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

Example 1 with ODESolver

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

the class SolverHandler method simulateAllTasks.

public HashMap<String, ODESolverResultSet> simulateAllTasks(CLIUtils utils, ExternalDocInfo externalDocInfo, SedML sedml, File outputDirForSedml, String outDir, String outputBaseDir, String sedmlLocation, boolean keepTempFiles, boolean exactMatchOnly) throws Exception {
    // create the VCDocument(s) (bioModel(s) + application(s) + simulation(s)), do sanity checks
    cbit.util.xml.VCLogger sedmlImportLogger = new LocalLogger();
    String inputFile = externalDocInfo.getFile().getAbsolutePath();
    String bioModelBaseName = org.vcell.util.FileUtils.getBaseName(inputFile);
    List<VCDocument> docs = null;
    // Key String is SEDML Task ID
    HashMap<String, ODESolverResultSet> resultsHash = new LinkedHashMap<String, ODESolverResultSet>();
    String docName = null;
    BioModel bioModel = null;
    Simulation[] sims = null;
    String outDirRoot = outputDirForSedml.toString().substring(0, outputDirForSedml.toString().lastIndexOf(System.getProperty("file.separator")));
    try {
        docs = XmlHelper.sedmlToBioModel(sedmlImportLogger, externalDocInfo, sedml, null, sedmlLocation, exactMatchOnly);
    } catch (Exception e) {
        System.err.println("Unable to Parse SED-ML into Bio-Model, failed with err: " + e.getMessage());
        throw e;
    }
    if (docs != null) {
        countBioModels = docs.size();
    }
    int simulationCount = 0;
    int bioModelCount = 0;
    boolean hasSomeSpatial = false;
    boolean bTimeoutFound = false;
    for (VCDocument doc : docs) {
        try {
            sanityCheck(doc);
        } catch (Exception e) {
            e.printStackTrace(System.err);
        // continue;
        }
        docName = doc.getName();
        bioModel = (BioModel) doc;
        sims = bioModel.getSimulations();
        for (Simulation sim : sims) {
            if (sim.getImportedTaskID() == null) {
                // this is a simulation not matching the imported task, so we skip it
                continue;
            }
            String logTaskMessage = "Initializing simulation... ";
            String logTaskError = "";
            long startTimeTask = System.currentTimeMillis();
            SimulationTask simTask;
            String kisao = "null";
            ODESolverResultSet odeSolverResultSet = null;
            SolverTaskDescription std = null;
            SolverDescription sd = null;
            try {
                SimulationOwner so = sim.getSimulationOwner();
                sim = new TempSimulation(sim, false);
                sim.setSimulationOwner(so);
                std = sim.getSolverTaskDescription();
                sd = std.getSolverDescription();
                kisao = sd.getKisao();
                if (kisao == null) {
                    throw new RuntimeException("KISAO is null.");
                }
                SimulationJob simJob = new SimulationJob(sim, 0, null);
                simTask = new SimulationTask(simJob, 0);
                Solver solver = SolverFactory.createSolver(outputDirForSedml, simTask, false);
                logTaskMessage += "done. Starting simulation... ";
                if (sd.isSpatial()) {
                    hasSomeSpatial = true;
                }
                // else
                if (solver instanceof AbstractCompiledSolver) {
                    ((AbstractCompiledSolver) solver).runSolver();
                    System.out.println(solver);
                    System.out.println(solver.getSolverStatus());
                    if (solver instanceof ODESolver) {
                        odeSolverResultSet = ((ODESolver) solver).getODESolverResultSet();
                    } else if (solver instanceof GibsonSolver) {
                        odeSolverResultSet = ((GibsonSolver) solver).getStochSolverResultSet();
                    } else if (solver instanceof HybridSolver) {
                        odeSolverResultSet = ((HybridSolver) solver).getHybridSolverResultSet();
                    } else {
                        String str = "Solver results are not compatible with CSV format. ";
                        System.err.println(str);
                    // keepTempFiles = true;		// temp fix for Jasraj
                    // throw new RuntimeException(str);
                    }
                } else if (solver instanceof AbstractJavaSolver) {
                    ((AbstractJavaSolver) solver).runSolver();
                    odeSolverResultSet = ((ODESolver) solver).getODESolverResultSet();
                    // must interpolate data for uniform time course which is not supported natively by the Java solvers
                    Task task = (Task) sedml.getTaskWithId(sim.getImportedTaskID());
                    assert task != null;
                    org.jlibsedml.Simulation sedmlSim = sedml.getSimulation(task.getSimulationReference());
                    if (sedmlSim instanceof UniformTimeCourse) {
                        odeSolverResultSet = CLIUtils.interpolate(odeSolverResultSet, (UniformTimeCourse) sedmlSim);
                        logTaskMessage += "done. Interpolating... ";
                    }
                } else {
                    // this should actually never happen...
                    String str = "Unexpected solver: " + kisao + " " + solver + ". ";
