fermipy.jobs subpackage¶
fermipy.jobs.link module¶
Module for class Link
, which wraps a single command line application.
-
class
fermipy.jobs.link.
Link
(**kwargs)[source]¶ Bases:
object
A wrapper for a command line application.
This class keeps track for the arguments to pass to the application as well as input and output files.
This can be used either with other
Link
objects to build aChain
, or as standalone wrapper to pass configuration to the application.Derived classes will need to override the appname and linkname-default class parameters.
Parameters: - appname (str) – Name of the application run by this
Link
- linkname_default (str) – Default name for
Link
of this type - default_options (dict) – Dictionry with options, defaults, helpstring and types
for the parameters associated with the
Link
- default_file_args (dict) – Dictionary specifying if particular parameters are associated with input or output files.
- linkname (str) – Name of this
Link
, used as a key to find it in aChain
. - link_prefix (str) – Optional prefix for this
Link
, used to distinguish between similarLink
objects on differentChain
objects. - args (dict) – Up-to-date dictionary with the arguments that will be passed to the application
- _options (dict) – Dictionary with the options that we are allowed to set and default values
- files (
FileDict
) – Object that keeps track of input and output files - jobs (
OrderedDict
) – Dictionary mapping keys toJobDetails
. This contains information about all the batch jobs associated to thisLink
-
appname
= 'dummy'¶
-
arg_names
¶ Return the list of arg names
-
check_input_files
(return_found=True, return_missing=True)[source]¶ Check if input files exist.
Parameters: Returns:
-
check_job_status
(key='__top__', fail_running=False, fail_pending=False, force_check=False)[source]¶ Check the status of a particular job
By default this checks the status of the top-level job, but can by made to drill into the sub-jobs.
Parameters: Returns: status – Job status flag
Return type: JobStatus
-
check_jobs_status
(fail_running=False, fail_pending=False)[source]¶ Check the status of all the jobs run from this link and return a status flag that summarizes that.
Parameters: Returns: status – Job status flag that summarizes the status of all the jobs,
Return type: JobStatus
-
check_output_files
(return_found=True, return_missing=True)[source]¶ Check if output files exist.
Parameters: Returns:
-
clean_jobs
(recursive=False)[source]¶ Clean out all of the jobs associated to this link.
For sub-classes, if recursive is True this also clean jobs from any internal
Link
-
clear_jobs
(recursive=True)[source]¶ Clear the self.jobs dictionary that contains information about jobs associated with this
Link
.For sub-classes, if recursive is True this also clean jobs from any internal
Link
-
command_template
()[source]¶ Build and return a string that can be used as a template invoking this chain from the command line.
The actual command can be obtainted by using
self.command_template().format(**self.args)
-
default_file_args
= {}¶
-
default_options
= {}¶
-
description
= 'Link to run dummy'¶
-
formatted_command
()[source]¶ Build and return the formatted command for this
Link
.This is exactly the command as called from the Unix command line.
-
full_linkname
¶ Return the linkname with the prefix attached This is useful to distinguish between links on different
Chain
objects.
-
get_failed_jobs
(fail_running=False, fail_pending=False)[source]¶ Return a dictionary with the subset of jobs that are marked as failed
Parameters: Returns: failed_jobs – Dictionary mapping from job key to
JobDetails
for the failed jobs.Return type:
-
get_jobs
(recursive=True)[source]¶ Return a dictionary with all the jobs
For sub-classes, if recursive is True this will include jobs from any internal
Link
-
linkname_default
= 'dummy'¶
-
missing_input_files
()[source]¶ Make and return a dictionary of the missing input files.
This returns a dictionary mapping filepath to list of
Link
that use the file as input.
-
missing_output_files
()[source]¶ Make and return a dictionary of the missing output files.
This returns a dictionary mapping filepath to list of links that produce the file as output.
