Index

A | B | C | D | E | F | G | H | I | J | L | M | P | Q | R | S | T | V | W

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)