HOWTO

==================================
Coastal Act Team  - 9/13/2019

Thanks to all the contributors. 
==================================

Forked latest version of the NEMS software program from the
official NEMS repository at https://github.com/NOAA-EMC/NEMS
git log:
    commit e05bf2a554544093f02bf177658ad432cbafbaa8
    Merge: c8e05a8 95c63cb
    Author: RatkoVasic-NOAA <37597874+RatkoVasic-NOAA@users.noreply.github.com>
    Date:   Fri Sep 13 15:13:28 2019 -0400

 
The purpose of this document is to setup, integrate, compile and run ESMF aware
applications, also known as NUOPC CAP using the NEMS framework which is also an
application of ESMF framework. The idea is to show, with an example, how to add
a new model into a couple system, using the NEMS program.  

To put it simply NEMS consists of a main program and a driver  where  different 
models can integrate into and exchange data at runtime in a standard manner. 

Figure below, depicts simplified relations among the ESMF-NUOPC & NEMS & MODELS 

 Model Coupling       Main Exec.      Models + Interface(CAP)
   Framework          & Driver           to ESMF & Makefile 
                                          Fragment for NEMS
 ==============      ==========       ====================== 
ESMF & NUOPC    -->     NEMS     -->   Mode1(1), Model(2), Model(3), ...

      |                   |                     |
      |                   |                     |
      V	                  V                     V

  libraries of        unifier to       models participating
callable functions    bring models     to be coupled together
designed to couple    together as an   through calls to ESMF & NUOPC(a.k.a CAP)  
     Models           executable       through makefile & manual setup to  NEMS
 
Note: 
     A CAP is a piece of program written in Fortran extending the model  source 
     code through calling the appropriate functions from ESMF & NUOPC frameworks.   
     The models can communicate with one another through CAPs.
  
     A makefile fragment is a section of a makefile that is cut from a makefile
	 and is written into a different file.   A makefile fragment is a part of a 
     whole. So all the parts must fit together like pieces of a puzzle in order
	 to complete the entire makefile. 

*****************************************************************
In rush to use NEMS - below are the required steps for your model
and your computing system and your machine name and your compiler
*****************************************************************
Assumptions:
   NWM     - is the model to be added to the NEMS system     - <MODEL>
   Hera    - is the user computer, machine name              - <COMPUTER>
   rdhpcs  - is the computing system where hera is a node of - <COMPUTING>
   intel   - is the compiler of choice in hera computer      - <COMPILER>
   ROOTDIR - is the directory of your choice in hera where you
             clone the NEMS in

cd ROOTDIR
   
1) git clone --recursive https://github.com/moghimis/ADC-WW3-NWM-NEMS
2) mkdir conf 
3) mkdir modulefiles
4) mkdir modulefiles/<COMPUTER>
5) vi modulefiles/<COMPUTER>/ESMF_NUOPC                           -- see TABLE 1
6) vi conf/configure.nems.<COMPUTER>.<COMPILER>                   -- see TABLE 2 
7) mkdir NEMS/src/incmake/env/<COMPUTING>                         -- if it doesn't exist
8) vi NEMS/src/incmake/env/<COMPUTING>/<COMPUTER>.<COMPILER>.mk   -- see step 4 item c below
9) vi NEMS/src/incmake/env/<COMPUTING>/detect.mk                  -- see TABLE 3
10) vi NEMS/src/incmake/buildenv.mk                                                                                       
  include $(call locate_incmake_file,env/<COMPUTER>/detect.mk)    -- add this line
  include $(call locate_incmake_file,env/uname/detect.mk)         -- must be the last in line
11) cp NEMS/src/incmake/example_component_FOO.mk NEMS/src/incmake/component_<COMPUTER>.mk  
12) vi NEMS/src/incmake/component_<MODEL>.mk                      -- see TABLE 4 
13) vi NEMS/src/module_EARTH_GRID_COMP.F90                        -- copy lines 171 and 3869 and change model name
14) Adjust your model makefile                                    -- see TABLE 5 and component_<MODEL>.mk (step 12)

TABLE 0 depicts above steps in form of tree structure


************************************************************************************
Below instrutions show how to add a new model for the coupling with other models and
how to compile and integrate with the NEMS framwork.
************************************************************************************
 
NEMS is designed to work with different earth system models developed in variety
of Linux based computer systems.   There are two parts for the user to  acheive
to integrate into NEMS program. Apart from developing a NUOPC CAP for the model
to participate in a coupling project, user should write a makefile fragment  in 
the model's makefile to comply with NEMS workflow for a successful integration.
The second part of the user's action requires configuration, setup, and  coding
into NEMS source files. We start with the sencond part first. The first part is
described on step 7. 


