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Better error message if a ReactionMethod fails at runtime, including @generated dispatch #139

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Better error message if a ReactionMethod fails at runtime, including @generated dispatch #139

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a09898f
Better error message if a ReactionMethod fails at runtime
sjdaines Nov 28, 2024
99e0f25
implement try-catch for generated dispatch
sjdaines Nov 29, 2024
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114 changes: 83 additions & 31 deletions src/Model.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -246,7 +246,7 @@ function create_model_from_config(
catch e
error("$(typeof(e)) while reading .yaml config file(s) $(abspath.(config_files)).\n"*
"If the error isn't obvious by looking at the file(s) (often this is a whitespace issue), "*
"try an online YAML validator eg http://www.yamllint.com")
"install the VS Code YAML plugin, or try an online YAML validator eg http://www.yamllint.com")
end

conf_model = data[configmodel]
Expand Down Expand Up @@ -778,12 +778,19 @@ function dispatch_methodlist(
dl::ReactionMethodDispatchListNoGen,
deltat::Float64=0.0
)
lasti = -1

for i in eachindex(dl.methods)
call_method(dl.methods[i], dl.vardatas[i], dl.cellranges[i], deltat)
end
try
for i in eachindex(dl.methods)
lasti = i
call_method(dl.methods[i], dl.vardatas[i], dl.cellranges[i], deltat)
end
catch
lasti != -1 && _dispatch_methodlist_methoderror(dl.methods[lasti][])
rethrow()
end

return nothing
return nothing
end

function dispatch_methodlist(
Expand All @@ -792,67 +799,112 @@ function dispatch_methodlist(
deltat::Float64=0.0
)

for j in eachindex(dl.methods)
methodref = dl.methods[j]
if has_modified_parameters(pa, methodref)
call_method(methodref, get_parameters(pa, methodref), dl.vardatas[j], dl.cellranges[j], deltat)
else
call_method(methodref, dl.vardatas[j], dl.cellranges[j], deltat)
lasti = -1

try
for i in eachindex(dl.methods)
lasti = i
methodref = dl.methods[i]
if has_modified_parameters(pa, methodref)
call_method(methodref, get_parameters(pa, methodref), dl.vardatas[i], dl.cellranges[i], deltat)
else
call_method(methodref, dl.vardatas[i], dl.cellranges[i], deltat)
end
end
end
catch
lasti != -1 && _dispatch_methodlist_methoderror(dl.methods[lasti][])
rethrow()
end

return nothing
return nothing
end

@generated function dispatch_methodlist(
dl::ReactionMethodDispatchList{M, V, C},
deltat::Float64=0.0
deltat::Float64=0.0,
) where {M, V, C}

# Write out unrolled loop as an expression
# See https://discourse.julialang.org/t/manually-unroll-operations-with-objects-of-tuple/11604

ex = quote ; end # empty expression
for j=1:fieldcount(M)
push!(ex.args,
unrollex = quote ; end # empty expression
for i=1:fieldcount(M)
push!(unrollex.args,
quote
lasti = $i
# let
# call_method(dl.methods[$j][], dl.vardatas[$j][], dl.cellranges[$j], deltat)
# call_method(dl.methods[$i][], dl.vardatas[$i][], dl.cellranges[$i], deltat)
# pass Ref to function to reduce compile time
call_method(dl.methods[$j], dl.vardatas[$j], dl.cellranges[$j], deltat)
call_method(dl.methods[$i], dl.vardatas[$i], dl.cellranges[$i], deltat)
# end
end
)
)
end

# interpolate the unrolled loop into a try-catch
ex = quote
lasti = -1

try
$unrollex
catch
lasti != -1 && _dispatch_methodlist_methoderror(dl.methods[lasti][])
rethrow()
end

return nothing
end
push!(ex.args, quote; return nothing; end)

return ex
end


@generated function dispatch_methodlist(
dl::ReactionMethodDispatchList{M, V, C},
pa::ParameterAggregator,
deltat::Float64=0.0
) where {M, V, C}

# See https://discourse.julialang.org/t/manually-unroll-operations-with-objects-of-tuple/11604

ex = quote ; end # empty expression
for j=1:fieldcount(M)
push!(ex.args,
# Write out unrolled loop as an expression
# See https://discourse.julialang.org/t/manually-unroll-operations-with-objects-of-tuple/11604
unrollex = quote ; end # empty expression
for i=1:fieldcount(M)
push!(unrollex.args,
quote
if has_modified_parameters(pa, dl.methods[$j])
call_method(dl.methods[$j], get_parameters(pa, dl.methods[$j]), dl.vardatas[$j], dl.cellranges[$j], deltat)
lasti = $i
if has_modified_parameters(pa, dl.methods[$i])
call_method(dl.methods[$i], get_parameters(pa, dl.methods[$i]), dl.vardatas[$i], dl.cellranges[$i], deltat)
else
call_method(dl.methods[$j], dl.vardatas[$j], dl.cellranges[$j], deltat)
call_method(dl.methods[$i], dl.vardatas[$i], dl.cellranges[$i], deltat)
end
end
)
end
push!(ex.args, quote; return nothing; end)

