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Compatible with Julia 1.9.3 Jupyter Notebooks? #6

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SimonStier opened this issue Oct 21, 2023 · 3 comments
Open

Compatible with Julia 1.9.3 Jupyter Notebooks? #6

SimonStier opened this issue Oct 21, 2023 · 3 comments

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@SimonStier
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I was trying to run

using Pkg; Pkg.add("BattMo")

within a Julia 1.9.3 Jupyter Notebooks, but precompilations fails:

...
  ✓ Jutul
  ✗ BattMo
  97 dependencies successfully precompiled in 88 seconds. 61 already precompiled.
  1 dependency errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the package
  1 dependency had warnings during precompilation:
┌ Roots [f2b01f46-fcfa-551c-844a-d8ac1e96c665]
│  ┌ Warning: Replacing docs for `Roots.Roots :: Union{}` in module `Roots`
│  └ @ Base.Docs docs/Docs.jl:243

[ Info: Precompiling BattMo [6f0c0536-3c2c-4762-a987-c605a8a6f898]
ERROR: LoadError: MethodError: no method matching update_before_step!(::Jutul.JutulStorage{Nothing}, ::BattMo.CurrentAndVoltageDomain, ::Jutul.SimulationModel{BattMo.CurrentAndVoltageDomain, BattMo.CurrentAndVoltageSystem, Jutul.FullyImplicitFormulation, Jutul.DefaultContext}, ::Float64, ::NamedTuple{(:policy,), Tuple{BattMo.SimpleCVPolicy{Float64}}}; time::Float64, recorder::Jutul.ProgressRecorder, update_explicit::Bool)

Closest candidates are:
  update_before_step!(::Any, ::BattMo.CurrentAndVoltageDomain, ::Jutul.SimulationModel{BattMo.CurrentAndVoltageDomain, BattMo.CurrentAndVoltageSystem}, ::Any, ::Any; time) got unsupported keyword arguments "recorder", "update_explicit"
   @ BattMo /opt/julia/packages/BattMo/ayys7/src/models/current_and_voltage_boundary.jl:208
  update_before_step!(::Any, ::Any, ::Any, ::Any, ::Any; time, recorder, update_explicit)
   @ Jutul /opt/julia/packages/Jutul/hWGJY/src/models.jl:924
  update_before_step!(::Any, ::Any, ::Any, ::Any; kwarg...)
   @ Jutul /opt/julia/packages/Jutul/hWGJY/src/models.jl:918
  ...
@moyner
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moyner commented Oct 21, 2023

Hi Simon, this is caused by the latest release of the upstream Jutul package. I have pushed a new release of BattMo.jl that should appear in the package manager soon: JuliaRegistries/General#93830

Alternatively, as a quick-fix, you can install the earlier version of Jutul explicitly in your environment to fix it:

Pkg.add(name="Jutul", version="0.2.14")

Hopefully that should make it work.

@simontaurus
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Thanks, that helped.

The example now runs, except the plotting (maybe unrelated)

using BattMo
# Simulate case
states, reports, extra, exported = run_battery("p2d_40");
# Plot result
using GLMakie
voltage = map(state -> state[:BPP][:Phi][1], states)
t = cumsum(extra[:timesteps])
fig = Figure()
ax = Axis(fig[1, 1], ylabel = "Voltage / V", xlabel = "Time / s", title = "Discharge curve")
lines!(ax, t, voltage)
display(fig)
[ Info: Precompiling GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a]
Invalid instruction at 0x7fbd14dc019b: 0xc5, 0xfb, 0x92, 0xce, 0x62, 0xf1, 0x7e, 0x09, 0x10, 0xc1, 0x31, 0xc9, 0x3d, 0x80, 0x00

[407513] signal (4.2): Illegal instruction
in expression starting at /opt/julia/packages/Makie/NrrbP/src/layouting/transformation.jl:362
exp_impl at ./special/exp.jl:282 [inlined]
exp10 at ./special/exp.jl:325
#890 at /opt/julia/packages/Makie/NrrbP/src/layouting/transformation.jl:364 [inlined]
call_composed at ./operators.jl:1034 [inlined]
#_#97 at ./operators.jl:1031 [inlined]
ComposedFunction at ./operators.jl:1031
unknown function (ip: 0x7fbd39b3b676)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
_#42 at /opt/julia/packages/Makie/NrrbP/src/types.jl:423
ReversibleScale at /opt/julia/packages/Makie/NrrbP/src/types.jl:413
unknown function (ip: 0x7fbd39b3b0d1)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:971
eval at ./boot.jl:370 [inlined]
include_string at ./loading.jl:1903
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457
jfptr_include_35036.clone_1 at /opt/julia-1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
jl_f__call_latest at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/builtins.c:774
include at /opt/julia/packages/Makie/NrrbP/src/Makie.jl:1
unknown function (ip: 0x7fbd39b05ee2)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_eval_module_expr at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:971
eval at ./boot.jl:370 [inlined]
include_string at ./loading.jl:1903
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457 [inlined]
include_package_for_output at ./loading.jl:2049
jfptr_include_package_for_output_38866.clone_1 at /opt/julia-1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:971
eval at ./boot.jl:370 [inlined]
include_string at ./loading.jl:1903
include_string at ./loading.jl:1913 [inlined]
exec_options at ./client.jl:305
_start at ./client.jl:522
jfptr__start_40034.clone_1 at /opt/julia-1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
true_main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:573
jl_repl_entrypoint at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:717
main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/cli/loader_exe.c:59
unknown function (ip: 0x7fbd50ee4d8f)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 10796794 (Pool: 10793186; Big: 3608); GC: 17
ERROR: LoadError: Failed to precompile Makie [ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a] to "/opt/julia/compiled/v1.9/Makie/jl_1lC48a".
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 /opt/julia/packages/GLMakie/wkomB/src/GLMakie.jl:1
in expression starting at stdin:3

Failed to precompile GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a] to "/opt/julia/compiled/v1.9/GLMakie/jl_qxtDsH".

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

@moyner
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moyner commented Oct 24, 2023

I'm glad it runs! I think the error is related to compilation of the GLMakie package. You could try with CairoMakie instead - the plots will not be interactive, but it may be better than nothing.

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3 participants
@moyner @simontaurus @SimonStier