Setting up ELM-FATES!

by Bharat Sharma bharat.sharma.neu@gmail.com

Updated on Jun 20, 2023

Optional: The following instructions are compatible with the Docker. Please follow the instructions to install the docker.

Updated on Jun 20, 2023

Cloning E3SM from Ryan's Github

git clone git@github.com:rgknox/E3SM.git

cd E3SM

Checkout E3SM branch compatible w/FATES nutrients

git checkout rgknox/lnd/update-suppl-fates-uptake-api25

Update submodules which downloads FATES

git submodule update --init

Updated on Jun 20, 2023

Add Ryan’s FATES repository as a source

cd components/elm/src/external_models/fates/
git remote add rgknox_repo git@github.com:rgknox/fates.git
git remote -v
git fetch rgknox_repo

Updated on Jun 20, 2023

Checkout the nutrient branch

git fetch --all --tags (fetching all tags)

git checkout tags/sci.1.61.0_api.25.0.0

Creating branch from the tag

git checkout -b bharat-tag-sci.1.61.0_api.25.0.0 sci.1.61.0_api.25.0.0

Updated on Jun 20, 2023

Getting the updated logging fix

git remote add anthony_repo git@github.com:walkeranthonyp/fates.git

git remote -v

git fetch anthony_repo

git checkout logging-bugfix
git fetch

Updated on Jun 20, 2023

E3SM: rgknox/lnd/update-suppl-fates-uptake-api25
FATES: tags/sci.1.61.0_api.25.0.0
Logging: walkeranthonyp/logging-bugfix

files modified:

modified:   cime_config/machines/cmake_macros/gnu_cades.cmake
modified:   components/elm/cime_config/config_component.xml
modified:   components/elm/cime_config/config_compsets.xml
modified:   components/elm/src/external_models/fates (new commits)

Updated on Jun 20, 2023

Details on the modifications

Added following lines in config_compsets.xml

<compset>
  <alias>I20TRELMFATES</alias>
  <lname>20TR_DATM%QIA_ELM%BGC-FATES_SICE_SOCN_MOSART_SGLC_SWAV</lname>
</compset>

Added following lines in config_component.xml

<!--value compset="20TR.*_ELM%[^_]*BGC">20thC_bgc_transient</value -->
<value compset="20TR.*_ELM%[^_]*BGC">20thC_transient</value>

Added following lines in gnu_cades.cmake

set(SCXX "g++")
set(CXX_LINKER "CXX")

Commented following lines in externals/scorpio/src/clib/pioc_support.c

/*if ((file->mode & NC_64BIT_DATA) == NC_64BIT_DATA)
{
file->mode &= ~NC_64BIT_DATA;
}*/

Updated on Jun 20, 2023

Use Call Scripts to run FATES model via OLMT

Updated on Jun 20, 2023

After the simulaions are run successfully, you can use the ELM_postprocessR, developed by Dr. Anthony Walker, to contatenate and plot some initial plots.

After the FATES sims are done:

1. PostprocessorR: to create summary nc files and plots 1.1. files to work on: postprocessR_FACE_bharat.bs or postprocessR_FACE_bharat2.bs Submit the post processor jobs: submit_pp.sbatch

   1. post postprocessor: FATESFACE These codes/repo uses the outputs of postprocessorR to generate plots for presentations.