Add support for fusion container custom options

This commit add the ability to provide custom container options where using fusion file system, using the following setting: docker.fusionOptions = "<CUSTOM OPTIONS>"> When omitted the following default is used docker.fusionOptions = "--rm --privileged" Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
nextflow-io · Dec 26, 2022 · 56e29d3 · 56e29d3
1 parent 393a489
commit 56e29d3
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Showing 6 changed files with 45 additions and 8 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy
@@ -87,12 +87,14 @@ abstract class ContainerBuilder<V extends ContainerBuilder> {
     String getImage() { image }
 
     V addRunOptions(String str) {
-        runOptions.add(str)
+        if( str )
+            runOptions.add(str)
         return (V)this
     }
 
     V addEngineOptions(String str) {
-        engineOptions.add(str)
+        if( str )
+            engineOptions.add(str)
         return (V)this
     }
 

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
@@ -18,12 +18,14 @@
 package nextflow.container
 
 import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
 
 /**
  * Models container engine configuration
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
+@Slf4j
 @CompileStatic
 class ContainerConfig extends LinkedHashMap {
 
@@ -76,4 +78,20 @@ class ContainerConfig extends LinkedHashMap {
             return Boolean.parseBoolean(result.toString())
         return false
     }
+
+    String fusionOptions() {
+        final result = get('fusionOptions')
+        return result!=null ? result : defaultFusionOptions()
+    }
+
+    protected String defaultFusionOptions() {
+        final eng = getEngine()
+        if( !eng )
+            return null
+        if( eng=='docker' || eng=='podman' )
+            return '--rm --privileged'
+        // default to null
+        log.warn "Fusion file system is not supported by '$eng' container engine"
+        return null
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
@@ -65,8 +65,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
     @Override
     SingularityBuilder addRunOptions(String str) {
-        runOptions.add(str)
-        return this
+        super.addRunOptions(str)
     }
 
     @Override

diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionHelper.groovy
@@ -50,9 +50,8 @@ class FusionHelper {
         final engine = containerConfig.getEngine()
         final containerBuilder = ContainerBuilder.create(engine, containerName)
                 .addMountWorkDir(false)
-                .addRunOptions('--rm')
+                .addRunOptions(containerConfig.fusionOptions())
                 .params(containerConfig)
-                .params(privileged: true)
 
         // add fusion env vars
         for(Map.Entry<String,String> it : launcher.fusionEnv()) {

diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
@@ -62,4 +62,23 @@ class ContainerConfigTest extends Specification {
 
     }
 
+    def 'should get fusion options' () {
+        when:
+        def cfg = new ContainerConfig(OPTS)
+
+        then:
+        cfg.fusionOptions() == EXPECTED
+
+        where:
+        OPTS                                            | EXPECTED
+        [:]                                             | null
+        [engine:'docker']                               | '--rm --privileged'
+        [engine:'podman']                               | '--rm --privileged'
+        and:
+        [engine:'docker', fusionOptions:'--cap-add foo']| '--cap-add foo'
+        [engine:'podman', fusionOptions:'--cap-add bar']| '--cap-add bar'
+        and:
+        [engine:'sarus', fusionOptions:'--other']       | '--other'
+    }
+
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy
@@ -76,8 +76,8 @@ class FusionHelperTest extends Specification {
         [engine:'docker']       | [:]               | 'image:1'     | ['echo', 'hello']     | ["sh", "-c", "docker run -i --rm --privileged image:1 echo 'hello'"]
         [engine:'docker']       | [FOO:'one']       | 'image:2'     | ['echo', 'hello']     | ["sh", "-c", "docker run -i -e \"FOO=one\" --rm --privileged image:2 echo 'hello'"]
         and:
-        [engine:'singularity']  | [:]               | 'image:1'     | ['echo', 'hello']     | ["sh", "-c", "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} singularity exec --rm image:1 echo 'hello'"]
-        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | ['echo', 'hello']     | ["sh", "-c", "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=one singularity exec --rm image:1 echo 'hello'"]
+        [engine:'singularity']  | [:]               | 'image:1'     | ['echo', 'hello']     | ["sh", "-c", "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} singularity exec image:1 echo 'hello'"]
+        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | ['echo', 'hello']     | ["sh", "-c", "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=one singularity exec image:1 echo 'hello'"]
 
     }