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GC error on Julia master #3

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vchuravy opened this issue Jan 13, 2022 · 1 comment
Open

GC error on Julia master #3

vchuravy opened this issue Jan 13, 2022 · 1 comment

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@vchuravy
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As seen on PkgEval https://s3.amazonaws.com/julialang-reports/nanosoldier/pkgeval/by_hash/ff8b327_vs_29ea1fe/Air.1.8.0-DEV-593ff735b36.log

vchuravy@odin ~/b/julia> ./julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.8.0-DEV.1261 (2022-01-10)
 _/ |\__'_|_|_|\__'_|  |  vc/funcinfo/c4ca9dc171* (fork: 1 commits, 4 days)
|__/                   |

(@v1.8) pkg> activate --temp
  Activating new project at `/tmp/jl_SuLou8`

(jl_SuLou8) pkg> add Air
    Updating registry at `~/.julia/registries/Experimental`
    Updating git-repo `https://github.com/vchuravy/Experimental`
    Updating registry at `~/.julia/registries/General`
    Updating git-repo `https://github.com/JuliaRegistries/General.git`
   Resolving package versions...
   Installed Air ─ v0.1.1
    Updating `/tmp/jl_SuLou8/Project.toml`
  [0c3b9dc7] + Air v0.1.1
    Updating `/tmp/jl_SuLou8/Manifest.toml`
  [0c3b9dc7] + Air v0.1.1
  [34da2185] + Compat v3.41.0
  [864edb3b] + DataStructures v0.18.11
  [ffbed154] + DocStringExtensions v0.8.6
⌅ [e30172f5] + Documenter v0.26.3
⌅ [b5f81e59] + IOCapture v0.1.1
  [682c06a0] + JSON v0.21.2
  [bac558e1] + OrderedCollections v1.4.1
  [69de0a69] + Parsers v2.1.3
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [8bb1440f] + DelimitedFiles
  [8ba89e20] + Distributed
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [b77e0a4c] + InteractiveUtils
  [b27032c2] + LibCURL v0.6.3
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.8.0
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [1a1011a3] + SharedArrays
  [6462fe0b] + Sockets
  [2f01184e] + SparseArrays
  [10745b16] + Statistics
  [fa267f1f] + TOML v1.0.0
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v0.5.0+0
  [deac9b47] + LibCURL_jll v7.73.0+4
  [29816b5a] + LibSSH2_jll v1.9.1+2
  [c8ffd9c3] + MbedTLS_jll v2.24.0+2
  [14a3606d] + MozillaCACerts_jll v2020.7.22
  [4536629a] + OpenBLAS_jll v0.3.17+2
  [83775a58] + Zlib_jll v1.2.12+1
  [8e850b90] + libblastrampoline_jll v3.1.0+0
  [8e850ede] + nghttp2_jll v1.41.0+1
  [3f19e933] + p7zip_jll v16.2.1+1
        Info Packages marked with ⌅ have new versions available but cannot be upgraded. To see why use `status --outdated`
Precompiling project...
  12 dependencies successfully precompiled in 7 seconds. 3 already precompiled.

