drmaa-pbs's Introduction

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)

drmaa-pbs's People

Contributors

Stargazers

Watchers

drmaa-pbs's Issues

Do not parse XMLs manually

At the moment we have a bunch of if conditions for parsing the XMLs, and we also use regular expressions.

Yesterday I committed a fix for a NPE that happened because of one of these if's. This is still possible to happen, and makes our code less readable and brittle.

Recommend Projects