Merge pull request #162 from arangodb/bugfix/enforce-anti-affinity

Force volumes to unique nodes for production environments

Author: ewoutp

examples/production-cluster.yaml

@@ -0,0 +1,8 @@
+apiVersion: "database.arangodb.com/v1alpha"
+kind: "ArangoDeployment"
+metadata:
+  name: "production-cluster"
+spec:
+  mode: Cluster
+  image: arangodb/arangodb:3.3.10
+  environment: Production

pkg/apis/deployment/v1alpha/environment.go

@@ -47,6 +47,11 @@ func (e Environment) Validate() error {
 	}
 }
 
+// IsProduction returns true when the given environment is a production environment.
+func (e Environment) IsProduction() bool {
+	return e == EnvironmentProduction
+}
+
 // NewEnvironment returns a reference to a string with given value.
 func NewEnvironment(input Environment) *Environment {
 	return &input

pkg/deployment/resources/pvcs.go

@@ -43,6 +43,7 @@ func (r *Resources) EnsurePVCs() error {
 	owner := apiObject.AsOwner()
 	iterator := r.context.GetServerGroupIterator()
 	status := r.context.GetStatus()
+	enforceAntiAffinity := r.context.GetSpec().GetEnvironment().IsProduction()
 
 	if err := iterator.ForeachServerGroup(func(group api.ServerGroup, spec api.ServerGroupSpec, status *api.MemberStatusList) error {
 		for _, m := range *status {
@@ -51,7 +52,7 @@ func (r *Resources) EnsurePVCs() error {
 				role := group.AsRole()
 				resources := spec.Resources
 				finalizers := r.createPVCFinalizers(group)
-				if err := k8sutil.CreatePersistentVolumeClaim(kubecli, m.PersistentVolumeClaimName, deploymentName, ns, storageClassName, role, resources, finalizers, owner); err != nil {
+				if err := k8sutil.CreatePersistentVolumeClaim(kubecli, m.PersistentVolumeClaimName, deploymentName, ns, storageClassName, role, enforceAntiAffinity, resources, finalizers, owner); err != nil {
 					return maskAny(err)
 				}
 			}

pkg/storage/pv_creator.go

@@ -24,6 +24,7 @@ package storage
 
 import (
 	"context"
+	"crypto/sha1"
 	"encoding/json"
 	"fmt"
 	"math/rand"
@@ -32,6 +33,7 @@ import (
 	"sort"
 	"strconv"
 	"strings"
+	"time"
 
 	"k8s.io/apimachinery/pkg/api/resource"
 
@@ -41,6 +43,8 @@ import (
 
 	api "github.com/arangodb/kube-arangodb/pkg/apis/storage/v1alpha"
 	"github.com/arangodb/kube-arangodb/pkg/storage/provisioner"
+	"github.com/arangodb/kube-arangodb/pkg/util/constants"
+	"github.com/arangodb/kube-arangodb/pkg/util/k8sutil"
 )
 
 const (
@@ -72,7 +76,24 @@ func (ls *LocalStorage) createPVs(ctx context.Context, apiObject *api.ArangoLoca
 		clients[i], clients[j] = clients[j], clients[i]
 	})
 
+	var nodeClientMap map[string]provisioner.API
 	for i, claim := range unboundClaims {
+		// Find deployment name & role in the claim (if any)
+		deplName, role, enforceAniAffinity := getDeploymentInfo(claim)
+		allowedClients := clients
+		if enforceAniAffinity && deplName != "" {
+			// Select nodes to choose from such that no volume in group lands on the same node
+			if nodeClientMap == nil {
+				nodeClientMap = createNodeClientMap(ctx, clients)
+			}
+			var err error
+			allowedClients, err = ls.filterAllowedNodes(nodeClientMap, deplName, role)
+			if err != nil {
+				log.Warn().Err(err).Msg("Failed to filter allowed nodes")
+				continue // We'll try this claim again later
+			}
+		}
+
 		// Find size of PVC
 		volSize := defaultVolumeSize
 		if reqStorage := claim.Spec.Resources.Requests.StorageEphemeral(); reqStorage != nil {
@@ -81,7 +102,7 @@ func (ls *LocalStorage) createPVs(ctx context.Context, apiObject *api.ArangoLoca
 			}
 		}
 		// Create PV
-		if err := ls.createPV(ctx, apiObject, clients, i, volSize); err != nil {
+		if err := ls.createPV(ctx, apiObject, allowedClients, i, volSize, claim, deplName, role); err != nil {
 			log.Error().Err(err).Msg("Failed to create PersistentVolume")
 		}
 	}
@@ -90,7 +111,7 @@ func (ls *LocalStorage) createPVs(ctx context.Context, apiObject *api.ArangoLoca
 }
 
