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

Example 31 with SimulationJob

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

the class RunSims method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    ClientSimManager clientSimManager = (ClientSimManager) hashTable.get("clientSimManager");
    // DocumentManager documentManager = (DocumentManager)hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    JobManager jobManager = (JobManager) hashTable.get("jobManager");
    Simulation[] simulations = (Simulation[]) hashTable.get("simulations");
    Hashtable<Simulation, Throwable> failures = new Hashtable<Simulation, Throwable>();
    if (simulations != null && simulations.length > 0) {
        // we need to get the new ones if a save occurred...
        if (hashTable.containsKey(SaveDocument.DOC_KEY)) {
            VCDocument savedDocument = (VCDocument) hashTable.get(SaveDocument.DOC_KEY);
            Simulation[] allSims = null;
            if (savedDocument instanceof BioModel) {
                allSims = ((BioModel) savedDocument).getSimulations();
            } else if (savedDocument instanceof MathModel) {
                allSims = ((MathModel) savedDocument).getSimulations();
            }
            Vector<Simulation> v = new Vector<Simulation>();
            for (int i = 0; i < simulations.length; i++) {
                for (int j = 0; j < allSims.length; j++) {
                    if (simulations[i].getName().equals(allSims[j].getName())) {
                        v.add(allSims[j]);
                        break;
                    }
                }
            }
            simulations = (Simulation[]) BeanUtils.getArray(v, Simulation.class);
        }
        for (Simulation sim : simulations) {
            try {
                int dimension = sim.getMathDescription().getGeometry().getDimension();
                if (clientSimManager.getSimulationStatus(sim).isCompleted()) {
                    // completed
                    String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_1, sim.getName());
                    String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                    if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                        continue;
                    }
                }
                DataProcessingInstructions dataProcessingInstructions = sim.getDataProcessingInstructions();
                try {
                    if (dataProcessingInstructions != null) {
                        dataProcessingInstructions.getSampleImageFieldData(sim.getVersion().getOwner());
                    }
                } catch (Exception ex) {
                    DialogUtils.showErrorDialog(documentWindowManager.getComponent(), "Problem found in simulation '" + sim.getName() + "':\n" + ex.getMessage());
                    continue;
                }
                if (dimension > 0) {
                    MeshSpecification meshSpecification = sim.getMeshSpecification();
                    boolean bCellCentered = sim.hasCellCenteredMesh();
                    if (meshSpecification != null && !meshSpecification.isAspectRatioOK(bCellCentered)) {
                        String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_2, sim.getName(), "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (dimension < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered)));
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                    if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.Smoldyn)) {
                        if (!isSmoldynTimeStepOK(sim)) {
                            double s = smoldynTimestepVars.getSpatialResolution();
                            double dMax = smoldynTimestepVars.getMaxDiffusion();
                            double condn = (s * s) / (2.0 * dMax);
                            String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_3, Double.toString(s), Double.toString(dMax), Double.toString(condn));
                            DialogUtils.showErrorDialog(documentWindowManager.getComponent(), warningMessage);
                            continue;
                        }
                    }
                    // check the number of regions if the simulation mesh is coarser.
                    Geometry mathGeometry = sim.getMathDescription().getGeometry();
                    ISize newSize = meshSpecification.getSamplingSize();
                    ISize defaultSize = mathGeometry.getGeometrySpec().getDefaultSampledImageSize();
                    if (!sim.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
                        int defaultTotalVolumeElements = mathGeometry.getGeometrySurfaceDescription().getVolumeSampleSize().getXYZ();
                        int newTotalVolumeElements = meshSpecification.getSamplingSize().getXYZ();
                        if (defaultTotalVolumeElements > newTotalVolumeElements) {
                            // coarser
                            Geometry resampledGeometry = (Geometry) BeanUtils.cloneSerializable(mathGeometry);
                            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
                            geoSurfaceDesc.setVolumeSampleSize(newSize);
                            geoSurfaceDesc.updateAll();
                            if (mathGeometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                                mathGeometry.getGeometrySurfaceDescription().updateAll();
                            }
                            int defaultNumGeometricRegions = mathGeometry.getGeometrySurfaceDescription().getGeometricRegions().length;
                            int numGeometricRegions = geoSurfaceDesc.getGeometricRegions().length;
                            if (numGeometricRegions != defaultNumGeometricRegions) {
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_4, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), numGeometricRegions, defaultNumGeometricRegions);
                                String result = PopupGenerator.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                        if (mathGeometry.getGeometrySpec().hasImage()) {
                            // if it's an image.
                            if (defaultSize.getX() + 1 < newSize.getX() || defaultSize.getY() + 1 < newSize.getY() || defaultSize.getZ() + 1 < newSize.getZ()) {
                                // finer
                                String defaultSizeString = (defaultSize.getX() + 1) + (dimension > 1 ? " x " + (defaultSize.getY() + 1) : "") + (dimension > 2 ? " x " + (defaultSize.getZ() + 1) : "");
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_5, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), defaultSizeString, defaultSizeString);
                                String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                    }
                    boolean bGiveWarning = false;
                    for (int i = 0; i < sim.getScanCount(); i++) {
                        if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE)) {
                            SimulationJob simJob = new SimulationJob(sim, i, null);
                            if (simJob.getSimulationSymbolTable().hasTimeVaryingDiffusionOrAdvection()) {
                                bGiveWarning = true;
                                break;
                            }
                        }
                    }
                    if (bGiveWarning) {
                        String warningMessage = VCellErrorMessages.RunSims_6;
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                }
                SimulationInfo simInfo = sim.getSimulationInfo();
                if (simInfo != null) {
                    // 
                    // translate to common ancestral simulation (oldest mathematically equivalent simulation)
                    // 
                    SimulationStatus simulationStatus = jobManager.startSimulation(simInfo.getAuthoritativeVCSimulationIdentifier(), sim.getScanCount());
                    // updateStatus
                    clientSimManager.updateStatusFromStartRequest(sim, simulationStatus);
                } else {
                    // this should really not happen...
                    throw new RuntimeException(">>>>>>>>>> trying to run an unsaved simulation...");
                }
            } catch (Throwable exc) {
                exc.printStackTrace(System.out);
                failures.put(sim, exc);
            }
        }
    }
    // we deal with individual request failures here, passing down only other things (that break the whole thing down) to dispatcher
    if (!failures.isEmpty()) {
        Enumeration<Simulation> en = failures.keys();
        while (en.hasMoreElements()) {
            Simulation sim = en.nextElement();
            Throwable exc = (Throwable) failures.get(sim);
            // // updateStatus
            // SimulationStatus simulationStatus = clientSimManager.updateStatusFromStartRequest(sim, true, exc.getMessage());
            // notify user
            PopupGenerator.showErrorDialog(documentWindowManager, "Failed to start simulation'" + sim.getName() + "'\n" + exc.getMessage());
        }
    }
}