Assumptions:
   NWM     - is the model to be added to the NEMS system 
   Hera    - is the user computer, machine name
   rdhpcs  - is the computing system where hera is a node of
   intel   - is the compiler of choice in hera computer with the version of interest
   ROOTDIR - is the directory of your choice in hera

1) cd <ROOTDIR>

2) Get the source codes into <ROOTDIR>

   a) git clone https://github.com/NOAA-EMC/NEMS
      
	  The above command only gets the NEMS code from the official repository. 
	  Most likely, users are required permission from the NEMS administrator
      to access this repo.	  

      Or get the development (a.k.a dev) version of the NEMS code to follow
	  the instruction easier.

   b) git clone --recursive https://github.com/moghimis/ADC-WW3-NWM-NEMS
   
      The development version includes the NEMS code and few model codes
	  such as ADCIRC, WW3, ATMESH.  This version is located in a private 
	  github repository at https://github.com/moghimis . 
	  
	  To clone from dev you should have an account on  github repository
	  with a valid email, username, and a password. You also required to 
	  request a collaborator access to this repo. by sending an email to 
	  saeed.moghimi@noaa.gov. 
   
      During cloning from dev, github asks for a username and password, 
	  which are those you use to login to your github account.

      After the first clone, you should use "git pull" command to access 
	  the latest changes from dev repo.
	
	For user who used 2a), contents are put into TABLEs and they are located
	at the end of instructions. 

3) Setup and configure user environment required by NEMS

    a) Create 4 directories: compsets\   conf\   modulefiles\   parm\  in <ROOTDIR> if
       they do not exist. 
	  
	   Note: These 4 directories are user directories and may or may not be saved as part 
	         of the NEMS source codes. However, there are name dependencies in NEMS code 
			 to these directories.	  

             You should have 5 directories, including NEMS, if cloned by way of 2a). 
             You should have 5 directories, including NEMS, and many models that are
			 integrated into this development version of NEMS (github version), if 
			 cloned by way of 2b).
   
             Since this document is describing the addition of NWM, the final product is 
             also included in development version. As such you should also see NWM final 
		     product & to checkout each step of the instruction as you arrive to them.
		 
    b) mkdir modulefiles/hera           --  this should match the machine name 
   
    c) vi modulefiles/hera/ESMF_NUOPC   --  could be any name 
   
	   Note: This file is to set the compilation  environments for this version of  NEMS and 
	         ESMF and all the participant coupled models. Examples are MPI libraries, NETCDF, 
		     HDF, SZIP, ESMF, Compilers, and more. See <ROOTDIR>/modulefiles/hera/ESMF_NUOPC
			
		 	 The module file name can be any name, however, the directory name "modulefiles" 
		 	 is expected. See <ROOTDIR>/NEMS/src/incmake/configure_vars.mk for detail.
			
             During runtime the contents of this modulefile will be copied into "modules.nems"
			 located at the <ROOTDIR>/NEMS/src/conf/modules.nems
   
    d) vi conf/configure.nems.hera.intel  
      
	   Note: This makefile fragment is the common part of a makefile that applies to all the
             participant coupled models including NEMS itself in Hera computer using intel
			 compiler. See the contents in <ROOTDIR>/conf/configure.nems.hera.intel
	  
	         The name of this makefile is constructed by appending the machine name, "hera", 
	         dotted with compiler selected, "intel", to the constant "configure.nems", formula
			 is configure.nems.{COMPUTER}.{COMPILER}
			    
             We suggest to copy contents of another makefile into this file and modify according
			 to your system. Make sure CC, FC and F77 compiler options are set to the intended 
			 compilers.

    e) Place holder for the <ROOTDIR>/compsets and <ROOTDIR>/parm - TODO
	
4) Setup, configuration, and integration of the machine and user modulefile into NEMS system

    a) ls NEMS/src/incmake/env 
      
	   Look for directory named after your computing system (i.e. rdhpcs).
	  
