rms/org.eclipse.ptp.rm.smoa.core/src/org/eclipse/ptp/rm/smoa/core/rmsystem/SMOAResourceManagerMonitor.java - ptp/org.eclipse.ptp - Git at Google

 /*******************************************************************************
  * Copyright (c) 2010 Poznan Supercomputing and Networking Center
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
  * http://www.eclipse.org/legal/epl-v10.html
  *
  * Contributors:
  *     Jan Konczak (PSNC) - initial implementation
  ******************************************************************************/

 package org.eclipse.ptp.rm.smoa.core.rmsystem;

 import java.io.DataOutputStream;
 import java.io.IOException;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;

 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.ptp.core.attributes.ArrayAttribute;
 import org.eclipse.ptp.core.attributes.AttributeManager;
 import org.eclipse.ptp.core.attributes.BooleanAttribute;
 import org.eclipse.ptp.core.attributes.IntegerAttribute;
 import org.eclipse.ptp.core.attributes.StringAttribute;
 import org.eclipse.ptp.core.elements.IPJob;
 import org.eclipse.ptp.core.elements.attributes.ElementAttributes;
 import org.eclipse.ptp.core.elements.attributes.JobAttributes;
 import org.eclipse.ptp.remote.core.IRemoteConnection;
 import org.eclipse.ptp.remote.core.PTPRemoteCorePlugin;
 import org.eclipse.ptp.remote.core.exception.RemoteConnectionException;
 import org.eclipse.ptp.rm.smoa.core.SMOAConfiguration;
 import org.eclipse.ptp.rm.smoa.core.attrib.SMOAJobAttributes;
 import org.eclipse.ptp.rm.smoa.core.attrib.StringMapAttribute;
 import org.eclipse.ptp.rm.smoa.core.rservices.SMOAConnection;
 import org.eclipse.ptp.rm.smoa.core.rservices.SMOARemoteServices;
 import org.eclipse.ptp.rm.smoa.core.rtsystem.SMOARuntimeSystem;
 import org.eclipse.ptp.rm.smoa.core.util.NotifyShell;
 import org.eclipse.ptp.rtsystem.AbstractRuntimeResourceManagerMonitor;
 import org.eclipse.ptp.rtsystem.IRuntimeSystem;

 import com.smoa.comp.sdk.SMOAFactory;
 import com.smoa.comp.sdk.exceptions.InvalidRequestMessageException;
 import com.smoa.comp.sdk.exceptions.NotAuthorizedException;
 import com.smoa.comp.sdk.exceptions.UnsupportedFeatureException;
 import com.smoa.comp.sdk.jsdl.JSDL;
 import com.smoa.comp.sdk.types.ActivityEndpointReference;
 import com.smoa.comp.stubs.factory.ApplicationsType.Application;

 public class SMOAResourceManagerMonitor extends AbstractRuntimeResourceManagerMonitor {

 	/**
 	 * Extracts from the {@link AttributeManager} proper executable name and
 	 * arguments
 	 *
 	 * Returns the list containing program path and executable (as first
 	 * element) and all arguments (as next arguments)
 	 */
 	private static List<String> getExecAndArgs(AttributeManager attrs, IRemoteConnection conn, Application app) {
 		final List<String> result = new Vector<String>();

 		final BooleanAttribute debug = attrs.getAttribute(JobAttributes.getDebugFlagAttributeDefinition());

 		// // // // // // // //
 		// // // debug // // //

 		if (debug != null && debug.getValue() == true) {
 			String execPath = attrs.getAttribute(JobAttributes.getDebuggerExecutablePathAttributeDefinition()).getValue();

 			if (execPath == null || execPath.isEmpty()) {
 				execPath = "."; //$NON-NLS-1$
 			}

 			final String execName = attrs.getAttribute(JobAttributes.getDebuggerExecutableNameAttributeDefinition()).getValue();

 			final String execPathAndName = execPath + "/" + execName; //$NON-NLS-1$

 			result.add(execPathAndName);

 			/* Arguments */

 			final List<String> appArguments = attrs.getAttribute(JobAttributes.getDebuggerArgumentsAttributeDefinition())
 					.getValue();

 			if (conn.supportsTCPPortForwarding()) {
 				final Pattern portRegex = Pattern.compile("^--port=(\\d+)$"); //$NON-NLS-1$
 				final Pattern hostRegex = Pattern.compile("^--host=(.+)$"); //$NON-NLS-1$

 				Integer port = null;
 				String host = null;

 				for (final String arg : appArguments) {
 					Matcher m = portRegex.matcher(arg);
 					if (m.matches()) {
 						port = Integer.parseInt(m.group(1));
 					}
 					m = hostRegex.matcher(arg);
 					if (m.matches()) {
 						host = m.group(1);
 					}
 				}
 				if (port != null && host != null) {
 					try {
 						conn.forwardRemotePort(port, host, port);
 					} catch (final RemoteConnectionException e) {
 						NotifyShell.open(Messages.SMOAResourceManager_PortForwardingFailed_title,
 								Messages.SMOAResourceManager_PortForwardingFailed_text + e.getLocalizedMessage());
 					}
 				}
 			}

 			result.addAll(appArguments);

 			final String appString = attrs.getAttribute(SMOAJobAttributes.getAppNameDef()).getValue();
 			if (SMOAJobAttributes.NO_WRAPPER_SCRIPT.equals(appString) || app == null) {
 				result.add("--server=0"); //$NON-NLS-1$
 			}
 		}

