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

Example 21 with SimulationStatus

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

the class SimulationListPanel method deleteSimulations.

/**
 * Comment
 */
private void deleteSimulations() {
    int[] selections = getScrollPaneTable().getSelectedRows();
    StringBuilder simulationNames = new StringBuilder();
    ArrayList<Simulation> simList = new ArrayList<Simulation>();
    // Simulation[] allSims = getSimulationWorkspace().getSimulations();
    for (int i = 0; i < selections.length; i++) {
        Simulation sim = (Simulation) (ivjSimulationListTableModel1.getValueAt(selections[i]));
        SimulationStatus simStatus = getSimulationWorkspace().getSimulationStatus(sim);
        if (!simStatus.isRunning()) {
            simList.add(sim);
            simulationNames.append(sim.getName() + "\n");
        }
    }
    if (simList.size() == 0) {
        return;
    }
    String confirm = DialogUtils.showOKCancelWarningDialog(this, "Deleting", "You are going to delete the following simulation(s):\n\n" + simulationNames + "\n Continue?");
    if (confirm.equals(UserMessage.OPTION_CANCEL)) {
        return;
    }
    Simulation[] toDelete = (Simulation[]) BeanUtils.getArray(simList, Simulation.class);
    try {
        getSimulationWorkspace().deleteSimulations(toDelete);
    } catch (Throwable exc) {
        exc.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(this, "Could not delete all simulations\n" + exc.getMessage(), exc);
    }
    // unset selection - may not be needed...
    getScrollPaneTable().clearSelection();
}

Example 22 with SimulationStatus

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

the class SimulationStatusDetails method getSimulationStatusDisplay.

/**
 * Comment
 */
Object getSimulationStatusDisplay(int index) {
    SimulationStatus simStatus = simWorkspace.getSimulationStatus(sim);
    if (simStatus != null) {
        SimulationJobStatus jobStatus = simStatus.getJobStatus(index);
        Double progress = simStatus.getProgressAt(index);
        if (jobStatus != null) {
            if (progress != null && jobStatus.getSchedulerStatus().isRunning() && progress.doubleValue() > 0) {
                statusBars[index].setValue((int) (progress.doubleValue() * 100));
                return statusBars[index];
            } else {
                return jobStatus.getSimulationMessage().getDisplayMessage();
            }
        } else {
            return simStatus.getDetails();
        }
    }
    return null;
}

Example 23 with SimulationStatus

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

the class CheckBeforeDelete method checkLostResults.

/**
 * Insert the method's description here.
 * Creation date: (6/1/2004 3:44:03 PM)
 * @return cbit.vcell.solver.SolverResultSetInfo[]
 * @param mathmodel cbit.vcell.mathmodel.Mathmodel
 */
private Simulation[] checkLostResults(MathModel oldMathmodel, MathModel newlySavedMathmodel, cbit.vcell.clientdb.DocumentManager documentManager, Simulation[] submittedSimulations) throws Exception {
    // 
    // before deleting old version, prompt user if old simulation results will not be availlable in new edition
    // 
    Vector<Simulation> lostResultsSimulationList = new Vector<Simulation>();
    Simulation[] oldSimulations = oldMathmodel.getSimulations();
    for (int i = 0; i < oldSimulations.length; i++) {
        Simulation oldSimulation = oldSimulations[i];
        // SolverResultSetInfo rsInfo = null;
        SimulationStatus simStatus = null;
        SimulationInfo oldSimInfo = oldSimulation.getSimulationInfo();
        if (oldSimInfo != null) {
            // 
            // we need to ask for previous sim results (here we need possible translation to ask for parent's results).
            // 
            simStatus = documentManager.getServerSimulationStatus(oldSimInfo.getAuthoritativeVCSimulationIdentifier());
        }
        if (simStatus != null && simStatus.getHasData()) {
            // 
            // results exist in old version (the Mathmodel to be deleted) for SimulationInfo "oldSimInfo"
            // Users should be warned when they are going to loose any simulation results in any unexpected way.
            // 
            // WARN if the lost data is because new simulation is not mathematically equivalent to old edition
            // (different MathDescription key)
            // 
            // IGNORE if the lost data is from edits of a Simulation only (same MathDescription)
            // (same MathDescription key, different Simulation key)
            // 
            // IGNORE if Simulation has been deleted
            // (Simulation not found in current Mathmodel)
            // 
            // IGNORE if Simulation has been submitted for running
            // 
            boolean bDataInNewEdition = false;
            Simulation[] newSimulations = newlySavedMathmodel.getSimulations();
            Simulation correspondingSimulation = null;
            for (int j = 0; j < newSimulations.length; j++) {
                if (newSimulations[j].getName().equals(oldSimulation.getName())) {
                    correspondingSimulation = newSimulations[j];
                    if (correspondingSimulation.getKey().equals(oldSimulation.getKey())) {
                        // 
                        // exactly same simulation (same key), so no lost data
                        // 
                        bDataInNewEdition = true;
                    } else if (correspondingSimulation.getSimulationVersion().getParentSimulationReference() != null) {
                        // 
                        // new simulation changed but points to same results
                        // 
                        bDataInNewEdition = true;
                    }
                    break;
                }
            }
            if (!bDataInNewEdition && correspondingSimulation != null) {
                // 
                // result set (for "rsInfo") will be lost, should we ignore this fact?
                // 
                boolean bIgnore = false;
                // 
                // ignore if only Simulation has been edited (same MathDescription)
                // 
                MathDescription mdCorr = correspondingSimulation.getMathDescription();
                MathDescription mdOld = oldSimulation.getMathDescription();
                if (mdCorr.getKey().equals(mdOld.getKey())) {
                    bIgnore = true;
                }
                // 
                for (int j = 0; submittedSimulations != null && j < submittedSimulations.length; j++) {
                    if (correspondingSimulation.getName().equals(submittedSimulations[j].getName())) {
                        bIgnore = true;
                    }
                }
                // 
                if (!bIgnore) {
                    lostResultsSimulationList.add(correspondingSimulation);
                }
            }
        }
    }
    return (Simulation[]) BeanUtils.getArray(lostResultsSimulationList, Simulation.class);
}

