Community Coupler C-Coupler1 User's Guide
Contents
1. with more than 23000 lines of source code programmed by C Coupler team Guided by the objective coupling functions of C Coupler project C Coupler1 0 achieves the following functions 1 Flux computation C Coupler1 0 provides flux computation function for climate system models through integrating existing flux algorithms such as the flux algorithms in NCAR CPL6 Craig et al 2005 2 3D coupling Besides 2D coupling C Couplerl 0 provides 3D data 3 3 4 5 6 7 8 communication and 3D data remapping to support the coupling of 3D variables User friendliness C Coupler1 0 has not achieved all targets in user friendliness of the C Coupler project It tries to facilitate the work in running models on the C Coupler platform Modularity and extendibility C Coupler1 0 is a modularized library with object oriented code structure It provides Fortran interfaces for coupling component model and interfaces for integrating external algorithms External algorithms can be either in Fortran or C Parallelization C Coupler1 0 is a parallel library based on the MPI parallel programming model which achieves the same bit identical results when using any number of processor cores It supports model coupling in parallel and also supports the parallel execution of component models where 1D and 2D parallel decomposition on horizontal grid is supported It uses multiple executables for coupled models It enables direct coupling bet2. G W Yang Z Y Song and F L Qiao 2013b The Flexible Global Ocean Atmosphere Land System Model Grid point Version 2 FGOALS g2 Adv Atmos Sci 30 3 543 560 Lin P E and Coauthors 2013 Long term Stability and Oceanic Mean State Simulated by the Coupled Model FGOALS s2 Adv Atmos Sci 30 1 175 192 Liu H L Zhang X H Li W Yu Y Q Yu R C 2004a A eddy permitting oceanic general circulation model and its preliminary evaluations Adv Atmos Sci 21 675 690 29 Liu H L Y Q Yu W Li and X H Zhang 2004b Manual for LASG IAP Climate System Ocean Model LICOM1 0 Science Press Beijing 1 128 in Chinese Liu H L P F Lin Y Q Yu and X H Zhang 2012 The baseline evaluation of LASG IAP Climate system Ocean Model LICOM version 2 0 Acta Meteorologica Sinica Liu J Sensitivity of sea ice and ocean simulations to sea ice salinity in a coupled global climate model Science in China Series D Earth Sciences 53 6 911 916 2010 Liu L R Li G Yang B Wang L Li Y Pu 2014 Efficient Parallelization Strategies for the Finite Difference AGCM on Modern High Performance Computers Submited to Journal of Atmospheric and Oceanic Technology minor revision Oleson K W Y Dai and Coauthors 2004 Technical description of the Community Land Model CLM NTIS PB2004 105836 Redler R S Valcke and H Ritzdorf 2010 OASIS4 a coupling software for next generation
3. The version 2 of LICOM LICOM2 is used in FGOALS g2 Comparing with LICOMI1 0 and LICOM1 1 LICOM2 increases the horizontal resolutions 1 x1 horizontal resolution with 0 5 meridional resolution in the tropics and adjusts vertical resolution 10m each layer in the upper 150m firstly Wu et al 2005 Secondly the advection scheme is introduced Xiao et al 2006 Thirdly the physical processes are updated or improved Liu et al 2012 including the mixing schemes Canuto et al 2001 2002 Liu et al 2012 solar penetration scheme Lin et al 2007 Lin et al 2011 etc Liu et al 2012 Several updated schemes are not adopted in the latest versions of FGOALS Lin et al 2012 The details can be found in Liu et al 2012 and Lin et al 2012 2 1 3 Land surface models 2 1 3 1 CoLM and CLM3 CoLM Dai et al 2008 and CLM3 Oleson et al 2004 are two main branches of the early Common Land Model Dai et al 2003 2004 for further development of land surface models The Common Land Model is a third generation land surface model based on the Biosphere Atmosphere Transfer Scheme BATS the Institute of Atmospheric Physics Land Surface Model IAP94 and the Land Surface Model LSM Due to its outstanding simulation performance it was selected to be the land surface model in the CCSM Community Climate System Model model from the National Center for Atmospheric Research NCAR and was further developed by NCAR At the same tim
4. 013 1 023 doi 10 1175 BAMS 84 8 1013 Dai Y R E Dickinson and Y P Wang 2004 A two big leaf model for can opy temperature photosynthesis and stomatal conductance J Clim 17 2 281 28 2 299 doi 10 1175 1520 0442 2004 017 lt 228 1 ATMFCT gt 2 0 CO 2 Dai Y DY Ji 2008 The Common Land Model CoLM Technical Guide at http globalchange bnu edu cn download doc CoLM CoLM_Technical_Guide p df Hill C C DeLuca V Balaji M Suarez and A da Silva 2004 Architecture of the Earth System Modeling Framework Comput Sci Eng 6 18 28 Jacob R J Larson and E Ong 2005 M x N Communication and Parallel Interpolation in Community Climate System Model Version 3 Using the Model Coupling Toolkit Int J High Perform C 19 293 307 Larson J R Jacob and E Ong 2005 The Model Coupling Toolkit A New Fortran90 Toolkit for Building Multiphysics Parallel Coupled Models Int J High Perform C 19 277 292 Li L B Wang L Dong L Liu S Shen N Hu W Sun Y Wang W Huang X Shi Y Pu G Yang 2013a Evaluation of Grid point Atmospheric Model of IAP LASG version 2 GAMIL2 Advances in Atmospheric Sciences 30 3 855 867 Li L J P F Lin Y Q Yu B Wang T J Zhou L Liu J P Liu Q Bao S M Xu W Y Huang K Xia Y Pu L Dong S Shen Y M Liu N Hu M M Liu W Q Sun X J Shi W P Zheng B Wu M R Song H L Liu X H Zhang G X Wu W Xue X M Huang