 // createPV creates a PersistentVolume.
-func (ls *LocalStorage) createPV(ctx context.Context, apiObject *api.ArangoLocalStorage, clients []provisioner.API, clientsOffset int, volSize int64) error {
+func (ls *LocalStorage) createPV(ctx context.Context, apiObject *api.ArangoLocalStorage, clients []provisioner.API, clientsOffset int, volSize int64, claim v1.PersistentVolumeClaim, deploymentName, role string) error {
 	log := ls.deps.Log
 	// Try clients
 	for clientIdx := 0; clientIdx < len(clients); clientIdx++ {
@@ -117,7 +138,7 @@ func (ls *LocalStorage) createPV(ctx context.Context, apiObject *api.ArangoLocal
 				continue
 			}
 			// Create a volume
-			pvName := apiObject.GetName() + "-" + name
+			pvName := strings.ToLower(apiObject.GetName() + "-" + shortHash(info.NodeName) + "-" + name)
 			volumeMode := v1.PersistentVolumeFilesystem
 			nodeAff, err := createNodeAffinity(info.NodeName)
 			if err != nil {
@@ -131,6 +152,10 @@ func (ls *LocalStorage) createPV(ctx context.Context, apiObject *api.ArangoLocal
 						v1.AlphaStorageNodeAffinityAnnotation: nodeAff,
 						nodeNameAnnotation:                    info.NodeName,
 					},
+					Labels: map[string]string{
+						k8sutil.LabelKeyArangoDeployment: deploymentName,
+						k8sutil.LabelKeyRole:             role,
+					},
 				},
 				Spec: v1.PersistentVolumeSpec{
 					Capacity: v1.ResourceList{
@@ -147,6 +172,13 @@ func (ls *LocalStorage) createPV(ctx context.Context, apiObject *api.ArangoLocal
 					},
 					StorageClassName: apiObject.Spec.StorageClass.Name,
 					VolumeMode:       &volumeMode,
+					ClaimRef: &v1.ObjectReference{
+						Kind:       "PersistentVolumeClaim",
+						APIVersion: "",
+						Name:       claim.GetName(),
+						Namespace:  claim.GetNamespace(),
+						UID:        claim.GetUID(),
+					},
 				},
 			}
 			// Attach PV to ArangoLocalStorage
@@ -159,6 +191,16 @@ func (ls *LocalStorage) createPV(ctx context.Context, apiObject *api.ArangoLocal
 				Str("name", pvName).
 				Str("node-name", info.NodeName).
 				Msg("Created PersistentVolume")
+
+			// Bind claim to volume
+			if err := ls.bindClaimToVolume(claim, pv.GetName()); err != nil {
+				// Try to delete the PV now
+				if err := ls.deps.KubeCli.CoreV1().PersistentVolumes().Delete(pv.GetName(), &metav1.DeleteOptions{}); err != nil {
+					log.Error().Err(err).Msg("Failed to delete PV after binding PVC failed")
+				}
+				return maskAny(err)
+			}
+
 			return nil
 		}
 	}
@@ -204,3 +246,96 @@ func createNodeAffinity(nodeName string) (string, error) {
 	}
 	return string(encoded), nil
 }
+
+// createNodeClientMap creates a map from node name to API.
+// Clients that do not respond properly on a GetNodeInfo request are
+// ignored.
+func createNodeClientMap(ctx context.Context, clients []provisioner.API) map[string]provisioner.API {
+	result := make(map[string]provisioner.API)
+	for _, c := range clients {
+		if info, err := c.GetNodeInfo(ctx); err == nil {
+			result[info.NodeName] = c
+		}
+	}
+	return result
+}
+
+// getDeploymentInfo returns the name of the deployment that created the given claim,
+// the role of the server that the claim is used for and the value for `enforceAntiAffinity`.
+// If not found, empty strings are returned.
+// Returns deploymentName, role, enforceAntiAffinity.
+func getDeploymentInfo(pvc v1.PersistentVolumeClaim) (string, string, bool) {
+	deploymentName := pvc.GetLabels()[k8sutil.LabelKeyArangoDeployment]
+	role := pvc.GetLabels()[k8sutil.LabelKeyRole]
+	enforceAntiAffinity, _ := strconv.ParseBool(pvc.GetAnnotations()[constants.AnnotationEnforceAntiAffinity]) // If annotation empty, this will yield false.
+	return deploymentName, role, enforceAntiAffinity
+}
+
+// filterAllowedNodes returns those clients that do not yet have a volume for the given deployment name & role.
+func (ls *LocalStorage) filterAllowedNodes(clients map[string]provisioner.API, deploymentName, role string) ([]provisioner.API, error) {
+	// Find all PVs for given deployment & role
+	list, err := ls.deps.KubeCli.CoreV1().PersistentVolumes().List(metav1.ListOptions{
+		LabelSelector: fmt.Sprintf("%s=%s,%s=%s", k8sutil.LabelKeyArangoDeployment, deploymentName, k8sutil.LabelKeyRole, role),
+	})
+	if err != nil {
+		return nil, maskAny(err)
+	}
+	excludedNodes := make(map[string]struct{})
+	for _, pv := range list.Items {
+		nodeName := pv.GetAnnotations()[nodeNameAnnotation]
+		excludedNodes[nodeName] = struct{}{}
+	}
+	result := make([]provisioner.API, 0, len(clients))
+	for nodeName, c := range clients {
+		if _, found := excludedNodes[nodeName]; !found {
+			result = append(result, c)
+		}
+	}
+	return result, nil
+}
+
+// bindClaimToVolume tries to bind the given claim to the volume with given name.
+// If the claim has been updated, the function retries several times.
+func (ls *LocalStorage) bindClaimToVolume(claim v1.PersistentVolumeClaim, volumeName string) error {
+	log := ls.deps.Log.With().Str("pvc-name", claim.GetName()).Str("volume-name", volumeName).Logger()
+	pvcs := ls.deps.KubeCli.CoreV1().PersistentVolumeClaims(claim.GetNamespace())
+
+	for attempt := 0; attempt < 10; attempt++ {
+		// Backoff if needed
+		time.Sleep(time.Millisecond * time.Duration(10*attempt))
+
+		// Fetch latest version of claim
+		updated, err := pvcs.Get(claim.GetName(), metav1.GetOptions{})
+		if k8sutil.IsNotFound(err) {
+			return maskAny(err)
+		} else if err != nil {
+			log.Warn().Err(err).Msg("Failed to load updated PersistentVolumeClaim")
+			continue
+		}
+
+		// Check claim. If already bound, bail out
+		if !pvcNeedsVolume(*updated) {
+			return maskAny(fmt.Errorf("PersistentVolumeClaim '%s' no longer needs a volume", claim.GetName()))
+		}
+
+		// Try to bind
+		updated.Spec.VolumeName = volumeName
+		if _, err := pvcs.Update(updated); k8sutil.IsConflict(err) {
+			// Claim modified already, retry
+			log.Debug().Err(err).Msg("PersistentVolumeClaim has been modified. Retrying.")
+		} else if err != nil {
+			log.Error().Err(err).Msg("Failed to bind PVC to volume")
+			return maskAny(err)
+		}
+		log.Debug().Msg("Bound volume to PersistentVolumeClaim")
+		return nil
+	}
+	log.Error().Msg("All attempts to bind PVC to volume failed")
+	return maskAny(fmt.Errorf("All attempts to bind PVC to volume failed"))
+}
+
+// shortHash creates a 6 letter hash of the given name.
+func shortHash(name string) string {
+	h := sha1.Sum([]byte(name))
+	return fmt.Sprintf("%0x", h)[:6]
+}

