Turing.jl: Support Julia 0.7/1.0

[xukai92]

There is a guide of what current packages should do to support the new package manager?

[yebai]

Not sure yet, there is a talk on Pkg3 from JuliaCon:

https://m.youtube.com/watch?v=GBi__3nF-rM

[xukai92]

So basically many things fail. Below are what I know so far

• ReverseDiff doesn't support 0.7 (https://github.com/JuliaDiff/ReverseDiff.jl/issues/109)
  
  
  
  • I can work around this by using Requires
  
  
• Mamba has a dependency which doesn't support 0.7
  
  
  
  • I will probably remove it anyway but I don't know what I should do now
  
  
• New coroutine interface - we didn't fix the warning in 0.6
  
  
  
  • I guess we should fix it first
  
  

[xukai92]

@yebai Can you take care of updating the coroutine thing?

[xukai92]

Oh I actually manage to hack it.

[xukai92]

After fixing things mentioned above, I meet a problem in out compiler. I guess there is some change which makes our implementation doesn't work any more. I pushed my branch (https://github.com/TuringLang/Turing.jl/tree/github.com/TuringLang/Turing.jl/issues/462) with temp-fixes described above which makes using Turing work. Now below fails and I haven't figured out why

using Turing
@model g() = begin
  x ~ Normal(0, 1)
end
g()
end

with error

ERROR: LoadError: MethodError: objects of type Int64 are not callable
Stacktrace:
 [1] eval at ./boot.jl:319 [inlined]
 [2] eval(::Expr) at ./client.jl:399
 [3] #g#3(::Dict{Symbol,Any}, ::Dict{Symbol,Any}, ::Function) at /Users/kai/.julia/dev/Turing/src/core/compiler.jl:323
 [4] g() at ./none:0
 [5] top-level scope at none:0
in expression starting at <macrocall>:0

[yebai]

I made some updates to the branch at the JuliaCon hackathon today. All the syntax errors should be fixed for 1.0 now. I still haven't nailed down the compiler error, but will continue working on it.

[xukai92]

Thanks @yebai and @trappmartin !

[xukai92]

I just pushed some commits to add Markdown to REQUIRE and resolve one syntax warning.

[trappmartin]

I resolved some syntax errors in the test. The compiler tests currently fail on my machine, and other tests probably too.

[revendrat]

Is Turing Julia 1.0 ready?

[trappmartin]

We are working on it. Stay tuned.

[xukai92]

I fixed the compiler issue. Please check my last two commits: 64b956b95499ccd1d81e1631983daf6ab1156991 and 24ba6cabd996530f4f560664b6622d86e7c86f9a

[xukai92]

Until now we can do the following

@model m(x) = begin
  a ~ Normal(0, 1)
  x ~ Nromal(a, 1)
end

mf = m(1)

But when I call mf() I still get an error:

julia> mf()
ERROR: type is immutable
Stacktrace:
 [1] setproperty! at ./sysimg.jl:19 [inlined]
 [2] observe(::Nothing, ::Normal{Float64}, ::Int64, ::Turing.VarReplay.VarInfo) at /Users/kai/.julia/dev/Turing/src/samplers/sampler.jl:92
 [3] ##m_model#368 at ./REPL[2]:65 [inlined]
 [4] ##m_model#368(::Turing.VarReplay.VarInfo, ::Nothing) at ./none:0
 [5] ##m_model#368() at ./none:1
 [6] top-level scope at none:0

[xukai92]

This may be related to my hack in 64b956b95499ccd1d81e1631983daf6ab1156991.

[yebai]

I fixed the compiler issue. Please check my last two commits: 64b956b and 24ba6ca

For better readability and maintainability, I think we should split the compiler into small functions and add tests to them.

[hessammehr]

@yebai, @xukai92 I just pushed a few quick fixes to this branch, one to get around the mutability error that @xukai92 is reporting. Feel free to cherry-pick or ignore altogether if not useful.

[yebai]

@hessammehr Many thanks! I’ve merged your PR. This is going a lot faster than I thought. We might be able to get Turing work on 1.0 this week!

[hessammehr]

@yebai No problem! I really hope so, and that we can do a clean refactor to make Turing more maintainable as well.

