add example with lammps pvc (#66)

* add example with lammps pvc

Signed-off-by: vsoch <[email protected]>

Author: vsoch

examples/addons/volumes/lammps-pvc.yaml

@@ -0,0 +1,56 @@
+apiVersion: flux-framework.org/v1alpha2
+kind: MetricSet
+metadata:
+  labels:
+    app.kubernetes.io/name: metricset
+    app.kubernetes.io/instance: metricset-sample
+  name: metricset-sample
+spec:
+  # Number of pods for lammps (one launcher, the rest workers)
+  pods: 4
+
+  # Keep interactive so we can decide when to quit
+  logging:
+    interactive: true
+
+  metrics:
+
+   # Running more scaled lammps is our main goal
+   - name: app-lammps
+
+     # This has intel mpi on rocky linux, per suggested by Google
+     image: ghcr.io/converged-computing/metric-lammps-intel-mpi:rocky
+
+     options:
+       command: lmp -v x 2 -v y 2 -v z 2 -in in.reaxc.hns -nocite
+       workdir: /opt/lammps/examples/reaxff/HNS
+       soleTenancy: "true"
+
+     # Add on hpctoolkit, will mount a volume and wrap lammps
+     addons:
+
+       - name: volume-pvc
+         options:
+           name: data
+           claimName: data
+           path: /storage
+           readOnly: "false"
+
+       - name: perf-hpctoolkit
+         options:           
+           mount: /opt/mnt
+           # This allows us to ask where is the event blocked / taking more time
+           events:  "-e REALTIME@10000"
+
+           # Use a custom container here too (we have for rocky and ubuntu)
+           image: ghcr.io/converged-computing/metric-hpctoolkit-view:rocky 
+           
+           # hpcrun needs to have mpirun in front of hpcrun <command> e.g.,
+           # mpirun <MPI args> hpcrun <hpcrun args> <app> <app args>
+           prefix: /opt/intel/mpi/2021.8.0/bin/mpirun --hostfile ./hostlist.txt -np 4 -map-by ppr:1:node
+
+           # Ensure the working directory is consistent
+           workdir: /opt/lammps/examples/reaxff/HNS
+
+           # Target container for entrypoint addition is the launcher, not workers
+           containerTarget: launcher

pkg/addons/addons.go

@@ -65,34 +65,34 @@ type AddonBase struct {
 	mapOptions  map[string]map[string]intstr.IntOrString
 }
 
-func (b AddonBase) SetOptions(metric *api.MetricAddon)                                   {}
-func (b AddonBase) CustomizeEntrypoints([]*specs.ContainerSpec, []*jobset.ReplicatedJob) {}
+func (b *AddonBase) SetOptions(metric *api.MetricAddon)                                   {}
+func (b *AddonBase) CustomizeEntrypoints([]*specs.ContainerSpec, []*jobset.ReplicatedJob) {}
 
-func (b AddonBase) Validate() bool {
+func (b *AddonBase) Validate() bool {
 	return true
 }
-func (b AddonBase) AssembleContainers() []specs.ContainerSpec {
+func (b *AddonBase) AssembleContainers() []specs.ContainerSpec {
 	return []specs.ContainerSpec{}
 }
 
 // Assemble Volumes (for now) just generates one
-func (b AddonBase) AssembleVolumes() []specs.VolumeSpec {
+func (b *AddonBase) AssembleVolumes() []specs.VolumeSpec {
 	return []specs.VolumeSpec{}
 }
 
-func (b AddonBase) Description() string {
+func (b *AddonBase) Description() string {
 	return b.Summary
 }
-func (b AddonBase) Name() string {
+func (b *AddonBase) Name() string {
 	return b.Identifier
 }
-func (b AddonBase) Options() map[string]intstr.IntOrString {
+func (b *AddonBase) Options() map[string]intstr.IntOrString {
 	return b.options
 }
-func (b AddonBase) ListOptions() map[string][]intstr.IntOrString {
+func (b *AddonBase) ListOptions() map[string][]intstr.IntOrString {
 	return b.listOptions
 }
-func (b AddonBase) MapOptions() map[string]map[string]intstr.IntOrString {
+func (b *AddonBase) MapOptions() map[string]map[string]intstr.IntOrString {
 	return b.mapOptions
 }
 

pkg/addons/commands.go

@@ -16,6 +16,11 @@ import (
 	jobset "sigs.k8s.io/jobset/api/jobset/v1alpha2"
 )
 
