Command line options
The full set of command line options for metawards is below;
usage: metawards [-h] [--version] [-c CONFIG] [-i INPUT] [-l [LINE [LINE ...]]] [-r [REPEATS [REPEATS ...]]] [-s SEED] [-a [ADDITIONAL [ADDITIONAL ...]]] [-o OUTPUT] [-d DISEASE] [-m MODEL] [-D DEMOGRAPHICS] [--start-date START_DATE] [--start-day START_DAY] [-p PARAMETERS] [-R REPOSITORY] [-P POPULATION] [-n NSTEPS] [-u USER_VARIABLES] [--iterator ITERATOR] [--extractor EXTRACTOR] [--mixer MIXER] [--mover MOVER] [--star-is-E] [--star-is-R] [--disable-star] [--UV UV] [--UV-max UV_MAX] [--theme THEME] [--no-spinner] [--no-progress] [--debug] [--debug-level DEBUG_LEVEL] [--outdir-scheme OUTDIR_SCHEME] [--nthreads NTHREADS] [--nprocs NPROCS] [--hostfile HOSTFILE] [--cores-per-node CORES_PER_NODE] [--auto-bzip] [--no-auto-bzip] [--force-overwrite-output] [--max-nodes MAX_NODES] [--max-links MAX_LINKS] [--profile] [--no-profile] [--mpi] [--scoop] MetaWards epidemic modelling - see https://metawards.org for more information. optional arguments: -h, --help show this help message and exit --version Print the version information about metawards (default: None) -c CONFIG, --config CONFIG Config file that can be used to set some or all of these command line options. (default: None) -i INPUT, --input INPUT Input file for the simulation that specifies the adjustable parameters to change for each run of the model. You must supply some input to run a model! (default: None) -l [LINE [LINE ...]], --line [LINE [LINE ...]] Line number (or line numbers) containing the values of adjustable parameters to run for this run (or runs) of the model If this isn't specified then model runs will be performed for adjustable parameters given on all lines from the input file. You can specify many numbers, and ranges are also accepted, e.g. '-l 5 6-10 12,13,14' etc. Note that the line numbers are 0-indexed, e.g. the first line of the file is line 0. Ranges are inclusive, so 3-5 is the same as 3 4 5 (default: None) -r [REPEATS [REPEATS ...]], --repeats [REPEATS [REPEATS ...]] The number of repeat runs of the model to perform for each value of the adjustable parameters. By default only a single run will be performed for each set of adjustable parameters. This complements the 'repeat' column in the input file (in which case the repeats are multipled). Also, multiple repeat values can be given, in which case each value corresponds to a different line in the input file (default: None) -s SEED, --seed SEED Random number seed for this run (default is to use a random seed) (default: None) -a [ADDITIONAL [ADDITIONAL ...]], --additional [ADDITIONAL [ADDITIONAL ...]] File (or files) containing additional seed of outbreak for the model. These are used to seed additional infections on specific days at different locations during a model run (default: None) -o OUTPUT, --output OUTPUT Path to the directory in which to place all output files (default 'output'). This directory will be subdivided if multiple adjustable parameter sets or repeats are used. (default: None) -d DISEASE, --disease DISEASE Name of the disease to model (default is 'ncov') (default: None) -m MODEL, --model MODEL Name of the input model data set for the network (default is '2011Data') (default: None) -D DEMOGRAPHICS, --demographics DEMOGRAPHICS Name of the demographics file that provides information about how a population is modelled as multiple demographics. If this is not supplied then the population is modelled as a single demographic (default: None) --start-date START_DATE Date of the start of the model outbreak. This accepts dates either is iso-format, or fuzzy dates such as 'monday', 'tomorrow' etc. This is used to work out which days are weekends, or to make it easier to specify time-based events. (default: None) --start-day START_DAY The start day of the model outbreak. By default the model outbreak starts on day zero (0), with each step of the model representing an additional day. Use this to start from a later day, which may be useful if you want to more quickly reach time based events. Note that the passed '--start-date' is always day 0, so day 10 has a date which is 10 days after start-date (default: None) -p PARAMETERS, --parameters PARAMETERS Name of the input parameter set used to control the simulation (default 'march29') (default: None) -R REPOSITORY, --repository REPOSITORY Path to the MetaWardsData repository. If unspecified this defaults to the value in the environment variable METAWARDSDATA or, if that isn't specified, to $HOME/GitHub/MetaWardsData [env var: METAWARDSDATA] (default: None) -P POPULATION, --population POPULATION Initial population (default 1000) (default: None) -n NSTEPS, --nsteps NSTEPS Maximum number of steps (days) to run for the simulation. Each step represents one day in the outbreak (default is to run for a maximum of two years - 730 days) (default: None) -u