Example 32 with SimulationJob

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

the class VCellSBMLSolver method solveVCell.

public File solveVCell(String filePrefix, File outDir, String sbmlFileName, SimSpec testSpec) throws IOException, SolverException, SbmlException {
    try {
        cbit.util.xml.VCLogger logger = new LocalLogger();
        // 
        // Instantiate an SBMLImporter to get the speciesUnitsHash - to compute the conversion factor from VC->SB species units.
        // and import SBML  (sbml->bioModel)
        org.vcell.sbml.vcell.SBMLImporter sbmlImporter = new org.vcell.sbml.vcell.SBMLImporter(sbmlFileName, logger, false);
        BioModel bioModel = sbmlImporter.getBioModel();
        if (bRoundTrip) {
            // Round trip the bioModel (bioModel->sbml->bioModel).
            // export bioModel as sbml and save
            String vcml_sbml = cbit.vcell.xml.XmlHelper.exportSBML(bioModel, 2, 1, 0, false, bioModel.getSimulationContext(0), null);
            // re-import bioModel from exported sbml
            XMLSource vcml_sbml_Src = new XMLSource(vcml_sbml);
            BioModel newBioModel = (BioModel) XmlHelper.importSBML(logger, vcml_sbml_Src, false);
            // have rest of code use the round-tripped biomodel
            bioModel = newBioModel;
        }
        // 
        // select only Application, generate math, and create a single Simulation.
        // 
        SimulationContext simContext = bioModel.getSimulationContext(0);
        MathMapping mathMapping = simContext.createNewMathMapping();
        MathDescription mathDesc = mathMapping.getMathDescription();
        simContext.setMathDescription(mathDesc);
        SimulationVersion simVersion = new SimulationVersion(new KeyValue("100"), "unnamed", null, null, null, null, null, null, null, null);
        Simulation sim = new Simulation(simVersion, mathDesc);
        sim.setName("unnamed");
        // if time factor from SBML is not 1 (i.e., it is not in secs but in minutes or hours), convert endTime to min/hr as : endTime*timeFactor
        // double endTime = testSpec.getEndTime()*timeFactor;
        double endTime = testSpec.getEndTime();
        sim.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, endTime));
        TimeStep timeStep = new TimeStep();
        sim.getSolverTaskDescription().setTimeStep(new TimeStep(timeStep.getMinimumTimeStep(), timeStep.getDefaultTimeStep(), endTime / 10000));
        sim.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec((endTime - 0) / testSpec.getNumTimeSteps()));
        sim.getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(testSpec.getAbsTolerance(), testSpec.getRelTolerance()));
        // sim.getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(1e-10, 1e-12));
        // Generate .idaInput string
        File idaInputFile = new File(outDir, filePrefix + SimDataConstants.IDAINPUT_DATA_EXTENSION);
        PrintWriter idaPW = new java.io.PrintWriter(idaInputFile);
        SimulationJob simJob = new SimulationJob(sim, 0, null);
        SimulationTask simTask = new SimulationTask(simJob, 0);
        IDAFileWriter idaFileWriter = new IDAFileWriter(idaPW, simTask);
        idaFileWriter.write();
        idaPW.close();
        // use the idastandalone solver
        File idaOutputFile = new File(outDir, filePrefix + SimDataConstants.IDA_DATA_EXTENSION);
        // String sundialsSolverExecutable = "C:\\Developer\\Eclipse\\workspace\\VCell 4.8\\SundialsSolverStandalone_NoMessaging.exe";
        String executableName = null;
        try {
            executableName = SolverUtilities.getExes(SolverDescription.IDA)[0].getAbsolutePath();
        } catch (IOException e) {
            throw new RuntimeException("failed to get executable for solver " + SolverDescription.IDA.getDisplayLabel() + ": " + e.getMessage(), e);
        }
        Executable executable = new Executable(new String[] { executableName, idaInputFile.getAbsolutePath(), idaOutputFile.getAbsolutePath() });
        executable.start();
        /*			// Generate .cvodeInput string
			File cvodeFile = new File(outDir,filePrefix+SimDataConstants.CVODEINPUT_DATA_EXTENSION);
			PrintWriter cvodePW = new java.io.PrintWriter(cvodeFile);
			SimulationJob simJob = new SimulationJob(sim, 0, null);
		    CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(cvodePW, simJob);
			cvodeFileWriter.write();
			cvodePW.close();

			// use the cvodeStandalone solver
			File cvodeOutputFile = new File(outDir,filePrefix+SimDataConstants.IDA_DATA_EXTENSION);
			String sundialsSolverExecutable = PropertyLoader.getRequiredProperty(PropertyLoader.sundialsSolverExecutableProperty);
			Executable executable = new Executable(new String[]{sundialsSolverExecutable, cvodeFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath()});
			executable.start();
*/
        // get the result
        ODESolverResultSet odeSolverResultSet = getODESolverResultSet(simJob, idaOutputFile.getPath());
