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Posted to commits@airavata.apache.org by ch...@apache.org on 2015/04/24 18:44:28 UTC
airavata git commit: removing extra scpace when adding email
addresses and test framework changes to ultrascan application
Repository: airavata
Updated Branches:
refs/heads/master 73da33a37 -> bf0f8efc8
removing extra scpace when adding email addresses and test framework changes to ultrascan application
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/bf0f8efc
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/bf0f8efc
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/bf0f8efc
Branch: refs/heads/master
Commit: bf0f8efc8ea9ae898e3c8b48c90b41fea3507f59
Parents: 73da33a
Author: Chathuri Wimalasena <ch...@apache.org>
Authored: Fri Apr 24 12:44:24 2015 -0400
Committer: Chathuri Wimalasena <ch...@apache.org>
Committed: Fri Apr 24 12:44:24 2015 -0400
----------------------------------------------------------------------
.../airavata/gfac/ssh/util/GFACSSHUtils.java | 2 +-
.../ComputeResourceRegister.java | 5 +-
.../ExperimentExecution.java | 144 ++++++++++---------
.../FrameworkBootstrapping.java | 4 +-
.../TestFrameworkProps.java | 10 ++
.../src/main/resources/test-framework.json | 7 +-
6 files changed, 93 insertions(+), 79 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/bf0f8efc/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 e94a499..bb580fb 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
@@ -301,7 +301,7 @@ public class GFACSSHUtils {
String userJobNotifEmailIds = ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_EMAILIDS);
if (userJobNotifEmailIds != null && !userJobNotifEmailIds.isEmpty()) {
if (emailIds != null && !emailIds.isEmpty()) {
- emailIds += (", " + userJobNotifEmailIds);
+ emailIds += ("," + userJobNotifEmailIds);
} else {
emailIds = userJobNotifEmailIds;
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/bf0f8efc/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ComputeResourceRegister.java
----------------------------------------------------------------------
diff --git a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ComputeResourceRegister.java b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ComputeResourceRegister.java
index 3ca61ba..b28b8b0 100644
--- a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ComputeResourceRegister.java
+++ b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ComputeResourceRegister.java
@@ -96,7 +96,7 @@ public class ComputeResourceRegister {
bigredResourceId = registerComputeHost("bigred2.uits.iu.edu", "IU BigRed II Cluster",
ResourceJobManagerType.PBS, "push", "/opt/torque/torque-5.0.1/bin/", SecurityProtocol.SSH_KEYS, 22, "aprun -n");
System.out.println("BigredII Resource Id is " + bigredResourceId);
- } else if (resourceName.contains("gorden")) {
+ } else if (resourceName.contains("gordon")) {
//Register BigRedII
gordenResourceId = registerComputeHost("gordon.sdsc.edu", "SDSC Gorden Cluster",
ResourceJobManagerType.PBS, "push", "/opt/torque/bin/", SecurityProtocol.SSH_KEYS, 22, "mpirun_rsh -hostfile $PBS_NODEFILE -np");
@@ -142,6 +142,7 @@ public class ComputeResourceRegister {
SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
sshJobSubmission.setResourceJobManager(resourceJobManager);
sshJobSubmission.setSecurityProtocol(securityProtocol);
+// sshJobSubmission.setMonitorMode(MonitorMode.JOB_EMAIL_NOTIFICATION_MONITOR);
sshJobSubmission.setSshPort(portNumber);
airavata.addSSHJobSubmissionDetails(computeResourceId, 1, sshJobSubmission);
@@ -214,7 +215,7 @@ public class ComputeResourceRegister {
bigRedCgatewayResourcePreferences = createComputeResourcePreference(resourceId, "TG-STA110014S", false, null, null, null,
"/N/dc2/scratch/cgateway/gta-work-dirs", loginUserName);
airavata.addGatewayComputeResourcePreference(gatewayResourceProfile.getGatewayID(), resourceId, bigRedCgatewayResourcePreferences);
- }else if (resourceId.contains("gorden") && loginUserName.equals("us3")){
+ }else if (resourceId.contains("gordon") && loginUserName.equals("us3")){
gordenUS3ResourcePreference = createComputeResourcePreference(resourceId, "uot111", false, null, JobSubmissionProtocol.SSH,
