ranjanan
commented
2 years ago Looks like something external is killing the test process?
Closed tommydevitt closed 9 months ago
ranjanan
commented
2 years ago Looks like something external is killing the test process?
tommydevitt
commented
2 years ago @ranjanan I'm not sure how to interpret the error, but looks like it has something to do with the required dependency "ImageCore" not loading? I ran Pkg.test("ImageCore") and got some warnings but ultimately "Testing ImageCore tests passed". Reran Pkg.test("Circuitscape") but still received "ERROR: Package Circuitscape errored during testing (received signal: KILL)".
ranjanan
commented
2 years ago Does It always error like:
ERROR: Package Circuitscape errored during testing (received signal: KILL)Specifically, does it always say KILL? Could you be running out of memory and receiving a SIGKILL?
tommydevitt
commented
2 years ago So far that's all it says. I don't know whether it's running out of memory. Using a MacBook Air M1 chip with 16 GB RAM.
ranjanan
commented
2 years ago I just ran tests on an M2 MacBook Pro with 16 GB RAM using Rosetta and tests passed for me. I am not sure why the OS is killing your tests.
tommydevitt
commented
2 years ago Do I need to install Rosetta?
ranjanan
commented
2 years ago You already have Rosetta - that's how you were able to run the tests using Julia 1.7
tommydevitt
commented
2 years ago OK thanks. Anything else you can think of to try?
ranjanan
commented
2 years ago Yes, could you cd into your Circuitscape directory and run tests directly? So, open Julia, run:
using Circuitscape
normpath(joinpath(Base.pathof(Circuitscape), "..", "..", "test")) |> cd
include("runtests.jl")and see what happens?
tommydevitt
commented
2 years ago julia> include("runtests.jl")
pwd = /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test
Test Summary: | Pass Total
Unit tests | 16 16
Raster Pairwise: Error During Test at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/src/utils.jl:308
Got exception outside of a @test
Reordering problem.
Stacktrace:
[1] check_error(ps::Pardiso.MKLPardisoSolver, err::Int32)
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:80
[2] ccall_pardiso(ps::Pardiso.MKLPardisoSolver, N::Int64, nzval::Vector{Float64}, colptr::Vector{Int64}, rowval::Vector{Int64}, NRHS::Int64, B::Vector{Float64}, X::Vector{Float64})
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:73
[3] pardiso(ps::Pardiso.MKLPardisoSolver, X::Vector{Float64}, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, B::Vector{Float64})
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/Pardiso.jl:346
[4] #_#36
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:459 [inlined]
[5] MKLPardisoFactorize (repeats 2 times)
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:457 [inlined]
[6] solve_linear_system(factor::Circuitscape.MKLPardisoFactorize, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, rhs::Matrix{Float64})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:625
[7] solve(prob::Circuitscape.GraphProblem{Float64, Int64, Circuitscape.MKLPardisoSolver}, solver::Circuitscape.MKLPardisoSolver, flags::Circuitscape.RasterFlags, cfg::Dict{String, String}, log::Bool)
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:445
[8] single_ground_all_pairs (repeats 2 times)
@ ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:66 [inlined]
[9] _pt_file_no_polygons_path(rasterdata::Circuitscape.RasterData{Float64, Int64}, flags::Circuitscape.RasterFlags, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/pairwise.jl:63
[10] raster_pairwise(T::Type, V::Type, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/pairwise.jl:29
[11] _compute(T::Type, V::Type, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:43
[12] macro expansion
@ ./timing.jl:299 [inlined]
[13] compute(path::String)
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:31
[14] macro expansion
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:317 [inlined]
[15] macro expansion
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
[16] macro expansion
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:310 [inlined]
[17] macro expansion
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
[18] runtests(f::typeof(compute))
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:278
[19] top-level scope
@ ~/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:16
[20] include(fname::String)
@ Base.MainInclude ./client.jl:451
[21] top-level scope
@ REPL[3]:1
[22] eval
@ ./boot.jl:373 [inlined]
[23] eval_user_input(ast::Any, backend::REPL.REPLBackend)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150
[24] repl_backend_loop(backend::REPL.REPLBackend)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:246
[25] start_repl_backend(backend::REPL.REPLBackend, consumer::Any)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:231
[26] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:364
[27] run_repl(repl::REPL.AbstractREPL, consumer::Any)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:351
[28] (::Base.var"#936#938"{Bool, Bool, Bool})(REPL::Module)
@ Base ./client.jl:394
[29] #invokelatest#2
@ ./essentials.jl:716 [inlined]
[30] invokelatest
@ ./essentials.jl:714 [inlined]
[31] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool)
@ Base ./client.jl:379
[32] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:309
[33] _start()
@ Base ./client.jl:495
Raster Advanced: Error During Test at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/src/utils.jl:328
Got exception outside of a @test
Reordering problem.
