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

Example 1 with JobSubmissionInterface

use of org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface 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 JobSubmissionInterface

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

the class SSHAccountManager method setupSSHAccount.

/**
 * Add SSH key to compute resource on behalf of user.
 * @param gatewayId
 * @param computeResourceId
 * @param userId Airavata user id
 * @param sshCredential
 * @return a populated but not persisted UserComputeResourcePreference instance
 * @throws InvalidSetupException
 * @throws InvalidUsernameException
 */
public static UserComputeResourcePreference setupSSHAccount(String gatewayId, String computeResourceId, String userId, SSHCredential sshCredential) throws InvalidSetupException, InvalidUsernameException {
    // get compute resource preferences for the gateway and hostname
    RegistryService.Client registryServiceClient = getRegistryServiceClient();
    ComputeResourcePreference computeResourcePreference = null;
    ComputeResourceDescription computeResourceDescription = null;
    SSHJobSubmission sshJobSubmission = null;
    try {
        computeResourcePreference = registryServiceClient.getGatewayComputeResourcePreference(gatewayId, computeResourceId);
        computeResourceDescription = registryServiceClient.getComputeResource(computeResourceId);
        // Find the SSHJobSubmission
        for (JobSubmissionInterface jobSubmissionInterface : computeResourceDescription.getJobSubmissionInterfaces()) {
            if (jobSubmissionInterface.getJobSubmissionProtocol() == JobSubmissionProtocol.SSH) {
                sshJobSubmission = registryServiceClient.getSSHJobSubmission(jobSubmissionInterface.getJobSubmissionInterfaceId());
                break;
            }
        }
    } catch (TException e) {
        throw new RuntimeException("Failed to retrieve compute resource information for [" + gatewayId + "] and " + "[" + computeResourceId + "]: " + e.getMessage(), e);
    } finally {
        if (registryServiceClient.getInputProtocol().getTransport().isOpen()) {
            registryServiceClient.getInputProtocol().getTransport().close();
        }
        if (registryServiceClient.getOutputProtocol().getTransport().isOpen()) {
            registryServiceClient.getOutputProtocol().getTransport().close();
        }
    }
    if (sshJobSubmission == null) {
        throw new InvalidSetupException("Compute resource [" + computeResourceId + "] does not have an SSH Job Submission " + "interface.");
    }
    // get the account provisioner and config values for the preferences
    if (!computeResourcePreference.isSetSshAccountProvisioner()) {
        throw new InvalidSetupException("Compute resource [" + computeResourceId + "] does not have an SSH Account Provisioner " + "configured for it.");
    }
    // instantiate and init the account provisioner
    SSHAccountProvisioner sshAccountProvisioner = createSshAccountProvisioner(gatewayId, computeResourcePreference);
    boolean canCreateAccount = SSHAccountProvisionerFactory.canCreateAccount(computeResourcePreference.getSshAccountProvisioner());
    // First check if userId has an account
    boolean hasAccount = false;
    try {
        hasAccount = sshAccountProvisioner.hasAccount(userId);
    } catch (InvalidUsernameException e) {
        throw e;
    } catch (Exception e) {
        throw new RuntimeException("hasAccount call failed for userId [" + userId + "]: " + e.getMessage(), e);
    }
    if (!hasAccount && !canCreateAccount) {
        throw new InvalidSetupException("User [" + userId + "] doesn't have account and [" + computeResourceId + "] doesn't " + "have a SSH Account Provisioner that supports creating accounts.");
    }
    // TODO: create account for user if user doesn't have account
    String username = null;
    // Install SSH key
    try {
        username = sshAccountProvisioner.installSSHKey(userId, sshCredential.getPublicKey());
    } catch (InvalidUsernameException e) {
        throw e;
    } catch (Exception e) {
        throw new RuntimeException("installSSHKey call failed for userId [" + userId + "]: " + e.getMessage(), e);
    }
    // Verify can authenticate to host
    String sshHostname = getSSHHostname(computeResourceDescription, sshJobSubmission);
    int sshPort = sshJobSubmission.getSshPort();
    boolean validated = false;
    try {
        validated = SSHUtil.validate(sshHostname, sshPort, username, sshCredential);
    } catch (Exception e) {
        throw new RuntimeException("Failed to validate SSH public key installation for account for user [" + username + "] on host [" + sshHostname + "]: " + e.getMessage(), e);
    }
    if (!validated) {
        throw new RuntimeException("Failed to validate installation of key for [" + username + "] on [" + computeResourceDescription.getHostName() + "] using SSH Account Provisioner [" + computeResourcePreference.getSshAccountProvisioner() + "]");
    }
    // create the scratch location on the host
    String scratchLocation = sshAccountProvisioner.getScratchLocation(userId);
    try {
        SSHUtil.execute(sshHostname, sshPort, username, sshCredential, "mkdir -p " + scratchLocation);
    } catch (Exception e) {
        throw new RuntimeException("Failed to create scratch location [" + scratchLocation + "] for user [" + username + "] on host [" + sshHostname + "]: " + e.getMessage(), e);
    }
    UserComputeResourcePreference userComputeResourcePreference = new UserComputeResourcePreference();
    userComputeResourcePreference.setComputeResourceId(computeResourceId);
    userComputeResourcePreference.setLoginUserName(username);
    userComputeResourcePreference.setScratchLocation(scratchLocation);
    userComputeResourcePreference.setValidated(true);
    return userComputeResourcePreference;
}

