Index

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

A

AbortOnError (class in gc3libs.workflow)
add() (gc3libs.core.Core method)
(gc3libs.core.Engine method)
(gc3libs.session.Session method)
(gc3libs.workflow.DependentTaskCollection 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)
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)
AuxiliaryCommandError

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.batch.BatchSystem method)
(gc3libs.backends.LRMS method)
(gc3libs.backends.shellcmd.ShellcmdLrms method)
cat() (in module gc3libs.utils)
changed (gc3libs.workflow.RetryableTask attribute)
(gc3libs.workflow.TaskCollection attribute)
close() (gc3libs.backends.batch.BatchSystem method)
(gc3libs.backends.LRMS method)
(gc3libs.backends.shellcmd.ShellcmdLrms method)
(gc3libs.core.Core method)
(gc3libs.core.Engine method)
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
ConfigurationFileError
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)
DependentTaskCollection (class in gc3libs.workflow)
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
error_ignored() (in module gc3libs)
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)
fgrep() (in module gc3libs.utils)
FilesystemStore (class in gc3libs.persistence)
(class in gc3libs.persistence.filesystem)
filter() (gc3libs.core.MatchMaker 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.batch.BatchSystem method)
(gc3libs.Task method)
(gc3libs.backends.LRMS 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.ssh (module)
gc3libs.backends (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.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.LRMS 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.batch.BatchSystem method)
(gc3libs.backends.LRMS 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)
grep() (in module gc3libs.utils)

H

has_converged() (gc3libs.optimizer.EvolutionaryAlgorithm method)
History (class in gc3libs.utils)

I

Id (class in gc3libs.persistence.idfactory)
IdFactory (class in gc3libs.persistence)
(class in gc3libs.persistence.idfactory)
ifelse() (in module gc3libs.utils)
in_state() (gc3libs.Run method)
info (gc3libs.Run attribute)
input_filename_pattern (gc3libs.cmdline.SessionBasedScript 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)
iter_tasks() (gc3libs.workflow.TaskCollection method)
iter_workflow() (gc3libs.workflow.TaskCollection method)

J

Job
JobIdFactory (class in gc3libs.persistence)
(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.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.FilesystemStore 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_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)
(in module gc3libs.persistence.store)
make_task_controller() (gc3libs.cmdline.SessionBasedScript method)
MatchMaker (class in gc3libs.core)
MaximumCapacityReached
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)
move_recursively() (in module gc3libs.utils)
movefile() (in module gc3libs.utils)
movetree() (in module gc3libs.utils)

N

name() (in module gc3libs.debug)
new() (gc3libs.persistence.IdFactory method)
(gc3libs.Task method)
(gc3libs.persistence.idfactory.IdFactory method)
new_tasks() (gc3libs.cmdline.SessionBasedScript method)
next() (gc3libs.utils.ExponentialBackoff method)
(gc3libs.workflow.SequentialTaskCollection method)
NoAccessibleConfigurationFile
NoConfigurationFile
NoneAuth (class in gc3libs.authentication)
nonnegative_int() (in module gc3libs.cmdline)
NoResources
NoValidConfigurationFile

O

occurs() (in module gc3libs.utils)
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.batch.BatchSystem method)
(gc3libs.Task method)
(gc3libs.backends.LRMS method)
(gc3libs.backends.shellcmd.ShellcmdLrms method)
(gc3libs.core.Core method)
(gc3libs.core.Engine method)
(gc3libs.workflow.TaskCollection method)
Persistable (class in gc3libs.persistence)
(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)
Python Enhancement Proposals
PEP 8

Q

qsub_pbs() (gc3libs.Application method)
qsub_sge() (gc3libs.Application method)
Quantity (class in gc3libs.quantity)

R

rank() (gc3libs.core.MatchMaker method)
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.FilesystemStore 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.FilesystemStore method)
(gc3libs.persistence.sql.SqlStore method)
(gc3libs.persistence.store.Store method)
reserve() (gc3libs.persistence.IdFactory method)
(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.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)
Scheduler (class in gc3libs.core)
scheduler (class in gc3libs.core)
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)
setup_args() (gc3libs.cmdline.GC3UtilsScript method)
(gc3libs.cmdline.SessionBasedScript method)
SgeLrms (class in gc3libs.backends.sge)
sh_quote_safe() (in module gc3libs.utils)
sh_quote_safe_cmdline() (in module gc3libs.utils)
sh_quote_unsafe() (in module gc3libs.utils)
sh_quote_unsafe_cmdline() (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)
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
StopOnError (class in gc3libs.workflow)
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.batch.BatchSystem method)
(gc3libs.backends.LRMS 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
tempdir() (in module gc3libs.utils)
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)
touch() (in module gc3libs.utils)
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.batch.BatchSystem method)
(gc3libs.backends.LRMS 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.batch.BatchSystem method)
(gc3libs.backends.LRMS method)
(gc3libs.backends.shellcmd.ShellcmdLrms method)

W

wait() (gc3libs.Task method)
(gc3libs.utils.ExponentialBackoff method)
Walltime
write_contents() (in module gc3libs.utils)

Y

YieldAtNext (class in gc3libs.utils)