Examples with VCSimulationIdentifier cbit.vcell.solver.VCSimulationIdentifier used on opensource projects

Example 21 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class SimulationControllerImpl method stopSimulation.

/**
 * This method was created by a SmartGuide.
 * @throws JMSException
 * @throws AuthenticationException
 * @throws DataAccessException
 * @throws SQLException
 * @throws FileNotFoundException
 * @exception java.rmi.RemoteException The exception description.
 * @throws VCMessagingException
 */
public void stopSimulation(Simulation simulation) throws FileNotFoundException, SQLException, DataAccessException, AuthenticationException, JMSException, VCMessagingException {
    LocalVCMessageListener localVCMessageListener = new LocalVCMessageListener() {

        public void onLocalVCMessage(VCDestination destination, VCMessage objectMessage) {
            String messageTypeProperty = VCMessagingConstants.MESSAGE_TYPE_PROPERTY;
            String stopSimulationValue = MessageConstants.MESSAGE_TYPE_STOPSIMULATION_VALUE;
            if (destination == VCellTopic.ClientStatusTopic && objectMessage.getObjectContent() instanceof SimulationJobStatus) {
                onClientStatusTopic_SimulationJobStatus(objectMessage);
            } else if (destination == VCellTopic.ServiceControlTopic && objectMessage.getStringProperty(messageTypeProperty).equals(stopSimulationValue)) {
                onServiceControlTopic_StopSimulation(objectMessage);
            } else {
                throw new RuntimeException("SimulationControllerImpl.startSimulation().objectMessageListener:: expecting message with SimulationJobStatus to topic " + VCellTopic.ClientStatusTopic.getName() + ": received \"" + objectMessage.show() + "\" on destination \"" + destination + "\"");
            }
        }
    };
    LocalVCMessageAdapter vcMessageSession = new LocalVCMessageAdapter(localVCMessageListener);
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simulation.getKey(), simulation.getVersion().getOwner());
    simulationDispatcherEngine.onStopRequest(vcSimID, localVCellConnection.getUserLoginInfo().getUser(), simulationDatabase, vcMessageSession);
    vcMessageSession.deliverAll();
}

Example 22 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class SimulationControllerImpl method onSimJobQueue_SimulationTask.

private void onSimJobQueue_SimulationTask(VCMessage vcMessage) {
    SimulationTask simTask = null;
    try {
        SimulationTaskMessage simTaskMessage = new SimulationTaskMessage(vcMessage);
        simTask = simTaskMessage.getSimulationTask();
        LocalSolverController solverController = getOrCreateSolverController(simTask);
        // can only start after updating the database is done
        solverController.startSimulationJob();
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        KeyValue simKey = simTask.getSimKey();
        VCSimulationIdentifier vcSimID = simTask.getSimulationJob().getVCDataIdentifier().getVcSimID();
        int jobIndex = simTask.getSimulationJob().getJobIndex();
        int taskID = simTask.getTaskID();
        SimulationJobStatus newJobStatus = new SimulationJobStatus(VCellServerID.getSystemServerID(), vcSimID, jobIndex, null, SchedulerStatus.FAILED, taskID, SimulationMessage.jobFailed(e.getMessage()), null, null);
        SimulationJobStatusEvent event = new SimulationJobStatusEvent(this, Simulation.createSimulationID(simKey), newJobStatus, null, null, vcSimID.getOwner().getName());
        fireSimulationJobStatusEvent(event);
    }
}

Example 23 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class SimulationControllerImpl method startSimulation.

/**
 * This method was created by a SmartGuide.
 * @exception java.rmi.RemoteException The exception description.
 */
public void startSimulation(Simulation simulation) throws Exception {
    LocalVCMessageListener localVCMessageListener = new LocalVCMessageListener() {

        public void onLocalVCMessage(VCDestination destination, VCMessage vcMessage) {
            if (destination == VCellTopic.ClientStatusTopic && vcMessage.getObjectContent() instanceof SimulationJobStatus) {
                onClientStatusTopic_SimulationJobStatus(vcMessage);
            } else if (destination == VCellQueue.SimJobQueue && vcMessage.getStringProperty(VCMessagingConstants.MESSAGE_TYPE_PROPERTY).equals(MessageConstants.MESSAGE_TYPE_SIMULATION_JOB_VALUE)) {
                onSimJobQueue_SimulationTask(vcMessage);
            } else {
                throw new RuntimeException("SimulationControllerImpl.startSimulation().objectMessageListener:: expecting object message with SimulationJobStatus to topic " + VCellTopic.ClientStatusTopic.getName() + ": received \"" + vcMessage.show() + "\"");
            }
        }
    };
    LocalVCMessageAdapter vcMessageSession = new LocalVCMessageAdapter(localVCMessageListener);
    removeSimulationJobStatusListener(localVCellConnection.getMessageCollector());
    addSimulationJobStatusListener(localVCellConnection.getMessageCollector());
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simulation.getKey(), simulation.getVersion().getOwner());
    simulationDispatcherEngine.onStartRequest(vcSimID, localVCellConnection.getUserLoginInfo().getUser(), simulation.getScanCount(), simulationDatabase, vcMessageSession, vcMessageSession);
    vcMessageSession.deliverAll();
    for (int jobIndex = 0; jobIndex < simulation.getScanCount(); jobIndex++) {
        SimulationJobStatus latestSimJobStatus = simulationDatabase.getLatestSimulationJobStatus(simulation.getKey(), jobIndex);
        simulationDispatcherEngine.onDispatch(simulation, latestSimJobStatus, simulationDatabase, vcMessageSession);
        vcMessageSession.deliverAll();
    }
}

Example 24 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class SimulationDatabaseDirect method translateToSimulationJobStatusTransient.

private SimulationJobStatus translateToSimulationJobStatusTransient(SimulationJobStatusPersistent simJobStatus) {
    VCellServerID serverID = simJobStatus.getServerID();
    VCSimulationIdentifier vcSimID = simJobStatus.getVCSimulationIdentifier();
    int jobIndex = simJobStatus.getJobIndex();
    Date submitDate = simJobStatus.getSubmitDate();
    SchedulerStatus schedulerStatus = SimulationJobStatus.SchedulerStatus.valueOf(simJobStatus.getSchedulerStatus().name());
    int taskID = simJobStatus.getTaskID();
    SimulationMessage simMessage = SimulationMessage.fromSerializedMessage(simJobStatus.getSimulationMessage().toSerialization());
    Date queueDate = simJobStatus.getSimulationQueueEntryStatus().getQueueDate();
    int queuePriority = simJobStatus.getSimulationQueueEntryStatus().getQueuePriority();
    SimulationQueueID queueId = SimulationJobStatus.SimulationQueueID.valueOf(simJobStatus.getSimulationQueueEntryStatus().getQueueID().name());
    SimulationQueueEntryStatus simQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, queueId);
    SimulationExecutionStatus simExecStatus = new SimulationExecutionStatus(simJobStatus.getSimulationExecutionStatus().getStartDate(), simJobStatus.getSimulationExecutionStatus().getComputeHost(), simJobStatus.getSimulationExecutionStatus().getLatestUpdateDate(), simJobStatus.getSimulationExecutionStatus().getEndDate(), simJobStatus.getSimulationExecutionStatus().hasData(), simJobStatus.getSimulationExecutionStatus().getHtcJobID());
    SimulationJobStatus simJobStatusTransient = new SimulationJobStatus(serverID, vcSimID, jobIndex, submitDate, schedulerStatus, taskID, simMessage, simQueueStatus, simExecStatus);
    return simJobStatusTransient;
}

Example 25 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier 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);
    }
}