USER_VARIABLES, --user-variables USER_VARIABLES Name of the file containing user-defined custom variables. These provide extra information that can be read by the custom integrators or custom extractors. (default: None) --iterator ITERATOR Name of the iterator to use to advance the outbreak at each step (day). For a full explanation see the tutorial at https://metawards.org (default: None) --extractor EXTRACTOR Name of the extractor to use to extract information during a model run. For a full explanation see the tutorial at https://metawards.org (default: None) --mixer MIXER Name of the mixer to use to mix information from multiple demographics together during a model run. For a full explanation see the tutorial at https://metawards.org (default: None) --mover MOVER Name of the mover to use to move the population between demographics during a model run. For a full explanation see the tutorial at https://metawards.org (default: None) --star-is-E Set the state 0 (* state) as an extra latent state, as opposed to an extra R state (default: None) --star-is-R Set the state 0 (* state) as an extra R state (the default). Individuals in this state are calculated as 'R', even though they will progress on the next day to the E state (default: None) --disable-star Disable the * state. Now state 0 is the first and only latent state. There is no star state. (default: None) --UV UV Value for the UV parameter for the model (default is 0.0) (default: None) --UV-max UV_MAX Date when the seasonal adjustment should be at its maximum. By default, this is January 1st on the assumption that disease spread is stronger in the (Northern) winter (default: None) --theme THEME The theme to use to color the output. Use '--theme simple' if you prefer a simple and colorless output. (default: None) --no-spinner Disable the spinner that spins when little output is being printed to the screen. (default: None) --no-progress Disable the progress bars that show progress. (default: None) --debug Enable debugging output. This is useful for MetaWards developers or if you are writing your own iterators, extractors etc. (default: None) --debug-level DEBUG_LEVEL Limit debug output to the specified level. (default: None) --outdir-scheme OUTDIR_SCHEME Set the naming scheme for output directory names for multiple model runs. Options are either 'fingerprint' to use the model fingerprint, 'sequential' for sequential numbering, or 'uid' to generate a unique ID. (default: None) --nthreads NTHREADS Number of threads over which parallelise an individual model run. The total number of cores used by metawards will be nprocesses x nthreads [env var: OMP_NUM_THREADS] (default: None) --nprocs NPROCS The number of processes over which to parallelise the different model runs for different adjustable parameter sets and repeats. By default this will automatically work out the number of processes based on the way metawards is launched. Use this option if you want to specify the number of processes manually. (default: None) --hostfile HOSTFILE The hostfile containing the names of the compute nodes over which to run a parallel job. If this is not set, the program will attempt to automatically get this information from the cluster queueing system. Use this if the auto-detection fails (default: None) --cores-per-node CORES_PER_NODE Set the number of processor cores available on each of the compute nodes in the cluster that will be used to run the models (if a cluster is used). If this is not set then the program will attempt to get this information from the cluster queueing system. Use this option if the auto-detection fails. (default: None) --auto-bzip Automatically bz2 compress all output files as they are written. (default: None) --no-auto-bzip Do not automatically bz2 compress all output files as they are written. (default: None) --force-overwrite-output Whether or not to force overwriting of any existing output. Using this option will tell metawards that it is safe to delete the contents of the output directory specified in by '--output' if it already exists. Dangerous as this can remove existing output files (default: False) --max-nodes MAX_NODES Maximum number of nodes that can be read (default: None) --max-links MAX_LINKS Maximum number of links that can be read (default: None) --profile Enable profiling of the code (default: None) --no-profile Disable profiling of the code (default: None) --mpi Force use of MPI to parallelise across runs (default: None) --scoop Force use of scoop to parallelise across runs (default: None) Args that start with '--' (eg. --version) can also be set in a config file (specified via -c). Config file syntax allows: key=value, flag=true, stuff=[a,b,c] (for details, see syntax at https://goo.gl/R74nmi). If an arg is specified in more than one place, then commandline values override environment variables which override config file values which override defaults.