Processing Data in Batch Mode using LCSim XML

Basics

This tutorial explains how to run org.lcsim in a batch computing environment, such as on a unix command line or from a shell script, which could be run on the grid.

If you have not gotten here by following the LCSim Tutorials, then backup and read or review as necessary.

Setup

Follow the instructions for building lcsim software using maven2.

You can now run lcsim from the command-line using the java command.

java -server -jar ./target/lib/lcsim-[VERSION].jar [XML]

The VERSION is replaced by your lcsim build version. And XML is a file in the lcsim recon XML format.

java -server -jar ./target/lib/lcsim-1.11-SNAPSHOT.jar ./myJob.xml

Simple Example

The JobManager class processes your job, which is written in an xml format.

Here is a simple example which will print the event number.

<lcsim>
    <inputFiles>
        <file>./myEvents.slcio</file>
    </inputFiles>
    <control>
        <numberOfEvents>100</numberOfEvents>
    </control>
    <execute>
        <driver name="EventMarkerDriver"/>
    </execute>
    <drivers>
        <driver name="EventMarkerDriver"
                type="org.lcsim.job.EventMarkerDriver">
            <eventInterval>1</eventInterval>
        </driver>
    </drivers>
</lcsim>

The inputFiles section is a list of one or more LCIO input file paths that will be processed.

The control section sets the jobs run parameters. Here we set the maximum numberOfEvents.

The execute section is a list of drivers to be executed in order. The name field of the driver element must correspond with a valid driver.

Finally, the drivers section describes the drivers that will be run on the input file. Certain types of Driver parameters can be set in this section. Here the interval for event printing is set as eventInterval, which is an integer.

The signature for this method looks like this.

public void setEventInterval(int eventInterval);

The JobManager is able to convert from xml to these simple setters using Javabeans. All Java primitive types are accepted, as are 1d arrays of these types. The method must have a single argument only.

LCSim XML Format

This shows all possible XML elements in the LCSim format.

<lcsim>
    <inputFiles>
        <fileUrl />
        <file />
    </inputFiles>
    <control>
        <dryRun />
        <logFile />
        <cacheDirectory />
        <skipEvents />
        <numberOfEvents />
        <verbose />
        <printDriverStatistics />
        <printSystemProperties />
        <printUserClassPath />
        <printDriversDetailed />
    </control>
    <classpath>
        <jarUrl />
        <jar />
    </classpath>
    <define>
        <anExampleVariable/>
    </define>
    <execute>
        <driver name="ExampleDriver" />
    </execute>
    <drivers>
        <driver name="ExampleDriver" type="org.lcsim.example.ExampleDriver">
            <exampleParam />
        </driver>
    </drivers>
</lcsim>

Each of these xml sections will be explained in greater detail below.

Input Files

The <inputFiles> section contains a list of local or remote files to be processed.

These can be <file> elements which contain a relative or absolute path to a file on the local file system.

<inputFiles>
    <file>/path/to/local/datafile.slcio</file>
</inputFiles>

Remote files that accessible via a public URL can be accessed using a <fileUrl> element.

<inputFiles>
    <fileUrl>ftp://example.org/datafile.slcio</fileUrl>
</inputFiles>

These remote files will be downloaded to the cache directory, which is ~/.cache, by default. A different local cache directory can be specified using the <cacheDirectory> tag (covered below).

The <inputFiles> section can contain a mixture of <file> and <fileUrl> objects.

Some batch systems may not support remote file access via URL. Check with your administrator.

Job Control

The <control> section contains parameters that control the batch job, including the number of events to run and whether various debugging output should be printed.

Setting <dryRun> to true means that the job manager will create the drivers but will not run the job. This can be used to check that your driver setup and arguments are correct.

The <logFile> element is used to specify a log file location. If no log file is specified, the job output goes to the terminal screen.

The <cacheDirectory> specifies the root directory to be used for caching remote data files.