        // remove CVOde input and output files ??
        idaInputFile.delete();
        idaOutputFile.delete();
        // 
        // print header
        // 
        File outputFile = new File(outDir, "results" + filePrefix + ".csv");
        java.io.PrintStream outputStream = new java.io.PrintStream(new java.io.BufferedOutputStream(new java.io.FileOutputStream(outputFile)));
        outputStream.print("time");
        for (int i = 0; i < testSpec.getVarsList().length; i++) {
            outputStream.print("," + testSpec.getVarsList()[i]);
        }
        outputStream.println();
        // 
        // extract data for time and species
        // 
        double[][] data = new double[testSpec.getVarsList().length + 1][];
        int column = odeSolverResultSet.findColumn("t");
        data[0] = odeSolverResultSet.extractColumn(column);
        int origDataLength = data[0].length;
        for (int i = 0; i < testSpec.getVarsList().length; i++) {
            column = odeSolverResultSet.findColumn(testSpec.getVarsList()[i]);
            if (column == -1) {
                Variable var = simJob.getSimulationSymbolTable().getVariable(testSpec.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 " + testSpec.getVarsList()[i] + " in simulation");
                }
            } else {
                data[i + 1] = odeSolverResultSet.extractColumn(column);
            }
        }
        // 
        // for each time, print row
        // 
        int index = 0;
        double[] sampleTimes = new double[testSpec.getNumTimeSteps() + 1];
        for (int i = 0; i <= testSpec.getNumTimeSteps(); i++) {
            sampleTimes[i] = endTime * i / testSpec.getNumTimeSteps();
        }
        Model vcModel = bioModel.getModel();
        ReservedSymbol kMole = vcModel.getKMOLE();
        for (int i = 0; i < sampleTimes.length; i++) {
            // 
            while (true) {
                // 
                if (index == odeSolverResultSet.getRowCount() - 1) {
                    if (data[0][index] == sampleTimes[i]) {
                        break;
                    } else {
                        throw new RuntimeException("sampleTime does not match at last time point");
                    }
                }
                // 
                if (data[0][index + 1] > sampleTimes[i]) {
                    break;
                }
                // 
                // sampleTime must be later in our data list.
                // 
                index++;
            }
            // if data[0][index] == sampleTime no need to interpolate
            if (data[0][index] == sampleTimes[i]) {
                // 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 (timeFactor != 1.0) {
                // outputStream.print(data[0][index]/timeFactor);
                // } else {
                outputStream.print(data[0][index]);
                // }
                for (int j = 0; j < testSpec.getVarsList().length; j++) {
                    // SBMLImporter.SBVCConcentrationUnits spConcUnits = speciesUnitsHash.get(testSpec.getVarsList()[j]);
                    // if (spConcUnits != null) {
                    // VCUnitDefinition sbunits = spConcUnits.getSBConcentrationUnits();
                    // VCUnitDefinition vcunits = spConcUnits.getVCConcentrationUnits();
                    // SBMLUnitParameter unitFactor = SBMLUtils.getConcUnitFactor("spConcParam", vcunits, sbunits, kMole);
                    // 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]);
                // }
                }
                // System.out.println("No interpolation needed!");
                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 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 (timeFactor != 1.0) {
                // outputStream.print(sampleTimes[i]/timeFactor);
                // } else {
                outputStream.print(sampleTimes[i]);
                // }
                for (int j = 0; j < testSpec.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);
                    }
                    // // Currently using 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 = taylorInterpolation(sampleTimes[i], times, speciesVals);
                    // interpolatedValue = interpolatedValue * unitFactor.getExpression().evaluateConstant(); 		//earlier, hack unitfactor = 0.000001
                    // System.out.println("Sample time: " + sampleTimes[i] + ", between time[" + index + "]=" + data[0][index]+" and time["+(index+1)+"]="+(data[0][index+1])+", interpolated = "+interpolatedValue);
                    outputStream.print("," + interpolatedValue);
                }
                outputStream.println();
            }
        }
        outputStream.close();
        return outputFile;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        // File outputFile = new File(outDir,"results" + filePrefix + ".csv");
        throw new SolverException(e.getMessage());
    }
}

