Examples with GATInvocationException org.gridlab.gat.GATInvocationException used on opensource projects

Example 41 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class LoadLevelerFileAdaptor method copyDir.

protected void copyDir(File sourceFile, File destFile) throws GATInvocationException {
    String sourcePath = sourceFile.getPath();
    String destPath = destFile.getPath();
    if (logger.isDebugEnabled()) {
        logger.debug("copyDir '" + sourcePath + "' to '" + destPath + "'");
    }
    boolean existingDir = false;
    if (destFile.exists()) {
        // check whether the target is an existing file
        if (!destFile.isDirectory()) {
            throw new GATInvocationException("cannot overwrite non-directory '" + destPath + "' with directory '" + sourcePath + "'!");
        } else {
            existingDir = true;
        }
    }
    if (!existingDir) {
    // copy dir a to b will result in a new directory b with contents
    // that is a copy of the contents of a.
    } else if (gatContext.getPreferences().containsKey("file.directory.copy") && ((String) gatContext.getPreferences().get("file.directory.copy")).equalsIgnoreCase("contents")) {
    // don't modify the dest dir, so copy dir a to dir b ends up as
    // copying a/* to b/*, note that a/dir/* also ends up in b/*
    } else {
        // dest.
        if (sourcePath.length() > 0) {
            int start = sourcePath.lastIndexOf(File.separator) + 1;
            String separator = "";
            if (!destPath.endsWith(File.separator)) {
                separator = File.separator;
            }
            destPath = destPath + separator + sourcePath.substring(start);
            destFile = new File(destPath);
        }
    }
    if (logger.isDebugEnabled()) {
        logger.debug("destPath = " + destPath);
    }
    if (gatContext.getPreferences().containsKey("file.create") && ((String) gatContext.getPreferences().get("file.create")).equalsIgnoreCase("true")) {
        destFile.mkdirs();
    } else {
        // if source is a dir 'dir1' and dest is a dir 'dir2' then the
        // result of dir1.copy(dir2) will be dir2/dir1/.. so even if the
        // 'file.create' flag isn't set, create the dir1 in dir2 before
        // copying the files.
        boolean mkdir = destFile.mkdir();
        if (logger.isDebugEnabled()) {
            logger.debug("mkdir: " + mkdir);
        }
    }
    // list all the files and copy recursively.
    File[] files = sourceFile.listFiles();
    if (files == null) {
        if (logger.isDebugEnabled()) {
            logger.debug("copyDirectory: no files in src directory: " + sourcePath);
        }
        return;
    }
    for (File file : files) {
        if (logger.isDebugEnabled()) {
            logger.debug("copyDirectory: file to copy = " + file);
        }
        String newDestString = destPath;
        newDestString += File.separator + file.getName();
        if (logger.isDebugEnabled()) {
            logger.debug("new dest: " + newDestString);
            logger.debug("src is file: " + file.isFile());
            logger.debug("src is dir: " + file.isDirectory());
        }
        File newDest = new File(newDestString);
        if (file.isFile()) {
            if (logger.isDebugEnabled()) {
                logger.debug("copyDir: copying " + file);
            }
            copy(file, newDest);
        } else if (file.isDirectory()) {
            copyDir(file, newDest);
        } else {
            throw new GATInvocationException("don't know how to handle file: " + file.getPath() + " (links are not supported).");
        }
    }
}

Example 42 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class LoadLevelerResourceBrokerAdaptor method submitJob.

