Examples with SimulationStatusPersistent cbit.vcell.server.SimulationStatusPersistent used on opensource projects

Example 11 with SimulationStatusPersistent

use of cbit.vcell.server.SimulationStatusPersistent in project vcell by virtualcell.

the class LocalUserMetaDbServerMessaging method getSimulationStatus.

/**
 * Insert the method's description here.
 * Creation date: (9/1/2004 11:27:01 AM)
 * @return cbit.vcell.solver.SolverResultSetInfo
 * @param simKey cbit.sql.KeyValue
 * @throws RemoteException
 */
public SimulationStatusPersistent[] getSimulationStatus(org.vcell.util.document.KeyValue[] simulationKeys) throws DataAccessException, ObjectNotFoundException {
    try {
        log.print("LocalUserMetaDbServerMessaging.getSimulationStatus(key=" + simulationKeys + ")");
        SimulationStatusPersistent[] simulationStatus = dbServerProxy.getSimulationStatus(simulationKeys);
        return simulationStatus;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 12 with SimulationStatusPersistent

use of cbit.vcell.server.SimulationStatusPersistent in project vcell by virtualcell.

the class VCComprehensiveStatistics method collectBioModelStats.

private void collectBioModelStats(long startDateInMs, long endDateInMs) throws DataAccessException {
    retrieveUsers();
    for (User user : userList) {
        if (!userConstraintList.contains(user.getName())) {
            continue;
        }
        if (!internalDeveloper.contains(user.getName())) {
            boolean bInternal = internalUsers.contains(user.getName());
            ModelStat modelStat = bioModelStats[bInternal ? 0 : 1];
            BioModelInfo[] bioModelInfos = dbServerImpl.getBioModelInfos(user, false);
            for (BioModelInfo bmi : bioModelInfos) {
                Date createDate = bmi.getVersion().getDate();
                long t = createDate.getTime();
                // }
                if (t < startDateInMs || t > endDateInMs) {
                    continue;
                }
                // modelStat.count_model ++;
                try {
                    BigString bioModelXML = dbServerImpl.getBioModelXML(user, bmi.getVersion().getVersionKey());
                    BioModel bioModel = (BioModel) waitForModel(bioModelXML, false);
                    if (bioModel == null) {
                        System.out.println("----------          Skipped BioModel " + bmi.getVersion() + "          ----------");
                        continue;
                    }
                    modelStat.count_model++;
                    for (SimulationContext simContext : bioModel.getSimulationContexts()) {
                        modelStat.count_geoDimApplications[simContext.getGeometry().getDimension()]++;
                        if (simContext.isStoch()) {
                            modelStat.count_app_stochastic++;
                        } else {
                            modelStat.count_app_deterministic++;
                        }
                    }
                    boolean bHasCompletedSim = false;
                    for (Simulation sim : bioModel.getSimulations()) {
                        SimulationStatusPersistent ss = dbServerImpl.getSimulationStatus(sim.getKey());
                        if (ss != null) {
                            for (int scan = 0; scan < sim.getScanCount(); scan++) {
                                SimulationJobStatusPersistent jobStatus = ss.getJobStatus(scan);
                                if (jobStatus != null) {
                                    if (jobStatus.getSchedulerStatus() == SchedulerStatus.COMPLETED) {
                                        bHasCompletedSim = true;
                                        long elapsed = jobStatus.getEndDate().getTime() - jobStatus.getStartDate().getTime();
                                        if (elapsed < 2 * MINUTE_IN_MS) {
                                            modelStat.runningTimeHistogram[0]++;
                                        } else if (elapsed < 5 * MINUTE_IN_MS) {
                                            modelStat.runningTimeHistogram[1]++;
                                        } else if (elapsed < 20 * MINUTE_IN_MS) {
                                            modelStat.runningTimeHistogram[2]++;
                                        } else if (elapsed < HOUR_IN_MS) {
                                            modelStat.runningTimeHistogram[3]++;
                                        } else if (elapsed < DAY_IN_MS) {
                                            modelStat.runningTimeHistogram[4]++;
