Index

A

abort_session() (gc3utils.commands.cmd_gsession method) add() (gc3libs.core.Core method) (gc3libs.core.Engine method) (gc3libs.session.Session method) (gc3libs.workflow.ParallelTaskCollection method) (gc3libs.workflow.TaskCollection method) add_params() (gc3libs.authentication.Auth method) adjoin() (gc3libs.url.Url method) after_main_loop() (gc3libs.cmdline.SessionBasedScript method) API append() (gc3libs.utils.History method) Application (class in gc3libs) application_name (gc3libs.Application attribute) ApplicationDescriptionError AppPotApplication (class in gc3libs.application.apppot)

Arc1Lrms (class in gc3libs.backends.arc1) ARC_CACHE_TIME (gc3libs.Default attribute) ARC_LOST_JOB_TIMEOUT (gc3libs.Default attribute) ArcLrms (class in gc3libs.backends.arc0) attach() (gc3libs.Task method) (gc3libs.workflow.ParallelTaskCollection method) (gc3libs.workflow.SequentialTaskCollection method) (gc3libs.workflow.TaskCollection method) Auth (class in gc3libs.authentication) auth_factory (gc3libs.config.Configuration attribute) authenticated() (gc3libs.backends.LRMS static method) AuthError aux_files() (gc3libs.application.codeml.CodemlApplication static method)

B

backup() (in module gc3libs.utils) basename_sans() (in module gc3libs.utils) BatchSystem (class in gc3libs.backends.batch)

before_main_loop() (gc3libs.cmdline.SessionBasedScript method) bsub() (gc3libs.Application method)

C

cache_for() (in module gc3libs.utils) cancel_job() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.batch.BatchSystem method) (gc3libs.backends.shellcmd.ShellcmdLrms method) cat() (in module gc3libs.utils) changed (gc3libs.workflow.RetryableTask attribute) (gc3libs.workflow.TaskCollection attribute) close() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.batch.BatchSystem method) (gc3libs.backends.shellcmd.ShellcmdLrms method) (gc3libs.core.Core method) (gc3libs.core.Engine method) cmd_gclean (class in gc3utils.commands) cmd_gcloud (class in gc3utils.commands) cmd_gget (class in gc3utils.commands) cmd_ginfo (class in gc3utils.commands) cmd_gkill (class in gc3utils.commands) cmd_gresub (class in gc3utils.commands) cmd_gselect (class in gc3utils.commands) cmd_gservers (class in gc3utils.commands) cmd_gsession (class in gc3utils.commands) cmd_gstat (class in gc3utils.commands) cmd_gtail (class in gc3utils.commands) cmdline() (gc3libs.Application method) CodemlApplication (class in gc3libs.application.codeml)

Command-line Command-line option compatible_resources() (gc3libs.Application method) compute_nr_of_slots() (in module gc3libs.backends.sge) ComputeTargetVals (class in gc3libs.optimizer.drivers) Configuration (class in gc3libs.config) ConfigurationError configure_logger() (in module gc3libs) copy() (gc3libs.utils.Struct method) copy_recursively() (in module gc3libs.utils) CopyError copyfile() (in module gc3libs.utils) copytree() (in module gc3libs.utils) Core (class in gc3libs.core) count() (in module gc3libs.utils) count_jobs() (in module gc3libs.backends.pbs) (in module gc3libs.backends.sge) (in module gc3libs.backends.slurm) CPU Time create_engine() (in module gc3libs)

D

DataStagingError de_opt() (gc3libs.optimizer.drivers.SequentialDriver method) Default (class in gc3libs) defproperty() (in module gc3libs.utils) delete_session() (gc3utils.commands.cmd_gsession method) deploy_configuration_file() (in module gc3libs.utils) destroy() (gc3libs.session.Session method)

detach() (gc3libs.Task method) DetachedFromGridError DifferentialEvolutionAlgorithm (class in gc3libs.optimizer.dif_evolution) dirname() (in module gc3libs.utils) draw_population() (in module gc3libs.optimizer) DuplicateEntryError Duration (class in gc3libs.quantity)

