Examples with JobStatus org.apache.airavata.model.status.JobStatus used on opensource projects

Example 1 with JobStatus

use of org.apache.airavata.model.status.JobStatus in project airavata by apache.

the class GFacEngineImpl method executeCancel.

private void executeCancel(TaskContext taskContext, JobSubmissionTask jSTask) throws GFacException {
    try {
        JobStatus oldJobStatus = jSTask.cancel(taskContext);
        // If Job was in Queued state when cancel command runs, then there won't be any email from this job.
        ProcessContext pc = taskContext.getParentProcessContext();
        JobMonitor monitorService = Factory.getMonitorService(pc.getMonitorMode());
        monitorService.canceledJob(pc.getJobModel().getJobId());
    } catch (TaskException e) {
        throw new GFacException("Error while cancelling job");
    } catch (AiravataException e) {
        throw new GFacException("Error wile getting monitoring service");
    }
}

Example 2 with JobStatus

use of org.apache.airavata.model.status.JobStatus in project airavata by apache.

the class GFacEngineImpl method executeTaskListFrom.

private void executeTaskListFrom(ProcessContext processContext, String startingTaskId) throws GFacException {
    // checkpoint
    if (processContext.isInterrupted() && processContext.getProcessState() != ProcessState.MONITORING) {
        GFacUtils.handleProcessInterrupt(processContext);
        return;
    }
    List<TaskModel> taskList = processContext.getTaskList();
    Map<String, TaskModel> taskMap = processContext.getTaskMap();
    boolean fastForward = true;
    for (String taskId : processContext.getTaskExecutionOrder()) {
        if (fastForward) {
            if (taskId.equalsIgnoreCase(startingTaskId)) {
                fastForward = false;
            } else {
                continue;
            }
        }
        TaskModel taskModel = taskMap.get(taskId);
        processContext.setCurrentExecutingTaskModel(taskModel);
        TaskTypes taskType = taskModel.getTaskType();
        TaskContext taskContext = getTaskContext(processContext);
        taskContext.setTaskModel(taskModel);
        ProcessStatus status = null;
        switch(taskType) {
            case ENV_SETUP:
                status = new ProcessStatus(ProcessState.CONFIGURING_WORKSPACE);
                status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                processContext.setProcessStatus(status);
                GFacUtils.saveAndPublishProcessStatus(processContext);
                // checkpoint
                if (processContext.isInterrupted()) {
                    GFacUtils.handleProcessInterrupt(processContext);
                    return;
                }
                configureWorkspace(taskContext, processContext.isRecovery());
                // checkpoint
                if (processContext.isInterrupted()) {
                    GFacUtils.handleProcessInterrupt(processContext);
                    return;
                }
                break;
            case DATA_STAGING:
                try {
                    // checkpoint
                    if (processContext.isInterrupted()) {
                        GFacUtils.handleProcessInterrupt(processContext);
                        return;
                    }
                    DataStagingTaskModel subTaskModel = (DataStagingTaskModel) taskContext.getSubTaskModel();
                    DataStageType type = subTaskModel.getType();
                    switch(type) {
                        case INPUT:
                            status = new ProcessStatus(ProcessState.INPUT_DATA_STAGING);
                            status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                            processContext.setProcessStatus(status);
                            GFacUtils.saveAndPublishProcessStatus(processContext);
                            taskContext.setProcessInput(subTaskModel.getProcessInput());
                            inputDataStaging(taskContext, processContext.isRecovery());
                            break;
                        case OUPUT:
                            status = new ProcessStatus(ProcessState.OUTPUT_DATA_STAGING);
                            status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                            processContext.setProcessStatus(status);
                            GFacUtils.saveAndPublishProcessStatus(processContext);
                            taskContext.setProcessOutput(subTaskModel.getProcessOutput());
                            outputDataStaging(taskContext, processContext.isRecovery(), false);
                            break;
                        case ARCHIVE_OUTPUT:
                            status = new ProcessStatus(ProcessState.OUTPUT_DATA_STAGING);
                            status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                            processContext.setProcessStatus(status);
