Error in precompiling packages

Hello, trying to run the following code and having issues with package precompilation from an existing Project.toml file on a new machine. Flux is just an example package, there are ~40 more packages which error out but the stacktrace is too long and I figured it’s the same issue. If any other extra information is necessary - please let me know. Otherwise any help is greatly appreciated (I realise that some directory is missing, but not sure how to properly create it).

(@v1.8) pkg> activate .                                                                                                                                                                                     
Activating project at `/disk/scratch/s1788788/NODE_work/recode_v1`                                                                                                                                                                                                                                                                                                                                                
(node_work) pkg> status                                                                                                                                                                                   
Project node_work v0.1.0                                                                                                                                                                                  
Status `/disk/scratch/s1788788/NODE_work/recode_v1/Project.toml`                                                                                                                                            
[6e4b80f9] BenchmarkTools v1.3.2                                                                                                                                                                          
[aae7a2af] DiffEqFlux v1.52.0                                                                                                                                                                             
[0c46a032] DifferentialEquations v7.6.0                                                                                                                                                                   
[31c24e10] Distributions v0.25.79                                                                                                                                                                         
[5789e2e9] FileIO v1.16.0                                                                                                                                                                                 
[587475ba] Flux v0.13.8                                                                                                                                                                                   
[c8e1da08] IterTools v1.4.0                                                                                                                                                                               
[033835bb] JLD2 v0.4.28                                                                                                                                                                                   
[d3d80556] LineSearches v7.2.0                                                                                                                                                                            
[429524aa] Optim v1.7.3                                                                                                                                                                                   
[7f7a1694] Optimization v3.9.2                                                                                                                                                                            
[36348300] OptimizationOptimJL v0.1.4                                                                                                                                                                     
[d330b81b] PyPlot v2.11.0                                                                                                                                                                                 
[295af30f] Revise v3.4.0                                                                                                                                                                                  
[ade2ca70] Dates                                                                                                                                                                                                                                                                                                                                                                                                  
julia> import Flux                                                                                                                                                                                        
[ Info: Precompiling Flux [587475ba-b771-5e3f-ad9e-33799f191a9c]                                                                                                                                          
ERROR: LoadError: InitError: could not load library "/afs/inf.ed.ac.uk/user/s17/s1788788/.julia/artifacts/abf4b5086b4eb867021118c85b2cc11a15b764a9/lib/libopenspecfun.so"                                 
/afs/inf.ed.ac.uk
/user/s17/s1788788/.julia/artifacts/abf4b5086b4eb867021118c85b2cc11a15b764a9/lib/libopenspecfun.so: cannot open shared object file: No such file or directory                           
 Stacktrace:                                                                                                                                                                                                
[1] dlopen(s::String, flags::UInt32; throw_error::Bool)                                                                                                                                                     
@ Base.Libc.Libdl ./libdl.jl:117                                                                                                                                                                        
[2] dlopen(s::String, flags::UInt32)                                                                                                                                                                        
@ Base.Libc.Libdl ./libdl.jl:116                                                                                                                                                                        
[3] macro expansion                                                                                                                                                                                         
@ ~/.julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
[4] __init__()
@ OpenSpecFun_jll ~/.julia/packages/OpenSpecFun_jll/1Zaof/src/wrappers/x86_64-linux-gnu-libgfortran5.jl:9
[5] _include_from_serialized(pkg::Base.PkgId, path::String, depmods::Vector{Any})
@ Base ./loading.jl:831
[6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt64)
@ Base ./loading.jl:1039
[7] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1315                                                                                                                                                                                
[8] _require_prelocked(uuidkey::Base.PkgId)                                                                                                                                                                 
@ Base ./loading.jl:1200                                                                                                                                                                                
[9] macro expansion                                                                                                                                                                                         
@ ./loading.jl:1180 [inlined]                                                                                                                                                                          
[10] macro expansion                                                                                                                                                                                         
@ ./lock.jl:223 [inlined]                                                                                                                                                                              
[11] require(into::Module, mod::Symbol)                                                                                                                                                                      
@ Base ./loading.jl:1144                                                                                                                                                                               
[12] include                                                                                                                                                                                                 
@ ./Base.jl:419 [inlined]                                                                                                                                                                              
[13] 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:1554                                                                                                                                                                               
[14] top-level scope                                                                                                                                                                                         
@ stdin:1                                                                                                                                                                                             
during initialization of module OpenSpecFun_jll                                                                                                                                                           
in expression starting at /afs/inf.ed.ac.uk/user/s17/s1788788/.julia/packages/SpecialFunctions/hefUc
/src/SpecialFunctions.jl:1                                                                           
in expression starting at stdin:1                                                                                                                                                                         
ERROR: LoadError: Failed to precompile SpecialFunctions [276daf66-3868-5448-9aa4-cd146d93841b] to /afs/inf.ed.ac.uk/user/s17/s1788788/.julia/compiled/v1.8/SpecialFunctions/jl_TAanta.                    
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:1707                                                                                                                                                                                
[3] compilecache                                                                                                                                                                                            
@ ./loading.jl:1651 [inlined]                                                                                                                                                                           
[4] _require(pkg::Base.PkgId)                                                                                                                                                                               
@ Base ./loading.jl:1337                                                                                                                                                                                
[5] _require_prelocked(uuidkey::Base.PkgId)                                                                                                                                                                 
@ Base ./loading.jl:1200                                                                                                                                                                                
[6] macro expansion                                                                                                                                                                                         
@ ./loading.jl:1180 [inlined]                                                                                                                                                                           
[7] macro expansion                                                                                                                                                                                         
@ ./lock.jl:223 [inlined]                                                                                                                                                                               
[8] require(into::Module, mod::Symbol)                                                                                                                                                                      
@ Base ./loading.jl:1144                                                                                                                                                                                
[9] include
@ ./Base.jl:419 [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, UInt64}}, 
source::Nothing)
@ Base ./loading.jl:1554
[11] top-level scope
@ stdin:1
in expression starting at /afs/inf.ed.ac.uk/user/s17/s1788788/.julia/packages/Flux/FKl3M/src/Flux.jl:1
in expression starting at stdin:1                                                                                                                                                                         ERROR: Failed to precompile Flux [587475ba-b771-5e3f-ad9e-33799f191a9c] to /afs/inf.ed.ac.uk/user/s17/s1788788/.julia/compiled/v1.8/Flux/jl_0re63l.                                                       
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:1707                                                                                                                                                                                
[3] compilecache                                                                                                                                                                                            
@ ./loading.jl:1651 [inlined]                                                                                                                                                                           
[4] _require(pkg::Base.PkgId)                                                                                                                                                                               
@ Base ./loading.jl:1337                                                                                                                                                                                
[5] _require_prelocked(uuidkey::Base.PkgId)                                                                                                                                                                 
@ Base ./loading.jl:1200                                                                                                                                                                                
[6] macro expansion
@ ./loading.jl:1180 [inlined]
[7] macro expansion                                                                                                                                                                                     @ ./lock.jl:223 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1144

The first thing to do is to check if you actually have the referenced file /afs/inf.ed.ac.uk/user/s17/s1788788/.julia/artifacts/abf4b5086b4eb867021118c85b2cc11a15b764a9/lib/libopenspecfun.so on your disk.

1 Like

Just checked, I do not, .../lib is empty.

Delete the entire directory /afs/inf.ed.ac.uk/user/s17/s1788788/.julia/artifacts/abf4b5086b4eb867021118c85b2cc11a15b764a9. It’ll be downloaded automatically next time it’s needed.

Yup, that did it, thanks!