ERROR: SuiteSparse.CHOLMOD.CHOLMODException("")

Question

ERROR: SuiteSparse.CHOLMOD.CHOLMODException("")

Mavisan6 opened this issue 3 years ago · comments

I have been trying to run Circuitscape but the following error came up:

ERROR: SuiteSparse.CHOLMOD.CHOLMODException("")
Stacktrace:
 [1] factorize_p!(::SuiteSparse.CHOLMOD.Sparse{Float64}, ::Float64, ::SuiteSparse.CHOLMOD.Factor{Float64}, ::Array{UInt8,1}) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\SuiteSparse\src\cholmod.jl:742
 [2] #cholesky!#6 at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\SuiteSparse\src\cholmod.jl:1306 [inlined]
 [3] cholesky(::SuiteSparse.CHOLMOD.Sparse{Float64}; shift::Float64, check::Bool, perm::Nothing) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\SuiteSparse\src\cholmod.jl:1346
 [4] cholesky at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\SuiteSparse\src\cholmod.jl:1339 [inlined]
 [5] #cholesky#9 at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\SuiteSparse\src\cholmod.jl:1458 [inlined]
 [6] cholesky at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\SuiteSparse\src\cholmod.jl:1458 [inlined]
 [7] construct_cholesky_factor at C:\Users\M533\.julia\packages\Circuitscape\9x9VD\src\core.jl:464 [inlined]
 [8] macro expansion at .\timing.jl:233 [inlined]
 [9] _cholmod_solver_path(::Circuitscape.GraphData{Float64,Int64}, ::Circuitscape.RasterFlags, ::Dict{String,String}, ::Bool, ::Int64) at C:\Users\M533\.julia\packages\Circuitscape\9x9VD\src\core.jl:332
 [10] single_ground_all_pairs(::Circuitscape.GraphData{Float64,Int64}, ::Circuitscape.RasterFlags, ::Dict{String,String}, ::Bool) at C:\Users\M533\.julia\packages\Circuitscape\9x9VD\src\core.jl:59
 [11] _pt_file_polygons_path(::Circuitscape.RasData{Float64,Int64}, ::Circuitscape.RasterFlags, ::Dict{String,String}) at C:\Users\M533\.julia\packages\Circuitscape\9x9VD\src\raster\pairwise.jl:105
 [12] raster_pairwise(::Type{T} where T, ::Type{T} where T, ::Dict{String,String}) at C:\Users\M533\.julia\packages\Circuitscape\9x9VD\src\raster\pairwise.jl:27
 [13] _compute(::Type{T} where T, ::Type{T} where T, ::Dict{String,String}) at C:\Users\M533\.julia\packages\Circuitscape\9x9VD\src\run.jl:42
 [14] macro expansion at .\timing.jl:233 [inlined]
 [15] compute(::String) at C:\Users\M533\.julia\packages\Circuitscape\9x9VD\src\run.jl:31
 [16] top-level scope at REPL[8]:1

Can anyone explain to me what it means and how to possibly fix it?
(I am new in using the software and the Julia programming language)

Vincent Landau · Answer 1 · Tue Oct 12 2021 05:49:04 GMT+0800 (China Standard Time)

Hi @Mavisan6 -- thanks for reaching out. If you don't mind, could you first provide information on what version of Circuitscape you are using? You can get this information by running using Pkg; Pkg.status("Circuitscape") in the Julia terminal. Thanks!

Mavisan6 · Answer 2 · Tue Oct 12 2021 15:49:04 GMT+0800 (China Standard Time)

Hi! I was using a .ini file as a template for mine, and that specified the version as 4.0.5, I kept the line as it was but maybe I should have changed it?

Vincent Landau · Answer 3 · Wed Oct 13 2021 00:04:20 GMT+0800 (China Standard Time)

Hi @Mavisan6, the INI version doesn't actually specify the version of CIrcuitscape. It is a carry-over from Circuitscape in Python. Could you run using Pkg; Pkg.status("Circuitscape") and post the output here?

Vincent Landau · Answer 4 · Wed Oct 13 2021 00:05:45 GMT+0800 (China Standard Time)

While you're at it, it would also be valuable if you could provide your input files, along with the INI file, so we can take a look and attempt to reproduce the problem on our side to debug.

