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
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.bsorpostprocessR_FACE_bharat2.bsSubmit 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