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2009 Stream 1 : User Interface
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The stream 1, named User Interface is a never end stream. In 2008, the main works in the stream have involved the ocean forcing interface (introduction of SBC module + on-the-fly interpolation) and the TOP interface. In 2009, the major expected improvement concerns the model output (introduce an easy and efficient way to add/remove model output fields (new IOM for output). Note also the starting of 2 years work on a simplification of the new configurations settings (CFG=Configuration manager). The actions of the stream are:
Substream 1.1: IOM for outputs
The defined strategy is built on the use of catalogues that are dynamically created
and written once for all at the end of step. The temporal mean is no more performed in the IO
library, but is done in NEMO. The write itself will use the new IOIPSL module, or a dimg
module. There is many improvements associated with this strategy. One example, a call to
iom_put (i.e. a write into a catalogue) can be done anywhere in the code. This will greatly
improve the code readability and will allow easy output of local variable.
Work :
(1) beta version expected in mid-February for the ocean (v3.2)
Status: Added in the trunk and validated (NEMO-paris, contribution from IPSL), see tickets #387 .
Ready for incorporation into v3.2
(2) Add a user-friendly interface (namelist or xml file) + a documentation (v3.2)
Status: Added the namelist and xml file in the trunk and validated (NEMO-paris, contribution from IPSL).
Documentation is missing.
(3) introduce IOM in the other components (LIM, TOP) (v3.2)
Status: Added in the trunk and validated for TOP (NEMO-paris), see tickets #437 .
On-going work for LIM 2 and 3.
(4) assessment of IOM behaviour on mpp computers (v3.3)
Status: to be done
Substream 1.2: NetCDF4 IO options
NetCDF4 offers the opportunity to employ dataset chunking and compression
algorithms to greatly reduce the volume of data written out by NEMO without any loss of
precision. NetCDF4.0.1 is the latest, full release of the library and this has been
successfully tested for use in NEMO by NOCS. Even with severe tests, involving ORCA025
configurations with biogeochemical tracers, there are no run-time performance issues
of any concern. In fact on some I/O limited clusters a speed enhancement is achieved
because the benefits of writing out fewer data outweigh the computational costs of in-memory
compression. The great benefit though is in the reduction of filesizes, for example:
File name Disk usage for netCDF3.X (MBytes) Disk usage for netCDF4.0 (Mbytes) Reduction factor *grid T*.nc 1500 586 2.56 *grid U*.nc 677 335 2.02 *grid V*.nc 677 338 2.00 *grid W*.nc 3300 929 3.55 *icemod*.nc 208 145 1.43 Table 11: Effect of chunking and compression on the size of the NEMO 3.0 output files. For each file name the usage is the sum of all 221 individual processor output files.
The code changes required to use netcdf4 within NEMO are relatively straight-forward and involve minor changes to: iom_def.F90, iom.F90, iom_nf90.F90 and restart.F90 in the NEMO code and: histcom.f90 in IOIPSL. Changes are also required in the relevant makefiles to link in the netcdf4 library (-lnetcdff -lnetcdf) and the HDF5 and compression libraries that underlie netcdf4 (-lhdf5_fortran -lhdf5 -lhdf5_hl -lz). The need to make changes to IOIPSL routines makes providing a solution which supports both netcdf3 and netcdf4 difficult (preprocessor keys are not used in IOIPSL). This requires some discussion. The uptake of netcdf4 in NEMO may also be restricted by slow uptake of 3rd party software providers. Any compilable code can simply be relinked to the new libraries. Existing utilities will then be able to read netCDF4 files (and write netCDF3 files). Code changes are only necessary if it is required to write new netCDF4 files. However, commercial packages, such as IDL, will need netCDF4 support provided by the vendor (planned for early 2010). Other packages may fare better; NOCS has been able to compile netCDF4-compatible versions of Ferret and a netCDF4-compatible version of the mexnc toolkit for use with matlab (versions 2008a onwards). Details are available on request.
Substream 1.3 : Configuration manager
Create the configuration tools (CFG-tools): user-friendly interface, the tools, and the
documentation associated to the creation of a new model configuration, and especially
configurations defined as a zoom of an ORCA configuration. The tools include the generation
of a grid, a bathymetry, an initial state, a forcing data set, and open boundary conditions.
Manpower will be demanded in the My_Ocean FP7 European project (MCS) to build the tool.
Work :
(1) collect the existing tools (OPABAT, ROMS-tools, etc
(2) Define the structure and implement a 1st version of the CFG-tools. (v3.3)
Status : beginning August the 1st, within MyOcean? (Brice Lemaire position)
Substream 1.4 :bio interfaces
Interface for other bio-models in TOP
Status : probably postponed for one year (==> 2010).
Substream 1.5 : reference manuels
LIM and TOP (TRP) paper documentation using Latex (similar to the NEMO ocean engine documentation.
Work :
(1) Create the TRP documentation (2 w) (v3.3)
(2) participate to the writing of LIM3 documentation realised at UCL (1 w) (v3.3)
(3) review of the TRP and LIM3 documentation (NOCS team, 2 w) (v3.3)
Status : expected to start during the second part of year 2009.
Substream 1.6 :Reference configurations
Add new standard configurations to be used as NEMO tutorial, developer validation
and benchmark purposes in order to illustrate the existing system potentiality.
Work :
(1) illustration of the on-the-fly interpolation (v3.3)
(2) illustration of the different type of vertical coordinate (v3.3)
(3) illustration of AGRIF zoom with sea-ice (v3.3)
(4) illustration of off-line tracer computation (v3.3)
Status : expected to start during the second part of year 2009.