5. 19 6 3 SAA ETA 20 6 4 Frequency of writing restart file sse 20 6 5 Nonleap year and leap year rennen enne nnne enne 20 6 6 X Experiment description eos ee eR e Pin RH ENSE e SIN A Ea SEEE 21 6L Parallelset ngs i s sone dee O 21 6 8 A rrt uper pa ierra e err pete 21 6 9 Directories of source code rennen iai tinneas 22 6 10 Namelist of component model 23 To Computer sy stems is ca eiecti et a en UD e RO DEZ RT Ee LX LENZ RE En seat 24 7 1 Recommended system setups asie eiaeia e ei aeaaea aeiia naar iri ias 24 7 2 High performance computers essent enne 24 8 sDownl ad c toUere t it ae reet 25 9 Frequently Asked Questions ts piriana rdeci asian piigi pra iiia 26 10 Copyright ster pee T a a NE 27 iu EM 28 1 Introduction 1 1 Brief introduction to coupler Climate system model or earth system model is an important tool for global climate change study It is always a coupled model consisting of several component models which are coupled together with a coupler to simultaneously simulate the variation of atmosphere ocean land surface sea ice etc With the fast development of science and technology there are more and more coupled models as well as component models in the world For example there are more than 50 coupled model versions participating in the Coupled Model Intercomparison Project Phase 5 CMIP5 Coupler Valcke et al 2012 is a key component for model developmen
6. J Anderson I Held M Winton J Durachta S Malyshev and R J Stouffer 2006 The Exchange Grid a mechanism for data exchange between Earth System components on independent grids In Proceedings of the 2005 International Conference on Parallel Computational Fluid Dynamics College Park MD USA Elsevier 2006 Bellenger H Guilyardi E Leloup J Lengaigne M Vialard J 2013 ENSO representation in climate models from CMIP3 to CMIP5 Climate Dyn DOI 10 1007 s00382 013 1783 z Canuto V M A Howard Y Cheng and M S Dubovikov 2001 Ocean Turbulence Part I One Point Closure Model Momentum and Heat Vertical Diffusivities J Phys Oceanogr 31 1413 1426 Canuto V M A Howard Y Cheng and M S Dubovikov 2002 Ocean Turbulence Part II Vertical Diffusivities of Momentum Heat Salt Mass and Passive Scalars J Phys Oceanogr 32 240 264 Craig A P M Vertenstein and R Jacob 2012 A New Flexible Coupler for Earth System Modeling developed for CCSM4 and CESM1 Int J High Perform C 26 1 31 42 doi 10 1177 1094342011428141 Craig A P R L Jacob B Kauffman T Bettge J W Larson E T Ong C H Q Ding Y He 2005 CPL6 The New Extensible High Performance Parallel Coupler for the Community Climate System Model International Journal of High Performance Computing Applications 19 3 309 327 Dai Y et al 2003 The Common Land Model CLM Bull Am Meteorol Soc 84 1
7. linux stands for common single node server with multiple cores 7ansuol00 stands for the high performance computer Tansuo100 in Tsinghua University JAP_avatar stand for the high performance computer avatar in Institute of Atmospheric Physics IAP Chinese Academy of Sciences CAS FIO HPC stands for a high performance computer in the First Institution of Oceanography FIO State Oceanic Administration SOA If users want to use the C Coupler platform on new high performance computer we d like to help migrate to the computer and integrate the configuration information of the computer into the C Coupler platform 24 S Download Users can download a model experiment as well as the C Coupler model platform from a SVN server of the C Coupler platform in a simple way Given that exp_setups tar is a package of experimental setups of an experiment users can download this experiment with command checkout_experiment exp_setups tar local_env where checkout_experiment is a script which has been introduced in Section 3 4 and local_env is a file with environment variables Table 4 lists out all environment variables in local_env After downloading the experiment users can follow Section 4 to create configure compile and run the experiment The local computer for downloading the experiment must have installed two kinds of tools SVN and FTP such as wget Iftp and curl Table 4 Environment variables for downloading experiment En
8. or library specifies its own 22 directories of source code Given a component model comp_name with type comp_type its directories of source code are specified in file config comp type comp name form src sh Given a library with name ib name ts directories of source code are specified in file config lib lib_name form src sh Please clean related objective and executable files after modifying source code directories 6 10 Namelist of component model Given a component model comp name with type comp type its namelist is generated by file config comp type comp name config sh Please modify config sh to modify the namelist Please do not modify the namelist file under the run directory of the model experiment 23 7 Computer systems 7 1 Recommended system setups We recommend users to use Linux operating system for the C Coupler platform as well as models and experiments We propose users to use Intel compiler including Fortran C and C with the version around 11 and Intel MPI library with the version around 3 for compiling the source code For Netcdf library we propose to use the version around 4 7 2 High performance computers Currently the C Coupler platform successfully runs on several high performance computers Under the directory config common machine of the C Coupler model platform there are 4 machines corresponding to the environment variable MACH generic linux Tansuol00 IAP avatar and FIO_HPC generic
