Running HPS Java

Before You Start

Before reading these instructions, you will want to read Installing HPS Java, which explains how to build or get an HPS Java distribution jar file.

Distribution Jars

The distribution jar file contains all of the project's dependencies in a distribution that can be run standalone using the java command.  The distribution will have "-bin" in the name.

The jar file will be found in your copy of HPS Java after you have built the project locally.  You can use a simple ls command to check that it was built correctly.

ls distribution/target/hps-distribution-*-bin.jar

Any references to hps-distribution-bin.jar in command line syntax within these instructions should be replaced by the complete path to the distribution jar which was built.

Running the Jar File

The distribution jar can be run in two basic ways.  You may run the default main method using the -jar switch, or the -cp switch can be used along with the path to a class's main method.

Running the Job Manager

Using the -jar switch from the command line will run the JobManager which processes LCIO files using a steering file configuration.

java -jar ./distribution/target/hps-distribution-bin.jar [args]

Without any arguments, it will print the command line options and then exit.

Running a Specific Class's Main Method

You can also run the main method from any class in the jar, for example:

java -cp ./distribution/target/hps-distribution-bin.jar org.hps.evio.EvioToLcio [args]

If there is a "class not found" error, then check the following: the correctness of the path to the jar, the existence and proper definition of a main method within the Java class, and the read permissions on the jar file.

A class can only be accessed from the command line if it defines a valid main method.

package org.example;
 
public class MyClass {
    public static void main(String[] args) {
        System.out.println("hello main");
    }
}

To be directly accessible from the command line, a class must also have the following features.

• It must be marked as public.
• It must have a public static method called main (as shown above).
• The main method must have an array of strings as an input variable.

Assuming that MyClass was bundled inside the distribution (which it isn't), then it could be run from the command line as follows:

java -cp ./distribution/target/hps-distribution-bin.jar org.example.MyClass arg1 arg2 [...]

Most classes that implement a command line interface will print out a help message when run with no additional options e.g.

java -cp ./distribution/target/hps-distribution-bin.jar org.hps.evio.EvioToLcio

By convention, the -h switch is also usually used to print out a help menu.

java -cp ./distribution/target/hps-distribution-bin.jar org.hps.evio.EvioToLcio -h

The specific command line syntax is unfortunately not standardized across all tools in the project and will depend on what was implemented in that class by the particular author.

Running Tests

mvn test -Dtest=[TestClassName]

mvn verify -Dit.test=[TestClassName]

Command Line Tools

Job Manager

The JobManager runs a series of Drivers defined in an lcsim xml file on input events from one or more LCIO files.  The XML steering file may contain lists of input file tags, or the input files may(more typically) be supplied by command line arguments.  

Job Manager Command Line Usage

[1026 $] java -jar ./hps-java-trunk/distribution/target/hps-distribution-3.6-SNAPSHOT-bin.jar
Feb 18, 2016 4:02:27 PM org.lcsim.job.JobControlManager printHelp
INFO: java org.lcsim.job.JobControlManager [options] steeringFile.xml
usage:
 -b,--batch               Run in batch mode in which plots will not be
                          shown.
 -D,--define <arg>        Define a variable with form [name]=[value]
 -d,--detector <arg>      user supplied detector name (careful!)
 -e,--event-print <arg>   Event print interval
 -h,--help                Print help and exit
 -i,--input-file <arg>    Add an LCIO input file to process
 -n,--nevents <arg>       Set the max number of events to process
 -p,--properties <arg>    Load a properties file containing variable
                          definitions
 -r,--resource            Use a steering resource rather than a file
 -R,--run <arg>           user supplied run number (careful!)
 -s,--skip <arg>          Set the number of events to skip
 -w,--rewrite <arg>       Rewrite the XML file with variables resolved
 -x,--dry-run             Perform a dry run which does not process events

Job Manager Command Line Options

The steering file is a mandtaory argument, and it is supplied as an extra argument rather than as a command switch.

If a detector name and run number are both supplied as arguments from the command line, then the conditions system will be initialized and frozen, meaning that subsequent event numbers from data will be ignored.

Here is an example command using most of these switches together.

java -jar ./hps-java-trunk/distribution/target/hps-distribution-bin.jar -b -DoutputFile=output -d HPS-EngRun2015-Nominal-v3 -e 100 -i input.slcio \
-n 1000 -p myvars.prop -r -R 5772 -s 10 -w myjob.xml -x /org/hps/steering/dummy.lcsim

The above command is actually nonsense and will not work!  

EvioToLcio

The EvioToLcio tool converts EVIO files to LCIO format and optionally may run a steering file job on the in-memory events.  This scheme allows the conversion and reconstruction to run within the same job for efficiency.

EvioToLcio Command Line Usage

[1037 $] java -cp ./distribution/target/hps-distribution-3.6-SNAPSHOT-bin.jar org.hps.evio.EvioToLcio
EvioToLcio [options] [evioFiles]
usage:
 -b         enable headless mode in which plots will not show
 -d <arg>   detector name (required)
 -D <arg>   define a steering file variable with format -Dname=value
 -f <arg>   text file containing a list of EVIO files
 -h         print help and exit
 -L <arg>   log level (INFO, FINE, etc.)
 -l <arg>   path of output LCIO file
 -m <arg>   set the max event buffer size
 -M         use memory mapping instead of sequential reading
 -n <arg>   maximum number of events to process in the job
 -r         interpret steering from -x argument as a resource instead of a
            file
 -R <arg>   fixed run number which will override run numbers of input
            files
 -t <arg>   specify a conditions tag to use
 -v         print EVIO XML for each event
 -x <arg>   LCSim steeering file for processing the LCIO events

EvioToLcio Command Line Options Table

Here is an example showing how to use most of these command line options.

java -jar ./hps-java-trunk/distribution/target/hps-distribution-bin.jar org.hps.evio.EvioToLcio -b -DoutputFile=output -l lcio_file_output -m 50 \
-v -M -n 1000 -d HPS-EngRun2015-Nominal-v3 -R 5772 -t pass1 -r -x /org/hps/steering/dummy.lcsim file1.evio file2.evio file3.evio [etc.]

Some of these arguments are similar to the job manager, but the steering file is supplied in a different way.  Evio2Lcio also uses a command switch to specifiy the steering file, whereas the job manager expects this as an extra argument without a command switch.

Run Scripts

Run scripts that wrap a number of HPS Java command line utilities are generated when building the distribution.  These can be used to easily run tools in the project without typing the full java command.

After the build completes, they should be found in this HPS Java directory.

distribution/target/appassembler/bin/

For instance, the EvioToLcio utility can be run using this script.

distribution/target/appassembler/bin/evio2lcio.sh [...]

These scripts have several advantages over running the java commands yourself.

• A full classpath is created in the script so it is not necessary to use the distribution jar.
• Reasonable JVM options are set such as the min heap size.
• Logging is configured automatically by a default logging properties file.
• You do not need to type all the Java boilerplate commands like "java -jar".
• You do not need to know the corresponding class's full name in order to run its command line utility.

Using symlinks to these scripts should work fine e.g.

ln -s distribution/target/appassembler/bin/evio2lcio.sh
./evio2lcio.sh

When using these scripts, you cannot directly supply Java system properties, so the JAVA_OPTS variable should be used instead.

export JAVA_OPTS="-Dorg.hps.conditions.enableSvtAlignmentConstants"

The full list of Java system properties to be used should be included in this variable.  You should not set the options -Xmx or -Djava.util.logging.config.class, as these are set by each script.

Steering Files

Steering File Locations

The standard location for steering files is steering-files/src/main/resources/org/hps/steering/ in HPS Java.

This folder is organized into the following sub-directories which contain sets of related steering files.

These steering files can be accessed using their path on disk, or they may be referenced as classpath resources.  The exact syntax will depend on the command line tool.

For example, a steering file resource can be accessed like this using the job manager:

java -jar ./hps-java/distribution/target/hps-distribution-bin.jar -x /org/hps/steering/recon/EngineeringRun2015FullRecon.lcsim [...]

The same steering file could also be accessed as a file from the local copy of HPS Java.

java -jar ./hps-java/distribution/target/hps-distribution-bin.jar hps-java-trunk/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015FullRecon.lcsim [...]

You can use a file rather than a resource if you running a steering file which is not checked into HPS Java or you are using a modified steering file that has not been packaged into the distribution jar.

Steering File Variables

Suppose a steering file contains the following variable definition:

<driver name="MyDriver" type="org.example.MyDriver">
    <someNumber>${numVar}</someNumber>
</driver>

The variable would then need to be resolved with a command such as:

 java -cp ./distribution/target/hps-distribution-bin.jar org.hps.evio.EvioToLcio -DnumVar=1234 [...]

All variables defined in the XML steering files must be resolved from the command line or an error will occur and the job will terminate.

System Properties

The command line tools may be affected by some Java system properties.

These values are set as system properties in Java itself rather than the command line tool.

java -Dorg.hps.conditions.enableSvtAlignmentConstants [...]

When set in this way, these values are accessible to the framework as Java system properties.

Java Arguments

The JVM accepts a number of command line arguments that alter its behavior.

In particular, when running java you will likely want to increase the default heap space, as the default is generally too low for running full reconstruction jobs.

This command will change the heap space to 2 gigabytes:

java -Xmx2g [...]

Also, you may want to run the JVM in server mode.

java -server [...]

The server JVM has been optimized for performance speed rather than responsiveness, and it should run faster than the default client JVM.

Logging and Debugging

Logging Config

HPS Java uses the built-in logging facilities of Java which are described in the logging package documentation.

Each package in HPS Java has a default level which is set in the following config file:

logging/src/main/resources/org/hps/logging/config/logging.properties

This config, or any other custom logging config, can be activated from the command line by setting the config file property to its path as a Java argument.

java -Djava.util.logging.config.file=logging/src/main/resources/org/hps/logging/config/logging.properties [...]

Alternately, you may also activate a Java class which will load this configuration.

java -Djava.util.logging.config.class=org.hps.logging.config.DefaultLoggingConfig [...]

Log Levels

These are the available log levels, in descending order.

Log Levels Table

Each logger inherits by default from the global log setting.

This is defined in the config file as follows.

# default global level
.level = WARNING

If a package's log level is not explicitly configured, then it will inherit the default WARNING log level from the global logger.

Defining Loggers

In the config file, loggers are defined and configured by their package rather than class.

# evio
org.hps.evio.level = CONFIG

In the above config, any logger within the org.hps.evio package will have a log level of CONFIG.

A class's logger is typically defined within the codebase using the following template.

package org.example;
 
import java.util.logging.Logger;
 
class MyClass {
 
    static private final Logger LOGGER = Logger.getLogger(MyClass.class.getPackage().getName());
 
    void someMethod() {
        LOGGER.info("some method was called");
    }
}

The handler and the level should not be assigned within the code, because changing the level would require recompilation.  Instead, the level should be defined using the config file as described above.