NNlib not defined error when loading model saved with BSON

[John-Boik]

It appears that code in the Flux documentation about saving and loading models does not work (with Ubuntu 19.10 and Julia 1.5.0 at least). The code, from https://fluxml.ai/Flux.jl/v0.8/saving/ is:

using BSON: @save, @load
using Flux
model = Chain(Dense(10,5,relu),Dense(5,2),softmax)
@save "mymodel.bson" model
@load "mymodel.bson" model

On my machine, the load line generates the error:

ERROR: LoadError: UndefVarError: NNlib not defined
Stacktrace:
 [1] (::BSON.var"#29#30")(::Module, ::String) at /home/jboik/.julia/packages/BSON/XAts7/src/extensions.jl:20
 [2] BottomRF at ./reduce.jl:81 [inlined]
 [3] _foldl_impl(::Base.BottomRF{BSON.var"#29#30"}, ::Module, ::Array{Any,1}) at ./reduce.jl:58
 [4] foldl_impl at ./reduce.jl:48 [inlined]
 [5] mapfoldl_impl(::typeof(identity), ::BSON.var"#29#30", ::NamedTuple{(:init,),Tuple{Module}}, ::Array{Any,1}) at ./reduce.jl:44
 [6] mapfoldl(::Function, ::Function, ::Array{Any,1}; kw::Base.Iterators.Pairs{Symbol,Module,Tuple{Symbol},NamedTuple{(:init,),Tuple{Module}}}) at ./reduce.jl:160
 [7] _mapreduce_dim at ./reducedim.jl:315 [inlined]
 [8] #mapreduce#620 at ./reducedim.jl:310 [inlined]
 [9] #reduce#622 at ./reducedim.jl:359 [inlined]
 [10] resolve(::Array{Any,1}) at /home/jboik/.julia/packages/BSON/XAts7/src/extensions.jl:20
 [11] (::BSON.var"#33#34")(::Dict{Symbol,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/extensions.jl:53
 [12] _raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:79
 [13] raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:89
 [14] (::BSON.var"#21#22"{IdDict{Any,Any}})(::Dict{Symbol,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:94
 [15] applychildren!(::BSON.var"#21#22"{IdDict{Any,Any}}, ::Array{Any,1}) at /home/jboik/.julia/packages/BSON/XAts7/src/BSON.jl:28
 [16] raise_recursive at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:94 [inlined]
 [17] (::BSON.var"#17#19"{IdDict{Any,Any}})(::Array{Any,1}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:79
 [18] applychildren!(::BSON.var"#17#19"{IdDict{Any,Any}}, ::Dict{Symbol,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/BSON.jl:21
 [19] _raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:79
 [20] raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:89
 [21] (::BSON.var"#21#22"{IdDict{Any,Any}})(::Dict{Symbol,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:94
 [22] applychildren!(::BSON.var"#21#22"{IdDict{Any,Any}}, ::Array{Any,1}) at /home/jboik/.julia/packages/BSON/XAts7/src/BSON.jl:28
 [23] raise_recursive at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:94 [inlined]
 [24] (::BSON.var"#17#19"{IdDict{Any,Any}})(::Array{Any,1}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:79
 [25] applychildren!(::BSON.var"#17#19"{IdDict{Any,Any}}, ::Dict{Symbol,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/BSON.jl:21
 [26] _raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:79
 [27] raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:89
 [28] (::BSON.var"#21#22"{IdDict{Any,Any}})(::Dict{Symbol,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:94
 [29] applychildren!(::BSON.var"#21#22"{IdDict{Any,Any}}, ::Array{Any,1}) at /home/jboik/.julia/packages/BSON/XAts7/src/BSON.jl:28
 [30] raise_recursive at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:94 [inlined]
 [31] (::BSON.var"#17#19"{IdDict{Any,Any}})(::Array{Any,1}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:79
 [32] applychildren!(::BSON.var"#17#19"{IdDict{Any,Any}}, ::Dict{Symbol,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/BSON.jl:21
 [33] _raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:79
 [34] raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:89
 [35] (::BSON.var"#43#44")(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/extensions.jl:138
 [36] raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:88
 [37] (::BSON.var"#18#20"{IdDict{Any,Any}})(::Dict{Symbol,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:82
 [38] applychildren!(::BSON.var"#18#20"{IdDict{Any,Any}}, ::Dict{Symbol,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/BSON.jl:21
 [39] _raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:82
 [40] raise_recursive(::Dict{Symbol,Any}, ::IdDict{Any,Any}) at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:89
 [41] raise_recursive at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:99 [inlined]
 [42] load at /home/jboik/.julia/packages/BSON/XAts7/src/read.jl:104 [inlined]
 [43] macro expansion at /home/jboik/.julia/packages/BSON/XAts7/src/BSON.jl:52 [inlined]

using NNlib does not solve the problem.
John

[John-Boik]

