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Offload publishing to separate jobs #5618
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be14ac2
Initial publish dir offloading implementation
jorgee 1f0dfec
fix unit test
jorgee ed27414
add integration test
jorgee 5b9fe68
add header
jorgee 0f394ec
Update modules/nextflow/src/main/groovy/nextflow/Session.groovy [skip…
jorgee 832834f
group copies and retries
jorgee ac04d04
fix minor issue
jorgee 9ac038f
fix unit test
jorgee 2c5c185
fix integration test
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221 changes: 221 additions & 0 deletions
221
modules/nextflow/src/main/groovy/nextflow/processor/PublishOffloadManager.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,221 @@ | ||
| /* | ||
| * Copyright 2013-2024, Seqera Labs | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
|
|
||
| package nextflow.processor | ||
|
|
||
| import groovy.transform.PackageScope | ||
| import groovy.util.logging.Slf4j | ||
| import nextflow.Nextflow | ||
| import nextflow.Session | ||
| import nextflow.executor.Executor | ||
| import nextflow.executor.ExecutorFactory | ||
| import nextflow.extension.FilesEx | ||
| import nextflow.fusion.FusionHelper | ||
| import nextflow.script.BaseScript | ||
| import nextflow.script.BodyDef | ||
| import nextflow.script.ProcessConfig | ||
| import nextflow.util.ArrayTuple | ||
|
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||
| import java.nio.file.Path | ||
| import java.util.concurrent.atomic.AtomicInteger | ||
|
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| @Slf4j | ||
| class PublishOffloadManager { | ||
| Map<Integer, ArrayTuple> runningPublications= new HashMap<Integer, ArrayTuple>(10) | ||
| static final Map SUPPORTED_SCHEMES = [awsbatch:['s3'], local:['file']] | ||
| static final String S5CMD_CONTAINER = 'jorgeejarquea/s5cmd_aws:0.0.1' | ||
| static final String PUBLISH_FUNCTION = 'nxf_publish' | ||
| private Session session | ||
| private PublishTaskProcessor publishProcessor | ||
| private List<String> commands = new LinkedList<String>() | ||
| private boolean closed = false | ||
| private int batchSize | ||
| /** | ||
| * Unique offloaded index number | ||
| */ | ||
| final protected AtomicInteger indexCount = new AtomicInteger() | ||
|
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| PublishOffloadManager(Session session, int batchSize) { | ||
| this.session = session; | ||
| this.batchSize = batchSize; | ||
| } | ||
| @PackageScope | ||
| TaskProcessor getPublishProcessor(){ publishProcessor } | ||
|
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| void init(){ | ||
| //Try with template | ||
| BodyDef body = new BodyDef({ | ||
| def file = PublishOffloadManager.class.getResource('copy-group-template.sh') | ||
| return file.text | ||
| },'publish file process', 'shell') | ||
| this.publishProcessor = createProcessor( "publish_process", body ) | ||
|
|
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| } | ||
|
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| private boolean checkOffload(Path source, Path destination, String executor){ | ||
| return this.batchSize > 0 && source.scheme in SUPPORTED_SCHEMES[executor] && destination.scheme in SUPPORTED_SCHEMES[executor]; | ||
| } | ||
|
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| private void invokeProcessor(inputValue) { | ||
| final params = new TaskStartParams(TaskId.next(), publishProcessor.indexCount.incrementAndGet()) | ||
| final values = new ArrayList(1) | ||
| values[0] = inputValue | ||
| final args = new ArrayList(2) | ||
| args[0] = params | ||
| args[1] = values | ||
| publishProcessor.invokeTask(args.toArray()) | ||
| } | ||
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| private synchronized boolean tryOffload(String command, Path origin, Path destination, PublishRetryConfig retryConfig, boolean failOnError){ | ||
| if (checkOffload(origin, destination, publishProcessor.executor.name)) { | ||
| final id = indexCount.incrementAndGet() | ||
| runningPublications.put(id, Nextflow.tuple(origin, destination, failOnError)) | ||
| commands.add(generateExecutionCommand(id, command, origin, destination, retryConfig)) | ||
| if (commands.size() == this.batchSize){ | ||
| invokeProcessor(commands.join(";")) | ||
| commands.clear() | ||
| } | ||
| return true | ||
| } | ||
| return false | ||
| } | ||
|
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||
| private isFusionEnabled(){ | ||
| return FusionHelper.isFusionEnabled(session) | ||
| } | ||
|
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| private useS5cmd(){ | ||
| return ( (!isFusionEnabled()) && (ExecutorFactory.getDefaultExecutorName(session) == 'awsbatch') ) | ||
| } | ||
|
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| private String generateExecutionCommand(Integer id, String command, Path origin, Path destination, PublishRetryConfig retryConfig){ | ||
| return "$PUBLISH_FUNCTION ${retryConfig.maxAttempts} ${retryConfig.delay.toMillis()} ${retryConfig.jitter} ${retryConfig.maxDelay.toMillis()} " + | ||