 		// // // // // // // //
 		// // / / run / / // //
 		else {
 			String execPath = attrs.getAttribute(JobAttributes.getExecutablePathAttributeDefinition()).getValue();

 			if (execPath == null || execPath.isEmpty()) {
 				execPath = "."; //$NON-NLS-1$
 			}

 			final String execName = attrs.getAttribute(JobAttributes.getExecutableNameAttributeDefinition()).getValue();

 			final String execPathAndName = execPath + "/" + execName; //$NON-NLS-1$

 			result.add(execPathAndName);

 			/* Arguments */

 			final List<String> appArguments = attrs.getAttribute(JobAttributes.getProgramArgumentsAttributeDefinition()).getValue();
 			result.addAll(appArguments);
 		}

 		return result;
 	}

 	/** Current configuration of this RM */
 	/* package access */SMOAConfiguration configuration;

 	/** Assigns sequential run number for each configuration */
 	private final Map<String, Integer> executeCount = new HashMap<String, Integer>();

 	public SMOAResourceManagerMonitor(SMOAResourceManagerConfiguration config) {
 		super(config);
 		configuration = config;
 	}

 	/**
 	 * Creates script if the user selected an application only.
 	 *
 	 * @param args
 	 *            - user arguments
 	 * @param app
 	 *            - user application
 	 * @param out
 	 *            - file name for stdout
 	 * @param err
 	 *            - file name for stderr
 	 * @param os
 	 *            - output stream for the script
 	 * @param make
 	 *            - if the user wants us to run 'make'
 	 * @param customMakeCommand
 	 *            - non-null if user wants to use custom run command
 	 */
 	private void createScript(List<String> args, String app, String out, String err, DataOutputStream os, boolean make,
 			String customMakeCommand) throws IOException {
 		os.writeBytes("rm -f " + out + " " + err + "\n"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$

 		final StringBuilder redirect = new StringBuilder();
 		redirect.append(" >> "); //$NON-NLS-1$
 		redirect.append(out);
 		redirect.append(" 2>> "); //$NON-NLS-1$
 		redirect.append(err);

 		if (make) {
 			os.writeBytes("echo $(date)   Running make >> " + err + "\n"); //$NON-NLS-1$ //$NON-NLS-2$
 			os.writeBytes("{ "); //$NON-NLS-1$
 			if (customMakeCommand != null) {
 				os.writeBytes(customMakeCommand);
 			} else {
 				os.writeBytes("make clean && make"); //$NON-NLS-1$
 			}
 			os.writeBytes(" ; } "); //$NON-NLS-1$
 			os.writeBytes(redirect.toString());
 			os.writeBytes("\n"); //$NON-NLS-1$
 			os.writeBytes("MAKEOUT=$?\n"); //$NON-NLS-1$
 			os.writeBytes("if [ ${MAKEOUT} -ne 0 ]\n"); //$NON-NLS-1$
 			os.writeBytes("then\n"); //$NON-NLS-1$
 			os.writeBytes("  echo $(date)   Make failed! Quitting. >> " + err //$NON-NLS-1$
 					+ "\n"); //$NON-NLS-1$
 			os.writeBytes("  exit ${MAKEOUT}\n"); //$NON-NLS-1$
 			os.writeBytes("fi\n"); //$NON-NLS-1$
 		}

 		os.writeBytes("STDBUF=$(which stdbuf)\n"); //$NON-NLS-1$
 		os.writeBytes("if [ \"${STDBUF}\" ]\n"); //$NON-NLS-1$
 		os.writeBytes("then\n"); //$NON-NLS-1$
 		os.writeBytes("  STDBUF=\"${STDBUF} -oL -eL \"\n"); //$NON-NLS-1$
 		os.writeBytes("fi\n"); //$NON-NLS-1$
 		os.writeBytes("echo $(date)   Starting task >> " + err + "\n"); //$NON-NLS-1$ //$NON-NLS-2$
 		os.writeBytes("{ time ${STDBUF}"); //$NON-NLS-1$

 		// app
 		os.writeBytes(app);

 		// arguments
 		for (final String arg : args) {
 			os.write(' ');
 			os.writeBytes(arg);
 		}

 		os.writeBytes(" ; }"); //$NON-NLS-1$

 		os.writeBytes(redirect.toString());
 		os.write('\n');

 		os.writeBytes("OUT=$?\n"); //$NON-NLS-1$
 		os.writeBytes("echo $(date)   Finished! >> " + err + "\n"); //$NON-NLS-1$ //$NON-NLS-2$
 		os.writeBytes("exit ${OUT}\n"); //$NON-NLS-1$

