Examples with SimulationTask cbit.vcell.messaging.server.SimulationTask used on opensource projects

Example 16 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask in project vcell by virtualcell.

the class RunFakeSimOp method runFVSolverStandalone.

private static void runFVSolverStandalone(File simulationDataDir, Simulation sim, ClientTaskStatusSupport progressListener) throws Exception {
    int jobIndex = 0;
    SimulationTask simTask = new SimulationTask(new SimulationJob(sim, jobIndex, null), 0);
    SolverUtilities.prepareSolverExecutable(sim.getSolverTaskDescription().getSolverDescription());
    FVSolverStandalone fvSolver = new FVSolverStandalone(simTask, simulationDataDir, false);
    fvSolver.startSolver();
    // fvSolver.runSolver();
    SolverStatus status = fvSolver.getSolverStatus();
    while (status.getStatus() != SolverStatus.SOLVER_FINISHED && status.getStatus() != SolverStatus.SOLVER_ABORTED && status.getStatus() != SolverStatus.SOLVER_STOPPED) {
        if (progressListener != null) {
            progressListener.setProgress((int) (fvSolver.getProgress() * 100));
            if (progressListener.isInterrupted()) {
                fvSolver.stopSolver();
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
        try {
            Thread.sleep(1000);
        } catch (InterruptedException ex) {
            ex.printStackTrace(System.out);
        // catch interrupted exception and ignore it, otherwise it will popup a dialog in user interface saying"sleep interrupted"
        }
        status = fvSolver.getSolverStatus();
    }
    if (status.getStatus() != SolverStatus.SOLVER_FINISHED) {
        throw new Exception("Sover did not finish normally." + status);
    }
}

Example 17 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask in project vcell by virtualcell.

the class StochtestRunService method runsolver.

private static void runsolver(Simulation newSimulation, File baseDirectory, int numRuns, TimeSeriesMultitrialData timeSeriesMultitrialData) {
    Simulation versSimulation = null;
    File destDir = null;
    boolean bTimeout = false;
    // int progress = 1;
    for (int trialIndex = 0; trialIndex < numRuns; trialIndex++) {
        System.out.println("\n=====================================\n\nStarting trial " + (trialIndex + 1) + " of " + numRuns + "\n\n==============================\n");
        long startTime = System.currentTimeMillis();
        // }
        try {
            versSimulation = new TempSimulation(newSimulation, false);
            // printout(ruleBasedTestDir.getAbsolutePath());
            destDir = new File(baseDirectory, timeSeriesMultitrialData.datasetName);
            SimulationTask simTask = new SimulationTask(new SimulationJob(versSimulation, 0, null), 0);
            Solver solver = ClientSimManager.createQuickRunSolver(destDir, simTask);
            solver.startSolver();
            while (true) {
                try {
                    Thread.sleep(250);
                } catch (InterruptedException e) {
                    e.printStackTrace();
                }
                if (System.currentTimeMillis() - startTime > 30 * 1000) {
                    // timeout after 30 seconds .. otherwise multiple runs will take forever
                    bTimeout = true;
                    solver.stopSolver();
                    throw new RuntimeException("timed out");
                }
                SolverStatus solverStatus = solver.getSolverStatus();
                if (solverStatus != null) {
                    if (solverStatus.getStatus() == SolverStatus.SOLVER_ABORTED) {
                        throw new RuntimeException(solverStatus.getSimulationMessage().getDisplayMessage());
                    }
                    if (solverStatus.getStatus() != SolverStatus.SOLVER_STARTING && solverStatus.getStatus() != SolverStatus.SOLVER_READY && solverStatus.getStatus() != SolverStatus.SOLVER_RUNNING) {
                        break;
                    }
                }
            }
            SimulationData simData = new SimulationData(simTask.getSimulationJob().getVCDataIdentifier(), destDir, null, null);
            ODEDataBlock odeDataBlock = simData.getODEDataBlock();
            ODESimData odeSimData = odeDataBlock.getODESimData();
            timeSeriesMultitrialData.addDataSet(odeSimData, trialIndex);
        } catch (Exception e) {
            e.printStackTrace();
            File file = new File(baseDirectory, Simulation.createSimulationID(versSimulation.getKey()) + "_solverExc.txt");
            StochtestFileUtils.writeMessageTofile(file, e.getMessage());
            if (bTimeout) {
                throw new RuntimeException("timed out");
            } else {
                throw new RuntimeException("solver failed : " + e.getMessage(), e);
            }
        }
        try {
            Thread.sleep(100);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
        StochtestFileUtils.clearDir(destDir);
    }
// printout("\n");
}

Example 18 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask in project vcell by virtualcell.

the class SbmlVcmlConverter method solveSimulation.

