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From sma...@apache.org
Subject git commit: Samples application as discussed in - AIRAVATA-1344
Date Fri, 11 Jul 2014 11:58:06 GMT
Repository: airavata
Updated Branches:
  refs/heads/master 5a4302152 -> b6392ef33


Samples application as discussed in - AIRAVATA-1344


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/b6392ef3
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/b6392ef3
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/b6392ef3

Branch: refs/heads/master
Commit: b6392ef33f780dc53ebe18f2782415820bffc543
Parents: 5a43021
Author: Suresh Marru <smarru@apache.org>
Authored: Fri Jul 11 07:57:55 2014 -0400
Committer: Suresh Marru <smarru@apache.org>
Committed: Fri Jul 11 07:57:55 2014 -0400

----------------------------------------------------------------------
 .../resources/php-cli-samples/getAppModule.php  |  68 ----
 .../getApplicationDeployment.php                |  46 +++
 .../php-cli-samples/getApplicationModule.php    |  68 ++++
 .../updateApplicationInterface.php              |  10 +-
 .../tools/RegisterSampleApplications.java       | 376 +++++++++++++++++++
 .../tools/RegisterSampleApplicationsUtils.java  | 154 ++++++++
 .../applicationDeploymentModel.thrift           |   2 +-
 7 files changed, 650 insertions(+), 74 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/b6392ef3/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAppModule.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAppModule.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAppModule.php
deleted file mode 100644
index e28dbac..0000000
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAppModule.php
+++ /dev/null
@@ -1,68 +0,0 @@
-<?php
-/**
- * Bundle all thrift and Airavata stubs into a include file. This is simple but not so elegant
way.
- *  Contributions welcome to improve writing PHP Client Samples.
- *
- */
-include 'getAiravataClient.php';
-global $airavataclient;
-global $transport;
-
-use Airavata\API\Error\AiravataClientException;
-use Airavata\API\Error\AiravataSystemException;
-use Airavata\API\Error\InvalidRequestException;
-use Thrift\Exception\TTransportException;
-
-use Airavata\Model\AppCatalog\AppDeployment\ApplicationModule;
-
-
-if (count($argv) < 2) {
-    exit("Please provide an appModuleID. \n");
-}
-
-$appModuleId = $argv[1];
-
-$applicationModule = get_appModule($appModuleId);
-
-var_dump($applicationModule);
-
-$transport->close();
-
-/**
- * Get the appModule with the given ID
- * @param $appModuleId
- * @return null
- */
-function get_appModule($appModuleId)
-{
-    global $airavataclient;
-
-    try
-    {
-        return $airavataclient->getApplicationModule($appModuleId);
-    }
-    catch (InvalidRequestException $ire)
-    {
-        echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
-    }
-    catch (AiravataClientException $ace)
-    {
-        echo 'AiravataClientException!<br><br>' . $ace->getMessage();
-    }
-    catch (AiravataSystemException $ase)
-    {
-        echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
-    }
-    catch (TTransportException $tte)
-    {
-        echo 'TTransportException!<br><br>' . $tte->getMessage();
-    }
-    catch (\Exception $e)
-    {
-        echo 'Exception!<br><br>' . $e->getMessage();
-    }
-
-}
-
-?>
-

