1. ROMS/TOMS Web Sites & ROMS: NetCDF and Matlab
David Robertson and Hernan Arango
IMCS, Rutgers University
New Brunswick, NJ, USA

2. Web Statistics
2004 new users: 204
2005 new users: 267
2006 new users: 288
2007 new users: 367
2008 new users: 533
2009 new users: 131

3. Web Statistics Mar. ‘09 Oct. ‘08 Country Users 1 United States 502 2
China
161 3 6
Australia 70
Spain 5
Japan 64 7
South Korea 62 8
India 61 4
France 60 9
Italy 53 10 11
Brazil 48
Mar. ‘09
Oct. ‘08
Country
Users 11 10
Canada 39 12
Germany 32 13 14
Mexico 29
Portugal 28 16
United Kingdom 15
Norway 26 17
Chile 21 18
Taiwan 19
Russia 20
Ireland

4. Overview Daily Update Email Forum Search Trac Website
Forum Posts
Trac Ticket Activity (New & Resolved)
Revisions
Forum Search
Trac Website
ROMS Documentation Projects
WikiROMS
Tutorial Movies and Animations

5. NetCDF-4/HDF5 Capabilities: Allows for multiple unlimited dimensions
Data compression
Parallel file access
Grouping
Caveats:
Compression cannot be used to write in parallel (PARALLEL_IO)
Parallel I/O only in MPI (not shared memory)
Separate compilation for every combination of I/0 (parallel v. serial), compiler (PGI, Intel, etc.), and MPI implementation (MPICH2, OpenMPI, etc.)
Parallel I/O is slower than serial in ROMS

6. NetCDF and Matlab® Considerations
Interfaces:
mexcdf
mexnc
snctools
NetCDF-java
Native Matlab (R2008b and newer)
NetCDF Version:
NetCDF-3
NetCDF-4/HDF5 (must be linked staticly, no shared libraries)
NetCDF File Type:
Classic (NetCDF-3)
HDF5 (NetCDF-4)
Misc:
File compression (NetCDF-4/HDF5 only)
OpenDAP URLs

7. mexnc Flowchart Matlab® Version mexnc.mex exists? R2008b or newer No
R2008a or older
Yes
mexnc.mex capabilities
NetCDF-4/HDF5
NetCDF-3
Native Matlab®
NetCDF
mexnc.mex

8. mexnc Flowchart Matlab® Version USE_TMW on? R2008b or newer Yes
R2008a or older No
mexnc.mex
Native Matlab®
NetCDF

9. snctools Flowchart (line colors indicate file type)
NetCDF file type
mexnc.mex capabilities
NetCDF-4/HDF5
NetCDF-4/HDF5
snctools – 2.9.7
NetCDF-3
NetCDF-3
URL (read only)
Java Available?
Matlab® Version
Error, no method
available to read file. No
R2008a or older
Yes
R2008b or newer
Native Matlab
NetCDF
Java ToolsUI.jar
mexnc.mex

10. snctools Flowchart: Reading (grey lines indicate Matlab version
line colors indicate file type)
Matlab® Version
NetCDF file type
R2008b or newer
snctools
NetCDF-3
R2008a or older
NetCDF-4/HDF5
URL
USE_JAVA on?
Java ToolsUI.jar
Yes
mexnc.mex No
Native Matlab®
NetCDF

11. snctools Flowchart: Writing (grey lines indicate Matlab version
line color indicates file type)
Matlab Version
R2008b or newer
NetCDF file type
snctools
NetCDF-3
R2008a or older
NetCDF-4/HDF5
mexnc.mex
Native Matlab
NetCDF

12. ROMS Matlab Pre- and Post-Processing Scripts
NetCDF Interface:
snctools users should be aware that mexnc, native Matlab NetCDF, and these scripts return arrays with the indices in the order in which the variable is written to the NetCDF file. snctools will give you the array with the indices in the opposite order.
Since ROMS is a Fortran code, ROMS arrays in output files are stored in (i, j, k) order.
These scripts use mexnc for the backend
mexnc.m is required regardless of Matlab version
For NetCDF-4/HDF5 capability you need to compile the mexnc mex file yourself
mexnc does not use the java ToolsUI.jar file so no OpenDAP
NetCDF v4.1 will have build-in OpenDAP capabilities