9. A component model always simulates a component or a process of the earth Component models are classified into categories e g atmosphere model land model ocean model sea ice model wave model etc Coupled model A coupled model always consists of several component models Experiment model An experiment model is a version of model which is ready for simulation Generally it can be any kind of models such as single column model stand alone component model regional coupling model air sea coupling model nested model climate system model earth system model etc On the C Coupler platform we always use compset to stand for experiment model Experiment models are always built from existing component models or existing coupled models such as the models participating CMIP5 An experiment model can also be new version of coupled model with several component models which are never coupled together before Model experiment Model experiment is a simulation based on certain experimental setups of an experiment model for scientific research purposes A new model experiment can be evolved from existing model experiments C Coupler platform The C Coupler platform is a platform also known as runtime environment for using the models with C Coupler for simulation It 5 provides the functions of creating configuring compiling running and downloading model experiment This user reference manual is mainly for introducing the C Coupler
10. Community Coupler C Coupler1 User s Guide Li Liu Ruizhe Li Cheng Zhang Guangwen Yang Bin Wang liuli cess tsinghua edu cn Ministry of Education Key Laboratory for Earth System Modeling Center for Earth System Science CESS Tsinghua University Beijing China 1 February 2014 Content IS AAA A ce PH GER RR ER RET ERAS 1 1 1 Brief introduction to coupler essent 1 1 2 C Coupler profecia tirada pee de ree eie iria 1 1 3 AA eee deett eri am ee Ree ME 3 1 4 General terms for C Coupler eese rennen nennen 5 1 5 How to use C Coupler platform essent nnns 6 2 Models on C Coupler platformasi hoaina aa ii 7 2 1 Component models tee diei o e e b EU SE E Re RETE 7 2 1 1 Atmosphere models 5 1 Snnt REI RTT RR E EANDEM 7 DAME AMI os etc ER RR UE pie PE 7 2 1 2 Ocean model ette eret ida 8 AA EICOM2 otn OO RN 8 2 1 3 Land surface models eie ite det eet to tre ei FO PI ER ERES Exin 8 2413 1 COEM and GDMO ae eb ad 8 2 1 4 SEA ICS models A 9 24b RN 9 2 2 AAA ane HE RE RD PH ETHER CERT HARUM 9 2 2 1 EGOALS 92 teet inet PP EH 9 2 3 Bxpernmentmodels eet Pe titre reete de tte Pe eth dta eee Tenuta dete evene 9 2 3 1 PG OAL SE 9C deze euet terium t tete nete te vb cade 9 2 3 2 GAMI 2 SOL esis hier rre frt crede t e e i CELER ibs ER ERE MER ER ERR ERE 10 2 3 3 Cr AMIE2 GEM S ida 10 3 Directory structures of C Coupler platform sese 11 3 1 Main directo
11. Efficient parallelization C Coupler itself will be parallelized It will provide parallel I O for models With the development of models as well as 2 C Coupler we will continuously improve the parallel efficiency especially when the resolution gets higher 8 Standardization C Coupler will provide uniform standards for integrating component models and external algorithms to facilitate the sharing of component models and algorithms among various coupled models 9 Automatic error detection C Coupler will provide various kinds of automatic error detection to help users to detect and fix bugs in constructing a coupled model 10 Reliability We will build an increasing number of test cases for C Coupler based on the various coupled models using it Before releasing a new version C Coupler must pass all test cases 11 Reproducibility of model simulation results C Coupler platform will provide the function of managing model simulation It will formulate the rules for reproducing simulation results The information for reproducing simulation results will be automatically generated by the C Coupler platform 12 Free and good service As the team of developing C Coupler we will try our best to provide free and good service for various users Any new requirements are possibly included in the future plan of C Coupler development 13 C Coupler1 0 C Coupler1 0 is the first version of C Coupler for public use It is mainly programmed by C
12. del experiment from a default setup or from an existing experiment We encourage users to use an existing experiment but not a default setup to minimize modification of configuration information for a new experiment 4 2 1 New model experiment from default setup To create a new model experiment from a default setup users should run command create_newcase experiment env under the directory scripts of the C Coupler model platform where create newcase is the script for creating experiment and experiment env is a parameter file with environment variables of the experiment COMPSET CASEROOT and MACH must be set in experiment env If CODEROOT CONFIGROOT and DATAROOT are set in experiment env they will be used as private environment variables of the experiment For example with the environment variables in Table 2 users can create an experiment of model FGOALS gc under the directory home liuli model_experiments FGOALS gc RCP26 Table 2 An example of environment variables for creating a new experiment COMPSET FGOALS gc CASEROOT home liuli model_experiments FGOALS gc RCP26 MACH Tansuo100 CODEROOT home liuli C Coupler platform C Coupler Model Platform models CONFIGROOT home liuli C Coupler platform C Coupler Model Platform models DATAROOT home liuli C Coupler_platform inputdata 15 4 2 2 New experiment from an existing experiment The C Coupler platform provides the utility of creating a new exper
13. del platform where model_name is the experiment model It contains a subdirectory coupler and a file compset settings The subdirectory coupler stores the configuration files for driving C Coupler runtime software system There are two sections in the file compset settings common and model Section common records overall information of the experiment model including component models libraries and a template of namelist Section model records information of each component model including realname real name of the component model grid label of model grid type type of component model including atm ocn Ind sice wave cpl etc etc 18 6 Configuration Information of Model Experiment We suggest users go to the private working directory of a model experiment to check and modify configuration information of this model experiment Please do not modify the shared directory config of the whole C Coupler platform Please do not modify any file under subdirectory run of experiment working directory such as namelist files because these files are temporal and generated by the scripts configure and compile according to the configuration files under directory config of experiment working directory Note that the experiment model compset for an experiment cannot be modified If users want use another experiment model for simulation please create a new experiment For reproducibility of model simulation result if the configuration informatio
