Examples with SimulationData cbit.vcell.simdata.SimulationData used on opensource projects

Example 6 with SimulationData

use of cbit.vcell.simdata.SimulationData 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 7 with SimulationData

use of cbit.vcell.simdata.SimulationData 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");
}