Example 24 with SimulationStatus

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

the class RunSims method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    ClientSimManager clientSimManager = (ClientSimManager) hashTable.get("clientSimManager");
    // DocumentManager documentManager = (DocumentManager)hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    JobManager jobManager = (JobManager) hashTable.get("jobManager");
    Simulation[] simulations = (Simulation[]) hashTable.get("simulations");
    Hashtable<Simulation, Throwable> failures = new Hashtable<Simulation, Throwable>();
    if (simulations != null && simulations.length > 0) {
        // we need to get the new ones if a save occurred...
        if (hashTable.containsKey(SaveDocument.DOC_KEY)) {
            VCDocument savedDocument = (VCDocument) hashTable.get(SaveDocument.DOC_KEY);
            Simulation[] allSims = null;
            if (savedDocument instanceof BioModel) {
                allSims = ((BioModel) savedDocument).getSimulations();
            } else if (savedDocument instanceof MathModel) {
                allSims = ((MathModel) savedDocument).getSimulations();
            }
            Vector<Simulation> v = new Vector<Simulation>();
            for (int i = 0; i < simulations.length; i++) {
                for (int j = 0; j < allSims.length; j++) {
                    if (simulations[i].getName().equals(allSims[j].getName())) {
                        v.add(allSims[j]);
                        break;
                    }
                }
            }
            simulations = (Simulation[]) BeanUtils.getArray(v, Simulation.class);
        }
        for (Simulation sim : simulations) {
            try {
                int dimension = sim.getMathDescription().getGeometry().getDimension();
                if (clientSimManager.getSimulationStatus(sim).isCompleted()) {
                    // completed
                    String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_1, sim.getName());
                    String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                    if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                        continue;
                    }
                }
                DataProcessingInstructions dataProcessingInstructions = sim.getDataProcessingInstructions();
                try {
                    if (dataProcessingInstructions != null) {
                        dataProcessingInstructions.getSampleImageFieldData(sim.getVersion().getOwner());
                    }
                } catch (Exception ex) {
                    DialogUtils.showErrorDialog(documentWindowManager.getComponent(), "Problem found in simulation '" + sim.getName() + "':\n" + ex.getMessage());
                    continue;
                }
                if (dimension > 0) {
                    MeshSpecification meshSpecification = sim.getMeshSpecification();
                    boolean bCellCentered = sim.hasCellCenteredMesh();
                    if (meshSpecification != null && !meshSpecification.isAspectRatioOK(bCellCentered)) {
                        String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_2, sim.getName(), "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (dimension < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered)));
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                    if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.Smoldyn)) {
                        if (!isSmoldynTimeStepOK(sim)) {
                            double s = smoldynTimestepVars.getSpatialResolution();
                            double dMax = smoldynTimestepVars.getMaxDiffusion();
                            double condn = (s * s) / (2.0 * dMax);
                            String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_3, Double.toString(s), Double.toString(dMax), Double.toString(condn));
                            DialogUtils.showErrorDialog(documentWindowManager.getComponent(), warningMessage);
                            continue;
                        }
                    }
                    // check the number of regions if the simulation mesh is coarser.
                    Geometry mathGeometry = sim.getMathDescription().getGeometry();
                    ISize newSize = meshSpecification.getSamplingSize();
                    ISize defaultSize = mathGeometry.getGeometrySpec().getDefaultSampledImageSize();
                    if (!sim.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
                        int defaultTotalVolumeElements = mathGeometry.getGeometrySurfaceDescription().getVolumeSampleSize().getXYZ();