E

Engine (class in gc3libs.core) Enum (class in gc3libs.utils) Error every_main_loop() (gc3libs.cmdline.SessionBasedScript method) EvolutionaryAlgorithm (class in gc3libs.optimizer)

evolve() (gc3libs.optimizer.dif_evolution.DifferentialEvolutionAlgorithm method) (gc3libs.optimizer.EvolutionaryAlgorithm method) evolve_fn() (gc3libs.optimizer.dif_evolution.DifferentialEvolutionAlgorithm static method) exitcode (gc3libs.Run attribute) expansions() (gc3libs.template.Template method) (in module gc3libs.template) ExponentialBackoff (class in gc3libs.utils)

F

FatalError fetch_output() (gc3libs.Application method) (gc3libs.Task method) (gc3libs.core.Core method) (gc3libs.core.Engine method) fetch_output_error() (gc3libs.Application method) FilesystemStore (class in gc3libs.persistence.filesystem) filter_by_iofile() (gc3utils.commands.cmd_gselect method) filter_by_regexp() (gc3utils.commands.cmd_gselect method) filter_by_state() (gc3utils.commands.cmd_gselect method) filter_by_submission_date() (gc3utils.commands.cmd_gselect method)

first() (in module gc3libs.utils) flush() (gc3libs.session.Session method) forget() (gc3libs.session.Session method) format_arg_value() (in module gc3libs.debug) format_message() (gc3libs.utils.History method) free() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.Task method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.batch.BatchSystem method) (gc3libs.backends.shellcmd.ShellcmdLrms method) (gc3libs.core.Core method) (gc3libs.core.Engine method) (gc3libs.workflow.TaskCollection method) free_slots (gc3libs.backends.shellcmd.ShellcmdLrms attribute) from_template() (in module gc3libs.utils)

G

GamessApplication (class in gc3libs.application.gamess) GamessAppPotApplication (class in gc3libs.application.gamess) gc3libs (module) gc3libs.application (module) gc3libs.application.apppot (module) gc3libs.application.codeml (module) gc3libs.application.demo (module) gc3libs.application.gamess (module) gc3libs.application.rosetta (module) gc3libs.application.turbomole (module) gc3libs.authentication (module) gc3libs.authentication.grid (module) gc3libs.authentication.ssh (module) gc3libs.backends (module) gc3libs.backends.arc0 (module) gc3libs.backends.arc1 (module) gc3libs.backends.batch (module) gc3libs.backends.lsf (module) gc3libs.backends.pbs (module) gc3libs.backends.sge (module) gc3libs.backends.shellcmd (module) gc3libs.backends.slurm (module) gc3libs.backends.transport (module) gc3libs.cmdline (module) gc3libs.config (module) gc3libs.core (module) gc3libs.debug (module) gc3libs.exceptions (module) gc3libs.optimizer (module) gc3libs.optimizer.dif_evolution (module) gc3libs.optimizer.drivers (module) gc3libs.optimizer.extra (module)