/*
     * (non-Javadoc)
     * 
     * @see org.gridlab.gat.resources.ResourceBroker#submitJob(org.gridlab.gat.resources.JobDescription)
     */
public Job submitJob(AbstractJobDescription abstractDescription, MetricListener listener, String metricDefinitionName) throws GATInvocationException {
    if (!(abstractDescription instanceof JobDescription)) {
        throw new GATInvocationException("can only handle JobDescriptions: " + abstractDescription.getClass());
    }
    JobDescription description = (JobDescription) abstractDescription;
    SoftwareDescription sd = description.getSoftwareDescription();
    if (sd == null) {
        throw new GATInvocationException("The job description does not contain a software description");
    }
    if (description.getProcessCount() < 1) {
        throw new GATInvocationException("Adaptor cannot handle: process count < 1: " + description.getProcessCount());
    }
    if (description.getResourceCount() != 1) {
        throw new GATInvocationException("Adaptor cannot handle: resource count > 1: " + description.getResourceCount());
    }
    String home = System.getProperty("user.home");
    if (home == null) {
        throw new GATInvocationException("loadleveler broker could not get user home dir");
    }
    Sandbox sandbox = new Sandbox(gatContext, description, "localhost", home, true, true, false, false);
    LoadLevelerJob loadlevelerJob = new LoadLevelerJob(gatContext, description, sandbox);
    Job job = null;
    if (description instanceof WrapperJobDescription) {
        WrapperJobCpi tmp = new WrapperJobCpi(gatContext, loadlevelerJob, listener, metricDefinitionName);
        listener = tmp;
        job = tmp;
    } else {
        job = loadlevelerJob;
    }
    if (listener != null && metricDefinitionName != null) {
        Metric metric = loadlevelerJob.getMetricDefinitionByName(metricDefinitionName).createMetric(null);
        loadlevelerJob.addMetricListener(listener, metric);
    }
    loadlevelerJob.setState(Job.JobState.PRE_STAGING);
    loadlevelerJob.waitForTrigger(Job.JobState.PRE_STAGING);
    sandbox.prestage();
    String exe;
    if (sandbox.getResolvedExecutable() != null) {
        exe = sandbox.getResolvedExecutable().getPath();
    // try to set the executable bit, it might be lost
    /* CDIAZ: The command "exe" can be also in a remote host
             * 		  The command must have the right permissions in the remote host
            try {
                new CommandRunner("chmod", "+x", exe);
            } catch (Throwable t) {
                // ignore
            }
            */
    } else {
        exe = getExecutable(description);
    }
    String[] args = getArgumentsArray(description);
    // Directory where the loadleveler command will be executed
    java.io.File f = new java.io.File(sandbox.getSandboxPath());
    if (!f.exists()) {
        throw new GATInvocationException("Unable to find directory " + f.getAbsolutePath());
    }
    // Check and set the environment for a blaunch command
    Map<String, Object> env = sd.getEnvironment();
    this.prepareBLaunchEnv(env);
    // Encapsulate the original command into a blaunch command
    String host = brokerURI.getHost();
    String newExe = this.getLoadLevelerCommand();
    String[] newArgs = this.getLoadLevelerArgs(host, exe, args);
    System.out.println("[AFTER] exe: " + newExe);
    System.out.println("[AFTER] llspawan.stdio args:");
    for (int i = 0; i < newArgs.length; i++) System.out.print(" " + newArgs[i]);
    System.out.println();
    ProcessBundle bundle = new ProcessBundle(description.getProcessCount(), newExe, newArgs, f, env);
    loadlevelerJob.setSubmissionTime();
    loadlevelerJob.setState(Job.JobState.SCHEDULED);
    try {
        loadlevelerJob.setState(Job.JobState.RUNNING);
        loadlevelerJob.waitForTrigger(Job.JobState.RUNNING);
        loadlevelerJob.setStartTime();
        bundle.startBundle();
        loadlevelerJob.setProcess(bundle);
        if (logger.isDebugEnabled()) {
            logger.debug("Job with PID: " + LOADL_PID + " is executed on host " + host);
        }
    } catch (IOException e) {
        throw new CommandNotFoundException("LoadLevelerResourceBrokerAdaptor", e);
    }
    if (!sd.streamingStderrEnabled()) {
        try {
            if (sd.getStderr() != null) {
                OutputStream err = GAT.createFileOutputStream(gatContext, sd.getStderr());
                // to file
                StreamForwarder forwarder = new StreamForwarder(bundle.getStderr(), err, sd.getExecutable() + " [stderr]");
                loadlevelerJob.setErrorStream(forwarder);
                if (logger.isDebugEnabled()) {
                    logger.debug("Created stderr forwarder to file " + sd.getStderr());
                }
            } else {
                // or throw it away
                new StreamForwarder(bundle.getStderr(), null, sd.getExecutable() + " [stderr]");
            }
        } catch (GATObjectCreationException e) {
            throw new GATInvocationException("Unable to create file output stream for stderr!", e);
        }
    }
    if (!sd.streamingStdoutEnabled()) {
        // read away the stdout
        try {
            if (sd.getStdout() != null) {
                // to file
                OutputStream out = GAT.createFileOutputStream(gatContext, sd.getStdout());
                StreamForwarder forwarder = new StreamForwarder(bundle.getStdout(), out, sd.getExecutable() + " [stdout]");
                loadlevelerJob.setOutputStream(forwarder);
                if (logger.isDebugEnabled()) {
                    logger.debug("Created stdout forwarder to file " + sd.getStdout());
                }
            } else {
                // or throw it away
                new StreamForwarder(bundle.getStdout(), null, sd.getExecutable() + " [stdout]");
            }
        } catch (GATObjectCreationException e) {
            throw new GATInvocationException("Unable to create file output stream for stdout!", e);
        }
    }
    if (!sd.streamingStdinEnabled() && sd.getStdin() != null) {
        // forward the stdin from file
        try {
            InputStream in = GAT.createFileInputStream(gatContext, sd.getStdin());
            bundle.setStdin(sd.getExecutable(), in);
        } catch (GATObjectCreationException e) {
            throw new GATInvocationException("Unable to create file input stream for stdin!", e);
        }
    }
    loadlevelerJob.monitorState();
    return job;
}

Example 43 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class LsfFileAdaptor method listFiles.

