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From scnakand...@apache.org
Subject [2/2] airavata-sandbox git commit: adding airavata layered prototype
Date Tue, 27 Jun 2017 16:19:00 GMT
adding airavata layered prototype


Project: http://git-wip-us.apache.org/repos/asf/airavata-sandbox/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata-sandbox/commit/43a79e3a
Tree: http://git-wip-us.apache.org/repos/asf/airavata-sandbox/tree/43a79e3a
Diff: http://git-wip-us.apache.org/repos/asf/airavata-sandbox/diff/43a79e3a

Branch: refs/heads/master
Commit: 43a79e3a5df6f8ed71ac439c71c322ece54b38a2
Parents: 85fb44b
Author: scnakandala <supun.nakandala@gmail.com>
Authored: Tue Jun 27 12:18:54 2017 -0400
Committer: scnakandala <supun.nakandala@gmail.com>
Committed: Tue Jun 27 12:18:54 2017 -0400

----------------------------------------------------------------------
 airavata-layered-architecture/pom.xml           |  58 +++
 .../airavata/resources/Authentication.java      |  30 ++
 .../apache/airavata/resources/OutputParser.java |  66 ++++
 .../apache/airavata/resources/ServerInfo.java   |  49 +++
 .../resources/batch/BatchJobOutputParser.java   |  89 +++++
 .../airavata/resources/batch/GroovyMap.java     |  93 +++++
 .../resources/batch/HPCBatchResource.java       | 200 ++++++++++
 .../batch/JobManagerConfiguration.java          |  51 +++
 .../airavata/resources/batch/JobStatus.java     |  28 ++
 .../resources/batch/JobSubmissionOutput.java    |  88 +++++
 .../resources/batch/PBSJobConfiguration.java    | 120 ++++++
 .../resources/batch/RawCommandInfo.java         |  41 ++
 .../apache/airavata/resources/batch/Script.java |  61 +++
 .../apache/airavata/runners/CommandOutput.java  |  57 +++
 .../airavata/runners/ssh/SSHApiException.java   |  35 ++
 .../runners/ssh/SSHCommandOutputReader.java     |  90 +++++
 .../runners/ssh/SSHKeyAuthentication.java       |  92 +++++
 .../apache/airavata/runners/ssh/SSHRunner.java  | 394 +++++++++++++++++++
 .../airavata/runners/ssh/SSHServerInfo.java     |  52 +++
 .../airavata/runners/ssh/SSHUserInfo.java       |  66 ++++
 .../resources/batch/PBS_Groovy.template         |  34 ++
 .../java/org/apache/airavata/Constants.java     |  30 ++
 .../resources/batch/HPCBatchResourceTest.java   |  86 ++++
 .../airavata/runners/ssh/SSHRunnerTest.java     |  63 +++
 .../src/test/resources/code_tf.py               |  30 ++
 .../src/test/resources/job_tf.pbs               |  18 +
 .../src/test/resources/ssh/id_rsa               |  30 ++
 .../src/test/resources/ssh/id_rsa.pub           |   1 +
 .../src/test/resources/ssh/known_hosts          |   0
 29 files changed, 2052 insertions(+)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/pom.xml
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/pom.xml b/airavata-layered-architecture/pom.xml
new file mode 100644
index 0000000..ff289c6
--- /dev/null
+++ b/airavata-layered-architecture/pom.xml
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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>
+
+    <groupId>org.apache.airavata</groupId>
+    <artifactId>airavata</artifactId>
+    <version>1.0-SNAPSHOT</version>
+
+    <dependencies>
+        <dependency>
+            <groupId>com.jcraft</groupId>
+            <artifactId>jsch</artifactId>
+            <version>0.1.53</version>
+        </dependency>
+        <dependency>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
+            <version>19.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.codehaus.groovy</groupId>
+            <artifactId>groovy-templates</artifactId>
+            <version>2.4.7</version>
+        </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.5</version>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+            <version>1.7.10</version>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.5.1</version>
+                <configuration>
+                    <source>1.8</source>
+                    <target>1.8</target>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/Authentication.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/Authentication.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/Authentication.java
new file mode 100644
index 0000000..426f55e
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/Authentication.java
@@ -0,0 +1,30 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class Authentication {
+    private final static Logger logger = LoggerFactory.getLogger(Authentication.class);
+
+    protected String userName;
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/OutputParser.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/OutputParser.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/OutputParser.java
new file mode 100644
index 0000000..de523e4
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/OutputParser.java
@@ -0,0 +1,66 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources;
+
+import org.apache.airavata.resources.batch.JobStatus;
+
+import java.util.Map;
+
+public interface OutputParser {
+    /**
+     * This can be used to parseSingleJob the result of a job submission to get the JobID
+     * @param rawOutput
+     * @return the job id as a String, or null if no job id found
+     */
+    public String parseJobSubmission(String rawOutput)throws Exception;
+
+
+    /**
+     * Parse output return by job submission task and identify jobSubmission failures.
+     * @param rawOutput
+     * @return true if job submission has been failed, false otherwise.
+     */
+    public boolean isJobSubmissionFailed(String rawOutput);
+
+
+    /**
+     * This can be used to get the job status from the output
+     * @param jobID
+     * @param rawOutput
+     */
+    public JobStatus parseJobStatus(String jobID, String rawOutput)throws Exception;
+
+    /**
+     * This can be used to parseSingleJob a big output and get multipleJob statuses
+     * @param statusMap list of status map will return and key will be the job ID
+     * @param rawOutput
+     */
+    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput)throws Exception;
+
+    /**
+     * filter the jobId value of given JobName from rawOutput
+     * @param jobName
+     * @param rawOutput
+     * @return
+     * @throws Exception
+     */
+    public String parseJobId(String jobName, String rawOutput) throws Exception;
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/ServerInfo.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/ServerInfo.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/ServerInfo.java
new file mode 100644
index 0000000..0bb46f5
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/ServerInfo.java
@@ -0,0 +1,49 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources;
+
+public class ServerInfo {
+
+    public static enum ComProtocol {SSH, LOCAL}
+
+    protected String host;
+    protected String userName;
+    protected int port;
+    protected ComProtocol comProtocol;
+
+    public ServerInfo(){}
+
+    public ServerInfo(String userName, String host, ComProtocol comProtocol, int port) {
+        this.userName = userName;
+        this.host = host;
+        this.comProtocol = comProtocol;
+        this.port = port;
+    }
+
+    public String getHost() {
+        return host;
+    }
+
+    public String getUserName() {
+        return userName;
+    }
+
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/BatchJobOutputParser.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/BatchJobOutputParser.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/BatchJobOutputParser.java
new file mode 100644
index 0000000..2278663
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/BatchJobOutputParser.java
@@ -0,0 +1,89 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+import org.apache.airavata.resources.OutputParser;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Map;
+
+public class BatchJobOutputParser implements OutputParser {
+    private final static Logger logger = LoggerFactory.getLogger(BatchJobOutputParser.class);
+
+    /**
+     * This can be used to parseSingleJob the result of a job submission to get the JobID
+     *
+     * @param rawOutput
+     * @return the job id as a String, or null if no job id found
+     */
+    @Override
+    public String parseJobSubmission(String rawOutput) throws Exception {
+        return null;
+    }
+
+    /**
+     * Parse output return by job submission task and identify jobSubmission failures.