                    throw new RuntimeException(str);
                }
                if (solver.getSolverStatus().getStatus() == SolverStatus.SOLVER_FINISHED) {
                    // File aaa = new File("C:\\TEMP\\aaa.hdf5");
                    // CLIUtils.exportPDE2HDF5(sim, outputDirForSedml, aaa);
                    logTaskMessage += "done. ";
                    System.out.println("Succesful execution: Model '" + docName + "' Task '" + sim.getDescription() + "'.");
                    long endTimeTask = System.currentTimeMillis();
                    long elapsedTime = endTimeTask - startTimeTask;
                    int duration = (int) Math.ceil(elapsedTime / 1000.0);
                    String msg = "Running simulation " + simTask.getSimulation().getName() + ", " + elapsedTime + " ms";
                    System.out.println(msg);
                    // we only count the number of simulations (tasks) that succeeded
                    countSuccessfulSimulationRuns++;
                    utils.updateTaskStatusYml(sedmlLocation, sim.getImportedTaskID(), CLIUtils.Status.SUCCEEDED, outDir, duration + "", kisao);
                    utils.setOutputMessage(sedmlLocation, sim.getImportedTaskID(), outDir, "task", logTaskMessage);
                    CLIUtils.drawBreakLine("-", 100);
                } else {
                    System.err.println("Solver status: " + solver.getSolverStatus().getStatus());
                    System.err.println("Solver message: " + solver.getSolverStatus().getSimulationMessage().getDisplayMessage());
                    String error = solver.getSolverStatus().getSimulationMessage().getDisplayMessage() + " ";
                    throw new RuntimeException(error);
                }
            // CLIUtils.finalStatusUpdate( CLIUtils.Status.SUCCEEDED, outDir);
            } catch (Exception e) {
                // File aaa = new File("C:\\TEMP\\aaa.hdf5");
                // CLIUtils.exportPDE2HDF5(sim, outputDirForSedml, aaa);
                String error = "Failed execution: Model '" + docName + "' Task '" + sim.getDescription() + "'. ";
                System.err.println(error);
                long endTime = System.currentTimeMillis();
                long elapsedTime = endTime - startTimeTask;
                int duration = (int) Math.ceil(elapsedTime / 1000.0);
                String msg = "Running simulation for " + elapsedTime + " ms";
                System.out.println(msg);
                if (sim.getImportedTaskID() == null) {
                    String str = "'null' imported task id, this should never happen. ";
                    System.err.println();
                    logTaskError += str;
                } else {
                    utils.updateTaskStatusYml(sedmlLocation, sim.getImportedTaskID(), CLIUtils.Status.FAILED, outDir, duration + "", kisao);
                }
                // CLIUtils.finalStatusUpdate(CLIUtils.Status.FAILED, outDir);
                if (e.getMessage() != null) {
                    // something else than failure caught by solver instance during execution
                    logTaskError += (e.getMessage() + ". ");
                    System.err.println(e.getMessage());
                } else {
                    logTaskError += (error + ". ");
                }
                String type = e.getClass().getSimpleName();
                utils.setOutputMessage(sedmlLocation, sim.getImportedTaskID(), outDir, "task", logTaskMessage);
                utils.setExceptionMessage(sedmlLocation, sim.getImportedTaskID(), outDir, "task", type, logTaskError);
                String sdl = "";
                if (sd != null && sd.getShortDisplayLabel() != null && !sd.getShortDisplayLabel().isEmpty()) {
                    sdl = sd.getShortDisplayLabel();
                } else {
                    sdl = kisao;
                }
                if (logTaskError.contains("Process timed out")) {
                    if (bTimeoutFound == false) {
                        // don't repeat this for each task
                        String str = logTaskError.substring(0, logTaskError.indexOf("Process timed out"));
                        // truncate the rest of the spam
                        str += "Process timed out";
                        CLIStandalone.writeDetailedErrorList(outputBaseDir, bioModelBaseName + ",  solver: " + sdl + ": " + type + ": " + str);
                        bTimeoutFound = true;
                    }
                } else {
                    CLIStandalone.writeDetailedErrorList(outputBaseDir, bioModelBaseName + ",  solver: " + sdl + ": " + type + ": " + logTaskError);
                }
                CLIUtils.drawBreakLine("-", 100);
            }
            if (odeSolverResultSet != null) {
                resultsHash.put(sim.getImportedTaskID(), odeSolverResultSet);
            } else {
                // if any task fails, we still put it in the hash with a null value
                resultsHash.put(sim.getImportedTaskID(), null);
            }
            if (keepTempFiles == false) {
                CLIUtils.removeIntermediarySimFiles(outputDirForSedml);
            }
            simulationCount++;
        }
        bioModelCount++;
    }
    System.out.println("Ran " + simulationCount + " simulations for " + bioModelCount + " biomodels.");
    if (hasSomeSpatial) {
        CLIStandalone.writeSpatialList(outputBaseDir, bioModelBaseName);
    }
    return resultsHash;
}

