Add compression level namelist parameter

[aekiss]

Netcdf compression level affects cice runtime, e.g. in 3mo runs with daily output (/g/data3/hh5/tmp/cosima/access-om2-01/01deg_jra55v13_ryf8485_spinup7_newexe):

level                          Timer  12: ReadWrite   file size
0 (no compression*)               1510s                  1600Mb
1                                1833s                   252Mb
5                                2501s                   236Mb

It would be nice to be able to control this speed/space tradeoff via a namelist parameter setting the compression level.
There are only a few code changes required - see 9e69c99

*this test still used nf90_def_var_deflate, but at level 0 - perhaps it would be faster to skip nf90_def_var_deflate if level is 0. Before switching to netcdf4 (d2ef6b1) IO took about 1300s. It's unclear whether the extra 200s in the table is the cost of netcdf4 or the level-0 deflate step.

Slack discussion: https://arccss.slack.com/archives/C9Q7Y1400/p1557809112231100

[russfiedler]

@aekiss I note that in your deflate=0 test cases that you still have chunking and byte shuffling on. Not sure how much of this is contributing to the extra time (probably not much) but the byte shuffling is pointless unless compression is also on so it needs to be turned off if DeflateLevel==0

	vicen:_Storage = "chunked" ;
	vicen:_ChunkSizes = 1, 1, 675, 900 ;
	vicen:_DeflateLevel = 0 ;
	vicen:_Shuffle = "true" ;

[nichannah]

I have something ready which I am testing now. I will update exes soon and let you know.

The 'history_deflate_level' namelist parameter in setup_nml of cice_in.nml will set the netcdf4 deflation level. By default it is set to -1 which is deflation turned off. This is distinct from history_deflate_level = 0 in that the former does not use a compression algorithm at all. It will be interesting to see whether there is any performance difference between history_deflate_level = -1 and = 0.

Also shuffle is always turned off because apparently this doesn't help much for float data.

References: https://www.unidata.ucar.edu/blogs/developer/entry/netcdf_compression

[aekiss]

Thanks @nichannah this is looking good - is ccee631 ready to merge into master? It would be nice to have it for the RYF run we have planned.

[nichannah]

A new namelist option has been added to CICE setup_nml, history_deflate_level.

This defaults to -1 which is no deflation. Testing show an approx 5x space saving with:

history_deflate_level = 1