-
print_summary
(stream=<open file '<stdout>', mode 'w'>, indent='', recurse_level=2)[source]¶ Print a summary of the activity done by this
Link
.Parameters:
-
run
(stream=<open file '<stdout>', mode 'w'>, dry_run=False, stage_files=True, resubmit_failed=False)[source]¶ Runs this
Link
.This version is intended to be overwritten by sub-classes so as to provide a single function that behaves the same for all version of
Link
Parameters:
-
run_command
(stream=<open file '<stdout>', mode 'w'>, dry_run=False)[source]¶ Runs the command for this link. This method can be overridden by sub-classes to invoke a different command
Parameters: Returns: code – Return code from sub-process
Return type:
-
run_with_log
(dry_run=False, stage_files=True, resubmit_failed=False)[source]¶ Runs this link with output sent to a pre-defined logfile
Parameters:
-
topkey
= '__top__'¶
-
update_args
(override_args)[source]¶ Update the argument used to invoke the application
Note that this will also update the dictionary of input and output files.
Parameters: override_args (dict) – Dictionary of arguments to override the current values
-
usage
= 'dummy [options]'¶
- appname (str) – Name of the application run by this
-
fermipy.jobs.link.
add_argument
(parser, dest, info)[source]¶ Add an argument to an
argparse.ArgumentParser
objectParameters: - parser (
argparse.ArgumentParser
) – The parser in question - dest (str) – The destination for the argument
- info (
tuple
) – The information associated with the argument in question.
- parser (
-
fermipy.jobs.link.
check_files
(filelist, file_stage_manager=None, return_found=True, return_missing=True)[source]¶ Check that all files in a list exist
Parameters: - filelist (list) – The list of files we are checking for.
- file_stage_manager (
fermipy.jobs.file_archive.FileStageManager
) – A object that maps files to scratch space if needed. - return_found (list) – A list with the paths of the files that were found.
- return_missing (list) – A list with the paths of the files that were missing.
Returns:
-
fermipy.jobs.link.
convert_dict_to_option_dict
(input_dict)[source]¶ Convert a simple key-value dictionary to a dictionary of options tuples
-
fermipy.jobs.link.
convert_option_dict_to_dict
(option_dict)[source]¶ Convert a dictionary of options tuples to a simple key-value dictionary
-
fermipy.jobs.link.
convert_value_to_option_tuple
(value, helpstr=None)[source]¶ Convert a value to a tuple of the form expected by
Link.options
Parameters: - value – The value we are converting
- helpstr (str) – The help string that will be associated to this option.
Returns: option_info – A 3-tuple with default value, helpstring and type for this particular option.
Return type:
fermipy.jobs.chain module¶
The Chain
class inherits from Link
and allow chaining together several
applications into a single object.
-
class
fermipy.jobs.chain.
Chain
(**kwargs)[source]¶ Bases:
fermipy.jobs.link.Link
An object tying together a series of applications into a single application.
This class keep track of the arguments to pass to the applications as well as input and output files.
Note that this class is itself a
Link
. This allows you to write a python module that implements a chain and also has a __main__ function to allow it to be called from the shell.-
check_links_status
(fail_running=False, fail_pending=False)[source]¶ “Check the status of all the jobs run from the
Link
objects in thisChain
and return a status flag that summarizes that.Parameters: Returns: status – Job status flag that summarizes the status of all the jobs,
Return type: JobStatus
-
clear_jobs
(recursive=True)[source]¶ Clear a dictionary with all the jobs
If recursive is True this will include jobs from all internal
Link
-
get_jobs
(recursive=True)[source]¶ Return a dictionary with all the jobs
If recursive is True this will include jobs from all internal
Link
-
missing_input_files
()[source]¶ Make and return a dictionary of the missing input files.
This returns a dictionary mapping filepath to list of
Link
that use the file as input.
-
missing_output_files
()[source]¶ Make and return a dictionary of the missing output files.
This returns a dictionary mapping filepath to list of links that produce the file as output.
-
print_status
(indent='', recurse=False)[source]¶ Print a summary of the job status for each
Link
in thisChain
-
print_summary
(stream=<open file '<stdout>', mode 'w'>, indent='', recurse_level=2)[source]¶ Print a summary of the activity done by this
Chain
.Parameters:
-
fermipy.jobs.file_archive module¶
Classes and utilites to keep track of files associated to an analysis.
