Examples with ResourceJobManager org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager used on opensource projects

Example 1 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class ForkJobSubmissionTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    TaskStatus taskStatus = new TaskStatus(TaskState.CREATED);
    try {
        ProcessContext processContext = taskContext.getParentProcessContext();
        JobModel jobModel = processContext.getJobModel();
        jobModel.setTaskId(taskContext.getTaskId());
        RemoteCluster remoteCluster = processContext.getJobSubmissionRemoteCluster();
        GroovyMap groovyMap = GFacUtils.createGroovyMap(processContext, taskContext);
        jobModel.setJobName(groovyMap.get(Script.JOB_NAME).toString());
        ResourceJobManager resourceJobManager = GFacUtils.getResourceJobManager(processContext);
        JobManagerConfiguration jConfig = null;
        if (resourceJobManager != null) {
            jConfig = Factory.getJobManagerConfiguration(resourceJobManager);
        }
        JobStatus jobStatus = new JobStatus();
        File jobFile = GFacUtils.createJobFile(groovyMap, taskContext, jConfig);
        if (jobFile != null && jobFile.exists()) {
            jobModel.setJobDescription(FileUtils.readFileToString(jobFile));
            JobSubmissionOutput jobSubmissionOutput = remoteCluster.submitBatchJob(jobFile.getPath(), processContext.getWorkingDir());
            jobModel.setExitCode(jobSubmissionOutput.getExitCode());
            jobModel.setStdErr(jobSubmissionOutput.getStdErr());
            jobModel.setStdOut(jobSubmissionOutput.getStdOut());
            String jobId = jobSubmissionOutput.getJobId();
            if (jobId != null && !jobId.isEmpty()) {
                jobModel.setJobId(jobId);
                GFacUtils.saveJobModel(processContext, jobModel);
                jobStatus.setJobState(JobState.SUBMITTED);
                jobStatus.setReason("Successfully Submitted to " + taskContext.getParentProcessContext().getComputeResourceDescription().getHostName());
                jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                jobModel.setJobStatuses(Arrays.asList(jobStatus));
                GFacUtils.saveJobStatus(taskContext.getParentProcessContext(), jobModel);
                taskStatus = new TaskStatus(TaskState.COMPLETED);
                taskStatus.setReason("Submitted job to compute resource");
            }
            if (jobId == null || jobId.isEmpty()) {
                String msg = "expId:" + processContext.getProcessModel().getExperimentId() + " Couldn't find " + "remote jobId for JobName:" + jobModel.getJobName() + ", both submit and verify steps " + "doesn't return a valid JobId. " + "Hence changing experiment state to Failed";
                log.error(msg);
                ErrorModel errorModel = new ErrorModel();
                errorModel.setActualErrorMessage(msg);
                errorModel.setCreationTime(AiravataUtils.getCurrentTimestamp().getTime());
                GFacUtils.saveExperimentError(processContext, errorModel);
                GFacUtils.saveProcessError(processContext, errorModel);
                GFacUtils.saveTaskError(taskContext, errorModel);
                taskStatus.setState(TaskState.FAILED);
                taskStatus.setReason("Couldn't find job id in both submitted and verified steps");
            } else {
                GFacUtils.saveJobModel(processContext, jobModel);
            }
        } else {
            taskStatus.setState(TaskState.FAILED);
            if (jobFile == null) {
                taskStatus.setReason("JobFile is null");
            } else {
                taskStatus.setReason("Job file doesn't exist");
            }
        }
    } catch (ApplicationSettingsException e) {
        String msg = "Error occurred while creating job descriptor";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (AppCatalogException e) {
        String msg = "Error while instantiating app catalog";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (GFacException e) {
        String msg = "Error occurred while submitting the job";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (IOException e) {
        String msg = "Error while reading the content of the job file";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    }
    return taskStatus;
}