Example 33 with SimulationJob

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

the class FRAPStudy method runFVSolverStandalone_ref.

public static void runFVSolverStandalone_ref(File simulationDataDir, Simulation sim, ExternalDataIdentifier imageDataExtDataID, ExternalDataIdentifier roiExtDataID, ExternalDataIdentifier psfExtDataID, ClientTaskStatusSupport progressListener, boolean bCheckSteadyState) throws Exception {
    FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
    FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFunctionArgs.length];
    for (int i = 0; i < fieldDataIdentifierSpecs.length; i++) {
        if (fieldFunctionArgs[i].getFieldName().equals(imageDataExtDataID.getName())) {
            fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], imageDataExtDataID);
        } else if (fieldFunctionArgs[i].getFieldName().equals(roiExtDataID.getName())) {
            fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], roiExtDataID);
        } else if (fieldFunctionArgs[i].getFieldName().equals(psfExtDataID.getName())) {
            fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], psfExtDataID);
        } else {
            throw new RuntimeException("failed to resolve field named " + fieldFunctionArgs[i].getFieldName());
        }
    }
    int jobIndex = 0;
    SimulationTask simTask = new SimulationTask(new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs), 0);
    SolverUtilities.prepareSolverExecutable(sim.getSolverTaskDescription().getSolverDescription());
    // if we need to check steady state, do the following two lines
    if (bCheckSteadyState) {
        simTask.getSimulation().getSolverTaskDescription().setStopAtSpatiallyUniformErrorTolerance(ErrorTolerance.getDefaultSpatiallyUniformErrorTolerance());
    // simJob.getSimulation().getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(1e-6, 1e-2));
    }
    FVSolverStandalone fvSolver = new FVSolverStandalone(simTask, simulationDataDir, false);
    fvSolver.startSolver();
    SolverStatus status = fvSolver.getSolverStatus();
    while (status.getStatus() != SolverStatus.SOLVER_FINISHED && status.getStatus() != SolverStatus.SOLVER_ABORTED) {
        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 34 with SimulationJob

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

the class VCMongoMessage method addObject.