/**
 * solves the simulation that is passed in throught the simulation job.
 */
private static void solveSimulation(SimulationJob simJob, String filePathName, SimSpec argSimSpec) /* Hashtable argSpUnitsHash, double argTimeFactor, Model.ReservedSymbol kMoleSymbol*/
{
    ODESolverResultSet odeSolverResultSet = null;
    try {
        /*		// Generate .idaInput string		
		File idaInputFile = new File(filePathName.replace(".vcml", ".idaInput"));
		PrintWriter idaPW = new java.io.PrintWriter(idaInputFile);
		IDAFileWriter idaFileWriter = new IDAFileWriter(idaPW, simJob);
		idaFileWriter.write();
		idaPW.close();

		// use the SundialsStandaloneSolver
		File idaOutputFile = new File(filePathName.replace(".vcml", ".ida"));
		Executable executable = new Executable(new String[]{"SundialsSolverStandalone", idaInputFile.getAbsolutePath(), idaOutputFile.getAbsolutePath()});
		executable.start();
*/
        // Generate .cvodeInput string
        File cvodeInputFile = new File(filePathName.replace(".vcml", ".cvodeInput"));
        PrintWriter cvodePW = new java.io.PrintWriter(cvodeInputFile);
        SimulationTask simTask = new SimulationTask(simJob, 0);
        CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(cvodePW, simTask);
        cvodeFileWriter.write();
        cvodePW.close();
        // use the cvodeStandalone solver
        // use the SundialsStandaloneSolver
        File cvodeOutputFile = new File(filePathName.replace(".vcml", ".ida"));
        /*
		Executable executable = new Executable(new String[]{"d:/workspace/VCell_5.3_VCell/SundialsSolverStandalone_x64", cvodeInputFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath()});
		executable.start();
		*/
        // use the cvodeStandalone solver
        // use the SundialsStandaloneSolver
        File[] exes = SolverUtilities.getExes(SolverDescription.CombinedSundials);
        assert exes.length == 1 : "one and only one smoldyn solver expected";
        File sundialsExe = exes[0];
        Executable executable = new Executable(new String[] { sundialsExe.getAbsolutePath(), cvodeInputFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath() });
        executable.start();
        // get the result
        odeSolverResultSet = VCellSBMLSolver.getODESolverResultSet(simJob, cvodeOutputFile.getPath());
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Error running NativeIDA solver : " + e.getMessage());
    }
    // now write out the results into CSV file
    try {
        if (odeSolverResultSet != null) {
            File csvFile = new File(filePathName.replace(".vcml", ".csv"));
            PrintStream outputStream = new PrintStream(new BufferedOutputStream(new FileOutputStream(csvFile)));
            outputStream.print("time");
            for (int i = 0; i < argSimSpec.getVarsList().length; i++) {
                outputStream.print("," + argSimSpec.getVarsList()[i]);
            }
            outputStream.println();
            // extract data for time and species
            double[][] data = new double[argSimSpec.getVarsList().length + 1][];
            int column = odeSolverResultSet.findColumn("t");
            data[0] = odeSolverResultSet.extractColumn(column);
            int origDataLength = data[0].length;
            for (int i = 0; i < argSimSpec.getVarsList().length; i++) {
                column = odeSolverResultSet.findColumn(argSimSpec.getVarsList()[i]);
                if (column == -1) {
                    Variable var = simJob.getSimulationSymbolTable().getVariable(argSimSpec.getVarsList()[i]);
                    data[i + 1] = new double[data[0].length];
                    if (var instanceof cbit.vcell.math.Constant) {
                        double value = ((cbit.vcell.math.Constant) var).getExpression().evaluateConstant();
                        for (int j = 0; j < data[i + 1].length; j++) {
                            data[i + 1][j] = value;
                        }
                    } else {
                        throw new RuntimeException("Did not find " + argSimSpec.getVarsList()[i] + " in simulation");
                    }
                } else {
                    data[i + 1] = odeSolverResultSet.extractColumn(column);
                }
            }
            double endTime = (simJob.getSimulation().getSolverTaskDescription().getTimeBounds().getEndingTime());
            // for each time, print row
            int index = 0;
            double[] sampleTimes = new double[numTimeSteps + 1];
            for (int i = 0; i <= numTimeSteps; i++) {
                sampleTimes[i] = endTime * i / numTimeSteps;
            }
            for (int i = 0; i < sampleTimes.length; i++) {
                // find largest index whose time is not past sample time
                while (true) {
                    // if already at last time point, then if it equals the sampleTime, we're done if it doesn't then we don't have this time point.
                    if (index == odeSolverResultSet.getRowCount() - 1) {
                        if (data[0][index] == sampleTimes[i]) {
                            break;
                        } else {
                            throw new RuntimeException("sampleTime does not match at last time point");
                        }
                    }
                    // haven't gotten to last time point yet, stop when next time step is past sampleTime.
                    if (data[0][index + 1] > sampleTimes[i]) {
