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

A

afterExecute() - Method in IgBaseTask

Template method invoke after the task is executed

afterExecute() - Method in IgClosureTask

afterExecute() - Method in IgScriptTask

apply(TaskId, IgBaseTask) - Method in SchedulerAgent.MatchingResources

Autoscaler - Class in nextflow.scheduler

Implements an auto-scaling policy which adds new instances under scheduler request pressure and remove when those instances are idle

Autoscaler() - Constructor in Autoscaler

ONLY FOR TESTING PURPOSE

B

bean - Field in IgBaseTask

Holds the class attributes in this map.

beforeExecute() - Method in IgBaseTask

Template method invoked before the task is executed

beforeExecute() - Method in IgClosureTask

beforeExecute() - Method in IgScriptTask

C

cacheConfig(IgniteConfiguration) - Method in IgGridFactory

call() - Method in IgBaseTask

Invoke the task execution.

cancel() - Method in IgClosureTask

cancel() - Method in IgScriptTask

cancelTask(TaskId) - Method in Scheduler

Cancel the execution of a task

checkAndSet(def, String, def) - Method in IgGridFactory

checkIfCompleted() - Method in IgTaskHandler

checkIfRunning() - Method in IgTaskHandler

checkTaskCompleted(TaskId) - Method in Scheduler

Check if the task with the specified id has completed

checkTaskFailed(TaskId) - Method in IgExecutor

checkTaskFailed(TaskId) - Method in Scheduler

checkTaskStarted(TaskId) - Method in Scheduler

Check if the task with the specified id has started

cleanupLocalWorkDir() - Method in IgScriptTask

clone() - Method in Protocol.Resources

clone() - Method in Protocol.TaskHolder

close() - Method in Autoscaler

Shutdown the auto-scaler thread

close() - Method in OnlyCloseChannel

close(boolean) - Method in SchedulerAgent

Shutdown the scheduler agent

config() - Method in IgGridFactory

Main factory method, creates the IgniteConfiguration object @return

create(TaskPollingMonitor) - Method in IgConnector

create(ClusterConfig, Ignite) - Method in Protocol.NodeData

create(IgBaseTask, def) - Method in Protocol.TaskComplete

createGroovyHandler(TaskRun, IgExecutor) - Method in IgTaskHandler

createScriptHandler(TaskRun, IgExecutor) - Method in IgTaskHandler

createTaskHandler(TaskRun) - Method in IgExecutor

Creates an handler for the specified task

createTaskMonitor() - Method in IgExecutor

Creates the task monitor for this executor

D

delete(Object) - Method in IgLocalCacheStore

deleteAll(Collection<?>) - Method in IgLocalCacheStore

deserialize() - Method in IgBaseTask

dumpQueueStatus() - Method in IgExecutor

dumpScheduledTasksStatus() - Method in Scheduler

E

equals(Object) - Method in IgBaseTask

error(IgBaseTask, Throwable) - Method in Protocol.TaskComplete

execute0() - Method in IgBaseTask

The actual task executor code provided by the extending subclass

execute0() - Method in IgClosureTask

execute0() - Method in IgScriptTask

execute() - Method in IgBaseTask

Just a synonym for #call

F

G

getBeforeStartScript() - Method in IgScriptStagingStrategy

{@inheritDoc}

getClassLoaderFor(UUID) - Method in IgClosureTask

Create a java.lang.ClassLoader object for the specified session ID

getCluster() - Method in IgConnector

getClusterConfig() - Method in IgGridFactory

getContext() - Method in IgResultData

getLocalCacheDir() - Method in IgFileStagingStrategy

getStageInputFilesScript(Map<String, Path>) - Method in IgScriptStagingStrategy

Turn off file staging from the wrapper script returning a null string

getTaskId() - Method in IgBaseTask

getTaskMonitor() - Method in IgExecutor

getUnstageOutputFilesScript(List<String>, Path) - Method in IgScriptStagingStrategy