+     *
+     * @param rawOutput
+     * @return true if job submission has been failed, false otherwise.
+     */
+    @Override
+    public boolean isJobSubmissionFailed(String rawOutput) {
+        return false;
+    }
+
+    /**
+     * This can be used to get the job status from the output
+     *
+     * @param jobID
+     * @param rawOutput
+     */
+    @Override
+    public JobStatus parseJobStatus(String jobID, String rawOutput) throws Exception {
+        return null;
+    }
+
+    /**
+     * This can be used to parseSingleJob a big output and get multipleJob statuses
+     *
+     * @param userName
+     * @param statusMap list of status map will return and key will be the job ID
+     * @param rawOutput
+     */
+    @Override
+    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) throws Exception {
+
+    }
+
+    /**
+     * filter the jobId value of given JobName from rawOutput
+     *
+     * @param jobName
+     * @param rawOutput
+     * @return
+     * @throws Exception
+     */
+    @Override
+    public String parseJobId(String jobName, String rawOutput) throws Exception {
+        return null;
+    }
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/GroovyMap.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/GroovyMap.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/GroovyMap.java
new file mode 100644
index 0000000..8709e8f
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/GroovyMap.java
@@ -0,0 +1,93 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+import java.util.HashMap;
+import java.util.Optional;
+
+public class GroovyMap extends HashMap<String, Object> {
+
+
+    public GroovyMap() {
+        super();
+        // to mitigate groovy exception groovy.lang.MissingPropertyException: No such property: <name> for class: groovy.lang.Binding
+        addDefaultValues();
+    }
+
+    public GroovyMap add(Script name, Object value){
+        put(name.name, value);
+        return this;
+    }
+
+    @Override
+    public Object get(Object key) {
+        return super.getOrDefault(key, null);
+    }
+
+    public Object get(Script script) {
+        return get(script.name);
+    }
+
+    public Optional<String> getStringValue(Script script) {
+        Object obj = get(script);
+        if (obj instanceof String) {
+            return Optional.of((String) obj);
+        } else if (obj == null) {
+            return Optional.empty();
+        } else {
+            throw new IllegalArgumentException("Value is not String type");
+        }
+    }
+
+    private void addDefaultValues() {
+        this.add(Script.SHELL_NAME, null)
+                .add(Script.QUEUE_NAME, null)
+                .add(Script.NODES, null)
+                .add(Script.CPU_COUNT, null)
+                .add(Script.MAIL_ADDRESS, null)
+                .add(Script.ACCOUNT_STRING, null)
+                .add(Script.MAX_WALL_TIME, null)
+                .add(Script.JOB_NAME, null)
+                .add(Script.STANDARD_OUT_FILE, null)
+                .add(Script.STANDARD_ERROR_FILE, null)
+                .add(Script.QUALITY_OF_SERVICE, null)
+                .add(Script.RESERVATION, null)
+                .add(Script.EXPORTS, null)
+                .add(Script.MODULE_COMMANDS, null)
+                .add(Script.SCRATCH_LOCATION, null)
+                .add(Script.WORKING_DIR, null)
+                .add(Script.PRE_JOB_COMMANDS, null)
+                .add(Script.JOB_SUBMITTER_COMMAND, null)
+                .add(Script.EXECUTABLE_PATH, null)
+                .add(Script.INPUTS, null)
+                .add(Script.POST_JOB_COMMANDS, null)
+                .add(Script.USED_MEM, null)
+                .add(Script.PROCESS_PER_NODE, null)
+                .add(Script.CHASSIS_NAME, null)
+                .add(Script.INPUT_DIR, null)
+                .add(Script.OUTPUT_DIR, null)
+                .add(Script.USER_NAME, null)
+                .add(Script.GATEWAY_ID, null)
+                .add(Script.GATEWAY_USER_NAME, null)
+                .add(Script.APPLICATION_NAME, null);
+    }
+
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/HPCBatchResource.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/HPCBatchResource.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/HPCBatchResource.java
new file mode 100644
index 0000000..46f2a48
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/HPCBatchResource.java
@@ -0,0 +1,200 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+import com.jcraft.jsch.JSchException;
+import groovy.lang.Writable;
+import groovy.text.GStringTemplateEngine;
+import groovy.text.TemplateEngine;
+import org.apache.airavata.resources.Authentication;
+import org.apache.airavata.resources.OutputParser;
+import org.apache.airavata.resources.ServerInfo;
+import org.apache.airavata.runners.ssh.SSHCommandOutputReader;
+import org.apache.airavata.runners.ssh.SSHKeyAuthentication;
+import org.apache.airavata.runners.ssh.SSHRunner;
+import org.apache.airavata.runners.ssh.SSHServerInfo;
+import org.apache.commons.io.FileUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+
+public class HPCBatchResource {
+    private final static Logger logger = LoggerFactory.getLogger(HPCBatchResource.class);
+
+    private static final int MAX_RETRY_COUNT = 3;
+
+    private ServerInfo serverInfo;
+    private Authentication authentication;
+    private JobManagerConfiguration jobManagerConfiguration;
+    private OutputParser outputParser;
+
+    public HPCBatchResource(ServerInfo serverInfo, JobManagerConfiguration jobManagerConfiguration, Authentication
+            authentication) throws Exception {
+        if(!(serverInfo instanceof SSHServerInfo) || !(authentication instanceof SSHKeyAuthentication)){
+            throw new Exception("Currently only SSH based communication is enabled for HPCRemote clusters");
+        }
+        if(!(jobManagerConfiguration instanceof PBSJobConfiguration)){
+            throw new Exception("Currently only PBS job configuration is enabled");
+        }
+
+        this.serverInfo = (SSHServerInfo) serverInfo;
+        this.authentication = (SSHKeyAuthentication) authentication;
+        this.jobManagerConfiguration = jobManagerConfiguration;
+        this.outputParser = jobManagerConfiguration.getParser();
+    }
+
+    public JobSubmissionOutput submitBatchJob(String routingKey, GroovyMap groovyMap, String workingDirectory) throws Exception {
+        File tempJobFile = File.createTempFile("temp_job", jobManagerConfiguration.getScriptExtension());
+        FileUtils.writeStringToFile(tempJobFile, generateScript(groovyMap));
+
+        String jobScriptFilePath = tempJobFile.getPath();
+        JobSubmissionOutput jsoutput = new JobSubmissionOutput();
+        copyTo(routingKey, jobScriptFilePath, workingDirectory+"/demo_job"
+                + jobManagerConfiguration.getScriptExtension()); // scp script file to working directory
+        RawCommandInfo submitCommand = jobManagerConfiguration.getSubmitCommand(workingDirectory, workingDirectory+"/demo_job"
+                + jobManagerConfiguration.getScriptExtension());
+        submitCommand.setRawCommand("cd " + workingDirectory + " && " + submitCommand.getRawCommand());
+        SSHCommandOutputReader reader = executeCommand(routingKey, submitCommand);
+
+        jsoutput.setJobId(outputParser.parseJobSubmission(reader.getStdOutputString()));
+        if (jsoutput.getJobId() == null) {
+            if (outputParser.isJobSubmissionFailed(reader.getStdOutputString())) {
+                jsoutput.setJobSubmissionFailed(true);
+                jsoutput.setFailureReason("stdout : " + reader.getStdOutputString() +
+                        "\n stderr : " + reader.getStdErrorString());
+            }
+        }
+        jsoutput.setExitCode(reader.getExitCode());
+        if (jsoutput.getExitCode() != 0) {
