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JuliaArrays / AxisArrays.jl

Performant arrays where each dimension can have a named axis with values
http://JuliaArrays.github.io/AxisArrays.jl/latest/
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seg_fault precompiling AxisArrays v0.4.3 on julia-1.4.2 #183

Closed accopeland closed 4 years ago

accopeland commented 4 years ago

'using AxisArray' or Pkg.test("AxisArrays") produces a seg_fault during precompile on Julia-1.4.2 on Linux (4.12.14-lp150.12.79-default / Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz). I suspect this is not strictly an AxisArrays issue as I don't find any other reports and it works fine on MacOS.

FWIW, the machine is patched (bugs : cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds swapgs). 


julia> versioninfo()
Julia Version 1.4.2
Commit 44fa15b150* (2020-05-23 18:35 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
Environment:
  JULIA_NUM_THREADS = 8
  JULIA_PKGDIR = /global/cfs/cdirs/jgiqaqc/.julia

(wtf) pkg> st --manifest
Status `/global/projectb/scratch/copeland/Projects/2020/20200207-gpu/fastplot/wtf/Manifest.toml`
  [39de3d68] AxisArrays v0.4.3
  [da5c29d0] EllipsisNotation v0.4.0
  [8197267c] IntervalSets v0.5.1
  [c8e1da08] IterTools v1.3.0
  [b3c3ace0] RangeArrays v0.3.2
  [ade2ca70] Dates
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [de0858da] Printf
  [9a3f8284] Random
  [9e88b42a] Serialization
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [4ec0a83e] Unicode

(wtf) pkg> test AxisArrays
    Testing AxisArrays
Status `/tmp/jl_V5bHMX/Manifest.toml`
  [39de3d68] AxisArrays v0.4.3
  [187b0558] ConstructionBase v1.0.0
  [da5c29d0] EllipsisNotation v0.4.0
  [8197267c] IntervalSets v0.5.1
  [c8e1da08] IterTools v1.3.0
  [6fe1bfb0] OffsetArrays v1.0.4
  [b3c3ace0] RangeArrays v0.3.2
  [1986cc42] Unitful v1.2.1
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [de0858da] Printf
  [9a3f8284] Random
  [9e88b42a] Serialization
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [8dfed614] Test
  [4ec0a83e] Unicode

signal (11): Segmentation fault
in expression starting at /global/homes/c/copeland/.julia/packages/AxisArrays/IFpjG/src/AxisArrays.jl:8
_jl_restore_incremental at /buildworker/worker/package_linux64/build/src/dump.c:3269
jl_restore_incremental at /buildworker/worker/package_linux64/build/src/dump.c:3314
_include_from_serialized at ./loading.jl:681
_require_search_from_serialized at ./loading.jl:781
_require at ./loading.jl:1006
require at ./loading.jl:927
require at ./loading.jl:922
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2145 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2323
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1700 [inlined]
call_require at /buildworker/worker/package_linux64/build/src/toplevel.c:404 [inlined]
eval_import_path at /buildworker/worker/package_linux64/build/src/toplevel.c:441
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:661
jl_eval_module_expr at /buildworker/worker/package_linux64/build/src/toplevel.c:186
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:645
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:872
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:877
include at ./Base.jl:377
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2145 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2323
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1700 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:369
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:458
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:409 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:817
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:744
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:911
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:819
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:848
eval at ./boot.jl:331 [inlined]
eval at ./client.jl:449
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2145 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2323
top-level scope at ./none:3
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:813
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:769
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:848
eval at ./boot.jl:331
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2145 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2323
exec_options at ./client.jl:264
_start at ./client.jl:484
jfptr__start_2075.clone_1 at /global/cfs/cdirs/jgiqaqc/local/julia-1.4.2/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2145 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2323
jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1700 [inlined]
true_main at /buildworker/worker/package_linux64/build/ui/repl.c:96
main at /buildworker/worker/package_linux64/build/ui/repl.c:217
__libc_start_main at /lib64/libc.so.6 (unknown line)
_start at /global/cfs/cdirs/jgiqaqc/local/julia-1.4.2/bin/julia (unknown line)
Allocations: 2504 (Pool: 2495; Big: 9); GC: 0
ERROR: LoadError: Failed to precompile AxisArrays [39de3d68-74b9-583c-8d2d-e117c070f3a9] to /global/homes/c/copeland/.julia/compiled/v1.4/AxisArrays/zm48T_EK3H7.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::String) at ./client.jl:439
 [7] top-level scope at none:6
in expression starting at /global/homes/c/copeland/.julia/packages/AxisArrays/IFpjG/test/runtests.jl:1
ERROR: Package AxisArrays errored during testing
iamed2 commented 4 years ago

Yes I would say this is something to file in https://gitlab.com/JuliaLang/julia since it appears to happen while loading code from the precompile cache and AxisArrays doesn't affect that process.

accopeland commented 4 years ago

Makes sense, thank you for looking.