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From lah...@apache.org
Subject [1/2] airavata git commit: adding lsf support with tests
Date Sat, 07 Mar 2015 05:37:38 GMT
Repository: airavata
Updated Branches:
  refs/heads/master 9d80cf298 -> 565b5a3f4


adding lsf support with tests


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/5ff650f4
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/5ff650f4
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/5ff650f4

Branch: refs/heads/master
Commit: 5ff650f4c61a9ee7bfcf6f15ea984d74d545ec32
Parents: e9468ca
Author: Lahiru Gunathilake <glahiru@gmail.com>
Authored: Sat Mar 7 00:37:06 2015 -0500
Committer: Lahiru Gunathilake <glahiru@gmail.com>
Committed: Sat Mar 7 00:37:06 2015 -0500

----------------------------------------------------------------------
 .../client/samples/CreateLaunchExperiment.java  |  73 +++++-
 .../tools/RegisterSampleApplications.java       |  53 +++-
 .../server/src/main/resources/LSFTemplate.xslt  |  43 ++--
 .../server/src/main/resources/PBSTemplate.xslt  |   3 +-
 .../credential/store/client/TestSSLClient.java  |   2 +-
 .../store/store/impl/db/SSHCredentialTest.java  |   6 +-
 .../test/resources/airavata-server.properties   | 254 +++++++++++++++++++
 .../server/src/main/assembly/bin-assembly.xml   |   1 +
 .../airavata/gfac/server/GfacServerHandler.java |   1 -
 .../org/apache/airavata/gfac/RequestData.java   |   2 +
 .../gfac/gsissh/util/GFACGSISSHUtils.java       |  10 +-
 .../airavata/gfac/ssh/util/GFACSSHUtils.java    |  23 +-
 .../ssh/api/job/JobManagerConfiguration.java    |   9 +-
 .../gsi/ssh/api/job/LSFJobConfiguration.java    |  18 +-
 .../gsi/ssh/api/job/LSFOutputParser.java        |   1 +
 .../gsi/ssh/api/job/PBSJobConfiguration.java    |  15 ++
 .../gsi/ssh/api/job/SlurmJobConfiguration.java  |  15 ++
 .../gsi/ssh/impl/GSISSHAbstractCluster.java     |  10 +-
 .../airavata/gsi/ssh/impl/RawCommandInfo.java   |   8 +-
 .../impl/DefaultSSHApiTestWithMyProxyAuth.java  |  15 +-
 20 files changed, 500 insertions(+), 62 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
index 3fc74eb..bb2ae6e 100644
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
@@ -58,7 +58,7 @@ public class CreateLaunchExperiment {
     private static final String DEFAULT_GATEWAY = "php_reference_gateway";
     private static Airavata.Client airavataClient;
 
-    private static String echoAppId = "Echo_f828a575-7f17-4149-9d45-abe2aa9c6109";
+    private static String echoAppId = "Echo_802454e5-6358-4371-9a04-3d5d59cecbc7";
     private static String mpiAppId = "HelloMPI_720e159f-198f-4daa-96ca-9f5eafee92c9";
     private static String wrfAppId = "WRF_7ad5da38-c08b-417c-a9ea-da9298839762";
     private static String amberAppId = "Amber_a56d457c-f239-4c0b-ba00-66bda936f7bc";
@@ -69,15 +69,15 @@ public class CreateLaunchExperiment {
     private static String trinityAppId = "Trinity_e894acf5-9bca-46e8-a1bd-7e2d5155191a";
     private static String autodockAppId = "AutoDock_43d9fdd0-c404-49f4-b913-3abf9080a8c9";
 
-
     private static String localHost = "localhost";
     private static String trestlesHostName = "trestles.sdsc.xsede.org";
     private static String unicoreHostName = "fsd-cloud15.zam.kfa-juelich.de";
     private static String stampedeHostName = "stampede.tacc.xsede.org";
     private static String br2HostName = "bigred2.uits.iu.edu";
+    private static String umassrcHostName = "ghpcc06.umassrc.org";
 
     private static String gatewayId;
-    
+
  // unicore service endpoint url
     private static final String unicoreEndPointURL = "https://fsd-cloud15.zam.kfa-juelich.de:7000/INTEROP1/services/BESFactory?res=default_bes_factory";
     
@@ -88,7 +88,7 @@ public class CreateLaunchExperiment {
 //        createGateway();
 //        getGateway("testGatewayId");
 //      registerApplications(); // run this only the first time
-      createAndLaunchExp();
+        createAndLaunchExp();
     }
     
     private static String fsdResourceId;
@@ -154,13 +154,14 @@ public class CreateLaunchExperiment {
 //                final String expId = createExperimentForBR2Amber(airavataClient);
 //                final String expId = createExperimentWRFStampede(airavataClient);
 //                final String expId = createExperimentForStampedeAmber(airavataClient);
-                final String expId = createExperimentForTrestlesAmber(airavataClient);
+//                final String expId = createExperimentForTrestlesAmber(airavataClient);
 //                final String expId = createExperimentGROMACSStampede(airavataClient);
 //                final String expId = createExperimentESPRESSOStampede(airavataClient);
 //                final String expId = createExperimentLAMMPSStampede(airavataClient);
 //                final String expId = createExperimentNWCHEMStampede(airavataClient);
 //                final String expId = createExperimentTRINITYStampede(airavataClient);
 //                final String expId = createExperimentAUTODOCKStampede(airavataClient); // this is not working , we need to register AutoDock app on stampede
+                final String expId = createExperimentForLSF(airavataClient);
 //            	  final String expId = "Ultrascan_ln_eb029947-391a-4ccf-8ace-9bafebe07cc0";
                 System.out.println("Experiment ID : " + expId);
 //                updateExperiment(airavata, expId);
@@ -185,6 +186,8 @@ public class CreateLaunchExperiment {
         //Register all compute hosts
         registerSampleApplications.registerXSEDEHosts();
 
+        registerSampleApplications.registerNonXSEDEHosts();
+
         //Register Gateway Resource Preferences
         registerSampleApplications.registerGatewayResourceProfile();
 
@@ -1343,6 +1346,63 @@ public class CreateLaunchExperiment {
         return null;
     }
 