+            jsoutput.setJobSubmissionFailed(true);
+            jsoutput.setFailureReason("stdout : " + reader.getStdOutputString() +
+                    "\n stderr : " + reader.getStdErrorString());
+        }
+        jsoutput.setStdOut(reader.getStdOutputString());
+        jsoutput.setStdErr(reader.getStdErrorString());
+        return jsoutput;
+    }
+
+    public void copyTo(String routingKey, String localFile, String remoteFile) throws Exception {
+        int retry = 3;
+        while (retry > 0) {
+            try {
+                SSHRunner sshRunner = new SSHRunner();
+                logger.info("Transferring localhost:" + localFile  + " to " + serverInfo.getHost() + ":" + remoteFile);
+                sshRunner.scpTo("", localFile, remoteFile,  (SSHServerInfo) serverInfo, (SSHKeyAuthentication) authentication);
+                retry = 0;
+            } catch (Exception e) {
+                retry--;
+                if (retry == 0) {
+                    throw new Exception("Failed to scp localhost:" + localFile + " to " + serverInfo.getHost() +
+                            ":" + remoteFile, e);
+                } else {
+                    logger.info("Retry transfer localhost:" + localFile + " to " + serverInfo.getHost() + ":" +
+                            remoteFile);
+                }
+            }
+        }
+    }
+
+    public void copyFrom(String routingKey, String remoteFile, String localFile) throws Exception {
+        int retry = 0;
+        while(retry < MAX_RETRY_COUNT) {
+            try {
+                logger.info("Transferring " + serverInfo.getHost() + ":" + remoteFile + " To localhost:" + localFile);
+                SSHRunner sshRunner = new SSHRunner();
+                sshRunner.scpFrom(routingKey, remoteFile, localFile, (SSHServerInfo) serverInfo, (SSHKeyAuthentication)authentication);
+                retry=0;
+            } catch (Exception e) {
+                retry++;
+                if (retry == 0) {
+                    throw new Exception("Failed to scp " + serverInfo.getHost() + ":" + remoteFile + " to " +
+                            "localhost:" + localFile, e);
+                } else {
+                    logger.info("Retry transfer " + serverInfo.getHost() + ":" + remoteFile + "  to localhost:" + localFile);
+                }
+            }
+        }
+    }
+
+    public void makeDirectory(String routingKey, String directoryPath) throws Exception {
+        int retryCount = 0;
+        try {
+            while (retryCount < MAX_RETRY_COUNT) {
+                retryCount++;
+                logger.info("Creating directory: " + serverInfo.getHost() + ":" + directoryPath);
+                try {
+                    SSHRunner sshRunner = new SSHRunner();
+                    sshRunner.makeDirectory(routingKey, directoryPath, (SSHServerInfo) serverInfo, (SSHKeyAuthentication)authentication);
+                    break;  // Exit while loop
+                } catch (JSchException e) {
+                    if (retryCount == MAX_RETRY_COUNT) {
+                        logger.error("Retry count " + MAX_RETRY_COUNT + " exceeded for creating directory: "
+                                + serverInfo.getHost() + ":" + directoryPath, e);
+
+                        throw e;
+                    }
+                    logger.error("Issue with jsch, Retry creating directory: " + serverInfo.getHost() + ":" + directoryPath);
+                }
+            }
+        } catch (JSchException | IOException e) {
+            throw new Exception("Failed to create directory " + serverInfo.getHost() + ":" + directoryPath, e);
+        }
+    }
+
+    private SSHCommandOutputReader executeCommand(String routingKey, RawCommandInfo commandInfo) throws Exception {
+        String command = commandInfo.getCommand();
+        int retryCount = 0;
+        try {
+            while (retryCount < MAX_RETRY_COUNT) {
+                retryCount++;
+
+                SSHRunner sshRunner = new SSHRunner();
+                SSHCommandOutputReader commandOutput = sshRunner.executeCommand(routingKey, command, (SSHServerInfo)serverInfo, (SSHKeyAuthentication)authentication);
+                logger.info("Executing command {}", commandInfo.getCommand());
+                return commandOutput;
+            }
+            throw new Exception("Unable to execute command after "+retryCount+" retry attempts - " + command);
+        } catch (JSchException e) {
+            throw new Exception("Unable to execute command - " + command, e);
+        }
+    }
+
+
+    private String generateScript(GroovyMap groovyMap) throws Exception {
+        URL templateUrl = new URL("file://"+jobManagerConfiguration.getJobDescriptionTemplateName());
+        if (templateUrl == null) {
+            String error = "Template file '" + jobManagerConfiguration.getJobDescriptionTemplateName() + "' not found";
+            throw new Exception(error);
+        }
+        File template = new File(templateUrl.getPath());
+        TemplateEngine engine = new GStringTemplateEngine();
+        Writable make;
+        try {
+            make = engine.createTemplate(template).make(groovyMap);
+        } catch (Exception e) {
+            throw new Exception("Error while generating script using groovy map");
+        }
+        return make.toString();
+    }
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobManagerConfiguration.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobManagerConfiguration.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobManagerConfiguration.java
new file mode 100644
index 0000000..bc0bfcd
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobManagerConfiguration.java
@@ -0,0 +1,51 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+import org.apache.airavata.resources.OutputParser;
+
+public interface JobManagerConfiguration {
+    public static enum JobManagerCommand{JOB_MONITORING, SUBMISSION, DELETION};
+
+    public RawCommandInfo getCancelCommand(String jobID);
+
+    public String getJobDescriptionTemplateName();
+
+    public RawCommandInfo getMonitorCommand(String jobID);
+
+    public RawCommandInfo getUserBasedMonitorCommand(String userName);
+
+    public RawCommandInfo getJobIdMonitorCommand(String jobName , String userName);
+
+    public String getScriptExtension();
+
+    public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath);
+
+    public OutputParser getParser();
+
+    public String getInstalledPath();
+
+    public String getBaseCancelCommand();
+
+    public String getBaseMonitorCommand();
+
+    public String getBaseSubmitCommand();
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobStatus.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobStatus.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobStatus.java
new file mode 100644
index 0000000..faa17e2
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobStatus.java
@@ -0,0 +1,28 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class JobStatus {
+    private final static Logger logger = LoggerFactory.getLogger(JobStatus.class);
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobSubmissionOutput.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobSubmissionOutput.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobSubmissionOutput.java
new file mode 100644
index 0000000..44bec6b
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/JobSubmissionOutput.java
@@ -0,0 +1,88 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+public class JobSubmissionOutput {
+
+    private int exitCode = Integer.MIN_VALUE;
+    private String stdOut;
+    private String stdErr;
+    private String command;
+    private String jobId;
+    private boolean isJobSubmissionFailed;
+    private String failureReason;
+
+    public int getExitCode() {
+        return exitCode;
+    }
+
+    public void setExitCode(int exitCode) {
