[GRASS-user] execGRASS("r.diversity") Done. No rasters created (Large rasters)
Sandra MacFadyen
sandramf at live.co.za
Sat Jun 14 00:21:05 PDT 2014
Dear GRASS Users,
I am using r.diversity (GRASS GIS 7.0.0svn build 60785 win32) through R (R version 3.0.2 win32) on Windows 7 64bit.
Testing from GRASS and North_Carolina dataset's lsat5_1987_10 raster (cells=29535), [r.diversity --o input=lsat5_1987_10 at landsat prefix=lsat5_1987_div_ alpha=0.5 size=5] reports as Done with the different diversity rasters added to the location fine (see # North_Carolina# code and results below).
However, when running the same code on a larger image (cells=6746328) from my own location, although it reports Done, no rasters are created. If I subset the image (cells=1632830) and run it again its works (see # sub2Kruger # code and results below). So I'm guessing it is a memory issue? My question is, how can I run r.diversity on an entire Landsat scence (cells= 54886341) as illustrated in http://www.faunalia.eu/pdf/ECOINF_2013.pdf
Thank you :)
Sandra
# North_Carolina#
g.gisenv set=DEBUG=1
g.gisenv -n
g.region -p
g.region rast=lsat5_1987_10 at landsat
g.region -p
r.diversity --o input=lsat5_1987_10 at landsat prefix=lsat5_1987_div_ alpha=0.5 size=5
g.gisenv set=DEBUG=0
#------------------------------------
(Sat Jun 14 08:01:50 2014)
g.gisenv set=DEBUG=1
(Sat Jun 14 08:01:51 2014) Command finished (0 sec)
(Sat Jun 14 08:05:42 2014)
g.gisenv -n
MAPSET=PERMANENT
GISDBASE=C:\Users\Sands\Documents\grassdata
LOCATION_NAME=North_Carolina
GUI=wxpython
DEBUG=1
(Sat Jun 14 08:05:43 2014) Command finished (0 sec)
(Sat Jun 14 08:02:00 2014)
g.region -p
D1/1: <PROJ_EPSG> file not found for location
<North_Carolina>
projection: 99 (Lambert Conformal Conic)
zone: 0
datum: nad83
ellipsoid: a=6378137 es=0.006694380022900787
north: 221230
south: 219580
west: 637740
east: 639530
nsres: 10
ewres: 10
rows: 165
cols: 179
cells: 29535
(Sat Jun 14 08:02:00 2014) Command finished (0 sec)
(Sat Jun 14 08:02:09 2014)
g.region rast=lsat5_1987_10 at landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
(Sat Jun 14 08:02:10 2014) Command finished (0 sec)
(Sat Jun 14 08:02:18 2014)
g.region -p
D1/1: <PROJ_EPSG> file not found for location
<North_Carolina>
projection: 99 (Lambert Conformal Conic)
zone: 0
datum: nad83
ellipsoid: a=6378137 es=0.006694380022900787
north: 228513
south: 214975.5
west: 629992.5
east: 645012
nsres: 28.5
ewres: 28.5
rows: 475
cols: 527
cells: 250325
(Sat Jun 14 08:02:18 2014) Command finished (0 sec)
(Sat Jun 14 08:03:10 2014)
r.diversity --o input=lsat5_1987_10 at landsat prefix=lsat5_1987_div_ alpha=0.5 size=5
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: grass.script.core.start_command(): r.li.simpson --o
--q input=lsat5_1987_10 at landsat conf=conf_diversity_5.0
output=lsat5_1987_div__simpson_size_5.0
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster(): name=MASK mapset=PERMANENT
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat5_1987_div__simpson_size_5.0 compressed
D1/1: G_find_raster2():
name=lsat5_1987_div__simpson_size_5.0 mapset=PERMANENT
D1/1: G_find_raster2():
name=lsat5_1987_div__simpson_size_5.0 mapset=PERMANENT
D1/1: G_find_raster2():
name=lsat5_1987_div__simpson_size_5.0 mapset=PERMANENT
D1/1: grass.script.core.start_command(): r.li.shannon --o
--q input=lsat5_1987_10 at landsat conf=conf_diversity_5.0
output=lsat5_1987_div__shannon_size_5.0
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster(): name=MASK mapset=PERMANENT
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat5_1987_div__shannon_size_5.0 compressed
D1/1: G_find_raster2():
name=lsat5_1987_div__shannon_size_5.0 mapset=PERMANENT
D1/1: G_find_raster2():
name=lsat5_1987_div__shannon_size_5.0 mapset=PERMANENT
D1/1: G_find_raster2():
name=lsat5_1987_div__shannon_size_5.0 mapset=PERMANENT
D1/1: grass.script.core.start_command(): r.li.pielou --o --q
input=lsat5_1987_10 at landsat conf=conf_diversity_5.0
output=lsat5_1987_div__pielou_size_5.0
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster(): name=MASK mapset=PERMANENT
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat5_1987_div__pielou_size_5.0 compressed
D1/1: G_find_raster2(): name=lsat5_1987_div__pielou_size_5.0
mapset=PERMANENT
D1/1: G_find_raster2(): name=lsat5_1987_div__pielou_size_5.0
mapset=PERMANENT
D1/1: G_find_raster2(): name=lsat5_1987_div__pielou_size_5.0
mapset=PERMANENT
D1/1: grass.script.core.start_command(): r.li.renyi --o --q
output=lsat5_1987_div__renyi_size_5.0_alpha_0.5
input=lsat5_1987_10 at landsat conf=conf_diversity_5.0
alpha=0.5
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster2(): name=lsat5_1987_10 mapset=landsat
D1/1: G_find_raster(): name=MASK mapset=PERMANENT
D1/1: G_find_raster2(): name=lsat5_1987_10 at landsat mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat5_1987_div__renyi_size_5.0_alpha_0.5
compressed
D1/1: G_find_raster2():
name=lsat5_1987_div__renyi_size_5.0_alpha_0.5
mapset=PERMANENT
D1/1: G_find_raster2():
name=lsat5_1987_div__renyi_size_5.0_alpha_0.5
mapset=PERMANENT
D1/1: G_find_raster2():
name=lsat5_1987_div__renyi_size_5.0_alpha_0.5
mapset=PERMANENT
D1/1: grass.script.core.start_command(): g.message
message=Done.
