Hyperpod Cluster Debugger
AWS LabsOfficialPublished by AWS Labs
- Skill
- Review and audit
- Cloud and DevOps
- Apache-2.0
- Low risk
- Has scripts
AutoGineer summary
Written by AutoGineer from the skill’s own files, not by the author
The HyperPod Cluster Debugger is a read-only diagnostic tool designed to identify and resolve common failures in HyperPod clusters, including deployment errors, EFA health checks, lifecycle script failures, and capacity issues. It provides a structured workflow to collect cluster state via AWS APIs and SSM, mapping findings to specific remediation runbooks. The tool emphasizes safe operations by providing suggested commands for users to execute manually, ensuring that IaC-managed environments are not inadvertently drifted.
What it does
- Collects cluster state via AWS APIs and SSM for comprehensive diagnostic reporting.
- Validates pre-flight requirements including SGs, subnets, IAM, and capacity.
- Maps detected failures to specific remediation runbooks for EFA, EKS, SSM, and CloudFormation.
- Provides actionable, read-only diagnostic commands to identify root causes.
- Offers guidance on distinguishing between manual fixes and IaC-managed configurations.
- Generates diagnostic bundles to streamline escalation to AWS Support.
When to use it
- When a HyperPod cluster fails during creation or deployment.
- When diagnosing EKS access, node replacement, or autoscaler conflicts.
- When troubleshooting lifecycle script timeouts or failures.
- When verifying capacity availability in specific AZs before cluster creation.
- When investigating post-maintenance rollback states or dangling nodes.
Advantages
- Reduces manual troubleshooting time by automating the collection of cluster state.
- Provides clear, categorized remediation steps for complex HyperPod error signals.
- Promotes safe practices by preventing unintended configuration drift in IaC environments.
- Standardizes the diagnostic output for efficient escalation to AWS Support.
- Includes pre-flight validation to catch configuration errors before cluster deployment.
Usage examples
- “Diagnose my existing HyperPod cluster named my-cluster in us-west-2.”
- The tool runs the diagnostic script, collects state, and outputs a list of [PASS], [FAIL], or [WARN] items with pointers to specific remediation documentation.
- “Validate my network and IAM configuration before creating a new HyperPod cluster.”
- The tool performs a pre-flight check using the provided SG IDs and subnet IDs, verifying capacity and permissions to ensure a successful cluster creation.
Install
Download the skill as a ZIP:
https://mp-staging.autogineer.com/agent-skills/awslabs/hyperpod-cluster-debugger/downloadUnzip it into the cross-client skills folder of your project:
mkdir -p .agents/skills && unzip hyperpod-cluster-debugger.zip -d .agents/skills
Documentation by AWS Labs
HyperPod Cluster Debugger
Operating policy. Run read-only diagnostics yourself. Never run a command that changes cluster, node, or workload state — present each one as a Suggested command (run this yourself) block and wait for the customer to run it. Destructive order: investigate → reboot → replace (replace destroys root + secondary volumes; not supported on Slurm controller nodes).
Before any state-changing CLI: ask if it's IaC-managed. HyperPod clusters, SGs, EKS access entries, and IAM are usually provisioned via CloudFormation / CDK / Terraform. If yes, the fix belongs in IaC — running the CLI will drift and the next deploy reverts it. Use the CLI only when IaC is unavailable (locked out, predates IaC, mid-review).
scripts/diagnose-cluster.sh is read-only: it collects state via AWS APIs (and SSM for Slurm controller health) and prints each issue as [FAIL] ... → references/<file>.md § <section>.
| Reference | Open when |
|---|---|
| cluster-diagnostics-detail.md | Per-finding remediation runbook (§ A–L) |
| cluster-operations.md | Operational deep-dives (EFA SG, EKS access, SSM, Slurm, filesystem) |
| cloudformation-errors.md | § H needs the full per-resource CFN error catalog |
| capacity-planning.md | § B or --validate flags capacity / subnet sizing |
| lifecycle-scripts.md | § C points at a specific lifecycle failure |
| iam-permissions.md | Full IAM policy for the diagnostic |
Workflow
Collect HyperPod cluster name (not EKS name), region, exact error string.