DataMovementProtocol.SCP, "/home/us3/gordon/work/airavata", loginUserName);
airavata.addGatewayComputeResourcePreference(gatewayResourceProfile.getGatewayID(), resourceId, gordenUS3ResourcePreference);
http://git-wip-us.apache.org/repos/asf/airavata/blob/bf0f8efc/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ExperimentExecution.java
----------------------------------------------------------------------
diff --git a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ExperimentExecution.java b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ExperimentExecution.java
index 03da1e7..f13056a 100644
--- a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ExperimentExecution.java
+++ b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ExperimentExecution.java
@@ -246,9 +246,9 @@ public class ExperimentExecution {
resultWriter.println("End of Results for Experiment : " + expId );
resultWriter.println("=====================================================================");
}
- System.out.println(" Experiment Id : '" + expId
- + "' with state : '" + event.getState().toString() +
- " for Gateway " + event.getGatewayId());
+// System.out.println(" Experiment Id : '" + expId
+// + "' with state : '" + event.getState().toString() +
+// " for Gateway " + event.getGatewayId());
} catch (TException e) {
logger.error(e.getMessage(), e);
}
@@ -501,6 +501,7 @@ public class ExperimentExecution {
public void createUltrascanExperiment () throws Exception{
try {
TestFrameworkProps.Application[] applications = properties.getApplications();
+ int numberOfIterations = properties.getNumberOfIterations();
Map<String, String> userGivenAmberInputs = new HashMap<>();
for (TestFrameworkProps.Application application : applications){
if (application.getName().equals(TestFrameworkConstants.AppcatalogConstants.ULTRASCAN)){
@@ -508,82 +509,83 @@ public class ExperimentExecution {
}
}
- for (String gatewayId : csTokens.keySet()){
- String token = csTokens.get(gatewayId);
- Map<String, String> appsWithNames = appInterfaceMap.get(gatewayId);
- for (String appId : appsWithNames.keySet()){
- String appName = appsWithNames.get(appId);
- if (appName.equals(TestFrameworkConstants.AppcatalogConstants.ULTRASCAN)){
- List<InputDataObjectType> applicationInputs = airavata.getApplicationInputs(appId);
- List<OutputDataObjectType> appOutputs = airavata.getApplicationOutputs(appId);
- for (String inputName : userGivenAmberInputs.keySet()){
- for (InputDataObjectType inputDataObjectType : applicationInputs) {
- if (inputDataObjectType.getName().equalsIgnoreCase(inputName)) {
- inputDataObjectType.setValue(userGivenAmberInputs.get(inputName));
+ for (int i=0; i < numberOfIterations; i++){
+ for (String gatewayId : csTokens.keySet()){
+ String token = csTokens.get(gatewayId);
+ Map<String, String> appsWithNames = appInterfaceMap.get(gatewayId);
+ for (String appId : appsWithNames.keySet()){
+ String appName = appsWithNames.get(appId);
+ if (appName.equals(TestFrameworkConstants.AppcatalogConstants.ULTRASCAN)){
+ List<InputDataObjectType> applicationInputs = airavata.getApplicationInputs(appId);
+ List<OutputDataObjectType> appOutputs = airavata.getApplicationOutputs(appId);
+ for (String inputName : userGivenAmberInputs.keySet()){
+ for (InputDataObjectType inputDataObjectType : applicationInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase(inputName)) {
+ inputDataObjectType.setValue(userGivenAmberInputs.get(inputName));
+ }
}
}
- }
- List<Project> projectsPerGateway = projectsMap.get(gatewayId);
- String projectID = null;
- if (projectsPerGateway != null && !projectsPerGateway.isEmpty()){
- projectID = projectsPerGateway.get(0).getProjectID();
- }
- Experiment simpleExperiment =
- ExperimentModelUtil.createSimpleExperiment(projectID, testUser, "Ultrascan Experiment", "Ultrascan Experiment run", appId, applicationInputs);
- simpleExperiment.setExperimentOutputs(appOutputs);
- String experimentId;
- Map<String, String> computeResources = airavata.getAvailableAppInterfaceComputeResources(appId);
- if (computeResources != null && computeResources.size() != 0) {
- for (String id : computeResources.keySet()) {
- String resourceName = computeResources.get(id);