http://git-wip-us.apache.org/repos/asf/airavata/blob/b6392ef3/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationDeployment.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationDeployment.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationDeployment.php
new file mode 100644
index 0000000..c59d99c
--- /dev/null
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationDeployment.php
@@ -0,0 +1,46 @@
+<?php
+/**
+ * Bundle all thrift and Airavata stubs into a include file. This is simple but not so elegant
way.
+ *  Contributions welcome to improve writing PHP Client Samples.
+ *
+ */
+include 'getAiravataClient.php';
+global $airavataclient;
+global $transport;
+
+use Airavata\API\Error\AiravataClientException;
+use Airavata\API\Error\AiravataSystemException;
+use Airavata\API\Error\InvalidRequestException;
+use Thrift\Exception\TTransportException;
+
+use Airavata\Model\AppCatalog\AppDeployment\ApplicationModule;
+
+try {
+    if ($argc < 1) {
+        echo 'php getApplicationDeployment.php <Application Deployment Id>';
+    } else {
+        $appDeploymentId = $argv[1];
+
+        $appDeployment = $airavataclient->getApplicationDeployment($appDeploymentId);
+
+        if ($appDeployment) {
+            var_dump($appDeployment);
+        } else {
+            echo "\n Failed to fetch application deployment description. \n";
+        }
+    }
+
+} catch (InvalidRequestException $ire) {
+    echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
+} catch (AiravataClientException $ace) {
+    echo 'AiravataClientException!<br><br>' . $ace->getMessage();
+} catch (AiravataSystemException $ase) {
+    echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
+} catch (TTransportException $tte) {
+    echo 'TTransportException!<br><br>' . $tte->getMessage();
+} catch (\Exception $e) {
+    echo 'Exception!<br><br>' . $e->getMessage();
+}
+
+?>
+

http://git-wip-us.apache.org/repos/asf/airavata/blob/b6392ef3/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationModule.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationModule.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationModule.php
new file mode 100644
index 0000000..e28dbac
--- /dev/null
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationModule.php
@@ -0,0 +1,68 @@
+<?php
+/**
+ * Bundle all thrift and Airavata stubs into a include file. This is simple but not so elegant
way.
+ *  Contributions welcome to improve writing PHP Client Samples.
+ *
+ */
+include 'getAiravataClient.php';
+global $airavataclient;
+global $transport;
+
+use Airavata\API\Error\AiravataClientException;
+use Airavata\API\Error\AiravataSystemException;
+use Airavata\API\Error\InvalidRequestException;
+use Thrift\Exception\TTransportException;
+
+use Airavata\Model\AppCatalog\AppDeployment\ApplicationModule;
+
+
+if (count($argv) < 2) {
+    exit("Please provide an appModuleID. \n");
+}
+
+$appModuleId = $argv[1];
+
+$applicationModule = get_appModule($appModuleId);
+
+var_dump($applicationModule);
+
+$transport->close();
+
+/**
+ * Get the appModule with the given ID
+ * @param $appModuleId
+ * @return null
+ */
+function get_appModule($appModuleId)
+{
+    global $airavataclient;
+
+    try
+    {
+        return $airavataclient->getApplicationModule($appModuleId);
+    }
+    catch (InvalidRequestException $ire)
+    {
+        echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
+    }
+    catch (AiravataClientException $ace)
+    {
+        echo 'AiravataClientException!<br><br>' . $ace->getMessage();
+    }
+    catch (AiravataSystemException $ase)
+    {
+        echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
+    }
+    catch (TTransportException $tte)
+    {
+        echo 'TTransportException!<br><br>' . $tte->getMessage();
+    }
+    catch (\Exception $e)
+    {
+        echo 'Exception!<br><br>' . $e->getMessage();
+    }
+
+}
+
+?>
+

http://git-wip-us.apache.org/repos/asf/airavata/blob/b6392ef3/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateApplicationInterface.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateApplicationInterface.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateApplicationInterface.php
index baccbc3..5b96be8 100755
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateApplicationInterface.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateApplicationInterface.php
@@ -32,12 +32,12 @@ try
 
         $appInput1 = new InputDataObjectType();
         $appInput1->name = "Namelist_File";
-        $appInput1->userFriendlyDescription = "Namelist file";
+        $appInput1->userFriendlyDescription = "Namelist Configuration File";
         $appInput1->type = DataType::URI;
 
         $appInput2 = new InputDataObjectType();
-        $appInput2->name = "WRF Boundary File";
-        $appInput2->userFriendlyDescription = "Boundary file";
+        $appInput2->name = "WRF_Boundary_File";
+        $appInput2->userFriendlyDescription = "Boundary Conditions File";
         $appInput2->type = DataType::URI;
 