Run
scripts/diagnose-cluster.sh(or--validatefor pre-create).For every
[FAIL]line,Readthe referenced section.Present finding, root cause, and the Suggested-command block verbatim. Wait for customer approval.
Re-run the diagnostic to confirm.
Step 1: Run diagnostics
# Diagnose an existing cluster:
bash scripts/diagnose-cluster.sh --cluster <CLUSTER_NAME_OR_ARN> --region <REGION>
# Pre-flight (no cluster needed) — validates SGs, subnets, IAM, VPC endpoints,
# optionally S3 lifecycle scripts and per-AZ capacity:
bash scripts/diagnose-cluster.sh --validate --region <REGION> \
--sg-ids <sg-1,sg-2> --subnet-ids <sub-1,sub-2> [--iam-role <role-arn>] \
[--s3-uri s3://<BUCKET>/path/] [--instance-type ml.p5.48xlarge]Pass --instance-type when the target instance type is known — enables the per-AZ capacity check (warns if none of the provided subnets are in an AZ that offers that type, which causes insufficient-capacity failures at creation time).
Tags: [PASS] · [FAIL] (counted, has → references/... pointer) · [WARN] · [INFO]. Priorities: P0 blocks operation · P1 degraded · P2 informational.
Step 2: Match signal → section
Error messages / events:
| Signal | Section |
|---|---|
"EFA health checks did not run successfully" (public-doc verbatim signal) | A: EFA Health Checks |
| Insufficient-capacity or AZ-mismatch failure at creation | B: Capacity & AZ |
| Lifecycle-script failure or timeout during provisioning | C: Lifecycle Scripts |
| kubectl auth error (server asks for credentials / no API group list) | D: EKS Access |
InService but not all instances visible | E: Cluster Provisioning |
"Target is not connected" / SSM errors | F: SSM Connectivity |
Node replacement not happening / batch-replace not working | G: Node Replacement |
"Embedded stack failed" / any CloudFormation error | H: CloudFormation Errors |
UpdateClusterSoftware failed or cluster in post-maintenance rollback state | J: AMI & Cluster Updates |
Dangling / orphaned nodes in EKS vs list-cluster-nodes | K: Dangling Nodes & Cleanup |
| Cluster Autoscaler breaks after HyperPod attached | L: Autoscaler Compatibility |
| Slow I/O, FSx throughput saturated | cluster-operations.md § 9 |
| Slurm node name → instance ID lookup | I: Utilities |
A: EFA Health Checks
SG missing self-reference. Add inbound + outbound self-ref to every SG on the cluster, plus least-privilege egress for the AWS APIs the node needs (HTTPS 443 to S3 / ECR / SageMaker / SSM / STS / CloudWatch Logs — via VPC-endpoint prefix-lists when possible). Full procedure: cluster-diagnostics-detail.md § A.
B: Capacity & AZ
Instance type unavailable in the requested AZ. Verify with describe-instance-type-offerings, then change AZ, use Flexible Training Plans, or request ODCR. Full: § B · strategy: capacity-planning.md.
C: Lifecycle Scripts
Script failed or timed out during provisioning. Read CloudWatch under /aws/sagemaker/Clusters/<name>/<id> — common causes: missing S3 VPC endpoint, IAM gap, CRLF line endings, instance-group name mismatch. Full: § C · layout: lifecycle-scripts.md.
D: EKS Access / kubectl
IAM identity not in EKS access entries. Verify with sts get-caller-identity, create an access entry with admin policy, update kubeconfig. Full: § D.
E: Cluster Provisioning
InService without all instances is expected under Continuous Provisioning — failures surface as events, not cluster errors. For stuck Creating/Updating/Deleting: check CFN nested stacks (§ H), IAM, capacity, events; if stuck Deleting check VPC ENI dependencies. Full: § E.
F: SSM Connectivity
Target is not connected: use sagemaker-cluster:<CLUSTER_ID>_<GROUP>-<INSTANCE_ID> format (not raw EC2 ID), install session-manager-plugin, confirm node Running. Check IAM + VPC endpoints on timeouts. Full: § F.
