Difference between revisions of "Running MOM5"

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Running an ocean simulation using MOM5 requires three steps:
 
Running an ocean simulation using MOM5 requires three steps:
  
# Designing an experiment, including its numerical grids and forcing fields
+
#Designing an experiment, including its numerical grids and forcing fields  
# Configuring MOM's numerical settings and physical parameterisations
+
#Configuring MOM's numerical settings and physical parameterisations  
# Executing MOM and generating numerical output
+
#Executing MOM and generating numerical output  
  
 
This section focusses on the final step of model execution, as well as a cursory discussion of model configuration. It assumes that you have been provided with a pre-configured experiment, such as one of the MOM5 examples.
 
This section focusses on the final step of model execution, as well as a cursory discussion of model configuration. It assumes that you have been provided with a pre-configured experiment, such as one of the MOM5 examples.
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In general, model design and configuration is a complex process which can require a broad range of expertise. For more detailed discussions about experiment design, consult the MOM5 documentation and ocean modelling literature.
 
In general, model design and configuration is a complex process which can require a broad range of expertise. For more detailed discussions about experiment design, consult the MOM5 documentation and ocean modelling literature.
  
=Running MOM=  
+
= Running MOM =
  
 
Before beginning, make sure that you have an experiment ready for MOM simulation, as well as a compiled MOM5 executable. Whilst there are other ways of running MOM5, the recommended (and supported) way is to use [https://github.com/marshallward/payu | payu], an experiment running program.
 
Before beginning, make sure that you have an experiment ready for MOM simulation, as well as a compiled MOM5 executable. Whilst there are other ways of running MOM5, the recommended (and supported) way is to use [https://github.com/marshallward/payu | payu], an experiment running program.
  
==Loading payu==  
+
== Loading payu ==
  
 
Payu is available as a system wide loadable software module.
 
Payu is available as a system wide loadable software module.
<syntaxhighlight lang=bash>
+
<syntaxhighlight lang="bash">
 
module load payu
 
module load payu
 
</syntaxhighlight>
 
</syntaxhighlight>
should load the most recent version. You can check which versions are available like so:
+
should load the most recent version. You can check which versions are available like so: <syntaxhighlight lang="bash">
<syntaxhighlight lang=bash>
 
 
module avail payu
 
module avail payu
 
</syntaxhighlight>
 
</syntaxhighlight>
And which is currently loaded:
+
And which is currently loaded: <syntaxhighlight lang="bash">
<syntaxhighlight lang=bash>
 
 
module list
 
module list
 
</syntaxhighlight>
 
</syntaxhighlight>
  
==Configuring your workspace==  
+
== Configuring your workspace ==
  
 
Payu places the experiment configuration in a separate directory tree to the large input and output files. This is a deliberate design decision so that the smaller model configuration files can be in the user's home directory. This means they are backed up in case of catastrophic disk failure, and can be restored.
 
Payu places the experiment configuration in a separate directory tree to the large input and output files. This is a deliberate design decision so that the smaller model configuration files can be in the user's home directory. This means they are backed up in case of catastrophic disk failure, and can be restored.
  
 
Create a directory for your model experiment configurations:
 
Create a directory for your model experiment configurations:
<syntaxhighlight lang=bash>
+
<syntaxhighlight lang="bash">
 
mkdir -p experiments/mom
 
mkdir -p experiments/mom
 
cd experiments/mom
 
cd experiments/mom
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If the experiment you wish to copy has the automatic experiment logging feature turned on, then it can be as simple as
 
If the experiment you wish to copy has the automatic experiment logging feature turned on, then it can be as simple as
<syntaxhighlight lang=bash>
+
<syntaxhighlight lang="bash">
 
git clone /path/to/experiment/config
 
git clone /path/to/experiment/config
 
</syntaxhighlight>
 
</syntaxhighlight>
or if it is available as a repository on a server:
+
or if it is available as a repository on a server: <syntaxhighlight lang="bash">
<syntaxhighlight lang=bash>
 
 
git clone url
 
git clone url
 
</syntaxhighlight>
 
</syntaxhighlight>
  
 
For example, this will clone a standard 1/4 degree MOM-SIS configuration into a directory named gfdl_nyf_18080.
 
For example, this will clone a standard 1/4 degree MOM-SIS configuration into a directory named gfdl_nyf_18080.
<syntaxhighlight lang=bash>
+
<syntaxhighlight lang="bash">
 
git clone git@github.com:coecms/gfdl_nyf_1080.git
 
git clone git@github.com:coecms/gfdl_nyf_1080.git
 
</syntaxhighlight>
 
</syntaxhighlight>
To clone into a different directory name, specify a new name. For example, the following will clone the same configuration into a directory gfdl_nyf_1080_mycopy
+
To clone into a different directory name, specify a new name. For example, the following will clone the same configuration into a directory gfdl_nyf_1080_mycopy <syntaxhighlight lang="bash">
<syntaxhighlight lang=bash>
 
 
git clone git@github.com:coecms/gfdl_nyf_1080.git gfdl_nyf_1080_mycopy
 
git clone git@github.com:coecms/gfdl_nyf_1080.git gfdl_nyf_1080_mycopy
 
</syntaxhighlight>
 
</syntaxhighlight>
[[Category:mom5]][[Category:payu]]
+
 
 +
[[Category:MOM]]

Latest revision as of 00:42, 12 December 2019

Running an ocean simulation using MOM5 requires three steps:

  1. Designing an experiment, including its numerical grids and forcing fields
  2. Configuring MOM's numerical settings and physical parameterisations
  3. Executing MOM and generating numerical output

This section focusses on the final step of model execution, as well as a cursory discussion of model configuration. It assumes that you have been provided with a pre-configured experiment, such as one of the MOM5 examples.

In general, model design and configuration is a complex process which can require a broad range of expertise. For more detailed discussions about experiment design, consult the MOM5 documentation and ocean modelling literature.

Running MOM

Before beginning, make sure that you have an experiment ready for MOM simulation, as well as a compiled MOM5 executable. Whilst there are other ways of running MOM5, the recommended (and supported) way is to use | payu, an experiment running program.

Loading payu

Payu is available as a system wide loadable software module.

module load payu

should load the most recent version. You can check which versions are available like so:

module avail payu

And which is currently loaded:

module list

Configuring your workspace

Payu places the experiment configuration in a separate directory tree to the large input and output files. This is a deliberate design decision so that the smaller model configuration files can be in the user's home directory. This means they are backed up in case of catastrophic disk failure, and can be restored.

Create a directory for your model experiment configurations:

mkdir -p experiments/mom
cd experiments/mom

The easiest way to obtain the necessary configuration files is to copy an existing experiment. Preferably one that is as close as possible to the experimental configuration you wish to use.

If the experiment you wish to copy has the automatic experiment logging feature turned on, then it can be as simple as

git clone /path/to/experiment/config

or if it is available as a repository on a server:

git clone url

For example, this will clone a standard 1/4 degree MOM-SIS configuration into a directory named gfdl_nyf_18080.

git clone git@github.com:coecms/gfdl_nyf_1080.git

To clone into a different directory name, specify a new name. For example, the following will clone the same configuration into a directory gfdl_nyf_1080_mycopy

git clone git@github.com:coecms/gfdl_nyf_1080.git gfdl_nyf_1080_mycopy