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Posted to commits@airavata.apache.org by sh...@apache.org on 2014/12/24 16:28:28 UTC
airavata git commit: Handled output inclusive and exclusive
properties in gsissh provider and modified games and nwchem appliation
registration code
Repository: airavata
Updated Branches:
refs/heads/master c29d4040b -> 61d0c7369
Handled output inclusive and exclusive properties in gsissh provider and modified games and nwchem appliation registration code
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/61d0c736
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/61d0c736
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/61d0c736
Branch: refs/heads/master
Commit: 61d0c7369a68261a1018d5e6523674b23d5cd28a
Parents: c29d404
Author: shamrath <sh...@gmail.com>
Authored: Wed Dec 24 10:29:30 2014 -0500
Committer: shamrath <sh...@gmail.com>
Committed: Wed Dec 24 10:29:30 2014 -0500
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.../tools/RegisterSampleApplications.java | 31 +++++++++++---------
.../gfac/gsissh/util/GFACGSISSHUtils.java | 13 +++++++-
2 files changed, 29 insertions(+), 15 deletions(-)
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http://git-wip-us.apache.org/repos/asf/airavata/blob/61d0c736/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 19d0bfe..7a829fc 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
@@ -371,7 +371,7 @@ public class RegisterSampleApplications {
//Registering Lammps
registerLammpsInterface();
//Registrting Gamess
-// registerGamessInterface();
+ registerGamessInterface();
//Registering NWChem
registerNWChemInterface();
@@ -393,26 +393,26 @@ public class RegisterSampleApplications {
System.out.println("#### Registering Gamess Interface #### \n");
List<String> appModules = new ArrayList<String>();
- appModules.add(gamessDescription);
+ appModules.add(gamessModuleId);
List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
applicationInputs.add(RegisterSampleApplicationsUtils.createAppInput("gams_input", "",
- DataType.URI, null, 1, ValidityType.REQUIRED, CommandLineType.EXCLUSIVE, false, "Gamess Input file", null));
- applicationInputs.add(RegisterSampleApplicationsUtils.createAppInput("EXT_FILE", "",
- DataType.URI, null, 1, ValidityType.OPTIONAL, CommandLineType.INCLUSIVE, false, "Gamess EXT file", null));
+ DataType.URI, null, 1, ValidityType.REQUIRED, CommandLineType.INCLUSIVE, false, "Gamess Input file", null));
+// applicationInputs.add(RegisterSampleApplicationsUtils.createAppInput("EXT_FILE", "",
+// DataType.URI, null, 2, ValidityType.OPTIONAL, CommandLineType.EXCLUSIVE, false, "Gamess EXT file", null));
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("gams_output",
- "", DataType.URI, ValidityType.REQUIRED, CommandLineType.EXCLUSIVE));
- applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("dat_file",
"", DataType.URI, ValidityType.REQUIRED, CommandLineType.INCLUSIVE));
+ applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("dat_file",
+ "", DataType.URI, ValidityType.REQUIRED, CommandLineType.EXCLUSIVE));
applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("trj_file",
- "", DataType.URI, ValidityType.OPTIONAL, CommandLineType.INCLUSIVE));
+ "", DataType.URI, ValidityType.OPTIONAL, CommandLineType.EXCLUSIVE));
applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("rst_file",
- "", DataType.URI, ValidityType.OPTIONAL, CommandLineType.INCLUSIVE));
+ "", DataType.URI, ValidityType.OPTIONAL, CommandLineType.EXCLUSIVE));
applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("f10_file",
- "", DataType.URI, ValidityType.OPTIONAL, CommandLineType.INCLUSIVE));
+ "", DataType.URI, ValidityType.OPTIONAL, CommandLineType.EXCLUSIVE));
gamessInterfaceId = airavataClient.registerApplicationInterface(
@@ -710,12 +710,13 @@ public class RegisterSampleApplications {
appModules.add(nwChemModuleId);
InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Water_Molecule_Input", null,
- DataType.URI, null, 1,null, null, false, "Water Molecule Input File - water.nw", null);
+ DataType.URI, null, 1,ValidityType.REQUIRED , CommandLineType.INCLUSIVE, false, "Water Molecule Input File - water.nw", null);
List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
applicationInputs.add(input1);
- OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("NWChem_Execution_Log",null,DataType.URI, null, null);
+ OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("NWChem_Execution_Log",
+ null, DataType.URI, ValidityType.REQUIRED, CommandLineType.INCLUSIVE);
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
@@ -976,10 +977,12 @@ public class RegisterSampleApplications {
System.out.println("LAMMPS on stampede deployment Id " + lammpsAppDeployId);
//Register NWChem
+ List<String> nwChemModuleCmds = new ArrayList<String>();
+ nwChemModuleCmds.add("module load nwchem");
String nwChemAppDeployId = airavataClient.registerApplicationDeployment(
RegisterSampleApplicationsUtils.createApplicationDeployment(nwChemModuleId, stampedeResourceId,
- "/home1/01437/ogce/production/app_wrappers/nwchem_wrapper.sh", ApplicationParallelismType.MPI,
- nwChemDescription, null));
+ "nwchem", ApplicationParallelismType.MPI,
+ nwChemDescription, nwChemModuleCmds));
System.out.println("NWChem on stampede deployment Id " + nwChemAppDeployId);
//Register Trinity
http://git-wip-us.apache.org/repos/asf/airavata/blob/61d0c736/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 68e0072..266c0e4 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
@@ -43,6 +43,7 @@ import org.apache.airavata.gsi.ssh.util.CommonUtils;
import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
import org.apache.airavata.model.appcatalog.appinterface.CommandLineType;
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 org.apache.airavata.model.workspace.experiment.ComputationalResourceScheduling;
@@ -198,7 +199,6 @@ public class GFACGSISSHUtils {
List<String> inputValues = new ArrayList<String>();
MessageContext input = jobExecutionContext.getInMessageContext();
- Map<String, Object> inputs = input.getParameters();
// sort the inputs first and then build the command List
Comparator<InputDataObjectType> inputOrderComparator = new Comparator<InputDataObjectType>() {
@Override
@@ -228,6 +228,17 @@ public class GFACGSISSHUtils {
inputValues.add(inputDataObjectType.getValue());
}
}
+
+ Map<String, Object> outputParams = jobExecutionContext.getOutMessageContext().getParameters();
+ for (Object outputParam : outputParams.values()) {
+ if (outputParam instanceof OutputDataObjectType) {
+ OutputDataObjectType output = (OutputDataObjectType) outputParam;
+ if (output.getValue() != null && !output.getValue().equals("") && output.getAddedToCommandLine() != null
+ && output.getAddedToCommandLine() == CommandLineType.INCLUSIVE) {
+ inputValues.add(output.getValue());
+ }
+ }
+ }
jobDescriptor.setInputValues(inputValues);
jobDescriptor.setUserName(((GSISSHAbstractCluster) cluster).getServerInfo().getUserName());