Example 3 with JobSubmissionInterface

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

the class DocumentCreatorUtils method createJobSubmissionInterface.

public static JobSubmissionInterface createJobSubmissionInterface(String jobSubmissionInterfaceId, JobSubmissionProtocol jobSubmissionProtocolType, int priorityOrder) {
    JobSubmissionInterface jobSubmissionInterface = new JobSubmissionInterface();
    jobSubmissionInterface.setJobSubmissionInterfaceId(jobSubmissionInterfaceId);
    jobSubmissionInterface.setJobSubmissionProtocol(jobSubmissionProtocolType);
    jobSubmissionInterface.setPriorityOrder(priorityOrder);
    return jobSubmissionInterface;
}

Example 4 with JobSubmissionInterface

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

the class CreateLaunchBES method registerUnicoreEndpoint.

public static String registerUnicoreEndpoint(String hostName, String hostDesc, JobSubmissionProtocol protocol, SecurityProtocol securityProtocol) throws TException {
    ComputeResourceDescription computeResourceDescription = RegisterSampleApplicationsUtils.createComputeResourceDescription(hostName, hostDesc, null, null);
    fsdResourceId = airavataClient.registerComputeResource(new AuthzToken(""), computeResourceDescription);
    if (fsdResourceId.isEmpty())
        throw new AiravataClientException();
    System.out.println("FSD Compute ResourceID: " + fsdResourceId);
    JobSubmissionInterface jobSubmission = RegisterSampleApplicationsUtils.createJobSubmissionInterface(fsdResourceId, protocol, 2);
    UnicoreJobSubmission ucrJobSubmission = new UnicoreJobSubmission();
    ucrJobSubmission.setSecurityProtocol(securityProtocol);
    ucrJobSubmission.setUnicoreEndPointURL(unicoreEndPointURL);
    return jobSubmission.getJobSubmissionInterfaceId();
}

Example 5 with JobSubmissionInterface

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

the class OrchestratorUtils method getPreferredJobSubmissionInterface.

public static JobSubmissionInterface getPreferredJobSubmissionInterface(OrchestratorContext context, ProcessModel processModel, String gatewayId) throws RegistryException {
    try {
        String resourceHostId = processModel.getComputeResourceId();
        ComputeResourcePreference resourcePreference = getComputeResourcePreference(context, processModel, gatewayId);
        JobSubmissionProtocol preferredJobSubmissionProtocol = resourcePreference.getPreferredJobSubmissionProtocol();
        ComputeResourceDescription resourceDescription = context.getRegistry().getAppCatalog().getComputeResource().getComputeResource(resourceHostId);
        List<JobSubmissionInterface> jobSubmissionInterfaces = resourceDescription.getJobSubmissionInterfaces();
        Map<JobSubmissionProtocol, List<JobSubmissionInterface>> orderedInterfaces = new HashMap<>();
        List<JobSubmissionInterface> interfaces = new ArrayList<>();
        if (jobSubmissionInterfaces != null && !jobSubmissionInterfaces.isEmpty()) {
            for (JobSubmissionInterface submissionInterface : jobSubmissionInterfaces) {
                if (preferredJobSubmissionProtocol != null) {
                    if (preferredJobSubmissionProtocol.toString().equals(submissionInterface.getJobSubmissionProtocol().toString())) {
                        if (orderedInterfaces.containsKey(submissionInterface.getJobSubmissionProtocol())) {
                            List<JobSubmissionInterface> interfaceList = orderedInterfaces.get(submissionInterface.getJobSubmissionProtocol());
                            interfaceList.add(submissionInterface);
                        } else {
                            interfaces.add(submissionInterface);
                            orderedInterfaces.put(submissionInterface.getJobSubmissionProtocol(), interfaces);
                        }
                    }
                } else {
                    Collections.sort(jobSubmissionInterfaces, (jobSubmissionInterface, jobSubmissionInterface2) -> jobSubmissionInterface.getPriorityOrder() - jobSubmissionInterface2.getPriorityOrder());
                }
            }
            interfaces = orderedInterfaces.get(preferredJobSubmissionProtocol);
            Collections.sort(interfaces, (jobSubmissionInterface, jobSubmissionInterface2) -> jobSubmissionInterface.getPriorityOrder() - jobSubmissionInterface2.getPriorityOrder());
        } else {
            throw new RegistryException("Compute resource should have at least one job submission interface defined...");
        }
        return interfaces.get(0);
    } catch (AppCatalogException e) {
        throw new RegistryException("Error occurred while retrieving data from app catalog", e);
    }
}