Stacktrace:
[1] check_error(ps::Pardiso.MKLPardisoSolver, err::Int32)
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:80
[2] ccall_pardiso(ps::Pardiso.MKLPardisoSolver, N::Int64, nzval::Vector{Float64}, colptr::Vector{Int64}, rowval::Vector{Int64}, NRHS::Int64, B::Vector{Float64}, X::Vector{Float64})
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:73
[3] pardiso(ps::Pardiso.MKLPardisoSolver, X::Vector{Float64}, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, B::Vector{Float64})
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/Pardiso.jl:346
[4] #_#36
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:459 [inlined]
[5] MKLPardisoFactorize (repeats 2 times)
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:457 [inlined]
[6] solve_linear_system(factor::Circuitscape.MKLPardisoFactorize, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, rhs::Vector{Float64})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:625
[7] macro expansion
@ ./timing.jl:299 [inlined]
[8] multiple_solve(s::Circuitscape.MKLPardisoSolver, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, sources::Vector{Float64}, suppress_info::Bool)
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:330
[9] multiple_solver(cfg::Dict{String, String}, solver::Circuitscape.MKLPardisoSolver, a::SparseArrays.SparseMatrixCSC{Float64, Int64}, sources::Vector{Float64}, grounds::Vector{Float64}, finitegrounds::Vector{Float64})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:292
[10] advanced_kernel(prob::Circuitscape.AdvancedProblem{Float64, Int64, Circuitscape.MKLPardisoSolver}, flags::Circuitscape.RasterFlags, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:205
[11] raster_advanced(T::Type, V::Type, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:30
[12] _compute(T::Type, V::Type, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:45
[13] macro expansion
@ ./timing.jl:299 [inlined]
[14] compute(path::String)
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:31
[15] macro expansion
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:332 [inlined]
[16] macro expansion
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
[17] macro expansion
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:330 [inlined]
[18] macro expansion
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
[19] runtests(f::typeof(compute))
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:278
[20] top-level scope
@ ~/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:16
[21] include(fname::String)
@ Base.MainInclude ./client.jl:451
[22] top-level scope
@ REPL[3]:1
[23] eval
@ ./boot.jl:373 [inlined]
[24] eval_user_input(ast::Any, backend::REPL.REPLBackend)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150
[25] repl_backend_loop(backend::REPL.REPLBackend)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:246
[26] start_repl_backend(backend::REPL.REPLBackend, consumer::Any)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:231
[27] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:364
[28] run_repl(repl::REPL.AbstractREPL, consumer::Any)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:351
[29] (::Base.var"#936#938"{Bool, Bool, Bool})(REPL::Module)
@ Base ./client.jl:394
[30] #invokelatest#2
@ ./essentials.jl:716 [inlined]
[31] invokelatest
@ ./essentials.jl:714 [inlined]
[32] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool)
@ Base ./client.jl:379
[33] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:309
[34] _start()
@ Base ./client.jl:495
From worker 2: [ Info: 2022-07-08 21:32:08 : Solving point 1 of 10
From worker 3: [ Info: 2022-07-08 21:32:08 : Solving point 2 of 10
From worker 3: [ Info: 2022-07-08 21:32:08 : Solver used: AMG accelerated by CG
From worker 2: [ Info: 2022-07-08 21:32:08 : Solver used: AMG accelerated by CG
From worker 2: [ Info: 2022-07-08 21:32:13 : Time taken to construct preconditioner = 1.177736791 seconds
From worker 2: [ Info: 2022-07-08 21:32:13 : Time taken to solve linear system = 0.004022333 seconds
From worker 3: [ Info: 2022-07-08 21:32:13 : Time taken to construct preconditioner = 1.237418583 seconds
