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The interactions between two independent caches can cause problems. I should look at the netcdf cache and see how it interacts with the hdf5 cache. =Dennis Heimbigner Unidata On 12/15/2016 6:03 PM, Dave Allured - NOAA Affiliate wrote:
On Thu, Dec 15, 2016 at 4:46 PM, Chris Barker <chris.barker@xxxxxxxx <mailto:chris.barker@xxxxxxxx>> wrote: On Thu, Dec 15, 2016 at 1:00 PM, dmh@xxxxxxxx <mailto:dmh@xxxxxxxx> <dmh@xxxxxxxx <mailto: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 chunk 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 _______________________________________________ NOTE: All exchanges posted to Unidata maintained email lists are recorded in the Unidata inquiry tracking system and made publicly available through the web. Users who post to any of the lists we maintain are reminded to remove any personal information that they do not want to be made public. netcdfgroup mailing list netcdfgroup@xxxxxxxxxxxxxxxx For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/
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