Mavisan6 · Answer 5 · Wed Oct 13 2021 00:51:43 GMT+0800 (China Standard Time)

the version is 5.7.1

Mavisan6 · Answer 6 · Wed Oct 13 2021 00:58:13 GMT+0800 (China Standard Time)

here are the files:
https://drive.google.com/drive/folders/1iZ6iUXRWN4xr6ye4Sq9vC4PM9_sKvmbG?usp=sharing

Vincent Landau · Answer 7 · Wed Oct 13 2021 00:59:06 GMT+0800 (China Standard Time)

Thanks for sharing those! I will look into it and get back to you as soon as I can!

Vincent Landau · Answer 8 · Wed Oct 13 2021 01:02:31 GMT+0800 (China Standard Time)

@ranjanan before I get into reproducing, is there any reason to suspect that updated to 5.8 might fix this issue? @Mavisan6 you can update Circuitscape to the latest version by running using Pkg; Pkg.update("Circuitscape")

Mavisan6 · Answer 9 · Wed Oct 13 2021 01:10:17 GMT+0800 (China Standard Time)

I will do that and let you know then, thanks very much!!

Mavisan6 · Answer 10 · Wed Oct 13 2021 01:28:52 GMT+0800 (China Standard Time)

seems like the file is not in the registries folder:

ERROR: SystemError: opening file "C:\\Users\\M533\\.julia\\registries\\General\\Registry.toml": No such file or directory
Stacktrace:
 [1] systemerror(::String, ::Int32; extrainfo::Nothing) at .\error.jl:168
 [2] #systemerror#48 at .\error.jl:167 [inlined]
 [3] systemerror at .\error.jl:167 [inlined]
 [4] open(::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing) at .\iostream.jl:284
 [5] open at .\iostream.jl:273 [inlined]
 [6] open(::Base.var"#294#295"{Tuple{}}, ::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at .\io.jl:323
 [7] open at .\io.jl:323 [inlined]
 [8] read at .\io.jl:408 [inlined]
 [9] parsefile at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\ext\TOML\src\TOML.jl:50 [inlined]
 [10] read_registry(::String; cache::Bool) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\Types.jl:1044
 [11] read_registry at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\Types.jl:1039 [inlined]
 [12] (::Pkg.Types.var"#94#97"{Pkg.Types.Context,String,Pkg.Types.RegistrySpec})(::String) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\Types.jl:1016
 [13] mktempdir(::Pkg.Types.var"#94#97"{Pkg.Types.Context,String,Pkg.Types.RegistrySpec}, ::String; prefix::String) at .\file.jl:709
 [14] mktempdir at .\file.jl:707 [inlined] (repeats 2 times)
 [15] clone_or_cp_registries(::Pkg.Types.Context, ::Array{Pkg.Types.RegistrySpec,1}, ::String) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\Types.jl:980
 [16] clone_or_cp_registries at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\Types.jl:973 [inlined]
 [17] clone_default_registries(::Pkg.Types.Context; only_if_empty::Bool) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\Types.jl:874
 [18] clone_default_registries at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\Types.jl:862 [inlined]
 [19] up(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; level::Pkg.Types.UpgradeLevel, mode::Pkg.Types.PackageMode, update_registry::Bool, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:226
 [20] up at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:221 [inlined]
 [21] #up#37 at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:67 [inlined]
 [22] up at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:67 [inlined]
 [23] #up#36 at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:66 [inlined]
 [24] up at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:66 [inlined]
 [25] up(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:65
 [26] up(::String) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:65
 [27] top-level scope at REPL[4]:1

Vincent Landau · Answer 11 · Wed Oct 13 2021 01:41:06 GMT+0800 (China Standard Time)

Ah, looks like there was an issue building the registry, which can sometimes happen on Windows systems. Can you delete this folder: C://Users/M533/.julia/registries/General and try again?

Ranjan Anantharaman · Answer 12 · Tue Oct 19 2021 00:10:35 GMT+0800 (China Standard Time)

@Mavisan6 did you get a chance to delete your .julia and try again?

Mavisan6 · Answer 13 · Tue Oct 19 2021 04:52:40 GMT+0800 (China Standard Time)

I did and ran the experiment but the result was a grid raster file where all cells had the value of zero. However, this might be due to the input files provided

Ranjan Anantharaman · Answer 14 · Tue Oct 19 2021 04:54:13 GMT+0800 (China Standard Time)

Thank you. Let me know if that is not expected. If the original issue is resolved, let's close this issue and open a new one corresponding to the new issue.

Ranjan Anantharaman · Answer 15 · Tue Oct 19 2021 09:38:59 GMT+0800 (China Standard Time)

@Mavisan6 form your comment it sounds like the original issue was resolved, but if this particular issue pops up, feel free to reopen.