reV qa-qc

Execute the qa-qc step from a config file.

reV QA/QC performs quality assurance checks on reV output data. Users can specify the type of QA/QC that should be applied to each reV module.

The general structure for calling this CLI command is given below (add --help to print help info to the terminal).

reV qa-qc [OPTIONS]

Options

-c, --config_file <config_file>

Required Path to the qa-qc configuration file. Below is a sample template config

{
    "execution_control": {
        "option": "local",
        "allocation": "[REQUIRED IF ON HPC]",
        "walltime": "[REQUIRED IF ON HPC]",
        "qos": "normal",
        "memory": null,
        "queue": null,
        "feature": null,
        "conda_env": null,
        "module": null,
        "sh_script": null,
        "num_test_nodes": null,
        "max_workers": null
    },
    "log_directory": "./logs",
    "log_level": "INFO",
    "modules": "[REQUIRED]"
}

execution_control:
  option: local
  allocation: '[REQUIRED IF ON HPC]'
  walltime: '[REQUIRED IF ON HPC]'
  qos: normal
  memory: null
  queue: null
  feature: null
  conda_env: null
  module: null
  sh_script: null
  num_test_nodes: null
  max_workers: null
log_directory: ./logs
log_level: INFO
modules: '[REQUIRED]'

log_directory = "./logs"
log_level = "INFO"
modules = "[REQUIRED]"

[execution_control]
option = "local"
allocation = "[REQUIRED IF ON HPC]"
walltime = "[REQUIRED IF ON HPC]"
qos = "normal"

Parameters

execution_controldict

Dictionary containing execution control arguments. Allowed arguments are:

option:: ({‘local’, ‘kestrel’, ‘eagle’, ‘awspc’, ‘slurm’, ‘peregrine’}) Hardware run option. Determines the type of job scheduler to use as well as the base AU cost. The “slurm” option is a catchall for HPC systems that use the SLURM scheduler and should only be used if desired hardware is not listed above. If “local”, no other HPC-specific keys in are required in execution_control (they are ignored if provided).
allocation:: (str) HPC project (allocation) handle.
walltime:: (int) Node walltime request in hours.
qos:: (str, optional) Quality-of-service specifier. For Kestrel users: This should be one of {‘standby’, ‘normal’, ‘high’}. Note that ‘high’ priority doubles the AU cost. By default, "normal".
memory:: (int, optional) Node memory max limit (in GB). By default, None, which uses the scheduler’s default memory limit. For Kestrel users: If you would like to use the full node memory, leave this argument unspecified (or set to None) if you are running on standard nodes. However, if you would like to use the bigmem nodes, you must specify the full upper limit of memory you would like for your job, otherwise you will be limited to the standard node memory size (250GB).
max_workers:: (int, optional) Max number of workers to run for QA/QA. If None, uses all CPU cores. By default, None.
queue:: (str, optional; PBS ONLY) HPC queue to submit job to. Examples include: ‘debug’, ‘short’, ‘batch’, ‘batch-h’, ‘long’, etc. By default, None, which uses “test_queue”.
feature:: (str, optional) Additional flags for SLURM job (e.g. “-p debug”). By default, None, which does not specify any additional flags.
conda_env:: (str, optional) Name of conda environment to activate. By default, None, which does not load any environments.
module:: (str, optional) Module to load. By default, None, which does not load any modules.
sh_script:: (str, optional) Extra shell script to run before command call. By default, None, which does not run any scripts.
num_test_nodes:: (str, optional) Number of nodes to submit before terminating the submission process. This can be used to test a new submission configuration without sumbitting all nodes (i.e. only running a handful to ensure the inputs are specified correctly and the outputs look reasonable). By default, None, which submits all node jobs.

Only the option key is required for local execution. For execution on the HPC, the allocation and walltime keys are also required. All other options are populated with default values, as seen above.

log_directorystr

Path to directory where logs should be written. Path can be relative and does not have to exist on disk (it will be created if missing). By default, "./logs".

log_level{“DEBUG”, “INFO”, “WARNING”, “ERROR”}

String representation of desired logger verbosity. Suitable options are DEBUG (most verbose), INFO (moderately verbose), WARNING (only log warnings and errors), and ERROR (only log errors). By default, "INFO".

modulesdict

Dictionary of modules to QA/QC. Keys should be the names of the modules to QA/QC. The values are dictionaries that represent the config for the respective QA/QC step. Allowed config keys for QA/QC are the “property” attributes of QaQcModule.

Note that you may remove any keys with a null value if you do not intend to update them yourself.