Use ephemeral-storage for disk directive and k8s executor

docs/executor.rst

@@ -202,6 +202,7 @@ Resource requests and other job characteristics can be controlled via the follow
 
 * :ref:`process-accelerator`
 * :ref:`process-cpus`
+* :ref:`process-disk`
 * :ref:`process-memory`
 * :ref:`process-pod`
 * :ref:`process-time`

docs/process.rst

@@ -1898,6 +1898,7 @@ The ``pod`` directive allows the definition of the following options:
 ``env: <E>, config: <C/K>``                       Defines an environment variable with name ``E`` and whose value is given by the entry associated to the key with name ``K`` in the `ConfigMap <https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/>`_ with name ``C``.
 ``env: <E>, secret: <S/K>``                       Defines an environment variable with name ``E`` and whose value is given by the entry associated to the key with name ``K`` in the `Secret <https://kubernetes.io/docs/concepts/configuration/secret/>`_ with name ``S``.
 ``config: <C/K>, mountPath: </absolute/path>``    The content of the `ConfigMap <https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/>`_ with name ``C`` with key ``K`` is made available to the path ``/absolute/path``. When the key component is omitted the path is interpreted as a directory and all the ``ConfigMap`` entries are exposed in that path.
+``emptyDir: <V>, mountPath: </absolute/path>``    Mounts an `emptyDir <https://kubernetes.io/docs/concepts/storage/volumes/#emptydir>`_ with configuration ``V`` to the path ``/absolute/path``.
 ``secret: <S/K>, mountPath: </absolute/path>``    The content of the `Secret <https://kubernetes.io/docs/concepts/configuration/secret/>`_ with name ``S`` with key ``K`` is made available to the path ``/absolute/path``. When the key component is omitted the path is interpreted as a directory and all the ``Secret`` entries are exposed in that path.
 ``volumeClaim: <V>, mountPath: </absolute/path>`` Mounts a `Persistent volume claim <https://kubernetes.io/docs/concepts/storage/persistent-volumes/>`_ with name ``V`` to the specified path location. Use the optional ``subPath`` parameter to mount a directory inside the referenced volume instead of its root. The volume may be mounted with `readOnly: true`, but is read/write by default.
 ``imagePullPolicy: <V>``                          Specifies the strategy to be used to pull the container image e.g. ``imagePullPolicy: 'Always'``.

modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy

@@ -203,11 +203,14 @@ class K8sTaskHandler extends TaskHandler {
         // add computing resources
         final cpus = taskCfg.getCpus()
         final mem = taskCfg.getMemory()
+        final disk = taskCfg.getDisk()
         final acc = taskCfg.getAccelerator()
         if( cpus )
             builder.withCpus(cpus)
         if( mem )
             builder.withMemory(mem)
+        if( disk )
+            builder.withDisk(disk)
         if( acc )
             builder.withAccelerator(acc)
 

modules/nextflow/src/main/groovy/nextflow/k8s/model/PodMountEmptyDir.groovy

@@ -0,0 +1,52 @@
+/*
+ * Copyright 2020-2022, Seqera Labs
+ * 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.
+ */
+
+package nextflow.k8s.model
+
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+
+/**
+ * Model a K8s pod emptyDir mount
+ *
+ * See also https://kubernetes.io/docs/concepts/storage/volumes/#emptydir
+ *
+ * @author Ben Sherman <[email protected]>
+ */
+@CompileStatic
+@ToString(includeNames = true)
+@EqualsAndHashCode
+class PodMountEmptyDir {
+
+    String mountPath
+
+    Map emptyDir
+
+    PodMountEmptyDir( Map emptyDir, String mountPath ) {
+        assert emptyDir
+        assert mountPath
+
+        this.emptyDir = emptyDir
+        this.mountPath = mountPath
+    }
+
+    PodMountEmptyDir( Map entry ) {
+        this(entry.emptyDir as Map, entry.mountPath as String)
+    }
+
+}

modules/nextflow/src/main/groovy/nextflow/k8s/model/PodOptions.groovy

@@ -41,6 +41,8 @@ class PodOptions {
 
     private Collection<PodMountConfig> mountConfigMaps
 
+    private Collection<PodMountEmptyDir> mountEmptyDirs
+
     private Collection<PodMountSecret> mountSecrets
 