                        int newTotalVolumeElements = meshSpecification.getSamplingSize().getXYZ();
                        if (defaultTotalVolumeElements > newTotalVolumeElements) {
                            // coarser
                            Geometry resampledGeometry = (Geometry) BeanUtils.cloneSerializable(mathGeometry);
                            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
                            geoSurfaceDesc.setVolumeSampleSize(newSize);
                            geoSurfaceDesc.updateAll();
                            if (mathGeometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                                mathGeometry.getGeometrySurfaceDescription().updateAll();
                            }
                            int defaultNumGeometricRegions = mathGeometry.getGeometrySurfaceDescription().getGeometricRegions().length;
                            int numGeometricRegions = geoSurfaceDesc.getGeometricRegions().length;
                            if (numGeometricRegions != defaultNumGeometricRegions) {
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_4, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), numGeometricRegions, defaultNumGeometricRegions);
                                String result = PopupGenerator.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                        if (mathGeometry.getGeometrySpec().hasImage()) {
                            // if it's an image.
                            if (defaultSize.getX() + 1 < newSize.getX() || defaultSize.getY() + 1 < newSize.getY() || defaultSize.getZ() + 1 < newSize.getZ()) {
                                // finer
                                String defaultSizeString = (defaultSize.getX() + 1) + (dimension > 1 ? " x " + (defaultSize.getY() + 1) : "") + (dimension > 2 ? " x " + (defaultSize.getZ() + 1) : "");
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_5, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), defaultSizeString, defaultSizeString);
                                String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                    }
                    boolean bGiveWarning = false;
                    for (int i = 0; i < sim.getScanCount(); i++) {
                        if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE)) {
                            SimulationJob simJob = new SimulationJob(sim, i, null);
                            if (simJob.getSimulationSymbolTable().hasTimeVaryingDiffusionOrAdvection()) {
                                bGiveWarning = true;
                                break;
                            }
                        }
                    }
                    if (bGiveWarning) {
                        String warningMessage = VCellErrorMessages.RunSims_6;
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                }
                SimulationInfo simInfo = sim.getSimulationInfo();
                if (simInfo != null) {
                    // 
                    // translate to common ancestral simulation (oldest mathematically equivalent simulation)
                    // 
                    SimulationStatus simulationStatus = jobManager.startSimulation(simInfo.getAuthoritativeVCSimulationIdentifier(), sim.getScanCount());
                    // updateStatus
                    clientSimManager.updateStatusFromStartRequest(sim, simulationStatus);
                } else {
                    // this should really not happen...
                    throw new RuntimeException(">>>>>>>>>> trying to run an unsaved simulation...");
                }
            } catch (Throwable exc) {
                exc.printStackTrace(System.out);
                failures.put(sim, exc);
            }
        }
    }
    // we deal with individual request failures here, passing down only other things (that break the whole thing down) to dispatcher
    if (!failures.isEmpty()) {
        Enumeration<Simulation> en = failures.keys();
        while (en.hasMoreElements()) {
            Simulation sim = en.nextElement();
            Throwable exc = (Throwable) failures.get(sim);
            // // updateStatus
            // SimulationStatus simulationStatus = clientSimManager.updateStatusFromStartRequest(sim, true, exc.getMessage());
            // notify user
            PopupGenerator.showErrorDialog(documentWindowManager, "Failed to start simulation'" + sim.getName() + "'\n" + exc.getMessage());
        }
    }
}

Example 25 with SimulationStatus

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

the class HealthService method runsimLoop.