 	}

 	/**
 	 * In case the submission failed, we set the job state and forward error
 	 */
 	private IPJob jobControlFromJobException(Exception e, String jobId, AttributeManager attrs) {
 		final String subId = attrs.getAttribute(JobAttributes.getSubIdAttributeDefinition()).getValue();

 		attrs.addAttribute(PoolingIntervalsAndStatic.exceptionAttrDef.create(e.getLocalizedMessage()));
 		attrs.addAttribute(JobAttributes.getStateAttributeDefinition().create(JobAttributes.State.COMPLETED));
 		attrs.addAttribute(JobAttributes.getStatusAttributeDefinition().create(Messages.SMOAResourceManager_JobSubmissionFailed));

 		getRuntimeSystem().addJobSubmissionError(subId, e);

 		final IPJob newJob = super.doCreateJob(jobId, attrs);
 		return newJob;
 	}

 	/**
 	 * Adds the SMOA UUID of the activity to job properties
 	 */
 	private void setSmoaUid(String smoaUid, IPJob newJob) {
 		final AttributeManager am = new AttributeManager();

 		final Collection<IPJob> jc = new Vector<IPJob>();
 		jc.add(newJob);

 		am.addAttribute(SMOAJobAttributes.getSmoaUuidDef().create(smoaUid));

 		doUpdateJobs(jc, am);
 	}

 	/**
 	 * Triggered by fireCreateJobEvent by {@link SMOARuntimeSystem}, creates the
 	 * job and submits it to the SMOA Computing service.
 	 */
 	@Override
 	protected IPJob doCreateJob(String jobId, AttributeManager attrs) {

 		// all temporary files are timestamped with the time generated below:
 		final long time = System.currentTimeMillis();

 		final SMOAConnection connection = configuration.getConnection();
 		final SMOAFactory factory = connection.getFactory();

 		final String originalName = attrs.getAttribute(ElementAttributes.getNameAttributeDefinition()).getValueAsString();

 		// Name for SMOA Computing
 		final JSDL jsdl = new JSDL(originalName);
 		final List<String> arguments = jsdl.getArguments();

 		Integer count = executeCount.get(originalName);
 		if (count == null) {
 			executeCount.put(originalName, 0);
 			count = 0;
 		}

 		// Label for Eclipse
 		attrs.addAttribute(ElementAttributes.getNameAttributeDefinition().create(originalName + " (" + count + ")")); //$NON-NLS-1$ //$NON-NLS-2$

 		executeCount.put(originalName, ++count);

 		// Working directory
 		final String workDir = attrs.getAttribute(JobAttributes.getWorkingDirectoryAttributeDefinition()).getValue();
 		if (workDir != null) {
 			jsdl.setWorkingDirectory(workDir);
 		}

 		// Setting program
 		final SMOARemoteServices remoteServices = (SMOARemoteServices) PTPRemoteCorePlugin.getDefault().getRemoteServices(
 				configuration.getRemoteServicesId());

 		final String appString = attrs.getAttribute(SMOAJobAttributes.getAppNameDef()).getValue();
 		final Application app = configuration.getAppForName(appString);

 		final List<String> execArgsAndPath = getExecAndArgs(attrs, connection, app);

 		final String execPathAndName = execArgsAndPath.get(0);
 		final List<String> appArguments = execArgsAndPath.subList(1, execArgsAndPath.size());

 		jsdl.setOutput("stdout"); //$NON-NLS-1$
 		jsdl.setError("stderr"); //$NON-NLS-1$

 		// filenames for out and err, and filename for shell script to be
 		// executed or for the machine file
 		final String out = connection.getHomeDir() + "/.ptp_smoa_out_" + time; //$NON-NLS-1$
 		final String err = connection.getHomeDir() + "/.ptp_smoa_err_" + time; //$NON-NLS-1$
 		String machinefile = null;
 		String sh = null;

 		// Custom Make command
 		String customMakeCommand = null;

 		final BooleanAttribute ifCustomMake = attrs.getAttribute(SMOAJobAttributes.getIfCustomMakeDef());
 		if (ifCustomMake != null && ifCustomMake.getValue() != null && ifCustomMake.getValue()) {
 			final StringAttribute makeCommand = attrs.getAttribute(SMOAJobAttributes.getCustomMakeCommandDef());
 			if (makeCommand != null && makeCommand.getValue() != null && !makeCommand.getValue().isEmpty()) {
 				customMakeCommand = makeCommand.getValue();
 			}
 		}

 		// If wrapper script has to be used
 		if (SMOAJobAttributes.NO_WRAPPER_SCRIPT.equals(appString) || app == null) {

 			sh = connection.getHomeDir() + "/.ptp_smoa_sh_" + time; //$NON-NLS-1$

 			final BooleanAttribute makeAttr = attrs.getAttribute(SMOAJobAttributes.getMakeDef());
 			final boolean make = (makeAttr == null ? false : makeAttr.getValue());

