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[netCDF #ACI-624328]: Experiences from rechunking with nccopy

Hi Joe,

> I've been doing some rechunking of large files with nccopy, and have
> encountered two potential issues.
> 
> The first is that the -h switch seems to work only up to around 1.7
> GB. Specifying -h 2G or 5G doesn't seem to affect memory usage of
> the process, or its performance. This was tested with 4.3.1.1 on 64
> bit CentOS, and also with your prebuilt 64 bit Windows binaries (also
> 4.3.1.1).

What you're seeing is that the performance isn't limited by the chunk
cache size, it's limited by the actual I/O.  Although you requested 5
GBytes of chunk cache, the library doesn't malloc that much, but only
mallocs what it needs up to that amount.  So it doesn't need more than
1.7 GBytes for the output file chunk cache in your case.

Here's a demonstration you can see from the example file you sent,
where you want to rechunk the variable Tair:

  dimensions:
          lon = 720 ;
          lat = 360 ;
          time = UNLIMITED ; // (365 currently)
 ...
        double Tair(time, lat, lon) ;

from 365 x 360 x 720 to 60 x 60 x 60.  I renamed your input file
"htest.nc" and time each of the following commands after purging the
OS disk buffers, so the data is actually read from the disk rather
than from OS cache.  If I run (and time)

  $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -m 5g -h 5g htest.nc tmp.nc
  real  0m28.33s

But I get essentially the same time if I only reserve enough chunk
cache for one output chunk, 60*60*60*8 bytes:

  $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -m 5g -h 1.728m htest.nc 
tmp.nc
  real  0m27.89s

And I don't actually need to reserve any memory at all for the input
buffer, because all it needs is enough for one chunk of the input, and
it allocates that much by default:

  $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -h 1.728m htest.nc tmp.nc
  real  0m24.86s

But if I don't have enough chunk cache to hold at least one chunk of
the output file, it takes *much* longer:

  $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -h 1.727m htest.nc tmp.nc
  real  16m20.36s

Your results will vary with more variables and more times.  For
example, with 2 variables of the size of Tair, you need to hold two
chunks of output (about 3.5m), but in that case it turns out to be
good to specify a larger input file buffer: 

  $./purge; time nccopy -c 'time/60,lat/60,lon/60' -m 100m -h 3.5m htest2.nc 
tmp.nc
  real  2m49.04s

Incidentally, I get better performance on the small example by using
the "-w" option to use a diskless write and keep the output in memory
until the output is closed, not using -h at all:

  $ ./purge; time nccopy -c 'time/60,lat/60,lon/60' -m 100m -w htest2.nc tmp.nc
  real  2m13.14s

--Russ

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: ACI-624328
Department: Support netCDF
Priority: Normal
Status: Closed