                                        } else {
                                            modelStat.runningTimeHistogram[5]++;
                                        }
                                    }
                                    int dimension = sim.getMathDescription().getGeometry().getDimension();
                                    modelStat.count_geoDimSim[dimension]++;
                                    if (sim.getMathDescription().isNonSpatialStoch() || sim.getMathDescription().isSpatialStoch()) {
                                        modelStat.count_sim_stochastic++;
                                    } else {
                                        modelStat.count_sim_deterministic++;
                                    }
                                    if (dimension > 0) {
                                        if (sim.getSolverTaskDescription().getSolverDescription().isSemiImplicitPdeSolver()) {
                                            modelStat.count_semiSim++;
                                        } else {
                                            modelStat.count_fullySim++;
                                        }
                                    }
                                }
                            }
                        }
                    }
                    if (bHasCompletedSim) {
                        modelStat.count_model_simcomplete++;
                    }
                } catch (Exception e2) {
                    e2.printStackTrace(System.out);
                }
            }
        }
    }
    itemCount++;
    statOutputPW.println(itemCount + ". BioModel Statistics ");
    statOutputPW.println("====================================================");
    for (ModelStat modelStat : bioModelStats) {
        statOutputPW.println("\t" + modelStat.title);
        statOutputPW.println("========================================");
        statOutputPW.println("number of biomodels saved :\t" + modelStat.count_model);
        statOutputPW.println("number of biomodels that has at least 1 completed simulation :\t" + modelStat.count_model_simcomplete);
        statOutputPW.println();
        statOutputPW.println("Application statistics :");
        statOutputPW.println("number of application ODE :\t" + modelStat.count_geoDimApplications[0]);
        statOutputPW.println("number of application 1D :\t" + modelStat.count_geoDimApplications[1]);
        statOutputPW.println("number of application 2D :\t" + modelStat.count_geoDimApplications[2]);
        statOutputPW.println("number of application 3D :\t" + modelStat.count_geoDimApplications[3]);
        statOutputPW.println("number of application stochastic :\t" + modelStat.count_app_stochastic);
        statOutputPW.println("number of application deterministic :\t" + modelStat.count_app_deterministic);
        statOutputPW.println();
        statOutputPW.println("Simulation statistics (including all simulations (stopped, failed, completed) :");
        statOutputPW.println("number of run simulation ODE :\t" + modelStat.count_geoDimSim[0]);
        statOutputPW.println("number of run simulation 1D :\t" + modelStat.count_geoDimSim[1]);
        statOutputPW.println("number of run simulation 2D :\t" + modelStat.count_geoDimSim[2]);
        statOutputPW.println("number of run simulation 3D :\t" + modelStat.count_geoDimSim[3]);
        statOutputPW.println("number of run simulation Semi-Implicit :\t" + modelStat.count_semiSim);
        statOutputPW.println("number of run simulation Fully-Implicit :\t" + modelStat.count_fullySim);
        statOutputPW.println("number of run simulation stochastic :\t" + modelStat.count_sim_stochastic);
        statOutputPW.println("number of run simulation deterministic :\t" + modelStat.count_sim_deterministic);
        statOutputPW.println();
        statOutputPW.println("Running time histogram for completed simulations only:");
        statOutputPW.println("0 ~ 2min:\t" + modelStat.runningTimeHistogram[0]);
        statOutputPW.println("2 ~ 5min:\t" + modelStat.runningTimeHistogram[1]);
        statOutputPW.println("5 ~ 20min:\t" + modelStat.runningTimeHistogram[2]);
        statOutputPW.println("20min ~ 1hr:\t" + modelStat.runningTimeHistogram[3]);
        statOutputPW.println("1hr ~ 1day:\t" + modelStat.runningTimeHistogram[4]);
        statOutputPW.println(">1day:\t" + modelStat.runningTimeHistogram[5]);
        statOutputPW.println();
        statOutputPW.println();
        statOutputPW.flush();
    }
}