 			// Creating script
 			try {
 				final DataOutputStream os = new DataOutputStream(remoteServices.getFileManager(connection).getResource(sh)
 						.openOutputStream(0, null));
 				createScript(appArguments, execPathAndName, out, err, os, make, customMakeCommand);
 				os.close();
 			} catch (final IOException e) {
 				NotifyShell.open(Messages.SMOAResourceManager_7, e.getLocalizedMessage());
 				return jobControlFromJobException(e, jobId, attrs);
 			} catch (final CoreException e) {
 				NotifyShell.open(Messages.SMOAResourceManager_8, e.getLocalizedMessage());
 				return jobControlFromJobException(e, jobId, attrs);
 			}

 			jsdl.setExecutable("/bin/sh"); //$NON-NLS-1$
 			arguments.add(sh);
 		}
 		// If the built-in application has to be used
 		else {
 			machinefile = connection.getHomeDir() + "/.ptp_smoa_machinefile_" //$NON-NLS-1$
 					+ time;

 			jsdl.setApplicationName(app.getName());
 			jsdl.setApplicationVersion(app.getVersion());

 			arguments.add(execPathAndName);
 			arguments.addAll(appArguments);

 			jsdl.getEnvironment().put(SMOAJobAttributes.ENV_STDOUT, out);
 			jsdl.getEnvironment().put(SMOAJobAttributes.ENV_STDERR, err);
 			jsdl.getEnvironment().put(SMOAJobAttributes.ENV_MACHINEFILE, machinefile);

 			if (customMakeCommand != null) {
 				jsdl.getEnvironment().put(SMOAJobAttributes.ENV_MAKE_COMMAND, customMakeCommand);
 			}

 		}

 		// Others

 		final StringAttribute attribute1 = attrs.getAttribute(SMOAJobAttributes.getDescDef());
 		if (attribute1 != null && attribute1.getValue() != null && (!attribute1.getValue().isEmpty())) {
 			jsdl.setJobDescription(attribute1.getValue());
 		}

 		final StringAttribute attribute2 = attrs.getAttribute(SMOAJobAttributes.getNativeSpecDef());
 		if (attribute2 != null && attribute2.getValue() != null && (!attribute2.getValue().isEmpty())) {
 			jsdl.setNativeSpecification(attribute2.getValue());
 		}

 		final IntegerAttribute attribute3 = attrs.getAttribute(SMOAJobAttributes.getMinCpuDef());
 		if (attribute3 != null && attribute3.getValue() != null) {
 			jsdl.setMinCpu(attribute3.getValue());
 		}

 		final IntegerAttribute attribute4 = attrs.getAttribute(SMOAJobAttributes.getMaxCpuDef());
 		if (attribute4 != null && attribute4.getValue() != null) {
 			jsdl.setMaxCpu(attribute4.getValue());
 		}

 		final ArrayAttribute<String> attribute5 = attrs.getAttribute(SMOAJobAttributes.getPrefferedDef());
 		if (attribute5 != null && attribute5.getValue() != null) {
 			for (final String machineName : attribute5.getValue()) {
 				jsdl.getCandidateHosts().add(machineName);
 			}
 		}

 		final StringMapAttribute attribute6 = attrs.getAttribute(SMOAJobAttributes.getEnvDef());
 		if (attribute6 != null && (!attribute6.getValue().isEmpty())) {
 			jsdl.getEnvironment().putAll(attribute6.getValue());
 		}

 		final BooleanAttribute attribute7 = attrs.getAttribute(SMOAJobAttributes.getMakeDef());
 		if (attribute7 != null && attribute7.getValue()) {
 			jsdl.getEnvironment().put(SMOAJobAttributes.ENV_IF_MAKE, "1"); //$NON-NLS-1$
 		} else {
 			jsdl.getEnvironment().remove(SMOAJobAttributes.ENV_IF_MAKE);
 		}

 		final StringAttribute attribute8 = attrs.getAttribute(SMOAJobAttributes.getQueueNameDef());
 		if (attribute8 != null && attribute8.getValue() != null && (!attribute8.getValue().isEmpty())) {
 			jsdl.setQueueName(attribute8.getValue());
 		}

 		ActivityEndpointReference activityReference;

 		// Submitting the job
 		try {
 			activityReference = factory.createActivity(jsdl);
 		} catch (final InvalidRequestMessageException e) {
 			return jobControlFromJobException(e, jobId, attrs);
 		} catch (final NotAuthorizedException e) {
 			return jobControlFromJobException(e, jobId, attrs);
 		} catch (final UnsupportedFeatureException e) {
 			return jobControlFromJobException(e, jobId, attrs);
 		} catch (final Throwable t) {
 			throw new RuntimeException(t);
 		}

 		final IPJob jobControl = super.doCreateJob(jobId, attrs);

 		setSmoaUid(activityReference.getActivityUUID(), jobControl);

 		// Starting job monitoring thread
 		final JobThread jobThread = new JobThread(getResourceManager(), factory, activityReference, jobControl, out, err, sh,
 				machinefile);
 		getResourceManager().addJobThread(jobControl.getID(), jobThread);
 		jobThread.start();

 		return jobControl;
 	}

 	@Override
 	protected SMOAResourceManager getResourceManager() {
 		return (SMOAResourceManager) super.getResourceManager();
 	}

