g S
ys
Te
t
-F o llo w i
r rai n
ng
O
R es
e a rc h C o mm u ni
ty
ce
m
em
g
M o d e li n
Re
io
ean
l Oc
na
an
Op
&
ROMS: NetCDF and Matlab
David Robertson and Hernan Arango
New Brunswick, NJ, USA
te
y
e r ati
n it
o n al C o m m u
ROMS/TOMS Web Sites
IMCS, Rutgers University
M o d e lin g S y s
Web Statistics
100
90
80
70
60
50
40
30
20
10
0
2004
2005
2004
2005
2006
2007
2008
2009
2006
2007
new
new
new
new
new
new
users:
users:
users:
users:
users:
users:
2008
204
267
288
367
533
131
2009
Web Statistics
Oct. ‘08
Users
Mar. ‘09
Oct. ‘08
Mar. ‘09
Country
Country
Use
rs
1
1 United States
502
11 10 Canada
39
2
2 China
161
12 12 Germany
32
3
6 Australia
70
13 14 Mexico
29
3 Spain
70
14 13 Portugal
28
5
5 Japan
64
6
7 South Korea
62
16 15 Norway
26
7
8 India
61
17 17 Chile
21
8
4 France
60
18 18 Taiwan
19
9
9 Italy
53
19 19 Russia
18
48
20 20 Ireland
14
10 11 Brazil
16 United Kingdom
28
Overview
• Daily Update Email
• Forum Posts
• Trac Ticket Activity (New & Resolved)
• Revisions
• Forum Search
• Trac Website
• ROMS Documentation Projects
 WikiROMS
 Tutorial Movies and Animations
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
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
mexnc Flowchart
Matlab® Version
mexnc.mex exists?
R2008b or newer
No
R2008a or older
Yes
mexnc 2.9.4 – 2.9.7
mexnc.mex capabilities
NetCDF-4/HDF5
NetCDF-3
mexnc.mex
Native Matlab®
NetCDF
mexnc Flowchart
Matlab® Version
USE_TMW on?
R2008b or newer
Yes
R2008a or older
No
mexnc 2.9.10
mexnc.mex
Native Matlab®
NetCDF
snctools Flowchart (line colors indicate file type)
NetCDF file type
NetCDF-4/HDF5
snctools 2.9.4 – 2.9.7
Java Available?
Java ToolsUI.jar
NetCDF-4/HDF5
NetCDF-3
URL (read only)
Error, no method
available to read file.
mexnc.mex capabilities
NetCDF-3
Matlab® Version
No
R2008a or older
Yes
R2008b or newer
Native Matlab
NetCDF
mexnc.mex
snctools Flowchart: Reading
(grey lines indicate Matlab version
line colors indicate file type)
Matlab® Version
R2008b or newer
snctools 2.9.10
NetCDF file type
NetCDF-3
R2008a or older
NetCDF-4/HDF5
URL
USE_JAVA on?
Yes
Java ToolsUI.jar
No
mexnc.mex
Native Matlab®
NetCDF
snctools Flowchart: Writing
(grey lines indicate Matlab version
line color indicates file type)
Matlab Version
R2008b or newer
snctools 2.9.10
R2008a or older
NetCDF file type
NetCDF-3
NetCDF-4/HDF5
mexnc.mex
Native Matlab
NetCDF
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
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’,…);
----------
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’,…);
----------
mexnc(‘rename_dim’,…);
----------
nc_rename_dim(…);
netcdf.renameDim(…);
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_copy_att(…);
netcdf.copyAtt(…);
mexnc(‘copy_att’,…);
----------
nc_rename_att(…);
netcdf.renameAtt(…);
mexnc(‘rename_att’,…);
----------
nc_del_att(…);
netcdf.delAtt(…);
mexnc(‘del_att’,…);
----------
nc_attget(…);
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’,…);
----------
mexnc(‘rename_var’,…);
nc_varrename(…);
nc_rename_var(…);
nc_copy_var(…);
netcdf.renameVar(…);
----------
-----------
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_*’,…);
----------