+    public static String createExperimentForLSF(Airavata.Client client) throws TException {
+        try {
+            List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
+            InputDataObjectType input = new InputDataObjectType();
+            input.setName("Input_to_Echo");
+            input.setType(DataType.STRING);
+            input.setValue("Echoed_Output=Hello World");
+            input.setRequiredToAddedToCommandLine(true);
+            exInputs.add(input);
+
+            List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
+            OutputDataObjectType output = new OutputDataObjectType();
+            output.setName("output_file");
+            output.setType(DataType.URI);
+            output.setValue("");
+            exOut.add(output);
+
+            Project project = ProjectModelUtil.createProject("default", "lg11w", "test project");
+            String projectId = client.createProject(DEFAULT_GATEWAY, project);
+
+            Experiment simpleExperiment =
+                    ExperimentModelUtil.createSimpleExperiment(projectId, "lg11w", "sshEchoExperiment", "StressMem", echoAppId, exInputs);
+            simpleExperiment.setExperimentOutputs(exOut);
+
+            Map<String, String> computeResources = airavataClient.getAvailableAppInterfaceComputeResources(echoAppId);
+            if (computeResources != null && computeResources.size() != 0) {
+                for (String id : computeResources.keySet()) {
+                    String resourceName = computeResources.get(id);
+                    if (resourceName.equals(umassrcHostName)) {
+                        ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 10, 1, 1, "long", 60, 0, 1000, "airavata");
+                        UserConfigurationData userConfigurationData = new UserConfigurationData();
+                        userConfigurationData.setAiravataAutoSchedule(false);
+                        userConfigurationData.setOverrideManualScheduledParams(false);
+                        userConfigurationData.setComputationalResourceScheduling(scheduling);
+                        simpleExperiment.setUserConfigurationData(userConfigurationData);
+                        simpleExperiment.setEmailAddresses(Arrays.asList(new String[]{"test@umassmed.edu"}));
+                        return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
+                    }
+                }
+            }
+        } catch (AiravataSystemException e) {
+            logger.error("Error occured while creating the experiment...", e.getMessage());
+            throw new AiravataSystemException(e);
+        } catch (InvalidRequestException e) {
+            logger.error("Error occured while creating the experiment...", e.getMessage());
+            throw new InvalidRequestException(e);
+        } catch (AiravataClientException e) {
+            logger.error("Error occured while creating the experiment...", e.getMessage());
+            throw new AiravataClientException(e);
+        } catch (TException e) {
+            logger.error("Error occured while creating the experiment...", e.getMessage());
+            throw new TException(e);
+        }
+        return null;
+    }
+
+
     public static String createExperimentForBR2Amber(Airavata.Client client) throws TException {
         try {
 			List<InputDataObjectType> exInputs = client.getApplicationInputs(amberAppId);
@@ -1538,8 +1598,7 @@ public class CreateLaunchExperiment {
     public static void launchExperiment(Airavata.Client client, String expId)
             throws TException {
         try {
-//        	String tokenId = "5f116091-0ad3-4ab6-9df7-6ac909f21f8b";
-        	String tokenId ="aaaaaa";
+        	String tokenId ="aa-dcdb-48e3-9cd5-ac90b710d55e";
             client.launchExperiment(expId, tokenId);
         } catch (ExperimentNotFoundException e) {
             logger.error("Error occured while launching the experiment...", e.getMessage());

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/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
index 7f7ac1d..8ae2dd2 100644
--- 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
@@ -54,6 +54,8 @@ public class RegisterSampleApplications {
     private static String stampedeResourceId = "stampede.tacc.xsede.org_92ac5ed6-35a5-4910-82ef-48f128f9245a";
     private static String trestlesResourceId = "trestles.sdsc.xsede.org_db29986e-5a27-4949-ae7f-04a6012d0d35";
     private static String bigredResourceId = "bigred2.uits.iu.edu_3eae6e9d-a1a7-44ec-ac85-3796ef726ef1";
+    private static String lsfResourceId = "lsf_3eae6e9d-a1a7-44ec-ac85-3796ef726ef1";
+
     private static String fsdResourceId;
  // unicore service endpoint url
     private static final String unicoreEndPointURL = "https://fsd-cloud15.zam.kfa-juelich.de:7000/INTEROP1/services/BESFactory?res=default_bes_factory";
@@ -73,6 +75,7 @@ public class RegisterSampleApplications {
     private static final String monteXName = "TinkerMonte";
     private static final String gaussianName = "Gaussian";
     private static final String gamessName = "Gamess";
+    private static final String stressMemName = "StressMem";
 
     //Appplication Descriptions
     private static final String echoDescription = "A Simple Echo Application";
@@ -90,6 +93,7 @@ public class RegisterSampleApplications {
     private static final String gaussianDescription = "Grid Chem Gaussian Application";
     private static final String gamessDescription = "A Gamess Application";
 
+
     //App Module Id's
     private static String echoModuleId;
     private static String amberModuleId;
@@ -136,6 +140,7 @@ public class RegisterSampleApplications {
             //Register all compute hosts
             registerSampleApplications.registerXSEDEHosts();
 
+            registerSampleApplications.registerNonXSEDEHosts();
 
             //Register Gateway Resource Preferences
             registerSampleApplications.registerGatewayResourceProfile();
@@ -200,10 +205,24 @@ public class RegisterSampleApplications {
             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, "aprun -n");
             System.out.println("BigredII Resource Id is " + bigredResourceId);
-            
+
             fsdResourceId = registerUnicoreEndpoint("fsd-cloud15.zam.kfa-juelich.de", "interop host", JobSubmissionProtocol.UNICORE, SecurityProtocol.GSI);
             System.out.println("FSd Resource Id: "+fsdResourceId);
-            
+
+        } catch (TException e) {
+            e.printStackTrace();
+        }
+
+    }
+
+    public void registerNonXSEDEHosts() {
+        try {
+            System.out.println("\n #### Registering Non-XSEDE Computational Resources #### \n");
+
+            //Register LSF resource
+            lsfResourceId = registerComputeHost("ghpcc06.umassrc.org", "LSF Cluster",
+                    ResourceJobManagerType.LSF, "push", "source /etc/bashrc;/lsf/9.1/linux2.6-glibc2.3-x86_64/bin", SecurityProtocol.SSH_KEYS, 22, null);
+            System.out.println("LSF Resource Id is " + lsfResourceId);
 
         } catch (TException e) {
             e.printStackTrace();
@@ -317,7 +336,6 @@ public class RegisterSampleApplications {
                             gamessName, "17May13", gamessDescription));
             System.out.println("Gamess Module Id " + gamessModuleId);
 
-
         } catch (TException e) {
             e.printStackTrace();
         }
@@ -341,6 +359,7 @@ public class RegisterSampleApplications {
         //Registering FSD Apps
         registerFSDApps();
 
