ERROR: ArgumentError: column indices J[k] must satisfy 1 <= J[k] <= n

[wwucl2019]

Hi,

I am new to Circuitscape. I am jus trying to run the calculations in the network mode. I am sure I have followed the spirit of the input files given in the instructions, but kept getting the following error. I attached my input files here. Thanks.
mgNetworkVerify1_grounds_resistances.txt
mgNetworkVerify1_graph_resistances.txt
mgNetworkVerify1_sources.txt

julia> compute("/Users/weiwu/Documents/MATLAB/200/mgNetworkVerify1.ini")
[ Info: 2021-11-12 11:24:48 : Precision used: Double
┌ Info: 2021-11-12 11:24:48 : Circuitscape.jl starts counting nodes from 1, 
└ not 0. This will be reflected in the outputs.
ERROR: ArgumentError: column indices J[k] must satisfy 1 <= J[k] <= n
Stacktrace:
 [1] sparse!(I::Vector{Int64}, J::Vector{Int64}, V::Vector{Float64}, m::Int64, n::Int64, combine::typeof(+), klasttouch::Vector{Int64}, csrrowptr::Vector{Int64}, csrcolval::Vector{Int64}, csrnzval::Vector{Float64}, csccolptr::Vector{Int64}, cscrowval::Vector{Int64}, cscnzval::Vector{Float64})
   @ SparseArrays /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/SparseArrays/src/sparsematrix.jl:889
 [2] sparse(I::Vector{Int64}, J::Vector{Int64}, V::Vector{Float64}, m::Int64, n::Int64, combine::Function)
   @ SparseArrays /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/SparseArrays/src/sparsematrix.jl:798
 [3] sparse
   @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/SparseArrays/src/sparsematrix.jl:987 [inlined]
 [4] compute_advanced_data(data::Circuitscape.NetworkData{Float64, Int64}, flags::Circuitscape.NetworkFlags, cfg::Dict{String, String})
   @ Circuitscape ~/.julia/packages/Circuitscape/a9Quh/src/network/advanced.jl:30
 [5] network_advanced(T::Type, V::Type, cfg::Dict{String, String})
   @ Circuitscape ~/.julia/packages/Circuitscape/a9Quh/src/network/advanced.jl:10
 [6] _compute(T::Type, V::Type, cfg::Dict{String, String})
   @ Circuitscape ~/.julia/packages/Circuitscape/a9Quh/src/run.jl:55
 [7] macro expansion
   @ ./timing.jl:299 [inlined]
 [8] compute(path::String)
   @ Circuitscape ~/.julia/packages/Circuitscape/a9Quh/src/run.jl:31
 [9] top-level scope
   @ REPL[19]:1

[wwucl2019]

@andreasnoack @ViralBShah @tanmaykm @yeesian , any expert can help with this issue?

[francescmolne]

Hi @wwucl2019 , I'm having the same problem. Have you already found a solution? I'm trying, I'll keep you updated if I find a way...👍

[csadorf]

@francescmolne Have you been able to resolve the problem?

[wwucl2019]

@francescmolne , no I haven't. CS@julia not working for me, but GUI on Mac and Windows works fine. So strange.

[unkcpz]

Hi @wwucl2019, I give a quick look at this issue and the data you provided. It seems there is a 'j' index (j=92 from the file mgNetworkVerify1_graph_resistances.txt) of your data that exceeding the upbound of the J[end]=91 . Can you also describe how you get the input data? I think this is the source of the issue. But I only look it from data side with zero knowledge of how Circuitscape works.

Anyway, I think there should be an easy fix for the issue, maybe from Circuitscape side you can check the code below to see whether you can set the sparse matrix dimension based on the i,j index as default? (sparse(i,j,v,m,m) -> sparse(i,j,v))

function compute_advanced_data(data::NetworkData{T,V}, 
                            flags, cfg)::AdvancedProblem{T,V} where {T,V}


    i,j,v = data.coords


    idx = findfirst(x -> x < 1, i)
    idx != nothing && throw("Indices no good")
    idx = findfirst(x -> x < 1, j)
    idx != nothing && throw("Indices no good")


    m = max(i[end], j[end])
    A = sparse(i,j,v,m,m)

[ranjanan]

As @unkcpz helpfully points out, the issue is in the sparse matrix construction. #357 should fix it