Examples with SimulationTask cbit.vcell.messaging.server.SimulationTask used on opensource projects

Example 21 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask in project vcell by virtualcell.

the class SolverPreprocessor method main.

public static void main(java.lang.String[] args) {
    if (args.length < 2) {
        System.out.print(SolverPreprocessor.class.getName() + " ");
        System.out.println(Arrays.toString(args));
        System.out.println("Missing arguments: " + SolverPreprocessor.class.getName() + " [simulationTaskFile] [userdir] <parallel dir> ");
        System.exit(1);
    }
    File parallelDirectory = null;
    if (args.length >= 3) {
        parallelDirectory = new File(args[2]);
        if (!parallelDirectory.exists()) {
            parallelDirectory.mkdirs();
        }
        if (!parallelDirectory.isDirectory() || !parallelDirectory.canWrite()) {
            throw new IllegalArgumentException(parallelDirectory.getAbsolutePath() + " is not a writeable directory");
        }
    }
    Logging.init();
    try {
        PropertyLoader.loadProperties();
        // 
        File simulationFile = new File(args[0]);
        final SimulationTask simTask = XmlHelper.XMLToSimTask(FileUtils.readFileToString(simulationFile));
        if (parallelDirectory != null) {
            // simulation task needs to be written to the "parallel directory" (a temporary directory) here (it is local to the cluster).
            FileUtils.copyFile(simulationFile, new File(parallelDirectory, simulationFile.getName()));
        }
        File userDirectory = new File(args[1]);
        final String hostName = null;
        VCMongoMessage.serviceStartup(ServiceName.solverPreprocessor, Integer.valueOf(simTask.getSimKey().toString()), args);
        // 
        // JMX registration
        // 
        MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
        mbs.registerMBean(new VCellServiceMXBeanImpl(), new ObjectName(VCellServiceMXBean.jmxObjectName));
        final HTCSolver htcSolver = new HTCSolver(simTask, userDirectory, parallelDirectory) {

            public void startSolver() {
                try {
                    super.initialize();
                } catch (Exception e) {
                    e.printStackTrace();
                    SimulationMessage simMessage = SimulationMessage.jobFailed(e.getMessage());
                    try {
                        sendFailureAndExit(this, simTask, hostName, simMessage);
                    } catch (Exception e1) {
                        e1.printStackTrace();
                    }
                }
            }

            public void stopSolver() {
            }

            public double getCurrentTime() {
                return 0;
            }

            public double getProgress() {
                return 0;
            }
        };
        SolverListener solverListener = new SolverListener() {

            public void solverStopped(SolverEvent event) {
                VCMongoMessage.sendSolverEvent(event);
                try {
                    sendFailureAndExit(htcSolver, simTask, hostName, event.getSimulationMessage());
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }

            public void solverStarting(SolverEvent event) {
                VCMongoMessage.sendSolverEvent(event);
            }

            public void solverProgress(SolverEvent event) {
                VCMongoMessage.sendSolverEvent(event);
            }

            public void solverPrinted(SolverEvent event) {
                VCMongoMessage.sendSolverEvent(event);
            }

            public void solverFinished(SolverEvent event) {
                VCMongoMessage.sendSolverEvent(event);
            }

            public void solverAborted(SolverEvent event) {
                VCMongoMessage.sendSolverEvent(event);
                try {
                    sendFailureAndExit(htcSolver, simTask, hostName, event.getSimulationMessage());
                } catch (VCMessagingException e) {
                    e.printStackTrace();
                }
            }
        };
        htcSolver.addSolverListener(solverListener);
        htcSolver.startSolver();
        VCMongoMessage.sendInfo("preprocessor done");
        exitWithCode(0);
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        exitWithCode(-1);
    }
}

Example 22 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask in project vcell by virtualcell.

the class ClientSimManager method runQuickSimulation.

public void runQuickSimulation(final Simulation originalSimulation, ViewerType viewerType) {
    Collection<AsynchClientTask> taskList = new ArrayList<AsynchClientTask>();
    final SimulationOwner simulationOwner = simWorkspace.getSimulationOwner();
    // ----------- update math if it is from biomodel (simulationContext)
    if (simulationOwner instanceof SimulationContext) {
        Collection<AsynchClientTask> ut = ClientRequestManager.updateMath(documentWindowManager.getComponent(), ((SimulationContext) simulationOwner), false, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        taskList.addAll(ut);
    }
    // ----------- run simulation(s)
    final File localSimDataDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
    AsynchClientTask runSimTask = new AsynchClientTask("running simulation", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Simulation simulation = new TempSimulation(originalSimulation, false);
            SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
            Solver solver = createQuickRunSolver(localSimDataDir, simTask);
            if (solver == null) {
                throw new RuntimeException("null solver");
            }
            // check if spatial stochastic simulation (smoldyn solver) has data processing instructions with field data - need to access server for field data, so cannot do local simulation run.
            if (solver instanceof SmoldynSolver) {
                DataProcessingInstructions dpi = simulation.getDataProcessingInstructions();
                if (dpi != null) {
                    FieldDataIdentifierSpec fdis = dpi.getSampleImageFieldData(simulation.getVersion().getOwner());
                    if (fdis != null) {
                        throw new RuntimeException("Spatial Stochastic simulation '" + simulation.getName() + "' (Smoldyn solver) with field data (in data processing instructions) cannot be run locally at this time since field data needs to be retrieved from the VCell server.");
                    }
                }
            }
            solver.addSolverListener(new SolverListener() {