         $appInput3 = new InputDataObjectType();
@@ -46,11 +46,11 @@ try
         $appInput3->type = DataType::URI;
 
         $appOutput1 = new OutputDataObjectType();
-        $appOutput1->name = "WRF Standard Out";
+        $appOutput1->name = "WRF_Standard_Out";
         $appOutput1->type = DataType::STRING;
 
         $appOutput2 = new OutputDataObjectType();
-        $appOutput2->name = "WRF RSL Out";
+        $appOutput2->name = "WRF_RSL_Out";
         $appOutput2->type = DataType::STRING;
 
         $appInterface = $airavataclient->getApplicationInterface($appInterfaceId);

http://git-wip-us.apache.org/repos/asf/airavata/blob/b6392ef3/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
new file mode 100644
index 0000000..9db25fb
--- /dev/null
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
@@ -0,0 +1,376 @@
+/*
+ *
+ * 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.client.tools;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.UUID;
+
+import org.apache.airavata.api.Airavata;
+import org.apache.airavata.api.client.AiravataClientFactory;
+import org.apache.airavata.client.api.exception.AiravataAPIInvocationException;
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule;
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType;
+import org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription;
+import org.apache.airavata.model.appcatalog.appinterface.DataType;
+import org.apache.airavata.model.appcatalog.computeresource.*;
+import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference;
+import org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile;
+import org.apache.airavata.model.error.AiravataClientException;
+import org.apache.airavata.model.error.AiravataSystemException;
+import org.apache.airavata.model.error.InvalidRequestException;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.thrift.TException;
+
+public class RegisterSampleApplications {
+
+    public static final String THRIFT_SERVER_HOST = "localhost";
+    public static final int THRIFT_SERVER_PORT = 8930;
+    private final static Logger logger = LoggerFactory.getLogger(RegisterSampleApplications.class);
+    private static final String DEFAULT_USER = "default.registry.user";
+    private static final String DEFAULT_GATEWAY = "default.registry.gateway";
+    private static Airavata.Client airavataClient;
+
+    //Host Id's
+    private static String stampedeResourceId;
+    private static String trestlesResourceId;
+    private static String bigredResourceId;
+
+    //App Module Id's
+    private static String echoModuleId;
+    private static String amberModuleId;
+    private static String autoDockModuleId;
+    private static String espressoModuleId;
+    private static String gromacsModuleId;
+    private static String lammpsModuleId;
+    private static String nwChemModuleId;
+    private static String trinityModuleId;
+    private static String wrfModuleId;
+
+    public static void main(String[] args) {
+        try {
+            airavataClient = AiravataClientFactory.createAiravataClient(THRIFT_SERVER_HOST,
THRIFT_SERVER_PORT);
+            System.out.println("API version is " + airavataClient.getAPIVersion());
+
+            //Register all compute hosts
+            registerXSEDEHosts();
+
+            //Register all application modules
+            registerAppModules();
+
+            //Register all application deployments
+            registerAppDeployments();
+
+        } catch (Exception e) {
+            logger.error("Error while connecting with server", e.getMessage());
+            e.printStackTrace();
+        }
+    }
+
+    public static void registerXSEDEHosts() {
+        try {
+            System.out.println("\n #### Registering XSEDE Computational Resources #### \n");
+
+            //Register Stampede
+            stampedeResourceId = registerComputeHost("stampede.tacc.xsede.org", "TACC Stampede
Cluster",
+                    ResourceJobManagerType.SLURM, "push", "/usr/bin", SecurityProtocol.GSI,
2222);
+            System.out.println("Stampede Resource Id is " + stampedeResourceId);
+
+            //Register Trestles
+            trestlesResourceId = registerComputeHost("trestles.sdsc.xsede.org", "SDSC Trestles
Cluster",
+                    ResourceJobManagerType.PBS, "push", "/usr/bin", SecurityProtocol.GSI,
22);
+            System.out.println("Trestles Resource Id is " + trestlesResourceId);
+
+            //Register BigRedII
+            bigredResourceId = registerComputeHost("bigred2.uits.iu.edu", "IU BigRed II Cluster",
+                    ResourceJobManagerType.PBS, "push", "/opt/torque/torque-4.2.3.1/bin/",