+        registerLSFApps();
 
     }
 
@@ -493,8 +512,8 @@ public class RegisterSampleApplications {
             e.printStackTrace();
         }
     }
-    
-    
+
+
     public void registerMPIInterface() {
         try {
             System.out.println("#### Registering MPI Interface #### \n");
@@ -1084,6 +1103,22 @@ public class RegisterSampleApplications {
         }
     }
 
+    public void registerLSFApps() {
+        try {
+            System.out.println("#### Registering Application Deployments on Trestles #### \n");
+
+            //Register Echo
+            String echoAppDeployId = airavataClient.registerApplicationDeployment(DEFAULT_GATEWAY,
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(echoModuleId, lsfResourceId,
+                            "/home/lg11w/executables/echo.sh", ApplicationParallelismType.SERIAL,
+                            echoDescription, null, null, null));
+            System.out.println("Echo on trestles deployment Id " + echoAppDeployId);
+
+        } catch (TException e) {
+            e.printStackTrace();
+        }
+    }
+
     public void registerBigRedApps() {
         try {
             System.out.println("#### Registering Application Deployments on BigRed II #### \n");
@@ -1127,7 +1162,7 @@ public class RegisterSampleApplications {
             e.printStackTrace();
         }
     }
-    
+
     public void registerFSDApps() {
         try {
             System.out.println("#### Registering Application Deployments on FSD #### \n");
@@ -1207,6 +1242,10 @@ public class RegisterSampleApplications {
             ComputeResourcePreference bigRedResourcePreferences = RegisterSampleApplicationsUtils.
                     createComputeResourcePreference(bigredResourceId, "TG-STA110014S", false, null, null, null,
                             "/N/dc2/scratch/cgateway/gta-work-dirs");
+
+            ComputeResourcePreference lsfResourcePreferences = RegisterSampleApplicationsUtils.
+                    createComputeResourcePreference(lsfResourceId, "airavata", false, null, null, null,
+                            "/home/lg11w/mywork");
             
             ComputeResourcePreference fsdResourcePreferences = RegisterSampleApplicationsUtils.
                     createComputeResourcePreference(fsdResourceId, null, false, null, JobSubmissionProtocol.UNICORE, DataMovementProtocol.UNICORE_STORAGE_SERVICE,null);
@@ -1217,6 +1256,7 @@ public class RegisterSampleApplications {
             gatewayResourceProfile.addToComputeResourcePreferences(trestlesResourcePreferences);
             gatewayResourceProfile.addToComputeResourcePreferences(bigRedResourcePreferences);
             gatewayResourceProfile.addToComputeResourcePreferences(fsdResourcePreferences);
+            gatewayResourceProfile.addToComputeResourcePreferences(lsfResourcePreferences);
 
             String gatewayProfile = airavataClient.registerGatewayResourceProfile(gatewayResourceProfile);
             System.out.println("Gateway Profile is registered with Id " + gatewayProfile);
@@ -1232,6 +1272,7 @@ public class RegisterSampleApplications {
             properties.setProperty("stampedeResourceId", stampedeResourceId);
             properties.setProperty("trestlesResourceId", trestlesResourceId);
             properties.setProperty("bigredResourceId", bigredResourceId);
+            properties.setProperty("lsfResourceId", lsfResourceId);
 
             properties.setProperty("echoInterfaceId", echoInterfaceId);
             properties.setProperty("amberInterfaceId", amberInterfaceId);

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/configuration/server/src/main/resources/LSFTemplate.xslt
----------------------------------------------------------------------
diff --git a/modules/configuration/server/src/main/resources/LSFTemplate.xslt b/modules/configuration/server/src/main/resources/LSFTemplate.xslt
index ab9fbbd..7081260 100644
--- a/modules/configuration/server/src/main/resources/LSFTemplate.xslt
+++ b/modules/configuration/server/src/main/resources/LSFTemplate.xslt
@@ -9,47 +9,61 @@
     <xsl:output method="text" />
     <xsl:template match="/ns:JobDescriptor">
         <xsl:param name="quote">"</xsl:param>
-        #! /bin/bash
-        # LSF batch job submission script generated by Apache Airavata
-        #
+#! /bin/bash
+# LSF batch job submission script generated by Apache Airavata
+#
+        <xsl:choose>
+            <xsl:when test="ns:shellName">
+#BSUB -L <xsl:value-of select="ns:shellName"/>
+            </xsl:when></xsl:choose>
         <xsl:choose>
             <xsl:when test="ns:queueName">
-                #BSUB -n <xsl:value-of select="ns:queueName"/>
+#BSUB -q <xsl:value-of select="ns:queueName"/>
+            </xsl:when>
+        </xsl:choose>
+        <xsl:choose>
+            <xsl:when test="ns:nodes">
+#BSUB -n <xsl:value-of select="ns:nodes"/>
             </xsl:when>
         </xsl:choose>
         <xsl:choose>
             <xsl:when test="ns:mailAddress">
-                #BSUB -u <xsl:value-of select="ns:mailAddress"/>
+#BSUB -u <xsl:value-of select="ns:mailAddress"/>
             </xsl:when>
         </xsl:choose>
         <xsl:choose>
             <xsl:when test="ns:jobName">
-                #BSUB -J <xsl:value-of select="ns:jobName"/>
+#BSUB -J <xsl:value-of select="ns:jobName"/>
             </xsl:when>
         </xsl:choose>
         <xsl:choose>
-        <xsl:when test="ns:acountString">
-            #BSUB -P <xsl:value-of select="ns:acountString"/>
-        </xsl:when>
-       </xsl:choose>
+            <xsl:when test="ns:acountString">
+#BSUB -P <xsl:value-of select="ns:acountString"/>
+            </xsl:when>
+        </xsl:choose>
         <xsl:choose>
             <xsl:when test="ns:maxWallTime">
-                #BSUB -W<xsl:value-of select="ns:maxWallTime"/>
+#BSUB -W <xsl:value-of select="ns:maxWallTime"/>
             </xsl:when>
         </xsl:choose>
         <xsl:choose>
             <xsl:when test="ns:standardOutFile">
-                #BSUB -o <xsl:value-of select="ns:standardOutFile"/>
+#BSUB -o "<xsl:value-of select="ns:standardOutFile"/>"
             </xsl:when>
         </xsl:choose>
         <xsl:choose>
             <xsl:when test="ns:standardOutFile">
-                #BSUB -e <xsl:value-of select="ns:standardErrorFile"/>
+#BSUB -e "<xsl:value-of select="ns:standardErrorFile"/>"
+            </xsl:when>
+        </xsl:choose>
+        <xsl:choose>
+            <xsl:when test="ns:chassisName">
+#BSUB -m c<xsl:value-of select="ns:chassisName"/>
             </xsl:when>
         </xsl:choose>
         <xsl:choose>
             <xsl:when test="ns:usedMem">
-                #BSUB -R rusage[mem=<xsl:value-of select="ns:usedMem"/>]
+#BSUB -R rusage[mem=<xsl:value-of select="ns:usedMem"/>]
             </xsl:when>
         </xsl:choose>
 