Example 2 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class LocalJobSubmissionTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    TaskStatus taskStatus = new TaskStatus(TaskState.CREATED);
    try {
        ProcessContext processContext = taskContext.getParentProcessContext();
        JobModel jobModel = processContext.getJobModel();
        jobModel.setTaskId(taskContext.getTaskId());
        RemoteCluster remoteCluster = processContext.getJobSubmissionRemoteCluster();
        GroovyMap groovyMap = GFacUtils.createGroovyMap(processContext, taskContext);
        String jobId = AiravataUtils.getId("JOB_ID_");
        jobModel.setJobName(groovyMap.get(Script.JOB_NAME).toString());
        jobModel.setJobId(jobId);
        ResourceJobManager resourceJobManager = GFacUtils.getResourceJobManager(processContext);
        JobManagerConfiguration jConfig = null;
        if (resourceJobManager != null) {
            jConfig = Factory.getJobManagerConfiguration(resourceJobManager);
        }
        JobStatus jobStatus = new JobStatus();
        File jobFile = GFacUtils.createJobFile(groovyMap, taskContext, jConfig);
        if (jobFile != null && jobFile.exists()) {
            jobModel.setJobDescription(FileUtils.readFileToString(jobFile));
            GFacUtils.saveJobModel(processContext, jobModel);
            JobSubmissionOutput jobSubmissionOutput = remoteCluster.submitBatchJob(jobFile.getPath(), processContext.getWorkingDir());
            jobStatus.setJobState(JobState.SUBMITTED);
            jobStatus.setReason("Successfully Submitted to " + taskContext.getParentProcessContext().getComputeResourceDescription().getHostName());
            jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
            jobModel.setJobStatuses(Arrays.asList(jobStatus));
            // log job submit status
            GFacUtils.saveJobStatus(taskContext.getParentProcessContext(), jobModel);
            // for local, job gets completed synchronously
            // so changing job status to complete
            jobModel.setExitCode(jobSubmissionOutput.getExitCode());
            jobModel.setStdErr(jobSubmissionOutput.getStdErr());
            jobModel.setStdOut(jobSubmissionOutput.getStdOut());
            jobModel.setJobId(jobId);
            jobStatus.setJobState(JobState.COMPLETE);
            jobStatus.setReason("Successfully Completed " + taskContext.getParentProcessContext().getComputeResourceDescription().getHostName());
            jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
            jobModel.setJobStatuses(Arrays.asList(jobStatus));
            // log job complete status
            GFacUtils.saveJobStatus(taskContext.getParentProcessContext(), jobModel);
            taskStatus = new TaskStatus(TaskState.COMPLETED);
            taskStatus.setReason("Submitted job to compute resource");
        } else {
            taskStatus.setState(TaskState.FAILED);
            if (jobFile == null) {
                taskStatus.setReason("JobFile is null");
            } else {
                taskStatus.setReason("Job file doesn't exist");
            }
        }
    } catch (GFacException | IOException | AppCatalogException | ApplicationSettingsException e) {
        String msg = "Error occurred while submitting a local job";
        log.error(msg, e);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
        taskStatus.setState(TaskState.FAILED);
    }
    return taskStatus;
}

Example 3 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class DocumentCreatorNew method createStampedeAmberDocs.

public String createStampedeAmberDocs() throws InvalidRequestException, AiravataClientException, AiravataSystemException, TException, AppCatalogException {
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(stampedeHostAddress, null, null);
    host.addToHostAliases(stampedeHostAddress);
    host.addToIpAddresses(stampedeHostAddress);
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.SLURM, "/usr/bin/", null, "push");
    SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
    sshJobSubmission.setResourceJobManager(resourceJobManager);
    sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI);
    sshJobSubmission.setSshPort(2222);
    client.addSSHJobSubmissionDetails(authzToken, host.getComputeResourceId(), 1, sshJobSubmission);
    SCPDataMovement scpDataMovement = new SCPDataMovement();
    scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI);
    scpDataMovement.setSshPort(22);
    client.addSCPDataMovementDetails(authzToken, host.getComputeResourceId(), 1, scpDataMovement);
    ApplicationModule amodule = DocumentCreatorUtils.createApplicationModule("Amber", "12.0", null);
    amodule.setAppModuleId(client.registerApplicationModule(authzToken, DEFAULT_GATEWAY, amodule));
    ApplicationInterfaceDescription application = new ApplicationInterfaceDescription();
    application.setApplicationName("AmberBR2");
    application.addToApplicationModules(amodule.getAppModuleId());
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_HEAT_RST", "AMBER_HEAT_RST", null, null, DataType.URI));
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PROD_IN", "AMBER_PROD_IN", null, null, DataType.URI));
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PRMTOP", "AMBER_PRMTOP", null, null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.info", null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.mdcrd", null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.out", null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.rst", null, DataType.URI));
    application.setApplicationInterfaceId(client.registerApplicationInterface(authzToken, DEFAULT_GATEWAY, application));
    ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), amodule.getAppModuleId(), "/home1/01437/ogce/production/app_wrappers/amber_wrapper.sh", ApplicationParallelismType.SERIAL, "AmberStampede");
    deployment.setAppDeploymentId(client.registerApplicationDeployment(authzToken, DEFAULT_GATEWAY, deployment));
    client.addGatewayComputeResourcePreference(authzToken, getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/home1/01437/ogce", "TG-STA110014S", false, null, null, null));
    return host.getComputeResourceId() + "," + application.getApplicationInterfaceId();
}

