4.3. Compiling MITgcm for the PCB simulation

Selecting the number of CPUs for the PCB simulation

First, you need to decide whether you will run the MITgcm as a debugging simulation (with 13 CPUs), or as a full science simulation (with 96 CPUs). You can change the number of CPUs for your MITgcm simulation with the setcpus script:

To select a 13 CPU debugging simulation, type the following commands:

cd /n/regal/sunderland_lab/YOUR-USER-NAME/MITgcm_code/

./setcpus 13 pcb

Or to select a 96 CPU science simulation, type:

cd /n/regal/sunderland_lab/YOUR-USER-NAME/MITgcm_code/

./setcpus 96 pcb

The setcpus script will copy a couple of files into place with appropriate settings for each simulation.

Changing default PCB simulation parameter settings (if necessary)

First, if you need to override any of the default settings in the various header files which are located here:

MITgcm_code/verification/global_pcb_llc90/code

Be aware that the /verification/pcb/code/ directory does not contain all pcb simulation code. It only contains the header files that you need for the PCB simulation. Here is a list of notable files and settings:

File Modification

PROFILES_SIZE.h Changed parameter NOBSGLOB from 500 to 400000 to allow MITgcm to read certain files in the run/profiles directory

PCB_OPTIONS.h

You can define (or undefine) several C-preprocessor switches to turn activate (or deactivate) various PCB simulation options.

To activate an option, use #define OPTION-NAME
To deactivate an option, use #undef OPTION-NAME

Option	Description	Default status
`#define PCBRIVER`	Use a seprarate tracer for riverine PCBp	OFF
`#define PCBAREFRACTORY`	Use a separate tracer for refractory PCBa (either from river or from atmospheric deposition)	OFF
`#define PCBPRREFRACTORY`	Use a separate tracer for refractory PCBp (from rivers only)	OFF
`#define PCBPR_IRREDUCIBLE`	Is refractory PCBp irreducible?	OFF
`#define PCBPR_SLOWRELEASING`	Is refractory PCBp slow-releasing?	OFF
`#define WALSH_FILTER`	Activate Walsh & Nittrouer typology filter for riverine particles?	Activated when `#define HGPREFRACTORY` is ON
`#define walsh_depth`	disable sedimentation: 0: no disable 1: only river mouth 2: over depth <= 55 m (top 4 levels) 3: over depth <= 185 m (top 8 levels) 4: over river mouth AND depth shallower than 55 m	0
`#define USE_EXFIWR`	Use external forcing fields (needed for online run)	ON
`#define VARI_RED_POOL`	Is Hg2 reducible pool a function of DOC concentrations?	OFF

PCB_SIZE.h

You can modify tracer indices and size parameters for the PCB simulation if necessary:

Parameter	Description	Default status
`iPCBa`	PCBa tracer index	`1`
`iPCBp`	PCBp tracer index	`2`
`iPCBaR`	Refractory PCBa tracer index	`3` (when `#define PCBAREFRACTORY` is ON)
`iPCBPr`	Refractory PCBp tracer index	`4` (when `#define PCBAREFRACTORY` is ON) `3` (when `#define PCBAREFRACTORY` is OFF)
`nrmax`	Number of rivers	`1` (only when `#define PCBPRREFRACTORY` is ON)

You will probably not need to change any of the above settings unless you are making your own modifications to the PCB simulation.

Building the mitgcmuv executable for the PCB simulation

Once you are sure that you have made the proper settings in th global_pcb_llc90/code directory, change to the global_pcb_llc90/build directory:

cd ../build

and type the following commands:

premake

make -j13 depend 2>&1 | tee depend.log

make -j13 2>&1 | tee build.log

cp mitgcmuv ../run

Each of these commands will be described in more detail below:

Command	Description
`premake`	`premake` is an alias in your `~/.bashrc_mitgcm` file. `premake` calls the `MITgcm_code/tools/genmake` program, which Queries your computer system to find out where various libraries (i.e. MPI, netCDF, etc) are located, Uses the compilation options that you specify in the file `MITgcm_code/tools/build_options/inux_ifort_odyssey` Generates the main MITgcm makefiles. For more information about genmake, see the MITgcm User Manual, Chapter 3.4.2.
`make -j13 depend`	This command builds the “dependencies” listing and adds it to the Makefile. In other words, it tells the Makefile which source code files depend on which other files. This is done in order to reduce compilation time. NOTE: the `-j13` option tells the Make command to use 13 CPUs. This number should be the same as the number of CPUs your interactive session uses. This will reduce the overall compilation time. Using the >& build.log suffix sends the stdout and stderr output to the log file that you specify. Build errors (if any) will be in this file.
`make -j13`	Builds the MITgcm source code into an executable. A symbolic link to each Fortran (`.F`) and include file (`.h`) will be made in the `build/` directory. For each .F file, include files will be inlined and C-preprocessor switches evaluated. The resultant "clean" Fortran file will be saved with a .f extension. The *.f files will be compiled into an executable file named mitgcmuv. Using the >>& build.log suffix appends the stdout and stderr output to the log file that you specify. Compile errors (if any) will be in this file.
`cp mitgcmuv ../run`	Copies the `mitgcmuv` executable to the run directory, where it will be used to run MITgcm simulations.

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