OK, I see now. I am trying to load a BSON file in a module, not in Main. If I use calls like:
Core.eval(Main, :(import NNlib))
just before the load line, then it works.

[floswald]

that doesn't work for me :-(

here's my env

(LandUse) pkg> st
Project LandUse v0.1.0
Status `~/.julia/dev/LandUse/Project.toml`
  [fbb218c0] BSON v0.2.6
  [6e4b80f9] BenchmarkTools v0.5.0
  [a134a8b2] BlackBoxOptim v0.5.0
  [ad839575] Blink v0.12.4
  [336ed68f] CSV v0.7.10
  [052768ef] CUDA v2.4.1
  [35d6a980] ColorSchemes v3.10.2
  [a93c6f00] DataFrames v0.22.5
  [1313f7d8] DataFramesMeta v0.6.0
  [442a2c76] FastGaussQuadrature v0.4.6
  [587475ba] Flux v0.11.3
  [59287772] Formatting v0.4.2
  [60bf3e95] GLPK v0.14.5
  [7073ff75] IJulia v1.23.1
  [f7bf1975] Impute v0.6.1
  [c601a237] Interact v0.10.3
  [a98d9a8b] Interpolations v0.13.1
  [b6b21f68] Ipopt v0.6.5
  [682c06a0] JSON v0.21.1
  [4076af6c] JuMP v0.21.6
  [b964fa9f] LaTeXStrings v1.2.0
  [266f59ce] LaTeXTabulars v0.1.1
  [d3d80556] LineSearches v7.1.1
  [2fda8390] LsqFit v0.12.0
  [cc2ba9b6] MLDataUtils v0.5.3
  [76087f3c] NLopt v0.6.2
  [2774e3e8] NLsolve v4.5.1
  [872c559c] NNlib v0.7.9
  [429524aa] Optim v1.2.3
  [995b91a9] PlotUtils v1.0.10
  [91a5bcdd] Plots v1.10.2
  [92933f4c] ProgressMeter v1.5.0
  [d330b81b] PyPlot v2.9.0
  [fcd29c91] QuantEcon v0.16.2
  [295af30f] Revise v3.1.11
  [f2b01f46] Roots v1.0.7
  [102930c3] SmoothingSplines v0.3.0
  [2913bbd2] StatsBase v0.33.2
  [f3b207a7] StatsPlots v0.14.17
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [37e2e46d] LinearAlgebra
  [de0858da] Printf
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays

in the global scope that works

julia> using Flux, BSON

julia> BSON.@load "./out/mymodel.bson" x

julia> 

but when I do the same thing inside a module it doesn't. inside the module I have to do

using Flux
using BSON
# no using NNlib

Chain = BSON.load(joinpath(@__DIR__,"..","out","mymodel.bson"))[:x]

[darsnack]

Try the latest release of BSON.jl. It adds support for specifying the namespace. Inside your module you can do:

BSON.load(joinpath(@__DIR__,"..","out","mymodel.bson"), @__MODULE__)[:x]

Reference to docs: https://github.com/JuliaIO/BSON.jl#loading-custom-data-types-within-modules

[rkube]

I just hit this issue, but in a Pluto notebook.

[darsnack]

I'm not a Pluto expert, but I believe Pluto modifies the namespaces that your code runs under. I would try asking on the Pluto.jl issues and reference this issue. It's likely a Pluto-side tweak, but we can add the solution to the BSON.jl docs once it is found.

[lorenzoh]

Not a solution to the problem per se, but I've found JLD2.jl works in Pluto.jl notebooks. So if you don't find another way, you could load the model with BSON in a regular Julia session and save them with JLD2; then use JLD2 in Pluto to load it.

[DhairyaLGandhi]

Could you add using NNlib and try loading the model.