Sun N1 Grid Engine 6.1 User's Guide

Developing with the Java Language Binding

Important Files for the Java Language Binding

To use the DRMAA Java language binding implementation included with N1 Grid Engine 6.1, you need to know where to find the important files. The most important file is the DRMAA JAR file sge-root/lib/drmaa.jar. To compile your DRMAA application, you must include the DRMAA JAR file in your CLASSPATH . The DRMAA classes are documented in the DRMAA Javadoc^TM, located in the sge-root/doc/javadocs directory. To access the Javadocs, open the file sge-root/doc/javadocs/index.html in your browser . When you are ready to run your application, you also need the DRMAA shared library, sge-root/lib/arch/libdrmaa.so, which provides the required native routines.

Importing the DRMAA Java Classes and Packages

To use the DRMAA classes in your application, your classes should import the DRMAA classes or packages. In most cases, only the classes in the org.ggf.drmaa package will be used. You can import these packages individually or using a wildcard package import. In some rare cases, you might need to reference the N1 Grid Engine DRMAA implementation classes found in the com.sun.grid.drmaa package. In those cases, you can import the classes individually or you can import all the classes in a given package. The names of the com.sun.grid.drmaa classes do not overlap with the org.ggf.drmaa classes, so you can import both packages without creating a namespace collision.

Compiling Your Java Application

To compile your DRMAA application, you must include the sge-root/lib/drmaa.jar file in your CLASSPATH. The drmaa.jar file will not be included automatically when you set your environment using the settings.sh or settings.csh files.

How to Use DRMAA with NetBeans 5.`x`

To use the DRMAA classses with your NetBeans 5.0 or 5.5 project, follow these steps:

Click mouse button 3 on the project node and select Properties.

Determine whether your project generates a build file or uses an existing file.
- If your project uses a generated build file:
  1. Select Libraries in the left column.
  2. Click Add Library.
  3. Click Manage Libraries in the Libraries dialog box.
  4. Click New Library in the Library Management dialog box.
  5. Type DRMAA in the Library Name field in the New Library dialog box.
  6. Click OK to dismiss the New Library dialog box.
  7. Click Add JAR/Folder.
  8. Browse to the sge-root/lib directory in the file chooser dialog box and select the drmaa.jar file.
  9. Click Add JAR/Folder to dismiss the file chooser dialog box.
  10. Click OK to dismiss the Library Management dialog box.
  11. Select the DRMAA library and click Add Library to dismiss the Libraries dialog box.
- If your project uses an existing build file:
  1. Select Java Sources Classpath in the left column.
  2. Click Add JAR/Folder.
  3. Browse to the sge-root/lib directory in the file chooser dialog box and select the drmaa.jar file.
  4. Click Choose to dismiss the file chooser dialog box.

Click OK to dismiss the properties dialog box.

Verify that the DRMAA shared library is in the library search path.

To run your application from NetBeans, the DRMAA shared library file sge-root/lib/arch/libdrmaa.so must be included in the library search path (LD_LIBRARY_PATH on the Solaris Operating Environment and Linux). The sge-root/lib/arch directory is not included automatically when you set your environment using the settings.sh or settings.csh files.To set up the path for the shared library, perform one of the following:
- Set up your environment in the shell before launching NetBeans.
- Add to the netbeans-root/etc/netbeans.conf file to set up the environment, such as:
```
# Setup environment for SGE
. <sge-root>/<sge_cell>/common/settings.sh
ARCH=`$SGE_ROOT/util/arch`
LD_LIBRARY_PATH=$SGE_ROOT/lib/$ARCH; export LD_LIBRARY_PATH
```

Running Your Java Application

To run your compiled DRMAA application, verify the following:

The sge-root/lib/arch directory must be included in the library search path (LD_LIBRARY_PATH on the Solaris Operating Environment and Linux). The sge-root/lib/arch directory is not included automatically when you set your environment using the settings.sh or settings.csh files.
You must be logged into a machine that is an N1 Grid Engine submit host. If the machine is not an N1 Grid Engine submit host, all DRMAA method calls will fail, throwing a DrmCommunicationException.

Using the DRMAA 0.5 Java Language Binding

The DRMAA shared library, which is used by default, supports version 1.0 of the DRMAA Java Language Binding Specification. For reasons of backward compatibility, however, N1 Grid Engine also includes an implementation of the 0.5 version of the DRMAA Java Language Binding Specification. You should develop all new applications with the 1.0 shared library, but you might occasionally discover an application that requires the 0.5 implementation.

To use the 0.5 version of the drmaa.jar file, you should include the sge-root/lib/drmaa-0.5.jar file in your CLASSPATH either before or instead of the usual sge-root/lib/drmaa.jar file. In addition, the use of the 0.5 Java language binding requires enabling the 0.95 C language binding. See How to Use the DRMAA 0.95 C Language Binding.