SecurityProtocol.SSH_KEYS, 22);
+            System.out.println("BigredII Resource Id is " + bigredResourceId);
+
+        } catch (TException e) {
+            e.printStackTrace();
+        }
+
+    }
+
+    public static void registerAppModules() {
+        try {
+            System.out.println("\n #### Registering Application Modules #### \n");
+
+            //Register Echo
+            echoModuleId = airavataClient.registerApplicationModule(
+                    RegisterSampleApplicationsUtils.createApplicationModule(
+                            "Echo", "1.0", "A Simple Echo Application"));
+            System.out.println("Echo Module Id " + echoModuleId);
+
+            //Register Amber
+            amberModuleId = airavataClient.registerApplicationModule(
+                    RegisterSampleApplicationsUtils.createApplicationModule(
+                            "Amber", "12.0", "Amber Molecular Dynamics Package"));
+            System.out.println("Amber Module Id " + amberModuleId);
+
+            //Register AutoDock
+            autoDockModuleId = airavataClient.registerApplicationModule(
+                    RegisterSampleApplicationsUtils.createApplicationModule(
+                            "AutoDock", "4.2", "AutoDock suite of automated docking tools"));
+            System.out.println("AutoDock Module Id " + autoDockModuleId);
+
+            //Register ESPRESSO
+            espressoModuleId = airavataClient.registerApplicationModule(
+                    RegisterSampleApplicationsUtils.createApplicationModule(
+                            "ESPRESSO", "5.0.3", "Nanoscale electronic-structure calculations
and materials modeling"));
+            System.out.println("ESPRESSO Module Id " + espressoModuleId);
+
+            //Register GROMACS
+            gromacsModuleId = airavataClient.registerApplicationModule(
+                    RegisterSampleApplicationsUtils.createApplicationModule(
+                            "GROMACS", "4.6.5", "GROMACS Molecular Dynamics Package"));
+            System.out.println("GROMACS Module Id " + gromacsModuleId);
+
+            //Register LAMMPS
+            lammpsModuleId = airavataClient.registerApplicationModule(
+                    RegisterSampleApplicationsUtils.createApplicationModule(
+                            "LAMMPS", "20Mar14", "Large-scale Atomic/Molecular Massively
Parallel Simulator"));
+            System.out.println("LAMMPS Module Id " + lammpsModuleId);
+
+            //Register NWChem
+            nwChemModuleId = airavataClient.registerApplicationModule(
+                    RegisterSampleApplicationsUtils.createApplicationModule(
+                            "NWChem", "6.3", "Ab initio computational chemistry software
package"));
+            System.out.println("NWChem Module Id " + nwChemModuleId);
+
+            //Register Trinity
+            trinityModuleId = airavataClient.registerApplicationModule(
+                    RegisterSampleApplicationsUtils.createApplicationModule(
+                            "Trinity", "r20130225", "de novo reconstruction of transcriptomes
from RNA-seq data"));
+            System.out.println("Trinity Module Id " + trinityModuleId);
+
+            //Register WRF
+            wrfModuleId = airavataClient.registerApplicationModule(
+                    RegisterSampleApplicationsUtils.createApplicationModule(
+                            "WRF", "3.5.1", "Weather Research and Forecasting"));
+            System.out.println("WRF Module Id " + wrfModuleId);
+
+        } catch (TException e) {
+            e.printStackTrace();
+        }
+
+    }
+
+    public static void registerAppDeployments() {
+        System.out.println("\n #### Registering Application Deployments #### \n");
+
+        //Registering Stampede Apps
+        registerStampedeApps();
+
+        //Registering Trestles Apps
+        registerTrestlesApps();
+
+        //Registering BigRed II Apps
+        registerBigRedApps();
+    }
+
+    public static void registerStampedeApps() {
+        try {
+            System.out.println("#### Registering Application Deployments on Stampede ####
\n");
+
+            //Register Echo
+            String echoAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(echoModuleId,
stampedeResourceId,
+                            "/bin/echo", ApplicationParallelismType.SERIAL, "Echo Testing
Application"));
+            System.out.println("Echo on stampede deployment Id " + echoAppDeployId);
+
+            //Register Amber
+            String amberAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(amberModuleId,
