daylily-ephemeral-cluster 0.7.606

Infrastructure-as-code for ephemeral AWS ParallelCluster environments for bioinformatics

Daylily Ephemeral Cluster

Daylily provisions ephemeral AWS ParallelCluster environments for bioinformatics workloads. It combines a Python control plane, region-scoped reference data, head-node bootstrap, workflow launch helpers, and lifecycle operations so operators can create Slurm clusters when needed and tear them down cleanly when they do not.

What Daylily Covers

• Preflight validation for IAM, quotas, network prerequisites, local toolchain, and reference-bucket readiness
• Cluster creation through python -m daylily_ec create or the thin wrapper ./bin/daylily-create-ephemeral-cluster
• A region-scoped S3 and FSx for Lustre layout for shared references, staged inputs, and results
• Head-node bootstrap that installs DAY-EC, day-clone, and the packaged Daylily helpers
• Operator workflows for validation, staging, workflow launch, export, drift checks, and delete

Architecture Snapshot

1. daylily_ec is the control plane that runs preflight, renders cluster YAML, applies spot pricing, creates the cluster, and records state snapshots.
2. AWS ParallelCluster and Slurm provide the compute fabric.
3. A region-specific S3 bucket whose name includes omics-analysis backs FSx for Lustre so references and staged data are shared across the cluster.
4. The head node installs Daylily utilities from bin/ and workflow definitions from config/daylily_available_repositories.yaml.
5. Optional budgets and heartbeat notifications help operators track cost and stale resources.

Fast Path

Use the full runbook in docs/quickest_start.md. The shortest supported path from a repo checkout is:

./bin/check_prereq_sw.sh
./bin/init_dayec
conda activate DAY-EC

export AWS_PROFILE=daylily-service
export REGION_AZ=us-west-2c
export DAY_EX_CFG="$HOME/.config/daylily/daylily_ephemeral_cluster.yaml"

python -m daylily_ec preflight --region-az "$REGION_AZ" --profile "$AWS_PROFILE" --config "$DAY_EX_CFG"
python -m daylily_ec create --region-az "$REGION_AZ" --profile "$AWS_PROFILE" --config "$DAY_EX_CFG"

Before create, make sure the reference bucket for the target region exists and your config file points at it. docs/quickest_start.md shows the supported daylily-omics-references workflow and the template-copy step.

CLI Surface

The current CLI surface is:

• python -m daylily_ec version
• python -m daylily_ec info
• python -m daylily_ec create --region-az <region-az> ...
• python -m daylily_ec preflight --region-az <region-az> ...
• python -m daylily_ec drift --state-file <path> ...
• python -m daylily_ec resources-dir
• python -m daylily_ec pricing snapshot --region <region> --config config/day_cluster/prod_cluster.yaml

Run python -m daylily_ec --help for the current command tree.

Documentation

• docs/quickest_start.md: operator-first install and cluster creation runbook
• docs/operations.md: head-node validation, staging, launch, monitoring, export, and delete
• docs/overview.md: public-facing architecture, workflow narrative, cost context, and benchmark links
• docs/pip_install.md: pip-based usage and packaged resources
• docs/DAY_EC_ENVIRONMENT.md: local development environment and CLI diagnostics
• CONTRIBUTING.md: development and docs contribution guide
• docs/archive/README.md: historical material preserved for reference

Repository Highlights

• config/daylily_ephemeral_cluster_template.yaml: config triplets for cluster creation defaults
• config/daylily_cli_global.yaml: shared global settings deployed to head nodes
• config/daylily_available_repositories.yaml: workflow registry used by day-clone
• docs/benchmarks/: benchmark reference material used by the overview doc

Historical Material

Older long-form docs and retired notes live under docs/archive/. They are preserved for historical context and are not canonical for current operator workflows.