(jl_SuLou8) pkg> test Air
     Testing Air
      Status `/tmp/jl_XstNlg/Project.toml`
  [0c3b9dc7] Air v0.1.1
  [864edb3b] DataStructures v0.18.11
⌅ [e30172f5] Documenter v0.26.3
  [9a3f8284] Random `@stdlib/Random`
  [2f01184e] SparseArrays `@stdlib/SparseArrays`
  [8dfed614] Test `@stdlib/Test`
      Status `/tmp/jl_XstNlg/Manifest.toml`
  [0c3b9dc7] Air v0.1.1
  [34da2185] Compat v3.41.0
  [864edb3b] DataStructures v0.18.11
  [ffbed154] DocStringExtensions v0.8.6
⌅ [e30172f5] Documenter v0.26.3
⌅ [b5f81e59] IOCapture v0.1.1
  [682c06a0] JSON v0.21.2
  [bac558e1] OrderedCollections v1.4.1
  [69de0a69] Parsers v2.1.3
  [0dad84c5] ArgTools v1.1.1 `@stdlib/ArgTools`
  [56f22d72] Artifacts `@stdlib/Artifacts`
  [2a0f44e3] Base64 `@stdlib/Base64`
  [ade2ca70] Dates `@stdlib/Dates`
  [8bb1440f] DelimitedFiles `@stdlib/DelimitedFiles`
  [8ba89e20] Distributed `@stdlib/Distributed`
  [f43a241f] Downloads v1.6.0 `@stdlib/Downloads`
  [7b1f6079] FileWatching `@stdlib/FileWatching`
  [b77e0a4c] InteractiveUtils `@stdlib/InteractiveUtils`
  [b27032c2] LibCURL v0.6.3 `@stdlib/LibCURL`
  [76f85450] LibGit2 `@stdlib/LibGit2`
  [8f399da3] Libdl `@stdlib/Libdl`
  [37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra`
  [56ddb016] Logging `@stdlib/Logging`
  [d6f4376e] Markdown `@stdlib/Markdown`
  [a63ad114] Mmap `@stdlib/Mmap`
  [ca575930] NetworkOptions v1.2.0 `@stdlib/NetworkOptions`
  [44cfe95a] Pkg v1.8.0 `@stdlib/Pkg`
  [de0858da] Printf `@stdlib/Printf`
  [3fa0cd96] REPL `@stdlib/REPL`
  [9a3f8284] Random `@stdlib/Random`
  [ea8e919c] SHA v0.7.0 `@stdlib/SHA`
  [9e88b42a] Serialization `@stdlib/Serialization`
  [1a1011a3] SharedArrays `@stdlib/SharedArrays`
  [6462fe0b] Sockets `@stdlib/Sockets`
  [2f01184e] SparseArrays `@stdlib/SparseArrays`
  [10745b16] Statistics `@stdlib/Statistics`
  [fa267f1f] TOML v1.0.0 `@stdlib/TOML`
  [a4e569a6] Tar v1.10.0 `@stdlib/Tar`
  [8dfed614] Test `@stdlib/Test`
  [cf7118a7] UUIDs `@stdlib/UUIDs`
  [4ec0a83e] Unicode `@stdlib/Unicode`
  [e66e0078] CompilerSupportLibraries_jll v0.5.0+0 `@stdlib/CompilerSupportLibraries_jll`
  [deac9b47] LibCURL_jll v7.73.0+4 `@stdlib/LibCURL_jll`
  [29816b5a] LibSSH2_jll v1.9.1+2 `@stdlib/LibSSH2_jll`
  [c8ffd9c3] MbedTLS_jll v2.24.0+2 `@stdlib/MbedTLS_jll`
  [14a3606d] MozillaCACerts_jll v2020.7.22 `@stdlib/MozillaCACerts_jll`
  [4536629a] OpenBLAS_jll v0.3.17+2 `@stdlib/OpenBLAS_jll`
  [83775a58] Zlib_jll v1.2.12+1 `@stdlib/Zlib_jll`
  [8e850b90] libblastrampoline_jll v3.1.0+0 `@stdlib/libblastrampoline_jll`
  [8e850ede] nghttp2_jll v1.41.0+1 `@stdlib/nghttp2_jll`
  [3f19e933] p7zip_jll v16.2.1+1 `@stdlib/p7zip_jll`
        Info Packages marked with ⌅ have new versions available but cannot be upgraded. To see why use `status --outdated`
     Testing Running tests...

