[netcdfgroup] Strided reads slow with upgrade to 4.3.3.1

• To: "netcdfgroup@xxxxxxxxxxxxxxxx" <netcdfgroup@xxxxxxxxxxxxxxxx>
• Subject: [netcdfgroup] Strided reads slow with upgrade to 4.3.3.1
• From: Ellen Johnson <Ellen.Johnson@xxxxxxxxxxxxx>
• Date: Wed, 16 Sep 2015 14:35:59 +0000

Good morning all,
  We upgraded from netCDF 4.1.3 to netCDF 4.3.3.1 for MATLAB R2015b.  We 
recently had a customer report that strided reads (with strides other than 1) 
for their netCDF-4 file is much slower in MATLAB R2015b than in R2015a.
  I've seen several threads on the netCDF mailing list about this, and wanted 
to know if there's a solution or workaround for this.  I also see that it may 
have something to do with the fact that netCDF-4 files use HDF5 underneath and 
it may be related to an HDF5 performance issue.
  My question is why we don't see this in our prior MATLAB release R2015a, 
which used netCDF 4.1.3 (and HDF5 1.8.12).  We only see this in MATLAB after 
the upgrade to netCDF 4.3.3.1 (still using HDF5 1.8.12).
  I wrote a standalone C function outside of MATLAB calling netCDF 4.3.3.1 
directly, and I still see the slow strided reads outside of MATLAB.
  If anyone can provide and update, and why we only see this after upgrading to 
4.3.3.1, that would be much appreciated.
  Thank you!
     Ellen

Ellen Johnson
Senior Software Engineer
Image and Scientific File Formats

MATLAB Toolbox

MathWorks

1-508-647-8288

ellen.johnson@xxxxxxxxxxxxx