G: Node Replacement
Auto-repair: confirm NodeRecovery=Automatic, check Health Monitoring Agent (HMA) logs + node labels / Slurm reason, confirm capacity. Manual: reboot first, replace only if reboot fails. Replace requires the cluster to have been patched via UpdateClusterSoftware at least once and cannot target a Slurm controller node. Full: § G.
H: CloudFormation Errors
Embedded stack failed hides the real error. Drill into nested stacks via Events tab (filter Failed) until you reach a non-stack resource. CLI: describe-stack-events --query 'StackEvents[?ResourceStatus==\CREATE_FAILED`]'`. Also covers SLR creation failures and permission-boundary denials. Full: § H · catalog: cloudformation-errors.md.
I: Utilities
Map Slurm node names (ip-10-x-y-z) to HyperPod instance IDs via list-cluster-nodes or on-node /opt/ml/config/resource_config.json. Full: § I.
J: AMI & Cluster Updates
UpdateClusterSoftware fails and rolls back, or the cluster stays in a post-maintenance rollback state. Common causes: lifecycle script incompatible with new AMI, HMA version too old, insufficient rolling-update capacity. If the cluster has active nodes, collect diagnostics and escalate rather than delete-and-recreate. Full: § J.
K: Dangling Nodes & Cleanup
Nodes in kubectl get nodes but not in list-cluster-nodes (ghost EKS nodes), or the inverse (HyperPod nodes that never registered kubelet). Script flags both. Full: § K.
L: Autoscaler Compatibility
Cluster Autoscaler errors on HyperPod provider IDs and breaks autoscaling for all node groups. No officially endorsed workaround — escalate to AWS Support. Karpenter does not conflict with HyperPod nodes by default. Full: § L.
Prerequisites
awsCLI v2.13+ authenticated to the cluster's accountjq,python3,bash4.2+kubectlauthenticated to the EKS cluster (EKS checks skipped if absent)session-manager-plugin(Slurm controller health checks only)
IAM policy: references/iam-permissions.md.
Defaults
Region — required: pass
--regionor set$AWS_DEFAULT_REGION.Mode —
--cluster <NAME>(diagnose) or--validate(pre-create).Event window — up to 500 most recent events (5 × 100, paginated).
Colors — auto-disabled on non-TTY;
--no-colorto force off.
Error handling
| Failure | Script | Tell the customer |
|---|---|---|
aws sts get-caller-identity fails | Exit 1 | "Fix AWS credentials and rerun." |
| Cluster not found | Exit 1 after listing region's clusters | "Confirm HyperPod cluster name (not EKS) and region." |
sagemaker:* / ec2:* / eks:* / logs:* denied | Warn, add Missing IAM permission for <API>, continue | "Grant the listed IAM action and rerun." |
kubectl absent or unauthenticated | Skip EKS checks (access entries, add-ons, aws-auth, nodes) | "Install/authenticate kubectl." |
session-manager-plugin absent (Slurm) | Skip Slurm controller probe | "Install session-manager-plugin." |
| SSM throttled / times out (180s) | Retry with backoff; warn and continue if still failing | "Rerun later — script is idempotent." |
| CloudWatch log group not found | Skip CloudWatch check | "CloudWatch not configured on this cluster." |
Exit codes: 0 no critical failures · 1 one or more critical failures (cluster not found, fatal prerequisite missing, or any [FAIL] in diagnose or --validate mode). [WARN] lines do not affect the exit code.
Skill delegation
| Need | Use |
|---|---|
| Shell on nodes | hyperpod-ssm |
| Version comparison across nodes | hyperpod-version-checker |
Escalate to AWS Support
Escalate when:
EFA health checks fail despite correct SG rules.
Capacity errors persist despite a valid Flexible Training Plan / ODCR.
Node replacement fails repeatedly without clear events / log signal.
Cluster stuck in a non-terminal state (
Creating,Updating, or a post-maintenance rollback state) for an extended period.CloudFormation root-cause is an internal service error.
Before opening the case
Run these commands and attach the output. Goal: AWS Support has everything at case open.