       Note: There are two types of computing systems that NEMS is concerned with.
	   
	         case 1) The system contains many nodes(computers) such as "rdhpcs" with nodes known as
			         "hera", "gaea", "jet", ...
			   
	         case 2) The system is an stand alone system such as "wcoss"

    b) mkdir NEMS/src/incmake/env/rdhpcs  -- if it doesn't exist 
	
	   In our case "hera" is a machine belong to the "rdhpcs" where other nodes such as "gaea" and
	   "jet" were setup but "hera" was not. So we need to implement "hera" under its parent system 
	   "rdhpcs".

       In case 1), such as our case example, user should create the parent directory in <ROOTDIR>/ 
	   NEMS/src/incmake/env, if it doesn't exist.
	   
	   In case 2), machine name is also the parent and user should create the directory with the node
       name in <ROOTDIR>/NEMS/src/incmake/env, if it doesn't exist.	   
   
    c) vi NEMS/src/incmake/env/rdhpcs/hera.intel.mk
	
	   Under parent directory you must create a makefile fragment with this formula, defined by NEMS
	   {COMPUTER}.{COMPILER}.mk    
	   
	   Note: The parent and the node names are only "strings" and NEMS program does not care what they 
	         are called as long as you are consistant on using the same name in the right place.
	  
       Add below contents to this file or copy from another similar file and then  edit
   
       MACHINE_ID=hera
       FULL_MACHINE_ID=hera
       USE_MODULES=YES
       DEFAULT_MODULE=$(FULL_MACHINE_ID)/ESMF_NUOPC
       BUILD_TARGET=$(FULL_MACHINE_ID).$(NEMS_COMPILER)
       NEMS_COMPILER=intel
       MODULE_LOGIC=$(call ULIMIT_MODULE_LOGIC,200000)

       Note: The first and 2nd lines are the machine name, the third  line is a toggle set to "YES". 
	         This means that NEMS program expects a user defined module file set on the fourth line. 
			 This the user modulefile is the same modulefile we created previousely on step 3 item b
			 called <ROOTDIR>/modulefiles/hera/ESMF_NUOPC. 
			
			 See the file NEMS/src/incmake/configure_rules.mk for more information on the options.

    d) vi NEMS/src/incmake/env/rdhpcs/detect.mk

       The purpose of this file is to locate the machine and find the modules and model codes, etc.
       In order to do so, especially in case 2) where there are many computer nodes under one parent
	   computing system, the task is not that trivial. That is why selection of computing system name
	   and computer name are important to pay attention to.
	   
	   In our case example, file systems /scratch1 and /scratch2 are mounting points on "Hera" node.
	   As a result we added the following statement to the "detect.mk" file to find our machine.
	   
       ifneq (,$(and $(wildcard /scratch1),$(wildcard /scratch2)))
           NEMS_COMPILER?=intel
           $(call add_build_env,hera.$(NEMS_COMPILER),env/rdhpcs/hera.$(NEMS_COMPILER).mk) 
       ...
	   
	   After finding the computer, the code also calls the "add_build_env" function of the NEMS code 
	   and passes "hera.intel" and "NEMS/src/incmake/env/rdhpcs/hera.intel.mk", created on step 4c
	   as arguments to this function in order to build the required environment.
	   
	   In summary, you have to add such statements to each detect.mk file where each node under one 
	   parent can be identified uniquely. There is one such detect.mk file per computer name.

    e) vi NEMS/src/incmake/buildenv.mk 
	 
	   Add the newely created "detect.mk" file to the "buildenv.mk" above the "uname/detect.mk" line.
	   
	   include $(call locate_incmake_file,env/rdhpcs/detect.mk)
       include $(call locate_incmake_file,env/uname/detect.mk)      -- comes last
	  
	   Note: It is important to make sure uname/detect.mk line is always the last line after all other 
             detect.mk lines. Otherwise, uname/detect.mk, if executed, assumes sets the computer name  
             to the result of linux command "uname" which may or may not equate to the machine name you 
			 defined. 		 
		 
