Examples with JobModel org.apache.airavata.model.job.JobModel used on opensource projects

Example 1 with JobModel

use of org.apache.airavata.model.job.JobModel 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 2 with JobModel

use of org.apache.airavata.model.job.JobModel in project airavata by apache.

the class DefaultJobSubmissionTask method cancel.

@Override
public JobStatus cancel(TaskContext taskcontext) throws TaskException {
    ProcessContext processContext = taskcontext.getParentProcessContext();
    RemoteCluster remoteCluster = processContext.getJobSubmissionRemoteCluster();
    JobModel jobModel = processContext.getJobModel();
    int retryCount = 0;
    if (jobModel != null) {
        if (processContext.getProcessState() == ProcessState.EXECUTING) {
            while (jobModel.getJobId() == null) {
                log.info("Cancellation pause {} secs until process get jobId", pauseTimeInSec);
                try {
                    Thread.sleep(waitForProcessIdmillis);
                } catch (InterruptedException e) {
                // ignore
                }
            }
        }
        try {
            JobStatus oldJobStatus = remoteCluster.getJobStatus(jobModel.getJobId());
            while (oldJobStatus == null && retryCount <= 5) {
                retryCount++;
                Thread.sleep(retryCount * 1000);
                oldJobStatus = remoteCluster.getJobStatus(jobModel.getJobId());
            }
            if (oldJobStatus != null) {
                oldJobStatus = remoteCluster.cancelJob(jobModel.getJobId());
                return oldJobStatus;
            } else {
                throw new TaskException("Cancel operation failed, Job status couldn't find in resource, JobId " + jobModel.getJobId());
            }
        } catch (GFacException | InterruptedException e) {
            throw new TaskException("Error while cancelling job " + jobModel.getJobId(), e);
        }
    } else {
        throw new TaskException("Couldn't complete cancel operation, JobModel is null in ProcessContext.");
    }
}

Example 3 with JobModel

use of org.apache.airavata.model.job.JobModel 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 4 with JobModel

use of org.apache.airavata.model.job.JobModel 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 5 with JobModel

use of org.apache.airavata.model.job.JobModel in project airavata by apache.

the class AuroraJobSubmissionTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    // set to completed.
    TaskStatus taskStatus = new TaskStatus(TaskState.COMPLETED);
    ProcessContext processContext = taskContext.getParentProcessContext();
    JobModel jobModel = processContext.getJobModel();
    jobModel.setTaskId(taskContext.getTaskId());
    String jobIdAndName = "A" + GFacUtils.generateJobName();
    jobModel.setJobName(jobIdAndName);
    JobStatus jobStatus = new JobStatus();
    jobStatus.setJobState(JobState.SUBMITTED);
    try {
        JobKeyBean jobKey = new JobKeyBean(AuroraUtils.ENVIRONMENT, AuroraUtils.ROLE, jobIdAndName);
        IdentityBean owner = new IdentityBean(AuroraUtils.ROLE);
        GroovyMap groovyMap = GFacUtils.createGroovyMap(processContext, taskContext);
        groovyMap.add(Script.JOB_SUBMITTER_COMMAND, "sh");
        String templateFileName = GFacUtils.getTemplateFileName(ResourceJobManagerType.CLOUD);
        String script = GFacUtils.generateScript(groovyMap, templateFileName);
        Set<ProcessBean> processes = new LinkedHashSet<>();
        ProcessBean process_1 = new ProcessBean("main_process", script, false);
        processes.add(process_1);
        groovyMap.getStringValue(Script.STANDARD_OUT_FILE).ifPresent(stdout -> {
            ProcessBean stdOutProcess = new ProcessBean("stdout_copy_process", "cp .logs/main_process/0/stdout " + stdout, false);
            processes.add(stdOutProcess);
        });
        groovyMap.getStringValue(Script.STANDARD_ERROR_FILE).ifPresent(stderr -> {
            ProcessBean stdErrProcess = new ProcessBean("stderr_copy_process", "cp .logs/main_process/0/stderr " + stderr, false);
            processes.add(stdErrProcess);
        });
        ResourceBean resources = new ResourceBean(1.5, 512, 512);
        TaskConfigBean taskConfig = new TaskConfigBean("Airavata-Aurora-" + jobIdAndName, processes, resources);
        JobConfigBean jobConfig = new JobConfigBean(jobKey, owner, taskConfig, AuroraUtils.CLUSTER);
        String executorConfigJson = AuroraThriftClientUtil.getExecutorConfigJson(jobConfig);
        log.info("Executor Config for Job {} , {}", jobIdAndName, executorConfigJson);
        AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient();
        ResponseBean response = client.createJob(jobConfig);
        log.info("Response for job {}, {}", jobIdAndName, response);
        jobModel.setJobDescription(resources.toString());
        jobModel.setJobId(jobIdAndName);
        jobStatus.setReason("Successfully Submitted");
        jobModel.setJobStatuses(Arrays.asList(jobStatus));
        jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        taskContext.getParentProcessContext().setJobModel(jobModel);
        GFacUtils.saveJobModel(processContext, jobModel);
        GFacUtils.saveJobStatus(processContext, jobModel);
        taskStatus.setReason("Successfully submitted job to Aurora");
    } catch (Throwable e) {
        String msg = "Error occurred while submitting Aurora job";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        taskStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    }
    taskContext.setTaskStatus(taskStatus);
    try {
        GFacUtils.saveAndPublishTaskStatus(taskContext);
    } catch (GFacException e) {
        log.error("Error while saving task status", e);
    }
    return taskStatus;
}