Examples with VCSimulationIdentifier cbit.vcell.solver.VCSimulationIdentifier used on opensource projects

Example 36 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class VCellClientDataServiceImpl method displayPostProcessingDataInVCell.

@Override
public void displayPostProcessingDataInVCell(SimulationDataSetRef simulationDataSetRef) throws NumberFormatException, DataAccessException {
    User vcUser = vcellClient.getRequestManager().getDocumentManager().getUser();
    VCSimulationIdentifier vcSimId = new VCSimulationIdentifier(new KeyValue(simulationDataSetRef.getSimId()), vcUser);
    ClientDocumentManager clientDocumentManager = (ClientDocumentManager) vcellClient.getClientServerManager().getDocumentManager();
    SimulationOwner simulationOwner = null;
    if (simulationDataSetRef.isMathModel) {
        simulationOwner = clientDocumentManager.getMathModel(new KeyValue(simulationDataSetRef.getModelId()));
    } else {
        BioModel bioModel = clientDocumentManager.getBioModel(new KeyValue(simulationDataSetRef.getModelId()));
        simulationOwner = bioModel.getSimulationContext(simulationDataSetRef.getSimulationContextName());
    }
    ArrayList<AnnotatedFunction> outputFunctionsList = simulationOwner.getOutputFunctionContext().getOutputFunctionsList();
    OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
    VCSimulationDataIdentifier vcSimDataId = new VCSimulationDataIdentifier(vcSimId, simulationDataSetRef.getJobIndex());
    PDEDataManager pdeDataManager = (PDEDataManager) vcellClient.getRequestManager().getDataManager(outputContext, vcSimDataId, true);
    final ClientPDEDataContext newClientPDEDataContext = pdeDataManager.getPDEDataContext();
    // this was the code before the windows refactoring; appears to just always get the first window???
    // Enumeration<TopLevelWindowManager> windowManagers = vcellClient.getMdiManager().getWindowManagers();
    // final Window window = FindWindow.getWindow(windowManagers.nextElement().getComponent());
    Optional<TopLevelWindowManager> first = vcellClient.getMdiManager().getWindowManagers().stream().findFirst();
    VCAssert.assertTrue(first.isPresent(), "window manager not present?");
    final Window window = getWindow(first.get().getComponent());
    AsynchClientTask task = new AsynchClientTask("Display Post Processing Statistics", AsynchClientTask.TASKTYPE_SWING_NONBLOCKING, false, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            DataProcessingResultsPanel dataProcessingResultsPanel = new DataProcessingResultsPanel();
            dataProcessingResultsPanel.update(newClientPDEDataContext);
            DialogUtils.showComponentOKCancelDialog(window, dataProcessingResultsPanel, "Post Processing Statistics");
        }
    };
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    Vector<AsynchClientTask> tasksV = new Vector<AsynchClientTask>();
    tasksV.add(task);
    AsynchClientTask[] tasks = new AsynchClientTask[tasksV.size()];
    tasksV.copyInto(tasks);
    ClientTaskDispatcher.dispatch(window, hash, tasks, true);
}

Example 37 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class HybridSolverTester method makeAltCSV.

