Examples with SolverStatus cbit.vcell.solver.server.SolverStatus used on opensource projects

Example 21 with SolverStatus

use of cbit.vcell.solver.server.SolverStatus 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 22 with SolverStatus

use of cbit.vcell.solver.server.SolverStatus 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 23 with SolverStatus

use of cbit.vcell.solver.server.SolverStatus in project vcell by virtualcell.

the class NFSimSolver method initialize.

/**
 * This method takes the place of the old runUnsteady()...
 */
protected void initialize() throws SolverException {
    if (lg.isTraceEnabled())
        lg.trace("NFSimSolver.initialize()");
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
    writeFunctionsFile();
    String inputFilename = getInputFilename();
    if (lg.isTraceEnabled())
        lg.trace("NFSimSolver.initialize() inputFilename = " + getInputFilename());
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE));
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INPUT_FILE);
    try (PrintWriter pw = new PrintWriter(inputFilename)) {
        NFSimFileWriter stFileWriter = new NFSimFileWriter(pw, simTask, bMessaging);
        stFileWriter.write();
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not generate input file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException(e.getMessage());
    }
    PrintWriter lg = null;
    String logFilename = getLogFilename();
    String outputFilename = getOutputFilename();
    try {
        lg = new PrintWriter(logFilename);
        String shortOutputFilename = outputFilename.substring(1 + outputFilename.lastIndexOf("\\"));
        lg.println(NFSIM_DATA_IDENTIFIER + " " + shortOutputFilename);
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not generate log file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException(e.getMessage());
    } finally {
        if (lg != null) {
            lg.close();
        }
    }
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
    // get executable path+name.
    setMathExecutable(new MathExecutable(getMathExecutableCommand(), getSaveDirectory()));
// setMathExecutable(new
// cbit.vcell.solvers.MathExecutable(executableName + " gibson " +
// getBaseName() + ".stochInput" + " " + getBaseName() + ".stoch"));
}

Example 24 with SolverStatus

use of cbit.vcell.solver.server.SolverStatus in project vcell by virtualcell.

the class RunSimulation2DOp method runFVSolverStandalone.

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

Example 25 with SolverStatus

use of cbit.vcell.solver.server.SolverStatus in project vcell by virtualcell.

the class JavaSimulationExecutable method runSimulation.

private void runSimulation() throws SolverException {
    solver = SolverFactory.createSolver(new File(userDirectory), simulationTask, true);
    solver.addSolverListener(new SolverListener() {

        public final void solverAborted(SolverEvent event) {
            sendFailed(event.getSimulationMessage());
        }

        public final void solverFinished(SolverEvent event) {
            sendCompleted(event.getProgress(), event.getTimePoint(), event.getSimulationMessage());
        }

        public final void solverPrinted(SolverEvent event) {
            // can never get data messages here
            sendNewData(event.getProgress(), event.getTimePoint(), event.getSimulationMessage());
        }

        public final void solverProgress(SolverEvent event) {
            // can never get progress message here
            sendProgress(event.getProgress(), event.getTimePoint(), event.getSimulationMessage());
        }

        public final void solverStarting(SolverEvent event) {
            sendStarting(event.getSimulationMessage());
        }

        public final void solverStopped(SolverEvent event) {
            if (lg.isTraceEnabled())
                lg.trace("Caught solverStopped(" + event.getSource() + ")");
        // Don't send message anymore because the dispatcher will update the database anyway no matter if the worker responds
        // workerMessaging.sendStopped(event.getProgress(), event.getTimePoint());
        }
    });
    solver.startSolver();
    while (true) {
        try {
            Thread.sleep(500);
        } catch (InterruptedException e) {
        }
        cbit.vcell.solver.server.SolverStatus solverStatus = solver.getSolverStatus();
        if (solverStatus != null) {
            if (solverStatus.getStatus() != SolverStatus.SOLVER_STARTING && solverStatus.getStatus() != SolverStatus.SOLVER_READY && solverStatus.getStatus() != SolverStatus.SOLVER_RUNNING) {
                break;
            }
        }
    }
}