gc3libs.persistence (module) gc3libs.persistence.accessors (module) gc3libs.persistence.filesystem (module) gc3libs.persistence.idfactory (module) gc3libs.persistence.serialization (module) gc3libs.persistence.sql (module) gc3libs.persistence.store (module) gc3libs.quantity (module) gc3libs.session (module) gc3libs.template (module) gc3libs.url (module) gc3libs.utils (module) gc3libs.workflow (module) gc3utils (module) gc3utils.commands (module) gc3utils.frontend (module) GC3UtilsScript (class in gc3libs.cmdline) generic_filename_mapping() (in module gc3libs.backends.batch) GET (in module gc3libs.persistence.accessors) get() (gc3libs.authentication.Auth method) get_epilogue_script() (gc3libs.backends.batch.BatchSystem method) get_jobid_from_submit_output() (gc3libs.backends.batch.BatchSystem method) get_prologue_script() (gc3libs.backends.batch.BatchSystem method) get_resource_status() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.lsf.LsfLrms method) (gc3libs.backends.pbs.PbsLrms method) (gc3libs.backends.sge.SgeLrms method) (gc3libs.backends.shellcmd.ShellcmdLrms method) (gc3libs.backends.slurm.SlurmLrms method) get_resources() (gc3libs.core.Core method) (gc3libs.core.Engine method) get_results() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.batch.BatchSystem method) (gc3libs.backends.shellcmd.ShellcmdLrms method) getattr_nested() (in module gc3libs.utils) GetAttributeValue (class in gc3libs.persistence.accessors) GetItemValue (class in gc3libs.persistence.accessors) GetOnly (class in gc3libs.persistence.accessors) GetValue (class in gc3libs.persistence.accessors)

H

has_converged() (gc3libs.optimizer.EvolutionaryAlgorithm method)

History (class in gc3libs.utils)

I

Id (class in gc3libs.persistence.idfactory) IdFactory (class in gc3libs.persistence.idfactory) ifelse() (in module gc3libs.utils) in_state() (gc3libs.Run method) info (gc3libs.Run attribute) InputFileError InternalError InvalidArgument

InvalidOperation InvalidResourceName InvalidType InvalidUsage InvalidValue irange() (in module gc3libs.utils) is_class_private_name() (in module gc3libs.debug) is_classmethod() (in module gc3libs.debug)

J

Job	JobIdFactory (class in gc3libs.persistence.idfactory)

K

kill() (gc3libs.core.Core method) (gc3libs.Task method) (gc3libs.core.Engine method) (gc3libs.workflow.ParallelTaskCollection method) (gc3libs.workflow.SequentialTaskCollection method)

L

last() (gc3libs.utils.History method) list() (gc3libs.persistence.filesystem.FilesystemStore method) (gc3libs.persistence.sql.SqlStore method) (gc3libs.persistence.store.Store method) list_ids() (gc3libs.session.Session method) list_jobs() (gc3utils.commands.cmd_gsession method) list_names() (gc3libs.session.Session method) load() (gc3libs.config.Configuration method) (gc3libs.persistence.filesystem.FilesystemStore method) (gc3libs.persistence.sql.SqlStore method) (gc3libs.persistence.store.Store method) (gc3libs.session.Session method) LoadError

lock() (in module gc3libs.utils) Log (in module gc3libs.utils) log_stats() (in module gc3libs.optimizer.extra) LRMS (class in gc3libs.backends) LRMSSkipSubmissionToNextIteration LsfLrms (class in gc3libs.backends.lsf)

M

main() (in module gc3utils.frontend) make_auth() (gc3libs.config.Configuration method) make_directory_path() (gc3libs.cmdline.SessionBasedScript method) make_filesystemstore() (in module gc3libs.persistence.filesystem) make_resources() (gc3libs.config.Configuration method) make_sqlstore() (in module gc3libs.persistence.sql) make_store() (in module gc3libs.persistence.store)

make_task_controller() (gc3libs.cmdline.SessionBasedScript method) Memory (class in gc3libs.quantity) merge_file() (gc3libs.config.Configuration method) method_name() (in module gc3libs.debug) mkdir() (in module gc3libs.utils) mkdir_with_backup() (in module gc3libs.utils)

N

name() (in module gc3libs.debug) new() (gc3libs.persistence.idfactory.IdFactory method) (gc3libs.Task method) new_tasks() (gc3libs.cmdline.SessionBasedScript method) next() (gc3libs.utils.ExponentialBackoff method) (gc3libs.workflow.SequentialTaskCollection method)

NoConfigurationFile NoneAuth (class in gc3libs.authentication) nonnegative_int() (in module gc3libs.cmdline) NoResources

O

ONLY() (gc3libs.persistence.accessors.GetValue method)

