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

Example 26 with SimulationTask

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

the class HybridSolverTester method runHybridTest.

public void runHybridTest(String site) {
    try {
        double[] timePoints = null;
        File mathModelFile = new File(mathModelVCMLFileName);
        XMLSource vcmlSource = new XMLSource(mathModelFile);
        MathModel mathModel = XmlHelper.XMLToMathModel(vcmlSource);
        File simDataDir = mathModelFile.getParentFile();
        Simulation sim = mathModel.getSimulations()[0];
        // run multiple trials and each run will have a simID = origSimID + i
        for (int i = 0; i < numRuns; i++) {
            System.out.println("--------------Trial No: " + (startTrialNo + i) + "----------------");
            // replace random seed
            sim.getSolverTaskDescription().getSmoldynSimulationOptions().setRandomSeed(new Integer(startTrialNo + i));
            // create sim job
            int jobIndex = startTrialNo + i;
            SimulationTask simTask = new SimulationTask(new SimulationJob(sim, jobIndex, null), 0);
            /*
				 * When you want to run the multiple trials on local uncomment the line below.
				 */
            // ResourceUtil.prepareSolverExecutable(sim.getSolverTaskDescription().getSolverDescription());
            /*
				 * When you want to run the multiple trials on server (without VCell user interface), use the next line of code 
				 * Corresponding changes should be made in the shell script runhybridtest for the location of executable on server
				 */
            FVSolverStandalone fvSolver = new FVSolverStandalone(simTask, simDataDir, false);
            fvSolver.startSolver();
            SolverStatus status = fvSolver.getSolverStatus();
            while (status.getStatus() != SolverStatus.SOLVER_FINISHED && status.getStatus() != SolverStatus.SOLVER_ABORTED) {
                System.out.println("progress: " + (int) (fvSolver.getProgress() * 100) + "%");
                // ask status every 2 seconds
                Thread.sleep(2000);
                status = fvSolver.getSolverStatus();
            }
            if (status.getStatus() == SolverStatus.SOLVER_FINISHED) {
                // get data
                VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(sim.getVersion().getVersionKey(), sim.getVersion().getOwner());
                VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
                File hdf5File = new File(simDataDir, vcSimDataID.getID() + SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
                DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(vcSimDataID, false, null), hdf5File);
                if (i == 0) {
                    // do only one time
                    timePoints = dataProcessingOutputInfo.getVariableTimePoints();
                    for (int j = 0; j < varNames.length; j++) {
                        // row: numTimePoints, col:first col time + numRuns
                        double[][] data = new double[numRuns + 1][timePoints.length];
                        data[0] = timePoints;
                        results.add(data);
                    }
                }
                // write into results after each run
                for (int j = 0; j < varNames.length; j++) {
                    results.get(j)[i + 1] = dataProcessingOutputInfo.getVariableStatValues().get(varNames[j]);
                }
                // delete the file generated for this run
                deleteSimFiles(simDataDir, vcSimDataID);
            } else {
                throw new Exception("Sover did not finish normally." + status);
            }
        }
        // write to output file, tab delimited
        if (results != null && results.size() > 0) {
            for (int j = 0; j < varNames.length; j++) {
                File file = new File(simDataDir, "SimID_" + sim.getVersion().getVersionKey().toString() + "_" + varNames[j] + "_" + startTrialNo + ".txt");
                PrintWriter pw = new PrintWriter(file);
                double[][] data = results.get(j);
                if (data != null) {
                    for (int k = 0; k < data.length; k++) {
                        if (!bPrintTime && k == 0) {
                            continue;
                        }
                        String rowStr = (k == 0) ? "Time\t" : ("trialNo_" + (startTrialNo + k - 1) + "\t");
                        double[] rowData = data[k];
                        for (int q = 0; q < rowData.length; q++) {
                            rowStr += rowData[q] + "\t";
                        }
                        pw.println(rowStr);
                    }
                }
                pw.close();
            }
        }
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 27 with SimulationTask

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

the class RuleBasedTest method runsolver.

// private static void printout(String printThis){
// System.out.flush();
// disableSystemOut(false);
// System.out.print(printThis);
// System.out.flush();
// disableSystemOut(true);
// }
private static void runsolver(Simulation newSimulation, File baseDirectory, int numRuns, TimeSeriesMultitrialData timeSeriesMultitrialData) {
    Simulation versSimulation = null;
    File destDir = null;
    // int progress = 1;
    for (int trialIndex = 0; trialIndex < numRuns; trialIndex++) {
        // }
        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();
                }
                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");
            writeMessageTofile(file, e.getMessage());
        }
        try {
            Thread.sleep(100);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
        clearDir(destDir);
    }
// printout("\n");
}

Example 28 with SimulationTask

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

the class StandaloneRuleBasedTest method runsolver.

