Examples with VCMessageSession cbit.vcell.message.VCMessageSession used on opensource projects

Example 6 with VCMessageSession

use of cbit.vcell.message.VCMessageSession in project vcell by virtualcell.

the class HtcSimulationWorker method initQueueConsumer.

private void initQueueConsumer() {
    this.sharedMessageProducer = vcMessagingService.createProducerSession();
    QueueListener queueListener = new QueueListener() {

        @Override
        public void onQueueMessage(VCMessage vcMessage, VCMessageSession session) throws RollbackException {
            SimulationTask simTask = null;
            try {
                SimulationTaskMessage simTaskMessage = new SimulationTaskMessage(vcMessage);
                simTask = simTaskMessage.getSimulationTask();
                if (lg.isInfoEnabled()) {
                    lg.info("onQueueMessage() run simulation key=" + simTask.getSimKey() + ", job=" + simTask.getSimulationJobID() + ", task=" + simTask.getTaskID() + " for user " + simTask.getUserName());
                }
                PostProcessingChores rd = choresFor(simTask);
                HtcProxy clonedHtcProxy = htcProxy.cloneThreadsafe();
                if (lg.isInfoEnabled()) {
                    lg.info("onQueueMessage() submit job: simulation key=" + simTask.getSimKey() + ", job=" + simTask.getSimulationJobID() + ", task=" + simTask.getTaskID() + " for user " + simTask.getUserName());
                }
                HtcJobID pbsId = submit2PBS(simTask, clonedHtcProxy, rd);
                if (lg.isInfoEnabled()) {
                    lg.info("onQueueMessage() sending 'accepted' message for job: simulation key=" + simTask.getSimKey() + ", job=" + simTask.getSimulationJobID() + ", task=" + simTask.getTaskID() + " for user " + simTask.getUserName());
                }
                synchronized (sharedMessageProducer) {
                    WorkerEventMessage.sendAccepted(sharedMessageProducer, HtcSimulationWorker.class.getName(), simTask, ManageUtils.getHostName(), pbsId);
                }
                if (lg.isInfoEnabled()) {
                    lg.info("onQueueMessage() sent 'accepted' message for job: simulation key=" + simTask.getSimKey() + ", job=" + simTask.getSimulationJobID() + ", task=" + simTask.getTaskID() + " for user " + simTask.getUserName());
                }
            } catch (Exception e) {
                lg.error(e.getMessage(), e);
                if (simTask != null) {
                    try {
                        lg.error("failed to process simTask request: " + e.getMessage() + " for simulation key=" + simTask.getSimKey() + ", job=" + simTask.getSimulationJobID() + ", task=" + simTask.getTaskID() + " for user " + simTask.getUserName(), e);
                        synchronized (sharedMessageProducer) {
                            WorkerEventMessage.sendFailed(sharedMessageProducer, HtcSimulationWorker.class.getName(), simTask, ManageUtils.getHostName(), SimulationMessage.jobFailed(e.getMessage()));
                        }
                        lg.error("sent 'failed' message for simulation key=" + simTask.getSimKey() + ", job=" + simTask.getSimulationJobID() + ", task=" + simTask.getTaskID() + " for user " + simTask.getUserName(), e);
                    } catch (VCMessagingException e1) {
                        lg.error(e1.getMessage(), e);
                    }
                } else {
                    lg.error("failed to process simTask request: " + e.getMessage(), e);
                }
            }
        }
    };
    int numHtcworkerThreads = Integer.parseInt(PropertyLoader.getProperty(PropertyLoader.htcworkerThreadsProperty, "5"));
    this.pooledQueueConsumer = new VCPooledQueueConsumer(queueListener, numHtcworkerThreads, sharedMessageProducer);
    this.pooledQueueConsumer.initThreadPool();
    VCellQueue queue = VCellQueue.SimJobQueue;
    VCMessageSelector selector = vcMessagingService.createSelector(getJobSelector());
    String threadName = "SimJob Queue Consumer";
    queueConsumer = new VCQueueConsumer(queue, pooledQueueConsumer, selector, threadName, MessageConstants.PREFETCH_LIMIT_SIM_JOB_HTC);
    vcMessagingService.addMessageConsumer(queueConsumer);
}

