Examples with SolverListener cbit.vcell.solver.server.SolverListener used on opensource projects

Example 1 with SolverListener

use of cbit.vcell.solver.server.SolverListener in project vcell by virtualcell.

the class SimulationServiceImpl method computeModel.

private SimulationInfo computeModel(BioModel bioModel, SimulationSpec simSpec, ClientTaskStatusSupport statusCallback) {
    try {
        SimulationContext simContext = bioModel.getSimulationContext(0);
        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(statusCallback);
        Simulation newsim = simContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX, callback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
        SimulationInfo simulationInfo = new SimulationInfo();
        simulationInfo.setId(Math.abs(new Random().nextInt(1000000)));
        // ----------- run simulation(s)
        final File localSimDataDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
        Simulation simulation = new TempSimulation(newsim, false);
        final SimulationServiceContext simServiceContext = new SimulationServiceContext();
        simServiceContext.simInfo = simulationInfo;
        simServiceContext.simState = SimulationState.running;
        simServiceContext.simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
        simServiceContext.vcDataIdentifier = simServiceContext.simTask.getSimulationJob().getVCDataIdentifier();
        simServiceContext.solver = createQuickRunSolver(localSimDataDir, simServiceContext.simTask);
        simServiceContext.localSimDataDir = localSimDataDir;
        if (simServiceContext.solver == null) {
            throw new RuntimeException("null solver");
        }
        sims.put(simulationInfo.id, simServiceContext);
        simServiceContext.solver.addSolverListener(new SolverListener() {

            public void solverStopped(SolverEvent event) {
                simServiceContext.simState = SimulationState.failed;
                System.err.println("Simulation stopped");
            }

            public void solverStarting(SolverEvent event) {
                simServiceContext.simState = SimulationState.running;
                updateStatus(event);
            }

            public void solverProgress(SolverEvent event) {
                simServiceContext.simState = SimulationState.running;
                updateStatus(event);
            }

            public void solverPrinted(SolverEvent event) {
                simServiceContext.simState = SimulationState.running;
            }

            public void solverFinished(SolverEvent event) {
                try {
                    getDataSetController(simServiceContext).getDataSetTimes(simServiceContext.vcDataIdentifier);
                    simServiceContext.simState = SimulationState.done;
                } catch (DataAccessException e) {
                    simServiceContext.simState = SimulationState.failed;
                    e.printStackTrace();
                }
                updateStatus(event);
            }

            public void solverAborted(SolverEvent event) {
                simServiceContext.simState = SimulationState.failed;
                System.err.println(event.getSimulationMessage().getDisplayMessage());
            }

            private void updateStatus(SolverEvent event) {
                if (statusCallback == null)
                    return;
                statusCallback.setMessage(event.getSimulationMessage().getDisplayMessage());
                statusCallback.setProgress((int) (event.getProgress() * 100));
            }
        });
        simServiceContext.solver.startSolver();
        return simServiceContext.simInfo;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        // remember the exceptiopn ... fail the status ... save the error message
        return new SimulationInfo().setId(1);
    }
}

Example 2 with SolverListener

use of cbit.vcell.solver.server.SolverListener 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 3 with SolverListener

use of cbit.vcell.solver.server.SolverListener in project vcell by virtualcell.

the class SimulationServiceImpl method computeModel.

private SimulationInfo computeModel(VCDocument vcDoc, SimulationSpec simSpec, ClientTaskStatusSupport statusCallback) throws Exception {
    // try {
    Simulation newsim = null;
    if (vcDoc instanceof BioModel) {
        SimulationContext simContext = ((BioModel) vcDoc).getSimulationContext(0);
        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(statusCallback);
        newsim = simContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX, callback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
    } else if (vcDoc instanceof MathModel) {
        newsim = ((MathModel) vcDoc).addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX);
    } else {
        throw new IllegalArgumentException("computeModel expecting BioModel or MathModel but got " + vcDoc.getClass().getName());
    }
    GeometrySpec geometrySpec = newsim.getMathDescription().getGeometry().getGeometrySpec();
    VCImage image = geometrySpec.getImage();
    if (image != null) {
        newsim.getMeshSpecification().setSamplingSize(new ISize(image.getNumX(), image.getNumY(), image.getNumZ()));
    }
    // newsim.getMeshSpecification().setSamplingSize(new ISize(simContext.getGeometry().getGeometrySpec().getImage().getNumX(), simContext.getGeometry().getGeometrySpec().getImage().getNumY(), simContext.getGeometry().getGeometrySpec().getImage().getNumZ()));
    newsim.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, simSpec.getTotalTime()));
    newsim.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(simSpec.getOutputTimeStep()));
    SimulationInfo simulationInfo = new SimulationInfo(Math.abs(new Random().nextInt(1000000)));
    // ----------- run simulation(s)
    final File localSimDataDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
    Simulation simulation = new TempSimulation(newsim, false);
    final SimulationServiceContext simServiceContext = new SimulationServiceContext();
    simServiceContext.simInfo = simulationInfo;
    simServiceContext.simState = SimulationState.running;
    simServiceContext.simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
    simServiceContext.vcDataIdentifier = simServiceContext.simTask.getSimulationJob().getVCDataIdentifier();
    simServiceContext.solver = createQuickRunSolver(localSimDataDir, simServiceContext.simTask);
    simServiceContext.localSimDataDir = localSimDataDir;
    if (simServiceContext.solver == null) {
        throw new RuntimeException("null solver");
    }
    sims.put(simulationInfo.getLocalId(), simServiceContext);
    simServiceContext.solver.addSolverListener(new SolverListener() {