signal (11): Segmentation fault
in expression starting at /home/vchuravy/.julia/packages/Air/0ciXC/test/api.jl:4
gc_try_setmark at /home/vchuravy/src/julia/src/gc.c:1711 [inlined]
gc_mark_loop at /home/vchuravy/src/julia/src/gc.c:2303
_jl_gc_collect at /home/vchuravy/src/julia/src/gc.c:3044
ijl_gc_collect at /home/vchuravy/src/julia/src/gc.c:3273
maybe_collect at /home/vchuravy/src/julia/src/gc.c:884 [inlined]
ijl_gc_pool_alloc at /home/vchuravy/src/julia/src/gc.c:1211
jl_gc_alloc_ at /home/vchuravy/src/julia/src/julia_internal.h:359 [inlined]
jl_gc_alloc at /home/vchuravy/src/julia/src/gc.c:3318
_new_array_ at /home/vchuravy/src/julia/src/array.c:134
ijl_array_copy at /home/vchuravy/src/julia/src/array.c:1178
copy at ./array.jl:369 [inlined]
setindex at /home/vchuravy/.julia/packages/Air/0ciXC/src/api.jl:216 [inlined]
setindex at /home/vchuravy/.julia/packages/Air/0ciXC/src/ptree.jl:763
unknown function (ip: 0x7fbc1d2b46d5)
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
setindex at /home/vchuravy/.julia/packages/Air/0ciXC/src/pdict.jl:296
_pheap_swap at /home/vchuravy/.julia/packages/Air/0ciXC/src/pheap.jl:72
_pheap_fix_up at /home/vchuravy/.julia/packages/Air/0ciXC/src/pheap.jl:98
_pheap_fixw at /home/vchuravy/.julia/packages/Air/0ciXC/src/pheap.jl:156 [inlined]
push at /home/vchuravy/.julia/packages/Air/0ciXC/src/pheap.jl:183
push at /home/vchuravy/.julia/packages/Air/0ciXC/src/pwdict.jl:124 [inlined]
BottomRF at ./reduce.jl:81 [inlined]
afoldl at ./operators.jl:628
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
jl_apply at /home/vchuravy/src/julia/src/julia.h:1777 [inlined]
do_apply at /home/vchuravy/src/julia/src/builtins.c:713
_foldl_impl at ./tuple.jl:277 [inlined]
foldl_impl at ./reduce.jl:48 [inlined]
mapfoldl_impl at ./reduce.jl:44
unknown function (ip: 0x7fbc1d30356f)
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
#mapfoldl#254 at ./reduce.jl:162
mapfoldl##kw at ./reduce.jl:162 [inlined]
#mapreduce#258 at ./reduce.jl:294 [inlined]
mapreduce##kw at ./reduce.jl:294 [inlined]
#reduce#260 at ./reduce.jl:475 [inlined]
reduce##kw at ./reduce.jl:475
unknown function (ip: 0x7fbc1d3032cf)
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
PWDict at /home/vchuravy/.julia/packages/Air/0ciXC/src/pwdict.jl:70
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
jl_apply at /home/vchuravy/src/julia/src/julia.h:1777 [inlined]
do_apply at /home/vchuravy/src/julia/src/builtins.c:713
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
jl_apply at /home/vchuravy/src/julia/src/julia.h:1777 [inlined]
do_call at /home/vchuravy/src/julia/src/interpreter.c:126
eval_value at /home/vchuravy/src/julia/src/interpreter.c:215
eval_body at /home/vchuravy/src/julia/src/interpreter.c:468
eval_body at /home/vchuravy/src/julia/src/interpreter.c:523
eval_body at /home/vchuravy/src/julia/src/interpreter.c:523
eval_body at /home/vchuravy/src/julia/src/interpreter.c:523
eval_body at /home/vchuravy/src/julia/src/interpreter.c:523
jl_interpret_toplevel_thunk at /home/vchuravy/src/julia/src/interpreter.c:745
jl_toplevel_eval_flex at /home/vchuravy/src/julia/src/toplevel.c:888
jl_toplevel_eval_flex at /home/vchuravy/src/julia/src/toplevel.c:832
ijl_toplevel_eval_in at /home/vchuravy/src/julia/src/toplevel.c:947
eval at ./boot.jl:369 [inlined]
include_string at ./loading.jl:1251
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
_include at ./loading.jl:1308
include at ./client.jl:460
unknown function (ip: 0x7fbc1d29e062)
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