Example 4 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class DocumentCreatorNew method createLocalHostDocs.

public String createLocalHostDocs() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException {
    // Define compute resource host
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription("localhost", new ArrayList<String>(Arrays.asList(new String[] { "127.0.0.1" })), new ArrayList<String>(Arrays.asList(new String[] { "127.0.0.1" })));
    // host.setIsEmpty(true);
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    LOCALSubmission localSubmission = new LOCALSubmission();
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.FORK, null, null, null);
    localSubmission.setResourceJobManager(resourceJobManager);
    client.addLocalSubmissionDetails(authzToken, host.getComputeResourceId(), 1, localSubmission);
    LOCALDataMovement localDataMovement = new LOCALDataMovement();
    client.addLocalDataMovementDetails(authzToken, host.getComputeResourceId(), 1, localDataMovement);
    // Define application module
    ApplicationModule module = DocumentCreatorUtils.createApplicationModule("echo", "1.0.0", "Local host echo applications");
    module.setAppModuleId(client.registerApplicationModule(authzToken, DEFAULT_GATEWAY, module));
    // Define application interfaces
    ApplicationInterfaceDescription application = new ApplicationInterfaceDescription();
    // application.setIsEmpty(false);
    application.setApplicationName("SimpleEcho0");
    application.addToApplicationModules(module.getAppModuleId());
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", "Echo Input Data", null, DataType.STRING));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING));
    application.setApplicationInterfaceId(client.registerApplicationInterface(authzToken, DEFAULT_GATEWAY, application));
    // Define application deployment
    ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module.getAppModuleId(), "/bin/echo", ApplicationParallelismType.SERIAL, "Local echo app depoyment");
    deployment.setAppDeploymentId(client.registerApplicationDeployment(authzToken, DEFAULT_GATEWAY, deployment));
    // Define gateway profile
    ComputeResourcePreference computeResourcePreference = DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/tmp", null, false, null, null, null);
    gatewayResourceProfile = new GatewayResourceProfile();
    // gatewayResourceProfile.setGatewayID("default");
    gatewayResourceProfile.setGatewayID(DEFAULT_GATEWAY);
    gatewayResourceProfile.addToComputeResourcePreferences(computeResourcePreference);
    String gatewayId = client.registerGatewayResourceProfile(authzToken, gatewayResourceProfile);
    gatewayResourceProfile.setGatewayID(gatewayId);
    client.addGatewayComputeResourcePreference(authzToken, gatewayResourceProfile.getGatewayID(), host.getComputeResourceId(), computeResourcePreference);
    return host.getComputeResourceId() + "," + application.getApplicationInterfaceId();
}

Example 5 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class DocumentCreatorNew method createPBSDocsForOGCE_Echo.

