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.