The main class is FileArchive
, which keep track of all the files associated to an analysis.
The FileHandle
helper class encapsulates information on a particular file.
-
class
fermipy.jobs.file_archive.
FileArchive
(**kwargs)[source]¶ Bases:
object
Class that keeps track of the status of files used in an analysis
Parameters: - table_file (str) – Path to the file used to persist this
FileArchive
- table (
astropy.table.Table
) – Persistent representation of thisFileArchive
- cache (
OrderedDict
) – Transient representation of thisFileArchive
- base_path (str) – Base file path for all files in this
FileArchive
-
base_path
¶ Return the base file path for all files in this
FileArchive
-
classmethod
build_archive
(**kwargs)[source]¶ Return the singleton
FileArchive
instance, building it if needed
-
cache
¶ Return the transiet representation of this
FileArchive
-
classmethod
get_archive
()[source]¶ Return the singleton
FileArchive
instance
-
get_file_ids
(file_list, creator=None, status=0, file_dict=None)[source]¶ Get or create a list of file ids based on file names
Parameters: - file_list (list) – The paths to the file
- creatror (int) – A unique key for the job that created these files
- status (
FileStatus
) – Enumeration giving current status of files - file_dict (
FileDict
) – Mask giving flags set on this file - list of integers (Returns) –
-
get_file_paths
(id_list)[source]¶ Get a list of file paths based of a set of ids
Parameters: - id_list (list) – List of integer file keys
- list of file paths (Returns) –
-
get_handle
(filepath)[source]¶ Get the
FileHandle
object associated to a particular file
-
register_file
(filepath, creator, status=0, flags=0)[source]¶ Register a file in the archive.
If the file already exists, this raises a
KeyError
Parameters: - filepath (str) – The path to the file
- creatror (int) – A unique key for the job that created this file
- status (
FileStatus
) – Enumeration giving current status of file - flags (
FileFlags
) – Enumeration giving flags set on this file - FileHandle (Returns) –
-
table
¶ Return the persistent representation of this
FileArchive
-
table_file
¶ Return the path to the file used to persist this
FileArchive
-
update_file
(filepath, creator, status)[source]¶ Update a file in the archive
If the file does not exists, this raises a
KeyError
Parameters: - filepath (str) – The path to the file
- creatror (int) – A unique key for the job that created this file
- status (
FileStatus
) – Enumeration giving current status of file - FileHandle (Returns) –
- table_file (str) – Path to the file used to persist this
-
class
fermipy.jobs.file_archive.
FileDict
(**kwargs)[source]¶ Bases:
object
Small class to keep track of files used & createed by a link.
Parameters: -
chain_input_files
¶ Return a list of the input files needed by this chain.
For
Link
sub-classes this will return only those files that were not created by any internalLink
-
chain_output_files
¶ Return a list of the all the output files produced by this link.
For
Link
sub-classes this will return only those files that were not marked as internal files or marked for removal.
-
gzip_files
¶ Return a list of the files compressed by this link.
This returns all files that were explicitly marked for compression.
-
input_files
¶ Return a list of the input files needed by this link.
For
Link
sub-classes this will return the union of all the input files of each internalLink
.That is to say this will include files produced by one
Link
in aChain
and used as input to anotherLink
in theChain
-
input_files_to_stage
¶ Return a list of the input files needed by this link.
For
Link
sub-classes this will return the union of all the input files of each internalLink
.That is to say this will include files produced by one
Link
in aChain
and used as input to anotherLink
in theChain
-
internal_files
¶ Return a list of the intermediate files produced by this link.
This returns all files that were explicitly marked as internal files.
-
output_files
¶ Return a list of the output files produced by this link.
For
Link
sub-classes this will return the union of all the output files of each internalLink
.That is to say this will include files produced by one
Link
in aChain
and used as input to anotherLink
in theChain
-
output_files_to_stage
¶ Return a list of the input files needed by this link.
