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Test not running to completion on aarch64-linux #31
Description
The test that was introduced in 97724a424116e4401ac8da7878699885352c46ac
./src/splitcode --assign --lift ./func_tests/vcf_validation.fa.gz ./func_tests/test_1.vcf.gz CAST_EiJ --kmer-length=31 --kmer-output=./func_tests/test.kmers.1.txt
[fai_load] build FASTA index.
does never run to completion on aarch64-linux systems. The process is stuck at 100% cpu core usage.
Here is the non-changing part of the stack-trace:
#5 0x0000000000472ea0 in fai_build_core (bgzf=bgzf@entry=0x571c90) at faidx.c:103
#6 0x00000000004732dc in fai_build (fn=fn@entry=0x571970 ".//splitcode.lift.0h2kxalMGgWUjpbVk",
fai_file=fai_file@entry=0x571c00 ".//splitcode.lift.bBityyoVsF9AmnlRV.fai") at faidx.c:189
#7 0x000000000047366c in fai_load (fn=0x571970 ".//splitcode.lift.0h2kxalMGgWUjpbVk",
fai_file=0x571c00 ".//splitcode.lift.bBityyoVsF9AmnlRV.fai") at faidx.c:270
#8 0x00000000004524d8 in LiftWorkflow::modify_fasta (this=this@entry=0x7fffffa2a0)
at /nix/store/qbvp2h1f5a03nwmw0nwqimnk4kjhzv19-gcc-14-20241116/include/c++/14-20241116/bits/basic_string.h:227
#9 0x00000000004227c8 in ParseOptions (argc=argc@entry=8, argv=argv@entry=0x7fffffc758, opt=...)
at /home/zimward/splitcode/src/main.cpp:748
#10 0x000000000041a294 in main (argc=8, argv=0x7fffffc758) at /home/zimward/splitcode/src/main.cpp:1483
Activity
Yenaled commentedon Jan 8, 2025
It probably has to do with zlib-ng (now enabled by default) and should run if you compile splitcode with: cmake .. ZLIBNG_DISABLE=ON -BUILD_FUNCTESTING=ON
I'll see if I can fix it.
zimward commentedon Jan 8, 2025
The behavior doesn't change when built without zlib-ng.
Yenaled commentedon Jan 8, 2025
Thanks for checking — looks like I’ll need to look into it some more. A bit difficult since it works on all my systems.
zimward commentedon Jan 8, 2025
The way in which it's broken seems quite strange indeed as it passes most platforms (NixOS/nixpkgs#370167 (comment))
I have yet to try if it also happens using
binfmtemulation (qemu aarch64 emulation) but it probably does which should make debugging easier