private static void makeAltCSV(AltArgsHelper altArgsHelper, FileWriter fw, int runIndex, File userSimDataDir) throws Exception {
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(new KeyValue(altArgsHelper.simID), altArgsHelper.user);
    boolean bInit = runIndex == 0;
    ArrayList<Double> simTimes = new ArrayList<Double>();
    StringTokenizer st = null;
    if (altArgsHelper.times.equals("all")) {
    } else {
        st = new StringTokenizer(altArgsHelper.times, ":");
        while (st.hasMoreTokens()) {
            double timePoint = Double.parseDouble(st.nextToken());
            simTimes.add(timePoint);
        }
    }
    SimLocHelper simLocHelper0 = null;
    ArrayList<String> simVars = new ArrayList<String>();
    st = new StringTokenizer(altArgsHelper.varnames, ":");
    while (st.hasMoreTokens()) {
        String var = st.nextToken();
        simVars.add(var);
    }
    int jobCounter = 0;
    final int TIME_SPACE_EXTRA = 0;
    double[][][] trialData = null;
    while (true) {
        VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(vcSimID, jobCounter);
        SimulationData simData = null;
        DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = null;
        try {
            simData = new SimulationData(vcSimulationDataIdentifier, userSimDataDir, null, null);
            dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(vcSimulationDataIdentifier, true, null), new File(userSimDataDir, SimulationData.createCanonicalPostProcessFileName(vcSimulationDataIdentifier)));
        } catch (FileNotFoundException e) {
            if (jobCounter == 0) {
                System.out.println("found no trials matching SimID=" + altArgsHelper.simID + " in user dir " + userSimDataDir.getAbsolutePath());
            } else {
                System.out.println("found " + jobCounter + " trials in dir " + userSimDataDir.getAbsolutePath() + " matching SimID=" + altArgsHelper.simID);
            }
            break;
        } catch (Exception e) {
            e.printStackTrace();
        }
        if (dataProcessingOutputInfo == null) {
            System.out.println("No postprocessing found for " + jobCounter + " trials in dir " + userSimDataDir.getAbsolutePath() + " matching SimID=" + altArgsHelper.simID);
            jobCounter++;
            continue;
        }
        if (simLocHelper0 == null && !altArgsHelper.dataIndexes.equals(POSTPROC)) {
            simLocHelper0 = calcSimLocs(altArgsHelper.dataIndexes, simData.getMesh());
        }
        if (jobCounter == 0) {
            double[] allDatasetTimes = simData.getDataTimes();
            if (altArgsHelper.times.equals("all")) {
                for (double thisTime : allDatasetTimes) {
                    simTimes.add(thisTime);
                }
            } else {
                // Convert user input times to actual data times
                for (int times = 0; times < simTimes.size(); times++) {
                    double masterDelta = Double.POSITIVE_INFINITY;
                    double timePoint = -1;
                    for (int j = 0; j < allDatasetTimes.length; j++) {
                        double tempDelta = Math.abs(simTimes.get(times) - allDatasetTimes[j]);
                        if (tempDelta < masterDelta) {
                            masterDelta = tempDelta;
                            timePoint = allDatasetTimes[j];
                            if (tempDelta == 0) {
                                break;
                            }
                        }
                    }
                    System.out.println("User time=" + simTimes.get(times) + " converted to dataset time=" + timePoint);
                    simTimes.set(times, timePoint);
                }
            }
            trialData = new double[simTimes.size()][(simLocHelper0 == null ? 1 : simLocHelper0.boxToLocs.size())][simVars.size()];
        }
        if (bInit && jobCounter == 0) {
            // print state vars
            DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
            for (int j = 0; j < dataIdentifiers.length; j++) {
                System.out.println(dataIdentifiers[j]);
            }
            printheader(altArgsHelper, simTimes, simLocHelper0, simVars, fw, TIME_SPACE_EXTRA);
        }
        for (int times = 0; times < simTimes.size(); times++) {
            double timePoint = simTimes.get(times);
            for (int vars = 0; vars < simVars.size(); vars++) {
                double[] data = null;
                if (altArgsHelper.dataIndexes.equals(POSTPROC)) {
                    data = dataProcessingOutputInfo.getVariableStatValues().get(simVars.get(vars) + "_average");
                } else {
                    SimDataBlock simDataBlock = simData.getSimDataBlock(null, simVars.get(vars), timePoint);
                    data = simDataBlock.getData();
                }
                for (int locs = 0; locs < trialData[times].length; locs++) {
                    double val;
                    if (simLocHelper0 != null && simLocHelper0.boxToLocs.get(locs).size() == 1) {
                        // point
                        // System.out.println("pointIndex="+simLocHelper.boxToLocs.get(locs).get(0));
                        val = data[simLocHelper0.boxToLocs.get(locs).get(0)];
                    } else if (simLocHelper0 != null) {
                        // box, calculate the average, could be concentration or counts
                        double accum = 0;
                        for (Integer locIndex : simLocHelper0.boxToLocs.get(locs)) {
                            // System.out.println("boxIndex="+locIndex);
                            accum += data[locIndex];
                        }
                        val = accum / simLocHelper0.boxToLocs.get(locs).size();
                    } else {
                        // PostProcess
                        if (times < data.length) {
                            val = data[times];
                        } else {
                            val = Double.NaN;
                        }
                    }
                    trialData[times][locs][vars] = val;
                }
            }
        }
        fw.write("r=" + runIndex + " s=" + jobCounter + ",");
        for (int times = 0; times < simTimes.size(); times++) {
            for (int locs = 0; locs < trialData[times].length; locs++) {
                for (int vars = 0; vars < simVars.size(); vars++) {
                    // System.out.println("job="+jobCounter+" time="+simTimes.get(times)+" loc="+simLocHelper.boxToID.get(locs)+" var="+simVars.get(vars)+" data="+trialData[times][locs][vars]);
                    boolean isNan = Double.isNaN(trialData[times][locs][vars]);
                    fw.write((isNan ? "" : trialData[times][locs][vars]) + ",");
                }
                fw.write(",");
            }
            for (int timeSpace = 0; timeSpace < TIME_SPACE_EXTRA; timeSpace++) {
                fw.write(",");
            }
        }
        fw.write("\n");
        jobCounter++;
    }
    fw.flush();
}

