Comments (8)
@dnadeau4 following our discussion today here are the discussion points:
- What should defaults be, speed of read vs file sizes?
- Should shuffling and chunking be enabled by default?
- How should a user specify deflation (in the CMIP6_Amon.json tables) or in the CMOR3 driver file (my preference is driver file, the tables should only contain information not runtime options for CMOR3)
We'll need to consult with @taylor13 to finalize the default behavior of CMOR3
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@doutriaux1 has comments about this - regarding "standards". Long story short, a user should be able to over-ride the Table default at runtime, however including the attributes deflate
, deflate_level
and shuffle
in the Tables ensures that across variables the same default compression is applied regardless of whether the CMOR user is aware of the deflation functionality or not.
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Balaji is strongly advising for us to check out performance issues. GFDL
has all but ruled out any sort of compression. We'll talk Wednesday.
On 6/6/16 12:40 PM, Paul J. Durack wrote:
@doutriaux1 https://github.com/doutriaux1 has comments about this -
regarding "standards". Long story short, a user should be able to
over-ride the Table default at runtime, however including the
attributes |deflate|, |deflate_level| and |shuffle| in the Tables
ensures that across variables the same default compression is applied
regardless of whether the CMOR user is aware of the deflation
functionality or not.—
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@dnadeau4 has this implemented in 3.0.6
with the following (python) notation:
cmor.set_deflate(varid,1,1,1) ; # shuffle=1,deflate=1,deflate_level=1 ; CMOR 3.0.6+
cmor.write( ...
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You can put the shuffle/deflation flag in the tables or call cmor.set_deflate. I have also add the API to C and Fortran. By default everything is netcdf3, I would like to default to netcdf4 with no compression.
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@dnadeau4 I think defaulting to netcdf4
is a good idea - it is the requested format for CMIP6 as far as I know
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Just FYI, here is what the file sizes look like using various deflate_level
(level=X) flags with the AMIP boundary forcing datasets (1x1 lat/lon grid and 1752 timesteps):
variable | cdms2 deflated | CMOR3 no-deflation | CMOR3 level=1 | CMOR3 level=3 | CMOR3 level=9 |
---|---|---|---|---|---|
areacello | 32.8KB | 303.7KB | 41.4KB | - | - |
siconc | 29.3MB | 433.1MB | 44.6MB | 43.2MB | 39.9MB |
siconcbcs | 75.2MB | 433.1MB | 73.0MB | 72.3MB | 69.6MB |
tos | 225.9MB | 433.1MB | 177.1MB | 174.8MB | 171.3MB |
tosbcs | 239.2MB | 433.1MB | 185.1MB | 182.6MB | 178.4MB |
It would be useful to have associated timing/CPU load equivalents to validate the statement by Balaji
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create test Test/cmor_speed_and_compression_03.py
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