Repository: airavata Updated Branches: refs/heads/master 405d31d89 -> f88204404
fixing ultrascan jobs with app catalog changes Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/f8820440 Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/f8820440 Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/f8820440 Branch: refs/heads/master Commit: f88204404aa7fc65e793ad98478b6648feda0c12 Parents: 405d31d Author: Chathuri Wimalasena <kamalas...@gmail.com> Authored: Fri Nov 14 12:02:26 2014 -0500 Committer: Chathuri Wimalasena <kamalas...@gmail.com> Committed: Fri Nov 14 12:02:26 2014 -0500 ---------------------------------------------------------------------- .../samples/CreateLaunchExperimentUS3.java | 100 +++++++++---------- .../tools/RegisterOGCEUS3Application.java | 4 +- .../gfac/gsissh/util/GFACGSISSHUtils.java | 17 ++-- .../airavata/gfac/ssh/util/GFACSSHUtils.java | 1 - 4 files changed, 63 insertions(+), 59 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/f8820440/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java index b4f8d98..bbffe62 100644 --- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java +++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperimentUS3.java @@ -44,7 +44,7 @@ import java.util.Set; public class CreateLaunchExperimentUS3 { //FIXME: Read from a config file - public static final String THRIFT_SERVER_HOST = "gridfarm005.ucs.indiana.edu"; + public static final String THRIFT_SERVER_HOST = "localhost"; public static final int THRIFT_SERVER_PORT = 8930; private final static Logger logger = LoggerFactory.getLogger(CreateLaunchExperiment.class); private static final String DEFAULT_USER = "default.registry.user"; @@ -54,9 +54,9 @@ public class CreateLaunchExperimentUS3 { final Airavata.Client airavata = AiravataClientFactory.createAiravataClient(THRIFT_SERVER_HOST, THRIFT_SERVER_PORT); System.out.println("API version is " + airavata.getAPIVersion()); // addDescriptors(); -// final String expId = createUS3ExperimentForTrestles(airavata); + final String expId = createUS3ExperimentForTrestles(airavata); // final String expId = createUS3ExperimentForStampede(airavata); - final String expId = createUS3ExperimentForLonestar(airavata); +// final String expId = createUS3ExperimentForLonestar(airavata); // final String expId = createUS3ExperimentForAlamo(airavata); System.out.println("Experiment ID : " + expId); launchExperiment(airavata, expId); @@ -66,39 +66,39 @@ public class CreateLaunchExperimentUS3 { // } catch (InterruptedException e) { // e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. // } - Thread monitor = (new Thread(){ - public void run() { - Map<String, JobStatus> jobStatuses = null; - while (true) { - try { - jobStatuses = airavata.getJobStatuses(expId); - Set<String> strings = jobStatuses.keySet(); - for (String key : strings) { - JobStatus jobStatus = jobStatuses.get(key); - if(jobStatus == null){ - return; - }else { - if (JobState.COMPLETE.equals(jobStatus.getJobState())) { - System.out.println("Job completed Job ID: " + jobStatus.getJobState().toString()); - return; - }else{ - System.out.println("Job ID:" + key + jobStatuses.get(key).getJobState().toString()); - } - } - } - Thread.sleep(20000); - } catch (Exception e) { - e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. - } - } - } - }); - monitor.start(); - try { - monitor.join(); - } catch (InterruptedException e) { - e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. - } +// Thread monitor = (new Thread(){ +// public void run() { +// Map<String, JobStatus> jobStatuses = null; +// while (true) { +// try { +// jobStatuses = airavata.getJobStatuses(expId); +// Set<String> strings = jobStatuses.keySet(); +// for (String key : strings) { +// JobStatus jobStatus = jobStatuses.get(key); +// if(jobStatus == null){ +// return; +// }else { +// if (JobState.COMPLETE.equals(jobStatus.getJobState())) { +// System.out.println("Job completed Job ID: " + jobStatus.getJobState().toString()); +// return; +// }else{ +// System.out.println("Job ID:" + key + jobStatuses.get(key).getJobState().toString()); +// } +// } +// } +// Thread.sleep(20000); +// } catch (Exception e) { +// e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. +// } +// } +// } +// }); +// monitor.start(); +// try { +// monitor.join(); +// } catch (InterruptedException