[hessammehr]

Presently, I get the following confusing internal error message with @xukai92's code snippet.

using Turing
using Distributions
@model m(x) = begin
         a ~ Normal(0, 1)
         x ~ Normal(a, 1)
end
mf = m(1)
mf()

rec_backtrace at /home/Administrator/buildbot/worker/package_win64/build/src\stackwalk.c:94
record_backtrace at /home/Administrator/buildbot/worker/package_win64/build/src\task.c:246
jl_throw at /home/Administrator/buildbot/worker/package_win64/build/src\task.c:577
jl_type_error_rt at /home/Administrator/buildbot/worker/package_win64/build/src\rtutils.c:118
jl_type_error at /home/Administrator/buildbot/worker/package_win64/build/src\rtutils.c:124
jl_f_issubtype at /home/Administrator/buildbot/worker/package_win64/build/src\builtins.c:415
typeof_tfunc at .\compiler\tfuncs.jl:393
typeof_tfunc at .\compiler\tfuncs.jl:391
typeof_tfunc at .\compiler\tfuncs.jl:396
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2182
jl_apply at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:1538 [inlined]
jl_f__apply at /home/Administrator/buildbot/worker/package_win64/build/src\builtins.c:563
builtin_tfunction at .\compiler\tfuncs.jl:1170
builtin_tfunction at .\compiler\tfuncs.jl:1079
abstract_call at .\compiler\abstractinterpretation.jl:551
abstract_eval_call at .\compiler\abstractinterpretation.jl:798
abstract_eval at .\compiler\abstractinterpretation.jl:883
typeinf_local at .\compiler\abstractinterpretation.jl:1107
typeinf_nocycle at .\compiler\abstractinterpretation.jl:1163
typeinf at .\compiler\typeinfer.jl:15
typeinf_edge at .\compiler\typeinfer.jl:492
abstract_call_method at .\compiler\abstractinterpretation.jl:321
abstract_call_gf_by_type at .\compiler\abstractinterpretation.jl:81
abstract_call at .\compiler\abstractinterpretation.jl:769
abstract_eval_call at .\compiler\abstractinterpretation.jl:798
abstract_eval at .\compiler\abstractinterpretation.jl:883
typeinf_local at .\compiler\abstractinterpretation.jl:1107
typeinf_nocycle at .\compiler\abstractinterpretation.jl:1163
typeinf at .\compiler\typeinfer.jl:15
typeinf_edge at .\compiler\typeinfer.jl:492
abstract_call_method at .\compiler\abstractinterpretation.jl:321
abstract_call_gf_by_type at .\compiler\abstractinterpretation.jl:81
abstract_call at .\compiler\abstractinterpretation.jl:769
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2182
abstract_apply at .\compiler\abstractinterpretation.jl:477
abstract_call at .\compiler\abstractinterpretation.jl:525
abstract_eval_call at .\compiler\abstractinterpretation.jl:798
abstract_eval at .\compiler\abstractinterpretation.jl:883
typeinf_local at .\compiler\abstractinterpretation.jl:1107
typeinf_nocycle at .\compiler\abstractinterpretation.jl:1163
typeinf at .\compiler\typeinfer.jl:15
typeinf_edge at .\compiler\typeinfer.jl:492
abstract_call_method at .\compiler\abstractinterpretation.jl:321
abstract_call_gf_by_type at .\compiler\abstractinterpretation.jl:81
abstract_call at .\compiler\abstractinterpretation.jl:769
abstract_eval_call at .\compiler\abstractinterpretation.jl:798
abstract_eval at .\compiler\abstractinterpretation.jl:883
typeinf_local at .\compiler\abstractinterpretation.jl:1107
typeinf_nocycle at .\compiler\abstractinterpretation.jl:1163
typeinf at .\compiler\typeinfer.jl:15
typeinf_edge at .\compiler\typeinfer.jl:492
abstract_call_method at .\compiler\abstractinterpretation.jl:321
abstract_call_gf_by_type at .\compiler\abstractinterpretation.jl:81
abstract_call at .\compiler\abstractinterpretation.jl:769
abstract_eval_call at .\compiler\abstractinterpretation.jl:798
abstract_eval at .\compiler\abstractinterpretation.jl:883
typeinf_local at .\compiler\abstractinterpretation.jl:1107
typeinf_nocycle at .\compiler\abstractinterpretation.jl:1163
typeinf at .\compiler\typeinfer.jl:15
typeinf_edge at .\compiler\typeinfer.jl:492
abstract_call_method at .\compiler\abstractinterpretation.jl:321
abstract_call_gf_by_type at .\compiler\abstractinterpretation.jl:81
abstract_call at .\compiler\abstractinterpretation.jl:769
abstract_eval_call at .\compiler\abstractinterpretation.jl:798
abstract_eval at .\compiler\abstractinterpretation.jl:883
typeinf_local at .\compiler\abstractinterpretation.jl:1107
typeinf_nocycle at .\compiler\abstractinterpretation.jl:1163
typeinf at .\compiler\typeinfer.jl:15
typeinf_edge at .\compiler\typeinfer.jl:492
abstract_call_method at .\compiler\abstractinterpretation.jl:321
abstract_call_gf_by_type at .\compiler\abstractinterpretation.jl:81
abstract_call at .\compiler\abstractinterpretation.jl:769
abstract_eval_call at .\compiler\abstractinterpretation.jl:798
abstract_eval at .\compiler\abstractinterpretation.jl:883
typeinf_local at .\compiler\abstractinterpretation.jl:1107
typeinf_nocycle at .\compiler\abstractinterpretation.jl:1163
typeinf at .\compiler\typeinfer.jl:15
typeinf_ext at .\compiler\typeinfer.jl:567
typeinf_ext at .\compiler\typeinfer.jl:604
jfptr_typeinf_ext_1.clone_1 at C:\Users\Uigedail\AppData\Local\Julia-0.7.0\lib\julia\sys.dll (unknown line)
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2182
jl_apply at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:1538 [inlined]
jl_apply_with_saved_exception_state at /home/Administrator/buildbot/worker/package_win64/build/src\rtutils.c:257
jl_type_infer at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:275
jl_compile_method_internal at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1784 [inlined]
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1828
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2182
do_call at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:324
eval_value at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:428
eval_stmt_value at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:363 [inlined]
eval_body at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:682
jl_interpret_toplevel_thunk_callback at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:799
unknown function (ip: FFFFFFFFFFFFFFFE)
unknown function (ip: 0000000022A4990F)
unknown function (ip: FFFFFFFFFFFFFFFF)
jl_toplevel_eval_flex at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:831
jl_toplevel_eval_in at /home/Administrator/buildbot/worker/package_win64/build/src\builtins.c:633
eval at .\boot.jl:319
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2182
eval_user_input at C:\cygwin\home\Administrator\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v0.7\REPL\src\REPL.jl:85
macro expansion at C:\cygwin\home\Administrator\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v0.7\REPL\src\REPL.jl:117 [inlined]
#28 at .\task.jl:262
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1829
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2182
jl_apply at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:1538 [inlined]
start_task at /home/Administrator/buildbot/worker/package_win64/build/src\task.c:268
WARNING: Base.e is deprecated, use ℯ (\euler) or `Base.MathConstants.e`
 in module Turing
WARNING: Base.e is deprecated, use ℯ (\euler) or `Base.MathConstants.e`
 in module Turing
WARNING: Base.e is deprecated, use ℯ (\euler) or `Base.MathConstants.e`
 in module Turing
Internal error: encountered unexpected error in runtime:
TypeError(func=:<:, context="", expected=Type{T} where T, got=T0<:Real)
┌ Warning: broadcast will default to iterating over its arguments in the future. Wrap arguments of