stampedeResourceId,
+                            "/home1/01437/ogce/production/app_wrappers/amber_wrapper_simple.sh",
ApplicationParallelismType.MPI,
+                            "Amber Molecular Dynamics Package"));
+            System.out.println("Amber on stampede deployment Id " + amberAppDeployId);
+
+            //Register ESPRESSO
+            String espressoAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(espressoModuleId,
stampedeResourceId,
+                            "/home1/01437/ogce/production/app_wrappers/espresso_wrapper.sh",
ApplicationParallelismType.MPI,
+                            "Nanoscale electronic-structure calculations and materials modeling"));
+            System.out.println("ESPRESSO on stampede deployment Id " + espressoAppDeployId);
+
+            //Register GROMACS
+            String gromacsAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(gromacsModuleId,
stampedeResourceId,
+                            "/home1/01437/ogce/production/app_wrappers/gromacs_wrapper.sh",
ApplicationParallelismType.MPI,
+                            "GROMACS Molecular Dynamics Package"));
+            System.out.println("GROMACS on stampede deployment Id " + gromacsAppDeployId);
+
+            //Register LAMMPS
+            String lammpsAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(lammpsModuleId,
stampedeResourceId,
+                            "/home1/01437/ogce/production/app_wrappers/lammps_wrapper.sh",
ApplicationParallelismType.MPI,
+                            "Large-scale Atomic/Molecular Massively Parallel Simulator"));
+            System.out.println("LAMMPS on stampede deployment Id " + lammpsAppDeployId);
+
+            //Register NWChem
+            String nwChemAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(nwChemModuleId,
stampedeResourceId,
+                            "/home1/01437/ogce/production/app_wrappers/nwchem_wrapper.sh",
ApplicationParallelismType.MPI,
+                            "Ab initio computational chemistry software package"));
+            System.out.println("NWChem on stampede deployment Id " + nwChemAppDeployId);
+
+            //Register Trinity
+            String trinityAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(trinityModuleId,
stampedeResourceId,
+                            "/home1/01437/ogce/production/app_wrappers/trinity_wrapper.sh",
ApplicationParallelismType.MPI,
+                            "de novo reconstruction of transcriptomes from RNA-seq data"));
+            System.out.println("Trinity on stampede deployment Id " + trinityAppDeployId);
+
+            //Register WRF
+            String wrfAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(wrfModuleId,
stampedeResourceId,
+                            "/home1/01437/ogce/production/app_wrappers/wrf_wrapper_3.5.1.sh",
ApplicationParallelismType.MPI,
+                            "Weather Research and Forecasting"));
+            System.out.println("WRF on stampede deployment Id " + wrfAppDeployId);
+
+        } catch (TException e) {
+            e.printStackTrace();
+        }
+    }
+
+    public static void registerTrestlesApps() {
+        try {
+            System.out.println("#### Registering Application Deployments on Trestles ####
\n");
+
+            //Register Echo
+            String echoAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(echoModuleId,
trestlesResourceId,
+                            "/bin/echo", ApplicationParallelismType.SERIAL, "Echo Testing
Application"));
+            System.out.println("Echo on trestles deployment Id " + echoAppDeployId);
+
+            //Register Amber
+            String amberAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(amberModuleId,
trestlesResourceId,
+                            "/home/ogce/production/app_wrappers/amber_wrapper_simple.sh",
ApplicationParallelismType.MPI,
+                            "Amber Molecular Dynamics Package"));
+            System.out.println("Amber on trestles deployment Id " + amberAppDeployId);
+
+            //Register GROMACS
+            String gromacsAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(gromacsModuleId,
trestlesResourceId,
+                            "/home/ogce/production/app_wrappers/gromacs_wrapper.sh", ApplicationParallelismType.MPI,
+                            "GROMACS Molecular Dynamics Package"));
+            System.out.println("GROMACS on trestles deployment Id " + gromacsAppDeployId);
+
+            //Register LAMMPS
+            String lammpsAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(lammpsModuleId,
trestlesResourceId,