# 1. Cluster identity + status (confirms region, ARN, orchestrator, instance groups)
aws sagemaker describe-cluster --cluster-name <CLUSTER> --region <REGION>
# 2. Full cluster-level diagnostic bundle
bash scripts/diagnose-cluster.sh --cluster <CLUSTER> --region <REGION> > diag.txt
# 3. Per-node log/config bundle to S3 (delegates to hyperpod-issue-report skill)
# See skills/hyperpod-issue-report/SKILL.md for the exact invocation.Include in the case
Cluster name + ARN (or
ClusterIdsuffix) and AWS regionClusterStatus+FailureMessagefromdescribe-clusterTimestamp window (UTC start / end) of the failure
Exact error strings observed (copy verbatim from events / logs / console)
Affected instance IDs /
NodeLogicalIds / instance group namesdiag.txtfrom step 2 aboveS3 URI of the
hyperpod-issue-reportbundle from step 3
Files
- ATTRIBUTION.mdAdded by AutoGineer934 B
- LICENSELicence file added by AutoGineer9.9 KiB
- NOTICELicence file added by AutoGineer89 B
- SKILL.md14.1 KiB
- references/capacity-planning.md4.5 KiB
- references/cloudformation-errors.md5.8 KiB
- references/cluster-diagnostics-detail.md23.3 KiB
- references/cluster-operations.md11.5 KiB
- references/iam-permissions.md1.2 KiB
- references/lifecycle-scripts.md5.1 KiB
- scripts/diagnose-cluster.shScript69.0 KiB
references/cluster-operations.md
Cluster Operations Reference
Operational deep-dives for the hyperpod-cluster-debugger skill. See SKILL.md for the workflow entry points.
1. EFA Security Group (multi-SG clusters)
The EFA health check runs during instance provisioning, before lifecycle scripts execute. If it fails, lifecycle scripts never run and CloudWatch lifecycle logs are empty — the cluster event will say "EFA health checks did not run successfully".
When a cluster uses multiple security groups, all SGs must have the self-referencing rules. Check each:
for SG in $(aws sagemaker describe-cluster --cluster-name <C> --region <R> \
--query 'VpcConfig.SecurityGroupIds[]' --output text); do
echo "=== $SG ==="
aws ec2 describe-security-groups --group-ids $SG --region <R> \
--query 'SecurityGroups[0].{In:IpPermissions,Out:IpPermissionsEgress}'
doneFix commands are in cluster-diagnostics-detail.md § A.
2. Capacity
See capacity-planning.md.
3. Lifecycle scripts
See lifecycle-scripts.md.
4. EKS access control
Authentication modes
Access entries require API or API_AND_CONFIG_MAP. If the cluster is on CONFIG_MAP only, aws eks list-access-entries returns nothing useful; verify the mode with describe-cluster --query 'cluster.accessConfig.authenticationMode' and consult the EKS access-entries documentation for the switching procedure.
Access policies (EKS-native)
| Policy | Scope | Use case |
|---|---|---|
AmazonEKSClusterAdminPolicy | Cluster-wide | Full admin (debugging) |
AmazonEKSAdminPolicy | Namespace | Namespace admin (multi-tenant) |
AmazonEKSEditPolicy | Namespace | Read/write workloads |
AmazonEKSViewPolicy | Namespace | Read-only |
Troubleshooting kubectl auth
aws sts get-caller-identity # your identity
kubectl config current-context # which cluster kubeconfig points at
kubectl cluster-info # API server reachable?If using an assumed role: access entries reference the IAM role ARN, not the assumed-role session ARN.
Role ARN:
arn:aws:iam::123456789012:role/MyRoleSession ARN:
arn:aws:sts::123456789012:assumed-role/MyRole/session-name
5. Continuous Provisioning (EKS only)
The cluster transitions to InService once the control plane is ready; instances are created asynchronously and failures are reported as events, not cluster failures. Failed instances can be individually replaced.