             If you do not have your detect.mk file included, you will get an error from systems file
             NEMS/src/incmake/buildenv.mk.
		
5) Setup, configuration, and integration of the model specific compiled files into NEMS system
		
    a) cp NEMS/src/incmake/example_component_FOO.mk NEMS/src/incmake/component_NWM.mk 
	
	   Note: Each model is required to have a makefile fragment using formula component_{model_name}.mk
	         There is a system "example_component_FOO.mk" file that is for this purpose, to copy from it.
	      
		     The selected model_name is significant because this string is like a keyword and is shared
             between the model and the NEMS system. More on this later in this document.
        			 
    b) vi NEMS/src/incmake/component_NWM.mk
	   
	   Through this file NEMS dynamically communicates information about the model's compiled modules location
	   as well as source files location.
	   
	   1) Edit the file by changing the word "FOO" to "NWM" and "foo" to "nwm" without double quotes.
	   
	   2) Further edit this file to match your model's compilation and linkage process. It is best to look
          at this 3 files at the same time to see the connections.
		  
	      - NEMS/src/incmake/component_NWM.mk
		  - $(ROOTDIR)/NWM_INSTALL/nwm.mk  
		  - <ROOTDIR>/NWM/trunk/NDHMS/CPL/NUOPC_cpl/Makefile around line 200, rule $(CAP_MK)
		  
		  OR checkout ADCIRC
		  
	      - NEMS/src/incmake/component_ADCIRC.mk
		  - $(ROOTDIR)/ADCIRC_INSTALL/adcirc.mk 
		  - <ROOTDIR>/ADCIRC/cpl/nuopc/makefile.adc_cap.nuopc lines 73-95

6) Integration of the model CAP into NEMS system

   a) vi NEMS/src/module_EARTH_GRID_COMP.F90 
   
      Edit to add below statements tailored to your model name into two places in this file:

      #ifdef FRONT_NWM
        use FRONT_NWM,        only: NWM_SS  => SetServices
      #endif

      And further down the file also add:

      #ifdef FRONT_NWM
        call NUOPC_DriverAddComp(driver, trim(prefix), NWM_SS, &
             petList=petList, comp=comp, rc=rc)
          if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
                    line=__LINE__, file=trim(name)//":"//__FILE__)) return   
      #else
        write (msg, *) "Model '", trim(model), "' was requested, "// &
                             "but is not available in the executable!"
        call ESMF_LogSetError(ESMF_RC_NOT_VALID, msg=msg, line=__LINE__, &
                                             file=__FILE__, rcToReturn=rc)
        return  ! bail out
      #endif

7) Model makefile specific fragment for NEMS 

   Each model's makefile has to provide following information to the NEMS system:
   
   ESMF_DEP_FRONT     = nwm_nuopc_cap
   ESMF_DEP_INCPATH   = /scratch2/COASTAL/coastal/save/NAMED_STORMS/NEMS_APP/NWM/trunk/NDHMS/CPL/NUOPC_cpl 
                        /scratch2/COASTAL/coastal/save/NAMED_STORMS/NEMS_APP/NWM_INSTALL
   ESMF_DEP_CMPL_OBJS =
   ESMF_DEP_LINK_OBJS = /scratch2/COASTAL/coastal/save/NAMED_STORMS/NEMS_APP/NWM_INSTALL/libnwm_nuopc.a
   ESMF_DEP_SHRD_PATH =
   ESMF_DEP_SHRD_LIBS =
   
   These information are writen to the file $(ROOTDIR)/NWM_INSTALL/nwm.mk from the model's makefile. Related
   section of NWM makefile is shown below:
   
   CAP_DEP_FRONT := nwm_nuopc_cap    # for NEMS, must be same name as its module
   CAP_VERS      := VERSION
   CAP_MK        := nwm.mk           # for NEMS


