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Update graham NEMO build docs re: change to StdEnv/2023 #46

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Update graham NEMO build docs re: change to StdEnv/2023 #46

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Delete trailing whitespace
douglatornell Mar 18, 2024
bd12245
Update graham docs re: change to StdEnv/2023
douglatornell Mar 18, 2024
b5e295d
Chg to Intel module load for graham StdEnv/2023
douglatornell May 8, 2024
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38 changes: 20 additions & 18 deletions code-notes/salishsea-nemo/quickstart/graham.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
Working on ``graham``: NEMO v3.6
********************************

This section describes the steps to set up and run the SalishSeaCast NEMO version 3.6 code on the
This section describes the steps to set up and run the SalishSeaCast NEMO version 3.6 code on the
Digital Research Alliance of Canada `graham.computecanada.ca`_ HPC cluster.

.. _graham.computecanada.ca: https://docs.alliancecan.ca/wiki/Graham
Expand All @@ -15,7 +15,7 @@ The process described here should be applicable with little or no change to the
.. _Alliance HPC clusters: https://docs.alliancecan.ca/wiki/Getting_started#What_systems_are_available?

Before going through the process described here,
you should have completed the steps in :ref:`moaddocs:InitialSetupOnGraham`
you should have completed the steps in :ref:`moaddocs:InitialSetupOnGraham`


Modules setup
Expand All @@ -26,8 +26,10 @@ On ``graham`` the module loads that are required to build and run NEMO are:

.. code-block:: bash

module load netcdf-fortran-mpi/4.6.0
module load perl/5.30.2
module load StdEnv/2023
module load intel/2023.2.1
module load netcdf-fortran-mpi/4.6.1
module load perl/5.36.1

You can manually load the modules each time you log in,
or you can add the above lines to your :file:`$HOME/.bashrc` file so that they are
Expand Down Expand Up @@ -169,12 +171,12 @@ Please see the :ref:`moaddocs:XIOS-2-docs` section of the :ref:`UBC-EOAS-MOAD-do
Compile NEMO-3.6
================

Compile the ``SalishSeaCast`` NEMO configuration and link it to XIOS-2,
Compile the ``SalishSeaCast`` NEMO configuration and link it to XIOS-2,
and compile the :program:`rebuild_nemo` tool.
The NEMO ARCH files use the :envvar:`XIOS_HOME` environment variable to find the XIOS-2 library
The NEMO ARCH files use the :envvar:`XIOS_HOME` environment variable to find the XIOS-2 library
you built above.
:envvar:`XIOS_HOME` *must* be an absolute path to your XIOS-2 clone directory.
You can set :envvar:`XIOS_HOME` on the command-line before the :command:`makenemo`
You can set :envvar:`XIOS_HOME` on the command-line before the :command:`makenemo`
and :command:`maketools` commands as shown below,
or you can set and export the value of :envvar:`XIOS_HOME` in your :file:`$HOME/.bashrc` file.

Expand All @@ -188,7 +190,7 @@ or you can set and export the value of :envvar:`XIOS_HOME` in your :file:`$HOME/
It typically takes about 3.5 minutes to build a NEMO configuration on ``graham``,
and about 15 seconds to build ``REBUILD_NEMO``.

To build a configuration other than ``SalishSeaCast``,
To build a configuration other than ``SalishSeaCast``,
replace ``SalishSeaCast`` with the name of the configuration to be built, e.g. ``SMELT``:

.. code-block:: bash
Expand All @@ -214,7 +216,7 @@ replace ``SalishSeaCast`` with the name of the configuration.
Prepare and Execute Runs
========================

The :file:`SS-run-sets/v202111/` directory in the :ref:`SS-run-sets-SalishSea` repo contains
The :file:`SS-run-sets/v202111/` directory in the :ref:`SS-run-sets-SalishSea` repo contains
version controlled sample run description files and namelist segment files.
In your own directory in that repo copy, edit,
and version control those files to define the runs that you want to execute.
Expand All @@ -225,7 +227,7 @@ The namelists are described in the `NEMO-3.6 Book`_.

.. _NEMO-3.6 Book: https://zenodo.org/records/3248739

Please see the sections below for details of using forcing climatology and
Please see the sections below for details of using forcing climatology and
shared daily forcing files in your runs,
and examples of run description and namelist file sections.

Expand All @@ -246,13 +248,13 @@ something like:
salishsea_cmd.run INFO: Created run directory /scratch/dlatorne/20mar17nowcast16x34_2017-10-06T101548.694389-0700
salishsea_cmd.run INFO: Submitted batch job 1578481

:command:`salishsea run` has a number of command-line option flags that are useful for controlling
:command:`salishsea run` has a number of command-line option flags that are useful for controlling
details of how runs are executed,
and for debugging your YAML files and the symlinks in the temporary run directory.
Please see :command:`salishsea help run` or the
Please see :command:`salishsea help run` or the
:ref:`SalishSeaCmd package docs <salishseacmd:salishsea-run>`.

You can use the batch job number with :command:`squeue --job` and :command:`sacct --job`
You can use the batch job number with :command:`squeue --job` and :command:`sacct --job`
to monitor the execution status of your job.

The command alias:
Expand All @@ -268,21 +270,21 @@ You can use as:
* :command:`sq -u $USER` to see all of your queued jobs
* :command:`sq -A rrg-allen,def-allen` to see all of the group's queued jobs
* :command:`sq --job job-number`,
where `job-number` is the batch job number provided in the output of a :command:`salishsea run`
where `job-number` is the batch job number provided in the output of a :command:`salishsea run`
command,
to see the information about a specific job

When the job completes the results should have been gathered in the directory you specified
When the job completes the results should have been gathered in the directory you specified
in the :command:`salishsea run` command and the temporary run directory should have been deleted.


Forcing Climatology and Daily Files
===================================

Model runs use a mixture of climatology and daily forcing from other operational models
Model runs use a mixture of climatology and daily forcing from other operational models
or observations:

* Atmospheric forcing is almost always from the Environment and Climate Change Canada (ECCC)
* Atmospheric forcing is almost always from the Environment and Climate Change Canada (ECCC)
`High Resolution Deterministic Prediction System`_ (HRDPS) model hourly forecasts.

.. _High Resolution Deterministic Prediction System: https://eccc-msc.github.io/open-data/msc-data/nwp_hrdps/readme_hrdps_en/
Expand All @@ -296,7 +298,7 @@ or observations:
Temperature and chemistry of the river run-offs are climatological.

* Tracers at the northern boundary in Johnstone Strait are climatological.
On the western boundary at the mouth of the Juan de Fuca Strait we have hourly tracer fields
On the western boundary at the mouth of the Juan de Fuca Strait we have hourly tracer fields
from the University of Washington `LiveOcean model`_ since 4-Feb-2017
for temperature,
salinity,
Expand Down
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