private static void addObject(Document dbObject, SolverEvent solverEvent) {
    AbstractSolver solver = (AbstractSolver) solverEvent.getSource();
    dbObject.put(MongoMessage_simProgress, solverEvent.getProgress());
    dbObject.put(MongoMessage_simTime, solverEvent.getTimePoint());
    addObject(dbObject, solverEvent.getSimulationMessage());
    dbObject.put(MongoMessage_solverEventType, solverEvent.getType());
    SimulationJob simJob = solver.getSimulationJob();
    dbObject.put(MongoMessage_simId, simJob.getVCDataIdentifier().getSimulationKey().toString());
    dbObject.put(MongoMessage_jobIndex, solver.getJobIndex());
    dbObject.put(MongoMessage_serverId, VCellServerID.getSystemServerID().toString());
}

Example 35 with SimulationJob

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

the class SimulationStateMachine method onDispatch.

public synchronized void onDispatch(Simulation simulation, SimulationJobStatus oldSimulationJobStatus, SimulationDatabase simulationDatabase, VCMessageSession session) throws VCMessagingException, DataAccessException, SQLException {
    updateSolverProcessTimestamp();
    VCSimulationIdentifier vcSimID = oldSimulationJobStatus.getVCSimulationIdentifier();
    int taskID = oldSimulationJobStatus.getTaskID();
    if (!oldSimulationJobStatus.getSchedulerStatus().isWaiting()) {
        VCMongoMessage.sendInfo("onDispatch(" + vcSimID.getID() + ") Can't start, simulation[" + vcSimID + "] job [" + jobIndex + "] task [" + taskID + "] is already dispatched (" + oldSimulationJobStatus.getSchedulerStatus().getDescription() + ")");
        throw new RuntimeException("Can't start, simulation[" + vcSimID + "] job [" + jobIndex + "] task [" + taskID + "] is already dispatched (" + oldSimulationJobStatus.getSchedulerStatus().getDescription() + ")");
    }
    FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = simulationDatabase.getFieldDataIdentifierSpecs(simulation);
    SimulationTask simulationTask = new SimulationTask(new SimulationJob(simulation, jobIndex, fieldDataIdentifierSpecs), taskID);
    double requiredMemMB = simulationTask.getEstimatedMemorySizeMB();
    double allowableMemMB = Double.parseDouble(PropertyLoader.getRequiredProperty(PropertyLoader.limitJobMemoryMB));
    final SimulationJobStatus newSimJobStatus;
    if (requiredMemMB > allowableMemMB) {
        // 
        // fail the simulation
        // 
        Date currentDate = new Date();
        // new queue status
        SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(currentDate, PRIORITY_DEFAULT, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
        SimulationExecutionStatus newSimExeStatus = new SimulationExecutionStatus(null, null, new Date(), null, false, null);
        newSimJobStatus = new SimulationJobStatus(VCellServerID.getSystemServerID(), vcSimID, jobIndex, oldSimulationJobStatus.getSubmitDate(), SchedulerStatus.FAILED, taskID, SimulationMessage.jobFailed("simulation required " + requiredMemMB + "MB of memory, only " + allowableMemMB + "MB allowed"), newQueueStatus, newSimExeStatus);
        simulationDatabase.updateSimulationJobStatus(newSimJobStatus);
        StatusMessage message = new StatusMessage(newSimJobStatus, simulation.getVersion().getOwner().getName(), null, null);
        message.sendToClient(session);
    } else {
        // 
        // dispatch the simulation, new queue status
        // 
        Date currentDate = new Date();
        SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(currentDate, PRIORITY_DEFAULT, SimulationJobStatus.SimulationQueueID.QUEUE_ID_SIMULATIONJOB);
        SimulationExecutionStatus newSimExeStatus = new SimulationExecutionStatus(null, null, new Date(), null, false, null);
        newSimJobStatus = new SimulationJobStatus(VCellServerID.getSystemServerID(), vcSimID, jobIndex, oldSimulationJobStatus.getSubmitDate(), SchedulerStatus.DISPATCHED, taskID, SimulationMessage.MESSAGE_JOB_DISPATCHED, newQueueStatus, newSimExeStatus);
        SimulationTaskMessage simTaskMessage = new SimulationTaskMessage(simulationTask);
        simTaskMessage.sendSimulationTask(session);
        simulationDatabase.updateSimulationJobStatus(newSimJobStatus);
        StatusMessage message = new StatusMessage(newSimJobStatus, simulation.getVersion().getOwner().getName(), null, null);
        message.sendToClient(session);
    }
// addStateMachineTransition(new StateMachineTransition(new DispatchStateMachineEvent(taskID), oldSimulationJobStatus, newSimJobStatus));
}