14. e the Common Land Model was further developed by the cooperation between Beijing Normal University and University of Texas at Austin 2 1 4 Sea ice models 2 1 4 1 CICE4 LASG The CICE4 LASG is an improved version of CICE4 Los Alamos sea ice model version 4 0 http climate lanl gov Models CICE It is the sea ice component in the FGOALS g2 model The main difference between CICE4 LASG and CICE4 is the simulation of sea ice salinity CICE4 uses an unchanged vertical salinity profile while CICE4 LASG formulates salinity variations and designs a simple parameterization accordingly More information about CICE4 LASG could be found in Wang et al 2009 and Liu 2010 2 2 Coupled models 2 2 1 FGOALS g2 FGOALS g2 Flexible Global Ocean Atmosphere Land System Model Grid point version2 Li et al 2013b is a coupled climate system model developed mainly in the LASG IAP FGOALS g2 consists of GAMIL2 LICOM2 CICE4_LASG and CLM3 using NCAR coupler CPL6 for model coupling Recently FGOALS g participated in several model intercomparison projects e g CMIP5 and PMIP3 Paleoclimate Modelling Intercomparison Project Phase 3 and showed good performance on ENSO Bellenger et al 2013 and other aspects 2 3 Experiment models 2 3 1 FGOALS gc FGOALS gc is a version of FGOALS g2 by replacing the coupler CPL6 with C Coupler1 0 In FGOALS gc C Coupler1 0 integrates the scientific algorithms in CPL6 such as flux algorithms and work
15. e simulation time restarted from The format of variable run restart date is YYYY MM DD When these variables are different from that in the restart data files simulation cannot be restarted 3 Configure the current experiment 6 3 Start time and stop time Variables run_start_date and run_start_second in Section common of file config common case conf specify the start time of model experiment while run_stop_date and run_stop_second specify the stop time The format of variables run_start_date and run_stop_date is Y Y Y Y MM DD Please configure the model experiment after the modification Frequency of writing restart file Variables rest freq unit and rest freq count in Section common of file config common case conf specify the frequency of writing restart file rest freq unit is the unit of frequency which can be seconds days months or years For example given rest freq unit days and rest freq count 5 the frequency of writing restart file is per 5 days Please configure the model experiment after the modification 6 5 Nonleap year and leap year Variable leap year in Section common of file config common case conf specifies whether leap year is on If it is true leap year is on Otherwise leap year is off 20 Please configure the model experiment after the modification 6 6 Experiment description Variable case_desc in Section common of file config common case conf specifies the desc
16. earth system modeling Geosci Model Dev 3 87 104 doi 10 5194 gmd 3 87 2010 2010 Valcke S V Balaji A Craig C DeLuca R Dunlap R W Ford R Jacob J Larson R O Kuinghttons G D Riley and M Vertenstein 2012 Coupling technologies for Earth System Modelling Geosci Model Dev 5 1589 1596 2012 Valcke S 2013 The OASIS3 coupler A European climate modelling community software Geosci Model Dev 6 373 388 doi 10 5194 gmd 6 373 2013 Wang B H Wan Z Z Ji X Zhang R C Yu Y Q Yu and H L Liu 2004 Design of a new dynamical core for global atmospheric models based on some efficient numerical methods Science in China A 47 4 21 Wang X C J P Liu Y Q Yu H L Liu and L J Li 2009 Numerical simulation of polar climate with FGOALS g1 1 Acta Meteorologica Sinica 67 961 972 in Chinese 30 Wu F H Liu W Li and X Zhang 2005 Effect of adjusting vertical resolution on the eastern equatorial Pacific cold tongue Acta Meteor Sinica 24 1 12 Xiao C 2006 Adoption of a two step shape preserving advection scheme in an OGCM and its coupled experiment M S thesis Institute of Atmospheric Physics Chinese Academy of Sciences 89pp in Chinese Yoshimura H and S Yukimoto 2008 Development of a Simple Coupler Scup for Earth System Modeling Meteorology and Geophysics 59 19 29 Yu R 1994 A test for numerical weather prediction of real time for china flood s
17. eason precipitation in 1993 by a regional eta coordinate model Scientia Atmospherica Sinica 18 284 292 Zhang X and X Liang 1989 A numerical world ocean general circulation model Adv Atmos Sci 6 43 61 31
18. ecified in file config comp_type comp_name compiler cfg Given a library with name ib_name its specific compilation optimizations are specified in file config lib lib name compiler cfg The common compilation options depend on the machine computer platform that the model experiment runs on Given a machine with name mach_name the common compilation options are specified in file config common machine mach_name common_compiler mach_name cfg Please clean related objective and executable files after modifying compilation options The following table shows the meaning of main variables in the common_compiler mach_name cfg file Variable Meaning FC Fortran compiler CC C compiler CXX C compiler CPP Tool for precompiling according to macro definition AR Tool for building library LD Linker for all objective files for generating executable file CFLAGS Compiling options for CC C compiler FFLAGS Compiling options for FC Fortran compiler CXXFLAGS Compiling options for CXX C compiler CPPFLAGS Compiling options for CPP precompiling LDFLAGS Compiling options for LD linker ULIBS Compiling options of linking libraries for LD linker NETCDFINC Directory of NetCDF header files NETCDFLIB Directory of NetCDF library files MPIINC Directory of MPI compiler header files MPILIB Directory of MPI compiler library files 6 9 Directories of source code On C Coupler platform each component model