private void runsimLoop() {
    try {
        Thread.sleep(SIMULATION_LOOP_START_DELAY);
    } catch (InterruptedException e1) {
    }
    UserLoginInfo userLoginInfo = new UserLoginInfo(testUserid, testPassword);
    while (true) {
        long id = simStartEvent();
        KeyValue savedBioModelKey = null;
        VCSimulationIdentifier runningSimId = null;
        try {
            RemoteProxyVCellConnectionFactory vcellConnectionFactory = new RemoteProxyVCellConnectionFactory(host, port, userLoginInfo);
            VCellConnection vcellConnection = vcellConnectionFactory.createVCellConnection();
            String vcmlString = IOUtils.toString(getClass().getResourceAsStream("/TestTemplate.vcml"));
            BioModel templateBioModel = XmlHelper.XMLToBioModel(new XMLSource(vcmlString));
            templateBioModel.clearVersion();
            String newBiomodelName = "test_" + System.currentTimeMillis();
            templateBioModel.setName(newBiomodelName);
            // remove all existing simulations from stored template model, and add new one
            while (templateBioModel.getNumSimulations() > 0) {
                templateBioModel.removeSimulation(templateBioModel.getSimulation(0));
            }
            MathMappingCallback callback = new MathMappingCallback() {

                @Override
                public void setProgressFraction(float fractionDone) {
                }

                @Override
                public void setMessage(String message) {
                }

                @Override
                public boolean isInterrupted() {
                    return false;
                }
            };
            templateBioModel.getSimulationContext(0).addNewSimulation("sim", callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
            BigString vcml = new BigString(XmlHelper.bioModelToXML(templateBioModel));
            String[] independentSims = new String[0];
            BigString savedBioModelVCML = vcellConnection.getUserMetaDbServer().saveBioModelAs(vcml, newBiomodelName, independentSims);
            BioModel savedBioModel = XmlHelper.XMLToBioModel(new XMLSource(savedBioModelVCML.toString()));
            savedBioModelKey = savedBioModel.getVersion().getVersionKey();
            Simulation sim = savedBioModel.getSimulation(0);
            VCSimulationIdentifier vcSimId = new VCSimulationIdentifier(sim.getKey(), sim.getVersion().getOwner());
            long eventTimestamp = System.currentTimeMillis();
            SimulationStatus simStatus = vcellConnection.getSimulationController().startSimulation(vcSimId, 1);
            simSubmitEvent(id, vcSimId);
            runningSimId = vcSimId;
            long startTime_MS = System.currentTimeMillis();
            while (simStatus.isActive()) {
                if ((System.currentTimeMillis() - startTime_MS) > SIMULATION_TIMEOUT) {
                    throw new RuntimeException("simulation took longer than " + SIMULATION_TIMEOUT + " to complete");
                }
                Thread.sleep(1000);
                MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
                if (messageEvents != null) {
                    for (MessageEvent event : messageEvents) {
                        if (event instanceof SimulationJobStatusEvent) {
                            SimulationJobStatusEvent jobEvent = (SimulationJobStatusEvent) event;
                            SimulationJobStatus jobStatus = jobEvent.getJobStatus();
                            VCSimulationIdentifier eventSimId = jobStatus.getVCSimulationIdentifier();
                            if (eventSimId.getOwner().equals(userLoginInfo.getUser()) && eventSimId.getSimulationKey().equals(sim.getKey())) {
                                simStatus = SimulationStatus.updateFromJobEvent(simStatus, jobEvent);
                            }
                        }
                    }
                }
            }
            runningSimId = null;
            if (!simStatus.isCompleted()) {
                throw new RuntimeException("failed: " + simStatus.getDetails());
            }
            simSuccess(id);
        } catch (Throwable e) {
            simFailed(id, e.getMessage());
        } finally {
            // cleanup
            try {
                RemoteProxyVCellConnectionFactory vcellConnectionFactory = new RemoteProxyVCellConnectionFactory(host, port, userLoginInfo);
                VCellConnection vcellConnection = vcellConnectionFactory.createVCellConnection();
                if (runningSimId != null) {
                    try {
                        vcellConnection.getSimulationController().stopSimulation(runningSimId);
                    } catch (Exception e) {
                        e.printStackTrace(System.out);
                    }
                }
                if (savedBioModelKey != null) {
                    vcellConnection.getUserMetaDbServer().deleteBioModel(savedBioModelKey);
                }
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
        try {
            Thread.sleep(SIMULATION_LOOP_SLEEP);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
    }
}