configuring roms for south of java

Configuring ROMS for South of Java

Kate Hedstrom, ARSC/UAFOctober, 2007

Requirements

• Input files– Grid– Initial conditions– Boundary conditions– Forcing

• Code changes– JAVA_1 cpp flag– ocean_java.in– makefile

Define Grid Coordinate System

• Provide a coastline file and point to it with XCOASTDATA

• Run xcoast• Set the map

projection

Specify the Grid Boundary

Save and Recompute Corners to Make a Rectangular Grid

Find lat,lon of Each Point, then Bathymetry

Land Mask

• The bathymetry finder will optionally set the land mask based on sea level

• The land mask might not be quite how you want it, so run editmask

• Interactive matlab tool needing a matlab coastline file too

Editmask

Smooth the Bathymetry

Another View

Bathymetric Slopes

Bathymetric Steepness

• Ratio of |h1-h2| / (h1+h2)

Grid Metrics on a Sphere

Initial and Boundary Files

• Matlab scripts to create them from the North Pacific run

• Requires matlab-netcdf interface• Requires rnt toolbox from Emanuelle

di Lorenzo• Tell rnt_gridinfo about both grids -

location of the files, vertical grid information

North Pacific at 18 km

• Run with CCSM CORE forcing and POP boundary conditions

• CORE files from 1958 through 2004• NPAC was run through 1976 so far• Pick a file from 1976 to use as initial

conditions 100 days before the end• Enrique saved four-day averages

Southern Boundary v

Initial Zeta

Forcing Files

• ROMS can now internally interpolate from coarse forcing files to the ROMS grid

• Liz Dobbins prepared the CORE (Large and Yeager) forcing files in a format that ROMS can use

• This saves a lot of time, effort, and disk space

ROMS Code

• Outline of the code• cpp• cppdefs.h• Modules• ocean.in• Note: understanding gnu make is

important, but not covered in this talk

ls roms

Atmosphere/ Lib/ User/Build/ makefile Waves/Compilers/ Master/Data/ ROMS/

I also have an Apps directory here for my applications.

ls ROMS

Adjoint/ License_ROMS.txtBin/ Modules/ SeaIce/Drivers/ Nonlinear/ Tangent/External/ Obsolete/ Utility/Functionals/ Programs/ VersionInclude/ Representer/

Most Important• Drivers

– Various model main programs• Nonlinear

– The regular ocean physics (forward model)• Modules

– Ocean model data types, with allocation and initialization routines

• Utility– File reading and writing routines and other

files common to the various models

Support

• Include– Include files, including cppdefs.h

• Bin– Perl and shell scripts

• Compilers– System-dependent parts of the makefile

• Lib– ARPACK and MCT libraries (optional)

• External– ASCII input files

Other

• Data Assimilation– Adjoint– Representer– Tangent

• SeaIce• Functionals

– Analytic expressions for initial conditions, etc.• Obsolete• Programs

cpp

• The C preprocessor, cpp, comes with some C compilers, or the functionality can be built into a C compiler

• Very simple macro processor• Used in ROMS primarily for conditional

compilation• We probably won’t switch to coco

when it becomes widely available

cpp Versions

• People started using the C preprocessor before there was a C standard - the Standard cpp isn’t quite the version we want

• Gnu “cpp -traditional” does the right thing for Fortran

File Inclusion

• In Fortran, you can include files with: include ‘file.h’• In cpp, the equivalent is: #include “file.h”• We use the cpp version to make sure

the #defines in the include files are seen

Macro Substitution

• A macro definition has the form: #define text replacement text• This is done in ROMS: #define WESTERN_EDGE Istr.eq.1• and used in: if (WESTERN_EDGE) then ….• Safe as long as the replacement text is

not much longer than the original

More on Macros

• Another type of macro substitution is like statement functions in Fortran

• Statement functions and the more modern inlined functions are better because the compiler can do type checking

Logical Macros

• A third kind of macro is something like: #define MASKING• or #define MASKING 1• These can be tested like: #ifdef MASKING (first case) #if MASKING (second case)• We use the first style for historical reasons,

gnu has officially gone to the second

Conditional Compilation

• ROMS uses conditional code everywhere. #ifdef ICE ! Stuff having to do with sea ice

#endif• If you want to find out about (say)

sediment code, do a search on SEDIMENT

More on Conditionals

• When setting up a problem of your own, it’s best to surround code you add with a unique cpp flag:

#define LOMBOK_STRAIT :

#ifdef LOMBOK_STRAIT

! My code

#endif

Still More

• The #define for our case is now happening in the makefile, passed in with a -DMY_CASE flag

• The name of our case is used in the search for an include file, -DROMS_HEADER=my_case.h

Even More

• The ROMS Makefile will take our .F files and run them through cpp for us before passing them to the compiler

• The intermediate files have a .f90 extension

• The compiler errors will refer to line numbers in the .f90 file, not the original source file

• Fix the .F file, but feel free to look at the .f90 files to see what happened

cppdefs.h• Every ROMS source file starts with: #include “cppdefs.h”• This file has been changed to contain

#if defined ROMS_HEADER# include ROMS_HEADER#endif

• The ROMS_HEADER variable comes from the makefile

Modules

• The model variables are stored in Fortran 90 modules defining specific types

• You no longer have to modify mod_param.F for your domain

Input file• ROMS has an ascii input file which it

reads during initialization• The file is not a namelist, but similar

in intent• It specifies things like:

– Number of timesteps– Number of gridpoints (Lm, Mm, N)– Parallel grid partitioning– Other input filenames, output options– Many others

Code Changes

• makefile - ROMS_APPLICATION := JAVA_1

• Create User/Include/java_1.h file with cpp options

• Specify grid dimensions in ocean_java.in

• User/Functionals/ana_hmixcoef.h - add sponge layer with #ifdef JAVA_1

Horizontal Viscosity

ocean_java.in

• ASCII input file for ROMS• Tells number of gridpoints• Provide the paths to the grid, forcing,

etc. files• Specify the timestep and timestep

ratio, viscosity values, etc.• Which fields do you want to output

and how often?

makefile

• Check the name of the compiler• Set Debug/MPI/OpenMP/Large as needed• Set name of application: JAVA_1• Provide number of grids (usually 1)• Check “uname -s” on your computer• Check location of netcdf library and set it

in the Compilers/system-compiler.mk fragment

• Type “make”

Run it!

• Create a working directory with:• oceanS• External/

– ocean_java.in– varinfo.dat

• Run the thing: ./oceanS < External/ocean_java.in

• It should spit out a lot of text• You can redirect this with: ./oceanS < External/ocean.in > ocean.out

• If successful, you will also obtain some other output files in NetCDF format

• Get bold and try it in parallel!– Change the makefile (MPI or OpenMP)– The executable will be called OceanM or

OceanO– If using MPI, run it with the input file as an

argument, not standard in:

./oceanM External/ocean_java.in