                public void solverStopped(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage(event.getSimulationMessage().getDisplayMessage());
                }

                public void solverStarting(SolverEvent event) {
                    String displayMessage = event.getSimulationMessage().getDisplayMessage();
                    System.out.println(displayMessage);
                    getClientTaskStatusSupport().setMessage(displayMessage);
                    if (displayMessage.equals(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT.getDisplayMessage())) {
                        getClientTaskStatusSupport().setProgress(75);
                    } else if (displayMessage.equals(SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE.getDisplayMessage())) {
                        getClientTaskStatusSupport().setProgress(90);
                    }
                }

                public void solverProgress(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage("Running...");
                    int progress = (int) (event.getProgress() * 100);
                    getClientTaskStatusSupport().setProgress(progress);
                }

                public void solverPrinted(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage("Running...");
                }

                public void solverFinished(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage(event.getSimulationMessage().getDisplayMessage());
                }

                public void solverAborted(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage(event.getSimulationMessage().getDisplayMessage());
                }
            });
            solver.startSolver();
            while (true) {
                try {
                    Thread.sleep(500);
                } catch (InterruptedException e) {
                }
                if (getClientTaskStatusSupport().isInterrupted()) {
                    solver.stopSolver();
                    throw UserCancelException.CANCEL_GENERIC;
                }
                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;
                    }
                }
            }
            ArrayList<AnnotatedFunction> outputFunctionsList = getSimWorkspace().getSimulationOwner().getOutputFunctionContext().getOutputFunctionsList();
            OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
            Simulation[] simsArray = new Simulation[] { simulation };
            hashTable.put("outputContext", outputContext);
            hashTable.put("simsArray", simsArray);
        }
    };
    taskList.add(runSimTask);
    // --------- add tasks from showSimResults : retrieve data, display results
    AsynchClientTask[] showResultsTask = showSimulationResults0(true, viewerType);
    for (AsynchClientTask task : showResultsTask) {
        taskList.add(task);
    }
    // ------- dispatch
    AsynchClientTask[] taskArray = new AsynchClientTask[taskList.size()];
    taskList.toArray(taskArray);
    ClientTaskDispatcher.dispatch(documentWindowManager.getComponent(), new Hashtable<String, Object>(), taskArray, true, true, null);
}

Example 23 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask in project vcell by virtualcell.

the class VCellClientDataServiceImpl method getSimsFromOpenModels.

@Override
public List<SimulationDataSetRef> getSimsFromOpenModels() {
    ArrayList<SimulationDataSetRef> simulationDataSetRefs = new ArrayList<SimulationDataSetRef>();
    for (TopLevelWindowManager windowManager : vcellClient.getMdiManager().getWindowManagers()) {
        Simulation[] simulations = null;
        VCDocument modelDocument = null;
        if (windowManager instanceof BioModelWindowManager) {
            BioModelWindowManager selectedBioWindowManager = (BioModelWindowManager) windowManager;
            BioModel bioModel = selectedBioWindowManager.getBioModel();
            simulations = bioModel.getSimulations();
            modelDocument = bioModel;
        // simOwnerCount = bioModel.getNumSimulationContexts();
        } else if (windowManager instanceof MathModelWindowManager) {
            MathModelWindowManager selectedMathWindowManager = (MathModelWindowManager) windowManager;
            MathModel mathModel = selectedMathWindowManager.getMathModel();
            simulations = mathModel.getSimulations();
            modelDocument = mathModel;
        // simOwnerCount = 1;
        }
        if (simulations != null) {
            for (Simulation simulation : simulations) {
                if (!isVtkSupported(simulation)) {
                    continue;
                }
                Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
                Extent extent = simulation.getMathDescription().getGeometry().getExtent();
                SimulationInfo simInfo = simulation.getSimulationInfo();
                SimulationStatus simStatus = vcellClient.getRequestManager().getServerSimulationStatus(simInfo);
                for (int jobIndex = 0; jobIndex < simulation.getScanCount(); jobIndex++) {
                    if (simStatus != null && simStatus.getHasData()) {
                        SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simulation, modelDocument, jobIndex, false);
                        simulationDataSetRefs.add(simulationDataSetReference);
                    }
                }
            }
        }
    }
    File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
    String[] simtaskFilenames = localSimDir.list((dir, name) -> (name.endsWith(".simtask.xml")));
    for (String simtaskFilename : simtaskFilenames) {
        try {
            SimulationTask simTask = XmlHelper.XMLToSimTask(org.apache.commons.io.FileUtils.readFileToString(new File(localSimDir, simtaskFilename)));
            VCDocument modelDocument = null;
            SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simTask.getSimulation(), modelDocument, simTask.getSimulationJob().getJobIndex(), true);
            simulationDataSetRefs.add(simulationDataSetReference);
        } catch (ExpressionException | XmlParseException | IOException e) {
            e.printStackTrace();
        }
    }
    return simulationDataSetRefs;
}

Example 24 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask in project vcell by virtualcell.

the class LocalSolverController method solverAborted.