Example 13 with SimulationStatusPersistent

use of cbit.vcell.server.SimulationStatusPersistent in project vcell by virtualcell.

the class TestMissingSimData method runSim.

private static void runSim(SimIDAndJobID simIDAndJobID) throws Exception {
    if (notCompletedSimIDs.contains(simIDAndJobID.simID.toString())) {
        // System.out.println("--skipping notCompleted");
        return;
    } else if (completedSimIDs.contains(simIDAndJobID.simID.toString())) {
        System.out.println("-----unexpected sim rerun already completed once");
        return;
    }
    VCSimulationIdentifier vcSimulationIdentifier = new VCSimulationIdentifier(simIDAndJobID.simID, simIDAndJobID.user);
    UserLoginInfo userLoginInfo = new UserLoginInfo(simIDAndJobID.user.getName(), new DigestedPassword("xoxoxox"));
    // getVcellClient().getClientServerManager().getConnectionStatus()
    VCellConnection vcellConnection = userConnections.get(simIDAndJobID.user);
    try {
        if (vcellConnection != null) {
            vcellConnection.getMessageEvents();
        }
    } catch (Exception e) {
        e.printStackTrace();
        // assume disconnected
        vcellConnection = null;
    }
    if (vcellConnection == null) {
        VCellBootstrap vCellBootstrap = getVCellBootstrap("rmi-alpha.cam.uchc.edu", 40106, "VCellBootstrapServer", 12, false);
        vcellConnection = vCellBootstrap.getVCellConnection(userLoginInfo);
        userConnections.put(simIDAndJobID.user, vcellConnection);
    }
    SimulationStatusPersistent finalSimStatus = null;
    try {
        SimulationStatusPersistent simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
        System.out.println("initial status=" + simulationStatus);
        BigString simXML = vcellConnection.getUserMetaDbServer().getSimulationXML(vcSimulationIdentifier.getSimulationKey());
        Simulation sim = XmlHelper.XMLToSim(simXML.toString());
        SolverDescription solverDescription = sim.getSolverTaskDescription().getSolverDescription();
        if (solverDescription.equals(SolverDescription.StochGibson) || solverDescription.equals(SolverDescription.FiniteVolume)) {
            // These 2 solvers give too much trouble so skip
            System.out.println("--skipping solver");
            // notCompletedSimIDs.add(simIDAndJobID.simID.toString());
            return;
        }
        int scanCount = sim.getScanCount();
        vcellConnection.getSimulationController().startSimulation(vcSimulationIdentifier, scanCount);
        long startTime = System.currentTimeMillis();
        while (simulationStatus.isStopped() || simulationStatus.isCompleted() || simulationStatus.isFailed()) {
            Thread.sleep(250);
            simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
            MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
            if ((System.currentTimeMillis() - startTime) > 60000) {
                System.out.println("-----Sim finished too fast or took too long to start");
                return;
            }
        // System.out.println(simulationStatus);
        }
        SimulationStatusPersistent lastSimStatus = simulationStatus;
        while (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed()) {
            Thread.sleep(3000);
            simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
            if (!simulationStatus.toString().equals(lastSimStatus.toString())) {
                lastSimStatus = simulationStatus;
                System.out.println("running status=" + simulationStatus);
            }
            // System.out.println(simulationStatus);
            MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
        // for (int i = 0; messageEvents != null && i < messageEvents.length; i++) {
        // System.out.println(messageEvents[i]);
        // }
        }
        finalSimStatus = simulationStatus;
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        return;
    } finally {
        System.out.println("final status=" + finalSimStatus + "\n");
        if (finalSimStatus == null || !finalSimStatus.isCompleted()) {
            notCompletedSimIDs.add(simIDAndJobID.simID.toString());
        } else {
            completedSimIDs.add(simIDAndJobID.simID.toString());
        }
    }
}

