 @@
     public VertexFileScanOperatorDescriptor(JobSpecification spec, RecordDescriptor rd, List<InputSplit> splits,
             String[] scheduledLocations, IConfigurationFactory confFactory) throws HyracksException {
         super(spec, 0, 1);
-        this.splits = splits;
+        List<FileSplit> fileSplits = new ArrayList<FileSplit>();
+        for (int i = 0; i < splits.size(); i++) {
+            fileSplits.add((FileSplit) splits.get(i));
+        }
+        this.splitsFactory = new FileSplitsFactory(fileSplits);
         this.confFactory = confFactory;
         this.scheduledLocations = scheduledLocations;
         this.executed = new boolean[scheduledLocations.length];
@@ -76,6 +80,8 @@
     public IOperatorNodePushable createPushRuntime(final IHyracksTaskContext ctx,
             IRecordDescriptorProvider recordDescProvider, final int partition, final int nPartitions)
             throws HyracksDataException {
+        final List<FileSplit> splits = splitsFactory.getSplits();
+
         return new AbstractUnaryOutputSourceOperatorNodePushable() {
             private Configuration conf = confFactory.createConfiguration();
 
@@ -116,7 +122,7 @@
              * @throws InterruptedException
              */
             @SuppressWarnings("unchecked")
-            private void loadVertices(final IHyracksTaskContext ctx, int partitionId) throws IOException,
+            private void loadVertices(final IHyracksTaskContext ctx, int splitId) throws IOException,
                     ClassNotFoundException, InterruptedException, InstantiationException, IllegalAccessException {
                 ByteBuffer frame = ctx.allocateFrame();
                 FrameTupleAppender appender = new FrameTupleAppender(ctx.getFrameSize());
@@ -124,14 +130,8 @@
 
                 VertexInputFormat vertexInputFormat = BspUtils.createVertexInputFormat(conf);
                 TaskAttemptContext context = new TaskAttemptContext(conf, new TaskAttemptID());
-                InputSplit split = splits.get(partitionId);
+                InputSplit split = splits.get(splitId);
 
-                if (split instanceof FileSplit) {
-                    FileSplit fileSplit = (FileSplit) split;
-                    LOGGER.info("read file split: " + fileSplit.getPath() + " location:" + fileSplit.getLocations()[0]
-                            + " start:" + fileSplit.getStart() + " length:" + split.getLength() + " partition:"
-                            + partitionId);
-                }
                 VertexReader vertexReader = vertexInputFormat.createVertexReader(split, context);
                 vertexReader.initialize(split, context);
                 Vertex readerVertex = (Vertex) BspUtils.createVertex(conf);
@@ -142,7 +142,7 @@
                  * set context
                  */
                 Context mapperContext = new Mapper().new Context(conf, new TaskAttemptID(), null, null, null, null,
-                        splits.get(partitionId));
+                        splits.get(splitId));
                 Vertex.setContext(mapperContext);
 
                 /**