+                            "/home/ogce/production/app_wrappers/lammps_wrapper.sh", ApplicationParallelismType.MPI,
+                            "Large-scale Atomic/Molecular Massively Parallel Simulator"));
+            System.out.println("LAMMPS on trestles deployment Id " + lammpsAppDeployId);
+
+        } catch (TException e) {
+            e.printStackTrace();
+        }
+    }
+
+    public static void registerBigRedApps() {
+        try {
+            System.out.println("#### Registering Application Deployments on BigRed II ####
\n");
+
+            //Register Echo
+            String echoAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(echoModuleId,
bigredResourceId,
+                            "/bin/echo", ApplicationParallelismType.SERIAL, "Echo Testing
Application"));
+            System.out.println("Echo on bigredII deployment Id " + echoAppDeployId);
+
+            //Register Amber
+            String amberAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(amberModuleId,
bigredResourceId,
+                            "/N/u/cgateway/BigRed2/production/app_wrappers/amber_wrapper_simple.sh",
ApplicationParallelismType.MPI,
+                            "Amber Molecular Dynamics Package"));
+            System.out.println("Amber on bigredII deployment Id " + amberAppDeployId);
+
+            //Register AutoDock
+            String autoDockDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(nwChemModuleId,
bigredResourceId,
+                            "/N/u/cgateway/BigRed2/production/app_wrappers/auto_dock_wrapper.sh",
ApplicationParallelismType.MPI,
+                            "AutoDock suite of automated docking tools"));
+            System.out.println("AutoDock on bigredII deployment Id " + autoDockDeployId);
+
+            //Register GROMACS
+            String gromacsAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(gromacsModuleId,
bigredResourceId,
+                            "/N/u/cgateway/BigRed2/production/app_wrappers/gromacs_wrapper.sh",
ApplicationParallelismType.MPI,
+                            "GROMACS Molecular Dynamics Package"));
+            System.out.println("GROMACS on bigredII deployment Id " + gromacsAppDeployId);
+
+            //Register LAMMPS
+            String lammpsAppDeployId = airavataClient.registerApplicationDeployment(
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(lammpsModuleId,
bigredResourceId,
+                            "/N/u/cgateway/BigRed2/production/app_wrappers/lammps_wrapper.sh",
ApplicationParallelismType.MPI,
+                            "Large-scale Atomic/Molecular Massively Parallel Simulator"));
+            System.out.println("LAMMPS on bigredII deployment Id " + lammpsAppDeployId);
+
+        } catch (TException e) {
+            e.printStackTrace();
+        }
+    }
+
+    public static String registerComputeHost(String hostName, String hostDesc,
+                                             ResourceJobManagerType resourceJobManagerType,
+                                             String monitoringEndPoint, String jobMangerBinPath,
+                                             SecurityProtocol securityProtocol, int portNumber)
throws TException {
+
+        ComputeResourceDescription computeResourceDescription = RegisterSampleApplicationsUtils.
+                createComputeResourceDescription(hostName, hostDesc, null, null);
+
+        String computeResourceId = airavataClient.registerComputeResource(computeResourceDescription);
+
+        if (computeResourceId.isEmpty()) throw new AiravataClientException();
+
+        ResourceJobManager resourceJobManager = RegisterSampleApplicationsUtils.
+                createResourceJobManager(resourceJobManagerType, monitoringEndPoint, jobMangerBinPath,
null);
+
+        SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
+        sshJobSubmission.setResourceJobManager(resourceJobManager);
+        sshJobSubmission.setSecurityProtocol(securityProtocol);
+        sshJobSubmission.setSshPort(portNumber);
+        boolean sshAddStatus = airavataClient.addSSHJobSubmissionDetails(computeResourceId,
1, sshJobSubmission);
+
+        if (!sshAddStatus) throw new AiravataClientException();
+
+        SCPDataMovement scpDataMovement = new SCPDataMovement();
+        scpDataMovement.setSecurityProtocol(securityProtocol);
+        scpDataMovement.setSshPort(portNumber);
+        boolean scpAddStatus = airavataClient.addSCPDataMovementDetails(computeResourceId,
1, scpDataMovement);
+
+        if (!scpAddStatus) throw new AiravataClientException();
+
+        return computeResourceId;
+    }
+}
+