@@ -74,7 +88,6 @@
             <xsl:value-of select="."/><xsl:text>   </xsl:text>
         </xsl:for-each>
         <xsl:text>&#xa;</xsl:text>
-        ~/rabbitmq-java-client-bin-3.3.5/runjava.sh com.rabbitmq.examples.SimpleProducer amqp://<xsl:value-of select="ns:callBackIp"/><xsl:text> </xsl:text><xsl:value-of select="ns:userName"/>,<xsl:value-of select="ns:jobName"/><xsl:text> </xsl:text><xsl:value-of select="$quote"/><xsl:value-of select="$quote"/><xsl:text> </xsl:text><xsl:value-of select="ns:callBackPort"/>
     </xsl:template>
 
 </xsl:stylesheet>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/configuration/server/src/main/resources/PBSTemplate.xslt
----------------------------------------------------------------------
diff --git a/modules/configuration/server/src/main/resources/PBSTemplate.xslt b/modules/configuration/server/src/main/resources/PBSTemplate.xslt
index aa3cccc..7676883 100644
--- a/modules/configuration/server/src/main/resources/PBSTemplate.xslt
+++ b/modules/configuration/server/src/main/resources/PBSTemplate.xslt
@@ -96,7 +96,6 @@ cd <xsl:text>   </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text
       <xsl:value-of select="."/><xsl:text>   </xsl:text>
 </xsl:for-each>
     <xsl:text>&#xa;</xsl:text>
-~/rabbitmq-java-client-bin-3.3.5/runjava.sh com.rabbitmq.examples.SimpleProducer amqp://<xsl:value-of select="ns:callBackIp"/><xsl:text> </xsl:text><xsl:value-of select="ns:userName"/>,<xsl:value-of select="ns:jobName"/><xsl:text> </xsl:text><xsl:value-of select="$quote"/><xsl:value-of select="$quote"/><xsl:text> </xsl:text><xsl:value-of select="ns:callBackPort"/>
-</xsl:template>
+R</xsl:template>
 
 </xsl:stylesheet>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/client/TestSSLClient.java
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/client/TestSSLClient.java b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/client/TestSSLClient.java
index cc5ebb6..1d9f4d9 100644
--- a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/client/TestSSLClient.java
+++ b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/client/TestSSLClient.java
@@ -63,7 +63,7 @@ public class TestSSLClient {
             TProtocol protocol = new TBinaryProtocol(transport);
 
             CredentialStoreService.Client client = new CredentialStoreService.Client(protocol);
-//            testSSHCredential(client);
+            testSSHCredential(client);
             testCertificateCredential(client);
             transport.close();
         } catch (TTransportException e) {

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java b/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java
index 7f44125..4f72b46 100644
--- a/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java
+++ b/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java
@@ -43,8 +43,8 @@ public class SSHCredentialTest {
         String userName = "airavata";
         String password = "airavata";
         String gatewayId = "default";
-        String privateKeyPath = "/Users/chathuri/.ssh/id_dsa";
-        String pubKeyPath = "/Users/chathuri/.ssh/id_dsa.pub";
+        String privateKeyPath = "/Users/lginnali/.ssh/id_dsa";
+        String pubKeyPath = "/Users/lginnali/.ssh/id_dsa.pub";
 
         try {
             AiravataUtils.setExecutionAsServer();
@@ -67,7 +67,7 @@ public class SSHCredentialTest {
             pubKeyStream.close();
             sshCredential.setPrivateKey(bFilePub);
             sshCredential.setPublicKey(bFilePub);
-            sshCredential.setPassphrase("test");
+            sshCredential.setPassphrase("gjtlmiJdas7wph");
             writer.writeCredentials(sshCredential);
             System.out.println(token);
         } catch (ClassNotFoundException e) {