13. Dataset Inquiry Functions
NetCDF Operator Comparison
Dataset Functions
NetCDF
Native Matlab
mexnc
snctools
nc_create(…);
netcdf.create(…);
mexnc(‘create’,…);
nc_create_empty(…);
nc_open(…);
netcdf.open(…);
mexnc(‘open’,…);
nc_redef(…);
netcdf.reDef(…);
mexnc(‘redef’,…);
nc_endef(…);
netcdf.endDef(…);
mexnc(‘endef’,…);
nc_close(…);
netcdf.close(…);
mexnc(‘close’,…);
nc_sync(…);
netcdf.sync(…);
mexnc(‘sync’,…);
nc_abort(…);
netcdf.abort(…);
mexnc(‘abort’,…);
Dataset Inquiry Functions
NetCDF
Native Matlab
mexnc
snctools
nc_inq(…);
netcdf.inq(…);
mexnc(‘inq’,…);
nc_info(…);
nc_inq_ndims(…);
mexnc(‘inq_ndims’,…);
nc_inq_nvars(…);
mexnc(‘inq_nvars’,…);
nc_inq_natts(…);
mexnc(‘inq_natts’,…);
nc_inq_unlimdim(…);
mexnc(‘inq_unlimdim’,…);

14. NetCDF Operator Comparison (cont.)
Dimension Functions
NetCDF
Native Matlab
mexnc
snctools
nc_def_dim(…);
netcdf.defDim(…);
mexnc(‘def_dim’,…);
nc_add_dimension(…);
nc_inq_dimid(…);
netcdf.inqDimID(…);
mexnc(‘inq_dimid’,…);
nc_inq_dim(…);
netcdf.inqDim(…);
mexnc(‘inq_dim’,…);
nc_getdiminfo(…);
nc_inq_dimname(…);
mexnc(‘inq_dimname’,…);
nc_inq_dimlen(…);
mexnc(‘inq_dimlen’,…);
nc_rename_dim(…);
netcdf.renameDim(…);
mexnc(‘rename_dim’,…);
Attribute Functions
NetCDF
Native Matlab
mexnc
snctools
nc_put_att_*(…);
netcdf.putAtt(…);
mexnc(‘put_att_*’,…);
nc_attput(…);
nc_inq_att(…);
netcdf.inqAtt(…);
mexnc(‘inq_att’,…);
nc_info(…);
nc_inq_atttype(…);
mexnc(‘inq_atttype’,…);
nc_inq_attlen(…);
mexnc(‘inq_attlen’,…);
nc_inq_attname(…);
netcdf.inqAttName(…);
mexnc(‘inq_attname’,…);
nc_inq_attid(…);
netcdf.inqAttID(…);
mexnc(‘inq_attid’,…);
nc_get_att_*(…);
netcdf.getAtt(…);
mexnc(‘get_att_*’,…);
nc_attget(…);
nc_copy_att(…);
netcdf.copyAtt(…);
mexnc(‘copy_att’,…);
nc_rename_att(…);
netcdf.renameAtt(…);
mexnc(‘rename_att’,…);
nc_del_att(…);
netcdf.delAtt(…);
mexnc(‘del_att’,…);

15. General Variable Functions
NetCDF Operator Comparison (cont.)
General Variable Functions
NetCDF
Native Matlab
mexnc
snctools
nc_def_var(…);
netcdf.defVar(…);
mexnc(‘def_var’,…);
nc_addvar(…);
nc_inq_varid(…);
netcdf.inqVarID(…);
mexnc(‘inq_varid’,…);
nc_inq_var(…);
netcdf.inqVar(…);
mexnc(‘inq_var’,…);
nc_getvarinfo(…);
nc_inq_varname(…);
mexnc(‘inq_varname’,…);
nc_inq_vartype(…);
mexnc(‘inq_vartype’,…);
nc_inq_vardims(…);
mexnc(‘inq_varndims’,…);
nc_inq_vardimid(…);
mexnc(‘inq_vardimid’,…);
nc_inq_varnatts(…);
mexnc(‘inq_varnatts’,…);
nc_rename_var(…);
netcdf.renameVar(…);
mexnc(‘rename_var’,…);
nc_varrename(…);
nc_copy_var(…);

16. Variable I/O Functions (read) Variable I/O Functions (write)
NetCDF Operator Comparison (cont.)
Variable I/O Functions (read)
NetCDF
Native Matlab
mexnc
snctools
nc_get_var_*(…);
netcdf.getVar(…);
mexnc(‘get_var_*’,…);
nc_varget(…);
nc_get_var1_*(…);
mexnc(‘get_var1_*’,…);
nc_get_vara_*(…);
mexnc(‘get_vara_*’,…);
nc_get_vars_*(…);
mexnc(‘get_vars_*’,…);
nc_get_varm_*(…);
mexnc(‘get_varm_*’,…);
Variable I/O Functions (write)
NetCDF
Native Matlab
mexnc
snctools
nc_put_var_*(…);
netcdf.putVar(…);
mexnc(‘put_var_*’,…);
nc_varput(…);
nc_put_var1_*(…);
mexnc(‘put_var1_*’,…);
nc_put_vara_*(…);
mexnc(‘put_vara_*’,…);
nc_put_vars_*(…);
mexnc(‘put_vars_*’,…);
nc_put_varm_*(…);
mexnc(‘put_varm_*’,…);