For
Link
sub-classes this will return the union of all the input files of each internalLink
.That is to say this will include files produced by one
Link
in aChain
and used as input to anotherLink
in theChain
-
print_chain_summary
(stream=<open file '<stdout>', mode 'w'>, indent='')[source]¶ Print a summary of the files in this file dict.
This version uses chain_input_files and chain_output_files to count the input and output files.
-
print_summary
(stream=<open file '<stdout>', mode 'w'>, indent='')[source]¶ Print a summary of the files in this file dict.
This version explictly counts the union of all input and output files.
-
temp_files
¶ Return a list of the temporary files produced by this link.
This returns all files that were explicitly marked for removal.
-
-
class
fermipy.jobs.file_archive.
FileFlags
[source]¶ Bases:
object
Bit masks to indicate file types
-
gz_mask
= 8¶
-
in_ch_mask
= 23¶
-
in_stage_mask
= 33¶
-
input_mask
= 1¶
-
internal_mask
= 16¶
-
no_flags
= 0¶
-
out_ch_mask
= 22¶
-
out_stage_mask
= 34¶
-
output_mask
= 2¶
-
rm_mask
= 4¶
-
rmint_mask
= 20¶
-
stageable
= 32¶
-
-
class
fermipy.jobs.file_archive.
FileHandle
(**kwargs)[source]¶ Bases:
object
Class to keep track of infomration about a file file.
Parameters: -
append_to_table
(table)[source]¶ Add this instance as a row on a
astropy.table.Table
-
classmethod
create_from_row
(table_row)[source]¶ Build and return a
FileHandle
from anastropy.table.row.Row
-
classmethod
make_dict
(table)[source]¶ Build and return a dict of
FileHandle
from anastropy.table.Table
The dictionary is keyed by FileHandle.key, which is a unique integer for each file
-
static
make_table
(file_dict)[source]¶ Build and return an
astropy.table.Table
to storeFileHandle
-
update_table_row
(table, row_idx)[source]¶ Update the values in an
astropy.table.Table
for this instances
-
-
class
fermipy.jobs.file_archive.
FileStageManager
(scratchdir, workdir)[source]¶ Bases:
object
Small class to deal with staging files to and from a scratch area
-
construct_scratch_path
(dirname, basename)[source]¶ Construct and return a path in the scratch area.
This will be <self.scratchdir>/<dirname>/<basename>
-
get_scratch_path
(local_file)[source]¶ Construct and return a path in the scratch area from a local file.
-
static
make_scratch_dirs
(file_mapping, dry_run=True)[source]¶ Make any directories need in the scratch area
-
map_files
(local_files)[source]¶ Build a dictionary mapping local paths to scratch paths.
Parameters: - local_files (list) – List of filenames to be mapped to scratch area
- dict (Returns) – Mapping local_file : fullpath of scratch file
-
split_local_path
(local_file)[source]¶ Split the local path into a directory name and a file name
If local_file is in self.workdir or a subdirectory of it, the directory will consist of the relative path from workdir.
If local_file is not in self.workdir, directory will be empty.
Returns (dirname, basename)
-
-
class
fermipy.jobs.file_archive.
FileStatus
[source]¶ Bases:
object
Enumeration of file status types
-
exists
= 2¶
-
expected
= 1¶
-
missing
= 3¶
-
no_file
= 0¶
-
superseded
= 4¶
-
temp_removed
= 5¶
-
fermipy.jobs.job_archive module¶
Classes and utilites to keep track the various jobs that are running in an analysis pipeline.
The main class is JobArchive
, which keep track of all the jobs associated to an analysis.
The JobDetails
helper class encapsulates information on a instance of running a job.
-
class
fermipy.jobs.job_archive.
JobArchive
(**kwargs)[source]¶ Bases:
object
Class that keeps of all the jobs associated to an analysis.