http://git-wip-us.apache.org/repos/asf/airavata/blob/b6392ef3/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplicationsUtils.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplicationsUtils.java
b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplicationsUtils.java
new file mode 100644
index 0000000..f47b0aa
--- /dev/null
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplicationsUtils.java
@@ -0,0 +1,154 @@
+/*
+*
+* 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.client.tools;
+
+import org.airavata.appcatalog.cpi.AppCatalogException;
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule;
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType;
+import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
+import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
+import org.apache.airavata.model.appcatalog.computeresource.*;
+import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference;
+
+import java.util.Map;
+import java.util.Set;
+
+public class RegisterSampleApplicationsUtils {
+
+
+    public static ComputeResourcePreference
+        createComputeResourcePreference(String computeResourceId, String allocationProjectNumber,
+                                        boolean overridebyAiravata, String preferredBatchQueue,
+                                        String preferredJobSubmissionProtocol,String preferredDataMovementProtocol,
+                                        String scratchLocation) throws AppCatalogException
{
+        ComputeResourcePreference computeResourcePreference = new ComputeResourcePreference();
+        computeResourcePreference.setComputeResourceId(computeResourceId);
+        computeResourcePreference.setOverridebyAiravata(overridebyAiravata);
+        computeResourcePreference.setAllocationProjectNumber(allocationProjectNumber);
+        computeResourcePreference.setPreferredBatchQueue(preferredBatchQueue);
+        computeResourcePreference.setPreferredDataMovementProtocol(preferredDataMovementProtocol);
+        computeResourcePreference.setPreferredJobSubmissionProtocol(preferredJobSubmissionProtocol);
+        computeResourcePreference.setScratchLocation(scratchLocation);
+        return computeResourcePreference;
+    }
+
+    public static ApplicationDeploymentDescription createApplicationDeployment(
+           String appModuleId, String computeResourceId, String executablePath,
+           ApplicationParallelismType parallelism, String appDeploymentDescription) {
+        ApplicationDeploymentDescription deployment = new ApplicationDeploymentDescription();
+//		deployment.setIsEmpty(false);
+        deployment.setAppDeploymentDescription(appDeploymentDescription);
+        deployment.setAppModuleId(appModuleId);
+        deployment.setComputeHostId(computeResourceId);
+        deployment.setExecutablePath(executablePath);
+        deployment.setParallelism(parallelism);
+        return deployment;
+    }
+
+    public static ApplicationModule createApplicationModule(String appModuleName,
+                                                            String appModuleVersion, String
appModuleDescription) {
+        ApplicationModule module = new ApplicationModule();
+        module.setAppModuleDescription(appModuleDescription);
+        module.setAppModuleName(appModuleName);
+        module.setAppModuleVersion(appModuleVersion);
+        return module;
+    }
+
+    public static DataMovementInterface createDataMovementInterface(
+            String dataMovementInterfaceId,
+            DataMovementProtocol dataMovementProtocolType, int priorityOrder) {
+        DataMovementInterface dataMovementInterface = new DataMovementInterface();
+        dataMovementInterface.setDataMovementInterfaceId(dataMovementInterfaceId);
+        dataMovementInterface.setDataMovementProtocol(dataMovementProtocolType);
+        dataMovementInterface.setPriorityOrder(priorityOrder);
+        return dataMovementInterface;
+    }
+
+    public static JobSubmissionInterface createJobSubmissionInterface(
+            String jobSubmissionInterfaceId,