e) { +// e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. +// } // airavata.terminateExperiment(expId); @@ -193,7 +193,7 @@ public class CreateLaunchExperimentUS3 { InputDataObjectType input = new InputDataObjectType(); input.setName("input"); input.setType(DataType.URI); - input.setValue("file:///home/airavata/input/hpcinput.tar"); + input.setValue("file:///home/sgg/chathuri/laptop_backup/airavata/ultrascan_input/hpcinput.tar"); InputDataObjectType input1 = new InputDataObjectType(); input1.setName("walltime"); input1.setType(DataType.STRING); @@ -224,21 +224,21 @@ public class CreateLaunchExperimentUS3 { // exOut.add(output1); // exOut.add(output2); - // Project project = ProjectModelUtil.createProject("ultrascan", "ultrascan", "test project"); - //String projectId = client.createProject(project); + Project project = ProjectModelUtil.createProject("ultrascan", "ultrascan", "test project"); + String projectId = client.createProject(project); - Experiment simpleExperiment = ExperimentModelUtil.createSimpleExperiment("ultrascan_41574ef5-b054-4d03-ab20-2cfe768d5096", "ultrascan", "US3ExperimentTrestles", "US3AppTrestles", "ultrascan_e76ab5cf-79f6-44df-a244-10a734183fec", exInputs); + Experiment simpleExperiment = ExperimentModelUtil.createSimpleExperiment(projectId, "ultrascan", "US3ExperimentTrestles", "US3AppTrestles", "ultrascan_7ce6cd43-622c-44e0-87c5-fb7a6528c799", exInputs); simpleExperiment.setExperimentOutputs(exOut); - ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling("trestles.sdsc.xsede.org_1ccc526f-ab74-4a5a-970a-c464cb9def5a", 32, 2, 0, "shared", 30, 0, 0, "uot111"); + ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling("trestles.sdsc.xsede.org_72b9181b-7156-4975-a386-ed98b4949496", 32, 1, 0, "shared", 30, 0, 0, "sds128"); UserConfigurationData userConfigurationData = new UserConfigurationData(); - scheduling.setResourceHostId("trestles.sdsc.xsede.org_1ccc526f-ab74-4a5a-970a-c464cb9def5a"); + scheduling.setResourceHostId("trestles.sdsc.xsede.org_72b9181b-7156-4975-a386-ed98b4949496"); userConfigurationData.setAiravataAutoSchedule(false); userConfigurationData.setOverrideManualScheduledParams(false); AdvancedOutputDataHandling dataHandling = new AdvancedOutputDataHandling(); - dataHandling.setOutputDataDir("/home/airavata/output/"); + dataHandling.setOutputDataDir("/home/sgg/chathuri/laptop_backup/airavata"); userConfigurationData.setAdvanceOutputDataHandling(dataHandling); userConfigurationData.setComputationalResourceScheduling(scheduling); @@ -264,7 +264,7 @@ public class CreateLaunchExperimentUS3 { InputDataObjectType input = new InputDataObjectType(); input.setName("input"); input.setType(DataType.URI); - input.setValue("file:///home/airavata/input/hpcinput.tar"); + input.setValue("file:///home/sgg/chathuri/laptop_backup/airavata/ultrascan_input/hpcinput.tar"); InputDataObjectType input1 = new InputDataObjectType(); input1.setName("walltime"); input1.setType(DataType.STRING); @@ -296,15 +296,15 @@ public class CreateLaunchExperimentUS3 { // exOut.add(output1); // exOut.add(output2); -// Project project = ProjectModelUtil.createProject("project1", "admin", "test project"); -// String projectId = client.createProject(project); + Project project = ProjectModelUtil.createProject("project1", "admin", "test project"); + String projectId = client.createProject(project); - Experiment simpleExperiment = ExperimentModelUtil.createSimpleExperiment("ultrascan_41574ef5-b054-4d03-ab20-2cfe768d5096", "ultrascan", "US3ExperimentStampede", "US3AppStampede", "ultrascan_e76ab5cf-79f6-44df-a244-10a734183fec", exInputs); + Experiment simpleExperiment = ExperimentModelUtil.createSimpleExperiment(projectId, "ultrascan", "US3ExperimentStampede", "US3AppStampede", "ultrascan_7ce6cd43-622c-44e0-87c5-fb7a6528c799", exInputs); simpleExperiment.setExperimentOutputs(exOut); - ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling("stampede.tacc.xsede.org_af57850b-103b-49a1-aab2-27cb070d3bd9", 16, 2, 0, "normal", 30, 0, 0, "TG-MCB070039N"); + ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling("stampede.tacc.xsede.org_e59e046f-e0e1-49c4-8475-2fab2e35d044", 16, 2, 0, "normal", 30, 0, 0, "TG-MCB070039N"); - scheduling.setResourceHostId("stampede.tacc.xsede.org_af57850b-103b-49a1-aab2-27cb070d3bd9"); + scheduling.setResourceHostId("stampede.tacc.xsede.org_e59e046f-e0e1-49c4-8475-2fab2e35d044"); UserConfigurationData