From 2734bb92a62ad70eaef052b61b5befd5b9744781 Mon Sep 17 00:00:00 2001 From: Aidan Heerdegen Date: Wed, 13 May 2020 10:32:32 +1000 Subject: [PATCH 1/3] Added documentation for force flag --- docs/source/conf.py | 3 ++- docs/source/usage.rst | 23 +++++++++++++---------- 2 files changed, 15 insertions(+), 11 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 11757b52..9169d107 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -9,7 +9,8 @@ # 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' diff --git a/docs/source/usage.rst b/docs/source/usage.rst index 02d479e1..37053d61 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -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 @@ -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:: @@ -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 @@ -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 ------------------------------ From 2f6b570d1f7b0142a1b5a90446325bd0f0ddd547 Mon Sep 17 00:00:00 2001 From: Aidan Heerdegen Date: Wed, 13 May 2020 10:39:04 +1000 Subject: [PATCH 2/3] Fixed line length of conf file that PEP8 decided was too long --- docs/source/conf.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 9169d107..10e36984 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -9,7 +9,10 @@ # Sphinx setup #needs_sphinx = '1.0' -extensions = ['sphinx.ext.autodoc', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.autosectionlabel'] +extensions = ['sphinx.ext.autodoc', + 'sphinx.ext.ifconfig', + 'sphinx.ext.viewcode', + 'sphinx.ext.autosectionlabel'] autosectionlabel_maxdepth = 2 templates_path = ['_templates'] source_suffix = '.rst' From 27afcbd82a94a3c04922eb711a1562bce3c623bc Mon Sep 17 00:00:00 2001 From: Aidan Heerdegen Date: Wed, 13 May 2020 10:41:08 +1000 Subject: [PATCH 3/3] More PEP8 nonsense on a config file --- docs/source/conf.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 10e36984..71edc718 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -9,9 +9,9 @@ # 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']