A Simple User Guides for NESM-BGC

Yifei Dai [email protected], [email protected]

February, 2018

Earth System Modeling Center (ESMC) Nanjing University of Information Science and Technology(NUIST)

Getting start with NESM-BGC

The NESM is referred to Nanjing University of Information Science and Technology(NUIST)

Earth System Model (ESM). The BGC version of the NESM (NESM-BGC) is based on the

NESM v1, the component model, model structure and coupling strategy are described in Cao et al. (2015). It was established with the atmospheric model ECHAM v5.3, ocean model NEMO v3.4, sea ice model CICE v4.1 and coupler 3 of the Ocean-Atmosphere-Sea-Ice-Soil Model

Coupling Toolkit (OASIS3.0-MCT3). It is aiming to provide a numerical modeling platform for cross-disciplinary earth system studies, project future Earth’s climate and environment changes, as well conduct subseasonal-to-seasonal prediction.

This goal of this manual is targeted at introducing the technical aspect in compile and running the NESM v3 model. Here we will discuss the necessary environment settings, forcing data, model compile settings and job scripts in performing the coupled experiments. The model structure description can be referring to Cao et al. (2015), and the component model and coupler descriptions are introduced in Roeckner et al. (2003) Madec and NEMO team(2012), Hunke and Lipscomb(2010) and Craig et al. (2017), and the references are also provided in this folder.

1. Model source code and input data

The current version of model source code and data are provided with Zenodo link with the purpose of NESM-BGC manuscript review. In future, the code and data will be available at

NUIST data server center, which is in the process.

The model code is named as NESM-BGC.tar.gz and shared by Zenodo, you can download and unpack the model by tar –xzvf NESM-BGC.tar.gz.

The unpacked model folder included 3 subdirectories: Linux, run, src, and data.

o Linux: contains compiled executable files of each component model and related

libraries.

o Run: includes compile settings and run scripts

o Src: includes component model and coupler code

o Data: includes required input data

In Run folder, there are three sub-folders, compile and script.

 Compile: includes the environment settings for the model compile

 Scirpt: includes the running script

Here we won’t introduce the install of libraries as mentioned in previous section. And the model compile and run examples are based on University of Hawaii High Performance

Computer (UHHPC). The information of UHHPC can be available at http://www.hawaii.edu/its/ci/hpc-uh-information-technology-services/.

2. Environments setup

Before compiling the model, the following library is necessary:

1. Intel compiler

2. SLIB and Zlib

3. HDF5 library

4. NETCDF library with the version higher than v4.1.3

Before compile the model, you have to load the right compilers and the setup the libraries

###### compiler for NESMv3 ######### module purge module load intel/ics intel/impi . /opt/intel/composerxe/mkl/bin/mklvars.sh intel64

###### Libraries for NESMv3 ######### export NETCDF=/home/jiancao/tools/intel export NETCDF_LIB=$NETCDF/lib export NETCDF_INC=$NETCDF/include export PATH=$NETCDF/bin:$PATH export LD_LIBRARY_PATH=$NETCDF_LIB:$LD_LIBRARY_PATH export LD_RUN_PATH=$NETCDF_LIB:$LD_RUN_PATH export LD_INCLUDE_PATH=$NETCDF_INC:$LD_INCLUDE_PATH

3. Configure and compile model code

Download the code and data, and then unpack the file: cd $Yourdir tar –xzvf NESM-BGC.tar.gz

Then, you can start to compile the coupled model. Go to the compile folder and edit the folder and library information.

cd NESM-BGC/run/compile vi make.env

There are serval settings should be modified by user. Line 7 is the current main folder of model code. The MPI, NETCDF, HDF5, SLIB and ZLIB are specified between line 9 and line 34.

Please modify the ROOT directory of each library to your HPC settings. Then save the settings in make.env.

To compile coupled model: make nuist

The compile error and log information can be found in COMP.err and COMP.log under this folder. If there is no error in COMP.err, which means you successfully compiled the coupled model. Additionally, the ocean component model need a tool to combine the restart files since there are wrote at each computing cores. The ‘REBUILD’ tool is located in

$Yourdir/NESM-BGC/src/modelsrc/cploce/NEMO-OASIS3-MCT/TOOLS. It can be set up in two steps.

a) Compile: 5 cd $Yourdir/NESM-BGC/src/modelsrc/cploce/NEMO‐OASIS3‐MCT/TOOLS ./maketools ‐m ifort_linux ‐n REBUILD b) Add the path in bashrc export PATH=$Yourdir/NESM- BGC/src/modelsrc/cploce/NEMO‐OASIS3‐MCT/TOOLS/REBUILD:$PATH

Now the compling process is finished!!!

There are several option in clean the compiled information:

Make realclean : Clean all compiled information for the whole coupled system.

Make cleanecham: clean the AGCM compiled information

Make cleannemol: clean the OGCM compiled information

Make cleancice: clean the AGCM compiled information

Make clean: clean the coupler compiled information

4. Run model

4.1 Setup the experiment

We will introduce the input data structure before running a job. The input data is in the same directory of model code. You can find it in

cd $Yourdir/NESM-BGC/data There are five sub‐folders in this directory, which include the input file of AGCM, OGCM, Sea ice model, ocean biogeochemical model, and the coupler; in additional the restart file and greenhouse gas data is also provided in data and restart_pi

The echam5, cice, NEMO and OASIS folder include the atmospheric model, ocean model and sea ice model and OASIS coupler input files. The PISCES folder contains the ocean biogeochemical input files

Here we provide 1 script to perform the 1% CO2 experiment.

The first section of the script is the job system and HPC settings, they could be different in difference HPC. Here, we used the UHHPC as the example, and the steps as following:

The second section of the script is the experiment setting, as shown following:

The information in the first two sections could be modified by the users, while the rest of script is no need for modification.

4.2 Submit job:

Type 8 sbatch 1%test

5. Plot model results

The ocean and sea ice output NESM model are nc files, while one step is necessary to convert the AGCM output to nc file, which is the same as ECHAM6 model post process procedure. The afterburner tool can be download at https://code.mpimet.mpg.de/projects/afterburner.

PS: If you have any question in running the model, please contact me at [email protected] or [email protected].

Reference:

Cao, J., Wang, B., Xiang, B., Li, J., Wu, T., Fu, X., Wu, L. Min, J.: Major modes of short-term

climate variability in the newly developed NUIST Earth System Model (NESM). Adv.

Atmos. Sci., 32(5), 585–600, doi: 10.1007/s00376-014-4200-6, 2015.

Craig, A., S. Valcke, and L. Coquart, 2017: Development and performance of a new version of

the OASIS coupler, OASIS3-MCT_3.0. Geosci. Model Dev. Discuss., 1–23,

doi:10.5194/gmd-2017-64. https://www.geosci-model-dev-discuss.net/gmd-2017-64/.

Hunke, E. C., and Lipscomb, W. H.:CICE: The Los Alamos Sea Ice Model Documentation and

Software User’s Manual Version 4.1. LA-CC-06-012, T-3 Fluid Dynamics Group, Los

Alamos National Laboratory, Los Alamos N.M, 2010.

Roeckner, E., and Coauthors.: The atmospheric general circulation model ECHAM 5. PART I:

Model description. Rep. No. 349, Max-Planck-Institut f¨ur Meteorologie, Hamburg,

Germany, 2003.