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result_memory_usage.txt
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result_memory_usage.txt
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Weights creation took 0.028196096420288086 seconds
./data/natregimes.shp 999 brutal-force 1: 0.623711109161377 seconds
1.59 real 2.20 user 0.61 sys
76283904 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
28859 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
4 voluntary context switches
12221 involuntary context switches
/usr/bin/time -l python perf_pysal.py ./data/natregimes.shp HR60 999 1
Numba not installed
Weights creation took 0.7980890274047852 seconds, with transform and remove islands it took 0.8030571937561035 seconds
./data/natregimes.shp 999 1: 0.6306629180908203 seconds
4.79 real 11.15 user 1.78 sys
181473280 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
59051 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
17 messages sent
53 messages received
0 signals received
26 voluntary context switches
5783 involuntary context switches
/usr/bin/time -l Rscript perf_rgeoda.R ./data/natregimes.shp HR60 999 brutal-force 1
Loading required package: digest
Linking to GEOS 3.8.1, GDAL 3.1.4, PROJ 6.3.1
Reading layer `natregimes' from data source `/Users/xun/Github/libgeoda_paper/data/natregimes.shp' using driver `ESRI Shapefile'
Simple feature collection with 3085 features and 73 fields
geometry type: MULTIPOLYGON
dimension: XY
bbox: xmin: -124.7314 ymin: 24.95597 xmax: -66.96985 ymax: 49.37173
geographic CRS: WGS 84
user system elapsed
0.481 0.013 0.498
[1] "./data/natregimes.shp" "HR60" "999"
[4] "brutal-force" "1"
user system elapsed
0.615 0.000 0.615
2.16 real 2.03 user 0.11 sys
158724096 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
43264 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
82 voluntary context switches
34 involuntary context switches
/usr/bin/time -l Rscript perf_spdep.R ./data/natregimes.shp HR60 999 1
Linking to GEOS 3.8.1, GDAL 3.1.4, PROJ 6.3.1
Loading required package: sp
Loading required package: spData
Reading layer `natregimes' from data source `/Users/xun/Github/libgeoda_paper/data/natregimes.shp' using driver `ESRI Shapefile'
Simple feature collection with 3085 features and 73 fields
geometry type: MULTIPOLYGON
dimension: XY
bbox: xmin: -124.7314 ymin: 24.95597 xmax: -66.96985 ymax: 49.37173
geographic CRS: WGS 84
user system elapsed
2.583 0.121 2.704
[1] "./data/natregimes.shp" "HR60" "999"
[4] "1"
user system elapsed
1.344 0.080 1.423
7.85 real 7.41 user 0.43 sys
491085824 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
132313 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
17 voluntary context switches
41 involuntary context switches
/usr/bin/time -l Rscript perf_rgeoda.R ./data/natregimes.shp HR60 999 lookup-table 1
Loading required package: digest
Linking to GEOS 3.8.1, GDAL 3.1.4, PROJ 6.3.1
Reading layer `natregimes' from data source `/Users/xun/Github/libgeoda_paper/data/natregimes.shp' using driver `ESRI Shapefile'
Simple feature collection with 3085 features and 73 fields
geometry type: MULTIPOLYGON
dimension: XY
bbox: xmin: -124.7314 ymin: 24.95597 xmax: -66.96985 ymax: 49.37173
geographic CRS: WGS 84
user system elapsed
0.479 0.012 0.491
[1] "./data/natregimes.shp" "HR60" "999"
[4] "lookup-table" "1"
user system elapsed
0.056 0.000 0.056
1.58 real 1.46 user 0.10 sys
168402944 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
45650 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
10 voluntary context switches
39 involuntary context switches
/usr/bin/time -l Rscript perf_spdep.R ./data/NYC_Area2010_2data.shp CE01_02 999 1
Linking to GEOS 3.8.1, GDAL 3.1.4, PROJ 6.3.1
Loading required package: sp
Loading required package: spData
Reading layer `NYC_Area2010_2data' from data source `/Users/xun/Github/libgeoda_paper/data/NYC_Area2010_2data.shp' using driver `ESRI Shapefile'
Simple feature collection with 108487 features and 8 fields
geometry type: MULTIPOLYGON
dimension: XY
bbox: xmin: 1796733 ymin: 544070.8 xmax: 1991063 ymax: 677021.4
projected CRS: USA_Contiguous_Albers_Equal_Area_Conic