| "$id $command ${convertFilePath(origin)} ${convertFilePath(destination)}" | ||
| } | ||
|
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| private String convertFilePath(Path path) { | ||
| if (isFusionEnabled()) { | ||
| return FusionHelper.toContainerMount(path) | ||
| } else { | ||
| return FilesEx.toUriString(path) | ||
| } | ||
| } | ||
|
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| boolean tryMoveOffload(Path origin, Path destination, PublishRetryConfig retryConfig, boolean failOnError) { | ||
| String command = 'mv' | ||
| if ( useS5cmd() ) { | ||
| command = 's5cmd mv' | ||
| } | ||
| tryOffload(command, origin, destination, retryConfig, failOnError) | ||
| } | ||
|
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| boolean tryCopyOffload(Path origin, Path destination, PublishRetryConfig retryConfig, boolean failOnError) { | ||
| String command = 'cp' | ||
| if ( useS5cmd() ) { | ||
| command = 's5cmd cp' | ||
| } | ||
| tryOffload(command, origin, destination, retryConfig, failOnError) | ||
| } | ||
|
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| private PublishTaskProcessor createProcessor( String name, BodyDef body){ | ||
| assert body | ||
| assert session.script | ||
| log.debug("Creating processor $name") | ||
| // -- the config object | ||
| final processConfig = new ProcessConfig(session.script, name) | ||
| // Invoke the code block which will return the script closure to the executed. | ||
| // As side effect will set all the property declarations in the 'taskConfig' object. | ||
| if (useS5cmd()) { | ||
| processConfig.put('container', S5CMD_CONTAINER); | ||
| } | ||
| processConfig._in_val('executions') | ||
| processConfig._out_stdout() | ||
| if ( !body ) | ||
| throw new IllegalArgumentException("Missing script in the specified process block -- make sure it terminates with the script string to be executed") | ||
|
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| // -- apply settings from config file to process config | ||
| processConfig.applyConfig((Map)session.config.process, name, name, name) | ||
|
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| // -- get the executor for the given process config | ||
| final execObj = session.executorFactory.getExecutor(name, processConfig, body, session) | ||
|
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| // -- create processor class | ||
| new PublishTaskProcessor( name, execObj, session, session.script, processConfig, body, this ) | ||
| } | ||
|
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| synchronized void close() { | ||
| closed=true | ||
| if ( commands.size() ){ | ||
| invokeProcessor(commands.join(";")) | ||
| commands.clear() | ||
| } | ||
|
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| } | ||
| } | ||
|
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| @Slf4j | ||
| class PublishTaskProcessor extends TaskProcessor{ | ||
| PublishOffloadManager manager | ||
|
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| PublishTaskProcessor(String name, Executor executor, Session session, BaseScript baseScript, ProcessConfig processConfig, BodyDef bodyDef, PublishOffloadManager manager) { | ||
| super(name, executor, session, baseScript, processConfig, bodyDef) | ||
| this.manager = manager | ||
| } | ||
|
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| @Override | ||
| void finalizeTask0(TaskRun task) { | ||
| if( task.outputs.size() == 1 ){ | ||
| def value = task.outputs.values().first() | ||
| value = value instanceof Path ? value.text : value?.toString() | ||
| for ( String finishedCopy : value.split('\n') ){ | ||
| final result = finishedCopy.split(":") | ||
| if (result.size() == 2) { | ||
| final id = result[0] as Integer | ||
| final tuple = manager.runningPublications.remove(id) | ||
| final exitCode = result[1] as Integer | ||
| if( exitCode == 0 ){ | ||
| session.notifyFilePublish((Path) tuple.get(0), (Path) tuple.get(1)) | ||
| } else { | ||
| if (tuple.get(2) as Boolean) { | ||
| log.error("Publication of file ${tuple.get(0)} -> ${tuple.get(1)} failed.") | ||
| } else { | ||
| log.warn("Publication of file ${tuple.get(0)} -> ${tuple.get(1)} failed.") | ||
| } | ||
| printPublishTaskError(task) | ||
| } | ||
| } | ||
| } | ||
| } else { | ||
| log.error("Incorrect number of outputs in the publish task"); | ||
| } | ||
| } | ||
|
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| private void printPublishTaskError(TaskRun task){ | ||
| final List<String> message = [] | ||
| final max = 50 | ||
| final lines = task.dumpStderr(max) | ||
| message << "Executed publish task:" | ||
| if( lines ) { | ||
| message << "\nCommand error:" | ||
| for( String it : lines ) { | ||
| message << " ${stripWorkDir(it, task.workDir)}" | ||
| } | ||
| } | ||
| if( task?.workDir ) | ||
| message << "\nWork dir:\n ${task.workDirStr}" | ||
| log.debug(message.join('\n')) | ||
| } | ||
| } |
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In principle
elseis not needed