The <numberOfEvents> is the total number of events that will be run. All events will be processed if this argument is left blank.

The <skipEvents> argument tells the job manager to skip a number of events up-front before processing the rest.

The <verbose> tag should be set to true for verbose debugging output.

These tags can also be set to true to print out additional information about the job: <printDriverStatistics>, <printSystemProperties>, <printUserClassPath>, and <printDriversDetailed>.

Variable Definitions

Driver Execution

The <execute> section specifies the order in which the drivers will be called for each event. Each <driver> tag must have a unique name attribute value that matches the name of a driver defined in the <drivers> section (see next section).

Driver Definition

The <drivers> section contains definitions for all drivers that will be called in the job. These drivers need to be defined in the LCSim package jar or any of the jars in the <classpath>.

Driver Arguments

Using Javabeans, the job manager is able to convert simple XML text into parameter arguments for drivers. Only simple method signatures with single arguments are supported.

Here is a table of supported parameter types.

Types with a yes in the array1d or array2d columns support arrays of those dimensions. Arrays beyond two dimensions are not supported and would need to be read in manually by user code, perhaps using a method with a File or URL argument. Types that support expression evaluation have a yes in that column.

Driver Example

The easiest way to understand how the driver parameter conversion works is to study a simple example.

Here is an example Driver class.

public class MyDriver
{
    public void setX(int x);
    public void setX1(int[] x);
    public void setX2(int[][] x);
  
    public void setFile(File f);
    public void setUrl(URL url);
    public void setVector(Hep3Vector vec);
}

In a real Driver, the methods would be defined to set private variables to the argument values, but this is left out of the example for brevity.

This is the corresponding XML code in <drivers> that would set values for these parameters.

<driver name="MyDriver" type="org.lcsim.example.MyDriver">
    <x>1</x>
    <x1>1 2 3</x1>
    <x2>1 2 3; 4 5 6</x2>

    <file>/path/to/a/file.txt</file>
    <url>http://example.org/file.txt</url>
    <vector>1.0 2.0 3.0</vector>
</driver>

There are several important things to notice in this example.

By Javabeans' convention, the set methods are transformed into parameter names by removing the "set" string from the method name and making the first letter of the parameter lower case. Driver methods must begin with "set" or will not be accessible from LCSim XML.

Multi-dimensional arguments are space delimited, meaning String arguments should not have spaces. The rows in 2D arrays are separated by semicolons.

In the above example, integers are used for the 1D and 2D arrays, but other types support arrays, also. See the types table above for specifics.

Expression Evaluation

Guidelines for Creating Compatible Drivers

driver class must be public
drivers must have a public, no argument constructor
drivers should not do any initialization in their constructors; use detectorChanged() or startOfData() instead
driver set methods should always be of the form public void setParameter(type singleArg)
use of sub-drivers is discouraged due to these being inaccessible to the job manager, though it is still possible

Running a Specific LCSim Release

When an LCSim release is made, a zip file is created containing the LCSim jar and all its dependencies. Running a specific version of LCSim from the command line is as simple as downloading this zip file, unzipping it, and using the java command to run the jar with your XML input.

Retrieve the dependencies jar for the version you want to run.

wget http://www.lcsim.org/maven2/org/lcsim/lcsim/1.4/lcsim-1.4-deps.zip

You can also paste this URL into your browser, and a prompt should show asking whether to download it. (Specifics depend on your browser.)

Now, unzip the dependencies jar. All the jars will show up in a directory called lib/ in your current directory.

unzip lcsim-1.4-deps.zip

This uses the command line zip utility, but a zip program with a GUI such as WinZip or WinRar would work fine, too.

We're ready to run this version of lcsim. This step requires java 1.5 or greater to be installed and accessible from your command terminal.

java -server -jar ./lib/lcsim-1.4.jar ./myJob.xml

Each release is also tagged in the cvs, like lcsim-1_4, so checking it out and rebuilding yourself is another possibility. (Not covered here.)