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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Maybe this is a problem with your NetCDF internal chunks cache too small and related to this ticket:
<a href="https://trac.osgeo.org/gdal/ticket/5291">https://trac.osgeo.org/gdal/ticket/5291</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You can change this per-variable cache using this C function:
<a href="http://www.unidata.ucar.edu/software/netcdf/docs/group__variables.html#ga2788cbfc6880ec70c304292af2bc7546">
http://www.unidata.ucar.edu/software/netcdf/docs/group__variables.html#ga2788cbfc6880ec70c304292af2bc7546</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Else a workaround may be to rechunk your data using nccopy to have chunks of the same size than your reading window.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Another solution is to recompile your NetCDF library to set more chunks cache.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Julien<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">De :</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gdal-dev [mailto:gdal-dev-bounces@lists.osgeo.org]
<b>De la part de</b> Pablo Rozas Larraondo<br>
<b>Envoyé :</b> mardi 22 novembre 2016 08:53<br>
<b>À :</b> gdal-dev@lists.osgeo.org<br>
<b>Objet :</b> [gdal-dev] slow netCDF read times<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">Hello,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt"><br>
I've come across some NetCDF4 files where GDAL is taking a surprisingly long time to read data from them. For example this is an example public file containing precipitation data:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt"><a href="ftp://ftp.chg.ucsb.edu/pub/org/chg/products/CHIRPS-2.0/global_dekad/netcdf/chirps-v2.0.2015.dekads.nc" target="_blank">ftp://ftp.chg.ucsb.edu/pub/org/chg/products/CHIRPS-2.0/global_dekad/netcdf/chirps-v2.0.2015.dekads.nc</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">If I use GDAL to read a small top left block (500x500) from one of its time bands, it takes approximately 1 minute on my computer. Source code is available here:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt"><a href="https://gist.github.com/monkeybutter/769a24bcf87682171eb87ac05c9347c5" target="_blank">https://gist.github.com/monkeybutter/769a24bcf87682171eb87ac05c9347c5</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">The equivalent operation is completed in less than a second using the NetCDF library and even reading the whole file takes around 6 seconds with the same library.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">I've tried to profile the GDAL program to get more insight and understand what's causing the overhead with not much success. All I know is that the deflate function is using 96% of the resources. I also guess
that the way this file is chunked has something to do with its performance. Can anyone suggest any idea for better understanding what's happening here?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">Thank you for your help,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">Pablo<o:p></o:p></span></p>
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