- if (resourceName.equals(TestFrameworkConstants.AppcatalogConstants.TRESTLES_RESOURCE_NAME)) {
- ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "normal", 30, 0, 1, null);
- UserConfigurationData userConfigurationData = new UserConfigurationData();
- userConfigurationData.setAiravataAutoSchedule(false);
- userConfigurationData.setOverrideManualScheduledParams(false);
- userConfigurationData.setComputationalResourceScheduling(scheduling);
- simpleExperiment.setUserConfigurationData(userConfigurationData);
- experimentId = airavata.createExperiment(gatewayId, simpleExperiment);
- experimentsWithTokens.put(experimentId, token);
- experimentsWithGateway.put(experimentId, gatewayId);
- }else if (resourceName.equals(TestFrameworkConstants.AppcatalogConstants.STAMPEDE_RESOURCE_NAME)) {
- ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "normal", 30, 0, 1, null);
- UserConfigurationData userConfigurationData = new UserConfigurationData();
- userConfigurationData.setAiravataAutoSchedule(false);
- userConfigurationData.setOverrideManualScheduledParams(false);
- userConfigurationData.setComputationalResourceScheduling(scheduling);
- simpleExperiment.setUserConfigurationData(userConfigurationData);
- experimentId = airavata.createExperiment(gatewayId, simpleExperiment);
- experimentsWithTokens.put(experimentId, token);
- experimentsWithGateway.put(experimentId, gatewayId);
- createAmberWithErrorInputs(gatewayId, token, projectID, id, appId);
- createAmberWithErrorUserConfig(gatewayId, token, projectID, id, appId);
- } else if (resourceName.equals(TestFrameworkConstants.AppcatalogConstants.ALAMO_RESOURCE_NAME)) {
- ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "normal", 30, 0, 1, null);
- UserConfigurationData userConfigurationData = new UserConfigurationData();
- userConfigurationData.setAiravataAutoSchedule(false);
- userConfigurationData.setOverrideManualScheduledParams(false);
- userConfigurationData.setComputationalResourceScheduling(scheduling);
- simpleExperiment.setUserConfigurationData(userConfigurationData);
- experimentId = airavata.createExperiment(gatewayId, simpleExperiment);
- experimentsWithTokens.put(experimentId, token);
- experimentsWithGateway.put(experimentId, gatewayId);
- }else if (resourceName.equals(TestFrameworkConstants.AppcatalogConstants.GORDEN_RESOURCE_NAME)) {
- ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "normal", 30, 0, 1, null);
- UserConfigurationData userConfigurationData = new UserConfigurationData();
- userConfigurationData.setAiravataAutoSchedule(false);
- userConfigurationData.setOverrideManualScheduledParams(false);
- userConfigurationData.setComputationalResourceScheduling(scheduling);
- simpleExperiment.setUserConfigurationData(userConfigurationData);
- experimentId = airavata.createExperiment(gatewayId, simpleExperiment);
- experimentsWithTokens.put(experimentId, token);
- experimentsWithGateway.put(experimentId, gatewayId);
+ List<Project> projectsPerGateway = projectsMap.get(gatewayId);
+ String projectID = null;
+ if (projectsPerGateway != null && !projectsPerGateway.isEmpty()){
+ projectID = projectsPerGateway.get(0).getProjectID();
+ }
+ Experiment simpleExperiment =
+ ExperimentModelUtil.createSimpleExperiment(projectID, testUser, "TestFR_Ultrascan_Experiment", "Ultrascan Experiment run", appId, applicationInputs);
+ simpleExperiment.setExperimentOutputs(appOutputs);
+ String experimentId;
+ Map<String, String> computeResources = airavata.getAvailableAppInterfaceComputeResources(appId);
+ if (computeResources != null && computeResources.size() != 0) {
+ for (String id : computeResources.keySet()) {
+ String resourceName = computeResources.get(id);
+ if (resourceName.equals(TestFrameworkConstants.AppcatalogConstants.STAMPEDE_RESOURCE_NAME)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "normal", 30, 0, 1, null);
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ experimentId = airavata.createExperiment(gatewayId, simpleExperiment);
+ experimentsWithTokens.put(experimentId, token);
+ experimentsWithGateway.put(experimentId, gatewayId);
+ } else if (resourceName.equals(TestFrameworkConstants.AppcatalogConstants.TRESTLES_RESOURCE_NAME)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "normal", 30, 0, 1, null);
