Advanced run not completing (see also #131)

[SimonTapper]

I am trying to run Circuitscape in advanced mode (wall-to-wall), but the run never completes. It calculates the 'Time taken to solve the linear system' and then continues to process indefinitely (as far as I can tell). I have tried several versions of Julia (1.6.0, 1.6.3, 1.67, 1.72, 1.8), and it's the same situation in all of them. I have tried changing some aspects of the ini file (below), but have not succeeded. For example, I have tried with solver = cg+amg, with different ground and source asc files, and with different/additional arguments (e.g., write_cur_maps = 1).

[circuitscape options]
data_type = raster
scenario = advanced
ground_file_is_resistances = True
source_file = path to source.asc
ground_file = path to ground.asc
output_file = path to out.out
habitat_file = path to habitat file.asc
solver = cholmod
print_timings = True
write_cur_maps = True
connect_four_neighbors_only = False
connect_using_avg_resistances = True
habitat_map_is_resistances = True

I would be willing to share my data privately if requested.

Circuitscape version v5.11.2, obtained from running 'using Pkg; Pkg.status("Circuitscape")', with Julia versions 1.6, obtained from versioninfo().

[ranjanan]

Hi @SimonTapper, could you please share these files with me please? Also, when it gets stuck at the Julia prompt, could you hit Control+C? This will interrupt the process and we can see where it is getting stuck.

[ranjanan]

Have you also tried with solver = cg+amg?

[SimonTapper]

Hi Ranjan,
I have shared the files with you via Google Drive. It gets stuck after successfully completing time to taken to solve linear system. Would you like to me to post the corresponding error message that arises after hitting control+C? And yes, I have tried solver = cg+amg.

[ranjanan]

Yes, could you please post that error message here?

[SimonTapper]

Stacktrace:
  [1] Array
    @ ./boot.jl:448 [inlined]
  [2] Array
    @ ./boot.jl:457 [inlined]
  [3] similar
    @ ./array.jl:358 [inlined]
  [4] similar
    @ ./abstractarray.jl:740 [inlined]
  [5] _unsafe_getindex(#unused#::IndexLinear, A::Vector{Float64}, I::Vector{Int64})
    @ Base ./multidimensional.jl:850
  [6] _getindex
    @ ./multidimensional.jl:838 [inlined]
  [7] getindex
    @ ./abstractarray.jl:1170 [inlined]
  [8] advanced_kernel(prob::Circuitscape.AdvancedProblem{Float64, Int64, Circuitscape.CholmodSolver}, flags::Circuitscape.RasterFlags, cfg::Dict{String, String})
    @ Circuitscape ~/.julia/packages/Circuitscape/XpftG/src/raster/advanced.jl:221
  [9] raster_advanced(T::Type, V::Type, cfg::Dict{String, String})
    @ Circuitscape ~/.julia/packages/Circuitscape/XpftG/src/raster/advanced.jl:30
 [10] _compute(T::Type, V::Type, cfg::Dict{String, String})
    @ Circuitscape ~/.julia/packages/Circuitscape/XpftG/src/run.jl:45
 [11] macro expansion
    @ ./timing.jl:287 [inlined]
 [12] compute(path::String)
    @ Circuitscape ~/.julia/packages/Circuitscape/XpftG/src/run.jl:31
 [13] top-level scope
    @ REPL[3]:1```

[ranjanan]

All of the directions run for me with this PR. Let me make another release and ask you to update to the latest release and check.

[ranjanan]

Once this JuliaRegistries/General#74737 merges, please update Circuitscape to 5.12.1 and then try again.