 	@Override
 	protected SMOARuntimeSystem getRuntimeSystem() {
 		final IRuntimeSystem rs = super.getRuntimeSystem();
 		if (rs instanceof SMOARuntimeSystem) {
 			return (SMOARuntimeSystem) rs;
 		}
 		throw new RuntimeException();
 	}

 }
	/*******************************************************************************
	* Copyright (c) 2010 Poznan Supercomputing and Networking Center
	* All rights reserved. This program and the accompanying materials
	* are made available under the terms of the Eclipse Public License v1.0
	* which accompanies this distribution, and is available at
	* http://www.eclipse.org/legal/epl-v10.html
	*
	* Contributors:
	* Jan Konczak (PSNC) - initial implementation
	******************************************************************************/

	package org.eclipse.ptp.rm.smoa.core.rmsystem;

	import java.io.DataOutputStream;
	import java.io.IOException;
	import java.util.Collection;
	import java.util.HashMap;
	import java.util.List;
	import java.util.Map;
	import java.util.Vector;
	import java.util.regex.Matcher;
	import java.util.regex.Pattern;

	import org.eclipse.core.runtime.CoreException;
	import org.eclipse.ptp.core.attributes.ArrayAttribute;
	import org.eclipse.ptp.core.attributes.AttributeManager;
	import org.eclipse.ptp.core.attributes.BooleanAttribute;
	import org.eclipse.ptp.core.attributes.IntegerAttribute;
	import org.eclipse.ptp.core.attributes.StringAttribute;
	import org.eclipse.ptp.core.elements.IPJob;
	import org.eclipse.ptp.core.elements.attributes.ElementAttributes;
	import org.eclipse.ptp.core.elements.attributes.JobAttributes;
	import org.eclipse.ptp.remote.core.IRemoteConnection;
	import org.eclipse.ptp.remote.core.PTPRemoteCorePlugin;
	import org.eclipse.ptp.remote.core.exception.RemoteConnectionException;
	import org.eclipse.ptp.rm.smoa.core.SMOAConfiguration;
	import org.eclipse.ptp.rm.smoa.core.attrib.SMOAJobAttributes;
	import org.eclipse.ptp.rm.smoa.core.attrib.StringMapAttribute;
	import org.eclipse.ptp.rm.smoa.core.rservices.SMOAConnection;
	import org.eclipse.ptp.rm.smoa.core.rservices.SMOARemoteServices;
	import org.eclipse.ptp.rm.smoa.core.rtsystem.SMOARuntimeSystem;
	import org.eclipse.ptp.rm.smoa.core.util.NotifyShell;
	import org.eclipse.ptp.rtsystem.AbstractRuntimeResourceManagerMonitor;
	import org.eclipse.ptp.rtsystem.IRuntimeSystem;

	import com.smoa.comp.sdk.SMOAFactory;
	import com.smoa.comp.sdk.exceptions.InvalidRequestMessageException;
	import com.smoa.comp.sdk.exceptions.NotAuthorizedException;
	import com.smoa.comp.sdk.exceptions.UnsupportedFeatureException;
	import com.smoa.comp.sdk.jsdl.JSDL;
	import com.smoa.comp.sdk.types.ActivityEndpointReference;
	import com.smoa.comp.stubs.factory.ApplicationsType.Application;

	public class SMOAResourceManagerMonitor extends AbstractRuntimeResourceManagerMonitor {

	/**
	* Extracts from the {@link AttributeManager} proper executable name and
	* arguments
	*
	* Returns the list containing program path and executable (as first
	* element) and all arguments (as next arguments)
	*/
	private static List<String> getExecAndArgs(AttributeManager attrs, IRemoteConnection conn, Application app) {
	final List<String> result = new Vector<String>();

	final BooleanAttribute debug = attrs.getAttribute(JobAttributes.getDebugFlagAttributeDefinition());

	// // // // // // // //
	// // // debug // // //

	if (debug != null && debug.getValue() == true) {
	String execPath = attrs.getAttribute(JobAttributes.getDebuggerExecutablePathAttributeDefinition()).getValue();

	if (execPath == null \|\| execPath.isEmpty()) {
	execPath = "."; //$NON-NLS-1$
	}

	final String execName = attrs.getAttribute(JobAttributes.getDebuggerExecutableNameAttributeDefinition()).getValue();

	final String execPathAndName = execPath + "/" + execName; //$NON-NLS-1$

	result.add(execPathAndName);

	/* Arguments */

	final List<String> appArguments = attrs.getAttribute(JobAttributes.getDebuggerArgumentsAttributeDefinition())
	.getValue();

	if (conn.supportsTCPPortForwarding()) {
	final Pattern portRegex = Pattern.compile("^--port=(\\d+)$"); //$NON-NLS-1$
	final Pattern hostRegex = Pattern.compile("^--host=(.+)$"); //$NON-NLS-1$