// private static void printout(String printThis){
// System.out.flush();
// disableSystemOut(false);
// System.out.print(printThis);
// System.out.flush();
// disableSystemOut(true);
// }
private static void runsolver(Simulation newSimulation, File baseDirectory, int numRuns, TimeSeriesMultitrialData timeSeriesMultitrialData) {
    Simulation versSimulation = null;
    File destDir = null;
    // int progress = 1;
    for (int trialIndex = 0; trialIndex < numRuns; trialIndex++) {
        // }
        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();
                }
                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());
        }
        try {
            Thread.sleep(100);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
        StochtestFileUtils.clearDir(destDir);
    }
// printout("\n");
}

Example 29 with SimulationTask

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

the class VCellSBMLSolver method solve.

public File solve(String filePrefix, File outDir, String sbmlFileName, SimSpec testSpec) throws IOException, SolverException, SbmlException {
    try {
        cbit.util.xml.VCLogger sbmlImportLogger = new LocalLogger();
        // 
        // Instantiate an SBMLImporter to get the speciesUnitsHash - to compute the conversion factor from VC->SB species units.
        // and import SBML  (sbml->bioModel)
        BioModel bioModel = importSBML(sbmlFileName, sbmlImportLogger, false);
        // Hashtable<String, SBMLImporter.SBVCConcentrationUnits> speciesUnitsHash = sbmlImporter.getSpeciesUnitsHash();
        // double timeFactor = sbmlImporter.getSBMLTimeUnitsFactor();
        String vcml_1 = XmlHelper.bioModelToXML(bioModel);
        SBMLUtils.writeStringToFile(vcml_1, new File(outDir, filePrefix + ".vcml").getAbsolutePath(), true);
        if (bRoundTrip) {
            // Round trip the bioModel (bioModel->sbml->bioModel).
            // save imported "bioModel" as VCML
            // String vcml_1 = XmlHelper.bioModelToXML(bioModel);
            // SBMLUtils.writeStringToFile(vcml_1, new File(outDir,filePrefix+".vcml").getAbsolutePath());
            // export bioModel as sbml and save
            // String vcml_sbml = cbit.vcell.xml.XmlHelper.exportSBML(bioModel, 2, 1, bioModel.getSimulationContexts(0).getName());
            // SimulationJob simJob = new SimulationJob(bioModel.getSimulations(bioModel.getSimulationContexts(0))[0], null, 0);
            String vcml_sbml = cbit.vcell.xml.XmlHelper.exportSBML(bioModel, 2, 1, 0, false, bioModel.getSimulationContext(0), null);
            SBMLUtils.writeStringToFile(vcml_sbml, new File(outDir, filePrefix + ".vcml.sbml").getAbsolutePath(), true);
            // re-import bioModel from exported sbml
            XMLSource vcml_sbml_Src = new XMLSource(vcml_sbml);
            BioModel newBioModel = (BioModel) XmlHelper.importSBML(sbmlImportLogger, vcml_sbml_Src, false);
            String vcml_sbml_vcml = XmlHelper.bioModelToXML(newBioModel);
            SBMLUtils.writeStringToFile(vcml_sbml_vcml, new File(outDir, filePrefix + ".vcml.sbml.vcml").getAbsolutePath(), true);
            // 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();
        String vcml = mathDesc.getVCML();
        try (PrintWriter pw = new PrintWriter("vcmlTrace.txt")) {
            pw.println(vcml);
        }
        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(1e-10, 1e-12));
        // sim.getSolverTaskDescription().setErrorTolerance(new cbit.vcell.solver.ErrorTolerance(1e-10, 1e-12));
        // Generate .idaInput string
        /*			IDAFileWriter idaFileWriter = new IDAFileWriter(sim);
			File idaInputFile = new File(filePathName.replace(".vcml", ".idaInput"));
			PrintWriter idaPW = new java.io.PrintWriter(idaInputFile);
			idaFileWriter.writeInputFile(idaPW);
			idaPW.close();

			// use the idastandalone solver
			File idaOutputFile = new File(filePathName.replace(".vcml", ".ida"));
			Executable executable = new Executable("IDAStandalone " + idaInputFile + " " + idaOutputFile);
			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);
        SimulationTask simTask = new SimulationTask(simJob, 0);
        CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(cvodePW, simTask);
        cvodeFileWriter.write();
        cvodePW.close();
        // use the cvodeStandalone solver
        File cvodeOutputFile = new File(outDir, filePrefix + SimDataConstants.IDA_DATA_EXTENSION);
        String executableName = null;
        try {
            executableName = SolverUtilities.getExes(SolverDescription.CVODE)[0].getAbsolutePath();
        } catch (IOException e) {
            throw new RuntimeException("failed to get executable for solver " + SolverDescription.CVODE.getDisplayLabel() + ": " + e.getMessage(), e);
        }
        Executable executable = new Executable(new String[] { executableName, cvodeFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath() });
        executable.start();
        // get the result
        ODESolverResultSet odeSolverResultSet = getODESolverResultSet(simJob, cvodeOutputFile.getPath());
        // 
        // print header
        // 
        File outputFile = new File(outDir, filePrefix + ".vcell.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 (RuntimeException e) {
        e.printStackTrace(System.out);
        // rethrow without losing context
        throw e;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SolverException(e.getMessage(), e);
    }
}

Example 30 with SimulationTask

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