     private Collection<PodVolumeClaim> mountClaims
@@ -66,8 +68,9 @@ class PodOptions {
     PodOptions( List<Map> options=null ) {
         int size = options ? options.size() : 0
         envVars = new HashSet<>(size)
-        mountSecrets = new HashSet<>(size)
         mountConfigMaps = new HashSet<>(size)
+        mountEmptyDirs = new HashSet<>(size)
+        mountSecrets = new HashSet<>(size)
         mountClaims = new HashSet<>(size)
         automountServiceAccountToken = true
         tolerations = new ArrayList<Map>(size)
@@ -94,12 +97,15 @@ class PodOptions {
         else if( entry.env && entry.config ) {
             envVars << PodEnv.config(entry.env, entry.config)
         }
-        else if( entry.mountPath && entry.secret ) {
-            mountSecrets <<  new PodMountSecret(entry)
-        }
         else if( entry.mountPath && entry.config ) {
             mountConfigMaps << new PodMountConfig(entry)
         }
+        else if( entry.mountPath && entry.emptyDir ) {
+            mountEmptyDirs << new PodMountEmptyDir(entry)
+        }
+        else if( entry.mountPath && entry.secret ) {
+            mountSecrets <<  new PodMountSecret(entry)
+        }
         else if( entry.mountPath && entry.volumeClaim ) {
             mountClaims << new PodVolumeClaim(entry)
         }
@@ -148,6 +154,8 @@ class PodOptions {
 
     Collection<PodMountConfig> getMountConfigMaps() { mountConfigMaps }
 
+    Collection<PodMountEmptyDir> getMountEmptyDirs() { mountEmptyDirs }
+
     Collection<PodMountSecret> getMountSecrets() { mountSecrets }
 
     Collection<PodVolumeClaim> getVolumeClaims() { mountClaims }
@@ -210,6 +218,10 @@ class PodOptions {
         result.mountConfigMaps.addAll( mountConfigMaps )
         result.mountConfigMaps.addAll( other.mountConfigMaps )
 
+        // empty dirs
+        result.mountEmptyDirs.addAll( mountEmptyDirs )
+        result.mountEmptyDirs.addAll( other.mountEmptyDirs )
+
         // secrets
         result.mountSecrets.addAll( mountSecrets )
         result.mountSecrets.addAll( other.mountSecrets )

modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy

@@ -68,16 +68,20 @@ class PodSpecBuilder {
 
     String memory
 
+    String disk
+
     String serviceAccount
 
     boolean automountServiceAccountToken = true
 
     AcceleratorResource accelerator
 
-    Collection<PodMountSecret> secrets = []
-
     Collection<PodMountConfig> configMaps = []
 
+    Collection<PodMountEmptyDir> emptyDirs = []
+
+    Collection<PodMountSecret> secrets = []
+
     Collection<PodHostMount> hostMounts = []
 
     Collection<PodVolumeClaim> volumeClaims = []
@@ -167,6 +171,16 @@ class PodSpecBuilder {
         return this
     }
 
+    PodSpecBuilder withDisk(String disk) {
+        this.disk = disk
+        return this
+    }
+
+    PodSpecBuilder withDisk(MemoryUnit disk)  {
+        this.disk = "${disk.mega}Mi".toString()
+        return this
+    }
+
     PodSpecBuilder withAccelerator(AcceleratorResource acc) {
         this.accelerator = acc
         return this
@@ -223,6 +237,16 @@ class PodSpecBuilder {
         return this
     }
 
+    PodSpecBuilder withEmptyDirs( Collection<PodMountEmptyDir> emptyDirs ) {
+        this.emptyDirs.addAll(emptyDirs)
+        return this
+    }
+
+    PodSpecBuilder withEmptyDir( PodMountEmptyDir emptyDir ) {
+        this.emptyDirs.add(emptyDir)
+        return this
+    }
+
     PodSpecBuilder withSecrets( Collection<PodMountSecret> secrets ) {
         this.secrets.addAll(secrets)
         return this
@@ -262,12 +286,15 @@ class PodSpecBuilder {
         // -- env vars
         if( opts.getEnvVars() )
             envVars.addAll( opts.getEnvVars() )
-        // -- secrets
-        if( opts.getMountSecrets() )
-            secrets.addAll( opts.getMountSecrets() )
         // -- configMaps
         if( opts.getMountConfigMaps() )
             configMaps.addAll( opts.getMountConfigMaps() )
+        // -- emptyDirs
+        if( opts.getMountEmptyDirs() )
+            emptyDirs.addAll( opts.getMountEmptyDirs() )
+        // -- secrets
+        if( opts.getMountSecrets() )
+            secrets.addAll( opts.getMountSecrets() )
         // -- volume claims 
         if( opts.getVolumeClaims() )
             volumeClaims.addAll( opts.getVolumeClaims() )
@@ -334,6 +361,8 @@ class PodSpecBuilder {
             res.cpu = this.cpus
         if( this.memory )
             res.memory = this.memory
+        if( this.disk )
+            res['ephemeral-storage'] = this.disk
 
         final container = [ name: this.podName, image: this.imageName ]
         if( this.command )
@@ -445,6 +474,13 @@ class PodSpecBuilder {
             configMapToSpec(name, entry, mounts, volumes)
         }
 