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ experimentId = airavata.createExperiment(gatewayId, simpleExperiment);
+ experimentsWithTokens.put(experimentId, token);
+ experimentsWithGateway.put(experimentId, gatewayId);
+ }else if (resourceName.equals(TestFrameworkConstants.AppcatalogConstants.ALAMO_RESOURCE_NAME)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "batch", 30, 0, 1, null);
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ experimentId = airavata.createExperiment(gatewayId, simpleExperiment);
+ experimentsWithTokens.put(experimentId, token);
+ experimentsWithGateway.put(experimentId, gatewayId);
+ }else if (resourceName.equals(TestFrameworkConstants.AppcatalogConstants.GORDEN_RESOURCE_NAME)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "normal", 30, 0, 1, null);
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ experimentId = airavata.createExperiment(gatewayId, simpleExperiment);
+ experimentsWithTokens.put(experimentId, token);
+ experimentsWithGateway.put(experimentId, gatewayId);
+ }
}
}
}
}
}
}
+
}catch (Exception e){
logger.error("Error while creating Ultrascan experiment", e);
throw new Exception("Error while creating Ultrascan experiment", e);
http://git-wip-us.apache.org/repos/asf/airavata/blob/bf0f8efc/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java
----------------------------------------------------------------------
diff --git a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java
index 0d3f68d..d4878fd 100644
--- a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java
+++ b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java
@@ -85,8 +85,8 @@ public class FrameworkBootstrapping {
experimentExecution.createUltrascanExperiment();
// experimentExecution.createEchoExperiment();
// experimentExecution.createAmberExperiment();
-// experimentExecution.launchExperiments();
-// experimentExecution.monitorExperiments();
+ experimentExecution.launchExperiments();
+ experimentExecution.monitorExperiments();
}
} catch (Exception e) {
logger.error("Error occured while set up", e);
http://git-wip-us.apache.org/repos/asf/airavata/blob/bf0f8efc/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/TestFrameworkProps.java
----------------------------------------------------------------------
diff --git a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/TestFrameworkProps.java b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/TestFrameworkProps.java
index 158a2ec..ea9956a 100644
--- a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/TestFrameworkProps.java
+++ b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/TestFrameworkProps.java
@@ -40,10 +40,20 @@ public class TestFrameworkProps {
private Resource[] resources;
private Application[] applications;
private Error[] errors;
+ private int numberOfIterations;
+
public TestFrameworkProps() {
}
+ public int getNumberOfIterations() {
+ return numberOfIterations;
+ }
+
+ public void setNumberOfIterations(int numberOfIterations) {
+ this.numberOfIterations = numberOfIterations;
+ }
+
public int getGcount() {
return gcount;
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/bf0f8efc/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json
----------------------------------------------------------------------
diff --git a/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json b/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json
index e5526fa..f25b091 100644
--- a/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json
+++ b/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json
@@ -12,15 +12,16 @@
"resultFileLoc": "/tmp/test_framework_results/",
"skippedGateways": "default,php_reference_gateway,ultrascan,umass",
"injectErrors" : true,
+ "numberOfIterations" : 10,
"resources": [
{
"name": "trestles.sdsc.xsede.org",
- "loginUser": "ogce"
+ "loginUser": "us3"
},
{
"name": "stampede.tacc.xsede.org",
- "loginUser": "ogce"
+ "loginUser": "us3"
},
{
@@ -49,7 +50,7 @@
}
},
{
- "name": "ultrascan",
+ "name": "Ultrascan",
"inputs": {
"input": "/Users/chathuri/dev/airavata/source/php/inputs/hpcinput.tar",
"mgroupcount": "-mgroupcount=1",