19. ed models in a user friendly way and to integrate various models on the same model platform for sharing Under this mission C Coupler is designed to be a coupler framework which can generate various coupler instances for different kinds of coupled models with a series of objective coupling functions as follows 1 2 3 4 5 6 7 Flux computation C Coupler will integrate flux algorithms such as the algorithms to calculate flux variables between atmosphere and ocean to provide the function of flux computation 3D coupling Besides traditional 2D coupling C Coupler will provide 3D data communication and 3D data remapping to enable the coupling of 3D variables Model nesting C Coupler will support one way and two way model nesting to facilitate the work of nesting regional models Ensemble C Coupler will be able to integrate ensemble packages or ensemble algorithms Multiple instances of model simulation can be run simultaneously on the same platform User friendliness C Coupler will provide various coupling functions in a user friendly way C Coupler will try to facilitate the work in integrating component models constructing coupled models integrating external algorithms and running models Modularity and extendibility C Coupler will provide modular and extendible software framework for coupling various component models and integrating various algorithms such as flux algorithms and remapping algorithms
20. iling running and downloading model experiment config is used to store configuration information for component models experiment models machines etc After creating a new model experiment the working directory of the model experiment is created by the C Coupler platform Please do not change the directory structure of the C Coupler model platform and input data as possible 3 2 Directory structure of input data Similar to models the input data includes several sub directories e g atm ocn Ind sice cpl and grids to respectively store the input data of atmosphere models ocean models land surface models sea ice models couplers model grids etc Each sub directory stores the input data of several component models 3 3 Directory structure of models models includes several sub directories e g atm ocn Ind sice cpl and libs to respectively store the source code of atmosphere models ocean models land surface models sea ice models couplers libraries etc Each sub directory stores the source code of several component models or libraries C Coupler can work as a component or a library for coupling Currently its code is stored under the directories models cpl c coupler and models libs c_coupler 11 3 4 Directory structure of scripts Under script there are several scripts create_newcase configure compile clean runcase checkout experiment register_platform csh register platform sh The former five script
21. iment from an existing experiment Given an existing experiment old_exp with experimental setup package old_exp setup tar users can create a new experiment new_exp from old_exp setup tar under the following steps 1 Create the working directory of new_exp 2 Goto the working directory of new_exp and then untar old_exp setup tar 3 Modify environment variable MACH and set CODEROOT CONFIGROOT and DATAROOT as private environment variables in file config common env if necessary 4 3 Configure experiment To configure an experiment users should run command configure under the working directory of model experiment All experimental setups of the experiment are automatically packed into a tar file under sub directory configure_history where the time of configuring recorded in the file name is a keyword Before configuring users should view and modify configuration information experimental setups Please refer Section 6 for details 4 4 Compile experiment model To compile an experiment model users should run command compile under the experiment working directory of the model The log files of compilation are stored under the sub directory run of the experiment working directory Users can run command clean para to remove objective files produced by compilation where para means parameter for clean The parameter can be the name of a component model or a library or all For command clean all all files pr
22. ith several component models which are never coupled together before 2 1 Component models 2 1 1 Atmosphere models 2 1 1 1 GAMIL2 GAMIL is an AGCM developed mainly in the National Key Laboratory for Numerical Modeling of Atmospheric Sciences and Geophysical Fluid Dynamics LASG Institute of Atmospheric Physics IAP Chinese Academy of Sciences CAS which has taken part in various international model intercomparison projects and has been widely used for various science problems studies GAMIL is based on the Eulerian finite difference dynamical core Its discrete grid includes a hybrid horizontal grid with the Gaussian grid for low resolution or uniform grid for high resolution in the low and middle latitudes region and a weighted even area grid in the high latitudes and polar region and 26 0 vertical levels pressure normalized by surface pressure with the model top at 2 194hPa Its dynamical core includes a finite difference scheme that conserves mass and effective energy Wang et al 2004 and a two step shape preserving advection scheme for the moisture equation Yu 1994 GAMIL2 is the second version of GAMIL It is the atmospheric component of the climate system model FGOALS g2 More detailed information of GAMIL2 can be found in Li et al 2013a 2 1 2 Ocean models 2 1 2 1 LICOM2 LICOM is the fourth generation of LASG OGCM Liu et al 2004a 2004b since the first generation developed in 1989 Zhang and Liang 1989