jl_apply at /home/vchuravy/src/julia/src/julia.h:1777 [inlined]
do_call at /home/vchuravy/src/julia/src/interpreter.c:126
eval_value at /home/vchuravy/src/julia/src/interpreter.c:215
eval_stmt_value at /home/vchuravy/src/julia/src/interpreter.c:166 [inlined]
eval_body at /home/vchuravy/src/julia/src/interpreter.c:599
eval_body at /home/vchuravy/src/julia/src/interpreter.c:523
eval_body at /home/vchuravy/src/julia/src/interpreter.c:523
jl_interpret_toplevel_thunk at /home/vchuravy/src/julia/src/interpreter.c:745
jl_toplevel_eval_flex at /home/vchuravy/src/julia/src/toplevel.c:888
jl_toplevel_eval_flex at /home/vchuravy/src/julia/src/toplevel.c:832
ijl_toplevel_eval_in at /home/vchuravy/src/julia/src/toplevel.c:947
eval at ./boot.jl:369 [inlined]
include_string at ./loading.jl:1251
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
_include at ./loading.jl:1308
include at ./client.jl:460
unknown function (ip: 0x7fbc1d29e062)
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
jl_apply at /home/vchuravy/src/julia/src/julia.h:1777 [inlined]
do_call at /home/vchuravy/src/julia/src/interpreter.c:126
eval_value at /home/vchuravy/src/julia/src/interpreter.c:215
eval_stmt_value at /home/vchuravy/src/julia/src/interpreter.c:166 [inlined]
eval_body at /home/vchuravy/src/julia/src/interpreter.c:599
jl_interpret_toplevel_thunk at /home/vchuravy/src/julia/src/interpreter.c:745
jl_toplevel_eval_flex at /home/vchuravy/src/julia/src/toplevel.c:888
jl_toplevel_eval_flex at /home/vchuravy/src/julia/src/toplevel.c:832
ijl_toplevel_eval_in at /home/vchuravy/src/julia/src/toplevel.c:947
eval at ./boot.jl:369 [inlined]
exec_options at ./client.jl:280
_start at ./client.jl:506
jfptr__start_50857 at /home/vchuravy/builds/julia/usr/lib/julia/sys.so (unknown line)
_jl_invoke at /home/vchuravy/src/julia/src/gf.c:2285 [inlined]
ijl_apply_generic at /home/vchuravy/src/julia/src/gf.c:2486
jl_apply at /home/vchuravy/src/julia/src/julia.h:1777 [inlined]
true_main at /home/vchuravy/src/julia/src/jlapi.c:562
jl_repl_entrypoint at /home/vchuravy/src/julia/src/jlapi.c:706
main at /home/vchuravy/src/julia/cli/loader_exe.c:59
__libc_start_main at /usr/lib/libc.so.6 (unknown line)
_start at /home/vchuravy/builds/julia/usr/bin/julia (unknown line)
Allocations: 14659175 (Pool: 14653902; Big: 5273); GC: 18
ERROR: Package Air errored during testing (received signal: 11)

(jl_SuLou8) pkg>

Before I dive in to see if this is a JuliaLang proper bug, are you doing anything interesting with memory?
@noahbenson
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noahbenson commented Jan 13, 2022 •
edited
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Hmm, not that I'm aware of! I haven't really studied the Julia GC or allocation system in depth yet myself. All the allocations in Air, I believe, are either made via the copy() function or are just plain constructor allocations. Nor does Air ever call the GC nor deallocate memory itself.

Probably not related, but I recall noticing during tests that the GC could get temporarily pretty slow if you performed a lot of small allocations and deletions in one go (e.g., by building up a PDict from a very large Dict one key-value pair at a time). This isn't really a surprise, though; I mostly just noticed that it seemed to perform worse with these small allocations than the JVM did under a similar task. I haven't seen any crashes like this.

Let me know if I can be of any help with debugging this!

@vchuravy vchuravy mentioned this issue Jan 13, 2022
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@vchuravy @noahbenson