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Deployment Mode

Deployment mode uses Flower SuperLink and SuperNode processes. It is closer to a real federated deployment than local simulation and requires at least two client nodes.

Install and verify​

Install FedGWAS on the server node and on every participating client node:

python -m pip install FedGWAS
python -m pip install flwr

Each client node also needs access to PLINK-compatible genotype data and the configured PLINK executable. Confirm the Flower commands are available before starting the federation:

flower-superlink --help
flower-supernode --help
flwr --help

Data layout​

For local deployment tests, point each SuperNode at a center config. The shipped tiny correctness experiment uses:

experiments/correctness/tiny_even/configs/
  server/config.yaml
  center_1/config.yaml
  center_2/config.yaml

For your own data, copy the template and update paths, thresholds, and output directories:

cp configs/config_template.yaml configs/config.yaml

Start the federation​

Start SuperLink:

flower-superlink --insecure --fleet-api-address 127.0.0.1:9092

Start two SuperNodes in separate terminals:

flower-supernode \
  --insecure \
  --superlink 127.0.0.1:9092 \
  --clientappio-api-address 127.0.0.1:9094 \
  --node-config 'partition-id=0 num-partitions=2 config-file="experiments/correctness/tiny_even/configs/center_1/config.yaml"'
flower-supernode \
  --insecure \
  --superlink 127.0.0.1:9092 \
  --clientappio-api-address 127.0.0.1:9095 \
  --node-config 'partition-id=1 num-partitions=2 config-file="experiments/correctness/tiny_even/configs/center_2/config.yaml"'

Run the Fed-GWAS app​

flwr run . local-deployment --stream

local-deployment must point at the SuperLink Exec API port:

[tool.flwr.federations.local-deployment]
address = "127.0.0.1:9093"
insecure = true
options.num-supernodes = 2

Flower ports​

PortRole
9091ServerAppIo API
9092Fleet API; SuperNodes connect here
9093Exec API; flwr run connects here
9094+ClientAppIo API for each SuperNode

TLS​

For TLS-enabled runs, provide certificates to SuperLink and SuperNode:

flower-superlink \
  --ssl-ca-certfile <ca-cert> \
  --ssl-certfile <server-cert> \
  --ssl-keyfile <server-key>
flower-supernode \
  --superlink 127.0.0.1:9092 \
  --clientappio-api-address 127.0.0.1:9094 \
  --root-certificates <ca-cert>