Seems to me like an issue with the task.c shim.

[yebai]

Seems to me like an issue with the task.c shim.

Did you recompile task.c?

@hessammehr There is a variable name change in julia's task type. I just fixed it in Turing's task.c. We need to re-complile LibtaskBuilder2.

[xukai92]

I also get that error but still manage to initialise vi by calling mf().

---

Also, after making Chain mutable, we are in the stage where we are kind of blocked by Mamba.Chain. As I mentioned in the very beginning of this issue, I disabled Mamba.Chain. I simply did this by commenting out Mamba.Chain and defining a dummy AbstractChain type (see https://github.com/TuringLang/Turing.jl/blob/github.com/TuringLang/Turing.jl/issues/462/src/Turing.jl#L25-L28).

Now when I try to call sample(mf, IS(100)), I get

ERROR: MethodError: no method matching Turing.Chains(::Array{Float64,3}; names=AbstractString["a", "lp"])
Closest candidates are:
  Turing.Chains() at /Users/kai/.julia/dev/Turing/src/Turing.jl:28 got unsupported keyword argument "names"
Stacktrace:
 [1] flatten!(::Turing.Chain) at /Users/kai/.julia/dev/Turing/src/core/io.jl:121
 [2] Turing.Chain(::Float64, ::Array{Turing.Sample,1}) at /Users/kai/.julia/dev/Turing/src/core/io.jl:105
 [3] sample(::getfield(Main, Symbol("###m_model#368")), ::IS) at /Users/kai/.julia/dev/Turing/src/samplers/is.jl:50
 [4] top-level scope at none:0

which is because of the lack of the real implementation of Chain utility functions.

[yebai]

Update:

The task.c code has been updated to support Julia 1.0 (ref: https://github.com/hessammehr/LibtaskBuilder2/pull/1) .

I'm working on fixing task copying on the Julia side. The issue is that consume/produce has been removed from Julia 1.0. The new channel API does not work on copied coroutines. I'm investigating why that's the case.

[yebai]

Blocking issues for Julia 1.0

• AD: change to Flux.Tracked #457 Postponed, ForwardDiff is working fine!
• Mamba.Chain #413 Fixed by https://github.com/TuringLang/Chain.jl
• Task communication #466 Fixed by #468

[alstat]

Waiting for this, thanks for the hard work.