   $(CAP_MK): 
        @echo $(HR)
        @echo "Generating NUOPC Makefile Fragment"
        @echo
        @echo "# ESMF self-describing build dependency makefile fragment" > $(CAP_MK)
        @echo "" >> $(CAP_MK)
        @echo "ESMF_DEP_FRONT     = $(CAP_DEP_FRONT)" >> $(CAP_MK)
        @echo "ESMF_DEP_INCPATH   = $(CAP_DIR)" >> $(CAP_MK)
        @echo "ESMF_DEP_CMPL_OBJS = " >> $(CAP_MK)
        @echo "ESMF_DEP_LINK_OBJS = $(CAP_DIR)/$(CAP_LIB)" >> $(CAP_MK)
        @echo "ESMF_DEP_SHRD_PATH = " >> $(CAP_MK)
        @echo "ESMF_DEP_SHRD_LIBS = " >> $(CAP_MK)
   
    
   Note: The value of the ESMF_DEP_FRONT is the name of the model's CAP module name and not the model's 
         file name.

8) Model source code locations

   a) cp -rf nwm <ROOTDIR>/NWM
   
   NEMS system expects source codes of all the model participant to be available in the same level 
   directory as NEMS source code. This location is the <ROOTDIR> where we cloned the NEMS. As the last 
   step before compilation, copy your model into <ROOTDIR>
   
9) There are 3 files located in <ROOTDIR> worth noting

   a) model_configure 
   b) nems.configure
   c) build.sh
   d) nems.job
   
    
***************************
To build model(s) with NEMS
***************************

1) got to: <ROOTDIR>/NEMS

   clean and/or distclean before compiling
   
2) make -f GNUmakefile distclean_ADCIRC COMPONENTS="ADCIRC"
   make -f GNUmakefile distclean_NWM COMPONENTS="NWM"
   make -f GNUmakefile distclean_WW3DATA COMPONENTS="WW3DATA"
   make -f GNUmakefile distclean_ATMESH COMPONENTS="ATMESH"
   make -f GNUmakefile distclean_NEMS COMPONENTS="NEMS"
   
   Note: You have to make sure your component_<model_name>.mk and your model's 
         makefile has distclean rule build into it.
   
   build one or more model
   
3) make -f GNUmakefile build COMPONENTS="ADCIRC WW3DATA ATMESH NWM"
   make -f GNUmakefile build COMPONENTS="ADCIRC"

   OR simply, add the new model to <ROOTDIR>/build.sh and while in
   <ROOTDIR> type: ./build.sh


*********************************
TO run NEMS: TODO - workflow is in progress
*********************************

1) create a <RUNDIR> (better be outside of NEMSDIR!!)
2) copy all the input files/environ files/config files/etc/
   required by all the coupled models into <RUNDIR>
3) copy <ROOTDIR>nsem.job into <RUNDIR>
4) edit nsem.job file to adjsut the <ROOTDIR> and the NODE/TASK options
   per model_configure and nems.configure files
5) help yourself to edit any other variables in nsem.job file as needed
6) then run the command > sbatch nsem.job
7) check the process > squeue -u $USER

Note: There are two run time configuration files, required by NEMS. 
      Example of these two files are located in this directory for convenience.
      To use them, you should copy and rename them to exclude the ".sample".
      These two files are hard coded into the NEMS source codes and expected files
      names are: 
	  - model_configure and 
	  - nems.configure
	  
      The file <ROOTDIR>/nsem.job.sample is an example of SLURM job batch file.


******************************************************************
TABLE 0 - Schematic workflow of files involved in pre compilation 
****************************************************************** 
   <ROOTDIR>
   |
   |--- NEMS
   |     |
   |     |--- src/ --- module_EARTH_GRID_COMP.F90
   |           |
   |           |--- incmake/ --- buildenv.mk, component_NWM.mk, example_component_FOO.mk
   |           |       |
   |           |       |--- env/ --- rdhpcs/ --- detect.mk, hera.intel.mk 
   |           |       
   |		   |--- conf/ --- modules.nems
   |--- ModelA
   |
   |--- ModelA_INSTALL/ --- libmodelA.a, modelA.mk, modelA.mod 
   |
   |--- ModelB
   |
   |--- ModelB_INSTALL/ --- libmodelB.a, modelB.mk, modelB.mod
   |
   |--- ModelN
   |
   |--- ModelN_INSTALL/ --- libmodelN.a, modelN.mk, modelN.mod
   |
   |--- modulefiles/ --- hera/ --- ESMF_NUOPC
   |
   |--- conf/ --- configure.nems.hera.intel
   |
   |--- NEMS_RUN
   

*************************************************
TABLE 1 - Contents of modulefiles/hera/ESMF_NUOPC
*************************************************
#%Module
#
#    NEMS FV3 Prerequisites: Hera/Intel


# load programming environment
# this typically includes compiler, MPI and job scheduler
#

module load intel/18.0.5.274
module load szip/2.1
module load hdf5/1.10.4
module load impi/2018.0.4
module load netcdf/4.6.1

# environment for ESMF v8.0.0 beta snapshot 48g
module use /home/emc.nemspara/SOFT-hera/modulefiles
module load esmf/8.0.0bs48g

# add others for each model as needed

****************************************************
TABLE 2 - Contents of conf/configure.nems.hera.intel
****************************************************
# NEMS configuration file
#
# Platform: Hera
# Compiler: Intel with IntelMPI

SHELL           = /bin/sh


# Include the common configuration parts
include         $(TOP)/conf/configure.nems.NUOPC

# Other settings

NETCDF_INC   = -I$(NETCDF)/include
NETCDF_LIB   = -L$(NETCDF)/lib -lnetcdf

NEMSIO_INC   = -I${LIBDIR}/incmod/nemsio
NEMSIO_LIB   = -L${LIBDIR} -lnemsio
SYS_LIB      =

EXTLIBS      = $(NEMSIO_LIB) \
               $(NETCDF_LIB) \
               $(ESMF_LIB)   \
               $(SYS_LIB) -lm

EXTLIBS_POST = $(NEMSIO_LIB)  \
               $(ESMF_LIB)    \
               $(NETCDF_LIB)  \
               $(SYS_LIB)
#
FC          = mpiifort -g -qopenmp -mkl=sequential -align array32byte -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -qopenmp -convert big_endian -assume byterecl -mkl=sequential
F77         = mpiifort -g -qopenmp -mkl=sequential -align array32byte -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -qopenmp -convert big_endian -assume byterecl -mkl=sequential
FREE         = -free
FIXED        = -fixed
R8           = -r8

FINCS        = $(ESMF_INC) $(NEMSIO_INC) $(NETCDF_INC)
#TRAPS        = -g -fno-inline -no-ip -traceback -ftrapuv -fpe0 -ftz -check all -check noarg_temp_created -fp-stack-check

FFLAGS       = $(TRAPS) $(FINCS) -fp-model strict

OPTS_NMM     = -g -fno-inline -no-ip -traceback -ftrapuv -fpe0 -ftz -check all -check noarg_temp_created -fp-stack-check $(FREE)

FFLAGM_DEBUG =

FFLAGS_NMM   = $(MACROS_NWM) $(OPTS_NMM) $(FFLAGS)

FPP          = -fpp
CPP          = cpp -P -traditional
CPPFLAGS     = -DENABLE_SMP -DCHNK_RRTM=8

AR           = ar
ARFLAGS      = -r

RM           = rm

***********************************************************        
TABLE 3 - Contents of NEMS/src/incmake/env/rdhpcs/detect.mk
***********************************************************

ifneq (,$(and $(wildcard /scratch),$(wildcard /scratch3)))
  NEMS_COMPILER?=intel
  $(call add_build_env,theia.$(NEMS_COMPILER),env/rdhpcs/theia.$(NEMS_COMPILER).mk)
else
  ifneq (,$(and $(wildcard /scratch1),$(wildcard /scratch2)))
    NEMS_COMPILER?=intel
    $(call add_build_env,hera.$(NEMS_COMPILER),env/rdhpcs/hera.$(NEMS_COMPILER).mk)
  else
    ifneq (,$(and $(wildcard /lfs1),$(wildcard /lfs3)))
      NEMS_COMPILER?=intel
      $(call add_build_env,jet.$(NEMS_COMPILER),env/rdhpcs/jet.$(NEMS_COMPILER).mk)
    else
      ifneq (,$(shell hostname | grep -i gaea))
        NEMS_COMPILER?=intel
        $(call add_build_env,gaea.$(NEMS_COMPILER),env/rdhpcs/gaea.$(NEMS_COMPILER).mk)
      endif
    endif
  endif
endif

