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2009 Stream 1 : User Interface
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This is a continuing stream for which, in 2008, we have simplified the forcing interface (SBC module + on-the-fly interpolation) and the TOP interface. The major actions in 2009 will be to introduce an easy and efficient way to add/remove model output fields (new IOM for output) and the starting of 2 years work on a simplification of the new configurations settings (Configuration manager). The actions of the stream are:
Substream 1.1: IOM for outputs
Description and participants
IOM for outputs
Advancement
Substream 1.2: NetCDF4 IO options
Description and participants
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.
Advancement
Substream 1.3 : Configuration manager
Description and participants
Develop tools to build regional configurations
Advancement
Substream 1.4 :bio interfaces
Description and participants
Interface for other bio-models in TOP
Advancement
Substream 1.5 : reference manuels
Description and participants
Advancement
Substream 1.6 :Reference configurations