                            GFacUtils.saveAndPublishProcessStatus(processContext);
                            outputDataStaging(taskContext, processContext.isRecovery(), true);
                            break;
                    }
                    // checkpoint
                    if (processContext.isInterrupted()) {
                        GFacUtils.handleProcessInterrupt(processContext);
                        return;
                    }
                } catch (TException e) {
                    throw new GFacException(e);
                }
                break;
            case JOB_SUBMISSION:
                // checkpoint
                if (processContext.isInterrupted()) {
                    GFacUtils.handleProcessInterrupt(processContext);
                    return;
                }
                status = new ProcessStatus(ProcessState.EXECUTING);
                status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                processContext.setProcessStatus(status);
                GFacUtils.saveAndPublishProcessStatus(processContext);
                executeJobSubmission(taskContext, processContext.isRecovery());
                // Don't put any checkpoint in between JobSubmission and Monitoring tasks
                JobStatus jobStatus = processContext.getJobModel().getJobStatuses().get(0);
                if (jobStatus != null && (jobStatus.getJobState() == JobState.SUBMITTED || jobStatus.getJobState() == JobState.QUEUED || jobStatus.getJobState() == JobState.ACTIVE)) {
                    List<OutputDataObjectType> processOutputs = processContext.getProcessModel().getProcessOutputs();
                    if (processOutputs != null && !processOutputs.isEmpty()) {
                        for (OutputDataObjectType output : processOutputs) {
                            try {
                                if (output.isOutputStreaming()) {
                                    TaskModel streamingTaskModel = new TaskModel();
                                    streamingTaskModel.setTaskType(TaskTypes.OUTPUT_FETCHING);
                                    streamingTaskModel.setTaskStatuses(Arrays.asList(new TaskStatus(TaskState.CREATED)));
                                    streamingTaskModel.setCreationTime(AiravataUtils.getCurrentTimestamp().getTime());
                                    streamingTaskModel.setParentProcessId(processContext.getProcessId());
                                    TaskContext streamingTaskContext = getTaskContext(processContext);
                                    DataStagingTaskModel submodel = new DataStagingTaskModel();
                                    submodel.setType(DataStageType.OUPUT);
                                    submodel.setProcessOutput(output);
                                    URI source = new URI(processContext.getDataMovementProtocol().name(), processContext.getComputeResourceLoginUserName(), processContext.getComputeResourceDescription().getHostName(), 22, processContext.getWorkingDir() + output.getValue(), null, null);
                                    submodel.setSource(source.getPath());
                                    submodel.setDestination("dummy://temp/file/location");
                                    streamingTaskModel.setSubTaskModel(ThriftUtils.serializeThriftObject(submodel));
                                    String streamTaskId = (String) processContext.getExperimentCatalog().add(ExpCatChildDataType.TASK, streamingTaskModel, processContext.getProcessId());
                                    streamingTaskModel.setTaskId(streamTaskId);
                                    streamingTaskContext.setTaskModel(streamingTaskModel);
                                    executeDataStreaming(streamingTaskContext, processContext.isRecovery());
                                }
                            } catch (URISyntaxException | TException | RegistryException e) {
                                log.error("Error while streaming output " + output.getValue());
                            }
                        }
                    }
                }
                break;
            case MONITORING:
                status = new ProcessStatus(ProcessState.MONITORING);
                status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                processContext.setProcessStatus(status);
                GFacUtils.saveAndPublishProcessStatus(processContext);
                executeJobMonitoring(taskContext, processContext.isRecovery());
                break;
            case ENV_CLEANUP:
                // TODO implement environment clean up task logic
                break;
            default:
                throw new GFacException("Unsupported Task type");
        }
        if (processContext.isPauseTaskExecution()) {
            // If any task put processContext to wait, the same task must continue processContext execution.
            return;
        }
    }
    processContext.setComplete(true);
}

