rose_bunch§

For the running of multiple command variants in parallel under a single job, as defined by the application configuration.

Each variant of the command is run in the same working directory with its output directed to separate .out and .err files of the form:

bunch.<name>.out

Should you need separate working directories you should configure your command to create the appropriate subdirectory for working in.

Note

Under load balancing systems such as PBS or Slurm, you will need to set resource requests to reflect the resources required by running multiple commands at once e.g. if one command would require 1GB memory and you have configured your app to run up to four commands at once then you will need to request 4GB of memory.

Example§

meta=rose_bunch
mode=rose_bunch

[bunch]
command-format=echo arg1: %(arg1)s, arg2: %(arg2)s, command-instance: %(command-instances)s
command-instances = 4
fail-handle = abort
incremental = True
names = foo1 bar2 baz3 qux4
pool-size=2

[bunch-args]
arg1=1 2 3 4
arg2=foo bar baz qux

Configuration§

The application is normally configured in the rose_bunch[bunch] and rose_bunch[bunch-args] sections of the rose-app.conf file, but rose-app.conf[command] can be used too, see below for details.

Rose App rose_bunch
Config [bunch]
Config command-format= FORMAT

A Pythonic printf-style format string to construct the commands to run. Insert placeholders %(argname)s for substitution of the arguments specified under [bunch-args] to the invoked command. The placeholder %(command-instances)s is reserved for inserting an automatically generated index for the command invocation when using the command-instances setting. If not specified then the command to run is determined following the mode=command logic, see rose app-run for details, and arguments are made accessible to the command as environment variables.

Config command-instances= N

Allows the user to specify an integer value for the number of instances of a command they want to run. This generates the values used by the %(command-instances)s value in command-format. If [bunch]command-format is not specified then the command instance is passed as the COMMAND_INSTANCES environment variable instead. This is useful for cases where the only difference between invocations would be an index number e.g. ensemble members. Note indexes start at 0.

Config pool-size= N

Allows the user to limit the number of concurrently running commands. If not specified then all command variations will be run at the same time.

Config fail-mode= continue|abort
Default:continue

Specify what action you want the job to take on the failure of a command that it is trying to run. If set to continue all command variants will be run by the job and the job will return a non-zero exit code upon completion e.g. if three commands are to be run and the second one fails, all three will be run and the job will exit with a return code of 1. Alternatively, if fail-mode is set to abort then on failure of any one of the command variants it will stop trying to run any further variants N.B. the job will wait for any already running commands to finish before exiting. Commands that won’t be run due to aborting will be reported in the job output with a [SKIP] prefix when running in verbose mode. For example in the case of three command variants with a pool-size of 1 and fail-mode=abort, if the second variant failed then the job would exit with a non-zero error code without having run the third variant.

Config incremental= true|false
Default:true

If set to true then only failed commands will be re-run on retrying running of the job. If any changes are made to the configuration being run then all variants will be re-run. Similarly, running the app with the --new option to rose task-run will result in all commands being run. In verbose mode the app will report commands that won’t be run due to previous successes in the job output with a [PASS] prefix.

Config names= name1 name2 ...

Allows defining names for each of the command variants to be run, facilitating identification in logs. If not set then commands will be identified by their index. The number of entries in the names must be the same as the number of entries in each of the args to be used.

Config argument-mode= Default|izip|izip_longest|product
Default:Default

If set to a value other than Default then the values for each bunch-arg will be manipulated. izip will shrink all values so all have the same length as the shortest bunch-arg. izip_longest will pad out values for each bunch-arg with an empty string so that each bunch-arg is the same length as the longest one. product will expand all provided bunch-args to create each possible combination. See the itertools documentation in Python for more information.

Config [bunch-args]

This section is used to specify the various combinations of args to be passed to the command specified under [bunch]command-format, if defined, or rose-app.conf[command] otherwise.

Config argname= val1 val2 ...

Allows defining named lists of argument values to pass to the commands being run. Multiple named sets of arguments can be defined. Each argname can be referenced using %(argname)s in [bunch]command-format, if specified, or ${argname} environment variable otherwise. The only disallowed names are command-instances and COMMAND_INSTANCES, which are reserved for the auto-generated list of instances when the [bunch]command-instances=N option is used.