Example 2 with ODESolver

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

the class SolverHandler method simulateAllVcmlTasks.

@Deprecated
public HashMap<String, ODESolverResultSet> simulateAllVcmlTasks(File vcmlPath, File outputDir) throws Exception {
    // create the VCDocument(s) (bioModel(s) + application(s) + simulation(s)), do sanity checks
    List<VCDocument> docs = null;
    // Key String is SEDML Task ID
    HashMap<String, ODESolverResultSet> resultsHash = new LinkedHashMap<String, ODESolverResultSet>();
    String docName = null;
    BioModel bioModel = null;
    Simulation[] sims = null;
    VCDocument singleDoc = null;
    try {
        singleDoc = VCMLHandler.convertVcmlToVcDocument(vcmlPath);
    } catch (Exception e) {
        System.err.println("Unable to Parse SED-ML into Bio-Model, failed with err: " + e.getMessage());
        throw e;
    }
    try {
        sanityCheck(singleDoc);
    } catch (Exception e) {
        e.printStackTrace(System.err);
    }
    assert singleDoc != null;
    docName = singleDoc.getName();
    bioModel = (BioModel) singleDoc;
    sims = bioModel.getSimulations();
    for (Simulation sim : sims) {
        sim = new TempSimulation(sim, false);
        SolverTaskDescription std = sim.getSolverTaskDescription();
        SolverDescription sd = std.getSolverDescription();
        String kisao = sd.getKisao();
        SimulationJob simJob = new SimulationJob(sim, 0, null);
        SimulationTask simTask = new SimulationTask(simJob, 0);
        Solver solver = SolverFactory.createSolver(outputDir, simTask, false);
        ODESolverResultSet odeSolverResultSet = null;
        try {
            if (solver instanceof AbstractCompiledSolver) {
                ((AbstractCompiledSolver) solver).runSolver();
                if (solver instanceof ODESolver) {
                    odeSolverResultSet = ((ODESolver) solver).getODESolverResultSet();
                } else if (solver instanceof GibsonSolver) {
                    odeSolverResultSet = ((GibsonSolver) solver).getStochSolverResultSet();
                } else if (solver instanceof HybridSolver) {
                    odeSolverResultSet = ((HybridSolver) solver).getHybridSolverResultSet();
                } else {
                    System.err.println("Solver results are not compatible with CSV format");
                }
            // TODO: Add support for JAVA solvers and implement interpolation
            // odeSolverResultSet = CLIUtils.interpolate(odeSolverResultSet, (UniformTimeCourse) sedmlSim);
            } else {
                // this should actually never happen...
                throw new Exception("Unexpected solver: " + kisao + " " + solver);
            }
            if (solver.getSolverStatus().getStatus() == SolverStatus.SOLVER_FINISHED) {
                System.out.println("Succesful execution: Model '" + docName + "' Task '" + sim.getDescription() + "'.");
            } else {
                System.err.println("Solver status: " + solver.getSolverStatus().getStatus());
                System.err.println("Solver message: " + solver.getSolverStatus().getSimulationMessage().getDisplayMessage());
                throw new Exception();
            }
        } catch (Exception e) {
            System.err.println("Failed execution: Model '" + docName + "' Task '" + sim.getDescription() + "'.");
            if (e.getMessage() != null) {
                // something else than failure caught by solver instance during execution
                System.err.println(e.getMessage());
            }
        }
        if (odeSolverResultSet != null) {
            resultsHash.put(sim.getName(), odeSolverResultSet);
        }
        CLIUtils.removeIntermediarySimFiles(outputDir);
    }
    return resultsHash;
}