Turn off file unstage from the wrapper script returning a null string

getUptime() - Method in Protocol.NodeData

getValue() - Method in IgResultData

GRID_NAME - Field in IgGridFactory

H

hashCode() - Method in IgBaseTask

I

idle() - Method in Protocol.NodeData

IgBaseTask - Class in nextflow.executor

Models a task executed remotely in a Ignite cluster node

IgBaseTask() - Constructor in IgBaseTask

ONLY FOR TESTING PURPOSE

IgClosureTask - Class in nextflow.executor

Execute a groovy closure task in a remote Ignite node

IgClosureTask(TaskRun, UUID) - Constructor in IgClosureTask

IgConnector - Class in nextflow.executor

Creates an instance of the Ignite node

IgCustomS3IpFinder - Class in nextflow.daemon

@author Paolo Di Tommaso

IgDaemon - Class in nextflow.daemon

Launch the Ignite daemon

IgExecutor - Class in nextflow.executor

A Nextflow executor based on Ignite services

IgFileStagingStrategy - Class in nextflow.executor

Implements file staging strategy for a Ignite task.

IgGridFactory - Class in nextflow.daemon

Grid factory class.

IgGridFactory(String, Map) - Constructor in IgGridFactory

Create a grid factory object for the given role and configuration params

IgLocalCacheStore - Class in nextflow.util

Save the cache entries in the local file system

IgLocalCacheStore(Session) - Constructor in IgLocalCacheStore

ignite() - Method in IgGridFactory

IgResultData - Class in nextflow.executor

Models the result of a remote closure task execution

IgScriptStagingStrategy - Class in nextflow.executor

Implements a StagingStrategy interface extending the behavior of IgFileStagingStrategy so that it copies also the task control meta-files.

IgScriptTask - Class in nextflow.executor

Execute a remote script task into a remote Ignite cluster node

IgScriptTask(TaskRun, UUID) - Constructor in IgScriptTask

IgTaskHandler - Class in nextflow.executor

A task handler for Ignite cluster

init(Ignite, TaskPollingMonitor) - Method in Scheduler

Initialize the scheduler instance

instance() - Method in IgGridFactory

INSTANCE - Field in Protocol.NodeShutdown

INSTANCE - Field in Protocol.TaskAvail

Singleton object instance

isGroovy() - Method in IgTaskHandler

@return Whenever is a groovy closure task

isIdle(Duration) - Method in Protocol.NodeData

isOpen() - Method in OnlyCloseChannel

isScriptlet() - Method in IgTaskHandler

@return Whenever is a shell script task

isWaitingMoreThan(Duration) - Method in Protocol.TaskHolder

J

K

kill() - Method in IgTaskHandler

L

launch(Map) - Method in IgDaemon

load(K) - Method in IgLocalCacheStore

loadAll(Iterable<? extends K>) - Method in IgLocalCacheStore

loadCache(IgniteBiInClosure<K, V>, Object) - Method in IgLocalCacheStore

localWorkDir - Field in IgFileStagingStrategy

The local scratch dir where the task is actually executed in the remote node.

M

N

NODE_ROLE - Field in IgGridFactory

O

OnlyCloseChannel - Class in nextflow.util

Fake channel only supporting the close operation.

OnlyCloseChannel(Closeable) - Constructor in OnlyCloseChannel

P

position(long) - Method in OnlyCloseChannel

Protocol - Interface in nextflow.scheduler

Defines constants and message objects that implement the Ignite based distributed execution logic

Protocol.NodeData - Class in nextflow.scheduler

Protocol.NodeIdle - Class in nextflow.scheduler

Message sent to notify that a computing node is idle

Protocol.NodeRetired - Class in nextflow.scheduler

Event send from the agent to the scheduler to notify that an instance received a spot/preemptive termination notice

Protocol.NodeShutdown - Class in nextflow.scheduler

Message sent from the scheduler to notify the cluster shutdown

Protocol.Resources - Class in nextflow.scheduler

Model the resources available for task executions

Protocol.Resources(ClusterConfig) - Constructor in Protocol.Resources

Protocol.TaskAvail - Class in nextflow.scheduler

Message send to all cluster node to notify that a new task has been submitted for execution

Protocol.TaskCancel - Class in nextflow.scheduler

Message send to a scheduler agent to cancel a job execution

Protocol.TaskComplete - Class in nextflow.scheduler

Message send by a scheduler agent to notify that a task execution has completed

Protocol.TaskComplete() - Constructor in Protocol.TaskComplete

Protocol.TaskHolder - Class in nextflow.scheduler

Holds the metadata of a scheduled task

Protocol.TaskHolder(IgBaseTask) - Constructor in Protocol.TaskHolder

Protocol.TaskResources - Class in nextflow.scheduler

Model the computing resources required by a task

Protocol.TaskResources(TaskRun) - Constructor in Protocol.TaskResources

Protocol.TaskStart - Class in nextflow.scheduler

Message sent from a scheduler agent to the master node to notify that the task execution has started

