From 7bf6f7e319b53f0c76d3b90306c8704ea115a43a Mon Sep 17 00:00:00 2001 From: Jo Basevi Date: Mon, 23 Sep 2024 09:24:08 +1000 Subject: [PATCH] Update docs on model executable loaded via environment modules --- docs/source/config.rst | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/docs/source/config.rst b/docs/source/config.rst index ef7b9451..aa0fabd4 100644 --- a/docs/source/config.rst +++ b/docs/source/config.rst @@ -163,9 +163,12 @@ configuration. directory of the list takes precedence. ``exe`` - Binary executable for the model. This can either be a filename in the - laboratory's ``bin`` directory, or an absolute filepath. Various model - drivers typically define their own default executable names. + Binary executable for the model. This can be a filename or an absolute + filepath. If it's a filename, it needs be found in either the laboratory's + ``bin`` directory, or in paths added to ``$PATH`` by loaded environment + modules (see configuring :ref:`modules` for how to load + modules). + Various model drivers typically define their own default executable names. ``submodels`` If one is running a coupled model containing several submodels, then each @@ -551,6 +554,7 @@ Miscellaneous Ignore any restart files and repeat the initial run upon resubmission. This is generally only used for testing purposes, such as bit reproducibility. +.. _configuring-modules: ``modules`` Specify lists of environment modules and/or directories to load/use at the start of the PBS job, for example:: @@ -563,9 +567,11 @@ Miscellaneous - parallel-netcdf-1.12.3 - xerces-c-3.2.3 - This is seldom needed, because payu is good at automatically determining - the environment modules required by model executables. If the modules - require `module use` in order to be found, this command can also be run + As environment modules can be used to determine model executable paths, + the modules loaded are required to be unique. This means modules should be + specified with a version, and modules of the same name and version + should not be found in multiple module directories. + If the modules require `module use` in order to be found, this command can also be run prior to `payu run` instead of listing the directory under the `use` option, e.g.::