add new executor for Fujitsu Technical Computing Suite (TCS)

Author: exthnet

modules/nextflow/src/main/groovy/nextflow/executor/ExecutorFactory.groovy

@@ -61,7 +61,8 @@ class ExecutorFactory {
             'nqsii': NqsiiExecutor,
             'moab': MoabExecutor,
             'oar': OarExecutor,
-            'hq': HyperQueueExecutor
+            'hq': HyperQueueExecutor,
+            'tcs': TcsExecutor
     ]
 
     @PackageScope Map<String, Class<? extends Executor>> executorsMap

modules/nextflow/src/main/groovy/nextflow/executor/TcsExecutor.groovy

@@ -0,0 +1,204 @@
+/*
+ * 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.
+ */
+/*
+  Implemented by Satoshi Ohshima <[email protected]>
+  I referred to the other executors groovy implementations.
+  Resource requests and other job characteristics can be controlled via the following process directives:
+  - time
+  - clusterOptions
+  queue (resource group), cpu, node, and other options should be indicated by clusterOptions.
+  This is because they depend on target systems (required options are not the same) and can be controlled by "-L" options in arguments of pjsub command.
+
+  example of nextflow.config on Genkai (Kyushu University)
+    process {
+      executor = 'tcs'
+      time = '00:30:00'
+      clusterOptions = '-L rscgrp=a-batch -L vnode-core=4'
+    }
+
+  example of nextflow.config on Flow (Nagoya University)
+    process {
+      executor = 'tcs'
+      time = '00:30:00'
+      clusterOptions = '-L rscunit=cx -L rscgrp=cx-share -L gpu=1'
+    }
+
+ */
+
+package nextflow.executor
+
+import java.nio.file.Path
+import java.util.regex.Pattern
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.processor.TaskArrayRun
+import nextflow.processor.TaskRun
+/*
+ * Implements a executor for Fujitsu TCS
+ *
+ * See https://software.fujitsu.com/jp/manual/manualindex/p21000154.html (in Japanese)
+ */
+@Slf4j
+@CompileStatic
+class TcsExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
+
+	static private Pattern SUBMIT_REGEX = ~/\[INFO\] PJM 0000 pjsub Job (\d+) submitted./
+    /* modify jobname for TCS on Fugaku */
+    static String modName(String name1){
+		String name2 = name1.replaceAll("\\(", "")
+		String name3 = name2.replaceAll("\\)", "")
+		return name3
+	}
+
+    /**
+     * Gets the directives to submit the specified task to the cluster for execution
+     *
+     * @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
+
+        if( task instanceof TaskArrayRun ) {
+            final arraySize = task.getArraySize()
+            result << '--bulk --sparam' << "0-${arraySize - 1}".toString()
+        }
+
+        result << '-N' << modName(getJobNameFor(task))
+
+		result << '-o' << (task.isArray() ? '/dev/null' : quote(task.workDir.resolve(TaskRun.CMD_LOG)))
+        result << '-j' << ''
+        result << '-S' << ''
+
+        // max task duration
+        if( task.config.getTime() ) {
+            final duration = task.config.getTime()
+            result << "-L" << "elapse=${duration.format('HH:mm:ss')}".toString()
+        }
+
+        // -- at the end append the command script wrapped file name
+        addClusterOptionsDirective(task.config, result)
+
+        return result
+    }
+
+    /**
+     * 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 ) {
+        [ 'pjsub', '-N', modName(getJobNameFor(task)), scriptFile.getName() ]
+    }
+
+    protected String getHeaderToken() { '#PJM' }
+
+    /**
+     * Parse the string returned by the {@code pjsub} 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 ) {
+        for( String line : text.readLines() ) {
+			log.warn1 line
+            def m = SUBMIT_REGEX.matcher(line)
+            if( m.find() ) {
+                return m.group(1).toString()
+            }
+        }
+        throw new IllegalArgumentException("Invalid TCS submit response:\n$text\n\n")
+    }
+
+    @Override
+    protected List<String> getKillCommand() { ['pjdel'] }
+
+    @Override
+    protected List<String> queueStatusCommand(Object queue) {
+        //String cmd = 'pjstat | grep -v JOB_ID'
+        //if( queue ) cmd += ' ' + queue
+        //return ['bash','-c', "set -o pipefail; $cmd | { grep -E '(Job Id:|job_state =)' || true; }".toString()]
+		final result = ['pjstat']
+		return result
+    }
+
+    static private Map<String,QueueStatus> DECODE_STATUS = [
+            'ACC': QueueStatus.PENDING,
+            'QUE': QueueStatus.PENDING,
+            'RNA': QueueStatus.PENDING,
+            'RUN': QueueStatus.RUNNING,
+            'RNO': QueueStatus.RUNNING,
+            'EXT': QueueStatus.RUNNING,
+            'CCL': QueueStatus.DONE,
+            'HLD': QueueStatus.HOLD,
+            'ERR': QueueStatus.ERROR
+    ]
+
+    protected QueueStatus decode(String status) {
+        DECODE_STATUS.get(status)
+    }
+
+    @Override
+    protected Map<String, QueueStatus> parseQueueStatus(String text) {
+
+        final JOB_ID = 'Job Id:'
+        final JOB_STATUS = 'job_state ='
+        final result = new LinkedHashMap<String, QueueStatus>()
+
+        String id = null
+        String status = null
+        text.eachLine { line ->
+            if( line.startsWith(JOB_ID) ) {
+                id = fetchValue(JOB_ID, line)
+            }
+            else if( id ) {
+                status = fetchValue(JOB_STATUS, line)
+            }
+            result.put( id, decode(status) ?: QueueStatus.UNKNOWN )
+        }
+
+        return result
+    }
+
+    static String fetchValue( String prefix, String line ) {
+        final p = line.indexOf(prefix)
+        return p!=-1 ? line.substring(p+prefix.size()).trim() : null
+    }
+
+    static protected boolean matchOptions(String value) {
+        value ? SUBMIT_REGEX.matcher(value).find() : null
+    }
+
+    @Override
+    String getArrayIndexName() {
+        return 'TCS_SUBJOBID'
+    }
+
+    @Override
+    int getArrayIndexStart() {
+        return 0
+    }
+
+    @Override
+    String getArrayTaskId(String jobId, int index) {
+        assert jobId, "Missing 'jobId' argument"
+        return jobId.replace('[]', "[$index]")
+    }
+
+}