ParProcCo 2.0.0

Parallel Processing Coordinator. Splits dataset processing to run parallel cluster jobs and aggregates outputs

ParProcCo

Requires a YAML configuration file in grandparent directory of package, CONDA_PREFIX/etc or /etc

--- !PPCConfig
allowed_programs:
    rs_map: msmapper_utils
    blah1: whatever_package1
    blah2: whatever_package2
url: https://slurm.local:8443
extra_property_envs: # optional dictionary for slurm job properties and environment variables
    account: MY_ACCOUNT # env var that holds account

An entry point called ParProcCo.allowed_programs can be added to other packages' setup.py:

setup(
...
    entry_points={PPC_ENTRY_POINT: ['blah1 = whatever_package1']},
)

which will look for a module called blah1_wrapper in whatever_package1 package.

Testing

Tests can be run with

$ pytest tests

To test interactions with Slurm, set the following environment variables:

SLURM_REST_URL  # URL for server and port where the REST endpoints are hosted
SLURM_PARTITION # Slurm cluster parition 
SLURM_JWT       # JSON web token for access to REST endpoints