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Fix File staging race condition + beta AWS parallel downloader
This commit resolves a race condition in the FilePorter class which takes care of stading files from a remote file system to the workflow work directory. Along with this implements an experimental multi-part parallel downloader. To enable this feature use the env variable: export NXF_S3_DOWNLOAD_PARALLEL=true
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178
modules/nextflow/src/main/groovy/nextflow/util/ThreadPoolBuilder.groovy
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| /* | ||
| * Copyright 2020-2021, 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. | ||
| * | ||
| */ | ||
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| package nextflow.util | ||
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| import java.util.concurrent.BlockingQueue | ||
| import java.util.concurrent.LinkedBlockingQueue | ||
| import java.util.concurrent.RejectedExecutionHandler | ||
| import java.util.concurrent.ThreadFactory | ||
| import java.util.concurrent.ThreadPoolExecutor | ||
| import java.util.concurrent.TimeUnit | ||
| import java.util.concurrent.atomic.AtomicInteger | ||
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| import groovy.transform.CompileStatic | ||
| import groovy.util.logging.Slf4j | ||
| /** | ||
| * Builder class to create instance of {@link ThreadPoolExecutor} | ||
| * | ||
| * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com> | ||
| */ | ||
| @Slf4j | ||
| @CompileStatic | ||
| class ThreadPoolBuilder { | ||
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| static AtomicInteger poolCount = new AtomicInteger() | ||
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| private String name | ||
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| private int minSize | ||
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| private int maxSize | ||
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| private BlockingQueue<Runnable> workQueue | ||
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| private int queueSize = -1 | ||
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| private Long keepAliveTime | ||
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| private RejectedExecutionHandler rejectionPolicy | ||
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| private ThreadFactory threadFactory | ||
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| private boolean allowCoreThreadTimeout | ||
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| String getName() { name } | ||
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| int getMinSize() { minSize } | ||
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| int getMaxSize() { maxSize } | ||
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| int getQueueSize() { queueSize } | ||
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| BlockingQueue<Runnable> getWorkQueue() { workQueue } | ||
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| Long getKeepAliveTime() { keepAliveTime } | ||
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| RejectedExecutionHandler getRejectionPolicy() { rejectionPolicy } | ||
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| ThreadFactory getThreadFactory() { threadFactory } | ||
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| boolean getAllowCoreThreadTimeout() { allowCoreThreadTimeout } | ||
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| ThreadPoolBuilder withName(String name) { | ||
| if( name ) { | ||
| this.name = name | ||
| this.threadFactory = new CustomThreadFactory(name) | ||
| } | ||
| return this | ||
| } | ||
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| ThreadPoolBuilder withThreadFactory(ThreadFactory threadFactory) { | ||
| assert !name || !threadFactory, "Property 'threadFactory' or 'name' was already set" | ||
| this.threadFactory = threadFactory | ||
| return this | ||
| } | ||
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| ThreadPoolBuilder withRejectionPolicy(RejectedExecutionHandler rejectionPolicy) { | ||
| this.rejectionPolicy = rejectionPolicy | ||
| return this | ||
| } | ||
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| ThreadPoolBuilder withMinSize(int min) { | ||
| this.minSize = min | ||
| return this | ||
| } | ||
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| ThreadPoolBuilder withMaxSize(int max) { | ||
| this.maxSize = max | ||
| return this | ||
| } | ||
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| ThreadPoolBuilder withQueueSize(int size) { | ||
| this.queueSize = size | ||
| this.workQueue = new LinkedBlockingQueue<Runnable>(size) | ||
| return this | ||
| } | ||
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| ThreadPoolBuilder withQueue(BlockingQueue<Runnable> workQueue) { | ||
| this.workQueue = workQueue | ||
| return this | ||
| } | ||
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| ThreadPoolBuilder withKeepAliveTime( long millis ) { | ||
| keepAliveTime = millis | ||
| return this | ||
| } | ||
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| ThreadPoolBuilder withKeepAliveTime(Duration duration ) { | ||
| keepAliveTime = duration.toMillis() | ||
| return this | ||
| } | ||
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| ThreadPoolBuilder withAllowCoreThreadTimeout(boolean flag) { | ||
| this.allowCoreThreadTimeout = flag | ||
| return this | ||
| } | ||
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| ThreadPoolExecutor build() { | ||
| assert minSize <= maxSize | ||
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| if( !name ) | ||
| name = "nf-thread-pool-${poolCount.getAndIncrement()}" | ||
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| if(keepAliveTime==null) | ||
| keepAliveTime = 60_000 | ||
| if( workQueue==null ) | ||
| workQueue = new LinkedBlockingQueue<>() | ||
| if( rejectionPolicy==null ) | ||
| rejectionPolicy = new ThreadPoolExecutor.CallerRunsPolicy() | ||
| if( threadFactory==null ) | ||
| threadFactory = new CustomThreadFactory(name) | ||
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| log.debug "Creating thread pool '$name' minSize=$minSize; maxSize=$maxSize; workQueue=${workQueue.getClass().getSimpleName()}[${queueSize}]; allowCoreThreadTimeout=$allowCoreThreadTimeout" | ||
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| final result = new ThreadPoolExecutor( | ||
| minSize, | ||
| maxSize, | ||
| keepAliveTime, TimeUnit.MILLISECONDS, | ||
| workQueue, | ||
| threadFactory, | ||
| rejectionPolicy) | ||
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| result.allowCoreThreadTimeOut(allowCoreThreadTimeout) | ||
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| return result | ||
| } | ||
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| static ThreadPoolExecutor io(String name=null) { | ||
| io(10, 100, 10_000, name) | ||
| } | ||
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| static ThreadPoolExecutor io(int min, int max, int queue, String name=null) { | ||
| new ThreadPoolBuilder() | ||
| .withMinSize(min) | ||
| .withMaxSize(max) | ||
| .withQueueSize(queue) | ||
| .withName(name) | ||
| .build() | ||
| } | ||
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| } |
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