Address cdms2 slow read from multiple netcdf files accessed through spanning xml

[durack1]

It appears cdms2 is taking a very long time (tens of minutes) to read a subset of data from multiple netcdf files containing a continuous time axis. In particular the issue is appearing with very high resolution (daily, 2700 x 3600) surface ocean fields.

The slow read also happens when addressing the netcdf file(s) directly

The issue is apparent on the GFDL computing systems and has also been replicated on a workstation physical disk so it's likely a cdms2 problem rather than anything hardware related.

[doutriaux1]

i suspect the time dim to be the killer, will report here as soon as we found a solution or at least a reason why.

[durack1]

With compressed (and potentially shuffled) netcdf4 files potentially coming down the pipe with CMIP6 it could be a good time to revisit how cdms2 is calling the netcdf C API, and if some compression/shuffling magic is better done by the library than Cdunif, then switching this to use the library.. If data reads can be sped up by reading across certain dimensions (so it appeared that reading all lons, and subsetting lats was 2x faster than the inverse) it would be great if a read call automagically did that for the user..

[aashish24]

👍 Would using parallel netcdf help?

[doutriaux1]

I don't think so in this case, it would probably help a bit but not so much, most of the wasted time (I believe) is spent reading the time dimensions from each files and recomposing the time objects. Taking cdunif is pretty much out of question since it is what allows us for reading in multiple formats.
But @aashish24 you're right we should definitely take advantage of // netcdf anyway.

[durack1]

You folks might want to assign this as a 2.1 milestone to get if off the to-do list

[aashish24]

Done

[doutriaux1]

@durack1 it's not a fix but since our file are niceley ordered based on name, using -j option makes the re-reading fast.

[durack1]

I'll take another look at this when I go and look at the GFDL data again, I do think that it's going to cause problems in the CMIP6+ timeframe..

[doutriaux1]

@painter1 that is the bug I'm thinking is hitting us on rhea. Will take a look tomorrow

[doutriaux1]

@durack1 are the files still around? @painter1 thread seems to indicate -j helps. Can't reproduce locally on a tiny example.

[painter1]

When I looked at the -j option it didn't seem that it does much of anything relative to the default behavior, except that it disables the default behavior of linearizing time for very short time units. Maybe I missed something.

[durack1]

@doutriaux1 yep - ocean:/export/doutriaux1/Paul we last discussed this back in June last year..

[durack1]

@doutriaux1 can you assign the enhancement label please?

[doutriaux1]

@dnadeau4 assigning this to you but let's work on it together

[dnadeau4]

I think it affect using THREDDS as well. #1475 I would like to only read 1 time dimension at a time instead of loading everything in memory at once. Will start to investigate a solution.

[durack1]

@dnadeau4 happy to run any tweaks you have over the test case, we have it pretty well reproduced..

[dnadeau4]

I have made progress on this parallel issue. Everything is working well. In an parallel world, every node must open the file, create dimensions and create variables. Only slicing is different for each one.

Please run testing/cmds2/test_mpi_write_2.py on branch issue_479.

[durack1]

@dnadeau4 are the tweaks on the branch above addressing the slow read times which was the focus of this original issue?

[dnadeau4]

This is a write in parallel program. Nothing to do with the original issue.

The original issue will need a re-architecture of CDMS. CDMS read the entire array in memory. I would like to change the code just to return a empty handler and read slices of the array per user request. Of course if the user ask for the entire array it will still be slow, but it could be possible to read in parallel using multiple nodes. Something to think about.

[durack1]

@dnadeau4 if there is no "fix" for this issue, aside from a rearchitecture of cdms2, then close this issue and add the large grid test to the suite for testing when cdms2 is updated..