<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Sep 17, 2014 at 7:40 PM, Sandra MacFadyen <span dir="ltr"><<a href="mailto:sandramf@live.co.za" target="_blank">sandramf@live.co.za</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Markus,<br>
<br>
Excellent! Thanks to everyone for their help.<br>
I tested r.diversity in the new revision (61840) on a raster with 12933032 cells and it took under 3 minutes to complete r.li.simpson, r.li.shannon, r.li.pielou and r.li.renyi outputs.<br>
Amazing :)<br>
<br>
> execGRASS("r.diversity",flags="overwrite", parameters=list(input="flow", prefix="flow_div", alpha=0.5, size=3))<br>
> r.li.simpson complete. Raster map <flow_div_simpson_size_3.0> created.<br>
> r.li.shannon complete. Raster map <flow_div_shannon_size_3.0> created.<br>
> r.li.pielou complete. Raster map <flow_div_pielou_size_3.0> created.<br>
> r.li.renyi complete. Raster map <flow_div_renyi_size_3.0_alpha_0.5><br>
> created.<br>
> Done.<br>
<br>
Thanks again and keep well.<br>
<br></blockquote><div>Good to hear that. Can you say if the results are correct? I computed difference of one map before and after and it was OK. But it would be great to have more tests. Let's start with: does the result make sense?<br></div><div><br></div><div>Vaclav<br> <br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Cheers<br>
Sandra<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:neteler.osgeo@gmail.com">neteler.osgeo@gmail.com</a> [mailto:<a href="mailto:neteler.osgeo@gmail.com">neteler.osgeo@gmail.com</a>] On Behalf Of Markus Neteler<br>
Sent: 06 September 2014 05:15 AM<br>
To: Sandra MacFadyen<br>
Cc: GRASS user list; Duccio Rocchini; Luca Delucchi<br>
Subject: Re: [GRASS-user] execGRASS("r.diversity") Done. No rasters created (Large rasters)<br>
<br>
Dear Sandra,<br>
<br>
On Fri, Jun 20, 2014 at 7:49 AM, Markus Neteler <<a href="mailto:neteler@osgeo.org">neteler@osgeo.org</a>> wrote:<br>
> On Sat, Jun 14, 2014 at 9:21 AM, Sandra MacFadyen <<a href="mailto:sandramf@live.co.za">sandramf@live.co.za</a>> wrote:<br>
>> I am using r.diversity (GRASS GIS 7.0.0svn build 60785 win32) through<br>
>> R (R version 3.0.2 win32) on Windows 7 64bit.<br>
...<br>
>> However, when running the same code on a larger image (cells=6746328)<br>
>> from my own location, although it reports Done, no rasters are<br>
>> created. If I subset the image<br>
>> (cells=1632830) and run it again its works (see # sub2Kruger # code and results below).<br>
>> So I'm guessing it is a memory issue?<br>
...<br>
> ... it consumes a lot of memory... will check on a bigger machine,<br>
> perhaps a memory leak.<br>
<br>
The assumption turned out to be right and I think we got it today!<br>
<br>
Vaclav Petras checked it and discovered an "unfortunate" memory allocation which he fixed in r.li.* in revision <a href="http://trac.osgeo.org/grass/changeset/61812" target="_blank">http://trac.osgeo.org/grass/changeset/61812</a> ("<a href="http://r.li" target="_blank">r.li</a>: fix memory handling (memory leak in avl_to_array function))".<br>
<br>
Now <a href="http://r.li" target="_blank">r.li</a> has become very fast, on my laptop:<br>
<br>
GRASS 7.1.svn (nc_spm_08_grass7):~ > g.region -p rast=lsat5_1987_10 res=10 -a ...<br>
rows: 1355<br>
cols: 1503<br>
cells: 2036565<br>
<br>
GRASS 7.1.svn (nc_spm_08_grass7):~ > time -p r.li.simpson --o input=lsat5_1987_10@landsat conf=conf_diversity_5.0<br>
output=lsat5_1987_div__simpson_size_5.0<br>
r.li.simpson complete. Raster map <lsat5_1987_div__simpson_size_5.0><br>
created.<br>
--> 29.32 seconds<br>
<br>
or with a simulated higher resolution:<br>
<br>
GRASS 7.1.svn (nc_spm_08_grass7):~ > g.region -p rast=lsat5_1987_10<br>
res=5 -aprojection: 99 (Lambert Conformal Conic) ...<br>
rows: 2708<br>
cols: 3005<br>
cells: 8137540<br>
<br>
GRASS 7.1.svn (nc_spm_08_grass7):~ > time -p r.li.simpson --o input=lsat5_1987_10@landsat conf=conf_diversity_5.0<br>
output=lsat5_1987_div__simpson_size_5.0<br>
r.li.simpson complete. Raster map <lsat5_1987_div__simpson_size_5.0><br>
created.<br>
--> 227.37 seconds (used to be > 2 hours)<br>
<br>
So, to grab this improvement for Windows, grab the version from here:<br>
<a href="http://wingrass.fsv.cvut.cz/grass71/" target="_blank">http://wingrass.fsv.cvut.cz/grass71/</a><br>
<br>
(or via OSGeo4W installer). Be sure that the revision is at least<br>
r61812 which is indicated in the file name.<br>
<br>
Please let us know if all works to avoid that the change has any negative impact.<br>
Tests here did not show any changes in the output except for the speed improvement and solved memory leak.<br>
<br>
Subsequently also r.diversity should behave now.<br>
<br>
I'll backport it to GRASS 7.0 release branch after some testing.<br>
<br>
Markus<br>
<br>
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</blockquote></div><br></div></div>