drmaa-pbs

DRMAA PBS Java library, using command executions like qsub and qstat

This library is not complete, and implements DRMAA v1 by calling native commands (qsub, qstat, pbsnodes, etc).

Example

package org.biouno.drmaa_pbs;

import java.util.HashMap;
import java.util.Map;

import org.ggf.drmaa.DrmaaException;
import org.ggf.drmaa.JobTemplate;
import org.ggf.drmaa.Session;
import org.ggf.drmaa.SessionFactory;

public class Test {

    public static void main(String[] args) {
        SessionFactory sf = SessionFactory.getFactory();
        Session s = sf.getSession();

        try {
            // http://biouno.org/2014/06/21/java-drmaa-api-part-1/
            Map<String, String> options = new HashMap<String, String>();
            options.put("os", "UNIX");
            options.put("address", "localhost");
            options.put("port", "10022");
            options.put("username", "testuser");
            options.put("password", "testuser");
            options.put("connectionType", "SCP");
            ((SessionImpl) s).init("ssh", options);
            JobTemplate jt = new JobTemplateImpl();
            jt.setRemoteCommand("/home/testuser/torque.submit");
            String id = s.runJob(jt);
            int i = s.getJobProgramStatus(id);
            System.out.println(i);
            s.deleteJobTemplate(jt);
            System.out.println("Your job has been submitted with id " + id);
            s.exit();
        } catch (DrmaaException de) {
            de.printStackTrace(System.err);
        }

        System.out.println("OK!");
        System.exit(1);
    }

}

The output will be similar to.

Sep 26, 2015 1:26:16 PM org.biouno.drmaa_pbs.SessionImpl runJob
INFO: jobId: 9.localhost

32
Your job has been submitted with id 9.localhost
OK!

Changelog

• v0.3 - Implemented basic functions for running, stopping and monitoring jobs. Tested on NCI's Raijin which uses a modified version of Pbs Pro (thanks to @kevyin)