+        this.exitCode = exitCode;
+    }
+
+    public String getStdOut() {
+        return stdOut;
+    }
+
+    public void setStdOut(String stdOut) {
+        this.stdOut = stdOut;
+    }
+
+    public String getStdErr() {
+        return stdErr;
+    }
+
+    public void setStdErr(String stdErr) {
+        this.stdErr = stdErr;
+    }
+
+    public String getCommand() {
+        return command;
+    }
+
+    public void setCommand(String command) {
+        this.command = command;
+    }
+
+    public String getJobId() {
+        return jobId;
+    }
+
+    public void setJobId(String jobId) {
+        this.jobId = jobId;
+    }
+
+    public boolean isJobSubmissionFailed() {
+        return isJobSubmissionFailed;
+    }
+
+    public void setJobSubmissionFailed(boolean jobSubmissionFailed) {
+        isJobSubmissionFailed = jobSubmissionFailed;
+    }
+
+    public String getFailureReason() {
+        return failureReason;
+    }
+
+    public void setFailureReason(String failureReason) {
+        this.failureReason = failureReason;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/PBSJobConfiguration.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/PBSJobConfiguration.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/PBSJobConfiguration.java
new file mode 100644
index 0000000..07bccc0
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/PBSJobConfiguration.java
@@ -0,0 +1,120 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+import org.apache.airavata.resources.OutputParser;
+import org.apache.commons.io.FilenameUtils;
+
+import java.io.File;
+import java.util.Map;
+
+public class PBSJobConfiguration implements JobManagerConfiguration {
+
+    private final Map<JobManagerCommand, String> jobManagerCommands;
+    private String jobDescriptionTemplateName;
+    private String scriptExtension;
+    private String installedPath;
+    private OutputParser parser;
+
+    public PBSJobConfiguration(String jobDescriptionTemplateName, String scriptExtension, String installedPath,
+                               Map<JobManagerCommand, String> jobManagerCommands, OutputParser parser) {
+        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+        this.scriptExtension = scriptExtension;
+        this.parser = parser;
+        installedPath = installedPath.trim();
+        if (installedPath.endsWith("/")) {
+            this.installedPath = installedPath;
+        } else {
+            this.installedPath = installedPath + "/";
+        }
+        this.jobManagerCommands = jobManagerCommands;
+    }
+
+    public RawCommandInfo getCancelCommand(String jobID) {
+        return new RawCommandInfo(this.installedPath + jobManagerCommands.get(JobManagerCommand.DELETION).trim() + " " +
+                jobID);
+    }
+
+    public String getJobDescriptionTemplateName() {
+        return jobDescriptionTemplateName;
+    }
+
+    public void setJobDescriptionTemplateName(String jobDescriptionTemplateName) {
+        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+    }
+
+    public RawCommandInfo getMonitorCommand(String jobID) {
+        return new RawCommandInfo(this.installedPath + jobManagerCommands.get(JobManagerCommand.JOB_MONITORING).trim()
+                + " -f " + jobID);
+    }
+
+    public String getScriptExtension() {
+        return scriptExtension;
+    }
+
+    public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
+        return new RawCommandInfo(this.installedPath + jobManagerCommands.get(JobManagerCommand.SUBMISSION).trim() + " " +
+                workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
+    }
+
+    public String getInstalledPath() {
+        return installedPath;
+    }
+
+    public void setInstalledPath(String installedPath) {
+        this.installedPath = installedPath;
+    }
+
+    public OutputParser getParser() {
+        return parser;
+    }
+
+    public void setParser(OutputParser parser) {
+        this.parser = parser;
+    }
+
+    public RawCommandInfo getUserBasedMonitorCommand(String userName) {
+        return new RawCommandInfo(this.installedPath + jobManagerCommands.get(JobManagerCommand.JOB_MONITORING).trim()
+                + " -u " + userName);
+    }
+
+    @Override
+    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
+        // For PBS there is no option to get jobDetails by JobName, so we search with userName
+        return new RawCommandInfo(this.installedPath + jobManagerCommands.get(JobManagerCommand.JOB_MONITORING).trim()
+                + " -u " + userName + " -f  | grep \"Job_Name = " + jobName + "\" -B1");
+    }
+
+    @Override
+    public String getBaseCancelCommand() {
+        return jobManagerCommands.get(JobManagerCommand.DELETION).trim();
+    }
+
+    @Override
+    public String getBaseMonitorCommand() {
+        return jobManagerCommands.get(JobManagerCommand.JOB_MONITORING).trim();
+    }
+
+    @Override
+    public String getBaseSubmitCommand() {
+        return jobManagerCommands.get(JobManagerCommand.SUBMISSION).trim();
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/RawCommandInfo.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/RawCommandInfo.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/RawCommandInfo.java
new file mode 100644
index 0000000..3193505
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/RawCommandInfo.java
@@ -0,0 +1,41 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+public class RawCommandInfo {
+    private String rawCommand;
+
+    public RawCommandInfo(String cmd) {
+        this.rawCommand = cmd;
+    }
+
+    public String getCommand() {
+        return this.rawCommand;
+    }
+
+    public String getRawCommand() {
+        return rawCommand;
+    }
+
+    public void setRawCommand(String rawCommand) {
+        this.rawCommand = rawCommand;
+    }
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/Script.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/Script.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/Script.java
new file mode 100644
index 0000000..7f49753
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/resources/batch/Script.java
@@ -0,0 +1,61 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+public enum Script {
+
+    SHELL_NAME("shellName"),
+    QUEUE_NAME("queueName"),
+    NODES("nodes"),
+    CPU_COUNT("cpuCount"),
+    MAIL_ADDRESS("mailAddress"),
+    ACCOUNT_STRING("accountString"),
+    MAX_WALL_TIME("maxWallTime"),
+    JOB_NAME("jobName"),
+    STANDARD_OUT_FILE("standardOutFile"),
+    STANDARD_ERROR_FILE("standardErrorFile"),
+    QUALITY_OF_SERVICE("qualityOfService"),
+    RESERVATION("reservation"),
+    EXPORTS("exports"),
+    MODULE_COMMANDS("moduleCommands"),
+    SCRATCH_LOCATION("scratchLocation"),
+    WORKING_DIR("workingDirectory"),
+    PRE_JOB_COMMANDS("preJobCommands"),
+    JOB_SUBMITTER_COMMAND("jobSubmitterCommand"),
+    EXECUTABLE_PATH("executablePath"),
+    INPUTS("inputs"),
+    POST_JOB_COMMANDS("postJobCommands"),
+    USED_MEM("usedMem"),
+    PROCESS_PER_NODE("processPerNode"),
+    CHASSIS_NAME("chassisName"),
+    INPUT_DIR("inputDir"),
+    OUTPUT_DIR("outputDir"),
+    USER_NAME("userName"),
+    GATEWAY_ID("gatewayId"),
+    GATEWAY_USER_NAME("gatewayUserName"),
+    APPLICATION_NAME("applicationName"),
+    ;
+
+    String name;
+    Script(String name) {
+        this.name = name;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/CommandOutput.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/CommandOutput.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/CommandOutput.java
new file mode 100644
index 0000000..c3f8877
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/CommandOutput.java
@@ -0,0 +1,57 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.runners;
+
+
+import com.jcraft.jsch.Channel;
+
+import java.io.OutputStream;
+
+/**
+ * Output of a certain command.
