CustomSubmitter.java Source code

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Here is the source code for CustomSubmitter.java

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/*
Copyright (C) 2011-2012 Josh Kollat, Jon Herman, Patrick Reed and others.
    
The HBV Benchmark Problem is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
    
The HBV Benchmark Problem is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Lesser General Public License for more details.
    
You should have received a copy of the GNU Lesser General Public License
along with the HBV Benchmark Problem.  If not, see <http://www.gnu.org/licenses/>.
*/

import java.io.File;
import java.io.IOException;
import java.io.PrintStream;
import java.io.File;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.moeaframework.util.CommandLineUtility;
import org.moeaframework.util.pbs.PBSJob;
import org.moeaframework.util.pbs.PBSSubmitter;

import org.moeaframework.util.io.RedirectStream;

/**
 * Translates individual {@link PBSJob}s to valid PBS scripts and submits the
 * scripts using {@code qsub}.
 */
public class CustomSubmitter {

    /**
     * The queue to which the jobs are submitted. Set to {@code null} to use the
     * default PBS queue.
     */
    private final String queue;

    /**
     * The directory where output logs are written. Set to {@code null} to use
     * the default PBS behavior.
     */
    private final File outputDirectory;

    /**
     * The directory where error logs are written. Set to {@code null} to use
     * the default PBS behavior.
     */
    private final File errorDirectory;

    /**
     * Store the new line character to prevent repetitive calls to
     * {@code System.getProperty("line.separator")}.
     */
    private static String newLine = System.getProperty("line.separator");

    /**
     * Class constructor for a PBS submitter with the specified queue, output
     * directory, and error directory. The output and error directories may be
     * {@code null} to use the default PBS behavior for saving output and error
     * logs.
     * 
     * @param queue the queue to which the jobs are submitted; {@code null} to
     *        use the default PBS queue
     * @param outputDirectory the directory where output logs are written;
     *        {@code null} to use the default PBS behavior
     * @param errorDirectory the directory where error logs are written;
     *        {@code null} to use the default PBS behavior
     * @throws IOException if an I/O error occurred
     */
    public CustomSubmitter(String queue, File outputDirectory, File errorDirectory) throws IOException {
        super();
        this.queue = queue;
        this.outputDirectory = outputDirectory;
        this.errorDirectory = errorDirectory;

        // ensure output and error folders exist
        if ((outputDirectory != null) && !outputDirectory.exists()) {
            if (!outputDirectory.mkdirs()) {
                throw new IOException("unable to create output directory");
            }
        }

        if ((errorDirectory != null) && !errorDirectory.exists()) {
            if (!errorDirectory.mkdirs()) {
                throw new IOException("unable to create output directory");
            }
        }
    }

    /**
     * Translates the specified PBS job to a valid PBS script which can be
     * submitted to the system's {@code qsub} program.
     * 
     * @param job the PBS job
     * @return the PBS script sued to execute the specified PBS job
     */
    protected String toPBSScript(PBSJob job) {
        StringBuilder sb = new StringBuilder();

        sb.append("#PBS -N ").append(job.getName()).append(newLine);
        sb.append("#PBS -l nodes=").append(job.getNodes()).append(":nehalem:ppn=1").append(newLine);
        sb.append("#PBS -l walltime=").append(job.getWalltime()).append(":00:00").append(newLine);

        if (outputDirectory != null) {
            sb.append("#PBS -o ").append(new File(outputDirectory, job.getName()).getPath()).append(newLine);
        }

        if (errorDirectory != null) {
            sb.append("#PBS -e ").append(new File(errorDirectory, job.getName()).getPath()).append(newLine);
        }

        if (queue != null) {
            sb.append("#PBS -q ").append(queue).append(newLine);
        }

        for (String command : job.getCommands()) {
            sb.append(command).append(newLine);
        }

        return sb.toString();
    }

    /**
     * Submits the specified PBS job to the PBS queue using the {@code qsub}
     * program.
     * 
     * @param job the PBS job to be submitted
     * @throws IOException if an error occurred while invoking {@code qsub}
     */
    public void submit(PBSJob job) throws IOException {
        Process process = new ProcessBuilder("qsub").start();

        RedirectStream.redirect(process.getInputStream(), System.out);
        RedirectStream.redirect(process.getErrorStream(), System.err);

        String script = toPBSScript(job);
        System.out.println(script);

        PrintStream ps = new PrintStream(process.getOutputStream());
        ps.print(script);
        ps.close();

        try {
            int exitStatus = process.waitFor();

            if (exitStatus != 0) {
                throw new IOException("qsub terminated with exit status " + exitStatus);
            }
        } catch (InterruptedException e) {
            Thread.currentThread().interrupt();
        }
    }

}