pkg test failed #364

tommydevitt · 2022-07-05T18:59:50Z

Can anyone tell me why the circuitscape package test is failing?

julia> Pkg.test("Circuitscape")
     Testing Circuitscape
      Status `/private/var/folders/yz/3xvfplr51n76z_803r4cv68dvwgqdt/T/jl_Sedyrg/Project.toml`
  [2169fc97] AlgebraicMultigrid v0.4.2
  [c9ce4bd3] ArchGDAL v0.7.4
  [2b7a1792] Circuitscape v5.10.2
  [92fee26a] GZip v0.5.1
  [86223c79] Graphs v1.7.0
  [42fd0dbc] IterativeSolvers v0.9.2
  [46dd5b70] Pardiso v0.5.4
  [47aef6b3] SimpleWeightedGraphs v1.2.1
  [ade2ca70] Dates `@stdlib/Dates`
  [8bb1440f] DelimitedFiles `@stdlib/DelimitedFiles`
  [8ba89e20] Distributed `@stdlib/Distributed`
  [37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra`
  [56ddb016] Logging `@stdlib/Logging`
  [3fa0cd96] REPL `@stdlib/REPL`
  [1a1011a3] SharedArrays `@stdlib/SharedArrays`
  [2f01184e] SparseArrays `@stdlib/SparseArrays`
  [4607b0f0] SuiteSparse `@stdlib/SuiteSparse`
  [8dfed614] Test `@stdlib/Test`
      Status `/private/var/folders/yz/3xvfplr51n76z_803r4cv68dvwgqdt/T/jl_Sedyrg/Manifest.toml`
  [621f4979] AbstractFFTs v1.1.0
  [79e6a3ab] Adapt v3.3.3
  [2169fc97] AlgebraicMultigrid v0.4.2
  [c9ce4bd3] ArchGDAL v0.7.4
  [ec485272] ArnoldiMethod v0.2.0
  [fa961155] CEnum v0.4.2
  [d360d2e6] ChainRulesCore v1.15.0
  [9e997f8a] ChangesOfVariables v0.1.3
  [2b7a1792] Circuitscape v5.10.2
  [3da002f7] ColorTypes v0.11.3
  [c3611d14] ColorVectorSpace v0.9.9
  [5ae59095] Colors v0.12.8
  [34da2185] Compat v3.45.0
  [aa819f21] CompatHelper v3.3.0
  [9a962f9c] DataAPI v1.10.0
  [864edb3b] DataStructures v0.18.13
  [e2d170a0] DataValueInterfaces v1.0.0
  [3c3547ce] DiskArrays v0.2.13
  [ffbed154] DocStringExtensions v0.8.6
  [e2ba6199] ExprTools v0.1.8
  [53c48c17] FixedPointNumbers v0.8.4
  [add2ef01] GDAL v1.4.0
  [92fee26a] GZip v0.5.1
  [68eda718] GeoFormatTypes v0.3.0
  [cf35fbd7] GeoInterface v0.5.7
  [8f6bce27] GitForge v0.2.8
  [a2bd30eb] Graphics v1.1.2
  [86223c79] Graphs v1.7.0
  [cd3eb016] HTTP v0.9.17
  [a09fc81d] ImageCore v0.9.3
  [d25df0c9] Inflate v0.1.2
  [83e8ac13] IniFile v0.5.1
  [842dd82b] InlineStrings v1.1.2
  [3587e190] InverseFunctions v0.1.7
  [92d709cd] IrrationalConstants v0.1.1
  [42fd0dbc] IterativeSolvers v0.9.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.4.1
  [2535ab7d] JSON2 v0.3.4
  [2ab3a3ac] LogExpFunctions v0.3.15
  [1914dd2f] MacroTools v0.5.9
  [dbb5928d] MappedArrays v0.4.1
  [739be429] MbedTLS v1.0.3
  [78c3b35d] Mocking v0.7.3
  [e94cdb99] MosaicViews v0.3.3
  [1e8d2bf6] MultilineStrings v0.1.1
  [77ba4419] NaNMath v1.0.0
  [6fe1bfb0] OffsetArrays v1.12.5
  [bac558e1] OrderedCollections v1.4.1
  [5432bcbf] PaddedViews v0.5.11
  [46dd5b70] Pardiso v0.5.4
  [69de0a69] Parsers v2.3.1
  [21216c6a] Preferences v1.3.0
  [3cdcf5f2] RecipesBase v1.2.1
  [189a3867] Reexport v1.2.2
  [699a6c99] SimpleTraits v0.9.4
  [47aef6b3] SimpleWeightedGraphs v1.2.1
  [276daf66] SpecialFunctions v2.1.6
  [cae243ae] StackViews v0.1.1
  [90137ffa] StaticArrays v1.4.6
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.7.0
  [62fd8b95] TensorCore v0.1.1
  [f269a46b] TimeZones v1.7.3
  [5c2747f8] URIs v1.3.0
  [2e619515] Expat_jll v2.4.8+0
  [a7073274] GDAL_jll v300.500.0+1
  [d604d12d] GEOS_jll v3.10.2+0
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+2
  [aacddb02] JpegTurbo_jll v2.1.2+0
  [88015f11] LERC_jll v3.0.0+1
  [89763e89] Libtiff_jll v4.4.0+0
  [d3a379c0] LittleCMS_jll v2.12.0+0
  [856f044c] MKL_jll v2022.0.0+0
  [643b3616] OpenJpeg_jll v2.4.0+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [58948b4f] PROJ_jll v900.0.0+0
  [76ed43ae] SQLite_jll v3.38.4+0
  [3161d3a3] Zstd_jll v1.5.2+0
  [06c338fa] libgeotiff_jll v1.7.1+0
  [b53b4c65] libpng_jll v1.6.38+0
  [0dad84c5] ArgTools `@stdlib/ArgTools`
  [56f22d72] Artifacts `@stdlib/Artifacts`
  [2a0f44e3] Base64 `@stdlib/Base64`
  [ade2ca70] Dates `@stdlib/Dates`
  [8bb1440f] DelimitedFiles `@stdlib/DelimitedFiles`
  [8ba89e20] Distributed `@stdlib/Distributed`
  [f43a241f] Downloads `@stdlib/Downloads`
  [7b1f6079] FileWatching `@stdlib/FileWatching`
  [b77e0a4c] InteractiveUtils `@stdlib/InteractiveUtils`
  [4af54fe1] LazyArtifacts `@stdlib/LazyArtifacts`
  [b27032c2] LibCURL `@stdlib/LibCURL`
  [76f85450] LibGit2 `@stdlib/LibGit2`
  [8f399da3] Libdl `@stdlib/Libdl`
  [37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra`
  [56ddb016] Logging `@stdlib/Logging`
  [d6f4376e] Markdown `@stdlib/Markdown`
  [a63ad114] Mmap `@stdlib/Mmap`
  [ca575930] NetworkOptions `@stdlib/NetworkOptions`
  [44cfe95a] Pkg `@stdlib/Pkg`
  [de0858da] Printf `@stdlib/Printf`
  [3fa0cd96] REPL `@stdlib/REPL`
  [9a3f8284] Random `@stdlib/Random`
  [ea8e919c] SHA `@stdlib/SHA`
  [9e88b42a] Serialization `@stdlib/Serialization`
  [1a1011a3] SharedArrays `@stdlib/SharedArrays`
  [6462fe0b] Sockets `@stdlib/Sockets`
  [2f01184e] SparseArrays `@stdlib/SparseArrays`
  [10745b16] Statistics `@stdlib/Statistics`
  [4607b0f0] SuiteSparse `@stdlib/SuiteSparse`
  [fa267f1f] TOML `@stdlib/TOML`
  [a4e569a6] Tar `@stdlib/Tar`
  [8dfed614] Test `@stdlib/Test`
  [cf7118a7] UUIDs `@stdlib/UUIDs`
  [4ec0a83e] Unicode `@stdlib/Unicode`
  [e66e0078] CompilerSupportLibraries_jll `@stdlib/CompilerSupportLibraries_jll`
  [deac9b47] LibCURL_jll `@stdlib/LibCURL_jll`
  [29816b5a] LibSSH2_jll `@stdlib/LibSSH2_jll`
  [c8ffd9c3] MbedTLS_jll `@stdlib/MbedTLS_jll`
  [14a3606d] MozillaCACerts_jll `@stdlib/MozillaCACerts_jll`
  [4536629a] OpenBLAS_jll `@stdlib/OpenBLAS_jll`
  [05823500] OpenLibm_jll `@stdlib/OpenLibm_jll`
  [83775a58] Zlib_jll `@stdlib/Zlib_jll`
  [8e850b90] libblastrampoline_jll `@stdlib/libblastrampoline_jll`
  [8e850ede] nghttp2_jll `@stdlib/nghttp2_jll`
  [3f19e933] p7zip_jll `@stdlib/p7zip_jll`
     Testing Running tests...
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Circuitscape [2b7a1792-8151-5239-925d-e2b8fdfa3201]
│   exception = Required dependency ImageCore [a09fc81d-aa75-5fe9-8630-4744c3626534] failed to load from a cache file.
└ @ Base loading.jl:1132
pwd = /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test
Test Summary: | Pass  Total
Unit tests    |   16     16
ERROR: Package Circuitscape errored during testing (received signal: KILL)
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Types.jl:68
  [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
    @ Pkg.Operations /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1672
  [3] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:421
  [4] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:149
  [5] test(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:144
  [6] #test#87
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:142 [inlined]
  [7] test
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:142 [inlined]
  [8] #test#86
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
  [9] test(pkg::String)
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:141
 [10] top-level scope
    @ REPL[10]:1