+        // -- emptyDir volumes
+        for( PodMountEmptyDir entry : emptyDirs ) {
+            final name = nextVolName()
+            mounts << [name: name, mountPath: entry.mountPath]
+            volumes << [name: name, emptyDir: entry.emptyDir]
+        }
+
         // host mounts
         for( PodHostMount entry : hostMounts ) {
             final name = nextVolName()

modules/nextflow/src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy

@@ -32,8 +32,9 @@ class PodOptionsTest extends Specification {
         def options = new PodOptions(null)
         then:
         options.getEnvVars() == [] as Set
-        options.getMountSecrets() == [] as Set
         options.getMountConfigMaps() == [] as Set
+        options.getMountEmptyDirs() == [] as Set
+        options.getMountSecrets() == [] as Set
         options.getAutomountServiceAccountToken() == true
     }
 
@@ -95,6 +96,25 @@ class PodOptionsTest extends Specification {
     }
 
 
+    def 'should return emptyDir mounts' () {
+
+        given:
+        def options = [
+                [mountPath: '/scratch1', emptyDir: [medium: 'Memory']],
+                [mountPath: '/scratch2', emptyDir: [medium: 'Disk']]
+        ]
+
+        when:
+        def emptyDirs = new PodOptions(options).getMountEmptyDirs()
+        then:
+        emptyDirs.size() == 2
+        emptyDirs == [
+                new PodMountEmptyDir(options[0]),
+                new PodMountEmptyDir(options[1])
+        ] as Set
+    }
+
+
     def 'should return secret mounts' () {
 
         given:
@@ -225,6 +245,7 @@ class PodOptionsTest extends Specification {
                 [config: 'y', mountPath: '/y'],
                 [volumeClaim: 'z', mountPath: '/z'],
 
+                [emptyDir: [:], mountPath: 'scratch1'],
                 [securityContext: [runAsUser: 1000, fsGroup: 200, allowPrivilegeEscalation: true]],
                 [nodeSelector: 'foo=X, bar=Y'],
                 [automountServiceAccountToken: false],
@@ -282,6 +303,10 @@ class PodOptionsTest extends Specification {
                 new PodMountConfig('y', '/y'),
         ] as Set
 
+        opts.getMountEmptyDirs() == [
+                new PodMountEmptyDir([:], '/scratch1'),
+        ] as Set
+
         opts.getVolumeClaims() == [
                 new PodVolumeClaim('pvc','/mnt/claim'),
                 new PodVolumeClaim('z','/z'),

modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy

@@ -252,6 +252,7 @@ class PodSpecBuilderTest extends Specification {
                 .withCpus(8)
                 .withAccelerator( new AcceleratorResource(request: 5, limit:10, type: 'foo.org') )
                 .withMemory('100Gi')
+                .withDisk('10Gi')
                 .build()
 
         then:
@@ -270,8 +271,8 @@ class PodSpecBuilderTest extends Specification {
                                             [name:'DELTA', value:'world']
                                     ],
                                     resources:[
-                                            requests: ['foo.org/gpu':5, cpu:8, memory:'100Gi'],
-                                            limits:['foo.org/gpu':10, cpu:8, memory:'100Gi'] ]
+                                            requests: ['foo.org/gpu':5, cpu:8, memory:'100Gi', 'ephemeral-storage':'10Gi'],
+                                            limits:['foo.org/gpu':10, cpu:8, memory:'100Gi', 'ephemeral-storage':'10Gi'] ]
                                    ]
                            ]
                    ]
@@ -390,6 +391,42 @@ class PodSpecBuilderTest extends Specification {
 
     }
 
+    def 'should get empty dir mounts' () {
+
+        when:
+        def spec = new PodSpecBuilder()
+                .withPodName('foo')
+                .withImageName('busybox')
+                .withWorkDir('/path')
+                .withCommand(['echo'])
+                .withEmptyDir(new PodMountEmptyDir(mountPath: '/scratch1', emptyDir: [medium: 'Disk']))
+                .withEmptyDir(new PodMountEmptyDir(mountPath: '/scratch2', emptyDir: [medium: 'Memory']))
+                .build()
+        then:
+        spec ==  [
+                apiVersion: 'v1',
+                kind: 'Pod',
+                metadata: [name: 'foo', namespace: 'default'],
+                spec: [
+                        restartPolicy: 'Never',
+                        containers: [[
+                                name: 'foo',
+                                image: 'busybox',
+                                command: ['echo'],
+                                workingDir: '/path',
+                                volumeMounts: [
+                                        [name: 'vol-1', mountPath: '/scratch1'],
+                                        [name: 'vol-2', mountPath: '/scratch2']
+                                ]
+                        ]],
+                        volumes: [
+                                [name: 'vol-1', emptyDir: [medium: 'Disk']],
+                                [name: 'vol-2', emptyDir: [medium: 'Memory']]
+                        ]
+                ]
+        ]
+    }
+
     def 'should consume env secrets' () {
 
         when: