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Thanks for the reply :) I should have said that we have already considered chunking and have the file contiguous for now (going to have a look at chunking soon). But you are right if we had a chunked file that would probably have been the cause. Thanks Matt -------- Original message -------- From: Chris Barker - NOAA Federal <chris.barker@xxxxxxxx> Date: 28/10/2015 19:59 (GMT+00:00) To: Matthew Jones <M.Jones3@xxxxxxxxxxxxxxxxx> Cc: netcdfgroup@xxxxxxxxxxxxxxxx Subject: Re: [netcdfgroup] netcdf buffers I'm no expert (particularly not with HPC), but you could be seeing effects from chunking. Netcdf4/HDF5 groups the arrays in chunks to allow multiple unlimited dimensions and compression, etc. One result is that you can't read less than one chunk of data at once. So maximum performance is reached when you are reading one chunk at a time. Also, you want the chunking configuration to match your access patterns. The default may not be well suited to your use case. Google a bit for discussion of how to select good chunking. -CHB On Oct 28, 2015, at 10:57 AM, Matthew Jones <M.Jones3@xxxxxxxxxxxxxxxxx<mailto:M.Jones3@xxxxxxxxxxxxxxxxx>> wrote: Hi I am running some tests on an HPC cluster, altering the size of reads to test the performance of the file system. I am using python, and for sequential reads not using netCDF4 the read rate is pretty constant across different read sizes. However, when I introduce the netCDF4 library the smaller and larger reads see a dip in performance with a peak on the medium sized reads (creating a hill-like profile). The peak in the netCDF4 performance is at about the same read rate as the non-netCDF4 reads. The peak is at reads of about 1MB. We think this could be to do with buffering somewhere in the NetCDF library. Does anyone know of such buffering that we should be aware of? Many thanks Matt ---------------------------------------- Matthew Jones PhD Student Atmosphere, Oceans and Climate Department of Meteorology, University of Reading Room 288, ESSC, Harry Pitt Building, 3 Earley Gate, Reading, RG6 6AL, UK Ext: 5214 https://www.linkedin.com/pub/matthew-jones/8b/b81/25a http://www.met.reading.ac.uk/users/users/1887 _______________________________________________ netcdfgroup mailing list netcdfgroup@xxxxxxxxxxxxxxxx<mailto:netcdfgroup@xxxxxxxxxxxxxxxx> For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/
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