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/credential-store/credential-store-service/src/test/resources/airavata-server.properties
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/test/resources/airavata-server.properties b/modules/credential-store/credential-store-service/src/test/resources/airavata-server.properties
new file mode 100644
index 0000000..9bdce87
--- /dev/null
+++ b/modules/credential-store/credential-store-service/src/test/resources/airavata-server.properties
@@ -0,0 +1,254 @@
+#
+#
+# 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.
+#
+
+###########################################################################
+#
+#  This properties file provides configuration for all Airavata Services:
+#  API Server, Registry, Workflow Interpreter, GFac, Orchestrator
+#
+###########################################################################
+
+###########################################################################
+#  API Server Registry Configuration
+###########################################################################
+
+#for derby [AiravataJPARegistry]
+registry.jdbc.driver=org.apache.derby.jdbc.ClientDriver
+registry.jdbc.url=jdbc:derby://localhost:1527/persistent_data;create=true;user=airavata;password=airavata
+# MySql database configuration
+#registry.jdbc.driver=com.mysql.jdbc.Driver
+#registry.jdbc.url=jdbc:mysql://localhost:3306/persistent_data
+registry.jdbc.user=airavata
+registry.jdbc.password=airavata
+start.derby.server.mode=true
+validationQuery=SELECT 1 from CONFIGURATION
+jpa.cache.size=5000
+#jpa.connection.properties=MaxActive=10,MaxIdle=5,MinIdle=2,MaxWait=60000,testWhileIdle=true,testOnBorrow=true
+
+# Properties for default user mode
+default.registry.user=admin
+default.registry.password=admin
+default.registry.password.hash.method=SHA
+default.registry.gateway=php_reference_gateway
+
+#ip=127.0.0.1
+
+###########################################################################
+#  Application Catalog DB Configuration
+###########################################################################
+#for derby [AiravataJPARegistry]
+appcatalog.jdbc.driver=org.apache.derby.jdbc.ClientDriver
+appcatalog.jdbc.url=jdbc:derby://localhost:1527/app_catalog;create=true;user=airavata;password=airavata
+# MySql database configuration
+#appcatalog.jdbc.driver=com.mysql.jdbc.Driver
+#appcatalog.jdbc.url=jdbc:mysql://localhost:3306/app_catalog
+appcatalog.jdbc.user=airavata
+appcatalog.jdbc.password=airavata
+appcatalog.validationQuery=SELECT 1 from CONFIGURATION
+
+###########################################################################
+#  Server module Configuration
+###########################################################################
+
+servers=apiserver,orchestrator,gfac,credentialstore
+#shutdown.trategy=NONE
+shutdown.trategy=SELF_TERMINATE
+
+
+apiserver.server.host=localhost
+apiserver.server.port=8930
+apiserver.server.min.threads=50
+orchestrator.server.host=localhost
+orchestrator.server.port=8940
+gfac.server.host=localhost
+gfac.server.port=8950
+orchestrator.server.min.threads=50
+
+###########################################################################
+#  Job Scheduler can send informative email messages to you about the status of your job.
+# Specify a string which consists of either the single character "n" (no mail), or one or more
+#  of the characters "a" (send mail when job is aborted), "b" (send mail when job begins),
+# and "e" (send mail when job terminates).  The default is "a" if not specified.
+###########################################################################
+
+job.notification.enable=true
+#Provide comma separated email ids as a string if more than one
+job.notification.emailids=
+job.notification.flags=abe
+
+###########################################################################
+# Credential Store module Configuration
+###########################################################################
+start.credential.store=false
+credential.store.keystore.url=/Users/lginnali/Downloads/airavata_sym.jks
+credential.store.keystore.alias=airavata
+credential.store.keystore.password=airavata
+credential.store.jdbc.url=jdbc:derby://localhost:1527/persistent_data;create=true;user=airavata;password=airavata
+credential.store.jdbc.user=airavata
+credential.store.jdbc.password=airavata
+credential.store.jdbc.driver=org.apache.derby.jdbc.ClientDriver
+credential.store.server.host=localhost
+credential.store.server.port=8960
+credentialstore=org.apache.airavata.credential.store.server.CredentialStoreServer
+credential.store.thrift.server.keystore=/Users/chathuri/dev/airavata/credential-store/oa4mp/airavata.jks
+credential.store.thrift.server.keystore.password=airavata
+
+notifier.enabled=false
+#period in milliseconds
+notifier.duration=5000
+
+email.server=smtp.googlemail.com
+email.server.port=465
+email.user=airavata
+email.password=xxx
+email.ssl=true
+email.from=airavata@apache.org
+
+###########################################################################
+# Airavata GFac MyProxy GSI credentials to access Grid Resources.
+###########################################################################
+#
+# Security Configuration used by Airavata Generic Factory Service
+#  to interact with Computational Resources.
+#
+gfac.thread.pool.size=50
+airavata.server.thread.pool.size=50
+gfac=org.apache.airavata.gfac.server.GfacServer
+myproxy.server=myproxy.teragrid.org
+myproxy.username=ogce
+myproxy.password=
+myproxy.life=3600
+# XSEDE Trusted certificates can be downloaded from https://software.xsede.org/security/xsede-certs.tar.gz
+trusted.cert.location=/Users/lahirugunathilake/Downloads/certificates
+gfac.passive=true
+# SSH PKI key pair or ssh password can be used SSH based authentication is used.
+# if user specify both password authentication gets the higher preference
+
+################# ---------- For ssh key pair authentication ------------------- ################
+#public.ssh.key=/path to public key for ssh
+#private.ssh.key=/path to private key file for ssh
+#ssh.keypass=passphrase for the private key
+#ssh.username=username for ssh connection
+### Incase of password authentication.
+#ssh.password=Password for ssh connection
+
+
+
+###########################################################################
+# Airavata Workflow Interpreter Configurations
+###########################################################################
+
+#runInThread=true
+#provenance=true
+#provenanceWriterThreadPoolSize=20
+#gfac.embedded=true
+#workflowserver=org.apache.airavata.api.server.WorkflowServer
+
+
+###########################################################################
+# API Server module Configuration
+###########################################################################
+apiserver=org.apache.airavata.api.server.AiravataAPIServer
+
+###########################################################################
+# Workflow Server module Configuration
+###########################################################################
+
+workflowserver=org.apache.airavata.api.server.WorkflowServer
+
+###########################################################################
+# Advance configuration to change service implementations
+###########################################################################
+# If false, disables two phase commit when submitting jobs
+TwoPhase=true
+#
+# Class which implemented HostScheduler interface. It will determine the which host to submit the request
+#
+host.scheduler=org.apache.airavata.gfac.core.scheduler.impl.SimpleHostScheduler
+
+###########################################################################
+# Monitoring module Configuration
+###########################################################################
+
+#This will be the primary monitoring tool which runs in airavata, in future there will be multiple monitoring
+#mechanisms and one would be able to start a monitor
+monitors=org.apache.airavata.gfac.monitor.impl.pull.qstat.QstatMonitor,org.apache.airavata.gfac.monitor.impl.LocalJobMonitor
+
+
+###########################################################################
+# AMQP Notification Configuration
+###########################################################################
+
+
+amqp.notification.enable=1
+
+amqp.broker.host=localhost
+amqp.broker.port=5672
+amqp.broker.username=guest
+amqp.broker.password=guest
+
+amqp.sender=org.apache.airavata.wsmg.client.amqp.rabbitmq.AMQPSenderImpl
+amqp.topic.sender=org.apache.airavata.wsmg.client.amqp.rabbitmq.AMQPTopicSenderImpl
+amqp.broadcast.sender=org.apache.airavata.wsmg.client.amqp.rabbitmq.AMQPBroadcastSenderImpl
+
+#,org.apache.airavata.gfac.monitor.impl.push.amqp.AMQPMonitor
+#This is the amqp related configuration and this lists down the Rabbitmq host, this is an xsede specific configuration
+amqp.hosts=info1.dyn.teragrid.org,info2.dyn.teragrid.org
+proxy.file.path=/Users/lahirugunathilake/Downloads/x509up_u503876
+connection.name=xsede
+#publisher
+activity.listeners=org.apache.airavata.gfac.core.monitor.AiravataJobStatusUpdator,org.apache.airavata.gfac.core.monitor.AiravataTaskStatusUpdator,org.apache.airavata.gfac.core.monitor.AiravataWorkflowNodeStatusUpdator,org.apache.airavata.api.server.listener.AiravataExperimentStatusUpdator,org.apache.airavata.gfac.core.monitor.GfacInternalStatusUpdator,org.apache.airavata.workflow.engine.util.ProxyMonitorPublisher
+publish.rabbitmq=false
+status.publisher=org.apache.airavata.messaging.core.impl.RabbitMQStatusPublisher
+task.launch.publisher=org.apache.airavata.messaging.core.impl.RabbitMQTaskLaunchPublisher
+rabbitmq.broker.url=amqp://localhost:5672
+rabbitmq.status.exchange.name=airavata_rabbitmq_exchange
+rabbitmq.task.launch.exchange.name=airavata_task_launch_rabbitmq_exchange
+
+
+###########################################################################
+# Orchestrator module Configuration
+###########################################################################
+
+#job.submitter=org.apache.airavata.orchestrator.core.impl.GFACEmbeddedJobSubmitter
+job.submitter=org.apache.airavata.orchestrator.core.impl.GFACPassiveJobSubmitter
+#job.submitter=org.apache.airavata.orchestrator.core.impl.GFACRPCJobSubmitter
+job.validators=org.apache.airavata.orchestrator.core.validator.impl.SimpleAppDataValidator,org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator
+submitter.interval=10000
+threadpool.size=10
+start.submitter=true
+embedded.mode=true
+enable.validation=true
+orchestrator=org.apache.airavata.orchestrator.server.OrchestratorServer
+
+###########################################################################
+# Zookeeper Server Configuration
+###########################################################################
+
+embedded.zk=false
+zookeeper.server.host=localhost
+zookeeper.server.port=2181
+airavata-server=/api-server
+orchestrator-server=/orchestrator-server
+gfac-server=/gfac-server
+gfac-experiments=/gfac-experiments
+gfac-server-name=gfac-node0
+orchestrator-server-name=orch-node0
+airavata-server-name=api-node0

