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

Example 1 with JobSubmissionProtocol

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

the class Factory method getJobSubmissionRemoteCluster.

/**
 * Factory class manage reomete cluster map, this will solve too many connections/ sessions issues with cluster
 * communications.
 * @param processContext
 * @return
 * @throws GFacException
 * @throws AppCatalogException
 * @throws AiravataException
 */
public static RemoteCluster getJobSubmissionRemoteCluster(ProcessContext processContext) throws GFacException, AppCatalogException, AiravataException, CredentialStoreException {
    String computeResourceId = processContext.getComputeResourceId();
    JobSubmissionProtocol jobSubmissionProtocol = processContext.getJobSubmissionProtocol();
    String key = new StringBuilder(processContext.getComputeResourceLoginUserName()).append(':').append(jobSubmissionProtocol.name()).append(':').append(computeResourceId).append(':').append(processContext.getComputeResourceCredentialToken()).toString();
    RemoteCluster remoteCluster = remoteClusterMap.get(key);
    if (remoteCluster == null) {
        JobManagerConfiguration jobManagerConfiguration = getJobManagerConfiguration(processContext.getResourceJobManager());
        if (jobSubmissionProtocol == JobSubmissionProtocol.LOCAL || jobSubmissionProtocol == JobSubmissionProtocol.LOCAL_FORK) {
            remoteCluster = new LocalRemoteCluster(processContext.getComputeResourceServerInfo(), jobManagerConfiguration, null);
        } else if (jobSubmissionProtocol == JobSubmissionProtocol.SSH || jobSubmissionProtocol == JobSubmissionProtocol.SSH_FORK || jobSubmissionProtocol == JobSubmissionProtocol.CLOUD) {
            remoteCluster = new HPCRemoteCluster(processContext.getComputeResourceServerInfo(), jobManagerConfiguration, Factory.getComputerResourceSSHKeyAuthentication(processContext));
        } else {
            throw new GFacException("No remote cluster implementation map to job submission protocol " + jobSubmissionProtocol.name());
        }
        remoteClusterMap.put(key, remoteCluster);
    } else {
        AuthenticationInfo authentication = remoteCluster.getAuthentication();
        if (authentication instanceof SSHKeyAuthentication) {
            SSHKeyAuthentication sshKeyAuthentication = (SSHKeyAuthentication) authentication;
            if (!sshKeyAuthentication.getUserName().equals(processContext.getComputeResourceLoginUserName())) {
                JobManagerConfiguration jobManagerConfiguration = getJobManagerConfiguration(processContext.getResourceJobManager());
                if (jobSubmissionProtocol == JobSubmissionProtocol.SSH || jobSubmissionProtocol == JobSubmissionProtocol.SSH_FORK) {
                    remoteCluster = new HPCRemoteCluster(processContext.getComputeResourceServerInfo(), jobManagerConfiguration, Factory.getComputerResourceSSHKeyAuthentication(processContext));
                }
            }
        }
    }
    return remoteCluster;
}

Example 2 with JobSubmissionProtocol

use of org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol 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 3 with JobSubmissionProtocol

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

the class BESJobSubmissionTask method cancelJob.

/**
 * EndpointReference need to be saved to make cancel work.
 *
 * @param processContext
 * @throws GFacException
 */
public boolean cancelJob(ProcessContext processContext) throws GFacException {
    try {
        String activityEpr = processContext.getJobModel().getJobDescription();
        // initSecurityProperties(processContext);
        EndpointReferenceType eprt = EndpointReferenceType.Factory.parse(activityEpr);
        JobSubmissionProtocol protocol = processContext.getJobSubmissionProtocol();
        String interfaceId = processContext.getApplicationInterfaceDescription().getApplicationInterfaceId();
        String factoryUrl = null;
        if (protocol.equals(JobSubmissionProtocol.UNICORE)) {
            UnicoreJobSubmission unicoreJobSubmission = GFacUtils.getUnicoreJobSubmission(interfaceId);
            factoryUrl = unicoreJobSubmission.getUnicoreEndPointURL();
        }
        EndpointReferenceType epr = EndpointReferenceType.Factory.newInstance();
        epr.addNewAddress().setStringValue(factoryUrl);
        FactoryClient factory = new FactoryClient(epr, secProperties);
        factory.terminateActivity(eprt);
        return true;
    } catch (Exception e) {
        throw new GFacException(e.getLocalizedMessage(), e);
    }
}