Description
When I run Circuitscape in Julia I encounter this problem: it seems that not all points are solved. The process speeds up at some point and the cumulative current map output shows connectivity in only a part of the map. I assume that not all points are dealt with.
I use Julia 1.8.1. and the latest version of Circuitscape installed by Pkg.add(PackageSpec(name="Circuitscape", rev="master")).
EXAMPLE:
julia> compute("E:\ALEXANOR\UNI\RICERCA\Connectivity\circuitscape\da_parches\P_circuit.ini")
[ Info: 2022-09-18 02:45:50 : Logs will recorded to file: log_file
[ Info: 2022-09-18 02:45:50 : Precision used: Double
[ Info: 2022-09-18 02:45:50 : Reading maps
[ Info: 2022-09-18 02:45:50 : Resistance/Conductance map has 133121 nodes
[ Info: 2022-09-18 02:45:52 : There are 132515 points and 7559 connected components
[ Info: 2022-09-18 02:45:52 : Solving point 1 of 281
[ Info: 2022-09-18 02:45:52 : Solver used: CHOLMOD
[ Info: 2022-09-18 02:45:52 : Time taken to construct cholesky factor = 0.0032751
[ Info: 2022-09-18 02:45:52 : Time taken to solve linear system = 0.0002907 seconds
[ Info: 2022-09-18 02:45:52 : Solving point 2 of 281
[ Info: 2022-09-18 02:45:52 : Solver used: CHOLMOD
[ Info: 2022-09-18 02:45:52 : Time taken to construct cholesky factor = 0.0043229
[ Info: 2022-09-18 02:45:52 : Time taken to solve linear system = 0.0002755 seconds
[ Info: 2022-09-18 02:45:53 : Solving point 3 of 281
[ Info: 2022-09-18 02:45:53 : Solver used: CHOLMOD
[ Info: 2022-09-18 02:45:53 : Time taken to construct cholesky factor = 0.0032252
[ Info: 2022-09-18 02:45:53 : Time taken to solve linear system = 0.0003644 seconds
... after some seconds...
[ Info: 2022-09-18 02:45:54 : Solving point 18 of 281
[ Info: 2022-09-18 02:45:54 : Solver used: CHOLMOD
[ Info: 2022-09-18 02:45:54 : Solving point 19 of 281
[ Info: 2022-09-18 02:45:54 : Solver used: CHOLMOD
[ Info: 2022-09-18 02:45:55 : Solving point 20 of 281
[ Info: 2022-09-18 02:45:55 : Solver used: CHOLMOD
[ Info: 2022-09-18 02:45:55 : Solving point 21 of 281
[ Info: 2022-09-18 02:45:55 : Solver used: CHOLMOD
[ Info: 2022-09-18 02:45:55 : Solving point 22 of 281
[ Info: 2022-09-18 02:45:55 : Solver used: CHOLMOD
etc.
.... and finally.....
[ Info: 2022-09-18 02:46:36 : Solving point 281 of 281
[ Info: 2022-09-18 02:46:37 : Solver used: CHOLMOD
[ Info: 2022-09-18 02:46:37 : Time taken to complete job = 47.2072923
281×2 Matrix{Float64}:
1.0 0.0
2.0 0.0
3.0 0.0
4.0 0.0
5.0 0.0
6.0 0.0
7.0 0.0
8.0 0.0
9.0 0.0
10.0 0.0
11.0 0.0
12.0 0.0
13.0 0.0
⋮
270.0 -1.0
271.0 -1.0
272.0 -1.0
273.0 -1.0
274.0 -1.0
275.0 -1.0
276.0 -1.0
277.0 -1.0
278.0 -1.0
279.0 -1.0
280.0 -1.0
281.0 -1.0
julia>
Here is my ini file settings:
<[Options for advanced mode]
ground_file_is_resistances = True
remove_src_or_gnd = keepall
ground_file = (Browse for a ground point file)
use_unit_currents = False
source_file = (Browse for a current source file)
use_direct_grounds = False
[Mask file]
mask_file =
use_mask = False
[Calculation options]
low_memory_mode = False
parallelize = False
solver = cholmod
print_timings = 0
preemptive_memory_release = False
print_rusages = False
max_parallel = 0
[Short circuit regions (aka polygons)]
polygon_file = (Browse for a short-circuit region file)
use_polygons = False
[Options for one-to-all and all-to-one modes]
use_variable_source_strengths = False
variable_source_file = (Browse for a source strength file)
[Output options]
set_null_currents_to_nodata = False
set_focal_node_currents_to_zero = False
set_null_voltages_to_nodata = False
compress_grids = False
write_cur_maps = 1
write_volt_maps = 0
output_file = E:\ALEXANOR\UNI\RICERCA\Connectivity\circuitscape\da_parches\P_circuit.out
write_cum_cur_map_only = True
log_transform_maps = False
write_max_cur_maps = False
[Version]
version = 4.0.5
[Options for reclassification of habitat data]
reclass_file = (Browse for file with reclassification data)
use_reclass_table = False
[Logging Options]
log_level = INFO
log_file = E:\ALEXANOR\UNI\RICERCA\Connectivity\circuitscape\da_parches\P_circuit.log
profiler_log_file = None
screenprint_log = False
[Options for pairwise and one-to-all and all-to-one modes]
included_pairs_file = (Browse for a file with pairs to include or exclude)
use_included_pairs = False
point_file = E:\ALEXANOR\UNI\RICERCA\Connectivity\circuitscape\da_parches\P_conn.asc
[Connection scheme for raster habitat data]
connect_using_avg_resistances = False
connect_four_neighbors_only = False
[Habitat raster or graph]
habitat_map_is_resistances = False
habitat_file = E:\ALEXANOR\UNI\RICERCA\Connectivity\circuitscape\da_parches\P_sdm.asc
[Circuitscape mode]
data_type = raster
scenario = all-to-one
cholmod_batch_size = 100>