Description
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