From worker 3: [ Info: 2022-07-08 21:32:13 : Time taken to solve linear system = 0.004103167 seconds
From worker 3: [ Info: 2022-07-08 21:32:14 : Solving point 3 of 10
From worker 3: [ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 21:32:14 : Solving point 4 of 10
From worker 2: [ Info: 2022-07-08 21:32:14 : Solving point 5 of 10
From worker 3: [ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
From worker 2: [ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 21:32:14 : Time taken to construct preconditioner = 0.0002465 seconds
From worker 3: [ Info: 2022-07-08 21:32:14 : Time taken to solve linear system = 8.8125e-5 seconds
From worker 2: [ Info: 2022-07-08 21:32:14 : Time taken to construct preconditioner = 0.000197209 seconds
From worker 2: [ Info: 2022-07-08 21:32:14 : Time taken to solve linear system = 8.575e-5 seconds
From worker 2: [ Info: 2022-07-08 21:32:14 : Solving point 6 of 10
From worker 2: [ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 21:32:14 : Solving point 7 of 10
From worker 3: [ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 21:32:14 : Time taken to construct preconditioner = 7.3584e-5 seconds
From worker 3: [ Info: 2022-07-08 21:32:14 : Time taken to solve linear system = 7.2042e-5 seconds
From worker 2: [ Info: 2022-07-08 21:32:14 : Solving point 8 of 10
From worker 2: [ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
From worker 2: [ Info: 2022-07-08 21:32:14 : Time taken to construct preconditioner = 8.325e-5 seconds
From worker 2: [ Info: 2022-07-08 21:32:14 : Time taken to solve linear system = 7.3958e-5 seconds
From worker 3: [ Info: 2022-07-08 21:32:14 : Solving point 9 of 10
From worker 3: [ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
From worker 2: [ Info: 2022-07-08 21:32:14 : Solving point 10 of 10
From worker 2: [ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
From worker 5: [ Info: 2022-07-08 21:32:25 : Solving point 1 of 5
From worker 4: [ Info: 2022-07-08 21:32:25 : Solving point 2 of 5
From worker 5: [ Info: 2022-07-08 21:32:26 : Solver used: AMG accelerated by CG
From worker 4: [ Info: 2022-07-08 21:32:26 : Solver used: AMG accelerated by CG
From worker 4: [ Info: 2022-07-08 21:32:30 : Time taken to construct preconditioner = 1.146539792 seconds
From worker 5: [ Info: 2022-07-08 21:32:30 : Time taken to construct preconditioner = 1.16853475 seconds
From worker 5: [ Info: 2022-07-08 21:32:30 : Time taken to solve linear system = 0.003904917 seconds
From worker 4: [ Info: 2022-07-08 21:32:30 : Time taken to solve linear system = 0.00410575 seconds
From worker 4: [ Info: 2022-07-08 21:32:31 : Solving point 3 of 5
From worker 4: [ Info: 2022-07-08 21:32:31 : Solver used: AMG accelerated by CG
From worker 5: [ Info: 2022-07-08 21:32:31 : Solving point 4 of 5
From worker 4: [ Info: 2022-07-08 21:32:31 : Time taken to construct preconditioner = 9.1167e-5 seconds
From worker 5: [ Info: 2022-07-08 21:32:31 : Solver used: AMG accelerated by CG
From worker 4: [ Info: 2022-07-08 21:32:31 : Time taken to solve linear system = 1.8625e-5 seconds
From worker 5: [ Info: 2022-07-08 21:32:31 : Time taken to construct preconditioner = 7.2041e-5 seconds
From worker 5: [ Info: 2022-07-08 21:32:31 : Time taken to solve linear system = 1.75e-5 seconds
From worker 4: [ Info: 2022-07-08 21:32:31 : Solving point 5 of 5
From worker 4: [ Info: 2022-07-08 21:32:31 : Solver used: AMG accelerated by CG
From worker 4: [ Info: 2022-07-08 21:32:31 : Time taken to construct preconditioner = 4.1167e-5 seconds
From worker 4: [ Info: 2022-07-08 21:32:31 : Time taken to solve linear system = 9.833e-6 seconds
┌ Warning: 2022-07-08 21:32:31 : Code to include pairs is activated, some entries did not match with focal node file. Some focal nodes may have been dropped
└ @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/logging.jl:25
Test Summary: | Pass Error Total
Double Precision Tests | 383 2 385
Network Pairwise | 141 141
Network Advanced | 12 12
Raster Pairwise | 1 1
Raster Advanced | 1 1
Raster One to All | 134 134
Raster All to One | 96 96
ERROR: LoadError: Some tests did not pass: 383 passed, 0 failed, 2 errored, 0 broken.
