Examples with CVodeFileWriter cbit.vcell.solver.ode.CVodeFileWriter used on opensource projects

Example 1 with CVodeFileWriter

use of cbit.vcell.solver.ode.CVodeFileWriter in project vcell by virtualcell.

the class VCellSedMLSolver method solveCvode.

private static ODESolverResultSet solveCvode(File outDir, BioModel bioModel) throws Exception {
    String docName = bioModel.getName();
    Simulation sim = bioModel.getSimulation(0);
    File cvodeInputFile = new File(outDir, docName + SimDataConstants.CVODEINPUT_DATA_EXTENSION);
    PrintWriter cvodePW = new java.io.PrintWriter(cvodeInputFile);
    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
    String outDirPath = outDir.getAbsolutePath();
    int indexOfLastSlash = outDirPath.lastIndexOf("/");
    String task_name = outDirPath.substring(indexOfLastSlash + 1);
    String idaFilePath = outDirPath.substring(0, indexOfLastSlash);
    File cvodeOutputFile = new File(idaFilePath, task_name + SimDataConstants.IDA_DATA_EXTENSION);
    String executableName = null;
    try {
        // we need to specify the vCell install dir in the Eclipse Debug configuration, as VM argument
        // so that the code next knows where to look for the solver
        // -Dvcell.installDir=G:\dan\jprojects\git\vcell
        // OR
        // just type the string with the full path explicitly
        // OR
        // provide a .properties file in the working directory
        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, cvodeInputFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath() });
    executable.start();
    ODESolverResultSet odeSolverResultSet = VCellSBMLSolver.getODESolverResultSet(simJob, cvodeOutputFile.getPath());
    return odeSolverResultSet;
}

Example 2 with CVodeFileWriter

use of cbit.vcell.solver.ode.CVodeFileWriter 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 3 with CVodeFileWriter

use of cbit.vcell.solver.ode.CVodeFileWriter 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);
    }
}