GotCloud: Configuration

The GotCloud configuration file contains the run-time options, including software binaries and command line arguments. A default configuration file is automatically loaded. Users may specify their own configuration file specifying just the values different than the defaults. The configuration file is not required if there are no values to override.

• Default GotCloud configuration file is gotcloud/bin/gotcloudDefaults.conf
• Comments begin with a #
• Format: KEY = value
  • where KEY is the item being set and value is its new value
• Some settings can be defined both in the configuration file and on the GotCloud command-line
  • command-line options take priority over configuration file settings
• A KEY can be used in another KEY's value by specifying $(KEY)
  • Example:

    KEY1 = value1

    KEY2 = $(KEY1)/value2

    • When KEY2 is used, it will be equal to: value1/value2

Output Directory

• The output directory is required for running GotCloud, so GotCloud knows where to write its output

Configuration Key	Command-line Flag	Value Description
OUT_DIR	--outdir	output directory

Reference/Resource Files

• See GotCloud: Genetic Reference and Resource Files for reference/resource file configuration settings

Cluster Configuration

Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it.

• For any BATCH_TYPEs that run in batch mode, GotCloud generates a script that will wait until the step is complete before returning
  • In a sense, it "fakes" interactive mode for all batch types since it will not proceed until a command is finished
• If you are at UM and are using flux, you can specify either flux or pbs

Configuration Key	Command-line Flag	Value Description
BATCH_TYPE	--batchtype	type of cluster system
		Valid Values	Command to Launch	Command to Check for Completion
		mosix	mosbatch -E/tmp	N/A - interactive type
		sge	qsub	qstat -u $USER
		sgei	qrsh -now n	N/A - interactive type
		pbs	qsub	qstat -u $USER
		slurm	sbatch	squeue -u $USER
		slurmi		N/A - interactive type
		local	N/A - local command	N/A - interactive type
BATCH_OPTS	--batchopts	options to pass to your cluster type, example: -j36,37,38,39,40,41,45,46,47,48,49