/**
 * Invoked when the solver aborts a calculation (abnormal termination).
 * @param event indicates the solver and the event type
 */
public void solverAborted(SolverEvent event) {
    try {
        if (lg.isTraceEnabled())
            lg.trace("LocalSolverController Caught solverAborted(" + event.getSource().toString() + ",error='" + event.getSimulationMessage() + "')");
        SimulationJob simJob = getSimulationTask().getSimulationJob();
        if (serialParameterScanJobIndex >= 0) {
            SimulationTask newSimTask = new SimulationTask(new SimulationJob(simJob.getSimulation(), serialParameterScanJobIndex, simJob.getFieldDataIdentifierSpecs()), getSimulationTask().getTaskID());
            fireWorkerEvent(new WorkerEvent(WorkerEvent.JOB_FAILURE, this, newSimTask, hostname, event.getSimulationMessage()));
        } else {
            fireWorkerEvent(new WorkerEvent(WorkerEvent.JOB_FAILURE, this, getSimulationTask(), hostname, event.getSimulationMessage()));
        }
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
    }
}

Example 25 with SimulationTask

use of cbit.vcell.messaging.server.SimulationTask in project vcell by virtualcell.

the class OptXmlWriter method getModelXML.

public static Element getModelXML(PdeObjectiveFunction pdeObjectiveFunction, String[] parameterNames) {
    Element modelElement = new Element(OptXmlTags.Model_Tag);
    try {
        SpatialReferenceData refData = pdeObjectiveFunction.getReferenceData();
        double refDataEndTime = refData.getDataByRow(refData.getNumDataRows() - 1)[0];
        // 
        // post the problem either as an IDA or CVODE model
        // 
        org.vcell.util.document.SimulationVersion simVersion = new org.vcell.util.document.SimulationVersion(new KeyValue("12345"), "name", new org.vcell.util.document.User("user", new KeyValue("123")), new org.vcell.util.document.GroupAccessNone(), // versionBranchPointRef
        null, // branchID
        new java.math.BigDecimal(1.0), new java.util.Date(), org.vcell.util.document.VersionFlag.Archived, "", null);
        Simulation simulation = new Simulation(simVersion, pdeObjectiveFunction.getMathDescription());
        simulation.getMeshSpecification().setSamplingSize(refData.getDataISize());
        double[] times = refData.getDataByColumn(0);
        double minDt = Double.POSITIVE_INFINITY;
        for (int i = 1; i < times.length; i++) {
            minDt = Math.min(minDt, times[i] - times[i - 1]);
        }
        simulation.getSolverTaskDescription().setTimeBounds(new cbit.vcell.solver.TimeBounds(0.0, refDataEndTime));
        simulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolume);
        simulation.getSolverTaskDescription().setTimeStep(new TimeStep(minDt / 5, minDt / 5, minDt / 5));
        // clone and resample geometry
        Geometry resampledGeometry = null;
        try {
            resampledGeometry = (Geometry) BeanUtils.cloneSerializable(simulation.getMathDescription().getGeometry());
            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
            ISize newSize = simulation.getMeshSpecification().getSamplingSize();
            geoSurfaceDesc.setVolumeSampleSize(newSize);
            geoSurfaceDesc.updateAll();
        } catch (Exception e) {
            e.printStackTrace();
            throw new SolverException(e.getMessage());
        }
        SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, pdeObjectiveFunction.getFieldDataIDSs()), 0);
        StringWriter simulationInputStringWriter = new StringWriter();
        FiniteVolumeFileWriter fvFileWriter = new FiniteVolumeFileWriter(new PrintWriter(simulationInputStringWriter, true), simTask, resampledGeometry, pdeObjectiveFunction.getWorkingDirectory());
        fvFileWriter.write(parameterNames);
        simulationInputStringWriter.close();
        modelElement.setAttribute(OptXmlTags.ModelType_Attr, OptXmlTags.ModelType_Attr_FVSOLVER);
        CDATA simulationInputText = new CDATA(simulationInputStringWriter.getBuffer().toString());
        modelElement.addContent(simulationInputText);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new OptimizationException("failed to create fv input file: " + e.getMessage());
    }
    return modelElement;
}