Failing precompilation of LibTrixi.jl

[benegee]

Currently precompilation of libtrixi does not work on rocinante when starting from scratch. The error is:

Failed to precompile LibTrixi [7e097bd5-a775-4bc1-90b6-ad92bd7220c1] to "./julia-depot/compiled/v1.10/LibTrixi/jl_oEM50J".

[1404813] signal (11.1): Segmentation fault
in expression starting at none:0
opal_hwloc_base_free_topology at /lib/x86_64-linux-gnu/libopen-pal.so.40 (unknown line)
unknown function (ip: 0x7fffdb832d16)
mca_base_framework_close at /lib/x86_64-linux-gnu/libopen-pal.so.40 (unknown line)
opal_finalize at /lib/x86_64-linux-gnu/libopen-pal.so.40 (unknown line)
ompi_mpi_finalize at /lib/x86_64-linux-gnu/libmpi.so (unknown line)
MPI_Finalize at /mnt/ssd/home/bgeihe/MPI_Finalize_MWE/julia-depot/packages/MPI/z2owj/src/api/generated_api.jl:1872 [inlined]
Finalize at /mnt/ssd/home/bgeihe/MPI_Finalize_MWE/julia-depot/packages/MPI/z2owj/src/environment.jl:263
#7 at /mnt/ssd/home/bgeihe/MPI_Finalize_MWE/julia-depot/packages/MPI/z2owj/src/environment.jl:140
unknown function (ip: 0x7fffe0ded907)
_jl_invoke at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/gf.c:2894 [inlined]
ijl_apply_generic at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/gf.c:3076
_atexit at ./initdefs.jl:426
jfptr__atexit_79296.1 at /mnt/hd1/opt/julia/1.10.0/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/gf.c:2894 [inlined]
ijl_apply_generic at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
ijl_atexit_hook at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/init.c:280
jl_repl_entrypoint at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/src/jlapi.c:732
main at /cache/build/builder-amdci4-6/julialang/julia-release-1-dot-10/cli/loader_exe.c:58
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 509656 (Pool: 508643; Big: 1013); GC:

I tried to find a minimal setup: https://github.com/bgeihe/MPI_Finalize_MWE

• A fresh Julia project with dependencies "LibTrixi", "MPIPreferences", "Trixi", "XML2_jll"
• MPIPreferences is the real package and used to switch to system MPI
• XML2_jll also is the real package
• "LibTrixi" is a local (Pkg.develop) package which just does using Trixi
• "Trixi" is a local (Pkg.develop) package which does

  module Trixi
  using MPI
  using XML2_jll
  function __init__()
    provided = MPI.Init(threadlevel = MPI.THREAD_FUNNELED, finalize_atexit = true)
  end
  end

Workarounds so far:

• set finalize_atexit = false
• downgrade XML2_jll to v2.11.5+0

[sloede]

This is weird (and annoying). I don't see how XML2_jll could affect MPI. Were there any recent changes to XML2_jll that could shed some light on it?

[benegee]

I do not fully understand these jll packages yet. I can compare the produced tarballs. But are there corresponding build recipes anywhere?

[sloede]

But are there corresponding build recipes anywhere?

https://github.com/JuliaPackaging/Yggdrasil/blob/master/X/XML2/build_tarballs.jl

[benegee]

💡

https://github.com/JuliaPackaging/Yggdrasil/compare/ebf508b..8f03a6b
Hmm... gcc changed.