user system elapsed
1948.731 216.487 2165.408
[1] "./data/NYC_Area2010_2data.shp" "CE01_02"
[3] "999" "1"
user system elapsed
111.733 30.680 142.426
2315.69 real 2067.10 user 247.91 sys
4634091520 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
6085227 page reclaims
1718 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
637 voluntary context switches
17896 involuntary context switches
/usr/bin/time -l Rscript perf_rgeoda.R ./data/NYC_Area2010_2data.shp CE01_02 999 brutal-force 1
Loading required package: digest
Linking to GEOS 3.8.1, GDAL 3.1.4, PROJ 6.3.1
Reading layer `NYC_Area2010_2data' from data source `/Users/xun/Github/libgeoda_paper/data/NYC_Area2010_2data.shp' using driver `ESRI Shapefile'
Simple feature collection with 108487 features and 8 fields
geometry type: MULTIPOLYGON
dimension: XY
bbox: xmin: 1796733 ymin: 544070.8 xmax: 1991063 ymax: 677021.4
projected CRS: USA_Contiguous_Albers_Equal_Area_Conic
user system elapsed
3.271 0.126 3.411
[1] "./data/NYC_Area2010_2data.shp" "CE01_02"
[3] "999" "brutal-force"
[5] "1"
user system elapsed
31.95 0.02 31.98
39.16 real 38.65 user 0.43 sys
675368960 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
195556 page reclaims
111 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
305 voluntary context switches
620 involuntary context switches
Weights creation took 1.3009519577026367 seconds
./data/NYC_Area2010_2data.shp 999 brutal-force 1: 30.663637161254883 seconds
34.01 real 34.19 user 0.73 sys
345739264 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
94822 page reclaims
3540 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
882 voluntary context switches
9514 involuntary context switches
/usr/bin/time -l python perf_pysal.py ./data/NYC_Area2010_2data.shp CE01_02 999 1
Numba not installed
/Users/xun/Github/libgeoda_paper/venv/lib/python3.6/site-packages/libpysal/weights/weights.py:172: UserWarning: The weights matrix is not fully connected:
There are 215 disconnected components.
There are 155 islands with ids: 441, 1956, 2064, 2083, 2084, 2085, 2087, 2088, 2253, 2698, 2847, 3810, 3811, 3967, 4113, 4200, 4786, 5431, 5432, 6270, 6271, 6282, 7128, 7189, 8823, 8824, 10116, 10117, 11116, 11168, 12825, 13093, 13347, 15126, 15851, 15907, 16537, 17079, 18053, 19206, 20103, 20408, 20891, 23259, 23636, 25499, 25500, 25502, 25995, 26120, 26853, 26854, 27335, 27336, 27337, 28381, 28707, 31391, 31786, 31881, 31895, 32912, 32913, 32918, 33423, 33424, 35479, 35818, 35822, 36496, 37606, 38385, 40568, 41139, 42676, 46359, 46558, 46562, 48834, 49546, 53435, 53788, 53789, 57407, 59705, 65315, 66158, 66209, 66326, 66464, 67913, 68066, 69174, 71183, 71650, 71919, 72148, 72238, 72240, 72322, 72323, 72324, 72325, 72861, 73206, 73406, 73637, 73780, 74435, 74512, 74869, 75628, 76047, 76968, 77224, 77373, 78972, 80314, 80555, 80581, 81668, 81720, 83817, 84359, 85702, 86135, 86451, 86683, 86744, 87311, 87313, 87336, 88496, 89361, 89362, 89600, 89876, 90132, 90368, 91050, 91360, 91464, 91522, 91571, 91939, 92915, 94224, 97113, 97114, 97366, 99511, 102944, 106618, 107198, 108332.
warnings.warn(message)
Remove islands...
/Users/xun/Github/libgeoda_paper/venv/lib/python3.6/site-packages/libpysal/weights/weights.py:172: UserWarning: The weights matrix is not fully connected:
There are 60 disconnected components.
warnings.warn(message)
Weights creation took 20.145065307617188 seconds, with transform and remove islands it took 22.02610731124878 seconds
./data/NYC_Area2010_2data.shp 999 1: 46.72153282165527 seconds
81.69 real 459.24 user 94.60 sys
1103413248 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
312286 page reclaims
2627 page faults
0 swaps
0 block input operations
0 block output operations
17 messages sent
52 messages received
0 signals received
1251 voluntary context switches
1220494 involuntary context switches
/usr/bin/time -l python perf_pysal.py ./data/Chicago_parcels_points.shp EstBuild 999 1
Numba not installed
/Users/xun/Github/libgeoda_paper/venv/lib/python3.6/site-packages/libpysal/weights/weights.py:172: UserWarning: The weights matrix is not fully connected:
There are 73 disconnected components.