Done.
(Sat Jun 14 08:03:23 2014) Command finished (12 sec)
(Sat Jun 14 08:03:59 2014)
g.gisenv set=DEBUG=0
(Sat Jun 14 08:03:59 2014) Command finished (0 sec)
#XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
# sub2Kruger #
g.gisenv set=DEBUG=1
g.gisenv -n
g.region -p
g.region rast=lsat7_1993s1 at tSub2
g.region -p
r.diversity --o input= lsat7_1993s1 at tSub2 prefix=lsat7_1993s1_div_ alpha=0.5 size=5
r.in.gdal input=D:\lndsr.LE71999353-band1_utm_clip2.tif output=lsat7_1993s2 -e
g.region -p
r.diversity --o input=lsat7_1993s2 at tSub2 prefix=lsat7_1993s2_div_ alpha=0.5 size=5
g.gisenv set=DEBUG=0
#--------------------------------------------------
g.gisenv set=DEBUG=1
(Sat Jun 14 08:18:48 2014) Command finished (0 sec)
(Sat Jun 14 08:18:58 2014)
g.gisenv -n
MAPSET=tSub2
GISDBASE=C:\Users\Sands\Documents\grassdata\
LOCATION_NAME=sub2Kruger
GUI=wxpython
DEBUG=1
(Sat Jun 14 08:18:58 2014) Command finished (0 sec)
(Sat Jun 14 08:19:25 2014)
g.proj -p
-PROJ_INFO-------------------------------------------------
name : Universal Transverse Mercator
proj : utm
datum : wgs84
ellps : wgs84
zone : 36
south : defined
no_defs : defined
towgs84 : 0.000,0.000,0.000
-PROJ_UNITS------------------------------------------------
unit : meter
units : meters
meters : 1
(Sat Jun 14 08:19:25 2014) Command finished (0 sec)
(Sat Jun 14 08:20:18 2014)
g.region -p
D1/1: <PROJ_EPSG> file not found for location <sub2Kruger>
projection: 1 (UTM)
zone: -36
datum: wgs84
ellipsoid: wgs84
north: 7270285.00009493
south: 7207645.00009493
west: 342134.99995605
east: 439064.99995605
nsres: 30
ewres: 30
rows: 2088
cols: 3231
cells: 6746328
(Sat Jun 14 08:20:18 2014) Command finished (0 sec)
(Sat Jun 14 08:21:36 2014)
r.diversity input=lsat7_1993s1 at tSub2 prefix=lsat7_1993s1_div_ alpha=0.5 size=5
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: grass.script.core.start_command(): r.li.simpson --q
input=lsat7_1993s1 at tSub2 conf=conf_diversity_5.0
output=lsat7_1993s1_div__simpson_size_5.0
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster(): name=MASK mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat7_1993s1_div__simpson_size_5.0 compressed
D1/1: G_find_raster2():
name=lsat7_1993s1_div__simpson_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s1_div__simpson_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s1_div__simpson_size_5.0 mapset=tSub2
D1/1: grass.script.core.start_command(): r.li.shannon --q
input=lsat7_1993s1 at tSub2 conf=conf_diversity_5.0
output=lsat7_1993s1_div__shannon_size_5.0
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster(): name=MASK mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat7_1993s1_div__shannon_size_5.0 compressed
D1/1: G_find_raster2():
name=lsat7_1993s1_div__shannon_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s1_div__shannon_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s1_div__shannon_size_5.0 mapset=tSub2
D1/1: grass.script.core.start_command(): r.li.pielou --q
input=lsat7_1993s1 at tSub2 conf=conf_diversity_5.0
output=lsat7_1993s1_div__pielou_size_5.0
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster(): name=MASK mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat7_1993s1_div__pielou_size_5.0 compressed
D1/1: G_find_raster2():
name=lsat7_1993s1_div__pielou_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s1_div__pielou_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s1_div__pielou_size_5.0 mapset=tSub2
D1/1: grass.script.core.start_command(): r.li.renyi --q
output=lsat7_1993s1_div__renyi_size_5.0_alpha_0.5
input=lsat7_1993s1 at tSub2 conf=conf_diversity_5.0 alpha=0.5
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 mapset=tSub2
D1/1: G_find_raster(): name=MASK mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s1 at tSub2 mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat7_1993s1_div__renyi_size_5.0_alpha_0.5
compressed
D1/1: G_find_raster2():
name=lsat7_1993s1_div__renyi_size_5.0_alpha_0.5 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s1_div__renyi_size_5.0_alpha_0.5 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s1_div__renyi_size_5.0_alpha_0.5 mapset=tSub2
D1/1: grass.script.core.start_command(): g.message
message=Done.