// 
// public void createGramDocs() {
// //        /*
// //           creating host descriptor for gram
// //        */
// //        HostDescription host = new HostDescription(GlobusHostType.type);
// //        host.getType().setHostAddress(trestleshpcHostAddress);
// //        host.getType().setHostName(trestleshpcHostAddress);
// //        ((GlobusHostType) host.getType()).setGlobusGateKeeperEndPointArray(new String[]{gramAddress});
// //        ((GlobusHostType) host.getType()).setGridFTPEndPointArray(new String[]{gridftpAddress});
// //        try {
// //            airavataAPI.getApplicationManager().saveHostDescription(host);
// //        } catch (AiravataAPIInvocationException e) {
// //            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
// //        }
// //
// //
// //        /*
// //        * Service Description creation and saving
// //        */
// //        String serviceName = "SimpleEcho1";
// //        ServiceDescription serv = new ServiceDescription();
// //        serv.getType().setName(serviceName);
// //
// //        List<InputParameterType> inputList = new ArrayList<InputParameterType>();
// //        List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
// //
// //        InputParameterType input = InputParameterType.Factory.newInstance();
// //        input.setParameterName("echo_input");
// //        ParameterType parameterType = input.addNewParameterType();
// //        parameterType.setType(DataType.STRING);
// //        parameterType.setName("String");
// //
// //        OutputParameterType output = OutputParameterType.Factory.newInstance();
// //        output.setParameterName("echo_output");
// //        ParameterType parameterType1 = output.addNewParameterType();
// //        parameterType1.setType(DataType.STRING);
// //        parameterType1.setName("String");
// //
// //        inputList.add(input);
// //        outputList.add(output);
// //
// //        InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList.size()]);
// //        OutputParameterType[] outputParamList = outputList.toArray(new OutputParameterType[outputList.size()]);
// //
// //        serv.getType().setInputParametersArray(inputParamList);
// //        serv.getType().setOutputParametersArray(outputParamList);
// //        try {
// //            airavataAPI.getApplicationManager().saveServiceDescription(serv);
// //        } catch (AiravataAPIInvocationException e) {
// //            e.printStackTrace();
// //        }
// //
// //        /*
// //            Application descriptor creation and saving
// //         */
// //        ApplicationDescription appDesc = new ApplicationDescription(HpcApplicationDeploymentType.type);
// //        HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc.getType();
// //        ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
// //        name.setStringValue("EchoLocal");
// //        app.setApplicationName(name);
// //        ProjectAccountType projectAccountType = app.addNewProjectAccount();
// //        projectAccountType.setProjectAccountNumber("sds128");
// //
// //        QueueType queueType = app.addNewQueue();
// //        queueType.setQueueName("normal");
// //
// //        app.setCpuCount(1);
// //        app.setJobType(JobTypeType.SERIAL);
// //        app.setNodeCount(1);
// //        app.setProcessorsPerNode(1);
// //
// //        /*
// //           * Use bat file if it is compiled on Windows
// //           */
// //        app.setExecutableLocation("/bin/echo");
// //
// //        /*
// //           * Default tmp location
// //           */
// //        String tempDir = "/home/ogce/scratch";
// //        app.setScratchWorkingDirectory(tempDir);
// //        app.setMaxMemory(10);
// //
// //
// //        try {
// //            airavataAPI.getApplicationManager().saveApplicationDescription(serviceName, trestleshpcHostAddress, appDesc);
// //        } catch (AiravataAPIInvocationException e) {
// //            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
// //        }
// }
// 
public String createPBSDocsForOGCE_Echo() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException {
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(trestleshpcHostAddress, null, null);
    host.addToIpAddresses(trestleshpcHostAddress);
    host.addToHostAliases(trestleshpcHostAddress);
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.PBS, "/opt/torque/bin/", null, null);
    sshJobSubmission.setResourceJobManager(resourceJobManager);
    sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI);
    sshJobSubmission.setSshPort(22);
    client.addSSHJobSubmissionDetails(authzToken, host.getComputeResourceId(), 1, sshJobSubmission);
    SCPDataMovement scpDataMovement = new SCPDataMovement();
    scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI);
    scpDataMovement.setSshPort(22);
    client.addSCPDataMovementDetails(authzToken, host.getComputeResourceId(), 1, scpDataMovement);
    ApplicationModule module1 = DocumentCreatorUtils.createApplicationModule("echo", "1.2", null);
    module1.setAppModuleId(client.registerApplicationModule(authzToken, DEFAULT_GATEWAY, module1));
    ApplicationInterfaceDescription application = new ApplicationInterfaceDescription();
    // application.setIsEmpty(false);
    application.setApplicationName("SimpleEcho2");
    application.addToApplicationModules(module1.getAppModuleId());
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", "echo_input", null, DataType.STRING));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING));
    application.setApplicationInterfaceId(client.registerApplicationInterface(authzToken, DEFAULT_GATEWAY, application));
    ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module1.getAppModuleId(), "/home/ogce/echo.sh", ApplicationParallelismType.SERIAL, "Echo application");
    deployment.setAppDeploymentId(client.registerApplicationDeployment(authzToken, DEFAULT_GATEWAY, deployment));
    client.addGatewayComputeResourcePreference(authzToken, getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/oasis/scratch/trestles/ogce/temp_project/", "sds128", false, null, null, null));
    return host.getComputeResourceId() + "," + application.getApplicationInterfaceId();
}