Protocol.TaskStart() - Constructor in Protocol.TaskStart

Q

R

read(ByteBuffer) - Method in OnlyCloseChannel

readExitStatus() - Method in IgTaskHandler

register() - Method in IgExecutor

Initialize the executor by getting a reference to the Ignite connector

registerAddresses(Collection<InetSocketAddress>) - Method in IgCustomS3IpFinder

registerAutoscaler(Autoscaler) - Method in Scheduler

removeTaskCompleted(TaskId) - Method in Scheduler

Get the task runtime information and remove from the scheduledTasks structure

run() - Method in SchedulerAgent

Launch the scheduler agent execution logic.

S

schedule(IgBaseTask) - Method in Scheduler

Schedule one or more tasks for execution.

Scheduler - Class in nextflow.scheduler

Implements the scheduler controller logic

SchedulerAgent - Class in nextflow.scheduler

Implements the scheduler execution logic.

SchedulerAgent.MatchingResources - Class in nextflow.scheduler

Predicate that scans all tasks whose resource request match the ones available in the scheduler agent

SchedulerAgent.MatchingResources(Resources) - Constructor in SchedulerAgent.MatchingResources

SchedulerAgent(Ignite, ClusterConfig, UUID) - Constructor in SchedulerAgent

Initialise the scheduler agent

sessionEnd(boolean) - Method in IgLocalCacheStore

sessionId - Field in IgFileStagingStrategy

Session unique-id

SESSIONS_CACHE - Field in IgGridFactory

setContext(Map) - Method in IgResultData

setValue(def) - Method in IgResultData

shutdown(boolean) - Method in IgConnector

Shutdown all grid nodes

shutdownRemoteAgents() - Method in Scheduler

Shutdown scheduler remote agents by sending a Protocol.TOPIC_AGENT_EVENTS message

shutdownScheduler() - Method in Scheduler

Shutdown the scheduler object

size() - Method in OnlyCloseChannel

stage() - Method in IgFileStagingStrategy

Copies to the task input files to the execution folder, that is localWorkDir folder created when this method is invoked

stage() - Method in IgScriptStagingStrategy

{@inheritDoc}

stage() - Method in StagingStrategy

Copy the input files to the task local working directory (scratch).

StagingStrategy - Interface in nextflow.executor

Declares the operations to stage task input and unstage task outputs

start() - Method in IgGridFactory

Creates teh config object and starts a Ignite instance

submit() - Method in IgTaskHandler

T

task - Field in IgFileStagingStrategy

Task meta-data

toString() - Method in IgBaseTask

toString() - Method in IgScriptTask

toString() - Method in Protocol.NodeData

toString() - Method in Protocol.NodeRetired

toString() - Method in Protocol.Resources

toString() - Method in Protocol.TaskCancel

toString() - Method in Protocol.TaskComplete

toString() - Method in Protocol.TaskHolder

toString() - Method in Protocol.TaskResources

toString() - Method in Protocol.TaskStart

toString() - Method in SchedulerAgent.MatchingResources

truncate(long) - Method in OnlyCloseChannel

U

unregisterAddresses(Collection<InetSocketAddress>) - Method in IgCustomS3IpFinder

unstage() - Method in IgFileStagingStrategy

Copy back the task output files from the execution directory in the local node storage to the task nextflow.processor.TaskRun#getTargetDir()

unstage() - Method in IgScriptStagingStrategy

{@inheritDoc}

unstage() - Method in StagingStrategy

Copy the output files from task local working directory (scratch) to the shared working directory.

V

W

withComplete(TaskComplete) - Method in Protocol.TaskHolder

withStart(UUID) - Method in Protocol.TaskHolder

write(Entry<? extends K, ? extends V>) - Method in IgLocalCacheStore

write(ByteBuffer) - Method in OnlyCloseChannel

writeAll(Entry<? extends K, ? extends V>>) - Method in IgLocalCacheStore

X

Y

Z

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