[netcdf-java] Performance Issues and Buffering

• To: "netcdf-java@xxxxxxxxxxxxxxxx" <netcdf-java@xxxxxxxxxxxxxxxx>
• Subject: [netcdf-java] Performance Issues and Buffering
• From: Robin Moss <robin.moss@xxxxxxxxxxxxxx>
• Date: Tue, 28 Jun 2016 08:26:30 +0000

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 :), 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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