data/docker/swarm/README_stack_on_mac.md

1. Build Java and Python

pushd ../../
mvn clean install dependency:copy-dependencies -DskipTests=true
popd

poetry install -C ../../vcell-cli-utils
poetry install -C ../swarm/vcell-admin
poetry install -C ../../pythonCopasiOpt/vcell-opt
poetry install -C ../../pythonVtk
poetry install -C ../../python-utils
poetry install -C ../../python-restclient
poetry install -C ../../pythonData

2. Build and push Docker and Singularity containers (without building clients)

pushd ../build
./build.sh --skip-maven --skip-singularity --skip-sudo all ghcr.io/virtualcell dev
popd

on cluster (e.g. xanadu-76) as user vcell build vcell-opt singularity container

export TAG=dev
export TAG=7.6.0.31
export SINGULARITY_MODULE=singularity/vcell-3.10.0
export docker_image=ghcr.io/virtualcell/vcell-opt:${TAG}
export singularity_file=ghcr.io_virtualcell_vcell-opt_${TAG}.img
module load ${SINGULARITY_MODULE}
# singularity remote login -u <github_user> -p <github_token> docker://ghcr.io
singularity build --force ${singularity_file} docker://${docker_image}
cp ${singularity_file} /state/partition1/singularityImages/
cp ${singularity_file} /share/apps/vcell3/singularityImages/

also, make sure vcell-batch container is current.

1. build vcell-batch container as usual

2. create vcell-batch singularity image on server

   on cluster (e.g. xanadu-76) as user vcell build vcell-batch singularity container

export TAG=dev
export TAG=7.6.0.31
export SINGULARITY_MODULE=singularity/vcell-3.10.0
export docker_image=ghcr.io/virtualcell/vcell-batch:${TAG}
export singularity_file=ghcr.io_virtualcell_vcell-batch_${TAG}.img
module load ${SINGULARITY_MODULE}
#singularity remote login -u <github_user> -p <github_token> docker://ghcr.io
singularity build --force ${singularity_file} docker://${docker_image}
cp ${singularity_file} /state/partition1/singularityImages/
cp ${singularity_file} /share/apps/vcell3/singularityImages/

3. Update local configuration to run locally (stored in /docker_env.txt)

./localconfig_realslurm_postgres.sh TEST ghcr.io/virtualcell dev 7.5.0 1234 ../../docker_env_postgres.txt
./localconfig_realslurm_oracle.sh TEST ghcr.io/virtualcell dev 7.5.0 1234 ../../docker_env_oracle.txt

5. run local middleware services

   1. Postgres on 0.0.0.0 (not just loopback adapter)
   2. run local MongoDB on 0.0.0.0 (not just loopback adapter)

6. make sure ActiveMQ is still running on UCHC cluster according to config in docker-compose.yml

   • for example:
     • VCELL_JMS_SIM_HOST_EXTERNAL=vcell-node3.cam.uchc.edu
     • VCELL_JMS_SIM_PORT_EXTERNAL=61619
     • VCELL_JMS_SIM_RESTPORT_EXTERNAL=8164
   • this is needed so that batch and opt jobs running on Slurm can send status, and listen for kills.

7. execute docker compose using docker-compose.yml with environment variable configuration in docker_env_postgres.txt or docker_env_oracle.txt in IDE (intellij)

8. execute local VCell GUI (VCellClientMain) pointing to local backend (vcell-api port as defined in docker-compose.yml)