Parameters: - table_file (str) – Path to the file used to persist this
JobArchive
- table (
astropy.table.Table
) – Persistent representation of thisJobArchive
- table_ids (
astropy.table.Table
) – Ancillary table with information about file ids - file_archive (
FileArchive
) – Archive with infomation about all this files used and produced by this analysis
-
classmethod
build_archive
(**kwargs)[source]¶ Return the singleton
JobArchive
instance, building it if needed
-
classmethod
build_temp_job_archive
()[source]¶ Build and return a
JobArchive
using defualt locations of persistent files.
-
cache
¶ Return the transiet representation of this
JobArchive
-
file_archive
¶ Return the
FileArchive
with infomation about all the files used and produced by this analysis
-
classmethod
get_archive
()[source]¶ Return the singleton
JobArchive
instance
-
get_details
(jobname, jobkey)[source]¶ Get the
JobDetails
associated to a particular job instance
-
make_job_details
(row_idx)[source]¶ Create a
JobDetails
from anastropy.table.row.Row
-
register_job
(job_details)[source]¶ Register a job in this
JobArchive
-
register_job_from_link
(link, key, **kwargs)[source]¶ Register a job in the
JobArchive
from aLink
object
-
table
¶ Return the persistent representation of this
JobArchive
-
table_file
¶ Return the path to the file used to persist this
JobArchive
-
table_ids
¶ Return the rpersistent epresentation of the ancillary info of this
JobArchive
-
update_job
(job_details)[source]¶ Update a job in the
JobArchive
- table_file (str) – Path to the file used to persist this
-
class
fermipy.jobs.job_archive.
JobDetails
(**kwargs)[source]¶ Bases:
object
A simple structure to keep track of the details of each of the sub-proccess jobs.
Parameters: - dbkey (int) – A unique key to identify this job
- jobname (str) – A name used to idenfity this job
- jobkey (str) – A string to identify this instance of the job
- appname (str) – The executable inovked to run the job
- logfile (str) – The logfile for this job, may be used to check for success/ failure
- job_config (dict) – A dictionrary with the arguments for the job
- parent_id (int) – Unique key identifying the parent job
- infile_ids (list of int) – Keys to identify input files to this job
- outfile_ids (list of int) – Keys to identify output files from this job
- rmfile_ids (list of int) – Keys to identify temporary files removed by this job
- intfile_ids (list of int) – Keys to identify internal files
- status (int) – Current job status, one of the enums above
-
append_to_tables
(table, table_ids)[source]¶ Add this instance as a row on a
astropy.table.Table
-
check_status_logfile
(checker_func)[source]¶ Check on the status of this particular job using the logfile
-
classmethod
create_from_row
(table_row)[source]¶ Create a
JobDetails
from anastropy.table.row.Row
-
fullkey
¶ Return the fullkey for this job fullkey = <jobkey>@<jobname>
-
get_file_ids
(file_archive, creator=None, status=0)[source]¶ Fill the file id arrays from the file lists
Parameters: - file_archive (
FileArchive
) – Used to look up file ids - creator (int) – A unique key for the job that created these file
- status (
FileStatus
) – Enumeration giving current status thse files
- file_archive (
-
get_file_paths
(file_archive, file_id_array)[source]¶ Get the full paths of the files used by this object from the the id arrays
Parameters: - file_archive (
FileArchive
) – Used to look up file ids - file_id_array (
numpy.array
) – Array that remaps the file indexes
- file_archive (
-
classmethod
make_dict
(table)[source]¶ Build a dictionary map int to
JobDetails
from anastropy.table.Table
-
static
make_fullkey
(jobname, jobkey='__top__')[source]¶ Combine jobname and jobkey to make a unique key fullkey = <jobkey>@<jobname>
-
static
split_fullkey
(fullkey)[source]¶ Split fullkey to make extract jobname, jobkey fullkey = <jobkey>@<jobname>
-
topkey
= '__top__'¶
-
update_table_row
(table, row_idx)[source]¶ Add this instance as a row on a
astropy.table.Table
-
class
fermipy.jobs.job_archive.