# Poll instance creation:
watch -n 30 "aws sagemaker describe-cluster --cluster-name <C> --region <R> \
--query 'InstanceGroups[*].{Name:InstanceGroupName,Current:CurrentCount,Target:InstanceCount}' --output table"
# Poll cluster events:
watch -n 30 "aws sagemaker list-cluster-events --cluster-name <C> --region <R> \
--query 'ClusterEventSummaries[0:5].{Time:EventTime,Msg:Message}' --output table"Nodes in list-cluster-nodes but not in kubectl get nodes
Check lifecycle script logs — it registers the node with EKS
Verify the EKS endpoint is reachable from worker subnets
Check kubelet on the node via SSM
Verify the node's IAM role has
AmazonEKSWorkerNodePolicy
Cluster events are emitted for HyperPod EKS. For HyperPod Slurm, events are not yet surfaced — use CloudWatch logs and
list-cluster-nodesinstead.
6. SSM target format
See the hyperpod-ssm skill's SKILL.md for the target format (sagemaker-cluster:<CLUSTER_ID>_<GROUP>-<INSTANCE_ID>), prerequisites, and manual-command examples. HyperPod requires start-session — not send-command against raw instance IDs.
7. Node replacement (batch APIs)
Full Suggested-command blocks with preconditions + blast radius are in cluster-diagnostics-detail.md § G.2. Summary:
Cluster must be
InServiceBatch limit: 1-25 node IDs per call for both APIs
batch-replace-cluster-nodesdestroys root + secondary volumes and is not supported on Slurm controller nodes — back up firstMonitor with
list-cluster-eventsafter the callPrefer batch APIs over legacy paths (Slurm reason fields, K8s labels)
8. Slurm — controller operations
The per-node Slurm operations (resuming a single node, fixing a single Slurm state) live in the hyperpod-node-debugger skill. This section is controller-level only.
Diagnose controller health (via SSM on the controller)
scontrol ping # slurmctld responsive?
systemctl status slurmctld # service state
systemctl is-active munge && systemctl status munge # auth daemon (required)
systemctl is-active slurmdbd # accounting DB (if used)slurmctld down
journalctl -u slurmctld --since "1 hour ago" --no-pager | tail -100
tail -200 /var/log/slurm/slurmctld.logCommon causes and fixes:
OOM on controller: restart the service; investigate the job scale that triggered it.
Munge auth failure (
Invalid authentication credential): munge key mismatch. Re-sync/etc/munge/munge.keyto every node, restart munge + slurmctld.Accounting DB unreachable (slurmdbd + MariaDB / RDS): check network path and credentials. slurmctld won't start if accounting is required but unreachable.
Config error in
slurm.conf:slurmctld -D -vvv(foreground) prints the parse error. Roll back to the last known-good config.
Fix — restart slurmctld
Customer-run on the Slurm controller (via SSM) after the root cause is diagnosed. Running jobs, pending queue, and node states are preserved; caches and resource calculations reset. Brief scheduler pause.
sudo systemctl restart slurmctld
scontrol ping # expect "Slurmctld(primary) is UP"If slurm.conf is broken the service will not return — roll back the config first.
munge inactive
Diagnose:
systemctl status munge
ls -l /etc/munge/munge.key # expect munge:munge, mode 0400
sudo md5sum /etc/munge/munge.key # must match on controller + every compute nodeFix — start munge
Customer-run. Safe when munge is inactive and the key file is present and matches other nodes.
sudo systemctl start mungeIf md5 mismatches another node, jobs will still fail auth — re-distribute the controller's key cluster-wide and restart munge on every node.
Stuck jobs (PENDING / COMPLETING / CONFIGURING)
squeue -o "%i %j %T %R %N" --noheader | grep -iE "COMPLETING|CONFIGURING|PENDING"
scontrol show job <JOBID>
scancel <JOBID> # if safe to cancelCommon reason codes:
(Resources)— waiting for free nodes. Checksinfo -o "%P %a %l %D %T".(AssocGrpNodeLimit)/(QOSMaxJobsPerUserLimit)— quota-related.sacctmgr show assoc.(NodeDown)— partition has no healthy nodes. Use thehyperpod-node-debuggerskill.(BeginTime)— scheduled for a future start time.
Restarting slurmctld to clear stuck-job symptoms uses the same Suggested-command block as above (§ slurmctld down).
