Segfault in 1.7.0

[miakramer]

System info:

Julia 1.7.0
macOS 11.6.1
CPU: Intel(R) Core(TM) i7-4870HQ CPU @ 2.50GHz

Minimal example I've come up with:

using Turing
@model function f()
    x ~ Normal()
    x
end
model = f()
sample(model, SMC(), 1)

This results in:

signal (11): Segmentation fault: 11
in expression starting at REPL[4]:1
getproperty at ./task.jl:170 [inlined]
produce at /Users/Mia/.julia/packages/Libtask/OtgFl/src/ctask.jl:112
#3 at /Users/Mia/.julia/packages/Turing/uAz5c/src/core/container.jl:44 [inlined]
#1 at /Users/Mia/.julia/packages/Libtask/OtgFl/src/ctask.jl:65
unknown function (ip: 0x1349c652f)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
start_task at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
Allocations: 45060303 (Pool: 45045281; Big: 15022); GC: 46

Interestingly, we get a different failure with specific values for number of samples—the following is with sample(model, SMC(), 1000):

signal (11): Segmentation fault: 11
in expression starting at REPL[4]:1
gc_mark_loop at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
_jl_gc_collect at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_gc_collect at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_gc_pool_alloc at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_gc_alloc at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
array_resize_buffer at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_array_grow_at_end at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
_growend! at ./array.jl:948 [inlined]
push! at ./array.jl:995 [inlined]
scan_slot_def_use at ./compiler/ssair/slot2ssa.jl:41
slot2reg at ./compiler/optimize.jl:418 [inlined]
run_passes at ./compiler/optimize.jl:303
optimize at ./compiler/optimize.jl:296 [inlined]
_typeinf at ./compiler/typeinfer.jl:255
typeinf at ./compiler/typeinfer.jl:209
abstract_call_method_with_const_args at ./compiler/abstractinterpretation.jl:557
abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:113
abstract_call_known at ./compiler/abstractinterpretation.jl:1342
abstract_call at ./compiler/abstractinterpretation.jl:1397
abstract_call at ./compiler/abstractinterpretation.jl:1382
abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534
typeinf_local at ./compiler/abstractinterpretation.jl:1918
typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014
_typeinf at ./compiler/typeinfer.jl:226
typeinf at ./compiler/typeinfer.jl:209
abstract_call_method_with_const_args at ./compiler/abstractinterpretation.jl:557
abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:113
abstract_call_known at ./compiler/abstractinterpretation.jl:1342
abstract_call at ./compiler/abstractinterpretation.jl:1397
abstract_call at ./compiler/abstractinterpretation.jl:1382
abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534
typeinf_local at ./compiler/abstractinterpretation.jl:1900
typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014
_typeinf at ./compiler/typeinfer.jl:226
typeinf at ./compiler/typeinfer.jl:209
typeinf_edge at ./compiler/typeinfer.jl:823 [inlined]
abstract_call_method at ./compiler/abstractinterpretation.jl:504
abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:105
abstract_call_known at ./compiler/abstractinterpretation.jl:1342
abstract_call at ./compiler/abstractinterpretation.jl:1397
abstract_call at ./compiler/abstractinterpretation.jl:1382
abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534
typeinf_local at ./compiler/abstractinterpretation.jl:1918
typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014
_typeinf at ./compiler/typeinfer.jl:226
typeinf at ./compiler/typeinfer.jl:209
typeinf_edge at ./compiler/typeinfer.jl:823 [inlined]
abstract_call_method at ./compiler/abstractinterpretation.jl:504
abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:105
abstract_call_known at ./compiler/abstractinterpretation.jl:1342
abstract_call at ./compiler/abstractinterpretation.jl:1397
abstract_call at ./compiler/abstractinterpretation.jl:1382
abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534
typeinf_local at ./compiler/abstractinterpretation.jl:1918
typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014
_typeinf at ./compiler/typeinfer.jl:226
typeinf at ./compiler/typeinfer.jl:209
typeinf_edge at ./compiler/typeinfer.jl:823 [inlined]
abstract_call_method at ./compiler/abstractinterpretation.jl:504
abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:105
abstract_call_known at ./compiler/abstractinterpretation.jl:1342
abstract_call at ./compiler/abstractinterpretation.jl:1397
abstract_call at ./compiler/abstractinterpretation.jl:1382
abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534
typeinf_local at ./compiler/abstractinterpretation.jl:1918
typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014
_typeinf at ./compiler/typeinfer.jl:226
typeinf at ./compiler/typeinfer.jl:209
typeinf_edge at ./compiler/typeinfer.jl:823 [inlined]
abstract_call_method at ./compiler/abstractinterpretation.jl:504
abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:105
abstract_call at ./compiler/abstractinterpretation.jl:1395
abstract_call at ./compiler/abstractinterpretation.jl:1382
abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534
typeinf_local at ./compiler/abstractinterpretation.jl:1918
typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014
_typeinf at ./compiler/typeinfer.jl:226
typeinf at ./compiler/typeinfer.jl:209
typeinf_edge at ./compiler/typeinfer.jl:823 [inlined]
abstract_call_method at ./compiler/abstractinterpretation.jl:504
abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:105
abstract_call at ./compiler/abstractinterpretation.jl:1395
abstract_apply at ./compiler/abstractinterpretation.jl:987
abstract_call_known at ./compiler/abstractinterpretation.jl:1249
abstract_call at ./compiler/abstractinterpretation.jl:1397
abstract_call at ./compiler/abstractinterpretation.jl:1382
abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534
typeinf_local at ./compiler/abstractinterpretation.jl:1918
typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014
_typeinf at ./compiler/typeinfer.jl:226
typeinf at ./compiler/typeinfer.jl:209
typeinf_edge at ./compiler/typeinfer.jl:823 [inlined]
abstract_call_method at ./compiler/abstractinterpretation.jl:504
abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:105
abstract_call at ./compiler/abstractinterpretation.jl:1395
abstract_call at ./compiler/abstractinterpretation.jl:1382
abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534
typeinf_local at ./compiler/abstractinterpretation.jl:1918
typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014
_typeinf at ./compiler/typeinfer.jl:226
typeinf at ./compiler/typeinfer.jl:209
typeinf_edge at ./compiler/typeinfer.jl:823 [inlined]
abstract_call_method at ./compiler/abstractinterpretation.jl:504
abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:105
abstract_call at ./compiler/abstractinterpretation.jl:1395
abstract_call at ./compiler/abstractinterpretation.jl:1382
abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534
typeinf_local at ./compiler/abstractinterpretation.jl:1900
typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014
_typeinf at ./compiler/typeinfer.jl:226
typeinf at ./compiler/typeinfer.jl:209
typeinf_ext at ./compiler/typeinfer.jl:909
typeinf_ext_toplevel at ./compiler/typeinfer.jl:942
typeinf_ext_toplevel at ./compiler/typeinfer.jl:938
jfptr_typeinf_ext_toplevel_9965.clone_1 at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_type_infer at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_generate_fptr at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_compile_method_internal at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
start_task at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
Allocations: 45061933 (Pool: 45046905; Big: 15028); GC: 45

