GS Run Processor Manager

6.3	GS Run Processor Manager

The gsRunProcessorManager is a server application that provides a simple queuing system for processing jobs that can launch, abort and monitor jobs, and report job progress. The gsRunProcessorManager is the mechanism used to launch processing jobs from the GS Run Browser application.

The command to start the gsRunProcessorManager daemon (run as root) is:

/etc/init.d/gsRunProcessorManager start

The gsRunProcessorManager command structure and options are:

gsRunProcessorManager OPTIONS

Command	Description
gsRunProcessorManager	Front end for management of a shared compute resource of gsRunProcessor

Option	Description
--daemon	Run application as a daemon
-CFILE, --conf=FILE	Loads an alternate config file
-pPORT, --port=PORT	Attaches to port number (default=4540)
--pid=FILE	Writes process ID (pid) to a file
--portFile=FILE	Writes port number to a file
-v, --verbose	Increases verbosity
-V, --version	Displays the version of the software
-h, --help	Display argument help information

The gsRunProcessorManager is controlled by a single XML configuration file, gsRunProcessorManager_conf.xml, found in /etc/gsRunProcessorManager/. Alternate configuration files may be specified on the command line by specifying a parameter to the ‑CFILE or --conf=FILE option. The parameters in the configuration file are described below.

Parameter	Values	Description
enableQueue	True, False	Enables or disables job queuing mechanism
log  file	gsRunProcessorManager.log path (/var/log)	Specifies the path to output the gsRunProcessorManager log file
log  autorotate	True, False	Enables or disables log autorotate such that the log file is not overwritten for each processing job.
outputDirectory	Path to sequencing Run output data directory (/data)	Used to estimate if there is enough disk space available to start a new sequencing run
xmlrpc  port	Valid port number (4050)	Controls the port on which gsRunProcessor Manager listens for XML-RPC and HTTP requests
files  pid	gsRunProcessorManager.pid path (/var/run)	Specifies the path to output the gsRunProcessorManager pid file
files  port	gsRunProcessorManager.port path (/var/run)	Specifies the path to output the gsRunProcessorManager port file
mpi  enable	True, False	Enables or disables use of mpiexec for launching jobs. Equivalent to GS_LAUNCH_MODE=MPI.

The gsRunProcessorManager package also contains a small tool called gsRunProcessorManagerCtrl. It can be used to interact with the gsRunProcessorManager from command line scripts or other utilities.

gsRunProcessorManagerCtrl [OPTIONS] COMMAND [PARAMETERS]

Command	Description
gsRunProcessorManagerCtrl	Submits jobs to a gsRunProcessorManager. Not to be used directly, but to be called by shell scripts.

Commands	Description
Launch	Launches a processing job
Status	Gets the status of a processing job
Queue	Shows the status of the job queue
Abort	Interrupts processing of a job
queryVersion	Gets the version of the remote software

Option	Description
-HHOSTNAME, --host=HOSTNAME	Connects to host (default=localhost)
-m, --machine	Format output data suitable for scripting
-pPORT, --port=PORT	Uses port number (default=4540)
-v, --verbose	Increases verbosity
-V, --version	Displays the version of the software
-h, --help	Display argument help information