+ */
+public interface CommandOutput {
+
+    /**
+     * Gets the output of the command as a stream.
+     * @param  channel Command output as a stream.
+     */
+    void onOutput(Channel channel);
+
+    /**
+     * Gets standard error as a output stream.
+     * @return Command error as a stream.
+     */
+    OutputStream getStandardError();
+
+    /**
+     * The command exit code.
+     * @param code The program exit code
+     */
+    void exitCode(int code);
+
+    /**
+     * Return the exit code of the command execution.
+     * @return exit code
+     */
+    int getExitCode();
+
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHApiException.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHApiException.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHApiException.java
new file mode 100644
index 0000000..e117351
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHApiException.java
@@ -0,0 +1,35 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.runners.ssh;
+
+/**
+ * An exception class to wrap SSH command execution related errors.
+ */
+public class SSHApiException extends Exception {
+
+    public SSHApiException(String message) {
+        super(message);
+    }
+
+    public SSHApiException(String message, Exception e) {
+        super(message, e);
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHCommandOutputReader.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHCommandOutputReader.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHCommandOutputReader.java
new file mode 100644
index 0000000..cdc45a9
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHCommandOutputReader.java
@@ -0,0 +1,90 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.runners.ssh;
+
+import com.jcraft.jsch.Channel;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+public class SSHCommandOutputReader{
+
+    private static final Logger logger = LoggerFactory.getLogger(SSHCommandOutputReader.class);
+    String stdOutputString = null;
+    String stdErrorString = null;
+    ByteArrayOutputStream errorStream = new ByteArrayOutputStream();
+    private int exitCode;
+
+    public void onOutput(Channel channel) {
+        try {
+            this.setStdOutputString(getOutputStream(channel, channel.getInputStream()));
+            this.setStdErrorString(new String(errorStream.toByteArray(), "UTF-8"));
+            this.exitCode = channel.getExitStatus();
+        } catch (IOException e) {
+            logger.error(e.getMessage(), e);
+        }
+
+    }
+
+    private String getOutputStream(Channel channel, InputStream inputStream) throws IOException {
+        StringBuilder output = new StringBuilder("");
+        byte[] tmp = new byte[1024];
+        do {
+            while (inputStream.available() > 0) {
+                int i = inputStream.read(tmp, 0, 1024);
+                if (i < 0) break;
+                output.append(new String(tmp, 0, i));
+            }
+        } while (!channel.isClosed()) ;
+        return  output.toString();
+    }
+
+    public void setExitCode(int exitCode) {
+        this.exitCode = exitCode;
+    }
+
+    public int getExitCode() {
+        return exitCode;
+    }
+
+    public String getStdOutputString() {
+        return stdOutputString;
+    }
+
+    public void setStdOutputString(String stdOutputString) {
+        this.stdOutputString = stdOutputString;
+    }
+
+    public String getStdErrorString() {
+        return stdErrorString;
+    }
+
+    public void setStdErrorString(String stdErrorString) {
+        this.stdErrorString = stdErrorString;
+    }
+
+    public ByteArrayOutputStream getErrorStream() {
+        return errorStream;
+    }
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHKeyAuthentication.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHKeyAuthentication.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHKeyAuthentication.java
new file mode 100644
index 0000000..0acb357
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHKeyAuthentication.java
@@ -0,0 +1,92 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.runners.ssh;
+
+import org.apache.airavata.resources.Authentication;
+
+public class SSHKeyAuthentication extends Authentication{
+    private byte[] privateKey;
+    private byte[] publicKey;
+    private String passphrase;
+    private String knownHostsFilePath;
+    private String strictHostKeyChecking; // yes or no
+
+    public SSHKeyAuthentication(String userName, byte[] privateKey, byte[] publicKey, String passphrase, String knownHostsFilePath, boolean strictHostKeyChecking) {
+        this.userName = userName;
+        this.privateKey = privateKey;
+        this.publicKey = publicKey;
+        this.passphrase = passphrase;
+        this.knownHostsFilePath = knownHostsFilePath;
+        if(strictHostKeyChecking){
+            this.strictHostKeyChecking = "yes";
+        }else{
+            this.strictHostKeyChecking = "no";
+        }
+    }
+
+    public String getUserName() {
+        return userName;
+    }
+
+    public void setUserName(String userName) {
+        this.userName = userName;
+    }
+
+    public byte[] getPrivateKey() {
+        return privateKey;
+    }
+
+    public void setPrivateKey(byte[] privateKey) {
+        this.privateKey = privateKey;
+    }
+
+    public byte[] getPublicKey() {
+        return publicKey;
+    }
+
+    public void setPublicKey(byte[] publicKey) {
+        this.publicKey = publicKey;
+    }
+
+    public String getPassphrase() {
+        return passphrase;
+    }
+
+    public void setPassphrase(String passphrase) {
+        this.passphrase = passphrase;
+    }
+
+    public String getKnownHostsFilePath() {
+        return knownHostsFilePath;
+    }
+
+    public void setKnownHostsFilePath(String knownHostsFilePath) {
+        this.knownHostsFilePath = knownHostsFilePath;
+    }
+
+    public String getStrictHostKeyChecking() {
+        return strictHostKeyChecking;
+    }
+
+    public void setStrictHostKeyChecking(String strictHostKeyChecking) {
+        this.strictHostKeyChecking = strictHostKeyChecking;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHRunner.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHRunner.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHRunner.java
new file mode 100644
index 0000000..6bb29a9
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHRunner.java
@@ -0,0 +1,394 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.runners.ssh;
+
+import com.jcraft.jsch.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
+import java.util.*;
+
+public class SSHRunner {
+    private final static Logger log = LoggerFactory.getLogger(SSHRunner.class);
+
+    public Session createSSHSession(SSHServerInfo serverInfo, SSHKeyAuthentication authentication) throws JSchException {
+            JSch jSch = new JSch();
+            jSch.addIdentity(UUID.randomUUID().toString(), authentication.getPrivateKey(), authentication.getPublicKey(),
+                    authentication.getPassphrase().getBytes());
+            Session session = jSch.getSession(serverInfo.getUserName(), serverInfo.getHost(),
+                    serverInfo.getSshPort());
+            session.setUserInfo(new SSHUserInfo(serverInfo.getUserName(), null, authentication.getPassphrase()));
+            if (authentication.getStrictHostKeyChecking().equals("yes")) {
+                jSch.setKnownHosts(authentication.getKnownHostsFilePath());
+            } else {
+                session.setConfig("StrictHostKeyChecking", "no");
+            }