Example 7 with VCMessageSession

use of cbit.vcell.message.VCMessageSession in project vcell by virtualcell.

the class SolverPostprocessor method main.

public static void main(java.lang.String[] args) {
    if (args.length < NUM_STD_ARGS) {
        System.out.println("Usage: " + SolverPostprocessor.class.getName() + " simKey username userKey jobindex taskid solverExitCode [postProcessorCommandFile]");
        System.exit(1);
    }
    Logging.init();
    Log4jSessionLog log = new Log4jSessionLog(LOG_NAME);
    Logger lg = log.getLogger();
    VCMessagingService vcMessagingService = null;
    try {
        PropertyLoader.loadProperties(POST_PROCESSOR_PROPERTIES);
        ResourceUtil.setNativeLibraryDirectory();
        NativeLoader.setOsType(OsType.LINUX);
        KeyValue simKey = new KeyValue(args[0]);
        String userName = args[1];
        KeyValue userKey = new KeyValue(args[2]);
        int jobIndex = Integer.parseInt(args[3]);
        int taskID = Integer.parseInt(args[4]);
        int solverExitCode = Integer.parseInt(args[5]);
        User owner = new User(userName, userKey);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        String hostName = ManageUtils.getHostName();
        VCMongoMessage.serviceStartup(ServiceName.solverPostprocessor, Integer.valueOf(simKey.toString()), args);
        // 
        // JMX registration
        // 
        MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
        mbs.registerMBean(new VCellServiceMXBeanImpl(), new ObjectName(VCellServiceMXBean.jmxObjectName));
        vcMessagingService = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        vcMessagingService.setDelegate(new ServerMessagingDelegate());
        VCMessageSession session = vcMessagingService.createProducerSession();
        WorkerEventMessage workerEventMessage;
        if (solverExitCode == 0) {
            Exception postProcessingException = null;
            if (args.length > NUM_STD_ARGS) {
                String fname = args[NUM_STD_ARGS];
                if (lg.isDebugEnabled()) {
                    lg.debug("processing " + fname);
                }
                postProcessingException = runPostprocessingCommands(fname, lg);
            }
            if (lg.isDebugEnabled()) {
                lg.debug("postProcessingException is " + postProcessingException);
            }
            if (postProcessingException == null) {
                lg.debug("sendWorkerExitNormal");
                workerEventMessage = WorkerEventMessage.sendWorkerExitNormal(session, SolverPostprocessor.class.getName(), hostName, vcSimID, jobIndex, taskID, solverExitCode);
            } else {
                lg.debug("sendWorkerExitError postprocessing");
                workerEventMessage = WorkerEventMessage.sendWorkerExitError(session, postProcessingException, hostName, vcSimID, jobIndex, taskID, SimulationMessage.WorkerExited(postProcessingException));
            }
        } else {
            // solverExitCode != 0
            lg.debug("sendWorkerExitError solverExitCode");
            workerEventMessage = WorkerEventMessage.sendWorkerExitError(session, SolverPostprocessor.class.getName(), hostName, vcSimID, jobIndex, taskID, solverExitCode);
        }
        lg.debug(workerEventMessage);
        VCMongoMessage.sendWorkerEvent(workerEventMessage);
    } catch (Throwable e) {
        log.exception(e);
    } finally {
        if (vcMessagingService != null) {
            try {
                vcMessagingService.close();
            } catch (VCMessagingException e) {
                e.printStackTrace();
            }
        }
        ApplicationTerminator.beginCountdown(TimeUnit.SECONDS, 10, 0);
        VCMongoMessage.shutdown();
        System.exit(0);
    }
}

