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

Example 11 with SolverStatus

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

the class RunRefSimulationFastOp method runFVSolverStandalone.

private void runFVSolverStandalone(File simulationDataDir, Simulation sim, ExternalDataIdentifier initialConditionExtDataID, 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(initialConditionExtDataID.getName())) {
            fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], initialConditionExtDataID);
        } 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());
    }
    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 12 with SolverStatus

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

the class RunRefSimulationOp method runFVSolverStandalone.

private static void runFVSolverStandalone(File simulationDataDir, Simulation sim, ExternalDataIdentifier initialConditionExtDataID, 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(initialConditionExtDataID.getName())) {
            fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], initialConditionExtDataID);
        } 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());
    }
    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 13 with SolverStatus

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

the class RunFakeSimOp 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 14 with SolverStatus

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

the class StochtestRunService method runsolver.

private static void runsolver(Simulation newSimulation, File baseDirectory, int numRuns, TimeSeriesMultitrialData timeSeriesMultitrialData) {
    Simulation versSimulation = null;
    File destDir = null;
    boolean bTimeout = false;
    // int progress = 1;
    for (int trialIndex = 0; trialIndex < numRuns; trialIndex++) {
        System.out.println("\n=====================================\n\nStarting trial " + (trialIndex + 1) + " of " + numRuns + "\n\n==============================\n");
        long startTime = System.currentTimeMillis();
        // }
        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();
                }
                if (System.currentTimeMillis() - startTime > 30 * 1000) {
                    // timeout after 30 seconds .. otherwise multiple runs will take forever
                    bTimeout = true;
                    solver.stopSolver();
                    throw new RuntimeException("timed out");
                }
                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());
            if (bTimeout) {
                throw new RuntimeException("timed out");
            } else {
                throw new RuntimeException("solver failed : " + e.getMessage(), e);
            }
        }
        try {
            Thread.sleep(100);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
        StochtestFileUtils.clearDir(destDir);
    }
// printout("\n");
}

Example 15 with SolverStatus

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

the class SimulationControllerImpl method getSolverStatus.

/**
 * This method was created by a SmartGuide.
 * @return java.lang.String
 * @exception java.rmi.RemoteException The exception description.
 */
public SolverStatus getSolverStatus(SimulationInfo simulationInfo, int jobIndex, int taskID) throws PermissionException, DataAccessException {
    SimulationTaskID simTaskInfo = new SimulationTaskID(simulationInfo, jobIndex, taskID);
    LocalSolverController solverController = solverControllerHash.get(simTaskInfo);
    if (solverController == null) {
        return new SolverStatus(SolverStatus.SOLVER_READY, SimulationMessage.MESSAGE_SOLVER_READY);
    }
    return solverController.getSolverStatus();
}