	Integer port = null;
	String host = null;

	for (final String arg : appArguments) {
	Matcher m = portRegex.matcher(arg);
	if (m.matches()) {
	port = Integer.parseInt(m.group(1));
	}
	m = hostRegex.matcher(arg);
	if (m.matches()) {
	host = m.group(1);
	}
	}
	if (port != null && host != null) {
	try {
	conn.forwardRemotePort(port, host, port);
	} catch (final RemoteConnectionException e) {
	NotifyShell.open(Messages.SMOAResourceManager_PortForwardingFailed_title,
	Messages.SMOAResourceManager_PortForwardingFailed_text + e.getLocalizedMessage());
	}
	}
	}

	result.addAll(appArguments);

	final String appString = attrs.getAttribute(SMOAJobAttributes.getAppNameDef()).getValue();
	if (SMOAJobAttributes.NO_WRAPPER_SCRIPT.equals(appString) \|\| app == null) {
	result.add("--server=0"); //$NON-NLS-1$
	}
	}

	// // // // // // // //
	// // / / run / / // //
	else {
	String execPath = attrs.getAttribute(JobAttributes.getExecutablePathAttributeDefinition()).getValue();

	if (execPath == null \|\| execPath.isEmpty()) {
	execPath = "."; //$NON-NLS-1$
	}

	final String execName = attrs.getAttribute(JobAttributes.getExecutableNameAttributeDefinition()).getValue();

	final String execPathAndName = execPath + "/" + execName; //$NON-NLS-1$

	result.add(execPathAndName);

	/* Arguments */

	final List<String> appArguments = attrs.getAttribute(JobAttributes.getProgramArgumentsAttributeDefinition()).getValue();
	result.addAll(appArguments);
	}

	return result;
	}

	/** Current configuration of this RM */
	/* package access */SMOAConfiguration configuration;

	/** Assigns sequential run number for each configuration */
	private final Map<String, Integer> executeCount = new HashMap<String, Integer>();

	public SMOAResourceManagerMonitor(SMOAResourceManagerConfiguration config) {
	super(config);
	configuration = config;
	}

	/**
	* Creates script if the user selected an application only.
	*
	* @param args
	* - user arguments
	* @param app
	* - user application
	* @param out
	* - file name for stdout
	* @param err
	* - file name for stderr
	* @param os
	* - output stream for the script
	* @param make
	* - if the user wants us to run 'make'
	* @param customMakeCommand
	* - non-null if user wants to use custom run command
	*/
	private void createScript(List<String> args, String app, String out, String err, DataOutputStream os, boolean make,
	String customMakeCommand) throws IOException {
	os.writeBytes("rm -f " + out + " " + err + "\n"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$

	final StringBuilder redirect = new StringBuilder();
	redirect.append(" >> "); //$NON-NLS-1$
	redirect.append(out);
	redirect.append(" 2>> "); //$NON-NLS-1$
	redirect.append(err);

	if (make) {
	os.writeBytes("echo $(date) Running make >> " + err + "\n"); //$NON-NLS-1$ //$NON-NLS-2$
	os.writeBytes("{ "); //$NON-NLS-1$
	if (customMakeCommand != null) {
	os.writeBytes(customMakeCommand);
	} else {
	os.writeBytes("make clean && make"); //$NON-NLS-1$
	}
	os.writeBytes(" ; } "); //$NON-NLS-1$
	os.writeBytes(redirect.toString());
	os.writeBytes("\n"); //$NON-NLS-1$
	os.writeBytes("MAKEOUT=$?\n"); //$NON-NLS-1$
	os.writeBytes("if [ ${MAKEOUT} -ne 0 ]\n"); //$NON-NLS-1$
	os.writeBytes("then\n"); //$NON-NLS-1$
	os.writeBytes(" echo $(date) Make failed! Quitting. >> " + err //$NON-NLS-1$
	+ "\n"); //$NON-NLS-1$
	os.writeBytes(" exit ${MAKEOUT}\n"); //$NON-NLS-1$
	os.writeBytes("fi\n"); //$NON-NLS-1$
	}

	os.writeBytes("STDBUF=$(which stdbuf)\n"); //$NON-NLS-1$
	os.writeBytes("if [ \"${STDBUF}\" ]\n"); //$NON-NLS-1$
	os.writeBytes("then\n"); //$NON-NLS-1$
	os.writeBytes(" STDBUF=\"${STDBUF} -oL -eL \"\n"); //$NON-NLS-1$
	os.writeBytes("fi\n"); //$NON-NLS-1$
	os.writeBytes("echo $(date) Starting task >> " + err + "\n"); //$NON-NLS-1$ //$NON-NLS-2$
	os.writeBytes("{ time ${STDBUF}"); //$NON-NLS-1$

	// app
	os.writeBytes(app);

	// arguments
	for (final String arg : args) {
	os.write(' ');
	os.writeBytes(arg);
	}

	os.writeBytes(" ; }"); //$NON-NLS-1$

	os.writeBytes(redirect.toString());
	os.write('\n');

	os.writeBytes("OUT=$?\n"); //$NON-NLS-1$
	os.writeBytes("echo $(date) Finished! >> " + err + "\n"); //$NON-NLS-1$ //$NON-NLS-2$
	os.writeBytes("exit ${OUT}\n"); //$NON-NLS-1$