+            session.connect();
+
+        return session;
+    }
+
+    public String scpTo(String routingKey, String localFile, String remoteFile, SSHServerInfo serverInfo,
+                        SSHKeyAuthentication authentication) throws IOException, JSchException, SSHApiException {
+
+        Session session =  createSSHSession(serverInfo, authentication);
+
+        FileInputStream fis = null;
+        String prefix = null;
+        if (new File(localFile).isDirectory()) {
+            prefix = localFile + File.separator;
+        }
+        boolean ptimestamp = true;
+
+        // exec 'scp -t rfile' remotely
+        String command = "scp " + (ptimestamp ? "-p" : "") + " -t " + remoteFile;
+        Channel channel = session.openChannel("exec");
+
+        SSHCommandOutputReader stdOutReader = new SSHCommandOutputReader();
+        ((ChannelExec) channel).setCommand(command);
+        ((ChannelExec) channel).setErrStream(stdOutReader.getErrorStream());
+
+        // get I/O streams for remote scp
+        OutputStream out = channel.getOutputStream();
+        InputStream in = channel.getInputStream();
+
+        channel.connect();
+
+        if (checkAck(in) != 0) {
+            String error = "Error Reading input Stream";
+            log.error(error);
+            throw new SSHApiException(error);
+        }
+
+        File _lfile = new File(localFile);
+
+        if (ptimestamp) {
+            command = "T" + (_lfile.lastModified() / 1000) + " 0";
+            // The access time should be sent here,
+            // but it is not accessible with JavaAPI ;-<
+            command += (" " + (_lfile.lastModified() / 1000) + " 0\n");
+            out.write(command.getBytes());
+            out.flush();
+            if (checkAck(in) != 0) {
+                String error = "Error Reading input Stream";
+                log.error(error);
+                throw new SSHApiException(error);
+            }
+        }
+
+        // send "C0644 filesize filename", where filename should not include '/'
+        long filesize = _lfile.length();
+        command = "C0644 " + filesize + " ";
+        if (localFile.lastIndexOf('/') > 0) {
+            command += localFile.substring(localFile.lastIndexOf('/') + 1);
+        } else {
+            command += localFile;
+        }
+        command += "\n";
+        out.write(command.getBytes());
+        out.flush();
+        if (checkAck(in) != 0) {
+            String error = "Error Reading input Stream";
+            log.error(error);
+            throw new SSHApiException(error);
+        }
+
+        // send a content of localFile
+        fis = new FileInputStream(localFile);
+        byte[] buf = new byte[1024];
+        while (true) {
+            int len = fis.read(buf, 0, buf.length);
+            if (len <= 0) break;
+            out.write(buf, 0, len); //out.flush();
+        }
+        fis.close();
+        fis = null;
+        // send '\0'
+        buf[0] = 0;
+        out.write(buf, 0, 1);
+        out.flush();
+        if (checkAck(in) != 0) {
+            String error = "Error Reading input Stream";
+            log.error(error);
+            throw new SSHApiException(error);
+        }
+        out.close();
+        stdOutReader.onOutput(channel);
+
+
+        channel.disconnect();
+        if (stdOutReader.getStdErrorString().contains("scp:")) {
+            throw new SSHApiException(stdOutReader.getStdErrorString());
+        }
+
+        session.disconnect();
+
+        //since remote file is always a file  we just return the file
+        return remoteFile;
+    }
+
+    /**
+     * This method will copy a remote file to a local directory
+     *
+     * @param remoteFile remote file path, this has to be a full qualified path
+     * @param localFile  This is the local file to copy, this can be a directory too
+     * @return returns the final local file path of the new file came from the remote resource
+     */
+    public void scpFrom(String routingKey, String remoteFile, String localFile, SSHServerInfo serverInfo,
+                        SSHKeyAuthentication authentication) throws IOException,
+            JSchException, SSHApiException {
+        Session session = createSSHSession(serverInfo, authentication);
+        FileOutputStream fos = null;
+        try {
+            String prefix = null;
+            if (new File(localFile).isDirectory()) {
+                prefix = localFile + File.separator;
+            }
+
+            SSHCommandOutputReader stdOutReader = new SSHCommandOutputReader();
+
+            // exec 'scp -f remotefile' remotely
+            String command = "scp -f " + remoteFile;
+            Channel channel = session.openChannel("exec");
+            ((ChannelExec) channel).setCommand(command);
+            ((ChannelExec) channel).setErrStream(stdOutReader.getErrorStream());
+
+            // get I/O streams for remote scp
+            OutputStream out = channel.getOutputStream();
+            InputStream in = channel.getInputStream();
+
+            if (!channel.isClosed()){
+                channel.connect();
+            }
+
+            byte[] buf = new byte[1024];
+
+            // send '\0'
+            buf[0] = 0;
+            out.write(buf, 0, 1);
+            out.flush();
+
+            while (true) {
+                int c = checkAck(in);
+                if (c != 'C') {
+                    break;
+                }
+
+                // read '0644 '
+                in.read(buf, 0, 5);
+
+                long filesize = 0L;
+                while (true) {
+                    if (in.read(buf, 0, 1) < 0) {
+                        // error
+                        break;
+                    }
+                    if (buf[0] == ' ') break;
+                    filesize = filesize * 10L + (long) (buf[0] - '0');
+                }
+
+                String file = null;
+                for (int i = 0; ; i++) {
+                    in.read(buf, i, 1);
+                    if (buf[i] == (byte) 0x0a) {
+                        file = new String(buf, 0, i);
+                        break;
+                    }
+                }
+
+                //System.out.println("filesize="+filesize+", file="+file);
+
+                // send '\0'
+                buf[0] = 0;
+                out.write(buf, 0, 1);
+                out.flush();
+
+                // read a content of lfile
+                fos = new FileOutputStream(prefix == null ? localFile : prefix + file);
+                int foo;
+                while (true) {
+                    if (buf.length < filesize) foo = buf.length;
+                    else foo = (int) filesize;
+                    foo = in.read(buf, 0, foo);
+                    if (foo < 0) {
+                        // error
+                        break;
+                    }
+                    fos.write(buf, 0, foo);
+                    filesize -= foo;
+                    if (filesize == 0L) break;
+                }
+                fos.close();
+                fos = null;
+
+                if (checkAck(in) != 0) {
+                    String error = "Error transfering the file content";
+                    log.error(error);
+                    throw new SSHApiException(error);
+                }
+
+                // send '\0'
+                buf[0] = 0;
+                out.write(buf, 0, 1);
+                out.flush();
+            }
+            stdOutReader.onOutput(channel);
+            if (stdOutReader.getStdErrorString().contains("scp:")) {
