Index

A

activecount() (JobBatch.JobBatch method)

Automator (class in Automator) (module)

B

batch_tool (class in batch_tool) (module) batching_loop() (JobBatch.JobBatch method)

BatchRunner (class in BatchRunner) (module)

C

characterize_one_error() (Tool.Tool method) check_control_directories() (batch_tool.batch_tool method) check_for_cycle() (in module queue_manager) check_log_directory() (batch_tool.batch_tool method) check_running_jobs() (batch_tool.batch_tool method) check_status() (queue_manager.queue_manager method) choose_bolus() (queue_manager.queue_manager method) choose_max_bolus() (in module BatchRunner) choose_processors() (queue_manager.queue_manager method)

choose_queue() (queue_manager.queue_manager method) classify_errors() (Tool.Tool method) command_needs_no_config() (in module Automator) common_parsing() (in module BatchRunner) (in module JobGenerator) (in module Tool) complexity (module) configured_parser() (in module JobGenerator) CONTINUEFLAG (in module JobBatch) count() (JobBatch.JobBatch method)

D

determine_id() (in module queue_manager) determine_job() (in module queue_manager) determineSplit() (in module JobGenerator)

do_split() (in module JobGenerator) donecount() (JobBatch.JobBatch method) donejobs() (JobBatch.JobBatch method)

E

error_pid() (queue_manager.queue_manager method) errorcount() (JobBatch.JobBatch method) errorjobs() (JobBatch.JobBatch method)

evaluate_problems() (batch_tool.batch_tool method) examine_runbatch() (JobBatch.JobBatch method)

F

feed_batch() (JobBatch.JobBatch method) find_exemplar() (Tool.Tool method)

format_command() (queue_manager.queue_manager method)

G

generate_jobs() (BatchRunner.BatchRunner method)

H

HOSTMAPPING() (in module queue_manager)

I

ignoreable_warning() (queue_manager.queue_manager method) init_JobBatch() (BatchRunner.BatchRunner method) initialize() (Automator.Automator method)

initialize_begin_and_tutorial() (in module Tool) is_complete() (JobBatch.JobBatch method) is_correct() (JobBatch.JobBatch method)

J

job_statistics_header() (queue_manager.queue_manager method) JobBatch (class in JobBatch) (module)

JobGenerator (module) joblist() (JobBatch.JobBatch method)

L

LEGAL_STEPS (in module BatchRunner) local_queue_manager (module)

logfile() (JobBatch.JobBatch method) lsf_queue_manager (module)

M

main() (in module BatchRunner) (in module JobGenerator) make_touchoutput_tag() (in module JobGenerator) manage_job_creation() (BatchRunner.BatchRunner method)

manage_problem_details() (batch_tool.batch_tool method) minimum_memory() (queue_manager.queue_manager method)

P

pair_info() (in module JobGenerator) parse() (in module Automator) (in module BatchRunner) (in module JobGenerator) (in module batch_tool) pbs_queue_manager (module) pend_job() (JobBatch.JobBatch method) pendingcount() (JobBatch.JobBatch method) pendingjobs() (JobBatch.JobBatch method) populate_command() (in module queue_manager) prepare_configuration() (BatchRunner.BatchRunner method) print_outputs() (Tool.Tool method)

process_batchroot() (Automator.Automator method) process_output_problems() (batch_tool.batch_tool method) process_problems() (batch_tool.batch_tool method) process_special_terms() (in module JobGenerator) process_task() (in module Tool) process_times() (batch_tool.batch_tool method) processor_usage() (queue_manager.queue_manager method) purge() (Tool.Tool method)

Q

Q_LONG (in module queue_manager) Q_MEDIUM (in module queue_manager) Q_PARALLEL (in module queue_manager) Q_SHORT (in module queue_manager) Q_VERYLONG (in module queue_manager) qa_exec() (batch_tool.batch_tool method) qa_inconsistent_output() (batch_tool.batch_tool method)

qa_match_output() (batch_tool.batch_tool method) qa_non_empty_output() (batch_tool.batch_tool method) qa_output_generated() (batch_tool.batch_tool method) queue_manager (class in queue_manager) (module) queue_status() (queue_manager.queue_manager method) queuedjobs() (JobBatch.JobBatch method)

R

record_job_change() (JobBatch.JobBatch method) record_job_completion() (JobBatch.JobBatch method) record_job_error() (JobBatch.JobBatch method) record_job_queued() (JobBatch.JobBatch method) record_job_start() (JobBatch.JobBatch method) reduce_inodes() (BatchRunner.BatchRunner method) repend() (BatchRunner.BatchRunner method) repend_errors() (JobBatch.JobBatch method)

repend_runners() (JobBatch.JobBatch method) report_problem_details() (batch_tool.batch_tool method) reset() (Tool.Tool method) reset_jobcounter() (JobBatch.JobBatch method) restartable_error() (in module batch_tool) run() (Automator.Automator method) (BatchRunner.BatchRunner method) runningcount() (JobBatch.JobBatch method) runningjobs() (JobBatch.JobBatch method)

S

select_interface_specific_parameters() (queue_manager.queue_manager method) set_interface_specific_parameters() (queue_manager.queue_manager method) set_logging() (in module batch_tool) show_error() (Tool.Tool method) sleep_interval() (queue_manager.queue_manager method)

Stringency (class in Tool) submit() (queue_manager.queue_manager method) submit_job() (JobBatch.JobBatch method) summarize_status() (batch_tool.batch_tool method)

T

test_console_input() (in module batch_tool) Tool (class in Tool) (module)

tool_parser() (in module Tool)

V

validate_file() (in module Tool)

validate_queue() (BatchRunner.BatchRunner method)

W

write_command() (in module JobGenerator)