warnings.warn(message)
Weights creation took 29.743753910064697 seconds, with transform and remove islands it took 30.804020881652832 seconds
./data/Chicago_parcels_points.shp 999 1: 358.5050389766693 seconds
412.33 real 3461.79 user 730.23 sys
1294110720 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
419264 page reclaims
48 page faults
0 swaps
0 block input operations
0 block output operations
17 messages sent
52 messages received
0 signals received
27 voluntary context switches
7208091 involuntary context switches
/usr/bin/time -l Rscript perf_spdep.R ./data/Chicago_parcels_points.shp EstBuild 999 1
Linking to GEOS 3.8.1, GDAL 3.1.4, PROJ 6.3.1
Loading required package: sp
Loading required package: spData
Reading layer `Chicago_parcels_points' from data source `/Users/xun/Github/libgeoda_paper/data/Chicago_parcels_points.shp' using driver `ESRI Shapefile'
Simple feature collection with 321701 features and 6 fields
geometry type: POINT
dimension: XY
bbox: xmin: -88.26351 ymin: 41.46987 xmax: -87.52488 ymax: 42.15398
geographic CRS: WGS 84
user system elapsed
12570.801 3.449 12575.317
Warning message:
In st_centroid.sfc(st_geometry(dt)) :
st_centroid does not give correct centroids for longitude/latitude data
[1] "./data/Chicago_parcels_points.shp" "EstBuild"
[3] "999" "1"
user system elapsed
800.236 204.022 1004.287
13589.42 real 13380.33 user 207.98 sys
3610624000 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
983765 page reclaims
19 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
23 voluntary context switches
86767 involuntary context switches
/usr/bin/time -l ./perf_libgeoda ./data/natregimes.shp HR60 complete
Weights creation takes: 27 milliseconds.
perm: 999 threads: 1 avg of 3 runs: 562.667 milliseconds.
1.86 real 1.79 user 0.05 sys
12410880 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
2968 page reclaims
76 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
2 voluntary context switches
77 involuntary context switches
xuns-black-pro:libgeoda_paper xun$
/usr/bin/time -l ./perf_libgeoda ./data/natregimes.shp HR60 complete
Weights creation takes: 27 milliseconds.
perm: 999 threads: 1 avg of 3 runs: 562.667 milliseconds.
1.86 real 1.79 user 0.05 sys
12410880 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
2968 page reclaims
76 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
2 voluntary context switches
xuns-black-pro:libgeoda_paper xun$ /usr/bin/time -l ./perf_libgeoda ./data/NYC_Area2010_2data.shp CE01_02 complete
Weights creation takes: 1209 milliseconds.
perm: 999 threads: 1 avg of 3 runs: 28996.7 milliseconds.
88.96 real 88.76 user 0.17 sys
274579456 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
69561 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
3 voluntary context switches
626 involuntary context switches
xuns-black-pro:libgeoda_paper xun$ /usr/bin/time -l ./perf_libgeoda ./data/us-sdoh-2014.shp ep_unem complete
Weights creation takes: 915 milliseconds.
perm: 999 threads: 1 avg of 3 runs: 17348.7 milliseconds.
54.73 real 54.08 user 0.62 sys
375984128 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
91807 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
3 voluntary context switches
514 involuntary context switches
/usr/bin/time -l ./perf_libgeoda ./data/Chicago_parcels_points.shp EstBuild complete
Weights creation takes: 3057 milliseconds.
perm: 999 threads: 1 avg of 3 runs: 117637 milliseconds.
356.81 real 356.47 user 0.30 sys
258203648 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
63310 page reclaims
0 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
0 voluntary context switches
2199 involuntary context switches
/usr/bin/time -l python perf_pygeoda.py ./data/Chicago_parcels_points.shp EstBuild 999 brutal-force 1
Weights creation took 3.2569642066955566 seconds
./data/Chicago_parcels_points.shp 999 brutal-force 1: 132.47705817222595 seconds
137.54 real 138.10 user 0.59 sys
309952512 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
87477 page reclaims
975 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
394 voluntary context switches
3112 involuntary context switches
/usr/bin/time -l Rscript perf_rgeoda.R ./data/Chicago_parcels_points.shp EstBuild 999 brutal-force 1
Loading required package: digest
Linking to GEOS 3.8.1, GDAL 3.1.4, PROJ 6.3.1
Reading layer `Chicago_parcels_points' from data source `/Users/xun/Github/libgeoda_paper/data/Chicago_parcels_points.shp' using driver `ESRI Shapefile'
Simple feature collection with 321701 features and 6 fields
geometry type: POINT
dimension: XY
bbox: xmin: -88.26351 ymin: 41.46987 xmax: -87.52488 ymax: 42.15398
geographic CRS: WGS 84
user system elapsed
5.774 0.128 5.920
[1] "./data/Chicago_parcels_points.shp" "EstBuild"
[3] "999" "brutal-force"
[5] "1"
user system elapsed
117.271 0.113 117.432
130.09 real 129.42 user 0.52 sys
689676288 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
201179 page reclaims
126 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
212 voluntary context switches
1939 involuntary context switches