23. n of an experiment is modified users should configure the experiment run the command configure before running it Then configuration information of the experiment will be stored automatically to facilitate reproducing model simulation result 6 1 Experiment name and working directory The name of a model experiment is the same as the name of the working directory When users want to modify the experiment name or migrate the model experiment to another directory please take the following two steps 1 Move or copy the experiment to a new working directory 2 Configure the experiment under the new working directory with command configure Then users can run the experiment after compilation 6 2 Initial run or restart run There are two choices to start a simulation initial run and restart run For initial run please set variable run_type in Section common of file config common case conf to initial and then configure the experiment For restart run from the original experiment please take the following steps 19 1 Set variable run_type in Section common of file config common case conf to restart 2 Set variables original case name original config time run restart date and run restart second in Section common of file config common case conf Original case name and original config time specify the name and configuration time of the original experiment run restart date and run restart second specify th
24. oduced by compilation will be removed 16 4 5 Run experiment To run an experiment users should run command runcase under the experiment working directory Note that runcase is common to any kind of experiments on any kind of hardware platforms 17 5 Configuration information of models 5 1 Configuration information of component models The configuration information of a component model is under directory config model_type model_name of the C Coupler model platform where model_type and model_name are type and name of component model respectively There are six files including field_buf_register cfg private_field_attribute cfg config sh form_src sh compiler cfg and build sh File field_buf_register cfg records fields which should be registered by component model File private_field_attribute cfg records information for outputting private model fields not coupling fields of component model File config sh is a script for generating private namelist of component model File form_src sh is a script which specifies source code directories of component model File compiler cfg is a file which specifies private compiling options of component model File build sh is a script for compiling component model which can generate some header files 5 2 Configuration information of experiment models The configuration information of an experiment model is under directory config compset model_name of the C Coupler mo
25. platform 1 5 How to use C Coupler platform The C Coupler platform provides utilities to facilitate model experimenting shown in Figure 1 The first step is to create an experiment from a default setup or an existing experiment Then users can check and modify experimental setups under the working directory of the experiment After that user should configure the experiment and then compile the source code Before the compilation users can remove some objs or executables when necessary After the compilation users can run the experiment for simulation results If users want further simulation after analyzing simulation results they can improve experimental setups or create a new experiment Remove obj from p compilation H Check and modify experimental setup Configure experiment Compile model code Create experiment From default Experimental experiment results experiment From existing experiment Figure 1 Flowchart for model experimenting on C Coupler platform 2 Models on C Coupler platform Models on the C Coupler platform include component models coupled models and experiment models Any kinds of component models and coupled models can be integrated in Experiment models are always built from existing component models or existing coupled models using C Coupler for coupling and using the C Coupler platform for experimenting An experiment model can also be new version of coupled model w
26. ries of C Coupler platform eseesseeeeeeneeneenennn 11 3 2 Directory structure of input data essent 11 3 3 Directory structure of models esses eene 11 3 4 Directory structure of scripts riean a ata ikter atia nne 12 3 5 Directory structure of config esee eene nennen nennen nennen nennen 12 3 6 X Structure of working directory of model experiment sss 12 4 Create configure compile and run model experiment sene 14 4 1 Environment Variables M M 14 4 22 Create model ex periments tse tee iter ne det lea dboucesscungedaastondeoesntersestonses 15 4 2 1 New model experiment from default setup sse 15 4 2 2 New experiment from an existing experiment c occcnccncnnnnnnnnnnannnonnnanana cnn ncnncnnannnincnns 16 4 3 Configure experiment eie ettet bride eie IE Dr de ove deae ted etatis 16 4 4 Compile experiment mod l iia ii iaai aenta iae i Aeaeeia tao i eadair sitea taisit 16 A TN 17 5 Configuration information of models sse nennen 18 5 1 Configuration information of component models sse 18 5 2 Configuration information of experiment models sese 18 2 6 Configuration Information of Model Experiment sess 19 6 1 Experiment name and working directory coccoccncnnnnncnnananinonanananinana nana nn anna rnn anar cnn cnica 19 62 CUEVA ATT
