Index

A

add() (gc3libs.session.Session method) (gc3libs.workflow.ParallelTaskCollection method) (gc3libs.workflow.TaskCollection method) add_params() (gc3libs.authentication.Auth method) adjoin() (gc3libs.url.Url 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)

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.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.shellcmd.ShellcmdLrms method) cmdline() (gc3libs.Application method) CodemlApplication (class in gc3libs.application.codeml) Command-line Command-line option compatible_resources() (gc3libs.Application method) 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 count() (in module gc3libs.utils) CPU Time create_engine() (in module gc3libs)

D

DataStagingError Default (class in gc3libs) defproperty() (in module gc3libs.utils) deploy_configuration_file() (in module gc3libs.utils) destroy() (gc3libs.session.Session method)

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

E

Enum (class in gc3libs.utils) Error 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) fetch_output_error() (gc3libs.Application method) FilesystemStore (class in gc3libs.persistence.filesystem) 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.shellcmd.ShellcmdLrms 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.shellcmd (module) gc3libs.config (module) gc3libs.debug (module) gc3libs.exceptions (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.frontend (module) GET (in module gc3libs.persistence.accessors) get() (gc3libs.authentication.Auth method) get_resource_status() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.shellcmd.ShellcmdLrms method) get_results() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms 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

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.Task 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_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) LRMS (class in gc3libs.backends) LRMSSkipSubmissionToNextIteration

M

main() (in module gc3utils.frontend) make_auth() (gc3libs.config.Configuration 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)

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) next() (gc3libs.utils.ExponentialBackoff method) (gc3libs.workflow.SequentialTaskCollection method)

NoConfigurationFile NoneAuth (class in gc3libs.authentication) NoResources

O

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

OutputNotAvailableError

P

ParallelTaskCollection (class in gc3libs.workflow) peek() (gc3libs.backends.arc0.ArcLrms method) (gc3libs.Task method) (gc3libs.backends.LRMS method) (gc3libs.backends.arc1.Arc1Lrms method) (gc3libs.backends.shellcmd.ShellcmdLrms method) (gc3libs.workflow.TaskCollection method) Persistable (class in gc3libs.persistence.store) Persistent PlusInfinity (class in gc3libs.utils)

prettyprint() (in module gc3libs.utils) progress() (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.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) SequentialTaskCollection (class in gc3libs.workflow) Session (class in gc3libs.session) set_end_timestamp() (gc3libs.session.Session method) set_start_timestamp() (gc3libs.session.Session method) 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) signal (gc3libs.Run attribute) Singleton (class in gc3libs.utils) 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.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.Task 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.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.shellcmd.ShellcmdLrms method) update_job_state_error() (gc3libs.Application method) update_parameter_in_file() (in module gc3libs.utils) 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.shellcmd.ShellcmdLrms method)

W

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

write_contents() (in module gc3libs.utils)

X

xrsl() (gc3libs.Application method)