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Posted to commits@airavata.apache.org by la...@apache.org on 2015/03/19 16:03:09 UTC
[43/62] [abbrv] airavata git commit: Fixed AIRAVATA-1596
Fixed AIRAVATA-1596
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/b746118e
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/b746118e
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/b746118e
Branch: refs/heads/queue-gfac-rabbitmq
Commit: b746118e5cc06ac5698c9504f6a4b1c29bc802ca
Parents: 4000b82
Author: raminder <ra...@apache.org>
Authored: Tue Mar 10 23:28:07 2015 -0400
Committer: raminder <ra...@apache.org>
Committed: Tue Mar 10 23:28:07 2015 -0400
----------------------------------------------------------------------
.../tools/RegisterSampleApplications.java | 158 +++++++++++++++++--
1 file changed, 143 insertions(+), 15 deletions(-)
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http://git-wip-us.apache.org/repos/asf/airavata/blob/b746118e/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
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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 55dbcf8..58dafbb 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
@@ -55,6 +55,8 @@ public class RegisterSampleApplications {
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 alamoResourceId;
+
private static String fsdResourceId;
// unicore service endpoint url
@@ -76,7 +78,8 @@ public class RegisterSampleApplications {
private static final String gaussianName = "Gaussian";
private static final String gamessName = "Gamess";
private static final String stressMemName = "StressMem";
-
+ private static final String ultrascanName = "Ultrascan";
+
//Appplication Descriptions
private static final String echoDescription = "A Simple Echo Application";
private static final String amberDescription = "Assisted Model Building with Energy Refinement MD Package";
@@ -92,8 +95,8 @@ public class RegisterSampleApplications {
private static final String monteXDescription = "Grid Chem Tinker Monte Application";
private static final String gaussianDescription = "Grid Chem Gaussian Application";
private static final String gamessDescription = "A Gamess Application";
-
-
+ private static final String ultrascanDescription = "Ultrascan Application";
+
//App Module Id's
private static String echoModuleId;
private static String amberModuleId;
@@ -124,6 +127,8 @@ public class RegisterSampleApplications {
private static String wrfInterfaceId;
private static String phastaInterfaceId;
private static String gamessInterfaceId;
+ private static String ultrascanModuleId;
+ private static String ultrascanInterfaceId;
public RegisterSampleApplications(Airavata.Client airavataClient) {
this.airavataClient = airavataClient;
@@ -209,6 +214,12 @@ public class RegisterSampleApplications {
fsdResourceId = registerUnicoreEndpoint("fsd-cloud15.zam.kfa-juelich.de", "interop host", JobSubmissionProtocol.UNICORE, SecurityProtocol.GSI);
System.out.println("FSd Resource Id: "+fsdResourceId);
+ //Register Alamo
+ alamoResourceId = registerComputeHost("alamo.uthscsa.edu", "Alamo Cluster",
+ ResourceJobManagerType.PBS, "push", "/usr/bin/", SecurityProtocol.SSH_KEYS, 22, "/usr/bin/mpiexec -np");
+ System.out.println("Alamo Cluster " + alamoResourceId);
+
+
} catch (TException e) {
e.printStackTrace();
}
@@ -335,6 +346,11 @@ public class RegisterSampleApplications {
RegisterSampleApplicationsUtils.createApplicationModule(
gamessName, "17May13", gamessDescription));
System.out.println("Gamess Module Id " + gamessModuleId);
+ //Register Ultrascan
+ ultrascanModuleId = airavataClient.registerApplicationModule(DEFAULT_GATEWAY,
+ RegisterSampleApplicationsUtils.createApplicationModule(
+ ultrascanName, "1.0", ultrascanDescription));
+ System.out.println("Ultrascan Module Id " + ultrascanModuleId);
} catch (TException e) {
e.printStackTrace();
@@ -360,6 +376,9 @@ public class RegisterSampleApplications {
registerFSDApps();
registerLSFApps();
+
+ //Registering Alamo Apps
+ registerAlamoApps();
}
@@ -404,6 +423,9 @@ public class RegisterSampleApplications {
registerTinkerMonteInterface();
registerGaussianInterface();
+
+ // Register Ultrascan
+ registerUltrascanInterface();
}
@@ -432,7 +454,10 @@ public class RegisterSampleApplications {
"", DataType.URI, false, true));
applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("f10_file",
"", DataType.URI, false, true));
-
+ applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("STDOUT",
+ "", DataType.STDOUT, false, true));
+ applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("STDERR",
+ "", DataType.STDERR, false, true));
gamessInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription("gamess", "gamess",
@@ -458,11 +483,14 @@ public class RegisterSampleApplications {
List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
applicationInputs.add(input1);
- OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("echo_output",
- "", DataType.STRING, false, false);
+ OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",
+ "", DataType.STDOUT, false, false);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",
+ "", DataType.STDERR, false, false);
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
echoLocalInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(echoName, echoDescription,
@@ -531,11 +559,14 @@ public class RegisterSampleApplications {
List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
applicationInputs.add(input1);
- OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Sample_Output",
- "", DataType.STRING, false, false);
+ OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("STDOutput",
+ "", DataType.STDOUT, true, true);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDErr",
+ "", DataType.STDERR, true, true);
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
mpiInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
@@ -609,17 +640,19 @@ public class RegisterSampleApplications {
InputDataObjectType input3 = RegisterSampleApplicationsUtils.createAppInput("Parameter_Topology_File", null,
DataType.URI, null, 3,true, true, false, "Parameter and Topology coordinates", null);
-
+
List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
applicationInputs.add(input1);
applicationInputs.add(input2);
applicationInputs.add(input3);
- OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output",
- "", DataType.STRING, true, true);
+ OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
autoDockInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(autoDockName, autoDockDescription,
@@ -723,9 +756,14 @@ public class RegisterSampleApplications {
applicationInputs.add(input1);
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("LAMMPS_Simulation_Log",null,DataType.URI, true, true);
-
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
lammpsInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(lammpsName, lammpsDescription,
@@ -752,9 +790,14 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("NWChem_Execution_Log",
null, DataType.URI, true, false);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
nwChemInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(nwChemName, nwChemDescription,
@@ -786,10 +829,14 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Trinity_Execution_Log",null,DataType.URI, true, true);
OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("Trinity_FASTA_File",null,DataType.URI, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output4 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
+ applicationOutputs.add(output4);
trinityInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(trinityName, trinityDescription,
@@ -828,11 +875,16 @@ public class RegisterSampleApplications {
OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("WRF_Execution_Log",
"", DataType.URI, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output4 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
applicationOutputs.add(output2);
-
+ applicationOutputs.add(output3);
+ applicationOutputs.add(output4);
+
wrfInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(wrfName, wrfDescription,
appModules, applicationInputs, applicationOutputs));
@@ -866,12 +918,18 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("PHASTA_Execution_Log",null,DataType.URI, true, true);
OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("PHASTA_Output_tar",null,DataType.URI, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output4 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
+ applicationOutputs.add(output4);
- amberInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
+
+ phastaInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(phastaName, phastaDescription,
appModules, applicationInputs, applicationOutputs));
System.out.println("phasta Application Interface Id " + phastaInterfaceId);
@@ -911,10 +969,15 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("gaussian.out",
"", DataType.URI, true, true );
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
-
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
+
String addApplicationInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription("Gaussian", "Gaussian application",
appModules, applicationInputs, applicationOutputs));
@@ -958,9 +1021,14 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Diskoutputfile_with_dir",
"", DataType.URI, false, false);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
String addApplicationInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription("Tinker_Monte", "Monte application",
@@ -1254,6 +1322,9 @@ public class RegisterSampleApplications {
ComputeResourcePreference fsdResourcePreferences = RegisterSampleApplicationsUtils.
createComputeResourcePreference(fsdResourceId, null, false, null, JobSubmissionProtocol.UNICORE, DataMovementProtocol.UNICORE_STORAGE_SERVICE,null);
+ ComputeResourcePreference alamoResourcePreferences = RegisterSampleApplicationsUtils.
+ createComputeResourcePreference(alamoResourceId, null, false, null, JobSubmissionProtocol.SSH, DataMovementProtocol.SCP,"/home/us3/work/uslims3_cauma3-03896");
+
GatewayResourceProfile gatewayResourceProfile = new GatewayResourceProfile();
gatewayResourceProfile.setGatewayID(DEFAULT_GATEWAY);
gatewayResourceProfile.addToComputeResourcePreferences(stampedeResourcePreferences);
@@ -1298,5 +1369,62 @@ public class RegisterSampleApplications {
e.printStackTrace();
}
}
+ public void registerAlamoApps() {
+ try {
+ System.out.println("#### Registering Application Deployments on Alamo #### \n");
+
+ //Register Ultrascan on Alamo
+ List<String> ultrascanMouldes = new ArrayList<String>();
+ ultrascanMouldes.add("module load intel/2015/64");
+ ultrascanMouldes.add("module load openmpi/intel/1.8.4");
+ ultrascanMouldes.add("module load qt4/4.8.6");
+ ultrascanMouldes.add("module load ultrascan3/3.3");
+
+ String ultrascanAppDeployId = airavataClient.registerApplicationDeployment(DEFAULT_GATEWAY,
+ RegisterSampleApplicationsUtils.createApplicationDeployment(ultrascanModuleId, alamoResourceId,
+ "/home/us3/bin/us_mpi_analysis", ApplicationParallelismType.OPENMP, ultrascanDescription, ultrascanMouldes , null, null));
+ System.out.println("Ultrascan on alamo deployment Id " + ultrascanAppDeployId);
+
+ } catch (TException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void registerUltrascanInterface() {
+ try {
+ System.out.println("#### Registering Ultrascan Application Interface ####");
+
+ List<String> appModules = new ArrayList<String>();
+ appModules.add(ultrascanModuleId);
+
+ InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("input", null,
+ DataType.URI, null, 1, true, true, false, "input file", null);
+
+ List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
+ applicationInputs.add(input1);
+
+ OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("output/analysis-results.tar",
+ "", DataType.URI, true, true );
+
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",
+ "", DataType.STDOUT, true, true );
+
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",
+ "", DataType.STDERR, true, true );
+
+ List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
+ applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
+
+ String ultrascanInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
+ RegisterSampleApplicationsUtils.createApplicationInterfaceDescription("Ultrascan", "Ultrascan application",
+ appModules, applicationInputs, applicationOutputs));
+ System.out.println("Ultrascan Application Interface Id " + ultrascanInterfaceId);
+
+ } catch (TException e) {
+ e.printStackTrace();
+ }
+ }
}