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/distribution/server/src/main/assembly/bin-assembly.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/server/src/main/assembly/bin-assembly.xml b/modules/distribution/server/src/main/assembly/bin-assembly.xml
index 4f061e4..18ccad6 100644
--- a/modules/distribution/server/src/main/assembly/bin-assembly.xml
+++ b/modules/distribution/server/src/main/assembly/bin-assembly.xml
@@ -127,6 +127,7 @@
 				<include>gfac-config.xml</include>
 				<include>PBSTemplate.xslt</include>
 				<include>SLURMTemplate.xslt</include>
+				<include>LSFTemplate.xslt</include>
 				<include>SGETemplate.xslt</include>
 				<include>gsissh.properties</include>
 			</includes>

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java b/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
index 583ec07..1687462 100644
--- a/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
+++ b/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
@@ -31,7 +31,6 @@ import org.apache.airavata.common.utils.AiravataZKUtils;
 import org.apache.airavata.common.utils.Constants;
 import org.apache.airavata.common.utils.MonitorPublisher;
 import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
 import org.apache.airavata.gfac.core.cpi.GFac;
 import org.apache.airavata.gfac.core.utils.GFacThreadPoolExecutor;

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/RequestData.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/RequestData.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/RequestData.java
index 9f45ce6..000ea7d 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/RequestData.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/RequestData.java
@@ -49,6 +49,8 @@ public class RequestData {
     private int myProxyLifeTime = DEFAULT_LIFE_TIME;
 
 
+
+
     public RequestData() {
     }
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
index 7a432e8..631f59c 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
@@ -60,6 +60,8 @@ public class GFACGSISSHUtils {
     public static final String PBS_JOB_MANAGER = "pbs";
     public static final String SLURM_JOB_MANAGER = "slurm";
     public static final String SUN_GRID_ENGINE_JOB_MANAGER = "UGE";
+    public static final String LSF_JOB_MANAGER = "lsf";
+
     public static int maxClusterCount = 5;
     public static Map<String, List<Cluster>> clusters = new HashMap<String, List<Cluster>>();
 
@@ -138,6 +140,8 @@ public class GFACGSISSHUtils {
                                 jConfig = CommonUtils.getSLURMJobManager(installedParentPath);
                             } else if (SUN_GRID_ENGINE_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
                                 jConfig = CommonUtils.getSGEJobManager(installedParentPath);
+                            }else if(LSF_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
+                                jConfig = CommonUtils.getLSFJobManager(installedParentPath);
                             }
                         }
                         pbsCluster = new PBSCluster(serverInfo, tokenizedMyProxyAuthInfo, jConfig);
@@ -177,7 +181,7 @@ public class GFACGSISSHUtils {
 			if(ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_ENABLE).equalsIgnoreCase("true")){
 				jobDescriptor.setMailOptions(ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_FLAGS));
 				String emailids = ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_EMAILIDS);
-			
+
 				if(jobExecutionContext.getTaskData().isSetEmailAddresses()){
 					List<String> emailList = jobExecutionContext.getTaskData().getEmailAddresses();
 					String elist = GFacUtils.listToCsv(emailList, ',');
@@ -204,6 +208,7 @@ public class GFACGSISSHUtils {
         jobDescriptor.setStandardOutFile(jobExecutionContext.getStandardOutput());
         jobDescriptor.setStandardErrorFile(jobExecutionContext.getStandardError());
         String computationalProjectAccount = taskData.getTaskScheduling().getComputationalProjectAccount();
+        taskData.getEmailAddresses();
         if (computationalProjectAccount == null){
             ComputeResourcePreference computeResourcePreference = jobExecutionContext.getApplicationContext().getComputeResourcePreference();
             if (computeResourcePreference != null) {
@@ -311,6 +316,9 @@ public class GFACGSISSHUtils {
             }
             if (taskScheduling.getWallTimeLimit() > 0) {
                 jobDescriptor.setMaxWallTime(String.valueOf(taskScheduling.getWallTimeLimit()));
+                if(resourceJobManager.getResourceJobManagerType().equals(ResourceJobManagerType.LSF)){
+                    jobDescriptor.setMaxWallTimeForLSF(String.valueOf(taskScheduling.getWallTimeLimit()));
+                }
             }
 
             if (taskScheduling.getTotalPhysicalMemory() > 0) {

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
index a9e08d3..c4d25f5 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
@@ -25,6 +25,7 @@ import org.airavata.appcatalog.cpi.AppCatalogException;
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.common.utils.ServerSettings;
 import org.apache.airavata.credential.store.credential.impl.ssh.SSHCredential;
+import org.apache.airavata.gfac.Constants;
 import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.RequestData;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
@@ -41,6 +42,7 @@ import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
 import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration;
 import org.apache.airavata.gsi.ssh.impl.GSISSHAbstractCluster;
 import org.apache.airavata.gsi.ssh.impl.PBSCluster;
+import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
 import org.apache.airavata.gsi.ssh.util.CommonUtils;
 import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
 import org.apache.airavata.model.appcatalog.appinterface.DataType;
@@ -96,15 +98,21 @@ public class GFACSSHUtils {
 