27. ription of model experiment This description will be written into output data file through C Coupler I O utility Please configure the model experiment after its modification Experiment description is important for comparing evaluating and reproducing simulation result We propose the providers of experiment leave their names even email into the description 6 7 Parallel settings Variables num_thread num_x_proc num_y_proc and num_total_proc in Section model of file config common case conf specify parallel settings of the corresponding component model num_thread is the number of threads e g OpenMP threads num_x_proc and num_y_proc are the numbers of processes on two directions which is useful for 2D parallel decomposition These two variables must be set or unset at the same time num_total_proc is the number of total processes If num_x_proc and num_y_proc are set num_total_proc must be the multiple of um_x_proc and num_y_proc Please configure the model experiment after modifying parallel setting For the experiment models which use macro define to control parallelism but not namelist please clean obj files and recompile the source code 6 8 Compilation options The compilation options of a component model or library consist of its specific compilation options and common compilation options for the whole experiment model Given a component model comp_name with type comp_type its specific 21 compilation options are sp
28. s are used for creating configuring compiling deleting compiled objective files and running for model experiments checkout experiment is used for checking out a model experiment from a SVN server include configuration information source code and input data register platform csh and register platform sh are used for registering environment variables for the C Coupler model platform Besides these scripts there is a sub directory utils which stores the common tools for these scripts 3 5 Directory structure of config config includes several sub directories e g atm ocn Ind sice cpl lib compset and common which stores default configuration information for atmosphere models ocean models land surface models sea ice models couplers libraries experiment models and common tools Each sub directory stores the configuration information of several models or libraries 3 6 Structure of working directory of model experiment Each model experiment has its own working directory Users should go to the working directory for configuration compilation and execution of the model experiment After configuration under the working directory there are four scripts e g configure compile clean and runcase and several sub directories utils config configure history job logs and run These four scripts and utils are copied from the scripts directory of the C Coupler model platform config stores the configuration information related to
29. s as a component which takes physical processor cores FGOALS gc achieves the same bit identical simulation result no matter the number of processor cores for each component In the original version 9 FGOALS gc achieves the same bit identical simulation result with FGOALS g2 In the latest version of FGOALS gc GAMIL2 is updated the version with 2D parallel decomposition Liu et al 2014 and upgrade of TSPAS advection implementation 2 3 2 GAMIL2 sole GAMIL2 sole is a version of GAMIL2 for sole component run GAMIL2 sole shares the same version of GAMIL2 with FGOALS gc GAMIL2 sole achieves the same bit identical simulation result no matter the number of processor cores used 2 3 3 GAMIL2 CLM3 GAMIL2 CLM3 is a coupled model with GAMIL2 and CLM3 In GAMIL2 CLM3 C Coupler1 0 works as a library for coupling without taking additional processor cores GAMIL2 CLM3 achieves the same bit identical simulation result no matter the number of processor cores for each component 10 3 Directory structures of C Coupler platform 3 1 Main directories of C Coupler platform The C Coupler platform consists of two packages the C Coupler model platform and input data In the C Coupler model platform there are three main directories models scripts and config models is used to store source code of each component model and each library scripts is used to store scripts for using the C Coupler platform such as creating configuring comp
30. t It achieves effective interaction and parallel computation among multiple component models and controls the integration of the whole coupled model It also provides a platform to make scientists and engineers cooperate together Most of state of the art climate system models and earth system models are constructed with couplers With more and more component models e g land ice model chemistry model and biology model to be added into earth system model coupler becomes more and more important to the development of earth system models There are several existing couplers e g OASIS Redler et al 2010 Valcke 2013 MCT Larson et al 2005 Jacob et al 2005 ESMF coupler Hill et al 2004 FMS coupler Balaji et al 2006 Scup Yoshimura and Yukimoto 2008 CPL6 Craig et al 2005 CPL7 Craig et al 2012 etc 1 3 C Coupler project C Coupler with its platform also known as runtime environment is an open source community coupler developed in China There was no coupler developed for earth system model in China before The coupled models developed in China always 1 use CPL6 MCT and OASIS for model coupling For example almost all coupled models for CMIP5 developed by Chinese institutions use CPL6 To help the development of earth system models in China China initiated the C Coupler project in 2010 The most important mission of developing C Coupler is to provide various coupling functions for various coupl
