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Segmentation fault in doctest CI job around Polymake/CxxWrap init #4102

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lgoettgens opened this issue Sep 17, 2024 · 2 comments
Closed

Segmentation fault in doctest CI job around Polymake/CxxWrap init #4102

lgoettgens opened this issue Sep 17, 2024 · 2 comments
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bug Something isn't working CI nightly error with julia nightly or pre-releases package: Polymake

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@lgoettgens
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Starting this morging, we have seen a new-ish segmentation fault in the nightly doctest CI job. See e.g. https://github.com/oscar-system/Oscar.jl/actions/runs/10898508254/job/30241873534.
The issue is not completely reproducible, just restarting a failing job then succeeded when I just tried it.

Complete error log:

Precompiling packages...
Info Given Oscar was explicitly requested, output will be shown live 

[1854] signal 11 (1): Segmentation fault
in expression starting at /home/runner/work/Oscar.jl/Oscar.jl/src/imports.jl:14
jl_object_id__cold at /cache/build/tester-amdci5-[13](https://github.com/oscar-system/Oscar.jl/actions/runs/10898508254/job/30241873534#step:8:14)/julialang/julia-master/src/builtins.c:441
jl_idset_peek_bp at /cache/build/tester-amdci5-13/julialang/julia-master/src/idset.c:34
jl_idset_get at /cache/build/tester-amdci5-13/julialang/julia-master/src/idset.c:40
jl_as_global_root at /cache/build/tester-amdci5-13/julialang/julia-master/src/staticdata.c:2599 [inlined]
jl_as_global_root at /cache/build/tester-amdci5-13/julialang/julia-master/src/staticdata.c:2579
inst_datatype_inner at /cache/build/tester-amdci5-13/julialang/julia-master/src/jltypes.c:2275
jl_inst_arg_tuple_type at /cache/build/tester-amdci5-13/julialang/julia-master/src/jltypes.c:2498
arg_type_tuple at /cache/build/tester-amdci5-13/julialang/julia-master/src/gf.c:2373 [inlined]
jl_lookup_generic_ at /cache/build/tester-amdci5-13/julialang/julia-master/src/gf.c:3312 [inlined]
ijl_apply_generic at /cache/build/tester-amdci5-13/julialang/julia-master/src/gf.c:3359
initialize_julia_module at /home/runner/.julia/packages/CxxWrap/5IZvn/src/CxxWrap.jl:405
__init__ at /home/runner/.julia/packages/Polymake/0TLCt/src/Polymake.jl:108
jfptr___init___18577 at /home/runner/.julia/compiled/v1.12/Polymake/QizyK_lvNBj.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
jl_module_run_initializer at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:76
run_module_init at ./loading.jl:1373
register_restored_modules at ./loading.jl:1361
#_include_from_serialized#830 at ./loading.jl:1250
_include_from_serialized at ./loading.jl:1206 [inlined]
_include_from_serialized at ./loading.jl:1206 [inlined]
#_require_search_from_serialized#839 at ./loading.jl:2018
_require_search_from_serialized at ./loading.jl:1941
jfptr__require_search_from_serialized_35607.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
_require at ./loading.jl:2477
__require_prelocked at ./loading.jl:2343
jfptr___require_prelocked_60933.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
jl_f__call_in_world at /cache/build/tester-amdci5-13/julialang/julia-master/src/builtins.c:902
#invoke_in_world#2 at ./essentials.jl:1082 [inlined]
invoke_in_world at ./essentials.jl:1079 [inlined]
_require_prelocked at ./loading.jl:2330
macro expansion at ./loading.jl:2269 [inlined]
macro expansion at ./lock.jl:287 [inlined]
__require at ./loading.jl:2226
jfptr___require_60875.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
jl_f__call_in_world at /cache/build/tester-amdci5-13/julialang/julia-master/src/builtins.c:902
#invoke_in_world#2 at ./essentials.jl:1082 [inlined]
invoke_in_world at ./essentials.jl:1079 [inlined]
require at ./loading.jl:2219
jfptr_require_60872.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
call_require at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:510 [inlined]
eval_import_path at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:547
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:916
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:983
ijl_toplevel_eval at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1054
ijl_toplevel_eval_in at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1096
eval at ./boot.jl:439 [inlined]
include_string at ./loading.jl:2670
_include at ./loading.jl:2730
include at ./Base.jl:582
jfptr_include_37718.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
jl_f__call_latest at /cache/build/tester-amdci5-13/julialang/julia-master/src/builtins.c:883
include at /home/runner/work/Oscar.jl/Oscar.jl/src/Oscar.jl:20
unknown function (ip: 0x7f91e37005d2)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
do_call at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:125
eval_value at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:222
eval_stmt_value at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:173 [inlined]
eval_body at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:685
jl_interpret_toplevel_thunk at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:892
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1043
jl_eval_module_expr at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:221 [inlined]
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:845
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:983
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:983
ijl_toplevel_eval at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1054
ijl_toplevel_eval_in at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1096
eval at ./boot.jl:439 [inlined]
include_string at ./loading.jl:2670
_include at ./loading.jl:2730
include at ./Base.jl:582 [inlined]
include_package_for_output at ./loading.jl:2848
jfptr_include_package_for_output_617[14](https://github.com/oscar-system/Oscar.jl/actions/runs/10898508254/job/30241873534#step:8:15).1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
do_call at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:125
eval_value at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:222
eval_stmt_value at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:173 [inlined]
eval_body at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:685
jl_interpret_toplevel_thunk at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:892
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1043
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:983
ijl_toplevel_eval at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1054
ijl_toplevel_eval_in at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1096
eval at ./boot.jl:439 [inlined]
include_string at ./loading.jl:2670
include_string at ./loading.jl:2680 [inlined]
exec_options at ./client.jl:322
_start at ./client.jl:553
jfptr__start_632[16](https://github.com/oscar-system/Oscar.jl/actions/runs/10898508254/job/30241873534#step:8:17).1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
true_main at /cache/build/tester-amdci5-13/julialang/julia-master/src/jlapi.c:900
jl_repl_entrypoint at /cache/build/tester-amdci5-13/julialang/julia-master/src/jlapi.c:1059
main at /cache/build/tester-amdci5-13/julialang/julia-master/cli/loader_exe.c:58
unknown function (ip: 0x7f91e5029d8f)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 2506569 (Pool: 2506429; Big: 140); GC: 4
           ✗ Oscar
  0 dependencies successfully precompiled in 5 seconds. 118 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