/*
     * (non-Javadoc)
     * 
     * @see org.gridlab.gat.io.File#listFiles(java.io.FilenameFilter)
     */
public org.gridlab.gat.io.File[] listFiles(FilenameFilter arg0) throws GATInvocationException {
    File[] r = f.listFiles(arg0);
    ArrayList<File> l = new ArrayList<File>();
    for (int i = 0; i < r.length; i++) {
        if (!(ignoreHiddenFiles && r[i].isHidden())) {
            l.add(r[i]);
        }
    }
    org.gridlab.gat.io.File[] res = new org.gridlab.gat.io.File[r.length];
    for (int i = 0; i < res.length; i++) {
        try {
            res[i] = GAT.createFile(gatContext, localToURI(l.get(i).getPath()));
        } catch (Exception e) {
            throw new GATInvocationException("LsfFile", e);
        }
    }
    return res;
}

Example 44 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class LsfFileAdaptor method copyDir.

protected void copyDir(File sourceFile, File destFile) throws GATInvocationException {
    String sourcePath = sourceFile.getPath();
    String destPath = destFile.getPath();
    if (logger.isDebugEnabled()) {
        logger.debug("copyDir '" + sourcePath + "' to '" + destPath + "'");
    }
    boolean existingDir = false;
    if (destFile.exists()) {
        // check whether the target is an existing file
        if (!destFile.isDirectory()) {
            throw new GATInvocationException("cannot overwrite non-directory '" + destPath + "' with directory '" + sourcePath + "'!");
        } else {
            existingDir = true;
        }
    }
    if (!existingDir) {
    // copy dir a to b will result in a new directory b with contents
    // that is a copy of the contents of a.
    } else if (gatContext.getPreferences().containsKey("file.directory.copy") && ((String) gatContext.getPreferences().get("file.directory.copy")).equalsIgnoreCase("contents")) {
    // don't modify the dest dir, so copy dir a to dir b ends up as
    // copying a/* to b/*, note that a/dir/* also ends up in b/*
    } else {
        // dest.
        if (sourcePath.length() > 0) {
            int start = sourcePath.lastIndexOf(File.separator) + 1;
            String separator = "";
            if (!destPath.endsWith(File.separator)) {
                separator = File.separator;
            }
            destPath = destPath + separator + sourcePath.substring(start);
            destFile = new File(destPath);
        }
    }
    if (logger.isDebugEnabled()) {
        logger.debug("destPath = " + destPath);
    }
    if (gatContext.getPreferences().containsKey("file.create") && ((String) gatContext.getPreferences().get("file.create")).equalsIgnoreCase("true")) {
        destFile.mkdirs();
    } else {
        // if source is a dir 'dir1' and dest is a dir 'dir2' then the
        // result of dir1.copy(dir2) will be dir2/dir1/.. so even if the
        // 'file.create' flag isn't set, create the dir1 in dir2 before
        // copying the files.
        boolean mkdir = destFile.mkdir();
        if (logger.isDebugEnabled()) {
            logger.debug("mkdir: " + mkdir);
        }
    }
    // list all the files and copy recursively.
    File[] files = sourceFile.listFiles();
    if (files == null) {
        if (logger.isDebugEnabled()) {
            logger.debug("copyDirectory: no files in src directory: " + sourcePath);
        }
        return;
    }
    for (File file : files) {
        if (logger.isDebugEnabled()) {
            logger.debug("copyDirectory: file to copy = " + file);
        }
        String newDestString = destPath;
        newDestString += File.separator + file.getName();
        if (logger.isDebugEnabled()) {
            logger.debug("new dest: " + newDestString);
            logger.debug("src is file: " + file.isFile());
            logger.debug("src is dir: " + file.isDirectory());
        }
        File newDest = new File(newDestString);
        if (file.isFile()) {
            if (logger.isDebugEnabled()) {
                logger.debug("copyDir: copying " + file);
            }
            copy(file, newDest);
        } else if (file.isDirectory()) {
            copyDir(file, newDest);
        } else {
            throw new GATInvocationException("don't know how to handle file: " + file.getPath() + " (links are not supported).");
        }
    }
}

Example 45 with GATInvocationException

use of org.gridlab.gat.GATInvocationException in project compss by bsc-wdc.

the class LsfFileAdaptor method listFiles.

/*
     * (non-Javadoc)
     * 
     * @see org.gridlab.gat.io.File#listFiles(java.io.FileFilter)
     */
public org.gridlab.gat.io.File[] listFiles(FileFilter arg0) throws GATInvocationException {
    File[] r = f.listFiles(arg0);
    ArrayList<File> l = new ArrayList<File>();
    for (int i = 0; i < r.length; i++) {
        if (!(ignoreHiddenFiles && r[i].isHidden())) {
            l.add(r[i]);
        }
    }
    org.gridlab.gat.io.File[] res = new org.gridlab.gat.io.File[r.length];
    for (int i = 0; i < res.length; i++) {
        try {
            res[i] = GAT.createFile(gatContext, localToURI(l.get(i).getPath()));
        } catch (Exception e) {
            throw new GATInvocationException("LsfFile", e);
        }
    }
    return res;
}