Commit 65823feb authored by Javier Vegas-Regidor's avatar Javier Vegas-Regidor
Browse files

Updated documentation

parent e512b9a3
......@@ -53,8 +53,8 @@ Optional configurations
Type of the dataset to use. It can be exp, obs or recon. Default is exp.
* DATA_CONVENTION
Convention to use for file paths and names and variable naming among other things. Can be SPECS, PRIMAVERA or CMIP6.
Default is SPECS.
Convention to use for file paths and names and variable naming among other things. Can be SPECS, PREFACE,
PRIMAVERA or CMIP6. Default is SPECS.
* CDFTOOLS_PATH
Path to the folder containing CDFTOOLS executables. By default is empty, so CDFTOOLS binaries must be added to the
......@@ -65,6 +65,28 @@ Optional configurations
necessary when launching through a scheduler, as Earthdiagnostics can detect how many cores the scheduler has
allocated to it.
* AUTO_CLEAN
If True, EarthDiagnostics removes the temporary folder just after finsihing. If RAM_DISK is set to True, this value
is ignored and always Default is True
* RAM_DISK
If set to True, the temporary files is created at the /dev/shm partition. This partition is not mounted from a disk.
Instead, all files are created in the RAM memory, so hopefully this will improve performance at the cost of a much
higher RAM consumption. Default is False.
* MESH_MASK
Custom file to use instead of the corresponding mesh mask file.
* NEW_MASK_GLO
Custom file to use instead of the corresponding new mask glo file
* MASK_REGIONS
Custom file to use instead of the corresponding 2D regions file
* MASK_REGIONS_3D
Custom file to use instead of the corresponding 3D regions file
EXPERIMENT
----------
......@@ -117,6 +139,9 @@ This sections contains options related to the experiment's definition or configu
* CHUNKS
Number of chunks to run
* CHUNK_LIST
List of chunks to run. If empty, all diagnostics will be applied to all chunks
* CALENDAR
Calendar to use for date calculation. All calendars supported by Autosubmit are available. Default is 'standard'
......@@ -213,6 +238,17 @@ cmorized files.
* SOURCE
Default value is 'to be filled'
* VERSION
Dataset version to use (not present in all conventions)
* DEFAULT_OCEAN_GRID
Name of the default ocean grid for those conventions that require it (CMIP6 and PRIMAVERA). Default is gn.
* DEFAULT_ATMOS_GRID
Name of the default atmos grid for those conventions that require it (CMIP6 and PRIMAVERA). Default is gr.
* ACTIVITY
Name of the activity. Default is CMIP
THREDDS
-------
......
......@@ -16,15 +16,16 @@ system, the diagnostics will always use the number of cores that you reserved. I
system, the diagnostics will try to use all the cores on the machine. To avoid this, add the MAX_CORES parameter to the
DIAGNOSTICS section inside the diags.conf file that you are using.
NEMO files
----------
Cleaning temp file
------------------
By default, EarthDiagnostics removes the temporary directory after execution. This behaviour can be avoided be setting
ra
Unlike the bash version of the ocean diagnostics, this program keeps the NEMO files in the scratch folder so you can
launch different configurations for the same experiment with reduced start time. You will need to remove the experiment's
folder in the scratch directory at the end of the experiment to avoid wasting resources. To do this, just use
By default
.. code-block:: bash
earthdiags -f PATH_TO_CONF --clean
If you plan to run the earthdiagnostics only once, you can add this line after the execution
\ No newline at end of file
......@@ -37,8 +37,8 @@ Creating a config file
----------------------
Go to the folder where you installed the EarthDiagnostics. You will see a folder called earthdiagnostics,
and, inside it, a diags.conf file that can be used as a model for your config file. Create a copy of it wherever it
suites you.
and, inside it, the model_diags.conf file that can be used as a template for your config file. Create a copy of it
wherever it suites you.
Now open your brand new copy with your preferred text editor. The file contains commentaries explaining each
one of its options, so read it carefully and edit whatever you need. Don't worry about DIAGS option, we will
......@@ -53,21 +53,20 @@ whichever suits you better. From now on, we will assume that you are going to ru
.. hint::
For old Ocean Diagnostics users: you can use most of the old names as aliases to launch one or multiple diagnostics.
Check the ALIAS section on the diags.conf to see which ones are available.
Check the ALIAS section on the model_diags.conf to see which ones are available.
First, choose a variable that has daily data. Then replace the DIAGS option with the next one where $VARIABLE represents the
variable's name and $DOMAIN its domain (atmos, ocean, seaice, landice...)
First, choose a variable that has daily data. Then replace the DIAGS option with the next one where $VARIABLE represents
the variable's name and $DOMAIN its domain (atmos, ocean, seaice, landice...)
.. code-block:: sh
DIAGS = monmean,$VARIABLE,$DOMAIN
DIAGS = monmean,$DOMAIN,$VARIABLE
Prepare the run script
----------------------
Once you have configured your experiment you can execute any diagnostic with the provided launch_diags.sh script.
Create a copy and change the variables PATH_TO_CONF_FILE and PATH_TO_DIAGNOSTICS so they point to your conf file and
installation folder.
Once you have configured your experiment you can execute any diagnostic with the provided model_launch_diags.sh script.
Create a copy and change the variable PATH_TO_CONF_FILE so it points to your conf file .
Now, execute the script (or submit it to bsceslogin01, it has the correct header) and... that's it!
You will find your results directly on the storage and a folder for the temp files in the scratch named after the EXPID.
......
#!/usr/bin/env bash
#SBATCH -n 1
#SBATCH --time 7-00:00:00
#SBATCH --error=earthdiags.%J.err
#SBATCH --output=earthdiags.%J.out
PATH_TO_CONF_FILE=~jvegas/earthdiagnostics/diags.conf
module purge
module load earthdiagnostics
set -xv
earthdiags -lc DEBUG -f ${PATH_TO_CONF_FILE}
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