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Add support for Moab resource manager #1224
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modules/nextflow/src/main/groovy/nextflow/executor/MoabExecutor.groovy
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| /* | ||
| * Copyright 2013-2019, Centre for Genomic Regulation (CRG) | ||
| * | ||
| * 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.executor | ||
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| import java.nio.file.Path | ||
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| import groovy.util.logging.Slf4j | ||
| import nextflow.processor.TaskRun | ||
| /** | ||
| * Implements a executor for Moab batch scheduler cluster | ||
| * | ||
| * http://www.adaptivecomputing.com/moab-hpc-basic-edition/ | ||
| * | ||
| * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com> | ||
| */ | ||
| @Slf4j | ||
| class MoabExecutor extends AbstractGridExecutor { | ||
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| /** | ||
| * Gets the directives to submit the specified task to the cluster for execution | ||
| * | ||
| * See http://docs.adaptivecomputing.com/maui/commands/msub.php | ||
| * | ||
| * @param task A {@link TaskRun} to be submitted | ||
| * @param result The {@link List} instance to which add the job directives | ||
| * @return A {@link List} containing all directive tokens and values. | ||
| */ | ||
| protected List<String> getDirectives( TaskRun task, List<String> result ) { | ||
| assert result !=null | ||
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| result << '-N' << getJobNameFor(task) | ||
| result << '-o' << quote(task.workDir.resolve(TaskRun.CMD_LOG)) | ||
| result << '-j' << 'oe' | ||
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| // the requested queue name | ||
| if( task.config.queue ) { | ||
| result << '-q' << (String)task.config.queue | ||
| } | ||
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| if( task.config.cpus > 1 ) { | ||
| result << '-l' << "nodes=1:ppn=${task.config.cpus}" | ||
| } | ||
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| // max task duration | ||
| if( task.config.time ) { | ||
| final duration = task.config.getTime() | ||
| result << "-l" << "walltime=${duration.format('HH:mm:ss')}" | ||
| } | ||
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| // task max memory | ||
| if( task.config.memory ) { | ||
| // https://www.osc.edu/documentation/knowledge_base/out_of_memory_oom_or_excessive_memory_usage | ||
| result << "-l" << "mem=${task.config.memory.toString().replaceAll(/[\s]/,'').toLowerCase()}" | ||
| } | ||
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| // -- at the end append the command script wrapped file name | ||
| if( task.config.clusterOptions ) { | ||
| result << task.config.clusterOptions.toString() << '' | ||
| } | ||
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| return result | ||
| } | ||
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| @Override | ||
| String getHeaders( TaskRun task ) { | ||
| String result = super.getHeaders(task) | ||
| result += "cd ${quote(task.workDir)}\n" | ||
| return result | ||
| } | ||
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| /** | ||
| * The command line to submit this job | ||
| * | ||
| * @param task The {@link TaskRun} instance to submit for execution to the cluster | ||
| * @param scriptFile The file containing the job launcher script | ||
| * @return A list representing the submit command line | ||
| */ | ||
| List<String> getSubmitCommandLine(TaskRun task, Path scriptFile ) { | ||
| def cmd = new ArrayList(5) | ||
| cmd << 'msub' | ||
| cmd << '--xml' | ||
| cmd << scriptFile.name | ||
| return cmd | ||
| } | ||
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| protected String getHeaderToken() { '#MSUB' } | ||
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| /** | ||
| * Parse the string returned by the {@code qsub} command and extract the job ID string | ||
| * | ||
| * @param text The string returned when submitting the job | ||
| * @return The actual job ID string | ||
| */ | ||
| @Override | ||
| def parseJobId( String text ) { | ||
| String result | ||
| try { | ||
| result = new XmlSlurper() | ||
| .parseText(text) | ||
| .job[0] | ||
| .@JobID | ||
| .toString() | ||
| } | ||
| catch (Exception e) { | ||
| throw new IllegalArgumentException("Invalid Moab submit response:\n$text\n\n", e) | ||
| } | ||
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| if( !result ) | ||
| throw new IllegalArgumentException("Missing Moab submit job ID:\n$text\n\n") | ||
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| return result | ||
| } | ||
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| @Override | ||
| protected List<String> getKillCommand() { ['mjobctl', '-c'] } | ||
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| @Override | ||
| protected List<String> queueStatusCommand(Object queue) { | ||
| return ['showq', '--xml', '-w', "user="+System.getProperty('user.name')] | ||
| } | ||
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| static private Map<String,QueueStatus> DECODE_STATUS = [ | ||
| 'Running': QueueStatus.RUNNING, | ||
| 'Starting': QueueStatus.RUNNING, | ||
| 'Idle': QueueStatus.HOLD, | ||
| 'UserHold': QueueStatus.HOLD, | ||
| 'SystemHold': QueueStatus.HOLD, | ||
| 'Deferred': QueueStatus.HOLD, | ||
| 'NotQueued': QueueStatus.ERROR, | ||
| 'BatchHold': QueueStatus.ERROR, | ||
| ] | ||
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| protected QueueStatus decode(String status) { | ||
| DECODE_STATUS.get(status) | ||
| } | ||
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| @Override | ||
| protected Map<String, QueueStatus> parseQueueStatus(String xmlStatus) { | ||
| // parse XML string and and decode job states | ||
| final result = new LinkedHashMap() | ||
| try { | ||
| def data = new XmlSlurper().parseText(xmlStatus) | ||
| for( def queue : data.queue ) { | ||
| if( !queue.@count?.toInteger() ) | ||
| continue | ||
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| def state = queue.@option?.toString() | ||
| if( state=="active") | ||
| parseQueueJobNodes(queue, result, QueueStatus.RUNNING ) | ||
| else if( state=="eligible" ) | ||
| parseQueueJobNodes(queue, result, QueueStatus.PENDING ) | ||
| else | ||
| parseQueueJobNodes(queue, result ) | ||
| } | ||
| } | ||
| catch (Exception e) { | ||
| throw e | ||
| } | ||
| return result | ||
| } | ||
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| protected void parseQueueJobNodes(queueNode, Map result, QueueStatus state=null) { | ||
| for( def entry : queueNode.job ) { | ||
| final value = state ?: decode(entry.@State?.toString()) | ||
| result.put( entry.@JobID?.toString(), value ) | ||
| } | ||
| } | ||
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| protected List<String> killTaskCommand(def jobId) { | ||
| final result = getKillCommand() | ||
| if( jobId instanceof Collection ) { | ||
| result.add( jobId.join(',') ) | ||
| log.trace "Kill command: ${result}" | ||
| } | ||
| else { | ||
| result.add(jobId.toString()) | ||
| } | ||
| return result | ||
| } | ||
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| } |
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