OutputNotAvailableError

P

ParallelDriver (class in gc3libs.optimizer.drivers) ParallelTaskCollection (class in gc3libs.workflow) parse_qhost_f() (in module gc3libs.backends.sge) parse_qstat_f() (in module gc3libs.backends.sge) PbsLrms (class in gc3libs.backends.pbs) peek() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.Task method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.batch.BatchSystem method) (gc3libs.backends.shellcmd.ShellcmdLrms method) (gc3libs.core.Core method) (gc3libs.core.Engine method) (gc3libs.workflow.TaskCollection method) Persistable (class in gc3libs.persistence.store) Persistent plot_population (class in gc3libs.optimizer.extra) PlusInfinity (class in gc3libs.utils) populate() (in module gc3libs.optimizer)

positive_int() (in module gc3libs.cmdline) pre_run() (gc3libs.cmdline.GC3UtilsScript method) (gc3libs.cmdline.SessionBasedScript method) prettyprint() (in module gc3libs.utils) print_stats() (in module gc3libs.optimizer.extra) print_summary_table() (gc3libs.cmdline.SessionBasedScript method) print_tasks_table() (gc3libs.cmdline.SessionBasedScript method) process_args() (gc3libs.cmdline.SessionBasedScript method) progress() (gc3libs.core.Engine method) (gc3libs.Task method) (gc3libs.workflow.ParallelTaskCollection method) progressive_number() (in module gc3libs.utils) PROXY_VALIDITY_THRESHOLD (gc3libs.Default attribute) Python Enhancement Proposals PEP 8

Q

qsub_pbs() (gc3libs.Application method) qsub_sge() (gc3libs.Application method)

Quantity (class in gc3libs.quantity)

R

rank_resources() (gc3libs.Application method) read_contents() (in module gc3libs.utils) RecoverableDataStagingError RecoverableError register() (in module gc3libs.persistence.store) remove() (gc3libs.core.Core method) (gc3libs.core.Engine method) (gc3libs.persistence.filesystem.FilesystemStore method) (gc3libs.persistence.sql.SqlStore method) (gc3libs.persistence.store.Store method) (gc3libs.session.Session method) (gc3libs.workflow.TaskCollection method) replace() (gc3libs.persistence.filesystem.FilesystemStore method) (gc3libs.persistence.sql.SqlStore method) (gc3libs.persistence.store.Store method) reserve() (gc3libs.persistence.idfactory.IdFactory method) Resource

retry() (gc3libs.workflow.RetryableTask method) RetryableTask (class in gc3libs.workflow) returncode (gc3libs.Run attribute) RosettaApplication (class in gc3libs.application.rosetta) RosettaDockingApplication (class in gc3libs.application.rosetta) Run (class in gc3libs) Run.Arch (class in gc3libs) running() (gc3libs.Task method)

S

safe_repr() (in module gc3libs.utils) same_docstring_as() (in module gc3libs.utils) samefile() (in module gc3libs.utils) save() (gc3libs.persistence.filesystem.FilesystemStore method) (gc3libs.persistence.sql.SqlStore method) (gc3libs.persistence.store.Store method) (gc3libs.session.Session method) save_all() (gc3libs.session.Session method) sbatch() (gc3libs.Application method) select() (gc3libs.optimizer.dif_evolution.DifferentialEvolutionAlgorithm method) (gc3libs.optimizer.EvolutionaryAlgorithm method) select_resource() (gc3libs.core.Core method) (gc3libs.core.Engine method) SequentialDriver (class in gc3libs.optimizer.drivers) SequentialTaskCollection (class in gc3libs.workflow) Session (class in gc3libs.session) SessionBasedScript (class in gc3libs.cmdline) set_end_timestamp() (gc3libs.session.Session method) set_start_timestamp() (gc3libs.session.Session method) setup() (gc3libs.cmdline.GC3UtilsScript method) (gc3libs.cmdline.SessionBasedScript method) (gc3utils.commands.cmd_gservers method) setup_args() (gc3libs.cmdline.GC3UtilsScript method) (gc3libs.cmdline.SessionBasedScript method) (gc3utils.commands.cmd_gservers method) (gc3utils.commands.cmd_gtail method) SgeLrms (class in gc3libs.backends.sge) sh_quote_safe() (in module gc3libs.utils) sh_quote_unsafe() (in module gc3libs.utils) ShellcmdLrms (class in gc3libs.backends.shellcmd) shellexit_to_returncode() (gc3libs.Run static method) show_log() (gc3utils.commands.cmd_gsession method)