31. the current model experiment It is oriented from the config directory of the C Coupler model platform configure history stores the package of experimental setups after every configuration by users for reproducing model 12 simulation result job_logs stores the log of every model run run stores files related to model compiling and model run for each component model and library including namelist input data output data source code for compilation and objective and executable files produced by compilation Given a component model with name model_name and type e g atm ocn Ind sice model_type the namelist input data as well as output data are under the directory run model_type model_name data the objective files produced by compilation are under the directory run model_type model_name obj the executable file is under the directory run model_type model_name exe the log files of compilation are under the directory run model_type model_name build_logs and the log files of component model run are under the directory run model_type model_name run_logs 13 4 Create configure compile and run model experiment As shown in Section 1 5 users can create configure compile and run model experiment 4 1 Environment variables Table 1 lists out the environment variables for model experiments COMPSET CASEROOT and MACH are specific to each experiment As the C Coupler platform is a shared platform for various models and vario
32. us experiments DATAROOT CODEROOT and CONFIGROOT are always common environment variables Users can use command such as source register platform sh or source register_platform csh to set CODEROOT and CONFIGROOT as common environment variables and use command such as source register_inputdata sh or source register_inputdata csh to set DATAROOT as common environment variables Users can also set CODEROOT CONFIGROOT and DATAROOT as private environment variables of an experiment Table 1 Environment variables for model experiments Environment variables Description COMPSET compset_name COMPSET is the name of an experiment model which specifies the experiment model for model experiment CASEROOT case_dir CASEROOT specifies the working directory for model experiment where the last level specifies the name of model experiment MACH machine_name MACH specifies the machine to run the model experiment DATAROOT data_dir DATAROOT specifies the root directory of the input data which is always the directory inputdata of the C Coupler platform 14 CODEROOT code_dir CODEROOT specifies the root directory of model code which is always the directory models of the C Coupler model platform CONFIGROOT config_dir CODEROOT specifies the root directory of configuration information of the C Coupler model platform 4 2 Create model experiment There are two approaches to creating a mo
33. vironment variables Description USER username Username for downloading the experiment from the SVN server PASS WORD password Password for downloading the experiment from the SVN server DATAROOT dataroot_dir Local directory for storing input data of the experiment downloading from the SVN server PLATFORMROOT platformroot_dir Loca directory for storing the C Coupler model platform downloading from the SVN server 25 9 Frequently Asked Questions 1 Cannot find MPI and Netcdf header files when compiling Solution Please check the path of compiler use commands such as which mpliifort and then modify compiling option variables MPIINC MPILIB NETCDFINC and NETCDFLIB accordingly please refer Section 6 8 for details 2 Error happens when linking Netcdf library Solution Please check the version of Netcdf to verify the option of linking Netcdf library such as lnetcdf and Inetcdff and then modify compiling option variable VETCDFLIB accordingly please refer Section 6 8 for details 26 10 Copyright C Coupler and the C Coupler platform are protected by copyright and patent They are free and open source software for non commercial usage We encourage users to use them for model coupling simulation etc Models and experiments will keep their own copyrights on the C Coupler platform C Coupler and the C Coupler platform will not infringe these copyrights 27 References Balaji V
34. ween component models for better parallel performance where C Coupler does not take unique executable and processes processor cores Automatic error detection C Coupler1 0 provides several kinds of automatic error detection It can check the order of calling C Coupler interfaces in component models check the consistency of grids between component models and remapping weight files check whether component models provide sufficient coupling variables etc Reliability C Coupler1 0 has passed various test cases with more than 600 diagnostic statements intra its source code There are several standards for testing C Coupler e g C Coupler must achieve the same bit identical result no matter how many processor cores are used C Coupler must achieve the same bit identical result in restart run a coupled model can achieve the same bit identical result after replacing the original coupling approach with C Coupler etc Reproducibility of model simulation results C Coupler1 0 provides the 4 9 function of managing model simulation It formulates rules and automatically records information for reproducing simulation results Free and good service After the public release of C Coupler1 0 we will provide free and good service for constructing various coupled models with C Coupler1 0 1 4 General terms for C Coupler There are several general terms for C Coupler listed out as follows 1 2 3 4 5 Component model
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