+                throw new SSHApiException(stdOutReader.getStdErrorString());
+            }
+
+        } catch (Exception e) {
+            log.error(e.getMessage(), e);
+        } finally {
+            try {
+                if (fos != null) fos.close();
+                session.disconnect();
+            } catch (Exception ee) {
+            }
+        }
+    }
+
+    public void makeDirectory(String routingKey, String path, SSHServerInfo serverInfo, SSHKeyAuthentication authentication)
+            throws IOException, JSchException, Exception {
+
+        Session session = createSSHSession(serverInfo, authentication);
+
+        // exec 'scp -t rfile' remotely
+        String command = "mkdir -p " + path;
+        Channel channel = session.openChannel("exec");
+        SSHCommandOutputReader stdOutReader = new SSHCommandOutputReader();
+
+        ((ChannelExec) channel).setCommand(command);
+        ((ChannelExec) channel).setErrStream(stdOutReader.getErrorStream());
+
+        try {
+            channel.connect();
+        } catch (JSchException e) {
+
+            channel.disconnect();
+            log.error("Unable to retrieve command output. Command - " + command +
+                    " on server - " + session.getHost() + ":" + session.getPort() +
+                    " connecting user name - "
+                    + session.getUserName());
+            throw e;
+        }
+        stdOutReader.onOutput(channel);
+        if (stdOutReader.getStdErrorString().contains("mkdir:")) {
+            throw new Exception(stdOutReader.getStdErrorString());
+        }
+
+        channel.disconnect();
+        session.disconnect();
+    }
+
+    public List<String> listDirectory(String routingKey, String path, SSHServerInfo serverInfo, SSHKeyAuthentication authentication)
+            throws IOException, JSchException, Exception {
+
+        Session session = createSSHSession(serverInfo, authentication);
+
+        // exec 'scp -t rfile' remotely
+        String command = "ls " + path;
+        Channel channel = session.openChannel("exec");
+        SSHCommandOutputReader stdOutReader = new SSHCommandOutputReader();
+
+        ((ChannelExec) channel).setCommand(command);
+        ((ChannelExec) channel).setErrStream(stdOutReader.getErrorStream());
+
+        try {
+            channel.connect();
+        } catch (JSchException e) {
+
+            channel.disconnect();
+
+            throw new Exception("Unable to retrieve command output. Command - " + command +
+                    " on server - " + session.getHost() + ":" + session.getPort() +
+                    " connecting user name - "
+                    + session.getUserName(), e);
+        }
+        if (stdOutReader.getStdErrorString().contains("ls:")) {
+            throw new Exception(stdOutReader.getStdErrorString());
+        }
+        channel.disconnect();
+        session.disconnect();
+        return Arrays.asList(stdOutReader.getStdOutputString().split("\n"));
+    }
+
+    public SSHCommandOutputReader executeCommand(String routingKey, String command, SSHServerInfo serverInfo,
+                                              SSHKeyAuthentication authentication) throws Exception {
+
+        Session session = createSSHSession(serverInfo, authentication);
+
+        Map<String, String> results = new HashMap<>();
+
+        Channel channel = session.openChannel("exec");
+        SSHCommandOutputReader stdOutReader = new SSHCommandOutputReader();
+
+        ((ChannelExec) channel).setCommand(command);
+        ((ChannelExec) channel).setErrStream(stdOutReader.getErrorStream());
+
+        try {
+            channel.connect();
+        } catch (JSchException e) {
+
+            channel.disconnect();
+
+            throw new Exception("Unable to retrieve command output. Command - " + command +
+                    " on server - " + session.getHost() + ":" + session.getPort() +
+                    " connecting user name - "
+                    + session.getUserName(), e);
+        }
+        stdOutReader.onOutput(channel);
+        session.disconnect();
+
+        return stdOutReader;
+    }
+
+    public SSHCommandOutputReader executeCommand(String routingKey, String[] commands, SSHServerInfo serverInfo,
+                                              SSHKeyAuthentication authentication) throws Exception {
+        return executeCommand(routingKey, String.join(" && ", commands), serverInfo, authentication);
+    }
+
+    private int checkAck(InputStream in) throws IOException {
+        int b = in.read();
+        if (b == 0) return b;
+        if (b == -1) return b;
+
+        if (b == 1 || b == 2) {
+            StringBuffer sb = new StringBuffer();
+            int c;
+            do {
+                c = in.read();
+                sb.append((char) c);
+            }
+            while (c != '\n');
+            if (b == 1) { // error
+                System.out.print(sb.toString());
+            }
+            if (b == 2) { // fatal error
+                System.out.print(sb.toString());
+            }
+            log.warn(sb.toString());
+        }
+        return b;
+    }
+
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHServerInfo.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHServerInfo.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHServerInfo.java
new file mode 100644
index 0000000..6a99bc1
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHServerInfo.java
@@ -0,0 +1,52 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.runners.ssh;
+
+import org.apache.airavata.resources.ServerInfo;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class SSHServerInfo extends ServerInfo {
+    private final static Logger logger = LoggerFactory.getLogger(SSHServerInfo.class);
+
+    SSHKeyAuthentication authentication;
+    int sshPort;
+
+    public SSHServerInfo(String userName, String host, SSHKeyAuthentication authentication, int port){
+            super(userName, host, ComProtocol.SSH, port);
+            this.authentication = authentication;
+            this.sshPort = port;
+    }
+
+    public SSHServerInfo(String userName, String host, SSHKeyAuthentication authentication){
+        super(userName, host, ComProtocol.SSH, 22);
+        this.authentication = authentication;
+        this.sshPort = 22;
+    }
+
+    public SSHKeyAuthentication getAuthentication() {
+        return authentication;
+    }
+
+    public int getSshPort() {
+        return sshPort;
+    }
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHUserInfo.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHUserInfo.java b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHUserInfo.java
new file mode 100644
index 0000000..9f2792b
--- /dev/null
+++ b/airavata-layered-architecture/src/main/java/org/apache/airavata/runners/ssh/SSHUserInfo.java
@@ -0,0 +1,66 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.runners.ssh;
+
+import com.jcraft.jsch.UserInfo;
+
+public class SSHUserInfo implements UserInfo {
+
+    private String userName;
+    private String password;
+    private String passphrase;
+
+    public SSHUserInfo(String userName, String password, String passphrase) {
+        this.userName = userName;
+        this.password = password;
+        this.passphrase = passphrase;
+    }
+
+    @Override
+    public String getPassphrase() {
+        return null;
+    }
+
+    @Override
+    public String getPassword() {
+        return null;
+    }
+
+    @Override
+    public boolean promptPassword(String s) {
+        return false;
+    }
+
+    @Override