Verify after remediation
scontrol ping # "Slurmctld(primary) is UP"
sinfo # no "down*" or "drain" states
systemctl is-active slurmctld munge
scontrol show config | grep StateSaveLocation # must be persistent + writable9. Filesystem performance
Symptom: training bottlenecked by data loading, checkpoint save / load, or slow executable / script loading.
Diagnose on the node
mount | grep -E "fsx|nfs|lustre|ebs|nvme"
df -hT
iostat -x 1 5 # per-device throughput / IOPS / utilization
# FSx for Lustre:
lfs df -h # per-OST utilization (uneven = hotspot)
lfs getstripe <path> # striping config; wider = more parallelism
# FSx for OpenZFS / NFS:
nfsstat -m # per-mount retransmissions / wait times
nfsiostat 5 # ops/s, throughput, RTT
# EBS:
lsblk -o NAME,TYPE,SIZE,MOUNTPOINTCloudWatch (from your workstation)
# FSx for Lustre throughput saturation:
aws cloudwatch get-metric-statistics \
--namespace AWS/FSx --metric-name DataReadBytes \
--dimensions Name=FileSystemId,Value=<FSxId> \
--statistics Sum --period 300 \
--start-time "$(date -u -d '1 hour ago' +%Y-%m-%dT%H:%M:%SZ)" \
--end-time "$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
--region <REGION>
# Also: DataWriteBytes, FreeDataStorageCapacity, MetadataOperations
# EBS throughput / IOPS:
aws cloudwatch get-metric-statistics \
--namespace AWS/EBS --metric-name VolumeReadOps \
--dimensions Name=VolumeId,Value=<vol-id> \
--statistics Sum --period 60 \
--start-time "$(date -u -d '1 hour ago' +%Y-%m-%dT%H:%M:%SZ)" \
--end-time "$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
--region <REGION>
# Also: VolumeWriteOps, VolumeReadBytes, VolumeWriteBytes, BurstBalanceInterpret
| Signal | Interpretation | Action |
|---|---|---|
FSx Lustre DataReadBytes sustained at the ceiling | Throughput ceiling hit | Increase throughput-per-TiB or grow storage (throughput scales with size) |
| FSx Lustre metadata ops saturated | Small-file workload on Lustre | Move small-file traffic to FSx for OpenZFS; keep Lustre for large sequential I/O |
FSx OpenZFS TotalIOps near provisioned IOPS | IOPS ceiling hit | Increase provisioned IOPS |
EBS BurstBalance draining to 0 on gp2 | Baseline IOPS insufficient | Migrate to gp3 or io2 with provisioned IOPS / throughput |
iostat %util > 90% on a mount device | Local device saturated | If NVMe instance store: at hardware ceiling, change data layout |
| Slow only at checkpoint time | Write amplification (many small files) | Consolidate checkpoints; rank-0 writer patterns |
Choose the right filesystem
| Workload | Best fit |
|---|---|
| Large sequential reads (datasets >> 1 MiB), many-reader training | FSx for Lustre |
| Small-file / metadata-heavy / mixed random I/O | FSx for OpenZFS |
| Single-instance scratch | EBS gp3 or io2 |
| Highest per-GPU throughput, ephemeral | NVMe instance store (/opt/dlami/nvme) |
For HyperPod Slurm, the default lifecycle script supports FSx for OpenZFS for /home — evaluate it if home is on Lustre and you see metadata-op saturation.
Verify after remediation
CloudWatch: throughput / IOPS climbs past the old flat-line
Training step time drops; data-loading fraction of step time drops
iostat %utilstays below 80% under sustained load
Requirements and compatibility
Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta
“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.
Needs: Needs a command-line tool, Needs Python, Needs Node.js
Security
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Attribution and licence
- Published by
- AWS Labs
- Publisher
- AWS Labs (Official)
- Source
- awslabs/agent-plugins · plugins/sagemaker-ai/skills/hyperpod-cluster-debugger · commit fbefb37
- Licence
- Apache License 2.0 (redistribution allowed)
- LICENSE (added by AutoGineer from LICENSE)
- NOTICE (added by AutoGineer from NOTICE)
- ATTRIBUTION.md (written by AutoGineer)
- Synced
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