signal (11): Segmentation fault: 11
in expression starting at REPL[4]:1
gc_mark_loop at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
_jl_gc_collect at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_gc_collect at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_gc_pool_alloc at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_gc_alloc at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
_new_array_ at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
_new_array at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_alloc_array_1d at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
Array at ./boot.jl:457 [inlined]
Array at ./boot.jl:466 [inlined]
Array at ./baseext.jl:36 [inlined]
zeros at ./array.jl:525 [inlined]
zeros at ./array.jl:521 [inlined]
stat at ./stat.jl:149
ispath at ./stat.jl:456 [inlined]
#temp_cleanup_purge#21 at ./file.jl:529
temp_cleanup_purge##kw at ./file.jl:526 [inlined]
#838 at ./initdefs.jl:329
jfptr_YY.838_30047.clone_1 at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
_atexit at ./initdefs.jl:350
jfptr__atexit_38138.clone_1 at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_atexit_hook at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_exit at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_exit_thread0_cb at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
Allocations: 45891074 (Pool: 45875924; Big: 15150); GC: 45

[devmotion]

Thanks for the report! Turing is not compatible with Julia 1.7 yet. It is blocked by Libtask whose binary dependencies have to be linked against specific Julia versions and which is broken on Julia 1.7. Currently, Libtask is redesigned in a way that avoids these problems (but has some other limitations currently): TuringLang/Libtask.jl#93

See also #1737, #1734, #1714, and #1713.

[miakramer]

Gotcha! I'll close as dup of #1734

[rikhuijzer]

I'm pinning this issue for now since about one issue about this is opened per day currently.

To fix this, either switch back to use Julia 1.6 or wait for TuringLang/Libtask.jl#93 to be merged. Turing developers are working hard on fixing this issue as can be seen in TuringLang/Libtask.jl#93.

[ParadaCarleton]

(Reopened so we can keep track of this here and close the other issues on this)

[ParadaCarleton]

@KDr2 quick question, do you expect this to be fixed by the end of the week?

If not, @yebai would it maybe make sense to create a minimal "TuringTemp" package which is just Turing without the particle samplers?

[devmotion]

would it maybe make sense to create a minimal "TuringTemp" package which is just Turing without the particle samplers?

I don't have time for it anyway but I think it's not worth the effort to separate the particle filters since Turing works with the LTS version and people are working on support for Julia 1.7. Additionally, I think one should not spam the registry, at most one could create a temporary unregistered branch in the Turing repo that can be installed with something like ] add Turing#without_particlefilters (but as mentioned above I don't think it's worth it).