Example 38 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class HybridSolverTester method runHybridTest.

public void runHybridTest(String site) {
    try {
        double[] timePoints = null;
        File mathModelFile = new File(mathModelVCMLFileName);
        XMLSource vcmlSource = new XMLSource(mathModelFile);
        MathModel mathModel = XmlHelper.XMLToMathModel(vcmlSource);
        File simDataDir = mathModelFile.getParentFile();
        Simulation sim = mathModel.getSimulations()[0];
        // run multiple trials and each run will have a simID = origSimID + i
        for (int i = 0; i < numRuns; i++) {
            System.out.println("--------------Trial No: " + (startTrialNo + i) + "----------------");
            // replace random seed
            sim.getSolverTaskDescription().getSmoldynSimulationOptions().setRandomSeed(new Integer(startTrialNo + i));
            // create sim job
            int jobIndex = startTrialNo + i;
            SimulationTask simTask = new SimulationTask(new SimulationJob(sim, jobIndex, null), 0);
            /*
				 * When you want to run the multiple trials on local uncomment the line below.
				 */
            // ResourceUtil.prepareSolverExecutable(sim.getSolverTaskDescription().getSolverDescription());
            /*
				 * When you want to run the multiple trials on server (without VCell user interface), use the next line of code 
				 * Corresponding changes should be made in the shell script runhybridtest for the location of executable on server
				 */
            FVSolverStandalone fvSolver = new FVSolverStandalone(simTask, simDataDir, false);
            fvSolver.startSolver();
            SolverStatus status = fvSolver.getSolverStatus();
            while (status.getStatus() != SolverStatus.SOLVER_FINISHED && status.getStatus() != SolverStatus.SOLVER_ABORTED) {
                System.out.println("progress: " + (int) (fvSolver.getProgress() * 100) + "%");
                // ask status every 2 seconds
                Thread.sleep(2000);
                status = fvSolver.getSolverStatus();
            }
            if (status.getStatus() == SolverStatus.SOLVER_FINISHED) {
                // get data
                VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(sim.getVersion().getVersionKey(), sim.getVersion().getOwner());
                VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
                File hdf5File = new File(simDataDir, vcSimDataID.getID() + SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
                DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(vcSimDataID, false, null), hdf5File);
                if (i == 0) {
                    // do only one time
                    timePoints = dataProcessingOutputInfo.getVariableTimePoints();
                    for (int j = 0; j < varNames.length; j++) {
                        // row: numTimePoints, col:first col time + numRuns
                        double[][] data = new double[numRuns + 1][timePoints.length];
                        data[0] = timePoints;
                        results.add(data);
                    }
                }
                // write into results after each run
                for (int j = 0; j < varNames.length; j++) {
                    results.get(j)[i + 1] = dataProcessingOutputInfo.getVariableStatValues().get(varNames[j]);
                }
                // delete the file generated for this run
                deleteSimFiles(simDataDir, vcSimDataID);
            } else {
                throw new Exception("Sover did not finish normally." + status);
            }
        }
        // write to output file, tab delimited
        if (results != null && results.size() > 0) {
            for (int j = 0; j < varNames.length; j++) {
                File file = new File(simDataDir, "SimID_" + sim.getVersion().getVersionKey().toString() + "_" + varNames[j] + "_" + startTrialNo + ".txt");
                PrintWriter pw = new PrintWriter(file);
                double[][] data = results.get(j);
                if (data != null) {
                    for (int k = 0; k < data.length; k++) {
                        if (!bPrintTime && k == 0) {
                            continue;
                        }
                        String rowStr = (k == 0) ? "Time\t" : ("trialNo_" + (startTrialNo + k - 1) + "\t");
                        double[] rowData = data[k];
                        for (int q = 0; q < rowData.length; q++) {
                            rowStr += rowData[q] + "\t";
                        }
                        pw.println(rowStr);
                    }
                }
                pw.close();
            }
        }
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 39 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier 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 40 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier 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();
        }
    }
}