Setting up ELM-FATES!

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Setting up ELM-FATES!

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

Updated on Sep 01, 2023

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

Updated on Feb 14, 2024

Clone from Master

git clone https://github.com/E3SM-Project/E3SM.git

cd E3SM

Make a copy of master

git checkout -b E3SM_BS_config

Use the following command to download the submodules compatible with the E3SM

git submodule update --init --recursive

Updated on Feb 08, 2024

files modified:

modified:   cime_config/machines/cmake_macros/gnu_cades.cmake
modified:   cime_config/machines/config_machines.xml
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)
modified:   externals/scorpio/src/clib/pioc_support.c

For Baseline

Following changes are required for ORNL Baseline:

https://github.com/E3SM-Project/E3SM/commit/db3790d66664e5f80945e4b46122c1ad1129b8c8

We need a conda env: conda env create -f /ccsopen/home/zdr/OLMT.yml then run the following command in OLMT env:
MPICC="mpicc -shared" pip install --no-cache-dir --no-binary=mpi4py mpi4py

cime_config/machines/config_machines.xml

Edit the following line under cades machine options

cmake/3.20.3</command>

Updated on Sep 01, 2023

Details on the modifications

gnu_cades.cmake should be

string(APPEND FFLAGS " -O -fno-range-check")
set(HDF5_PATH "/software/dev_tools/swtree/cs400_centos7.2_pe2016-08/hdf5-parallel/1.8.17/centos7.2_gnu5.3.0")
set(NETCDF_PATH "/software/dev_tools/swtree/cs400_centos7.2_pe2016-08/netcdf-hdf5parallel/4.3.3.1/centos7.2_gnu5.3.0")
set(PNETCDF_PATH "/software/dev_tools/swtree/cs400_centos7.2_pe2016-08/pnetcdf/1.9.0/centos7.2_gnu5.3.0")
set(LAPACK_LIBDIR "/software/tools/compilers/intel_2017/mkl/lib/intel64")
string(APPEND SLIBS " -L${NETCDF_PATH}/lib -Wl,-rpath=${NETCDF_PATH}/lib -lnetcdff -lnetcdf")
set(MPICXX "mpic++")
set(SCXX "g++")
set(CXX_LINKER "CXX")

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>

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 Sep 01, 2023

Use Call Scripts to run FATES model via OLMT

Updated on Sep 01, 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:

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

Data that I use to run ELM-FATES

ORNL and Duke FACE Experiment Data: Google Drive link

My personal branches

E3SM

E3SM_BS_config : copy of master with config changes
fates-cnp-lambda : ryan’s cnp with ECA changes
master : master
ryan_bs_config : config + ryans: in E3SM_BS_config, I pulled fates-cnp-lambda

fates

FATES_BS_local: copy of the main
main: main/master