JobStatus
[source]¶ Bases:
object
Enumeration of job status types
-
done
= 5¶
-
failed
= 6¶
-
no_job
= -1¶
-
not_ready
= 1¶
-
partial_failed
= 7¶
-
pending
= 3¶
-
ready
= 2¶
-
removed
= 8¶
-
running
= 4¶
-
unknown
= 0¶
-
-
class
fermipy.jobs.job_archive.
JobStatusVector
[source]¶ Bases:
object
Vector that counts the status of jobs and returns an overall status flag based on those
-
n_done
¶ Return the number of successfully completed jobs
-
n_failed
¶ Return the number of failed jobs
-
n_pending
¶ Return the number jobs submitted to batch, but not yet running
-
n_running
¶ Return the number of running jobs
-
n_total
¶ Return the total number of jobs
-
n_waiting
¶ Return the number of jobs in various waiting states
-
fermipy.jobs.gtlink module¶
Utilities to chain together a series of ScienceTools apps
-
class
fermipy.jobs.gtlink.
Gtlink
(**kwargs)[source]¶ Bases:
fermipy.jobs.link.Link
A wrapper for a single ScienceTools application
This class keeps track for the arguments to pass to the application as well as input and output files.
This can be used either with other
Link
to build aChain
, or as as standalone wrapper to pass conifguration to the application.See help for
chain.Link
for additional details-
appname
= 'dummy'¶
-
command_template
()[source]¶ Build and return a string that can be used as a template invoking this chain from the command line.
The actual command can be obtainted by using
self.command_template().format(**self.args)
-
description
= 'Link to run dummy'¶
-
linkname_default
= 'dummy'¶
-
run_command
(stream=<open file '<stdout>', mode 'w'>, dry_run=False)[source]¶ Runs the command for this link. This method can be overridden by sub-classes to invoke a different command
Parameters: - stream (
file
) – Must have ‘write’ function - dry_run (bool) – Print command but do not run it
- stream (
-
update_args
(override_args)[source]¶ Update the argument used to invoke the application
See help for
chain.Link
for detailsThis calls the base class function then fills the parameters of the GtApp object
-
usage
= 'dummy [options]'¶
-
-
fermipy.jobs.gtlink.
build_gtapp
(appname, dry_run, **kwargs)[source]¶ Build an object that can run ScienceTools application
Parameters:
-
fermipy.jobs.gtlink.
extract_parameters
(pil, keys=None)[source]¶ Extract and return parameter names and values from a pil object
Parameters: - pil (
Pil
object) – - keys (list) – List of parameter names, if None, extact all parameters
Returns: out_dict – Dictionary with parameter name, value pairs
Return type: - pil (
-
fermipy.jobs.gtlink.
run_gtapp
(gtapp, stream, dry_run, **kwargs)[source]¶ Runs one on the ScienceTools apps
Taken from fermipy.gtanalysis.run_gtapp by Matt Wood
Parameters: - gtapp (
GtApp.GtApp
object) – The application (e.g., gtbin) - stream (stream object) – Must have ‘write’ function
- dry_run (bool) – Print command but do not run it
- kwargs (arguments used to invoke the application) –
- gtapp (
fermipy.jobs.batch module¶
Factory module to return the default interace to the batch farm
-
fermipy.jobs.batch.
get_batch_job_args
(job_time=1500)[source]¶ Get the correct set of batch jobs arguments.
Parameters: job_time (int) – Expected max length of the job, in seconds. This is used to select the batch queue and set the job_check_sleep parameter that sets how often we check for job completion. Returns: job_args – Dictionary of arguments used to submit a batch job Return type: dict
-
fermipy.jobs.batch.
get_batch_job_interface
(job_time=1500)[source]¶ Create a batch job interface object.
Parameters: job_time (int) – Expected max length of the job, in seconds. This is used to select the batch queue and set the job_check_sleep parameter that sets how often we check for job completion. Returns: job_interfact – Object that manages interactions with batch farm Return type: SysInterface
fermipy.jobs.scatter_gather module¶
Abstract interface for parallel execution of multiple jobs.
The main class is ScatterGather
, which can submit many instances
of a job with different configurations.
-
class
fermipy.jobs.scatter_gather.