        public void solverStopped(SolverEvent event) {
            simServiceContext.simState = SimulationState.failed;
            System.err.println("Simulation stopped");
        }

        public void solverStarting(SolverEvent event) {
            simServiceContext.simState = SimulationState.running;
            updateStatus(event);
        }

        public void solverProgress(SolverEvent event) {
            simServiceContext.simState = SimulationState.running;
            updateStatus(event);
        }

        public void solverPrinted(SolverEvent event) {
            simServiceContext.simState = SimulationState.running;
        }

        public void solverFinished(SolverEvent event) {
            try {
                getDataSetController(simServiceContext).getDataSetTimes(simServiceContext.vcDataIdentifier);
                simServiceContext.simState = SimulationState.done;
            } catch (DataAccessException e) {
                simServiceContext.simState = SimulationState.failed;
                e.printStackTrace();
            }
            updateStatus(event);
        }

        public void solverAborted(SolverEvent event) {
            simServiceContext.simState = SimulationState.failed;
            System.err.println(event.getSimulationMessage().getDisplayMessage());
        }

        private void updateStatus(SolverEvent event) {
            if (statusCallback == null)
                return;
            statusCallback.setMessage(event.getSimulationMessage().getDisplayMessage());
            statusCallback.setProgress((int) (event.getProgress() * 100));
        }
    });
    if (true) {
        // debug
        if (vcDoc instanceof BioModel) {
            XmlUtil.writeXMLStringToFile(XmlHelper.bioModelToXML(((BioModel) vcDoc)), "C:\\Users\\frm\\vcGititImageJWorkspace\\vcell\\imagej_BM_true.xml", true);
        } else if (vcDoc instanceof MathModel) {
            XmlUtil.writeXMLStringToFile(XmlHelper.mathModelToXML(((MathModel) vcDoc)), "C:\\Users\\frm\\vcGititImageJWorkspace\\vcell\\imagej_MM_true.xml", true);
        }
    }
    simServiceContext.solver.startSolver();
    return simServiceContext.simInfo;
// } catch (Exception e){
// e.printStackTrace(System.out);
// // remember the exceptiopn ... fail the status ... save the error message
// return new SimulationInfo();
// }
}

Example 4 with SolverListener

use of cbit.vcell.solver.server.SolverListener in project vcell by virtualcell.

the class AbstractSolver method fireSolverStarting.

/**
 * Method to support listener events.
 */
protected void fireSolverStarting(SimulationMessage message) {
    // Create event
    SolverEvent event = new SolverEvent(this, SolverEvent.SOLVER_STARTING, message, 0, 0, message.getHtcJobId());
    VCMongoMessage.sendSolverEvent(event);
    // Guaranteed to return a non-null array
    Object[] listeners = listenerList.getListenerList();
    // those that are interested in this event
    for (int i = listeners.length - 2; i >= 0; i -= 2) {
        if (listeners[i] == SolverListener.class) {
            ((SolverListener) listeners[i + 1]).solverStarting(event);
        }
    }
}

Example 5 with SolverListener

use of cbit.vcell.solver.server.SolverListener in project vcell by virtualcell.

the class AbstractSolver method fireSolverFinished.

/**
 * Method to support listener events.
 */
protected void fireSolverFinished() {
    // Create event
    SolverEvent event = new SolverEvent(this, SolverEvent.SOLVER_FINISHED, SimulationMessage.MESSAGE_SOLVEREVENT_FINISHED, getProgress(), getCurrentTime(), null);
    VCMongoMessage.sendSolverEvent(event);
    // Guaranteed to return a non-null array
    Object[] listeners = listenerList.getListenerList();
    // those that are interested in this event
    for (int i = listeners.length - 2; i >= 0; i -= 2) {
        if (listeners[i] == SolverListener.class) {
            ((SolverListener) listeners[i + 1]).solverFinished(event);
        }
    }
}