Example 8 with VCMessageSession

use of cbit.vcell.message.VCMessageSession in project vcell by virtualcell.

the class JavaSimulationExecutable method init.

protected void init() throws JMSException {
    // 
    // session used for sending worker events.
    // 
    this.workerEventSession = vcMessagingService.createProducerSession();
    // 
    // message consumer for Service Control topic message (to stop simulation).
    // 
    VCellTopic topic = VCellTopic.ServiceControlTopic;
    TopicListener listener = new TopicListener() {

        public void onTopicMessage(VCMessage vcMessage, VCMessageSession session) {
            if (lg.isTraceEnabled())
                lg.trace("JavaSimulationExecutable::onControlTopicMessage(): " + vcMessage.show());
            try {
                String msgType = vcMessage.getStringProperty(VCMessagingConstants.MESSAGE_TYPE_PROPERTY);
                if (msgType != null && msgType.equals(MessageConstants.MESSAGE_TYPE_STOPSIMULATION_VALUE)) {
                    Long longkey = vcMessage.getLongProperty(MessageConstants.SIMKEY_PROPERTY);
                    KeyValue simKey = new KeyValue(longkey + "");
                    int jobIndex = vcMessage.getIntProperty(MessageConstants.JOBINDEX_PROPERTY);
                    if (simKey.equals(simulationTask.getSimKey()) && jobIndex == simulationTask.getSimulationJob().getJobIndex()) {
                        solver.stopSolver();
                    }
                }
            } catch (MessagePropertyNotFoundException ex) {
                lg.error(ex.getMessage(), ex);
                return;
            }
        }
    };
    VCMessageSelector selector = null;
    String threadName = "Service Control Topic Consumer";
    VCTopicConsumer serviceControlConsumer = new VCTopicConsumer(topic, listener, selector, threadName, MessageConstants.PREFETCH_LIMIT_SERVICE_CONTROL);
    vcMessagingService.addMessageConsumer(serviceControlConsumer);
}

Example 9 with VCMessageSession

use of cbit.vcell.message.VCMessageSession in project vcell by virtualcell.

the class RestDatabaseService method getDataSetTimeSeries.

public DataSetTimeSeries getDataSetTimeSeries(SimDataValuesServerResource resource, User vcellUser) throws DataAccessException, ObjectNotFoundException, SQLException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String simId = resource.getAttribute(VCellApiApplication.SIMDATAID);
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String jobIndexString = resource.getAttribute(VCellApiApplication.JOBINDEX);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    int jobIndex = Integer.parseInt(jobIndexString);
    // TODO: pass in variables names from the query parameters.
    String[] variableNames = null;
    User owner = simRep.getOwner();
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        RpcDataServerProxy rpcDataServerProxy = new RpcDataServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        VCDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
        DataSetTimeSeries dataSetTimeSeries = rpcDataServerProxy.getDataSetTimeSeries(vcdID, variableNames);
        return dataSetTimeSeries;
    } finally {
        rpcSession.close();
    }
}

Example 10 with VCMessageSession

use of cbit.vcell.message.VCMessageSession in project vcell by virtualcell.

the class RestDatabaseService method startSimulation.

public SimulationRep startSimulation(BiomodelSimulationStartServerResource resource, User vcellUser) throws PermissionException, ObjectNotFoundException, DataAccessException, SQLException {
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String simId = resource.getAttribute(VCellApiApplication.SIMULATIONID);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    User owner = simRep.getOwner();
    if (!owner.compareEqual(vcellUser)) {
        throw new PermissionException("not authorized to start simulation");
    }
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
        try {
            userLoginInfo.setUser(vcellUser);
        } catch (Exception e) {
            e.printStackTrace();
            throw new DataAccessException(e.getMessage());
        }
        RpcSimServerProxy rpcSimServerProxy = new RpcSimServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        rpcSimServerProxy.startSimulation(vcellUser, vcSimID, simRep.getScanCount());
        return simRep;
    } finally {
        rpcSession.close();
    }
}