signal (gc3libs.Run attribute) Singleton (class in gc3libs.utils) SlurmLrms (class in gc3libs.backends.slurm) sql_next_id_factory() (in module gc3libs.persistence.sql) SqlStore (class in gc3libs.persistence.sql) Square (class in gc3libs.application.demo) StagedTaskCollection (class in gc3libs.workflow) State state (gc3libs.Run attribute) stats() (gc3libs.core.Engine method) (gc3libs.workflow.TaskCollection method) STDERR STDOUT stopped() (gc3libs.Task method) Store (class in gc3libs.persistence.store) string_to_boolean() (in module gc3libs.utils) stripped() (in module gc3libs.utils) Struct (class in gc3libs.utils) submit() (gc3libs.core.Core method) (gc3libs.Task method) (gc3libs.core.Engine method) (gc3libs.workflow.ParallelTaskCollection method) (gc3libs.workflow.SequentialTaskCollection method) submit_error() (gc3libs.Application method) submit_job() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.batch.BatchSystem method) (gc3libs.backends.shellcmd.ShellcmdLrms method) submitted() (gc3libs.Task method) substitute() (gc3libs.template.Template method)

T

Task (class in gc3libs) TaskCollection (class in gc3libs.workflow) TaskError Template (class in gc3libs.template) terminated() (gc3libs.application.codeml.CodemlApplication method) (gc3libs.Task method) (gc3libs.application.gamess.GamessApplication method) (gc3libs.application.rosetta.RosettaApplication method) (gc3libs.workflow.TaskCollection method) terminating() (gc3libs.Task method) test_file() (in module gc3libs.utils) to_bytes() (in module gc3libs.utils)

to_timedelta() (gc3libs.quantity.Duration method) trace() (in module gc3libs.debug) trace_class() (in module gc3libs.debug) trace_instancemethod() (in module gc3libs.debug) trace_module() (in module gc3libs.debug) TurbomoleApplication (class in gc3libs.application.turbomole) TurbomoleDefineApplication (class in gc3libs.application.turbomole)

U

UnexpectedStateError uniq() (in module gc3libs.utils) unknown() (gc3libs.Task method) UnknownJob UnknownJobState unlock() (in module gc3libs.utils) UnrecoverableDataStagingError UnrecoverableError update_job_state() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.batch.BatchSystem method) (gc3libs.backends.shellcmd.ShellcmdLrms method) (gc3libs.core.Core method) (gc3libs.core.Engine method)

update_job_state_error() (gc3libs.Application method) update_opt_state() (gc3libs.optimizer.EvolutionaryAlgorithm method) update_parameter_in_file() (in module gc3libs.utils) update_resources() (gc3libs.core.Core method) update_state() (gc3libs.Task method) (gc3libs.workflow.ParallelTaskCollection method) (gc3libs.workflow.RetryableTask method) (gc3libs.workflow.SequentialTaskCollection method) (gc3libs.workflow.TaskCollection method) Url (class in gc3libs.url) UrlKeyDict (class in gc3libs.url) UrlValueDict (class in gc3libs.url)

V

validate_data() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.batch.BatchSystem method) (gc3libs.backends.shellcmd.ShellcmdLrms method)

W

wait() (gc3libs.Task method) (gc3libs.utils.ExponentialBackoff method) Walltime

write_contents() (in module gc3libs.utils)

X

xrsl() (gc3libs.Application method)