                     Cluster pbsCluster = null;
                     try {
-                        TokenizedSSHAuthInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData);
+                        AuthenticationInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData);
                         String installedParentPath = jobExecutionContext.getResourceJobManager().getJobManagerBinPath();
                         if (installedParentPath == null) {
                             installedParentPath = "/";
                         }
 
-                        SSHCredential credentials = tokenizedSSHAuthInfo.getCredentials();// this is just a call to get and set credentials in to this object,data will be used
+                        SSHCredential credentials =((TokenizedSSHAuthInfo)tokenizedSSHAuthInfo).getCredentials();// this is just a call to get and set credentials in to this object,data will be used
+                        if(credentials.getPrivateKey()==null || credentials.getPublicKey()==null){
+                            // now we fall back to username password authentication
+                            Properties configurationProperties = ServerSettings.getProperties();
+                            tokenizedSSHAuthInfo = new DefaultPasswordAuthenticationInfo(configurationProperties.getProperty(Constants.SSH_PASSWORD));
+                        }
                         serverInfo.setUserName(credentials.getPortalUserName());
                         jobExecutionContext.getExperiment().setUserName(credentials.getPortalUserName());
+
                         // inside the pbsCluser object
 
                         String key = credentials.getPortalUserName() + jobExecutionContext.getHostName() + serverInfo.getPort();
@@ -147,8 +155,11 @@ public class GFACSSHUtils {
                                          jConfig = CommonUtils.getSLURMJobManager(installedParentPath);
                                      } else if (SUN_GRID_ENGINE_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
                                          jConfig = CommonUtils.getSGEJobManager(installedParentPath);
+                                     } else if (LSF_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
+                                         jConfig = CommonUtils.getLSFJobManager(installedParentPath);
                                      }
                                  }
+
                                 pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo,jConfig);
                                 List<Cluster> pbsClusters = null;
                                 if (!(clusters.containsKey(key))) {
@@ -322,7 +333,7 @@ public class GFACSSHUtils {
         List<String> inputValues = new ArrayList<String>();
         MessageContext input = jobExecutionContext.getInMessageContext();
 
-        // sort the inputs first and then build the command List
+        // sort the inputs first and then build the command ListR
         Comparator<InputDataObjectType> inputOrderComparator = new Comparator<InputDataObjectType>() {
             @Override
             public int compare(InputDataObjectType inputDataObjectType, InputDataObjectType t1) {
@@ -411,6 +422,12 @@ public class GFACSSHUtils {
             }
             if (taskScheduling.getWallTimeLimit() > 0) {
                 jobDescriptor.setMaxWallTime(String.valueOf(taskScheduling.getWallTimeLimit()));
+                if(resourceJobManager.getResourceJobManagerType().equals(ResourceJobManagerType.LSF)){
+                    jobDescriptor.setMaxWallTimeForLSF(String.valueOf(taskScheduling.getWallTimeLimit()));
+                }
+            }
+            if (taskScheduling.getTotalPhysicalMemory() > 0) {
+                jobDescriptor.setUsedMemory(taskScheduling.getTotalPhysicalMemory() + "");
             }
         } else {
             logger.error("Task scheduling cannot be null at this point..");

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobManagerConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobManagerConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobManagerConfiguration.java
index f68ba29..85a843e 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobManagerConfiguration.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobManagerConfiguration.java
@@ -37,6 +37,13 @@ public interface JobManagerConfiguration {
 	public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath);
 
 	public OutputParser getParser();
-	
+
 	public String getInstalledPath();
+
+	public String getBaseCancelCommand();
+
+	public String getBaseMonitorCommand();
+
+	public String getBaseSubmitCommand();
+
 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFJobConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFJobConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFJobConfiguration.java
index 018d49d..46fe9ad 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFJobConfiguration.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFJobConfiguration.java
@@ -80,7 +80,7 @@ public class LSFJobConfiguration implements JobManagerConfiguration {
 
     @Override
     public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
-        return new RawCommandInfo(this.installedPath + "bsub <" +
+        return new RawCommandInfo(this.installedPath + "bsub < " +
                 workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
     }
 
@@ -97,4 +97,20 @@ public class LSFJobConfiguration implements JobManagerConfiguration {
     public String getInstalledPath() {
         return installedPath;
     }
+
+
+    @Override
+    public String getBaseCancelCommand() {
+        return "bkill";
+    }
+
+    @Override
+    public String getBaseMonitorCommand() {
+        return "bjobs";
+    }
+
+    @Override
+    public String getBaseSubmitCommand() {
+        return "bsub";
+    }
 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFOutputParser.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFOutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFOutputParser.java
index 5490ff6..bd02e37 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFOutputParser.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFOutputParser.java
@@ -57,6 +57,7 @@ public class LSFOutputParser implements OutputParser {
     @Override
     public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) throws SSHApiException {
         logger.debug(rawOutput);
+
         String[]    info = rawOutput.split("\n");
 //        int lastStop = 0;
         for (String jobID : statusMap.keySet()) {

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
index 18ea772..e935dfb 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
@@ -95,4 +95,19 @@ public class PBSJobConfiguration implements JobManagerConfiguration {
     public RawCommandInfo getUserBasedMonitorCommand(String userName) {
         return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
     }
+
+    @Override
+    public String  getBaseCancelCommand() {
+        return "qdel";
+    }
+
+    @Override
+    public String  getBaseMonitorCommand() {
+        return "qstat";
+    }
+
+    @Override
+    public String getBaseSubmitCommand() {
+        return "qsub ";
+    }
 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmJobConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmJobConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmJobConfiguration.java
index 0b774ed..807ac42 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmJobConfiguration.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmJobConfiguration.java
@@ -94,4 +94,19 @@ public class SlurmJobConfiguration implements JobManagerConfiguration{
     public RawCommandInfo getUserBasedMonitorCommand(String userName) {
         return new RawCommandInfo(this.installedPath + "squeue -u " + userName);
     }
+
+    @Override
+    public String getBaseCancelCommand() {
+        return "scancel";
+    }
+
+    @Override
+    public String getBaseMonitorCommand() {
+        return "squeue";
+    }
+
+    @Override
+    public String getBaseSubmitCommand() {
+        return "sbatch";
+    }
 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
index dd7f2d9..0420cff 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
@@ -241,7 +241,7 @@ public class GSISSHAbstractCluster implements Cluster {
 