pkg/util/constants/constants.go

@@ -48,4 +48,6 @@ const (
 	FinalizerPodAgencyServing = "agent.database.arangodb.com/agency-serving"  // Finalizer added to Agents, indicating the need for keeping enough agents alive
 	FinalizerPVCMemberExists  = "pvc.database.arangodb.com/member-exists"     // Finalizer added to PVCs, indicating the need to keep is as long as its member exists
 	FinalizerDeplReplStopSync = "replication.database.arangodb.com/stop-sync" // Finalizer added to ArangoDeploymentReplication, indicating the need to stop synchronization
+
+	AnnotationEnforceAntiAffinity = "database.arangodb.com/enforce-anti-affinity" // Key of annotation added to PVC. Value is a boolean "true" or "false"
 )

pkg/util/k8sutil/pvc.go

@@ -23,9 +23,13 @@
 package k8sutil
 
 import (
+	"strconv"
+
 	"k8s.io/api/core/v1"
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"k8s.io/client-go/kubernetes"
+
+	"github.com/arangodb/kube-arangodb/pkg/util/constants"
 )
 
 // IsPersistentVolumeClaimMarkedForDeletion returns true if the pod has been marked for deletion.
@@ -42,14 +46,17 @@ func CreatePersistentVolumeClaimName(deploymentName, role, id string) string {
 // CreatePersistentVolumeClaim creates a persistent volume claim with given name and configuration.
 // If the pvc already exists, nil is returned.
 // If another error occurs, that error is returned.
-func CreatePersistentVolumeClaim(kubecli kubernetes.Interface, pvcName, deploymentName, ns, storageClassName, role string, resources v1.ResourceRequirements, finalizers []string, owner metav1.OwnerReference) error {
+func CreatePersistentVolumeClaim(kubecli kubernetes.Interface, pvcName, deploymentName, ns, storageClassName, role string, enforceAntiAffinity bool, resources v1.ResourceRequirements, finalizers []string, owner metav1.OwnerReference) error {
 	labels := LabelsForDeployment(deploymentName, role)
 	volumeMode := v1.PersistentVolumeFilesystem
 	pvc := &v1.PersistentVolumeClaim{
 		ObjectMeta: metav1.ObjectMeta{
 			Name:       pvcName,
 			Labels:     labels,
 			Finalizers: finalizers,
+			Annotations: map[string]string{
+				constants.AnnotationEnforceAntiAffinity: strconv.FormatBool(enforceAntiAffinity),
+			},
 		},
 		Spec: v1.PersistentVolumeClaimSpec{
 			AccessModes: []v1.PersistentVolumeAccessMode{