Example 3 with JobStatus

use of org.apache.airavata.model.status.JobStatus in project airavata by apache.

the class BESJobSubmissionTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    TaskStatus taskStatus = new TaskStatus(TaskState.CREATED);
    StorageClient sc = null;
    ProcessContext processContext = taskContext.getParentProcessContext();
    // FIXME - use original output dir
    setInputOutputLocations(processContext);
    try {
        // con't reuse if UserDN has been changed.
        secProperties = getSecurityConfig(processContext);
    // try secProperties = secProperties.clone() if we can't use already initialized ClientConfigurations.
    } catch (GFacException e) {
        String msg = "Unicorn security context initialization error";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        return taskStatus;
    }
    try {
        JobSubmissionProtocol protocol = processContext.getJobSubmissionProtocol();
        JobSubmissionInterface jobSubmissionInterface = GFacUtils.getPreferredJobSubmissionInterface(processContext);
        String factoryUrl = null;
        if (protocol.equals(JobSubmissionProtocol.UNICORE)) {
            UnicoreJobSubmission unicoreJobSubmission = GFacUtils.getUnicoreJobSubmission(jobSubmissionInterface.getJobSubmissionInterfaceId());
            factoryUrl = unicoreJobSubmission.getUnicoreEndPointURL();
        }
        EndpointReferenceType eprt = EndpointReferenceType.Factory.newInstance();
        eprt.addNewAddress().setStringValue(factoryUrl);
        String userDN = processContext.getProcessModel().getUserDn();
        CreateActivityDocument cad = CreateActivityDocument.Factory.newInstance();
        // create storage
        StorageCreator storageCreator = new StorageCreator(secProperties, factoryUrl, 5, null);
        sc = storageCreator.createStorage();
        JobDefinitionType jobDefinition = JSDLGenerator.buildJSDLInstance(processContext, sc.getUrl()).getJobDefinition();
        cad.addNewCreateActivity().addNewActivityDocument().setJobDefinition(jobDefinition);
        log.info("Submitted JSDL: " + jobDefinition.getJobDescription());
        // copy files to local
        copyInputFilesToLocal(taskContext);
        // upload files if any
        DataTransferrer dt = new DataTransferrer(processContext, sc);
        dt.uploadLocalFiles();
        JobModel jobDetails = new JobModel();
        jobDetails.setTaskId(taskContext.getTaskId());
        jobDetails.setProcessId(taskContext.getProcessId());
        FactoryClient factory = new FactoryClient(eprt, secProperties);
        log.info("Activity Submitting to {} ... \n", factoryUrl);
        CreateActivityResponseDocument response = factory.createActivity(cad);
        log.info("Activity Submitted to {} ... \n", factoryUrl);
        EndpointReferenceType activityEpr = response.getCreateActivityResponse().getActivityIdentifier();
        log.info("Activity : " + activityEpr.getAddress().getStringValue() + " Submitted.");
        // factory.waitWhileActivityIsDone(activityEpr, 1000);
        jobId = WSUtilities.extractResourceID(activityEpr);
        if (jobId == null) {
            jobId = new Long(Calendar.getInstance().getTimeInMillis()).toString();
        }
        log.info("JobID: " + jobId);
        jobDetails.setJobId(jobId);
        jobDetails.setJobDescription(activityEpr.toString());
        jobDetails.setJobStatuses(Arrays.asList(new JobStatus(JobState.SUBMITTED)));
        processContext.setJobModel(jobDetails);
        GFacUtils.saveJobModel(processContext, jobDetails);
        GFacUtils.saveJobStatus(processContext, jobDetails);
        log.info(formatStatusMessage(activityEpr.getAddress().getStringValue(), factory.getActivityStatus(activityEpr).toString()));
        waitUntilDone(eprt, activityEpr, processContext, secProperties);
        ActivityStatusType activityStatus = null;
        activityStatus = getStatus(factory, activityEpr);
        log.info(formatStatusMessage(activityEpr.getAddress().getStringValue(), activityStatus.getState().toString()));
        ActivityClient activityClient;
        activityClient = new ActivityClient(activityEpr, secProperties);
        // now use the activity working directory property
        dt.setStorageClient(activityClient.getUspaceClient());
        List<OutputDataObjectType> copyOutput = null;
        if ((activityStatus.getState() == ActivityStateEnumeration.FAILED)) {
            String error = activityStatus.getFault().getFaultcode().getLocalPart() + "\n" + activityStatus.getFault().getFaultstring() + "\n EXITCODE: " + activityStatus.getExitCode();
            log.error(error);
            JobState applicationJobStatus = JobState.FAILED;
            jobDetails.setJobStatuses(Arrays.asList(new JobStatus(applicationJobStatus)));
            sendNotification(processContext, jobDetails);
            try {
                Thread.sleep(5000);
            } catch (InterruptedException e) {
            }
            // What if job is failed before execution and there are not stdouts generated yet?
            log.debug("Downloading any standard output and error files, if they were produced.");
            copyOutput = dt.downloadRemoteFiles();
        } else if (activityStatus.getState() == ActivityStateEnumeration.CANCELLED) {
            JobState applicationJobStatus = JobState.CANCELED;
            jobDetails.setJobStatuses(Arrays.asList(new JobStatus(applicationJobStatus)));
            GFacUtils.saveJobStatus(processContext, jobDetails);
            throw new GFacException(processContext.getExperimentId() + "Job Canceled");
        } else if (activityStatus.getState() == ActivityStateEnumeration.FINISHED) {
            try {
                Thread.sleep(5000);
            } catch (InterruptedException ignored) {
            }
            JobState applicationJobStatus = JobState.COMPLETE;
            jobDetails.setJobStatuses(Arrays.asList(new JobStatus(applicationJobStatus)));
            GFacUtils.saveJobStatus(processContext, jobDetails);
            log.info("Job Id: {}, exit code: {}, exit status: {}", jobDetails.getJobId(), activityStatus.getExitCode(), ActivityStateEnumeration.FINISHED.toString());
            // if (activityStatus.getExitCode() == 0) {
            // } else {
            // dt.downloadStdOuts();
            // }
            copyOutput = dt.downloadRemoteFiles();
        }
        if (copyOutput != null) {
            copyOutputFilesToStorage(taskContext, copyOutput);
            for (OutputDataObjectType outputDataObjectType : copyOutput) {
                GFacUtils.saveExperimentOutput(processContext, outputDataObjectType.getName(), outputDataObjectType.getValue());
            }
        }
        // dt.publishFinalOutputs();
        taskStatus.setState(TaskState.COMPLETED);
    } catch (AppCatalogException e) {
        log.error("Error while retrieving UNICORE job submission..", e);
        taskStatus.setState(TaskState.FAILED);
    } catch (Exception e) {
        log.error("BES task failed... ", e);
        taskStatus.setState(TaskState.FAILED);
    }
    return taskStatus;
}

Example 4 with JobStatus

use of org.apache.airavata.model.status.JobStatus 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 5 with JobStatus

use of org.apache.airavata.model.status.JobStatus 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;
}