OrdinaryDiffEq fails to precompile in julia 1.7.2

jackblyle · March 3, 2022, 4:50am

I am suddenly getting an error when precompiling the OrdinaryDiffEq package. I originally ran into it in a jupyter-lab notebook (ipynb) that worked a few days ago. I then tried creating a new environment and I still get the problem.

Specific steps:

conda create -n sfsa1
conda activate sfsa1
conda install -c conda-forge julia
julia
returned Version 1.7.2 (2022-02-06)
using Pkg
Pkg.add(“OrdinaryDiffEq”)
much happy green stuff, then
✗ VectorizationBase
✗ SLEEFPirates
✗ SIMDDualNumbers
✗ LoopVectorization
✗ TriangularSolve
✗ RecursiveFactorization
✗ LinearSolve
✗ NonlinearSolve
✗ DiffEqBase
✗ OrdinaryDiffEq
101 dependencies successfully precompiled in 30 seconds
10 dependencies errored. To see a full report either run import Pkg; Pkg.precompile() or load the packages

julia> import Pkg; Pkg.precompile()
Precompiling project…
✗ VectorizationBase
✗ SLEEFPirates
✗ SIMDDualNumbers
✗ LoopVectorization
✗ TriangularSolve
✗ RecursiveFactorization
✗ LinearSolve
✗ NonlinearSolve
✗ DiffEqBase
✗ OrdinaryDiffEq
0 dependencies successfully precompiled in 22 seconds (101 already precompiled)

ERROR: The following 1 direct dependency failed to precompile:

OrdinaryDiffEq [1dea7af3-3e70-54e6-95c3-0bf5283fa5ed]

Failed to precompile OrdinaryDiffEq [1dea7af3-3e70-54e6-95c3-0bf5283fa5ed] to /home/jlyle/.conda/envs/sfsa1/share/julia/compiled/v1.7/OrdinaryDiffEq/jl_9oz7hR.
ERROR: LoadError: UndefVarError: num_cache_levels not defined
Stacktrace:
[1] include
@ ./Base.jl:418 [inlined]
[2] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1318
[3] top-level scope
@ none:1
[4] eval
@ ./boot.jl:373 [inlined]
[5] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[6] top-level scope
@ none:1
in expression starting at /home/jlyle/.julia/packages/VectorizationBase/yDGcX/src/VectorizationBase.jl:1
followed by more of the same.

Any ideas?

Ad Astra,

Jack

ChrisRackauckas · March 3, 2022, 12:28pm

@Elrod do you know what this is?

Elrod · March 3, 2022, 2:23pm

That sounds like it’s using CPUSummary 0.1.10, which is broken. 0.1.9 is also broken.
Using <=0.1.8, or >=0.1.11.
I’m not sure why the resolver would prefer a broken version, given newer non-broken alternatives.

Also, these show up because Hwloc failed to load.
This may indicate the check is bad, and returns a ton of false negatives.
Locally, it works.

jackblyle · March 3, 2022, 4:46pm

Gentlemen,

Thank you for looking into this, but what I am immediately looking for is a work-around. Do we know that version x.x.x of OrdinaryDiffEq works with julia 1.7.x for example. Or as a teaching moment, how do I check that myself?

Ad Astra,

Jack

ChrisRackauckas · March 3, 2022, 5:30pm

Anything like OrdinaryDiffEq v5 or above should be fine. That’s not your issue though. Sounds like it’s CPUSummary.jl, and figuring out why that went into a weird version is what’s essential.

Elrod · March 3, 2022, 7:01pm

] add CPUSummary
That should trigger it to update and fix the problem.
Please tell me the version.

giordano · March 3, 2022, 8:34pm

If a version is hopelessly broken it should be yanked from the registry

Elrod · March 3, 2022, 9:01pm

https://github.com/JuliaRegistries/General/pull/55916

EDIT: Merged, bad CPUSummary versions have been yanked.

jackblyle · March 4, 2022, 5:38am

(@sfsa1) pkg> add CPUSummary
Resolving package versions…
Updating ~/.conda/envs/sfsa1/share/julia/environments/sfsa1/Project.toml
[2a0fbf3d] + CPUSummary v0.1.10
No Changes to ~/.conda/envs/sfsa1/share/julia/environments/sfsa1/Manifest.toml

jackblyle · March 4, 2022, 5:41am

Here is the full error trace when trying to precompile:

julia> using OrdinaryDiffEq
[ Info: Precompiling OrdinaryDiffEq [1dea7af3-3e70-54e6-95c3-0bf5283fa5ed]
ERROR: LoadError: UndefVarError: num_cache_levels not defined
Stacktrace:
[1] include
@ ./Base.jl:418 [inlined]
[2] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1318
[3] top-level scope
@ none:1
[4] eval
@ ./boot.jl:373 [inlined]
[5] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[6] top-level scope
@ none:1
in expression starting at /home/jlyle/.julia/packages/VectorizationBase/yDGcX/src/VectorizationBase.jl:1
ERROR: LoadError: Failed to precompile VectorizationBase [3d5dd08c-fd9d-11e8-17fa-ed2836048c2f] to /home/jlyle/.conda/envs/sfsa1/share/julia/compiled/v1.7/VectorizationBase/jl_LH0w2b.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:997
[7] include
@ ./Base.jl:418 [inlined]
[8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1318
[9] top-level scope
@ none:1
[10] eval
@ ./boot.jl:373 [inlined]
[11] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[12] top-level scope
@ none:1
in expression starting at /home/jlyle/.julia/packages/LoopVectorization/tSQDi/src/LoopVectorization.jl:1
ERROR: LoadError: Failed to precompile LoopVectorization [bdcacae8-1622-11e9-2a5c-532679323890] to /home/jlyle/.conda/envs/sfsa1/share/julia/compiled/v1.7/LoopVectorization/jl_g20eGY.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:997
[7] include(mod::Module, _path::String)
@ Base ./Base.jl:418
[8] include(x::String)
@ RecursiveFactorization ~/.julia/packages/RecursiveFactorization/mIP2e/src/RecursiveFactorization.jl:1
[9] top-level scope
@ ~/.julia/packages/RecursiveFactorization/mIP2e/src/RecursiveFactorization.jl:3
[10] include
@ ./Base.jl:418 [inlined]
[11] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1318
[12] top-level scope
@ none:1
[13] eval
@ ./boot.jl:373 [inlined]
[14] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[15] top-level scope
@ none:1
in expression starting at /home/jlyle/.julia/packages/RecursiveFactorization/mIP2e/src/lu.jl:1
in expression starting at /home/jlyle/.julia/packages/RecursiveFactorization/mIP2e/src/RecursiveFactorization.jl:1
ERROR: LoadError: Failed to precompile RecursiveFactorization [f2c3362d-daeb-58d1-803e-2bc74f2840b4] to /home/jlyle/.conda/envs/sfsa1/share/julia/compiled/v1.7/RecursiveFactorization/jl_V48LiI.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:997
[7] include
@ ./Base.jl:418 [inlined]
[8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1318
[9] top-level scope
@ none:1
[10] eval
@ ./boot.jl:373 [inlined]
[11] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[12] top-level scope
@ none:1
in expression starting at /home/jlyle/.julia/packages/DiffEqBase/Y5mGv/src/DiffEqBase.jl:1
ERROR: LoadError: Failed to precompile DiffEqBase [2b5f629d-d688-5b77-993f-72d75c75574e] to /home/jlyle/.conda/envs/sfsa1/share/julia/compiled/v1.7/DiffEqBase/jl_348VQR.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:997
[7] include
@ ./Base.jl:418 [inlined]
[8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
@ Base ./loading.jl:1318
[9] top-level scope
@ none:1
[10] eval
@ ./boot.jl:373 [inlined]
[11] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[12] top-level scope
@ none:1
in expression starting at /home/jlyle/.julia/packages/OrdinaryDiffEq/Op0Oq/src/OrdinaryDiffEq.jl:1
ERROR: Failed to precompile OrdinaryDiffEq [1dea7af3-3e70-54e6-95c3-0bf5283fa5ed] to /home/jlyle/.conda/envs/sfsa1/share/julia/compiled/v1.7/OrdinaryDiffEq/jl_bBhx3g.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:997

DanDoe · August 31, 2022, 12:21pm

Same issue here, cannot figure out whats happening.

ERROR: LoadError: Failed to precompile OrdinaryDiffEq [1dea7af3-3e70-54e6-95c3-0bf5283fa5ed] to /home/daniel/.julia/compiled/v1.7/OrdinaryDiffEq/jl_zWlkoC.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
   @ Base ./loading.jl:1466
 [3] compilecache(pkg::Base.PkgId, path::String)
   @ Base ./loading.jl:1410
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1120
 [5] require(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1013
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:997

ChrisRackauckas · August 31, 2022, 1:39pm

That seems like a separate issue? The LoopVectorization stuff was found and handled. Can you open a separate thread and share information? You cutoff the stack trace before it gave the information

Also, I would highly recommend upgrading to v1.8 and sharing ]st which will tell us a lot more about the current packages on your system.