+            JobSubmissionProtocol jobSubmissionProtocolType, int priorityOrder) {
+        JobSubmissionInterface jobSubmissionInterface = new JobSubmissionInterface();
+        jobSubmissionInterface.setJobSubmissionInterfaceId(jobSubmissionInterfaceId);
+        jobSubmissionInterface.setJobSubmissionProtocol(jobSubmissionProtocolType);
+        jobSubmissionInterface.setPriorityOrder(priorityOrder);
+        return jobSubmissionInterface;
+    }
+
+    public static ComputeResourceDescription createComputeResourceDescription(
+            String hostName, String hostDesc, Set<String> hostAliases, Set<String>
ipAddresses) {
+        ComputeResourceDescription host = new ComputeResourceDescription();
+        host.setHostName(hostName);
+        host.setResourceDescription(hostDesc);
+        host.setIpAddresses(ipAddresses);
+        host.setHostAliases(hostAliases);
+        return host;
+    }
+
+    public static ResourceJobManager createResourceJobManager(
+            ResourceJobManagerType resourceJobManagerType, String pushMonitoringEndpoint,
String jobManagerBinPath,
+            Map<JobManagerCommand, String> jobManagerCommands) {
+        ResourceJobManager resourceJobManager = new ResourceJobManager();
+        resourceJobManager.setResourceJobManagerType(resourceJobManagerType);
+        resourceJobManager.setJobManagerBinPath(jobManagerBinPath);
+        resourceJobManager.setJobManagerCommands(jobManagerCommands);
+        resourceJobManager.setPushMonitoringEndpoint(pushMonitoringEndpoint);
+        return resourceJobManager;
+    }
+
+    public static InputDataObjectType createAppInput(String inputName, String argumentName,
String description, String value, org.apache.airavata.model.appcatalog.appinterface.DataType
type) {
+        InputDataObjectType input = new InputDataObjectType();
+//        input.setIsEmpty(false);
+        if (inputName != null) {
+            input.setName(inputName);
+        }
+        if (value != null) {
+            input.setValue(value);
+        }
+        if (type != null) {
+            input.setType(type);
+        }
+        if (argumentName != null) {
+            input.setApplicationArgument(argumentName);
+        }
+        if (description != null) {
+            input.setUserFriendlyDescription(description);
+        }
+        return input;
+    }
+
+    public static OutputDataObjectType createAppOutput(String inputName, String value, org.apache.airavata.model.appcatalog.appinterface.DataType
type) {
+        OutputDataObjectType outputDataObjectType = new OutputDataObjectType();
+//        outputDataObjectType.setIsEmpty(false);
+        if (inputName != null) {
+            outputDataObjectType.setName(inputName);
+        }
+        if (value != null) {
+            outputDataObjectType.setValue(value);
+        }
+        if (type != null) {
+            outputDataObjectType.setType(type);
+        }
+        return outputDataObjectType;
+    }
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/b6392ef3/airavata-api/thrift-interface-descriptions/applicationDeploymentModel.thrift
----------------------------------------------------------------------
diff --git a/airavata-api/thrift-interface-descriptions/applicationDeploymentModel.thrift
b/airavata-api/thrift-interface-descriptions/applicationDeploymentModel.thrift
index 4ee3978..9df1df3 100644
--- a/airavata-api/thrift-interface-descriptions/applicationDeploymentModel.thrift
+++ b/airavata-api/thrift-interface-descriptions/applicationDeploymentModel.thrift
@@ -120,7 +120,7 @@ struct ApplicationDeploymentDescription {
     2: required string appModuleId,
     3: required string computeHostId,
     4: required string executablePath,
-    5: required ApplicationParallelismType parallelism = ApplicationParallelismType.SERIAL
,
+    5: required ApplicationParallelismType parallelism = ApplicationParallelismType.SERIAL,
 	6: optional string appDeploymentDescription,
 	7: optional list<string> moduleLoadCmds,
 	8: optional list<SetEnvPaths> libPrependPaths,


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