OCI Container with all of the packages needed to run SciMLBenchmarks.jl fails

[jgforbes]

I started with the latest julia docker image and was able to run the BCR demonstration in the Bio benchamrk group with no problems. When I added all of the packages used by the other tests I am unable to get past the using statement of the the BCR demonstration. The output is below. Any ideas how I can make a container that can be used off line and have everything needed to run the benchmarks?

julia> using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, LinearSolvejulia> using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, LinearSolve [ Info: Precompiling Catalyst [479239e8-5488-4da2-87a7-35f2df7eef83] ERROR: LoadError: UndefVarError: nodevalue not defined Stacktrace: [1] getproperty(x::Module, f::Symbol) @ Base ./Base.jl:31 [2] top-level scope @ ~/.julia/packages/SymbolicUtils/ssQsQ/src/inspect.jl:4 [3] include(mod::Module, _path::String) @ Base ./Base.jl:457 [4] include(x::String) @ SymbolicUtils ~/.julia/packages/SymbolicUtils/ssQsQ/src/SymbolicUtils.jl:4 [5] top-level scope @ ~/.julia/packages/SymbolicUtils/ssQsQ/src/SymbolicUtils.jl:31 [6] include @ ./Base.jl:457 [inlined] [7] 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, UInt128}}, source::String) @ Base ./loading.jl:2049 [8] top-level scope @ stdin:3 in expression starting at /root/.julia/packages/SymbolicUtils/ssQsQ/src/inspect.jl:4 in expression starting at /root/.julia/packages/SymbolicUtils/ssQsQ/src/SymbolicUtils.jl:1 in expression starting at stdin:3 ERROR: LoadError: Failed to precompile SymbolicUtils [d1185830-fcd6-423d-90d6-eec64667417b] to "/root/.julia/compiled/v1.9/SymbolicUtils/jl_DjsQxi". Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:2300 [3] compilecache @ ./loading.jl:2167 [inlined] [4] _require(pkg::Base.PkgId, env::String) @ Base ./loading.jl:1805 [5] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:1660 [6] macro expansion @ ./loading.jl:1648 [inlined] [7] macro expansion @ ./lock.jl:267 [inlined] [8] require(into::Module, mod::Symbol) @ Base ./loading.jl:1611 [9] top-level scope @ ~/.julia/packages/ModelingToolkit/BsHty/src/ModelingToolkit.jl:41 [10] top-level scope @ ~/.julia/packages/ModelingToolkit/BsHty/src/ModelingToolkit.jl:6 [11] include @ ./Base.jl:457 [inlined] [12] 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, UInt128}}, source::String) @ Base ./loading.jl:2049 [13] top-level scope @ stdin:3 in expression starting at /root/.julia/packages/ModelingToolkit/BsHty/src/ModelingToolkit.jl:1 in expression starting at stdin:3 ERROR: LoadError: Failed to precompile ModelingToolkit [961ee093-0014-501f-94e3-6117800e7a78] to "/root/.julia/compiled/v1.9/ModelingToolkit/jl_LHmlpp". Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:2300 [3] compilecache @ ./loading.jl:2167 [inlined] [4] _require(pkg::Base.PkgId, env::String) @ Base ./loading.jl:1805 [5] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:1660 [6] macro expansion @ ./loading.jl:1648 [inlined] [7] macro expansion @ ./lock.jl:267 [inlined] [8] require(into::Module, mod::Symbol) @ Base ./loading.jl:1611 [9] include @ ./Base.jl:457 [inlined] [10] 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, UInt128}}, source::Nothing) @ Base ./loading.jl:2049 [11] top-level scope @ stdin:3 in expression starting at /root/.julia/packages/Catalyst/THzhm/src/Catalyst.jl:1 in expression starting at stdin:3 ERROR: Failed to precompile Catalyst [479239e8-5488-4da2-87a7-35f2df7eef83] to "/root/.julia/compiled/v1.9/Catalyst/jl_MnDlqx". Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:2300 [3] compilecache @ ./loading.jl:2167 [inlined] [4] _require(pkg::Base.PkgId, env::String) @ Base ./loading.jl:1805 [5] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:1660 [6] macro expansion @ ./loading.jl:1648 [inlined] [7] macro expansion @ ./lock.jl:267 [inlined] [8] require(into::Module, mod::Symbol) @ Base ./loading.jl:1611