	}

	/**
	* In case the submission failed, we set the job state and forward error
	*/
	private IPJob jobControlFromJobException(Exception e, String jobId, AttributeManager attrs) {
	final String subId = attrs.getAttribute(JobAttributes.getSubIdAttributeDefinition()).getValue();

	attrs.addAttribute(PoolingIntervalsAndStatic.exceptionAttrDef.create(e.getLocalizedMessage()));
	attrs.addAttribute(JobAttributes.getStateAttributeDefinition().create(JobAttributes.State.COMPLETED));
	attrs.addAttribute(JobAttributes.getStatusAttributeDefinition().create(Messages.SMOAResourceManager_JobSubmissionFailed));

	getRuntimeSystem().addJobSubmissionError(subId, e);

	final IPJob newJob = super.doCreateJob(jobId, attrs);
	return newJob;
	}

	/**
	* Adds the SMOA UUID of the activity to job properties
	*/
	private void setSmoaUid(String smoaUid, IPJob newJob) {
	final AttributeManager am = new AttributeManager();

	final Collection<IPJob> jc = new Vector<IPJob>();
	jc.add(newJob);

	am.addAttribute(SMOAJobAttributes.getSmoaUuidDef().create(smoaUid));

	doUpdateJobs(jc, am);
	}

	/**
	* Triggered by fireCreateJobEvent by {@link SMOARuntimeSystem}, creates the
	* job and submits it to the SMOA Computing service.
	*/
	@Override
	protected IPJob doCreateJob(String jobId, AttributeManager attrs) {

	// all temporary files are timestamped with the time generated below:
	final long time = System.currentTimeMillis();

	final SMOAConnection connection = configuration.getConnection();
	final SMOAFactory factory = connection.getFactory();

	final String originalName = attrs.getAttribute(ElementAttributes.getNameAttributeDefinition()).getValueAsString();

	// Name for SMOA Computing
	final JSDL jsdl = new JSDL(originalName);
	final List<String> arguments = jsdl.getArguments();

	Integer count = executeCount.get(originalName);
	if (count == null) {
	executeCount.put(originalName, 0);
	count = 0;
	}

	// Label for Eclipse
	attrs.addAttribute(ElementAttributes.getNameAttributeDefinition().create(originalName + " (" + count + ")")); //$NON-NLS-1$ //$NON-NLS-2$

	executeCount.put(originalName, ++count);

	// Working directory
	final String workDir = attrs.getAttribute(JobAttributes.getWorkingDirectoryAttributeDefinition()).getValue();
	if (workDir != null) {
	jsdl.setWorkingDirectory(workDir);
	}

	// Setting program
	final SMOARemoteServices remoteServices = (SMOARemoteServices) PTPRemoteCorePlugin.getDefault().getRemoteServices(
	configuration.getRemoteServicesId());

	final String appString = attrs.getAttribute(SMOAJobAttributes.getAppNameDef()).getValue();
	final Application app = configuration.getAppForName(appString);

	final List<String> execArgsAndPath = getExecAndArgs(attrs, connection, app);

	final String execPathAndName = execArgsAndPath.get(0);
	final List<String> appArguments = execArgsAndPath.subList(1, execArgsAndPath.size());

	jsdl.setOutput("stdout"); //$NON-NLS-1$
	jsdl.setError("stderr"); //$NON-NLS-1$

	// filenames for out and err, and filename for shell script to be
	// executed or for the machine file
	final String out = connection.getHomeDir() + "/.ptp_smoa_out_" + time; //$NON-NLS-1$
	final String err = connection.getHomeDir() + "/.ptp_smoa_err_" + time; //$NON-NLS-1$
	String machinefile = null;
	String sh = null;

	// Custom Make command
	String customMakeCommand = null;

	final BooleanAttribute ifCustomMake = attrs.getAttribute(SMOAJobAttributes.getIfCustomMakeDef());
	if (ifCustomMake != null && ifCustomMake.getValue() != null && ifCustomMake.getValue()) {
	final StringAttribute makeCommand = attrs.getAttribute(SMOAJobAttributes.getCustomMakeCommandDef());
	if (makeCommand != null && makeCommand.getValue() != null && !makeCommand.getValue().isEmpty()) {
	customMakeCommand = makeCommand.getValue();
	}
	}

	// If wrapper script has to be used
	if (SMOAJobAttributes.NO_WRAPPER_SCRIPT.equals(appString) \|\| app == null) {

	sh = connection.getHomeDir() + "/.ptp_smoa_sh_" + time; //$NON-NLS-1$

	final BooleanAttribute makeAttr = attrs.getAttribute(SMOAJobAttributes.getMakeDef());
	final boolean make = (makeAttr == null ? false : makeAttr.getValue());

