Add support for selecting minimum CPU platform on GCP (#1633)

Signed-off-by: hnawar <hnawar@google.com>

docs/google.rst

@@ -106,6 +106,7 @@ google.region                                  The Google *region* where the com
 google.zone                                    The Google *zone* where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Do not specify if a region is provided. See  `available Compute Engine regions and zones <https://cloud.google.com/compute/docs/regions-zones/>`_
 google.location                                The Google *location* where the job executions are deployed to Cloud Life Sciences API. See  `available Cloud Life Sciences API locations <https://cloud.google.com/life-sciences/docs/concepts/locations>`_ (default: the same as the region or the zone specified).
 google.enableRequesterPaysBuckets              When ``true`` uses the configured Google project id as the billing project for storage access. This is required when accessing data from *reqester pays enabled* buckets. See `Requester Pays on Google Cloud Storage documentation  <https://cloud.google.com/storage/docs/requester-pays>`_ (default: ``false``)
+google.lifeSciences.cpuPlatform                Set the minimum CPU Platform e.g `'Intel Skylake'`  See `Specifying a minimum CPU Platform for VM instances  <https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications>`_ (default: none).
 google.lifeSciences.bootDiskSize               Set the size of the virtual machine boot disk e.g `50.GB` (default: none).
 google.lifeSciences.copyImage                  The container image run to copy input and output files. It must include the ``gsutil`` tool (default: ``google/cloud-sdk:alpine``).
 google.lifeSciences.debug                      When ``true`` copies the `/google` debug directory in that task bucket directory (default: ``false``)

modules/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesConfig.groovy

@@ -52,6 +52,7 @@ class GoogleLifeSciencesConfig {
     String location
     boolean disableBinDir
     MemoryUnit bootDiskSize
+    String cpuPlatform
     boolean sshDaemon
     String sshImage
     Integer debugMode
@@ -109,6 +110,7 @@ class GoogleLifeSciencesConfig {
         final boolean disableBinDir = config.navigate('google.lifeSciences.disableRemoteBinDir',false)
         final preemptible = config.navigate("google.lifeSciences.preemptible", false) as boolean
         final bootDiskSize = config.navigate('google.lifeSciences.bootDiskSize') as MemoryUnit
+        final cpuPlatform = config.navigate('google.lifeSciences.cpuPlatform') as String
         final sshDaemon = config.navigate('google.lifeSciences.sshDaemon', false) as boolean
         final sshImage = config.navigate('google.lifeSciences.sshImage', DEFAULT_SSH_IMAGE) as String
         final copyImage = config.navigate('google.lifeSciences.copyImage', DEFAULT_COPY_IMAGE) as String
@@ -128,6 +130,7 @@ class GoogleLifeSciencesConfig {
                 preemptible: preemptible,
                 disableBinDir: disableBinDir,
                 bootDiskSize: bootDiskSize,
+                cpuPlatform: cpuPlatform,
                 debugMode: debugMode0(debugMode),
                 copyImage: copyImage,
                 sshDaemon: sshDaemon,

modules/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy

@@ -190,6 +190,10 @@ class GoogleLifeSciencesHelper {
         if( req.bootDiskSizeGb ) {
             vm.setBootDiskSizeGb(req.bootDiskSizeGb)
         }
+
+        if( req.cpuPlatform ) {
+            vm.setCpuPlatform(req.cpuPlatform)
+        }
 
         if( req.accelerator ) {
             final acc = new Accelerator().setType(req.accelerator.type).setCount(req.accelerator.request)

modules/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesSubmitRequest.groovy

@@ -59,6 +59,8 @@ class GoogleLifeSciencesSubmitRequest {
     Path workDir
 
     Integer bootDiskSizeGb
+
+    String cpuPlatform
 
     String entryPoint
 

modules/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesTaskHandler.groovy

@@ -299,6 +299,7 @@ class GoogleLifeSciencesTaskHandler extends TaskHandler {
         req.sharedMount = configureMount(DEFAULT_DISK_NAME, task.workDir.toString())
         req.accelerator = task.config.getAccelerator()
         req.location = executor.config.location
+        req.cpuPlatform = executor.config.cpuPlatform
         req.bootDiskSizeGb = executor.config.bootDiskSize?.toGiga() as Integer
         req.entryPoint = task.config.getContainerOptionsMap().getOrDefault('entrypoint', GoogleLifeSciencesConfig.DEFAULT_ENTRY_POINT)
         req.usePrivateAddress = executor.config.usePrivateAddress

modules/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesConfigTest.groovy

@@ -240,5 +240,18 @@ class GoogleLifeSciencesConfigTest extends Specification {
         config.enableRequesterPaysBuckets == true
 
     }
+
+    def 'should config cpuPlatform' () {
+        when:
+        def config = GoogleLifeSciencesConfig.fromSession0([google:[project:'foo', region:'x', lifeSciences: [:]]])
+        then:
+        config.cpuPlatform == null
+
+        when:
+        config = GoogleLifeSciencesConfig.fromSession0([google:[project:'foo', region:'x', lifeSciences: [cpuPlatform:'Intel Skylake']]])
+        then:
+        config.cpuPlatform == 'Intel Skylake'
+
+    }
 
 }

modules/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy

@@ -189,6 +189,7 @@ class GoogleLifeSciencesHelperTest extends GoogleSpecification {
                     preemptible: false,
                     accelerator: acc,
                     bootDiskSizeGb: 75,
+                    cpuPlatform: 'Intel Skylake',
                     usePrivateAddress: true ))
         then:
         with(resources3) {
@@ -202,6 +203,7 @@ class GoogleLifeSciencesHelperTest extends GoogleSpecification {
             getVirtualMachine().getAccelerators()[0].getCount()==4
             getVirtualMachine().getAccelerators()[0].getType()=='nvidia-tesla-k80'
             getVirtualMachine().getBootDiskSizeGb() == 75
+            getVirtualMachine().getCpuPlatform() == 'Intel Skylake'
             getVirtualMachine().getNetwork().getUsePrivateAddress()
         }
     }

modules/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesTaskHandlerTest.groovy

@@ -178,6 +178,7 @@ class GoogleLifeSciencesTaskHandlerTest extends GoogleSpecification {
         req.sharedMount.getDisk() == GoogleLifeSciencesTaskHandler.DEFAULT_DISK_NAME
         !req.sharedMount.getReadOnly()
         req.bootDiskSizeGb == null
+        req.cpuPlatform == null
         req.entryPoint == GoogleLifeSciencesConfig.DEFAULT_ENTRY_POINT
         !req.usePrivateAddress
 
@@ -211,6 +212,7 @@ class GoogleLifeSciencesTaskHandlerTest extends GoogleSpecification {
                     getPreemptible() >> true
                     getBootDiskSize() >> MemoryUnit.of('20 GB')
                     getUsePrivateAddress() >> true
+                    getCpuPlatform() >> 'Intel Skylake'
                 }
             }
         }
@@ -244,6 +246,7 @@ class GoogleLifeSciencesTaskHandlerTest extends GoogleSpecification {
         req.sharedMount.getDisk() == GoogleLifeSciencesTaskHandler.DEFAULT_DISK_NAME
         !req.sharedMount.getReadOnly()
         req.bootDiskSizeGb == 20
+        req.cpuPlatform =='Intel Skylake'
         req.entryPoint == GoogleLifeSciencesConfig.DEFAULT_ENTRY_POINT
         req.usePrivateAddress