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Assuming you have followed the instructions at Installing HPS Java, you can run the standalone jar file two ways.
Using the -jar switch from the command line will run the main from the class JobManager, which is listened in the manifest inside the jar.
java -jar ./distribution/target/hps-distribution-3.6-SNAPSHOT-bin.jar [args]
Without any arguments it will print the command line options and then exit.
You can also run the main method from any class in the jar.
All instructions given here assume you're using the steering files included with the release. If you write your own, you can point hps-java to it by omitting the "-r" and using the file path of your .lcsim file:
java -jar hps-distribution.jar -i recon.slcio my_steering_files/MyAnalysis.lcsim -DoutputFile=analysis_plots
The standard steering files are in trunk/steering-files/src/main/resources/org/hps/steering/.
Every package in hps-java does have a default level which comes from:
trunk/logging/src/main/resources/org/hps/logging/config/logging.properties
provided you set the system property as I described or use one of the wrapper scripts from distribution.
Or you can override the default levels by providing your own custom config using
java -D -Djava.util.logging.config.file=mylogging.properties
There you can set the log level of all the packages in your custom config.
This is handled by: https://docs.oracle.com/javase/7/docs/api/java/util/logging/package-summary.html
The levels in descending order are:
SEVERE (highest value)
WARNING
INFO
CONFIG
FINE
FINER
FINEST (lowest value)
ALL (Give all messages)
OFF (Suppress all messages)