You don't say *how* you are writing the data, other than "a row at a time".
Is the row dimension an unlimited dimension? (That is what I would
recommend trying.)
Or have you pre-allocated space in the variables and are now writing data
into that space?
Or are you reading the entire file, adding one row of data, then writing
the entire file? (That is bound to be slow when the number of rows gets
larger.)
On Tue, Jun 28, 2016 at 1:26 AM, Robin Moss <robin.moss@xxxxxxxxxxxxxx>
wrote:
> Hello,
>
>
>
> I’m hoping I can get some pointers to improve the way im using the NetCDF
> library.
>
>
>
> At the moment the processing I’m doing is writing to several different
> NetCDF files, multiple variables a row at a time. These are not currently
> multi-threaded.
>
>
>
> When the processed data is small I don’t see any issues (100’s of rows),
> however when I start running a bigger chain (10’s of thousands of rows) I
> see the performance of NetCDF Java plummet, a quick look at whats happening
> with VisualVM shows that most of my application times (~60%) is spent in
> `Nc4Iosp.writeData()`.
>
>
>
> Which leads me to believe I’m using the library wrong J, my initial
> thought having worked with the C Library directly before was to adjust the
> write buffer, but I don’t see any support for that in the Java lib and
> considering it would likely affect the C Lib I’m not sure it would help
> with the write data call.
>
>
>
> I had briefly looked into just buffering my rows so I write every 10-100
> rows to see what effect that would have on performance and memory usage,
> however I hit a bit of an issue with the variables that have an unlimited
> dimension of columns (most variables I have are row x column), in that I
> was unable to figure out how to create an Array that supported unlimited
> dimensions.
>
>
>
> We currently use the NetcdfFileWriter to writer data to the underlying
> NetCDF 4 files, I know the API suggests using the FileWriter2, but I
> couldn’t see a way to use that, that also allowed us to ‘stream’ data into
> the underlying files.
>
>
>
> Any suggestions would be greatly appreciated.
>
>
>
> Thanks,
>
> Robin
>
>
>
>
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--
Sincerely,
Bob Simons
IT Specialist
Environmental Research Division
NOAA Southwest Fisheries Science Center
99 Pacific St., Suite 255A (New!)
Monterey, CA 93940 (New!)
Phone: (831)333-9878 (New!)
Fax: (831)648-8440
Email: bob.simons@xxxxxxxx
The contents of this message are mine personally and
do not necessarily reflect any position of the
Government or the National Oceanic and Atmospheric Administration.
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