Java Application Examples

The following examples illustrate some application interactions that use the Java language bindings. You can find additional examples on the “How To” section of the Grid Engine Community Site.

Example 6–4 Starting and Stopping a Session

The following code segment shows the most basic DRMAA Java language binding program.

Everything that you as a programmer do with DRMAA, you do through a Session object. You get the Session object from a SessionFactory. You get the SessionFactory from the static SessionFactory.getFactory() method. The reason for this chain is that the org.ggf.drmaa.* classes should be considered an immutable package to be used by every DRMAA Java language binding implementation. Because the package is immutable, to load a specific implementation, the SessionFactory uses a system property to find the implementation's session factory, which it then loads. That session factory is then responsible for creating the session in whatever way it sees fit. It should be noted that even though there is a session factory, only one session may exist at a time.

On line 9, SessionFactory.getFactory() gets a session factory instance . On line 10, SessionFactory.getSession() gets the session instance. On line 13, Session.init() initializes the session. "" is passed in as the contact string to create a new session because no initialization arguments are needed.

Session.init() creates a session and starts an event client listener thread. The session is used for organizing jobs submitted through DRMAA, and the thread is used to receive updates from the queue master about the state of jobs and the system in general. Once Session.init() has been called successfully, the calling application must also call Session.exit() before terminating. If an application does not call Session.exit() before terminating, the queue master might be left with a dead event client handle, which can decrease queue master performance. Use the Runtime.addShutdownHook() method to make sure Session.exit() gets called.

At the end of the program, on line 14, Session.exit() cleans up the session and stops the event client listener thread. Most other DRMAA methods must be called before Session.exit(). Some functions, like Session.getContact(), can be called after Session.exit(), but these functions only provide general information. Any function that performs an action, such as Session.runJob() or Session.wait() must be called before Session.exit() is called. If such a function is called after Session.exit() is called, it will throw a NoActiveSessionException.

01: package com.sun.grid.drmaa.howto;
02:
03: import org.ggf.drmaa.DrmaaException;
04: import org.ggf.drmaa.Session;
05: import org.ggf.drmaa.SessionFactory;
06:
07: public class Howto1 {
08:    public static void main(String[] args) {
09:       SessionFactory factory = SessionFactory.getFactory();
10:       Session session = factory.getSession();
11:
12:       try {
13:          session.init("");
14:          session.exit();
15:       } catch (DrmaaException e) {
16:          System.out.println("Error: " + e.getMessage());
17:       }
18:    }
19: }

Example 6–5 Running a Job

The following code segment shows how to use the DRMAA Java language binding to submit a job to N1 Grid Engine. The beginning and end of this program are the same as Example 6–4. The differences are on lines 16-24.

On line 16 , DRMAA allocates a JobTemplate. A JobTemplate is an object that is used to store information about a job to be submitted. The same template can be reused for multiple calls to Session.runJob() or Session.runBulkJobs().

On line 17, the remoteCommand attribute is set. This attribute tells DRMAA where to find the program to run. Its value is the path to the executable. The path can be relative or absolute. If relative, the path is relative to the workingDirectory attribute, which defaults to the user's home directory. For more information on DRMAA attributes, see the DRMAA Javadoc or the drmaa_attributes man page. For this program to work, the script sleeper.sh must be in your default path.

On line 18, the args attribute is set. This attribute tells DRMAA what arguments to pass to the executable. For more information on DRMAA attributes, see the DRMAA Javadoc or the drmaa_attributes man page.

On line 20, Session.runJob() submits the job. This method returns the ID assigned to the job by the queue master. The job is now running as though submitted by qsub. At this point, calling Session.exit() or terminating the program will have no effect on the job.

To clean things up, the job template is deleted on line 24. This action frees the memory DRMAA set aside for the job template, but has no effect on submitted jobs.

01: package com.sun.grid.drmaa.howto;
02:
03: import java.util.Collections;
04: import org.ggf.drmaa.DrmaaException;
05: import org.ggf.drmaa.JobTemplate;
06: import org.ggf.drmaa.Session;
07: import org.ggf.drmaa.SessionFactory;
08:
09: public class Howto2 {
10:    public static void main(String[] args) {
11:       SessionFactory factory = SessionFactory.getFactory();
12:       Session session = factory.getSession();
13:
14:       try {
15:          session.init("");
16:          JobTemplate jt = session.createJobTemplate();
17:          jt.setRemoteCommand("sleeper.sh");
18:          jt.setArgs(Collections.singletonList("5"));
19:
20:          String id = session.runJob(jt);
21:
22:          System.out.println("Your job has been submitted with id " + id);
23:
24:          session.deleteJobTemplate(jt);
25:          session.exit();
26:       } catch (DrmaaException e) {
27:          System.out.println("Error: " + e.getMessage());
28:       }
29:    }
30: }