         StandardOutReader stdOutReader = new StandardOutReader();
         CommandExecutor.executeCommand(rawCommandInfo, this.getSession(), stdOutReader);
-        String outputifAvailable = getOutputifAvailable(stdOutReader, "Error reading output of job submission",rawCommandInfo.getBaseCommand(jobManagerConfiguration.getInstalledPath()));
+        String outputifAvailable = getOutputifAvailable(stdOutReader, "Error reading output of job submission",jobManagerConfiguration.getBaseCancelCommand());
         // this might not be the case for all teh resources, if so Cluster implementation can override this method
         // because here after cancelling we try to get the job description and return it back
         try {
@@ -274,7 +274,7 @@ public class GSISSHAbstractCluster implements Cluster {
         //Check whether pbs submission is successful or not, if it failed throw and exception in submitJob method
         // with the error thrown in qsub command
         //
-        String outputifAvailable = getOutputifAvailable(standardOutReader,"Error reading output of job submission",rawCommandInfo.getBaseCommand(jobManagerConfiguration.getInstalledPath()));
+        String outputifAvailable = getOutputifAvailable(standardOutReader,"Error reading output of job submission",jobManagerConfiguration.getBaseSubmitCommand());
         OutputParser outputParser = jobManagerConfiguration.getParser();
         return  outputParser.parseJobSubmission(outputifAvailable);
     }
@@ -411,7 +411,7 @@ public class GSISSHAbstractCluster implements Cluster {
         RawCommandInfo rawCommandInfo = jobManagerConfiguration.getMonitorCommand(jobID);
         StandardOutReader stdOutReader = new StandardOutReader();
         CommandExecutor.executeCommand(rawCommandInfo, this.getSession(), stdOutReader);
-        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !",rawCommandInfo.getBaseCommand(jobManagerConfiguration.getInstalledPath()));
+        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !",jobManagerConfiguration.getBaseMonitorCommand());
         JobDescriptor jobDescriptor = new JobDescriptor();
         jobManagerConfiguration.getParser().parseSingleJob(jobDescriptor, result);
         return jobDescriptor;
@@ -421,7 +421,7 @@ public class GSISSHAbstractCluster implements Cluster {
         RawCommandInfo rawCommandInfo = jobManagerConfiguration.getMonitorCommand(jobID);
         StandardOutReader stdOutReader = new StandardOutReader();
         CommandExecutor.executeCommand(rawCommandInfo, this.getSession(), stdOutReader);
-        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !", rawCommandInfo.getBaseCommand(jobManagerConfiguration.getInstalledPath()));
+        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !", jobManagerConfiguration.getBaseMonitorCommand());
         return jobManagerConfiguration.getParser().parseJobStatus(jobID, result);
     }
 
@@ -638,7 +638,7 @@ public class GSISSHAbstractCluster implements Cluster {
                 }
             }
         }
-        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !", rawCommandInfo.getBaseCommand(jobManagerConfiguration.getInstalledPath()));
+        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !", jobManagerConfiguration.getBaseMonitorCommand());
         jobManagerConfiguration.getParser().parseJobStatuses(userName, jobIDs, result);
     }
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/RawCommandInfo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/RawCommandInfo.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/RawCommandInfo.java
index ac88fe7..0e9d16e 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/RawCommandInfo.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/RawCommandInfo.java
@@ -48,13 +48,7 @@ public class RawCommandInfo implements CommandInfo {
     public String getRawCommand() {
         return rawCommand;
     }
-    /*
-     * To get command without the path and other parameters. This is required to read errors 
-     */
-    public String getBaseCommand(String installPath) {
-        return rawCommand.substring(rawCommand.lastIndexOf(installPath)+1, rawCommand.indexOf(" "));
-    }
-    
+
     public void setRawCommand(String rawCommand) {
         this.rawCommand = rawCommand;
     }

http://git-wip-us.apache.org/repos/asf/airavata/blob/5ff650f4/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
index 5a12723..0ca7546 100644
--- a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
+++ b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
@@ -26,6 +26,7 @@ import org.apache.airavata.gsi.ssh.api.*;
 import org.apache.airavata.gsi.ssh.api.authentication.GSIAuthenticationInfo;
 import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
 import org.apache.airavata.gsi.ssh.config.ConfigReader;
+import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
 import org.apache.airavata.gsi.ssh.impl.authentication.MyProxyAuthenticationInfo;
 import org.apache.airavata.gsi.ssh.util.CommonUtils;
 import org.slf4j.Logger;
@@ -49,17 +50,13 @@ public class DefaultSSHApiTestWithMyProxyAuth {
 
 
     public static void main(String[]ars){
-         String myProxyUserName = "ogce";
-         String myProxyPassword = "OGCE@xsede14";
-         String certificateLocation = "/Users/raminder/.globus/certificates";
+         String myProxyUserName = "lg11w";
 
-
-        GSIAuthenticationInfo authenticationInfo
-                = new MyProxyAuthenticationInfo(myProxyUserName, myProxyPassword, "myproxy.teragrid.org",
-                7512, 17280000, certificateLocation);
+        DefaultPasswordAuthenticationInfo authenticationInfo
+                = new DefaultPasswordAuthenticationInfo("");
 
         // Create command
-        CommandInfo commandInfo = new RawCommandInfo("/bin/ls");
+        CommandInfo commandInfo = new RawCommandInfo("source /etc/bashrc; bsub </home/lg11w/mywork/sshEchoExperiment_9d267072-ca65-4ca8-847a-cd3d130f6050/366787899.lsf");
 
         // Server info
         //Stampede
@@ -68,7 +65,7 @@ public class DefaultSSHApiTestWithMyProxyAuth {
 //        ServerInfo serverInfo = new ServerInfo(myProxyUserName, "trestles.sdsc.xsede.org", 22);
         
         //Lonestar
-         ServerInfo serverInfo = new ServerInfo(myProxyUserName, "lonestar.tacc.utexas.edu", 22);
+         ServerInfo serverInfo = new ServerInfo(myProxyUserName, "ghpcc06.umassrc.org", 22);
         // Output
         CommandOutput commandOutput = new SystemCommandOutput();
 


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