Fix Orphaned processes when using Singularity

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy

@@ -19,6 +19,7 @@ package nextflow.container
 
 import java.nio.file.Path
 
+import nextflow.executor.BashWrapperBuilder
 import nextflow.util.Escape
 import nextflow.util.MemoryUnit
 import nextflow.util.PathTrie
@@ -160,7 +161,7 @@ abstract class ContainerBuilder<V extends ContainerBuilder> {
         return run + ' ' + launcher
     }
 
-    String getKillCommand() { return '[[ "$pid" ]] && kill $pid 2>/dev/null' }
+    String getKillCommand() { BashWrapperBuilder.KILL_CMD }
 
     String getRemoveCommand() { return null }
 

modules/nextflow/src/test/groovy/nextflow/container/UdockerBuilderTest.groovy

@@ -115,7 +115,7 @@ class UdockerBuilderTest extends Specification {
             .stripIndent().trim()
 
         builder.getRemoveCommand() == null
-        builder.getKillCommand() == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        builder.getKillCommand() == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
     def 'should append the run command line with launcher' () {
@@ -132,7 +132,7 @@ class UdockerBuilderTest extends Specification {
                 .stripIndent().trim()
 
         builder.getRemoveCommand() == null
-        builder.getKillCommand() == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        builder.getKillCommand() == '[[ "$pid" ]] && nxf_kill $pid'
 
 
         when:
@@ -147,7 +147,7 @@ class UdockerBuilderTest extends Specification {
                 .stripIndent().trim()
 
         builder.getRemoveCommand() == null
-        builder.getKillCommand() == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        builder.getKillCommand() == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
 }

modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy

@@ -480,6 +480,7 @@ class BashWrapperBuilderTest extends Specification {
         binding.task_env == 'export FOO="aa"\nexport BAR="bb"\n'
         binding.container_env == null
         !binding.launch_cmd.contains('nxf_container_env')
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
     def 'should create secret env' () {
@@ -839,7 +840,7 @@ class BashWrapperBuilderTest extends Specification {
         sarus run --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
-        binding.kill_cmd == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
     def 'should create wrapper with sarus and environment'() {
@@ -856,7 +857,7 @@ class BashWrapperBuilderTest extends Specification {
         sarus run --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
-        binding.kill_cmd == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
         and:
         binding.container_env == '''\
                     nxf_container_env() {
@@ -881,7 +882,7 @@ class BashWrapperBuilderTest extends Specification {
         sarus run --mount=type=bind,source=/folder\\ with\\ blanks,destination=/folder\\ with\\ blanks --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
-        binding.kill_cmd == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
     def 'should create wrapper with sarus container custom options'() {
@@ -898,7 +899,7 @@ class BashWrapperBuilderTest extends Specification {
         sarus run --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" --mount=type=bind,source=/foo,destination=/bar busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
-        binding.kill_cmd == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
     def 'should create wrapper with shifter'() {
@@ -921,7 +922,7 @@ class BashWrapperBuilderTest extends Specification {
         shifter --image docker://ubuntu:latest /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
-        binding.kill_cmd == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
 
     }
 
@@ -936,7 +937,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
-        binding.kill_cmd == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
     def 'should create wrapper with singularity legacy entry'() {
@@ -950,7 +951,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
-        binding.kill_cmd == '[[ "$pid" ]] && kill $pid 2>/dev/null'
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
     def 'should create task and container env' () {