Oscar 

Failed to precompile Oscar [f1435218-dba5-11e9-1e4d-f1a5fab5fc13] to "/home/runner/.julia/compiled/v1.12/Oscar/jl_WjgMim".
[1854] signal 11 (1): Segmentation fault
in expression starting at /home/runner/work/Oscar.jl/Oscar.jl/src/imports.jl:14
jl_object_id__cold at /cache/build/tester-amdci5-13/julialang/julia-master/src/builtins.c:441
jl_idset_peek_bp at /cache/build/tester-amdci5-13/julialang/julia-master/src/idset.c:34
jl_idset_get at /cache/build/tester-amdci5-13/julialang/julia-master/src/idset.c:40
jl_as_global_root at /cache/build/tester-amdci5-13/julialang/julia-master/src/staticdata.c:2599 [inlined]
jl_as_global_root at /cache/build/tester-amdci5-13/julialang/julia-master/src/staticdata.c:2579
inst_datatype_inner at /cache/build/tester-amdci5-13/julialang/julia-master/src/jltypes.c:2275
jl_inst_arg_tuple_type at /cache/build/tester-amdci5-13/julialang/julia-master/src/jltypes.c:2498
arg_type_tuple at /cache/build/tester-amdci5-13/julialang/julia-master/src/gf.c:2373 [inlined]
jl_lookup_generic_ at /cache/build/tester-amdci5-13/julialang/julia-master/src/gf.c:3312 [inlined]
ijl_apply_generic at /cache/build/tester-amdci5-13/julialang/julia-master/src/gf.c:3359
initialize_julia_module at /home/runner/.julia/packages/CxxWrap/5IZvn/src/CxxWrap.jl:405
__init__ at /home/runner/.julia/packages/Polymake/0TLCt/src/Polymake.jl:108
jfptr___init___18577 at /home/runner/.julia/compiled/v1.12/Polymake/QizyK_lvNBj.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
jl_module_run_initializer at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:76
run_module_init at ./loading.jl:1373
register_restored_modules at ./loading.jl:1361
#_include_from_serialized#830 at ./loading.jl:1250
_include_from_serialized at ./loading.jl:1206 [inlined]
_include_from_serialized at ./loading.jl:1206 [inlined]
#_require_search_from_serialized#839 at ./loading.jl:2018
_require_search_from_serialized at ./loading.jl:1941
jfptr__require_search_from_serialized_35607.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
_require at ./loading.jl:2477
__require_prelocked at ./loading.jl:2343
jfptr___require_prelocked_60933.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
jl_f__call_in_world at /cache/build/tester-amdci5-13/julialang/julia-master/src/builtins.c:902
#invoke_in_world#2 at ./essentials.jl:1082 [inlined]
invoke_in_world at ./essentials.jl:1079 [inlined]
_require_prelocked at ./loading.jl:2330
macro expansion at ./loading.jl:2269 [inlined]
macro expansion at ./lock.jl:287 [inlined]
__require at ./loading.jl:2226
jfptr___require_60875.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
jl_f__call_in_world at /cache/build/tester-amdci5-13/julialang/julia-master/src/builtins.c:902
#invoke_in_world#2 at ./essentials.jl:1082 [inlined]
invoke_in_world at ./essentials.jl:1079 [inlined]
require at ./loading.jl:2219
jfptr_require_60872.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
call_require at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:510 [inlined]
eval_import_path at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:547
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:916
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:983
ijl_toplevel_eval at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1054
ijl_toplevel_eval_in at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1096
eval at ./boot.jl:439 [inlined]
include_string at ./loading.jl:2670
_include at ./loading.jl:2730
include at ./Base.jl:582
jfptr_include_37718.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
jl_f__call_latest at /cache/build/tester-amdci5-13/julialang/julia-master/src/builtins.c:883
include at /home/runner/work/Oscar.jl/Oscar.jl/src/Oscar.jl:20