# interpolate the unrolled loop into a try-catch
ex = quote
lasti = -1

try
$unrollex
catch
lasti != -1 && _dispatch_methodlist_methoderror(dl.methods[lasti][])
rethrow()
end

return nothing
end

return ex
end

function _dispatch_methodlist_methoderror(reactionmethod)
io = IOBuffer()
println(io, "dispatch_methodlist: a ReactionMethod failed:")
show(io, MIME"text/plain"(), reactionmethod)
@warn String(take!(io))
return
end

#################################
# Pretty printing
################################
Expand Down
26 changes: 16 additions & 10 deletions src/Reaction.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -324,11 +324,13 @@ end
add_method_do!(@nospecialize(reaction::AbstractReaction), @nospecialize(methodfn::Function), @nospecialize(vars::Tuple{Vararg{AbstractVarList}}); kwargs...) =
_add_method!(reaction, methodfn, vars, add_method_do!; kwargs...)

default_preparefn(m, vardata) = vardata

function _add_method!(
@nospecialize(reaction::AbstractReaction), @nospecialize(methodfn::Function), @nospecialize(vars::Tuple{Vararg{AbstractVarList}}), add_method_fn;
name=string(methodfn),
p=nothing,
preparefn=(m, vardata) -> vardata,
preparefn=default_preparefn,
operatorID=reaction.operatorID,
domain=reaction.domain
)
Expand Down Expand Up @@ -611,15 +613,19 @@ function Base.show(io::IO, react::AbstractReaction)
end

function Base.show(io::IO, ::MIME"text/plain", react::AbstractReaction)
println(io, typename(react))
println(io, " name='", react.name, "'")
println(io, " classname='", react.classname, "'")
println(io, " domain='", domainname(react), "'")
println(io, " operatorID=", react.operatorID)
println(io, " parameters=", get_parameters(react))
println(io, " methods_setup=", react.methods_setup)
println(io, " methods_initialize=", react.methods_initialize)
println(io, " methods_do=", react.methods_do)
dump_reaction(io, react)
end

function dump_reaction(io::IO, react::AbstractReaction; prefix="", show_parameters::Bool=true)
println(io, prefix, typename(react))
println(io, prefix, " name='", react.name, "'")
println(io, prefix, " classname='", react.classname, "'")
println(io, prefix, " domain='", domainname(react), "'")
println(io, prefix, " operatorID=", react.operatorID)
show_parameters && println(io, prefix, " parameters=", get_parameters(react))
println(io, prefix, " methods_setup=", react.methods_setup)
println(io, prefix, " methods_initialize=", react.methods_initialize)
println(io, prefix, " methods_do=", react.methods_do)
end

"""
Expand Down
17 changes: 15 additions & 2 deletions src/ReactionMethod.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -143,7 +143,7 @@ call_method_codefn(io::IO, codefn, method::ReactionMethod{M, R, P, 5}, vardata,

"""
get_variables_tuple(method::AbstractReactionMethod) -> (Vector{VariableReaction}, ...)

println(io, typename(react))
Get all [`VariableReaction`](@ref)s from `method` as a Tuple of `Vector{VariableReaction}`
"""
get_variables_tuple(@nospecialize(method::ReactionMethod); flatten=true) = Tuple(get_variables(vl; flatten) for vl in method.varlists)
Expand Down Expand Up @@ -209,7 +209,7 @@ get_rate_stoichiometry(@nospecialize(m::ReactionMethod)) = []
# Pretty printing
############################################

"compact form"
# compact form
function Base.show(io::IO, @nospecialize(method::ReactionMethod))
print(
io,
Expand All @@ -220,3 +220,16 @@ function Base.show(io::IO, @nospecialize(method::ReactionMethod))
")",
)
end

# multiline form
function Base.show(io::IO, ::MIME"text/plain", @nospecialize(method::ReactionMethod))
println(io, "ReactionMethod")
println(io, " fullname='", fullname(method), "'")
println(io, " methodfn=", string(method.methodfn))
println(io, " preparefn=", string(method.preparefn))
println(io, " domain='", method.domain.name , "'")
println(io, " operatorID=", method.operatorID, "'")

print(io, " reaction=")
dump_reaction(io, method.reaction; prefix=" ", show_parameters=false)
end
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