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Example 1 with SlurmProxy

use of cbit.vcell.message.server.htc.slurm.SlurmProxy in project vcell by virtualcell.

the class VCellServices method main.

/**
 * Starts the application.
 * @param args an array of command-line arguments
 */
public static void main(java.lang.String[] args) {
    OperatingSystemInfo.getInstance();
    if (args.length != 3 && args.length != 0) {
        System.out.println("Missing arguments: " + VCellServices.class.getName() + " [sshHost sshUser sshKeyFile] ");
        System.exit(1);
    }
    try {
        PropertyLoader.loadProperties(REQUIRED_SERVICE_PROPERTIES);
        ResourceUtil.setNativeLibraryDirectory();
        new LibraryLoaderThread(false).start();
        PythonSupport.verifyInstallation(new PythonPackage[] { PythonPackage.VTK, PythonPackage.THRIFT });
        CommandService commandService = null;
        if (args.length == 3) {
            String sshHost = args[0];
            String sshUser = args[1];
            File sshKeyFile = new File(args[2]);
            try {
                commandService = new CommandServiceSshNative(sshHost, sshUser, sshKeyFile);
                commandService.command(new String[] { "/usr/bin/env bash -c ls | head -5" });
                lg.trace("SSH Connection test passed with installed keyfile, running ls as user " + sshUser + " on " + sshHost);
            } catch (Exception e) {
                e.printStackTrace();
                try {
                    commandService = new CommandServiceSshNative(sshHost, sshUser, sshKeyFile, new File("/root"));
                    commandService.command(new String[] { "/usr/bin/env bash -c ls | head -5" });
                    lg.trace("SSH Connection test passed after installing keyfile, running ls as user " + sshUser + " on " + sshHost);
                } catch (Exception e2) {
                    e.printStackTrace();
                    throw new RuntimeException("failed to establish an ssh command connection to " + sshHost + " as user '" + sshUser + "' using key '" + sshKeyFile + "'", e);
                }
            }
            // can't make user directories, they are remote.
            AbstractSolver.bMakeUserDirs = false;
        } else {
            commandService = new CommandServiceLocal();
        }
        BatchSystemType batchSystemType = BatchSystemType.SLURM;
        HtcProxy htcProxy = null;
        switch(batchSystemType) {
            case SLURM:
                {
                    htcProxy = new SlurmProxy(commandService, PropertyLoader.getRequiredProperty(PropertyLoader.htcUser));
                    break;
                }
            default:
                {
                    throw new RuntimeException("unrecognized batch scheduling option :" + batchSystemType);
                }
        }
        int serviceOrdinal = 0;
        VCMongoMessage.serviceStartup(ServiceName.dispatch, new Integer(serviceOrdinal), args);
        // //
        // // JMX registration
        // //
        // MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
        // mbs.registerMBean(new VCellServiceMXBeanImpl(), new ObjectName(VCellServiceMXBean.jmxObjectName));
        ServiceInstanceStatus serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.MASTER, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
        ConnectionFactory conFactory = DatabaseService.getInstance().createConnectionFactory();
        KeyFactory keyFactory = conFactory.getKeyFactory();
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(conFactory, keyFactory);
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(conFactory);
        SimulationDatabase simulationDatabase = new SimulationDatabaseDirect(adminDbTopLevel, databaseServerImpl, true);
        Cachetable cacheTable = new Cachetable(MessageConstants.MINUTE_IN_MS * 20);
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty))));
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        // add dataJobListener
        DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
        VCMessagingService vcMessagingService = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        vcMessagingService.setDelegate(new ServerMessagingDelegate());
        VCellServices vcellServices = new VCellServices(htcProxy, vcMessagingService, serviceInstanceStatus, databaseServerImpl, dataServerImpl, simulationDatabase);
        dataSetControllerImpl.addDataJobListener(vcellServices);
        exportServiceImpl.addExportListener(vcellServices);
        vcellServices.init();
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
}
Also used : Cachetable(cbit.vcell.simdata.Cachetable) DataServerImpl(cbit.vcell.simdata.DataServerImpl) ServerMessagingDelegate(cbit.vcell.message.server.ServerMessagingDelegate) HtcProxy(cbit.vcell.message.server.htc.HtcProxy) CommandService(cbit.vcell.message.server.cmd.CommandService) VCMessagingService(cbit.vcell.message.VCMessagingService) ConnectionFactory(org.vcell.db.ConnectionFactory) SimulationDatabaseDirect(cbit.vcell.message.server.dispatcher.SimulationDatabaseDirect) CommandServiceLocal(cbit.vcell.message.server.cmd.CommandServiceLocal) ServiceInstanceStatus(cbit.vcell.message.server.ServiceInstanceStatus) DatabaseServerImpl(cbit.vcell.modeldb.DatabaseServerImpl) ExportServiceImpl(cbit.vcell.export.server.ExportServiceImpl) KeyFactory(org.vcell.db.KeyFactory) AdminDBTopLevel(cbit.vcell.modeldb.AdminDBTopLevel) SimulationDatabase(cbit.vcell.message.server.dispatcher.SimulationDatabase) LibraryLoaderThread(cbit.vcell.resource.LibraryLoaderThread) SlurmProxy(cbit.vcell.message.server.htc.slurm.SlurmProxy) VCMessagingException(cbit.vcell.message.VCMessagingException) Date(java.util.Date) DataSetControllerImpl(cbit.vcell.simdata.DataSetControllerImpl) BatchSystemType(cbit.vcell.server.HtcJobID.BatchSystemType) File(java.io.File) CommandServiceSshNative(cbit.vcell.message.server.cmd.CommandServiceSshNative)

Aggregations

ExportServiceImpl (cbit.vcell.export.server.ExportServiceImpl)1 VCMessagingException (cbit.vcell.message.VCMessagingException)1 VCMessagingService (cbit.vcell.message.VCMessagingService)1 ServerMessagingDelegate (cbit.vcell.message.server.ServerMessagingDelegate)1 ServiceInstanceStatus (cbit.vcell.message.server.ServiceInstanceStatus)1 CommandService (cbit.vcell.message.server.cmd.CommandService)1 CommandServiceLocal (cbit.vcell.message.server.cmd.CommandServiceLocal)1 CommandServiceSshNative (cbit.vcell.message.server.cmd.CommandServiceSshNative)1 SimulationDatabase (cbit.vcell.message.server.dispatcher.SimulationDatabase)1 SimulationDatabaseDirect (cbit.vcell.message.server.dispatcher.SimulationDatabaseDirect)1 HtcProxy (cbit.vcell.message.server.htc.HtcProxy)1 SlurmProxy (cbit.vcell.message.server.htc.slurm.SlurmProxy)1 AdminDBTopLevel (cbit.vcell.modeldb.AdminDBTopLevel)1 DatabaseServerImpl (cbit.vcell.modeldb.DatabaseServerImpl)1 LibraryLoaderThread (cbit.vcell.resource.LibraryLoaderThread)1 BatchSystemType (cbit.vcell.server.HtcJobID.BatchSystemType)1 Cachetable (cbit.vcell.simdata.Cachetable)1 DataServerImpl (cbit.vcell.simdata.DataServerImpl)1 DataSetControllerImpl (cbit.vcell.simdata.DataSetControllerImpl)1 File (java.io.File)1