1. Configuring ROMS for South of Java Kate Hedstrom, ARSC/UAF October, 2007

2. Requirements Input files –Grid –Initial conditions –Boundary conditions –Forcing Code changes –JAVA_1 cpp flag –ocean_java.in –makefile

3. Define Grid Coordinate System Provide a coastline file and point to it with XCOASTDATA Run xcoast Set the map projection

4. Specify the Grid Boundary

5. Save and Recompute Corners to Make a Rectangular Grid

6. Find lat,lon of Each Point, then Bathymetry

7. 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

8. Editmask

9. Smooth the Bathymetry

10. Another View

11. Bathymetric Slopes

12. Bathymetric Steepness Ratio of |h1-h2| / (h1+h2)

13. Grid Metrics on a Sphere

14. 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

16. 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

17. Southern Boundary v

18. Initial Zeta

19. 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

20. ROMS Code Outline of the code cpp cppdefs.h Modules ocean.in Note: understanding gnu make is important, but not covered in this talk

21. ls roms Atmosphere/ Lib/ User/ Build/ makefile Waves/ Compilers/ Master/ Data/ ROMS/ I also have an Apps directory here for my applications.

22. ls ROMS Adjoint/ License_ROMS.txt Bin/ Modules/ SeaIce/ Drivers/ Nonlinear/ Tangent/ External/ Obsolete/ Utility/ Functionals/ Programs/ Version Include/ Representer/

23. 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

24. 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

25. Other Data Assimilation –Adjoint –Representer –Tangent SeaIce Functionals –Analytic expressions for initial conditions, etc. Obsolete Programs

26. 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

27. 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

28. 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

29. 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

30. 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

31. 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

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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

38. 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

39. 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

40. Horizontal Viscosity

41. 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?

42. 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”

43. Run it! Create a working directory with: oceanS External/ –ocean_java.in –varinfo.dat Run the thing:./oceanS < External/ocean_java.in

44. It should spit out a lot of text You can redirect this with:./oceanS ocean.out If successful, you will also obtain some other output files in NetCDF format

45. 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