+const (
+	commandsName     = "commands"
+	perfCommandsName = "perf-commands"
+)
+
 // Perf addon expects the same command structure, but adds sys caps for trace and admin
 type PerfAddon struct {
 	CommandAddon
@@ -37,6 +42,11 @@ func (a *PerfAddon) CustomizeEntrypoints(
 	}
 }
 
+func (a *PerfAddon) SetOptions(metric *api.MetricAddon) {
+	a.Identifier = perfCommandsName
+	a.SetSharedCommandOptions(metric)
+}
+
 // addContainerCaps adds capabilities to a container spec
 func (a *PerfAddon) addContainerCaps(
 	cs []*specs.ContainerSpec,
@@ -92,8 +102,13 @@ func (m CommandAddon) Family() string {
 	return AddonFamilyApplication
 }
 
-// Set custom options / attributes for the metric
 func (a *CommandAddon) SetOptions(metric *api.MetricAddon) {
+	a.Identifier = commandsName
+	a.SetSharedCommandOptions(metric)
+}
+
+// Set custom options / attributes for the metric
+func (a *CommandAddon) SetSharedCommandOptions(metric *api.MetricAddon) {
 	target, ok := metric.Options["target"]
 	if ok {
 		a.target = target.StrVal
@@ -213,14 +228,14 @@ func init() {
 
 	// Config map volume type
 	base := AddonBase{
-		Identifier: "commands",
+		Identifier: commandsName,
 		Summary:    "customize a metric's entrypoints",
 	}
 	app := CommandAddon{AddonBase: base}
 	Register(&app)
 
 	base = AddonBase{
-		Identifier: "perf-commands",
+		Identifier: perfCommandsName,
 		Summary:    "customize a metric's entrypoints expecting performance tracing (adding ptrace and admin caps)",
 	}
 	cmd := CommandAddon{AddonBase: base}

pkg/addons/hpctoolkit.go

@@ -25,6 +25,9 @@ import (
 // hpcstruct hpctoolkit-sleep-measurements
 // hpcprof hpctoolkit-sleep-measurements
 // hpcviewer ./hpctoolkit-lmp-database
+const (
+	hpctoolkitIdentifier = "perf-hpctoolkit"
+)
 
 type HPCToolkit struct {
 	ApplicationAddon
@@ -121,6 +124,7 @@ func (a *HPCToolkit) SetOptions(metric *api.MetricAddon) {
 	a.volumeName = "hpctoolkit"
 	a.output = "hpctoolkit-result"
 	a.postAnalysis = true
+	a.Identifier = hpctoolkitIdentifier
 
 	// UseColor set to anything means to use it
 	output, ok := metric.Options["output"]
@@ -399,7 +403,7 @@ sleep infinity
 
 func init() {
 	base := AddonBase{
-		Identifier: "perf-hpctoolkit",
+		Identifier: hpctoolkitIdentifier,
 		Summary:    "performance tools for measurement and analysis",
 	}
 	app := ApplicationAddon{AddonBase: base}

pkg/addons/volumes.go

@@ -19,6 +19,14 @@ import (
 	"k8s.io/apimachinery/pkg/util/intstr"
 )
 
+const (
+	hostPathName = "volume-hostpath"
+	pvcName      = "volume-pvc"
+	emptyName    = "volume-empty"
+	secretName   = "volume-secret"
+	cmName       = "volume-cm"
+)
+
 type VolumeBase struct {
 	AddonBase
 	readOnly bool
@@ -98,6 +106,8 @@ func (v *ConfigMapVolume) Validate() bool {
 // Set custom options / attributes for the metric
 func (v *ConfigMapVolume) SetOptions(metric *api.MetricAddon) {
 
+	v.Identifier = cmName
+
 	// Set an empty list of items
 	v.items = map[string]string{}
 
@@ -190,6 +200,9 @@ func (v *PersistentVolumeClaim) Validate() bool {
 
 // Set custom options / attributes
 func (v *PersistentVolumeClaim) SetOptions(metric *api.MetricAddon) {
+
+	v.Identifier = pvcName
+
 	claimName, ok := metric.Options["claimName"]
 	if ok {
 		v.claimName = claimName.StrVal
@@ -207,8 +220,6 @@ func (v *PersistentVolumeClaim) AssembleVolumes() []specs.VolumeSpec {
 			},
 		},
 	}
-
-	// ConfigMaps have to be read only!
 	return []specs.VolumeSpec{{
 		Volume:   volume,
 		Path:     filepath.Dir(v.path),
@@ -236,6 +247,8 @@ func (v *SecretVolume) Validate() bool {
 