	// Creating script
	try {
	final DataOutputStream os = new DataOutputStream(remoteServices.getFileManager(connection).getResource(sh)
	.openOutputStream(0, null));
	createScript(appArguments, execPathAndName, out, err, os, make, customMakeCommand);
	os.close();
	} catch (final IOException e) {
	NotifyShell.open(Messages.SMOAResourceManager_7, e.getLocalizedMessage());
	return jobControlFromJobException(e, jobId, attrs);
	} catch (final CoreException e) {
	NotifyShell.open(Messages.SMOAResourceManager_8, e.getLocalizedMessage());
	return jobControlFromJobException(e, jobId, attrs);
	}

	jsdl.setExecutable("/bin/sh"); //$NON-NLS-1$
	arguments.add(sh);
	}
	// If the built-in application has to be used
	else {
	machinefile = connection.getHomeDir() + "/.ptp_smoa_machinefile_" //$NON-NLS-1$
	+ time;

	jsdl.setApplicationName(app.getName());
	jsdl.setApplicationVersion(app.getVersion());

	arguments.add(execPathAndName);
	arguments.addAll(appArguments);

	jsdl.getEnvironment().put(SMOAJobAttributes.ENV_STDOUT, out);
	jsdl.getEnvironment().put(SMOAJobAttributes.ENV_STDERR, err);
	jsdl.getEnvironment().put(SMOAJobAttributes.ENV_MACHINEFILE, machinefile);

	if (customMakeCommand != null) {
	jsdl.getEnvironment().put(SMOAJobAttributes.ENV_MAKE_COMMAND, customMakeCommand);
	}

	}

	// Others

	final StringAttribute attribute1 = attrs.getAttribute(SMOAJobAttributes.getDescDef());
	if (attribute1 != null && attribute1.getValue() != null && (!attribute1.getValue().isEmpty())) {
	jsdl.setJobDescription(attribute1.getValue());
	}

	final StringAttribute attribute2 = attrs.getAttribute(SMOAJobAttributes.getNativeSpecDef());
	if (attribute2 != null && attribute2.getValue() != null && (!attribute2.getValue().isEmpty())) {
	jsdl.setNativeSpecification(attribute2.getValue());
	}

	final IntegerAttribute attribute3 = attrs.getAttribute(SMOAJobAttributes.getMinCpuDef());
	if (attribute3 != null && attribute3.getValue() != null) {
	jsdl.setMinCpu(attribute3.getValue());
	}

	final IntegerAttribute attribute4 = attrs.getAttribute(SMOAJobAttributes.getMaxCpuDef());
	if (attribute4 != null && attribute4.getValue() != null) {
	jsdl.setMaxCpu(attribute4.getValue());
	}

	final ArrayAttribute<String> attribute5 = attrs.getAttribute(SMOAJobAttributes.getPrefferedDef());
	if (attribute5 != null && attribute5.getValue() != null) {
	for (final String machineName : attribute5.getValue()) {
	jsdl.getCandidateHosts().add(machineName);
	}
	}

	final StringMapAttribute attribute6 = attrs.getAttribute(SMOAJobAttributes.getEnvDef());
	if (attribute6 != null && (!attribute6.getValue().isEmpty())) {
	jsdl.getEnvironment().putAll(attribute6.getValue());
	}

	final BooleanAttribute attribute7 = attrs.getAttribute(SMOAJobAttributes.getMakeDef());
	if (attribute7 != null && attribute7.getValue()) {
	jsdl.getEnvironment().put(SMOAJobAttributes.ENV_IF_MAKE, "1"); //$NON-NLS-1$
	} else {
	jsdl.getEnvironment().remove(SMOAJobAttributes.ENV_IF_MAKE);
	}

	final StringAttribute attribute8 = attrs.getAttribute(SMOAJobAttributes.getQueueNameDef());
	if (attribute8 != null && attribute8.getValue() != null && (!attribute8.getValue().isEmpty())) {
	jsdl.setQueueName(attribute8.getValue());
	}

	ActivityEndpointReference activityReference;

	// Submitting the job
	try {
	activityReference = factory.createActivity(jsdl);
	} catch (final InvalidRequestMessageException e) {
	return jobControlFromJobException(e, jobId, attrs);
	} catch (final NotAuthorizedException e) {
	return jobControlFromJobException(e, jobId, attrs);
	} catch (final UnsupportedFeatureException e) {
	return jobControlFromJobException(e, jobId, attrs);
	} catch (final Throwable t) {
	throw new RuntimeException(t);
	}

	final IPJob jobControl = super.doCreateJob(jobId, attrs);

	setSmoaUid(activityReference.getActivityUUID(), jobControl);

	// Starting job monitoring thread
	final JobThread jobThread = new JobThread(getResourceManager(), factory, activityReference, jobControl, out, err, sh,
	machinefile);
	getResourceManager().addJobThread(jobControl.getID(), jobThread);
	jobThread.start();

	return jobControl;
	}

	@Override
	protected SMOAResourceManager getResourceManager() {
	return (SMOAResourceManager) super.getResourceManager();
	}

	@Override
	protected SMOARuntimeSystem getRuntimeSystem() {
	final IRuntimeSystem rs = super.getRuntimeSystem();
	if (rs instanceof SMOARuntimeSystem) {
	return (SMOARuntimeSystem) rs;
	}
	throw new RuntimeException();
	}

	}