Example 14 with SimulationStatusPersistent

use of cbit.vcell.server.SimulationStatusPersistent in project vcell by virtualcell.

the class TestMissingSimData method startClient.

private static void startClient(VCSimulationIdentifier vcSimulationIdentifier, UserLoginInfo userLoginInfo) throws Exception {
    ClientServerInfo clientServerInfo = ClientServerInfo.createRemoteServerInfo("vcellapi.cam.uchc.edu", 443, userLoginInfo.getUserName(), userLoginInfo.getDigestedPassword());
    VCellClient vCellClient = VCellClient.startClient(null, clientServerInfo);
    while (vCellClient.getClientServerManager() == null || vCellClient.getClientServerManager().getConnectionStatus() == null || vCellClient.getClientServerManager().getConnectionStatus().getStatus() != ConnectionStatus.CONNECTED) {
        Thread.sleep(1000);
        System.out.println("trying connect");
    }
    BigString simXML = vCellClient.getClientServerManager().getUserMetaDbServer().getSimulationXML(vcSimulationIdentifier.getSimulationKey());
    Simulation sim = XmlHelper.XMLToSim(simXML.toString());
    vCellClient.getClientServerManager().getJobManager().startSimulation(vcSimulationIdentifier, sim.getScanCount());
    SimulationStatusPersistent simulationStatus = null;
    while (true) {
        simulationStatus = vCellClient.getClientServerManager().getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
        System.out.println(simulationStatus);
        if (simulationStatus.isCompleted() || simulationStatus.isFailed()) {
            break;
        }
        Thread.sleep(1000);
    // MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
    // for (int i = 0; messageEvents != null && i < messageEvents.length; i++) {
    // System.out.println(messageEvents[i]);
    // }
    }
}

Example 15 with SimulationStatusPersistent

use of cbit.vcell.server.SimulationStatusPersistent in project vcell by virtualcell.

the class VCComprehensiveStatistics method collectMathModelStats.