 // Set custom options / attributes
 func (v *SecretVolume) SetOptions(metric *api.MetricAddon) {
+
+	v.Identifier = secretName
 	secretName, ok := metric.Options["secretName"]
 	if ok {
 		v.secretName = secretName.StrVal
@@ -281,6 +294,8 @@ func (v *HostPathVolume) Validate() bool {
 // Set custom options / attributes
 func (v *HostPathVolume) SetOptions(metric *api.MetricAddon) {
 
+	v.Identifier = hostPathName
+
 	// Name is required!
 	path, ok := metric.Options["hostPath"]
 	if ok {
@@ -319,6 +334,7 @@ func (v *EmptyVolume) Validate() bool {
 
 // Set custom options / attributes
 func (v *EmptyVolume) SetOptions(metric *api.MetricAddon) {
+	v.Identifier = emptyName
 	name, ok := metric.Options["name"]
 	if ok {
 		v.name = name.StrVal
@@ -347,7 +363,7 @@ func init() {
 
 	// Config map volume type
 	base := AddonBase{
-		Identifier: "volume-cm",
+		Identifier: cmName,
 		Summary:    "config map volume type",
 	}
 	volBase := VolumeBase{AddonBase: base}
@@ -356,7 +372,7 @@ func init() {
 
 	// Secret volume type
 	base = AddonBase{
-		Identifier: "volume-secret",
+		Identifier: secretName,
 		Summary:    "secret volume type",
 	}
 	volBase = VolumeBase{AddonBase: base}
@@ -365,7 +381,7 @@ func init() {
 
 	// Hostpath volume type
 	base = AddonBase{
-		Identifier: "volume-hostpath",
+		Identifier: hostPathName,
 		Summary:    "host path volume type",
 	}
 	volBase = VolumeBase{AddonBase: base}
@@ -374,7 +390,7 @@ func init() {
 
 	// persistent volume claim volume type
 	base = AddonBase{
-		Identifier: "volume-pvc",
+		Identifier: pvcName,
 		Summary:    "persistent volume claim volume type",
 	}
 	volBase = VolumeBase{AddonBase: base}
@@ -383,7 +399,7 @@ func init() {
 
 	// EmptyVolume
 	base = AddonBase{
-		Identifier: "volume-empty",
+		Identifier: emptyName,
 		Summary:    "empty volume type",
 	}
 	volBase = VolumeBase{AddonBase: base}

pkg/metrics/base.go

@@ -39,9 +39,10 @@ type BaseMetric struct {
 func (m *BaseMetric) RegisterAddon(addon *addons.Addon) {
 	a := (*addon)
 	if m.Addons == nil {
+		logger.Infof("🟧️ Resetting addons - they are unset.")
 		m.Addons = map[string]*addons.Addon{}
 	}
-	logger.Infof("🟧️ Registering addon %s", a)
+	logger.Infof("🟧️ Registering addon %s", a.Name())
 	m.Addons[a.Name()] = addon
 }
 
@@ -142,10 +143,10 @@ func (m BaseMetric) AddAddons(
 	// These are container specs that need to be written to configmaps
 	cms := []*specs.ContainerSpec{}
 
-	logger.Infof("🟧️ Addons to include %s\n", m.Addons)
 	for _, addon := range m.Addons {
 		a := (*addon)
 
+		logger.Infof("🟧️ Including Addon", a.Name())
 		volumes = append(volumes, a.AssembleVolumes()...)
 
 		// Assemble containers that addons provide, also as specs

pkg/metrics/metrics.go

@@ -85,10 +85,12 @@ func GetMetric(metric *api.Metric, set *api.MetricSet) (Metric, error) {
 		// Register addons, meaning adding the spec but not instantiating yet (or should we?)
 		for _, a := range metric.Addons {
 
+			logger.Infof("Attempting to add addon %s", a.Name)
 			addon, err := addons.GetAddon(&a)
 			if err != nil {
 				return nil, fmt.Errorf("Addon %s for metric %s did not validate", a.Name, metric.Name)
 			}
+			logger.Infof("Registering addon %s", a.Name)
 			m.RegisterAddon(&addon)
 		}