PbsTest.java

package org.molgenis.compute.host.test;

import java.io.IOException;

import org.apache.log4j.BasicConfigurator;
import org.apache.log4j.Logger;
import org.molgenis.compute.host.Job;
import org.molgenis.compute.host.Pbs;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;

public class PbsTest
{
	String host = "millipede.service.rug.nl";
	String user = "xxxx";
	String password = "xxxx";
	String workingDir = "molgenis_jobs";

	Logger logger = Logger.getLogger(PbsTest.class);

	@BeforeClass
	public void setup()
	{
		BasicConfigurator.configure();

		// load test settings from properties file outside svn???
	}

	// @Test
	// public void testLogMonitoring() throws IOException
	// {
	// JobManager pbs = new PbsSshJobManager(host, user, password);
	//
	// //just simple shell
	// Job job = new
	// Job("sleep 5\necho 20%\nsleep 5\necho 40%\nsleep 5\necho 60%\nsleep 5\necho 60%\nsleep 5\necho 100%\n");
	//
	// //of course you can use defaults ;-)
	// job.setQueue("short");
	// job.setName("myjob_"+UUID.randomUUID().toString().replace("-", ""));
	// job.setNodes("1:ppn=2");
	// job.setMem("2gb");
	// job.setWalltime("00:10:00");
	//
	// pbs.submit(job);
	//
	// logger.debug(job);
	//
	// // monitor until it is done
	// while (job.getState() != AbstractJobManager.JobState.COMPLETED
	// && job.getState() != AbstractJobManager.JobState.ERROR)
	// {
	// try
	// {
	// Thread.sleep(5000);
	// }
	// catch (InterruptedException e)
	// {
	// // TODO Auto-generated catch block
	// e.printStackTrace();
	// }
	// pbs.refresh(job);
	// logger.debug("current state: "+job);
	// }
	// pbs.refresh(job);
	//
	// logger.debug("done. log: \n" + job);
	// }
	//
	// @Test
	// public void testAllJobsMonitoring() throws IOException
	// {
	// Pbs pbs = new Pbs(host, user, password);
	//
	// for(PbsJob job: pbs.getQstat())
	// {
	// logger.debug(job);
	// }
	//
	// }

	@Test
	public void testSubmitMultiple() throws IOException, InterruptedException
	{
		Pbs pbs = new Pbs(host, user, password);
		pbs.setWorkingDir(workingDir);

		long time = System.currentTimeMillis();

		// submit script
		for (int i = 0; i < 5; i++)
		{
			Job job = new Job("sleep 120\necho \"hello\"\necho \"some error\" >2");

			// of course you can use defaults ;-)
			job.setQueue("short");
			job.setName("myjob" + i + "_" + time);
			job.setNodes("1:ppn=2");
			job.setMem("2gb");
			job.setWalltime("00:05:00");

			pbs.submit(job);

			Thread.sleep(1000);

			logger.debug(job);
		}

		// monitor until it is done

		while (pbs.hasActiveJobs())
		{
			logger.debug("jobs running: ");
			for (Job j : pbs.getJobs())
			{
				pbs.refresh(j);
				logger.debug("\n" + j);
			}

			try
			{
				Thread.sleep(30000);
			}
			catch (InterruptedException e)
			{
				// TODO Auto-generated catch block
				e.printStackTrace();
			}
			pbs.refreshJobs();
		}

		// one last view
		for (Job j : pbs.getJobs())
		{
			logger.debug("\n" + j);
		}
	}
}