                        break;
                    }
                    // sampleTime must be later in our data list.
                    index++;
                }
                // if (data[0][index] == sampleTimes[i]) {
                if (Math.abs(data[0][index] - sampleTimes[i]) < 1e-12) {
                    // if timeFactor is not 1.0, time is not in seconds (mins or hrs); if timeFactor is 60, divide sampleTime/60; if it is 3600, divide sampleTime/3600.
                    // if (argTimeFactor != 1.0) {
                    // outputStream.print(data[0][index]/argTimeFactor);
                    // } else {
                    outputStream.print(data[0][index]);
                    // }
                    for (int j = 0; j < argSimSpec.getVarsList().length; j++) {
                        // SBMLImporter.SBVCConcentrationUnits spConcUnits = (SBMLImporter.SBVCConcentrationUnits)argSpUnitsHash.get(argSimSpec.getVarsList()[j]);
                        // if (spConcUnits != null) {
                        // VCUnitDefinition sbunits = spConcUnits.getSBConcentrationUnits();
                        // VCUnitDefinition vcunits = spConcUnits.getVCConcentrationUnits();
                        // SBMLUnitParameter unitFactor = SBMLUtils.getConcUnitFactor("spConcParam", vcunits, sbunits, kMoleSymbol);
                        // outputStream.print("," + data[j + 1][index] * unitFactor.getExpression().evaluateConstant()); 		//earlier, hack unitfactor = 0.000001
                        // earlier, hack unitfactor = 0.000001
                        outputStream.print("," + data[j + 1][index]);
                    }
                    // }
                    outputStream.println();
                } else {
                    // if data[0][index] < sampleTime, must interpolate
                    double fraction = (sampleTimes[i] - data[0][index]) / (data[0][index + 1] - data[0][index]);
                    // if argTimeFactor is not 1.0, time is not in seconds (mins or hrs); if argTimeFactor is 60, divide sampleTime/60; if it is 3600, divide sampleTime/3600.
                    // if (argTimeFactor != 1.0) {
                    // outputStream.print(sampleTimes[i]/argTimeFactor);
                    // } else {
                    outputStream.print(sampleTimes[i]);
                    // }
                    for (int j = 0; j < argSimSpec.getVarsList().length; j++) {
                        double interpolatedValue = 0.0;
                        double[] speciesVals = null;
                        double[] times = null;
                        // Currently using 2nd order interpolation
                        if (index == 0) {
                            // can only do 1st order interpolation
                            times = new double[] { data[0][index], data[0][index + 1] };
                            speciesVals = new double[] { data[j + 1][index], data[j + 1][index + 1] };
                            interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
                        } else {
                            if (index >= 1 && index <= origDataLength - 3) {
                                double val_1 = Math.abs(sampleTimes[i] - data[0][index - 1]);
                                double val_2 = Math.abs(sampleTimes[i] - data[0][index + 2]);
                                if (val_1 < val_2) {
                                    times = new double[] { data[0][index - 1], data[0][index], data[0][index + 1] };
                                    speciesVals = new double[] { data[j + 1][index - 1], data[j + 1][index], data[j + 1][index + 1] };
                                } else {
                                    times = new double[] { data[0][index], data[0][index + 1], data[0][index + 2] };
                                    speciesVals = new double[] { data[j + 1][index], data[j + 1][index + 1], data[j + 1][index + 2] };
                                }
                                interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
                            } else {
                                times = new double[] { data[0][index - 1], data[0][index], data[0][index + 1] };
                                speciesVals = new double[] { data[j + 1][index - 1], data[j + 1][index], data[j + 1][index + 1] };
                                interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
                            }
                        }
                        // end if-else - calc of interpolated value
                        // interpolatedValue = interpolatedValue * unitFactor.getExpression().evaluateConstant();
                        outputStream.print("," + interpolatedValue);
                    }
                    // end for - sp values for each time point (row)
                    outputStream.println();
                }
            }
            outputStream.close();
        } else {
            throw new RuntimeException("Result set was null, could not write to CSV file");
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Errors saving results to CSV file" + e.getMessage());
    }
}

Example 19 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask 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 20 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask 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);
}