in expression starting at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:15okay, at least you didn't get the kill. One last thing. Can you run using Pkg; Pkg.update() and then run the tests again? I notice you're on a slightly older version of Circuitscape.
tommydevitt
commented
2 years ago OK, did that, but same (?) result:
julia> include("runtests.jl") ERROR: SystemError: opening file "/Users/tjd66/runtests.jl": No such file or directory Stacktrace: [1] systemerror(p::String, errno::Int32; extrainfo::Nothing) @ Base ./error.jl:174 [2] #systemerror#68 @ ./error.jl:173 [inlined] [3] systemerror @ ./error.jl:173 [inlined] [4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing) @ Base ./iostream.jl:293 [5] open @ ./iostream.jl:282 [inlined] [6] open(f::Base.var"#364#365"{String}, args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./io.jl:328 [7] open @ ./io.jl:328 [inlined] [8] read @ ./io.jl:436 [inlined] [9] _include(mapexpr::Function, mod::Module, _path::String) @ Base ./loading.jl:1249 [10] include(fname::String) @ Base.MainInclude ./client.jl:451 [11] top-level scope @ REPL[4]:1
julia> normpath(joinpath(Base.pathof(Circuitscape), "..", "..", "test")) |> cd
julia> using Circuitscape
julia> normpath(joinpath(Base.pathof(Circuitscape), "..", "..", "test")) |> cd
julia> include("runtests.jl") pwd = /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test Test Summary: | Pass Total Unit tests | 16 16 Raster Pairwise: Error During Test at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/src/utils.jl:308 Got exception outside of a @test Reordering problem. Stacktrace: [1] check_error(ps::Pardiso.MKLPardisoSolver, err::Int32) @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:80 [2] ccall_pardiso(ps::Pardiso.MKLPardisoSolver, N::Int64, nzval::Vector{Float64}, colptr::Vector{Int64}, rowval::Vector{Int64}, NRHS::Int64, B::Vector{Float64}, X::Vector{Float64}) @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mklpardiso.jl:73 [3] pardiso(ps::Pardiso.MKLPardisoSolver, X::Vector{Float64}, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, B::Vector{Float64}) @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/Pardiso.jl:346 [4] ##36 @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:459 [inlined] [5] MKLPardisoFactorize (repeats 2 times) @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:457 [inlined] [6] solve_linear_system(factor::Circuitscape.MKLPardisoFactorize, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, rhs::Matrix{Float64}) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:625 [7] solve(prob::Circuitscape.GraphProblem{Float64, Int64, Circuitscape.MKLPardisoSolver}, solver::Circuitscape.MKLPardisoSolver, flags::Circuitscape.RasterFlags, cfg::Dict{String, String}, log::Bool) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:445 [8] single_ground_all_pairs (repeats 2 times) @ ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:66 [inlined] [9] _pt_file_no_polygons_path(rasterdata::Circuitscape.RasterData{Float64, Int64}, flags::Circuitscape.RasterFlags, cfg::Dict{String, String}) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/pairwise.jl:63 [10] raster_pairwise(T::Type, V::Type, cfg::Dict{String, String}) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/pairwise.jl:29 [11] _compute(T::Type, V::Type, cfg::Dict{String, String}) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:43 [12] macro expansion @ ./timing.jl:299 [inlined] [13] compute(path::String) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:31 [14] macro expansion @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:317 [inlined] [15] macro expansion @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined] [16] macro expansion @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:310 [inlined] [17] macro expansion @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined] [18] runtests(f::typeof(compute)) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:278 [19] top-level scope @ ~/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:16 [20] include(fname::String) @ Base.MainInclude ./client.jl:451 [21] top-level scope @ REPL[8]:1 [22] eval @ ./boot.jl:373 [inlined] [23] eval_user_input(ast::Any, backend::REPL.REPLBackend) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150 [24] repl_backend_loop(backend::REPL.REPLBackend) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:246 [25] start_repl_backend(backend::REPL.REPLBackend, consumer::Any) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:231 [26] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:364 [27] run_repl(repl::REPL.AbstractREPL, consumer::Any) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:351 [28] (::Base.var"#936#938"{Bool, Bool, Bool})(REPL::Module) @ Base ./client.jl:394 [29] #invokelatest#2 @ ./essentials.jl:716 [inlined] [30] invokelatest @ ./essentials.jl:714 [inlined] [31] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool) @ Base ./client.jl:379 [32] exec_options(opts::Base.JLOptions) @ Base ./client.jl:309 [33] _start() @ Base ./client.jl:495 Raster Advanced: Error During Test at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/src/utils.jl:328 Got exception outside of a @test Not enough memory. Stacktrace: [1] check_error(ps::Pardiso.MKLPardisoSolver, err::Int32) @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:79 [2] ccall_pardiso(ps::Pardiso.MKLPardisoSolver, N::Int64, nzval::Vector{Float64}, colptr::Vector{Int64}, rowval::Vector{Int64}, NRHS::Int64, B::Vector{Float64}, X::Vector{Float64}) @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mklpardiso.jl:73 [3] pardiso(ps::Pardiso.MKLPardisoSolver, X::Vector{Float64}, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, B::Vector{Float64}) @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/Pardiso.jl:346 [4] ##36 @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:459 [inlined] [5] MKLPardisoFactorize (repeats 2 times) @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:457 [inlined] [6] solve_linear_system(factor::Circuitscape.MKLPardisoFactorize, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, rhs::Vector{Float64}) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:625 [7] macro expansion @ ./timing.jl:299 [inlined] [8] multiple_solve(s::Circuitscape.MKLPardisoSolver, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, sources::Vector{Float64}, suppress_info::Bool) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:330 [9] multiple_solver(cfg::Dict{String, String}, solver::Circuitscape.MKLPardisoSolver, a::SparseArrays.SparseMatrixCSC{Float64, Int64}, sources::Vector{Float64}, grounds::Vector{Float64}, finitegrounds::Vector{Float64}) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:292 [10] advanced_kernel(prob::Circuitscape.AdvancedProblem{Float64, Int64, Circuitscape.MKLPardisoSolver}, flags::Circuitscape.RasterFlags, cfg::Dict{String, String}) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:205 [11] raster_advanced(T::Type, V::Type, cfg::Dict{String, String}) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:30 [12] _compute(T::Type, V::Type, cfg::Dict{String, String}) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:45 [13] macro expansion @ ./timing.jl:299 [inlined] [14] compute(path::String) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:31 [15] macro expansion @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:332 [inlined] [16] macro expansion @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined] [17] macro expansion @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:330 [inlined] [18] macro expansion @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined] [19] runtests(f::typeof(compute)) @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:278 [20] top-level scope @ ~/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:16 [21] include(fname::String) @ Base.MainInclude ./client.jl:451 [22] top-level scope @ REPL[8]:1 [23] eval @ ./boot.jl:373 [inlined] [24] eval_user_input(ast::Any, backend::REPL.REPLBackend) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150 [25] repl_backend_loop(backend::REPL.REPLBackend) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:246 [26] start_repl_backend(backend::REPL.REPLBackend, consumer::Any) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:231 [27] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:364 [28] run_repl(repl::REPL.AbstractREPL, consumer::Any) @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:351 [29] (::Base.var"#936#938"{Bool, Bool, Bool})(REPL::Module) @ Base ./client.jl:394 [30] #invokelatest#2 @ ./essentials.jl:716 [inlined] [31] invokelatest @ ./essentials.jl:714 [inlined] [32] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool) @ Base ./client.jl:379 [33] exec_options(opts::Base.JLOptions) @ Base ./client.jl:309 [34] _start() @ Base ./client.jl:495 From worker 3: [ Info: 2022-07-08 23:16:03 : Solving point 2 of 10 From worker 2: [ Info: 2022-07-08 23:16:03 : Solving point 1 of 10 From worker 3: [ Info: 2022-07-08 23:16:04 : Solver used: AMG accelerated by CG From worker 2: [ Info: 2022-07-08 23:16:04 : Solver used: AMG accelerated by CG From worker 3: [ Info: 2022-07-08 23:16:08 : Time taken to construct preconditioner = 1.206053834 seconds From worker 3: [ Info: 2022-07-08 23:16:08 : Time taken to solve linear system = 0.004389292 seconds From worker 2: [ Info: 2022-07-08 23:16:08 : Time taken to construct preconditioner = 1.176347083 seconds From worker 2: [ Info: 2022-07-08 23:16:08 : Time taken to solve linear system = 0.003827583 seconds From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 3 of 10 From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 