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Added documentation for force flag #259

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May 13, 2020
Merged

Added documentation for force flag #259

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2734bb9
Added documentation for force flag
aidanheerdegen May 13, 2020
2f6b570
Fixed line length of conf file that PEP8 decided was too long
aidanheerdegen May 13, 2020
27afcbd
More PEP8 nonsense on a config file
aidanheerdegen May 13, 2020
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6 changes: 5 additions & 1 deletion docs/source/conf.py
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Expand Up @@ -9,7 +9,11 @@

# Sphinx setup
#needs_sphinx = '1.0'
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode']
extensions = ['sphinx.ext.autodoc',
'sphinx.ext.ifconfig',
'sphinx.ext.viewcode',
'sphinx.ext.autosectionlabel']
autosectionlabel_maxdepth = 2
templates_path = ['_templates']
source_suffix = '.rst'
#source_encoding = 'utf-8-sig'
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23 changes: 13 additions & 10 deletions docs/source/usage.rst
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Expand Up @@ -150,17 +150,16 @@ created manually:
Running your experiment
=======================

Once the laboratory has been created and the experiment has been configured, you
can check that the paths have been correctly specified by running::
Once the laboratory has been created and the experiment has been configured, as
an optioal step you can check that the paths have been correctly specified by
running::

payu setup

This creates the temporary ``work`` directory and is done automatically when
the model is run. If there any errors these can be fixed. ``payu`` will not
run the model if there is an existing ``work`` directory, so this must be
removed like so::

payu sweep
the model is run. If there any errors in the configuration, such as incorrect
or missing paths, these can be fixed. ``payu`` will not run the model if there
is an existing ``work`` directory, so this must be removed (see :ref:`Cleaning up`).

The ``setup`` command will also generate manifest files in the ``manifest``
directory. The manifest files track the executable, input and restart files used
Expand All @@ -175,6 +174,11 @@ Once you are satisfied the configuration is correct, and there is no existing

This will run the model once and store the output in the ```archive``` directory.

Optionally is there is an existing ``work`` directory the ``-f/--force`` flag
will automatically ``sweep`` any existing ``work`` directory::

payu run -f

To continue the simulation from its last point, type ``payu run`` again.

In order to schedule ``N`` successive runs, use the ``-n`` flag::
Expand All @@ -200,8 +204,8 @@ If you have instructed ``payu`` to run for a number of resubmits but for some
reason need to stop a run after the current run has completed create a file
called ``stop_run`` in the control directory.

It is possible to require that a run reproduce an existing run using the ``-r``
flag:
It is possible to require that a run reproduce an existing run using the
``-r/--reproduce`` flag:

payu run -r

Expand Down Expand Up @@ -231,7 +235,6 @@ This will delete the contents of ``work`` and move any model and scheduler logs
into a ``pbs_logs`` directory. Any model output in ``archive`` will not be
deleted.


Deleting an experiment archive
------------------------------

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