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NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
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Correction, inserted below. I said "increasing the per-variable chunk size", I meant to say "per-variable CACHE size". On Thu, Dec 15, 2016 at 6:03 PM, Dave Allured - NOAA Affiliate < dave.allured@xxxxxxxx> wrote: > On Thu, Dec 15, 2016 at 4:46 PM, Chris Barker <chris.barker@xxxxxxxx> > wrote: > >> On Thu, Dec 15, 2016 at 1:00 PM, dmh@xxxxxxxx <dmh@xxxxxxxx> wrote: >> >>> 1. Adding this feature to ncdump also requires adding >>> it to the netcdf-c library API. But providing some means >>> for client programs to pass thru parameter settings to the hdf5 lib >>> seems like a good idea. >>> >> >> absolutely! that would be very helpful. >> >> -CHB >> > > This may be premature. The netcdf API already has its own chunk cache > with at least two functions to adjust tuning parameters. It seems to me > that the netcdf facility would probably handle the current ncdump and gdal > cases nicely, though I have not tested it. Please see this relevant > documentation: > > http://www.unidata.ucar.edu/software/netcdf/docs/netcdf_perf_chunking.html > > Simon, you might want to ask your gdal maintainer to give this a try. If > it works, it should be simple and robust. I would suggest increasing the > per-variable CACHE size to at least 5 qualityFlags.nc uncompressed chunks, > and probably more. 5 is the number of chunks that span a single row for > this particular file. This advice presumes that your typical read pattern > is similar to ncdump, which I speculate is first across single whole rows, > as I said earlier. > > columns = 4865 ; > rows = 3682 ; > uint quality_flags(rows, columns) ; > quality_flags:_ChunkSizes = 891, 1177 ; > > 5 x 891 x 1177 x 4 bytes per uint uncompressed ~= 21 Mbytes > > Note this is likely to be a little larger than the default cache size in > the current netcdf-C library, thus explaining some of the slow read > behavior. > > You might also consider rechunking such data sets to smaller chunk size. > Nccopy and ncks can do that. Rechunking may depend on your anticipated > spatial read patterns, so give that a little thought. > > You might also consider reading the entire grid in a single get_vara call > to the netcdf API. That is what my fast fortran test program did. A naive > reader that, for example, loops over single rows may incur bad cache > activity that could be avoided. > > --Dave >
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