ScatterGather
(link, **kwargs)[source]¶ Bases:
fermipy.jobs.link.Link
Class to dispatch several jobs in parallel and collect and merge the results.
Sub-classes will need to generatare configuration for the jobs that they launch.
Parameters: -
appname
= 'dummy-sg'¶
-
build_job_configs
(args)[source]¶ Hook to build job configurations
Sub-class implementation should return:
- job_configs : dict
- Dictionary of dictionaries passed to parallel jobs
-
check_status
(stream=<open file '<stdout>', mode 'w'>, check_once=False, fail_pending=False, fail_running=False, no_wait=False, do_print=True, write_status=False)[source]¶ Loop to check on the status of all the jobs in job dict.
Parameters: - stream (
file
) – Stream that this function will print to, Must have ‘write’ function. - check_once (bool) – Check status once and exit loop.
- fail_pending (
bool
) – If True, consider pending jobs as failed - fail_running (
bool
) – If True, consider running jobs as failed - no_wait (bool) – Do not sleep before checking jobs.
- do_print (bool) – Print summary stats.
- write_status (bool) – Write the status the to log file.
Returns: status_vect – Vector that summarize the number of jobs in various states.
Return type: JobStatusVector
- stream (
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clean_jobs
(recursive=False)[source]¶ Clean up all the jobs associated with this object.
If recursive is True this also clean jobs dispatch by this object.
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clear_jobs
(recursive=True)[source]¶ Clear the self.jobs dictionary that contains information about jobs associated with this
ScatterGather
If recursive is True this will include jobs from all internal
Link
-
clientclass
= None¶
-
classmethod
create
(**kwargs)[source]¶ Build and return a
ScatterGather
object
-
default_options
= {}¶
-
default_options_base
= {'action': ('run', 'Action to perform', <type 'str'>), 'check_status_once': (False, 'Check status only once before proceeding', <type 'bool'>), 'dry_run': (False, 'Print commands, but do not execute them', <type 'bool'>), 'job_check_sleep': (300, 'Sleep time between checking on job status (s)', <type 'int'>), 'print_update': (False, 'Print summary of job status', <type 'bool'>)}¶
-
default_prefix_logfile
= 'scatter'¶
-
description
= 'Run multiple analyses'¶
-
get_jobs
(recursive=True)[source]¶ Return a dictionary with all the jobs
If recursive is True this will include jobs from all internal
Link
-
job_time
= 1500¶
-
print_summary
(stream=<open file '<stdout>', mode 'w'>, indent='', recurse_level=2)[source]¶ Print a summary of the activity done by this
Link
.Parameters:
-
print_update
(stream=<open file '<stdout>', mode 'w'>, job_stats=None)[source]¶ Print an update about the current number of jobs running
-
resubmit
(stream=<open file '<stdout>', mode 'w'>, fail_running=False)[source]¶ Function to resubmit failed jobs and collect results
Parameters: - stream (
file
) – Stream that this function will print to, Must have ‘write’ function. - fail_running (
bool
) – If True, consider running jobs as failed
Returns: status_vect – Vector that summarize the number of jobs in various states.
Return type: JobStatusVector
- stream (
-
run
(stream=<open file '<stdout>', mode 'w'>, dry_run=False, stage_files=True, resubmit_failed=True)[source]¶ Runs this
Link
.This version is intended to be overwritten by sub-classes so as to provide a single function that behaves the same for all version of
Link
Parameters:
-
run_jobs
(stream=<open file '<stdout>', mode 'w'>)[source]¶ Function to dipatch jobs and collect results
Parameters: stream ( file
) – Stream that this function will print to, Must have ‘write’ function.Returns: status_vect – Vector that summarize the number of jobs in various states. Return type: JobStatusVector
-
scatter_link
¶ Return the
Link
object used the scatter phase of processing
-
update_args
(override_args)[source]¶ Update the arguments used to invoke the application
Note that this will also update the dictionary of input and output files
Parameters: override_args (dict) – dictionary of arguments to override the current values
-
usage
= 'dummy-sg [options]'¶
-