private void collectMathModelStats(long startDateInMs, long endDateInMs) throws DataAccessException {
    retrieveUsers();
    List<String> internalDeveloper = Arrays.asList(VCComprehensiveStatistics.INTERNAL_DEVELOPERS);
    for (User user : userList) {
        if (!userConstraintList.contains(user.getName())) {
            continue;
        }
        if (!internalDeveloper.contains(user.getName())) {
            boolean bInternal = internalUsers.contains(user.getName());
            ModelStat modelStat = mathModelStats[bInternal ? 0 : 1];
            MathModelInfo[] mathModelInfos = dbServerImpl.getMathModelInfos(user, false);
            for (MathModelInfo mmi : mathModelInfos) {
                Date createDate = mmi.getVersion().getDate();
                long t = createDate.getTime();
                // }
                if (t < startDateInMs || t > endDateInMs) {
                    continue;
                }
                // modelStat.count_model ++;
                try {
                    BigString mathModelXML = dbServerImpl.getMathModelXML(user, mmi.getVersion().getVersionKey());
                    MathModel mathModel = (MathModel) waitForModel(mathModelXML, true);
                    if (mathModel == null) {
                        System.out.println("----------          Skipped MathModel " + mmi.getVersion() + "          ----------");
                        continue;
                    }
                    modelStat.count_model++;
                    boolean bHasCompletedSim = false;
                    for (Simulation sim : mathModel.getSimulations()) {
                        SimulationStatusPersistent ss = dbServerImpl.getSimulationStatus(sim.getKey());
                        for (int scan = 0; ss != null && scan < sim.getScanCount(); scan++) {
                            SimulationJobStatusPersistent jobStatus = ss.getJobStatus(scan);
                            if (jobStatus != null) {
                                if (jobStatus.getSchedulerStatus() == SchedulerStatus.COMPLETED) {
                                    bHasCompletedSim = true;
                                    long elapsed = jobStatus.getEndDate().getTime() - jobStatus.getStartDate().getTime();
                                    if (elapsed < 2 * MINUTE_IN_MS) {
                                        modelStat.runningTimeHistogram[0]++;
                                    } else if (elapsed < 5 * MINUTE_IN_MS) {
                                        modelStat.runningTimeHistogram[1]++;
                                    } else if (elapsed < 20 * MINUTE_IN_MS) {
                                        modelStat.runningTimeHistogram[2]++;
                                    } else if (elapsed < HOUR_IN_MS) {
                                        modelStat.runningTimeHistogram[3]++;
                                    } else if (elapsed < DAY_IN_MS) {
                                        modelStat.runningTimeHistogram[4]++;
                                    } else {
                                        modelStat.runningTimeHistogram[5]++;
                                    }
                                }
                                int dimension = sim.getMathDescription().getGeometry().getDimension();
                                modelStat.count_geoDimSim[dimension]++;
                                if (sim.getMathDescription().isNonSpatialStoch()) {
                                    modelStat.count_sim_stochastic++;
                                } else {
                                    modelStat.count_sim_deterministic++;
                                }
                                if (dimension > 0) {
                                    if (sim.getSolverTaskDescription().getSolverDescription().isSemiImplicitPdeSolver()) {
                                        modelStat.count_semiSim++;
                                    } else {
                                        modelStat.count_fullySim++;
                                    }
                                }
                            }
                        }
                    }
                    if (bHasCompletedSim) {
                        modelStat.count_model_simcomplete++;
                    }
                } catch (Exception e2) {
                    e2.printStackTrace(System.out);
                }
            }
        }
    }
    itemCount++;
    statOutputPW.println(itemCount + ". MathModel Statistics ");
    statOutputPW.println("====================================================");
    for (ModelStat modelStat : mathModelStats) {
        statOutputPW.println("\t" + modelStat.title);
        statOutputPW.println("========================================");
        statOutputPW.println("number of mathmodels saved :\t" + modelStat.count_model);
        statOutputPW.println("number of mathmodels that has at least 1 completed simulation :\t" + modelStat.count_model_simcomplete);
        statOutputPW.println();
        statOutputPW.println("Simulation statistics (including all simulations (stopped, failed, completed) :");
        statOutputPW.println("number of run simulation ODE :\t" + modelStat.count_geoDimSim[0]);
        statOutputPW.println("number of run simulation 1D :\t" + modelStat.count_geoDimSim[1]);
        statOutputPW.println("number of run simulation 2D :\t" + modelStat.count_geoDimSim[2]);
        statOutputPW.println("number of run simulation 3D :\t" + modelStat.count_geoDimSim[3]);
        statOutputPW.println("number of run simulation Semi-Implicit :\t" + modelStat.count_semiSim);
        statOutputPW.println("number of run simulation Fully-Implicit :\t" + modelStat.count_fullySim);
        statOutputPW.println("number of run simulation stochastic :\t" + modelStat.count_sim_stochastic);
        statOutputPW.println("number of run simulation deterministic :\t" + modelStat.count_sim_deterministic);
        statOutputPW.println();
        statOutputPW.println("Running time histogram for completed simulations only:");
        statOutputPW.println("0 ~ 2min:\t" + modelStat.runningTimeHistogram[0]);
        statOutputPW.println("2 ~ 5min:\t" + modelStat.runningTimeHistogram[1]);
        statOutputPW.println("5 ~ 20min:\t" + modelStat.runningTimeHistogram[2]);
        statOutputPW.println("20min ~ 1hr:\t" + modelStat.runningTimeHistogram[3]);
        statOutputPW.println("1hr ~ 1day:\t" + modelStat.runningTimeHistogram[4]);
        statOutputPW.println(">1day:\t" + modelStat.runningTimeHistogram[5]);
        statOutputPW.println();
        statOutputPW.println();
        statOutputPW.flush();
    }
}