ranjanan · 2022-07-05T19:02:49Z

Looks like something external is killing the test process?

tommydevitt · 2022-07-05T20:31:43Z

@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 · 2022-07-08T01:02:43Z

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 · 2022-07-08T18:15:30Z

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 · 2022-07-08T18:32:52Z

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 · 2022-07-08T18:36:12Z

Do I need to install Rosetta?

ranjanan · 2022-07-08T18:46:44Z

You already have Rosetta - that's how you were able to run the tests using Julia 1.7

tommydevitt · 2022-07-08T20:32:04Z

OK thanks. Anything else you can think of to try?

ranjanan · 2022-07-09T00:50:03Z

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 · 2022-07-09T02:34:01Z

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:15

ranjanan · 2022-07-09T03:12:16Z

okay, 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 · 2022-07-09T04:18:06Z

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/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[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/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[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 · 2023-08-11T13:17:01Z

@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 · 2023-12-12T21:52:53Z

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 · 2024-01-04T06:40:44Z

I can't imagine the Singularity container is different from running it regularly. Not sure what is causing this.

ViralBShah · 2024-01-04T06:48:28Z

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.

simonbyrne mentioned this issue Dec 13, 2022

Pkg.test: ERROR: Package ClimaCore errored during testing (received signal: KILL) JuliaLang/julia#47890

Open

ViralBShah mentioned this issue Aug 11, 2023

Error during Pkg.test("Circuitscape") #377

Closed

ViralBShah closed this as completed Jan 4, 2024

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pkg test failed #364

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