userConfigurationData = new UserConfigurationData(); userConfigurationData.setAiravataAutoSchedule(false); @@ -312,7 +312,7 @@ public class CreateLaunchExperimentUS3 { userConfigurationData.setComputationalResourceScheduling(scheduling); AdvancedOutputDataHandling dataHandling = new AdvancedOutputDataHandling(); - dataHandling.setOutputDataDir("/home/airavata/output/"); + dataHandling.setOutputDataDir("/home/sgg/chathuri/laptop_backup/airavata"); userConfigurationData.setAdvanceOutputDataHandling(dataHandling); simpleExperiment.setUserConfigurationData(userConfigurationData); http://git-wip-us.apache.org/repos/asf/airavata/blob/f8820440/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java index d6cd8f8..2b7c195 100644 --- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java +++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java @@ -32,8 +32,8 @@ public class RegisterOGCEUS3Application { // public static final String THRIFT_SERVER_HOST = "gridfarm005.ucs.indiana.edu"; // public static final int THRIFT_SERVER_PORT = 8930; private static final String DEFAULT_GATEWAY= "default"; - public static final String THRIFT_SERVER_HOST = "gw111.iu.xsede.org"; - public static final int THRIFT_SERVER_PORT = 9930; + public static final String THRIFT_SERVER_HOST = "localhost"; + public static final int THRIFT_SERVER_PORT = 8930; // private static final String DEFAULT_GATEWAY = "ultrascan"; private static Airavata.Client airavataClient; http://git-wip-us.apache.org/repos/asf/airavata/blob/f8820440/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 d040ca4..edd496a 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 @@ -42,10 +42,7 @@ import org.apache.airavata.gsi.ssh.impl.PBSCluster; import org.apache.airavata.gsi.ssh.util.CommonUtils; import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType; -import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface; -import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol; -import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission; -import org.apache.airavata.model.appcatalog.computeresource.SecurityProtocol; +import org.apache.airavata.model.appcatalog.computeresource.*; import org.apache.airavata.model.workspace.experiment.ComputationalResourceScheduling; import org.apache.airavata.model.workspace.experiment.TaskDetails; import org.slf4j.Logger; @@ -162,9 +159,17 @@ public class GFACGSISSHUtils { public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext, Cluster cluster) { JobDescriptor jobDescriptor = new JobDescriptor(); - ApplicationContext applicationContext = jobExecutionContext.getApplicationContext(); - ApplicationDeploymentDescription app = applicationContext.getApplicationDeploymentDescription(); TaskDetails taskData = jobExecutionContext.getTaskData(); + ResourceJobManager resourceJobManager = jobExecutionContext.getResourceJobManager(); + Map<JobManagerCommand, String> jobManagerCommands = resourceJobManager.getJobManagerCommands(); + if (jobManagerCommands != null && !jobManagerCommands.isEmpty()) { + for (JobManagerCommand command : jobManagerCommands.keySet()) { + if (command == JobManagerCommand.SUBMISSION) { + String commandVal = jobManagerCommands.get(command); + jobDescriptor.setJobSubmitter(commandVal); + } + } + } // this is common for any application descriptor jobDescriptor.setCallBackIp(ServerSettings.getIp()); jobDescriptor.setCallBackPort(ServerSettings.getSetting(org.apache.airavata.common.utils.Constants.GFAC_SERVER_PORT, "8950")); http://git-wip-us.apache.org/repos/asf/airavata/blob/f8820440/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 00b5e16..1e9b937 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 @@ -215,7 +215,6 @@ public class GFACSSHUtils { TaskDetails taskData = jobExecutionContext.getTaskData(); ResourceJobManager resourceJobManager = jobExecutionContext.getResourceJobManager(); Map<JobManagerCommand, String> jobManagerCommands = resourceJobManager.getJobManagerCommands(); - String jobManagerBinPath = resourceJobManager.getJobManagerBinPath(); if (jobManagerCommands != null && !jobManagerCommands.isEmpty()) { for (JobManagerCommand command : jobManagerCommands.keySet()) { if (command == JobManagerCommand.SUBMISSION) {