4 of 10 From worker 2: [ Info: 2022-07-08 23:16:09 : Solving point 5 of 10 From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to construct preconditioner = 0.000268542 seconds From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to solve linear system = 9.85e-5 seconds From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 6 of 10 From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 7 of 10 From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to construct preconditioner = 9.9167e-5 seconds From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to solve linear system = 7.7625e-5 seconds From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 8 of 10 From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to construct preconditioner = 6.6834e-5 seconds From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to solve linear system = 7.5791e-5 seconds From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 9 of 10 From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 10 of 10 From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG From worker 2: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG From worker 2: [ Info: 2022-07-08 23:16:09 : Time taken to construct preconditioner = 0.000213708 seconds From worker 2: [ Info: 2022-07-08 23:16:09 : Time taken to solve linear system = 9.15e-5 seconds From worker 5: [ Info: 2022-07-08 23:16:20 : Solving point 2 of 5 From worker 4: [ Info: 2022-07-08 23:16:20 : Solving point 1 of 5 From worker 5: [ Info: 2022-07-08 23:16:21 : Solver used: AMG accelerated by CG From worker 4: [ Info: 2022-07-08 23:16:21 : Solver used: AMG accelerated by CG From worker 5: [ Info: 2022-07-08 23:16:25 : Time taken to construct preconditioner = 1.214680958 seconds From worker 5: [ Info: 2022-07-08 23:16:25 : Time taken to solve linear system = 0.004146291 seconds From worker 4: [ Info: 2022-07-08 23:16:25 : Time taken to construct preconditioner = 1.173361292 seconds From worker 4: [ Info: 2022-07-08 23:16:25 : Time taken to solve linear system = 0.00401875 seconds From worker 5: [ Info: 2022-07-08 23:16:26 : Solving point 3 of 5 From worker 5: [ Info: 2022-07-08 23:16:26 : Solver used: AMG accelerated by CG From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to construct preconditioner = 9.0541e-5 seconds From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to solve linear system = 1.7084e-5 seconds From worker 5: [ Info: 2022-07-08 23:16:26 : Solving point 4 of 5 From worker 5: [ Info: 2022-07-08 23:16:26 : Solver used: AMG accelerated by CG From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to construct preconditioner = 3.2833e-5 seconds From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to solve linear system = 1.2666e-5 seconds From worker 5: [ Info: 2022-07-08 23:16:26 : Solving point 5 of 5 From worker 5: [ Info: 2022-07-08 23:16:26 : Solver used: AMG accelerated by CG From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to construct preconditioner = 3.9709e-5 seconds From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to solve linear system = 1.0917e-5 seconds ┌ Warning: 2022-07-08 23:16:27 : Code to include pairs is activated, some entries did not match with focal node file. Some focal nodes may have been dropped └ @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/logging.jl:25 Test Summary: | Pass Error Total Double Precision Tests | 383 2 385 Network Pairwise | 141 141 Network Advanced | 12 12 Raster Pairwise | 1 1 Raster Advanced | 1 1 Raster One to All | 134 134 Raster All to One | 96 96 ERROR: LoadError: Some tests did not pass: 383 passed, 0 failed, 2 errored, 0 broken. in expression starting at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:15
ViralBShah
commented
1 year ago @ranjanan Using this issue to discuss the Pkg test failures. It doesn't appear to be an issue with Circuitscape based on the issue Simon links to above.
ruegdeg
commented
10 months ago Dear all, I tried to make the Julia Circuitscape to work within a Singularity container, but always getting this error about SimpleWeightedGraphs: LoadError: MethodError: no method matching connected_components(::SimpleWeightedGraphs.SimpleWeightedGraph{Int32,Float64}) Closest candidates are: connected_components(!Matched::LightGraphs.AbstractGraph{T}) where T at /home/XX/.julia/packages/LightGraphs/IgJif/src/connectivity.jl:101 .. . . Any suggestions how to overcome this?
ViralBShah
commented
9 months ago I can't imagine the Singularity container is different from running it regularly. Not sure what is causing this.
ViralBShah
commented
9 months ago I'm closing this since it is quite old now. Please reopen a new issue if tests still failing. I just ran everything with Julia 1.10 and works fine.
Can anyone tell me why the circuitscape package test is failing?