[ Info: Precompiling Catalyst [479239e8-5488-4da2-87a7-35f2df7eef83] ERROR: LoadError: UndefVarError: nodevalue not defined Stacktrace: [1] getproperty(x::Module, f::Symbol) @ Base ./Base.jl:31 [2] top-level scope @ ~/.julia/packages/SymbolicUtils/ssQsQ/src/inspect.jl:4 [3] include(mod::Module, _path::String) @ Base ./Base.jl:457 [4] include(x::String) @ SymbolicUtils ~/.julia/packages/SymbolicUtils/ssQsQ/src/SymbolicUtils.jl:4 [5] top-level scope @ ~/.julia/packages/SymbolicUtils/ssQsQ/src/SymbolicUtils.jl:31 [6] include @ ./Base.jl:457 [inlined] [7] 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, UInt128}}, source::String) @ Base ./loading.jl:2049 [8] top-level scope @ stdin:3 in expression starting at /root/.julia/packages/SymbolicUtils/ssQsQ/src/inspect.jl:4 in expression starting at /root/.julia/packages/SymbolicUtils/ssQsQ/src/SymbolicUtils.jl:1 in expression starting at stdin:3 ERROR: LoadError: Failed to precompile SymbolicUtils [d1185830-fcd6-423d-90d6-eec64667417b] to "/root/.julia/compiled/v1.9/SymbolicUtils/jl_DjsQxi". Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:2300 [3] compilecache @ ./loading.jl:2167 [inlined] [4] _require(pkg::Base.PkgId, env::String) @ Base ./loading.jl:1805 [5] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:1660 [6] macro expansion @ ./loading.jl:1648 [inlined] [7] macro expansion @ ./lock.jl:267 [inlined] [8] require(into::Module, mod::Symbol) @ Base ./loading.jl:1611 [9] top-level scope @ ~/.julia/packages/ModelingToolkit/BsHty/src/ModelingToolkit.jl:41 [10] top-level scope @ ~/.julia/packages/ModelingToolkit/BsHty/src/ModelingToolkit.jl:6 [11] include @ ./Base.jl:457 [inlined] [12] 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, UInt128}}, source::String) @ Base ./loading.jl:2049 [13] top-level scope @ stdin:3 in expression starting at /root/.julia/packages/ModelingToolkit/BsHty/src/ModelingToolkit.jl:1 in expression starting at stdin:3 ERROR: LoadError: Failed to precompile ModelingToolkit [961ee093-0014-501f-94e3-6117800e7a78] to "/root/.julia/compiled/v1.9/ModelingToolkit/jl_LHmlpp". Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:2300 [3] compilecache @ ./loading.jl:2167 [inlined] [4] _require(pkg::Base.PkgId, env::String) @ Base ./loading.jl:1805 [5] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:1660 [6] macro expansion @ ./loading.jl:1648 [inlined] [7] macro expansion @ ./lock.jl:267 [inlined] [8] require(into::Module, mod::Symbol) @ Base ./loading.jl:1611 [9] include @ ./Base.jl:457 [inlined] [10] 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, UInt128}}, source::Nothing) @ Base ./loading.jl:2049 [11] top-level scope @ stdin:3 in expression starting at /root/.julia/packages/Catalyst/THzhm/src/Catalyst.jl:1 in expression starting at stdin:3 ERROR: Failed to precompile Catalyst [479239e8-5488-4da2-87a7-35f2df7eef83] to "/root/.julia/compiled/v1.9/Catalyst/jl_MnDlqx". Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:2300 [3] compilecache @ ./loading.jl:2167 [inlined] [4] _require(pkg::Base.PkgId, env::String) @ Base ./loading.jl:1805 [5] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:1660 [6] macro expansion @ ./loading.jl:1648 [inlined] [7] macro expansion @ ./lock.jl:267 [inlined] [8] require(into::Module, mod::Symbol) @ Base ./loading.jl:1611

[ChrisRackauckas]

Did you instantiate the manifest?