+    public boolean promptPassphrase(String s) {
+        return false;
+    }
+
+    @Override
+    public boolean promptYesNo(String s) {
+        return false;
+    }
+
+    @Override
+    public void showMessage(String s) {
+
+    }
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/main/resources/resources/batch/PBS_Groovy.template
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/main/resources/resources/batch/PBS_Groovy.template b/airavata-layered-architecture/src/main/resources/resources/batch/PBS_Groovy.template
new file mode 100644
index 0000000..7e30b7b
--- /dev/null
+++ b/airavata-layered-architecture/src/main/resources/resources/batch/PBS_Groovy.template
@@ -0,0 +1,34 @@
+#!${shellName}
+
+<%
+   if(shellName != null && shellName != "") out.print '#PBS -S ' + shellName + '\n'
+   if (queueName != null && queueName != "") out.print '#PBS -q ' + queueName + '\n'
+   if (jobName != null && jobName != "") out.print '#PBS -N ' + jobName + '\n'
+   if (mailAddress != null && mailAddress != "") out.print '#PBS -M ' + mailAddress + '\n'
+   if (accountString != null && accountString != "") out.print '#PBS -A ' + accountString + '\n'
+   if (maxWallTime != null && maxWallTime != "") out.print '#PBS -l walltime=' + maxWallTime + '\n'
+   if (jobSubmitterCommand != null && jobSubmitterCommand != "" && jobSubmitterCommand == "ccmrun")
+        out.print '#PBS -l gres=ccm \n'
+   if (standardOutFile != null && standardOutFile != "") out.print '#PBS -o ' + standardOutFile + '\n'
+   if (standardErrorFile != null && standardErrorFile != "") out.print '#PBS -e ' + standardErrorFile + '\n'
+   if (usedMem != null && usedMem != "") out.print '#PBS -l vmem=' + usedMem + 'M\n'
+   if (nodes != null && nodes != "" && processPerNode != null && processPerNode != "")
+        out.print '#PBS -l nodes=' + nodes + ':ppn=' + processPerNode + '\n'
+%>
+#PBS -m bea
+
+<% if (exports != null) for(com in exports)  out.print 'export ' + com +'\n'
+   if (moduleCommands != null) for(mc in moduleCommands)  out.print mc +'\n'
+   if (workingDirectory != null && workingDirectory != "")  out.print 'cd ' + workingDirectory +'\n'
+   if (preJobCommands != null) for(pjc in preJobCommands)  out.print pjc +'\n'
+   if (jobSubmitterCommand != null && jobSubmitterCommand != ""){
+     out.print jobSubmitterCommand + ' '
+     if(jobSubmitterCommand != "ccmrun"){
+        out.print cpuCount + ' '
+     }
+   }
+   if (executablePath != null && executablePath != "")  out.print  executablePath + ' '
+   if (inputs != null) for(input in inputs)  out.print input + ' '
+            out.print '\n'
+   if (postJobCommands != null) for(pjc in postJobCommands)  out.print pjc +'\n'
+%>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/test/java/org/apache/airavata/Constants.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/test/java/org/apache/airavata/Constants.java b/airavata-layered-architecture/src/test/java/org/apache/airavata/Constants.java
new file mode 100644
index 0000000..539cfb5
--- /dev/null
+++ b/airavata-layered-architecture/src/test/java/org/apache/airavata/Constants.java
@@ -0,0 +1,30 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class Constants {
+    private final static Logger logger = LoggerFactory.getLogger(Constants.class);
+
+    public static final String loginUserName = "snakanda";
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/43a79e3a/airavata-layered-architecture/src/test/java/org/apache/airavata/resources/batch/HPCBatchResourceTest.java
----------------------------------------------------------------------
diff --git a/airavata-layered-architecture/src/test/java/org/apache/airavata/resources/batch/HPCBatchResourceTest.java b/airavata-layered-architecture/src/test/java/org/apache/airavata/resources/batch/HPCBatchResourceTest.java
new file mode 100644
index 0000000..525e28f
--- /dev/null
+++ b/airavata-layered-architecture/src/test/java/org/apache/airavata/resources/batch/HPCBatchResourceTest.java
@@ -0,0 +1,86 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 at
+ *
+ *   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.airavata.resources.batch;
+
+import org.apache.airavata.Constants;
+import org.apache.airavata.runners.ssh.SSHKeyAuthentication;
+import org.apache.airavata.runners.ssh.SSHRunnerTest;
+import org.apache.airavata.runners.ssh.SSHServerInfo;
+import org.apache.commons.io.IOUtils;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.*;
+
+public class HPCBatchResourceTest {
+    private final static Logger logger = LoggerFactory.getLogger(HPCBatchResourceTest.class);
+
+    @Test
+    public void test() throws Exception {
+        SSHKeyAuthentication br2SshAuthentication = new SSHKeyAuthentication(
+                Constants.loginUserName,
+                IOUtils.toByteArray(SSHRunnerTest.class.getClassLoader().getResourceAsStream("ssh/id_rsa")),
+                IOUtils.toByteArray(SSHRunnerTest.class.getClassLoader().getResourceAsStream("ssh/id_rsa.pub")),
+                "dummy",
+                SSHRunnerTest.class.getClassLoader().getResource("ssh/known_hosts").getPath(),
+                false
+        );
+        SSHServerInfo br2 = new SSHServerInfo(Constants.loginUserName, "bigred2.uits.iu.edu", br2SshAuthentication,22);
+        Map<JobManagerConfiguration.JobManagerCommand, String> jobManagerCommands = new HashMap<>();
+        jobManagerCommands.put(JobManagerConfiguration.JobManagerCommand.SUBMISSION, "qsub");
+        jobManagerCommands.put(JobManagerConfiguration.JobManagerCommand.JOB_MONITORING, "qstat");
+        jobManagerCommands.put(JobManagerConfiguration.JobManagerCommand.DELETION, "qdel");
+
+        JobManagerConfiguration pbsJobConfiguration = new PBSJobConfiguration(PBSJobConfiguration.class.getClassLoader().
+                getResource("resources/batch/PBS_Groovy.template").getPath(), ".pbs",
+                "/opt/torque/torque-5.0.1/bin", jobManagerCommands, new BatchJobOutputParser());
+        HPCBatchResource hpcBatchResource = new HPCBatchResource(br2, pbsJobConfiguration, br2SshAuthentication);
+
+        GroovyMap jobSpecification = new GroovyMap();
+
+        jobSpecification.add(Script.NODES, 1);
+        jobSpecification.add(Script.PROCESS_PER_NODE, 16);
+        jobSpecification.add(Script.MAX_WALL_TIME, "00:30:00");
+
+        jobSpecification.add(Script.QUEUE_NAME, "debug_gpu");
+
+        jobSpecification.add(Script.MAIL_ADDRESS, "supun.nakandala@gmail.com");
+
+        List<String> moduleLoads = new ArrayList<>();
+        moduleLoads.add("module load ccm");
+        moduleLoads.add("module load singularity");
+        jobSpecification.add(Script.MODULE_COMMANDS, moduleLoads);
+
+        jobSpecification.add(Script.WORKING_DIR, "/N/dc2/scratch/snakanda/work-dirs");
+        List<String> inputs = new ArrayList<>();
+        inputs.add("~/airavata/code_tf.py");
+        jobSpecification.add(Script.INPUTS, inputs);
+        jobSpecification.add(Script.EXECUTABLE_PATH, "singularity exec /N/soft/cle5/singularity/images/tensorflow1.1-ubuntu-py2.7.11-test.img python");
+        jobSpecification.add(Script.JOB_SUBMITTER_COMMAND,"ccmrun");
+
+        jobSpecification.add(Script.STANDARD_OUT_FILE, "STDOUT.txt");
+        jobSpecification.add(Script.STANDARD_ERROR_FILE, "STDERR.txt");
+
+        String routingKey = UUID.randomUUID().toString();
+        hpcBatchResource.submitBatchJob(routingKey, jobSpecification, "~/airavata");
+    }
+}
\ No newline at end of file


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