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using GAP fails when julia is using multiple threads #960

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using GAP fails when julia is using multiple threads#960
@mjrodgers

Description

@mjrodgers
mjrodgers
opened on Jan 19, 2024

Edit (@thoma): As a workaround, start julia with --gcthreads=1.

When starting julia using multiple threads (julia -t 4), using GAP can fail. This also seems to leave julia in a fragile state, and I get a segfault when quitting.

Interestingly, using GAP seems to work fine if I launch julia using 3 threads, but 4 is a problem.

I'm running on an Intel Mac running Sonoma 14.2.1, julia 1.10.0, GAP 0.10.1

(base) ➜  ~ julia -t 4
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.0 (2023-12-25)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using GAP
 ┌───────┐   GAP 4.12.2 of 2022-12-18
 │  GAP  │   https://www.gap-system.org
 └───────┘   Architecture: x86_64-apple-darwin14-julia1.10-64-kv8
 Configuration:  gmp 6.2.1, Julia GC, Julia 1.10.0, readline
 Loading the library Error, IS_SUBSET_FLAGS: <flags1> must be a flags list (not a plain list) in
  IS_SUBSET_FLAGS( imp2[1], imp[2]
 ) at /Users/mrodgers/.julia/artifacts/b5c2f0f824457e5c391fb24916f94d5d91c62c4f/share/gap/lib/filter.g:151 called from
InstallTrueMethodNewFilter( tofilt, from
 ); at /Users/mrodgers/.julia/artifacts/b5c2f0f824457e5c391fb24916f94d5d91c62c4f/share/gap/lib/filter.g:298 called from
<function "InstallTrueMethod">( <arguments> )
 called from read-eval loop at /Users/mrodgers/.julia/artifacts/b5c2f0f824457e5c391fb24916f94d5d91c62c4f/share/gap/lib/pcgsspec.gd:253
ERROR: InitError: GAP variable _JULIAINTERFACE_ERROR_BUFFER not bound
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] getproperty(::GAP.GlobalsType, name::Symbol)
    @ GAP ~/.julia/packages/GAP/aJO9M/src/globals.jl:42
  [3] error_handler()
    @ GAP ~/.julia/packages/GAP/aJO9M/src/GAP.jl:72
  [4] initialize(argv::Vector{String})
    @ GAP ~/.julia/packages/GAP/aJO9M/src/GAP.jl:154
  [5] __init__()
    @ GAP ~/.julia/packages/GAP/aJO9M/src/GAP.jl:294
  [6] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1128
  [7] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1116
  [8] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1061
  [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
    @ Base ./loading.jl:1575
 [10] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1932
 [11] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1806
 [12] #invoke_in_world#3
    @ Base ./essentials.jl:921 [inlined]
 [13] invoke_in_world
    @ Base ./essentials.jl:918 [inlined]
 [14] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1797
 [15] macro expansion
    @ Base ./loading.jl:1784 [inlined]
 [16] macro expansion
    @ Base ./lock.jl:267 [inlined]
 [17] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1747
 [18] #invoke_in_world#3
    @ Base ./essentials.jl:921 [inlined]
 [19] invoke_in_world
    @ Base ./essentials.jl:918 [inlined]
 [20] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1740
during initialization of module GAP

julia>

julia> exit()

[37561] signal (11): Segmentation fault: 11
in expression starting at REPL[2]:1
ExecProccall0args at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
ExecSeqStat at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
EXEC_CURR_FUNC at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
DoExecFunc1args at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
DoOperation1Args at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
DoProperty at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
EvalFunccall1args at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
EvalUnknownBool at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
EvalNot at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
ExecWhile2 at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
ExecSeqStat2 at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
EXEC_CURR_FUNC at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
DoExecFunc0args at /Users/mrodgers/.julia/artifacts/a7bcd955e05e9f268114b41a0606a2fc5e3dbb06/lib/libgap.8.dylib (unknown line)
_call_gap_func at /Users/mrodgers/.julia/packages/GAP/aJO9M/src/ccalls.jl:318 [inlined]
GapObj at /Users/mrodgers/.julia/packages/GAP/aJO9M/src/ccalls.jl:301
unknown function (ip: 0x10250361c)
_jl_invoke at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:0 [inlined]
ijl_apply_generic at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:3076
#1 at /Users/mrodgers/.julia/packages/GAP/aJO9M/src/GAP.jl:256
unknown function (ip: 0x1025032f1)
_jl_invoke at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:0 [inlined]
ijl_apply_generic at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:3076
_atexit at ./initdefs.jl:428
jfptr__atexit_79385.1 at /Applications/Julia-1.10.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
_jl_invoke at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:0 [inlined]
ijl_apply_generic at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/./julia.h:1982 [inlined]
ijl_atexit_hook at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/init.c:280
ijl_exit at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/init.c:207
exit at ./initdefs.jl:28 [inlined]
exit at ./initdefs.jl:29
jfptr_exit_79210.1 at /Applications/Julia-1.10.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
_jl_invoke at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:0 [inlined]
ijl_apply_generic at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/./julia.h:1982 [inlined]
do_call at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/interpreter.c:126
eval_body at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/interpreter.c:0
jl_interpret_toplevel_thunk at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/interpreter.c:775
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/toplevel.c:934
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/toplevel.c:877
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/toplevel.c:877
ijl_toplevel_eval at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/toplevel.c:943 [inlined]
ijl_toplevel_eval_in at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/toplevel.c:985
eval at ./boot.jl:385 [inlined]
eval_user_input at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:150
repl_backend_loop at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:246
#start_repl_backend#46 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:231
start_repl_backend at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:228
_jl_invoke at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:0 [inlined]
ijl_apply_generic at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:3076
#run_repl#59 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:389
run_repl at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:375
jfptr_run_repl_91808.1 at /Applications/Julia-1.10.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
_jl_invoke at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:0 [inlined]
ijl_apply_generic at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:3076
#1013 at ./client.jl:432
jfptr_YY.1013_82797.1 at /Applications/Julia-1.10.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
_jl_invoke at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:0 [inlined]
ijl_apply_generic at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/./julia.h:1982 [inlined]
jl_f__call_latest at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/builtins.c:812
#invokelatest#2 at ./essentials.jl:887 [inlined]
invokelatest at ./essentials.jl:884 [inlined]
run_main_repl at ./client.jl:416
exec_options at ./client.jl:333
_start at ./client.jl:552
jfptr__start_82823.1 at /Applications/Julia-1.10.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
_jl_invoke at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:0 [inlined]
ijl_apply_generic at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/./julia.h:1982 [inlined]
true_main at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/jlapi.c:582
jl_repl_entrypoint at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-10/src/jlapi.c:731
Allocations: 848880 (Pool: 846702; Big: 2178); GC: 3
[1]    37561 segmentation fault  julia -t 4

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