Done.
(Sat Jun 14 08:22:43 2014) Command finished (1 min 6 sec)
(Sat Jun 14 08:38:34 2014)
r.in.gdal input=D:\lndsr.LE71999353-band1_utm_clip2.tif output=lsat7_1993s2 -e
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster(): name=MASK mapset=tSub2
D1/1: Creating support files for lsat7_1993s2
D1/1: close lsat7_1993s2 compressed
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
Raster map <lsat7_1993s2> created.
Region for the current mapset updated
r.in.gdal complete.
(Sat Jun 14 08:38:35 2014) Command finished (1 sec)
(Sat Jun 14 08:41:03 2014)
g.region -p
D1/1: <PROJ_EPSG> file not found for location <sub2Kruger>
projection: 1 (UTM)
zone: -36
datum: wgs84
ellipsoid: wgs84
north: 7250125.00009493
south: 7213705.00009493
west: 354434.99995605
east: 394784.99995605
nsres: 30
ewres: 30
rows: 1214
cols: 1345
cells: 1632830
(Sat Jun 14 08:41:04 2014) Command finished (0 sec)
(Sat Jun 14 08:21:36 2014)
r.diversity input=lsat7_1993s2 at tSub2 prefix=lsat7_1993s2_div_ alpha=0.5 size=5
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: grass.script.core.start_command(): r.li.simpson --q
input=lsat7_1993s2 at tSub2 conf=conf_diversity_5.0
output=lsat7_1993s2_div__simpson_size_5.0
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster(): name=MASK mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat7_1993s2_div__simpson_size_5.0 compressed
D1/1: G_find_raster2():
name=lsat7_1993s2_div__simpson_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s2_div__simpson_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s2_div__simpson_size_5.0 mapset=tSub2
D1/1: grass.script.core.start_command(): r.li.shannon --q
input=lsat7_1993s2 at tSub2 conf=conf_diversity_5.0
output=lsat7_1993s2_div__shannon_size_5.0
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster(): name=MASK mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat7_1993s2_div__shannon_size_5.0 compressed
D1/1: G_find_raster2():
name=lsat7_1993s2_div__shannon_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s2_div__shannon_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s2_div__shannon_size_5.0 mapset=tSub2
D1/1: grass.script.core.start_command(): r.li.pielou --q
input=lsat7_1993s2 at tSub2 conf=conf_diversity_5.0
output=lsat7_1993s2_div__pielou_size_5.0
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster(): name=MASK mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat7_1993s2_div__pielou_size_5.0 compressed
D1/1: G_find_raster2():
name=lsat7_1993s2_div__pielou_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s2_div__pielou_size_5.0 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s2_div__pielou_size_5.0 mapset=tSub2
D1/1: grass.script.core.start_command(): r.li.renyi --q
output=lsat7_1993s2_div__renyi_size_5.0_alpha_0.5
input=lsat7_1993s2 at tSub2 conf=conf_diversity_5.0 alpha=0.5
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 mapset=tSub2
D1/1: G_find_raster(): name=MASK mapset=tSub2
D1/1: G_find_raster2(): name=lsat7_1993s2 at tSub2 mapset=
D1/1: r.li.daemon pathSetup: [C:\Users\Sands\AppData\Roa
ming\GRASS7\r.li\conf_diversity_5.0]
D1/1: close lsat7_1993s2_div__renyi_size_5.0_alpha_0.5
compressed
D1/1: G_find_raster2():
name=lsat7_1993s2_div__renyi_size_5.0_alpha_0.5 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s2_div__renyi_size_5.0_alpha_0.5 mapset=tSub2
D1/1: G_find_raster2():
name=lsat7_1993s2_div__renyi_size_5.0_alpha_0.5 mapset=tSub2
D1/1: grass.script.core.start_command(): g.message
message=Done.
Done.
(Sat Jun 14 08:22:43 2014) Command finished (1 min 6 sec)
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