unknown function (ip: 0x7f91e37005d2)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:2220 [inlined]
do_call at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:125
eval_value at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:222
eval_stmt_value at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:[17](https://github.com/oscar-system/Oscar.jl/actions/runs/10898508254/job/30241873534#step:8:18)3 [inlined]
eval_body at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:685
jl_interpret_toplevel_thunk at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:892
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1043
jl_eval_module_expr at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:221 [inlined]
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:845
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:983
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:983
ijl_toplevel_eval at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1054
ijl_toplevel_eval_in at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1096
eval at ./boot.jl:439 [inlined]
include_string at ./loading.jl:2670
_include at ./loading.jl:2730
include at ./Base.jl:582 [inlined]
include_package_for_output at ./loading.jl:2848
jfptr_include_package_for_output_61714.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:22[20](https://github.com/oscar-system/Oscar.jl/actions/runs/10898508254/job/30241873534#step:8:21) [inlined]
do_call at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:125
eval_value at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:222
eval_stmt_value at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:173 [inlined]
eval_body at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:685
jl_interpret_toplevel_thunk at /cache/build/tester-amdci5-13/julialang/julia-master/src/interpreter.c:892
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1043
jl_toplevel_eval_flex at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:983
ijl_toplevel_eval at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1054
ijl_toplevel_eval_in at /cache/build/tester-amdci5-13/julialang/julia-master/src/toplevel.c:1096
eval at ./boot.jl:439 [inlined]
include_string at ./loading.jl:2670
include_string at ./loading.jl:2680 [inlined]
exec_options at ./client.jl:322
_start at ./client.jl:553
jfptr__start_63[21](https://github.com/oscar-system/Oscar.jl/actions/runs/10898508254/job/30241873534#step:8:22)6.1 at /opt/hostedtoolcache/julia/nightly/x64/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-13/julialang/julia-master/src/julia.h:[22](https://github.com/oscar-system/Oscar.jl/actions/runs/10898508254/job/30241873534#step:8:23)20 [inlined]
true_main at /cache/build/tester-amdci5-13/julialang/julia-master/src/jlapi.c:900
jl_repl_entrypoint at /cache/build/tester-amdci5-13/julialang/julia-master/src/jlapi.c:1059
main at /cache/build/tester-amdci5-13/julialang/julia-master/cli/loader_exe.c:58
unknown function (ip: 0x7f91e5029d8f)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: [25](https://github.com/oscar-system/Oscar.jl/actions/runs/10898508254/job/30241873534#step:8:26)06569 (Pool: 2506429; Big: 140); GC: 
Error: Process completed with exit code 1.
@lgoettgens lgoettgens added bug Something isn't working nightly error with julia nightly or pre-releases package: Polymake CI labels Sep 17, 2024
@benlorenz
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I think this is #3296

@lgoettgens
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Indeed. Duplicate of #3296

@lgoettgens lgoettgens closed this as not planned Won't fix, can't repro, duplicate, stale Sep 17, 2024
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