********************************************************
TABLE 4 - Contents of NEMS/src/incmake/component_NWM.mk
********************************************************
# Location of the ESMF makefile fragment for this component:
nwm_mk = $(NWM_BINDIR)/nwm.mk
all_component_mk_files+=$(nwm_mk)

# Location of source code and installation
NWM_SRCDIR?=$(ROOTDIR)/NWM/trunk/NDHMS
NWM_BINDIR?=$(ROOTDIR)/NWM_INSTALL

# Make sure the expected directories exist and are non-empty:
$(call require_dir,$(NWM_SRCDIR),NWM source directory)


# Rule for building this component:
build_NWM: $(nwm_mk)


env_file=$(NWM_SRCDIR)/setEnvar.sh
esmf_env=$(NWM_SRCDIR)/esmf-impi-env.sh
comp_opt=3

# HOW to source env here??
#
NWM_ALL_OPTS= \
  COMP_SRCDIR="$(NWM_SRCDIR)" \
  COMP_BINDIR="$(NWM_BINDIR)" \
  MACHINE_ID="$(MACHINE_ID)"


$(nwm_mk): configure $(CONFDIR)/configure.nems
        @echo ""
        +$(MODULE_LOGIC) ; cd $(NWM_SRCDIR) ; exec ./compile_nuopc_NoahMP.sh $(env_file) $(esmf_env) $(comp_opt)
        +$(MODULE_LOGIC) ; cd $(NWM_SRCDIR)/CPL/NUOPC_cpl ; exec $(MAKE) -f Makefile nuopcinstall \
          $(NWM_ALL_OPTS) DESTDIR=/ "INSTDIR=$(NWM_BINDIR)"
        @echo ""
        test -d "$(NWM_BINDIR)"
        @echo ""
        test -s $(nwm_mk)

# Rule for cleaning the SRCDIR and BINDIR:
clean_NWM:
        @echo ""
        +-cd $(NWM_SRCDIR) ; exec $(MAKE) -f Makefile.nuopc nuopcclean

distclean_NWM: clean_NWM
        @echo ""
        rm -rf $(NWM_BINDIR)

distclean_NUOPC:
        @echo ""
        +-cd $(NWM_SRCDIR) ; exec $(MAKE) -C CPL/NUOPC_cpl -f Makefile nuopcclean
        rm -rf $(NWM_BINDIR)

***********************************************************
TABLE 5 - <ROOTDIR>/NWM/trunk/NDHMS/CPL/NUOPC_cpl/Makefile
***********************************************************
CAP_DEP_FRONT := nwm_nuopc_cap    # for NEMS, must be same name as its module
CAP_VERS      := VERSION
CAP_MK        := nwm.mk           # for NEMS


$(CAP_MK): 
        @echo $(HR)
        @echo "Generating NUOPC Makefile Fragment"
        @echo
        @echo "# ESMF self-describing build dependency makefile fragment" > $(CAP_MK)
        @echo "" >> $(CAP_MK)
        @echo "ESMF_DEP_FRONT     = $(CAP_DEP_FRONT)" >> $(CAP_MK)
        @echo "ESMF_DEP_INCPATH   = $(CAP_DIR)" >> $(CAP_MK)
        @echo "ESMF_DEP_CMPL_OBJS = " >> $(CAP_MK)
        @echo "ESMF_DEP_LINK_OBJS = $(CAP_DIR)/$(CAP_LIB)" >> $(CAP_MK)
        @echo "ESMF_DEP_SHRD_PATH = " >> $(CAP_MK)
        @echo "ESMF_DEP_SHRD_LIBS = " >> $(CAP_MK)

=====================================================   


Please add contents as needed into <ROOTDIR>.gitignore file: