Fix problem that Nextflow Executions stuck on Kubernetes

modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy

@@ -418,48 +418,50 @@ class TraceRecord implements Serializable {
      */
 
     TraceRecord parseTraceFile( Path file ) {
+        try (BufferedReader reader = new BufferedReader(new FileReader(file.toFile()))) {
 
-        final text = file.text
-
-        final lines = text.readLines()
-        if( !lines )
-            return this
-        if( lines[0] != 'nextflow.trace/v2' )
-            return parseLegacy(file, lines)
-
-        for( int i=0; i<lines.size(); i++ ) {
-            final pair = lines[i].tokenize('=')
-            final name = pair[0]
-            final value = pair[1]
-            if( value == null )
-                continue
-
-            switch (name) {
-                case '%cpu':
-                case '%mem':
-                    // fields '%cpu' and '%mem' are expressed as percent value
-                    this.put(name, parseInt(value, file, name) / 10F)
-                    break
-
-                case 'rss':
-                case 'vmem':
-                case 'peak_rss':
-                case 'peak_vmem':
-                    // these fields are provided in KB, so they are normalized to bytes
-                    def val = parseLong(value, file, name) * 1024
-                    this.put(name, val)
-                    break
-
-                case 'cpu_model':
-                    this.put(name, value)
-                    break
-
-                default:
-                    def val = parseLong(value, file, name)
-                    this.put(name, val)
-                    break
+            String line
+            if( ( line = reader.readLine() ) == null ) {
+                return this
+            } else if ( line != 'nextflow.trace/v2' ) {
+                return parseLegacy(file, file.readLines())
             }
 
+            while(( line = reader.readLine() ) != null ) {
+                final pair = line.tokenize('=')
+                final name = pair[0]
+                final value = pair[1]
+                if( value == null )
+                    continue
+
+                switch (name) {
+                    case '%cpu':
+                    case '%mem':
+                        // fields '%cpu' and '%mem' are expressed as percent value
+                        this.put(name, parseInt(value, file, name) / 10F)
+                        break
+
+                    case 'rss':
+                    case 'vmem':
+                    case 'peak_rss':
+                    case 'peak_vmem':
+                        // these fields are provided in KB, so they are normalized to bytes
+                        def val = parseLong(value, file, name) * 1024
+                        this.put(name, val)
+                        break
+
+                    case 'cpu_model':
+                        this.put(name, value)
+                        break
+
+                    default:
+                        def val = parseLong(value, file, name)
+                        this.put(name, val)
+                        break
+                }
+            }
+        } catch (IOException e) {
+            e.printStackTrace();
         }
 
         return this

modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy

@@ -16,6 +16,9 @@
 
 package nextflow.processor
 
+import spock.lang.TempDir
+
+import java.nio.file.Path
 import java.util.concurrent.atomic.LongAdder
 
 import nextflow.Session
@@ -33,6 +36,9 @@ class TaskHandlerTest extends Specification {
 
     def static final long KB = 1024
 
+    @TempDir
+    Path folder
+
     def 'test get trace record'() {
 
         given:
@@ -42,7 +48,6 @@ class TaskHandlerTest extends Specification {
         '''
                 .leftTrim()
 
-        def folder = TestHelper.createInMemTempDir()
         folder.resolve( TaskRun.CMD_TRACE ).text = traceText
 
         def config = [

modules/nextflow/src/test/groovy/nextflow/trace/TraceFileObserverTest.groovy

@@ -15,6 +15,9 @@
  */
 
 package nextflow.trace
+
+import spock.lang.TempDir
+
 import java.nio.file.Files
 
 import nextflow.Session
@@ -28,7 +31,9 @@ import nextflow.processor.TaskStatus
 import nextflow.util.CacheHelper
 import nextflow.util.Duration
 import spock.lang.Specification
-import test.TestHelper
+
+import java.nio.file.Path
+
 /**
  *
  * @author Paolo Di Tommaso <[email protected]>
@@ -37,6 +42,9 @@ class TraceFileObserverTest extends Specification {
 
     final static long MB = 1024 * 1024
 
+    @TempDir
+    Path tempDir
+
     def setupSpec() {
         TraceRecord.TIMEZONE = TimeZone.getTimeZone('UTC') // note: set the timezone to be sure the time string does not change on CI test servers
     }
@@ -235,7 +243,7 @@ class TraceFileObserverTest extends Specification {
 
         given:
         final KB = 1024L
-        final file = TestHelper.createInMemTempFile('trace')
+        final file = Files.createTempFile(tempDir,'trace', '.txt')
         file.text =  '''
                 pid state %cpu %mem vmem rss peak_vmem peak_rss rchar wchar syscr syscw read_bytes write_bytes
                 18 0 7999 46 7868980 6694900 7876620 6702144 2147483647 2147483647 44001533 148401890 2147483647 2147483647

modules/nextflow/src/test/groovy/nextflow/trace/TraceRecordTest.groovy

@@ -18,9 +18,13 @@ package nextflow.trace
 
 import groovy.json.JsonSlurper
 import spock.lang.Specification
+import spock.lang.TempDir
 import spock.lang.Unroll
 import test.TestHelper
 
+import java.nio.file.Files
+import java.nio.file.Path
+
 /**
  *
  * @author Paolo Di Tommaso <[email protected]>
@@ -33,6 +37,9 @@ class TraceRecordTest extends Specification {
         TraceRecord.TIMEZONE = TimeZone.getTimeZone('UTC') // note: set the timezone to be sure the time string does not change on CI test servers
     }
 
+    @TempDir
+    Path tempDir
+
     def 'test get field'() {
 
         given:
@@ -153,7 +160,7 @@ class TraceRecordTest extends Specification {
     def 'should parse a trace file and return a TraceRecord object'() {
 
         given:
-        def file = TestHelper.createInMemTempFile('trace')
+        def file = Files.createTempFile(tempDir,'trace', '.txt')
         file.text = '''\
             nextflow.trace/v2
             realtime=12021
@@ -200,7 +207,7 @@ class TraceRecordTest extends Specification {
     def 'should parse a legacy trace file and return a TraceRecord object'() {
 
         given:
-        def file = TestHelper.createInMemTempFile('trace')
+        def file = Files.createTempFile(tempDir,'trace', '.txt')
         file.text =  '''
         pid state %cpu %mem vmem rss peak_vmem peak_rss rchar wchar syscr syscw read_bytes write_bytes
         1 0 10 20 11084 1220 21084 2220 4790 12 11 1 20 30