realloc(): invalid pointer
#22
Comments
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Seems likely to have been introduced by #20, based on the backtrace. |
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I just ran all the CSV.jl tests and didn't see any issues; is there a way you could share the file, even if only privately? (quinn.jacobd@gmail.com) |
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I'll try to pull the data tomorrow |
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@simonbyrne, do you have any ideas on what might be happening here? My two thoughts are
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The second one could be the case. Tough to say without a reproducible example. |
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It appears that the issue has to do with using PackageCompiler. I can reproduce the problem by running the tests for Parsers. The issue can be reproduced using this Dockerfile: FROM julia:1.0.3-stretch
RUN apt-get update && apt-get install -y gcc && \
julia -e 'using Pkg; Pkg.add("PackageCompiler"); using PackageCompiler; compile_package(force=true)'
RUN julia -e 'using Pkg, PackageCompiler; Pkg.add(PackageSpec(name="Parsers", version="0.2.20"))'
# Fails with "Task cannot be serialized"
# RUN julia -e 'using PackageCompiler; compile_package("Parsers", force=true)'
RUN echo "using Parsers" > userimg.jl && \
julia -e 'using PackageCompiler: build_sysimg, default_sysimg_path; build_sysimg(default_sysimg_path(), "userimg.jl")'
CMD ["julia", "-e", "using Pkg; Pkg.test(\"Parsers\")"]$ docker build -t parsers .
...
$ docker run --rm parsers
...
*** Error in `/usr/local/julia/bin/julia': realloc(): invalid next size: 0x00007f0cb087c4d0 ***
...
signal (6): Aborted
in expression starting at /root/.julia/packages/Parsers/v5u2B/test/floats.jl:1
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x7f0cb58d8bff)
unknown function (ip: 0x7f0cb58defc5)
unknown function (ip: 0x7f0cb58e213b)
realloc at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
jl_gc_counted_realloc_with_old_size at /buildworker/worker/package_linux64/build/src/gc.c:2777
__gmpz_realloc at /usr/local/julia/bin/../lib/julia/libgmp.so (unknown line)
__gmpz_mul at /usr/local/julia/bin/../lib/julia/libgmp.so (unknown line)
mul! at ./gmp.jl:132 [inlined]
mul! at ./gmp.jl:134 [inlined]
scale at /root/.julia/packages/Parsers/v5u2B/src/floats.jl:80 [inlined]
scale at /root/.julia/packages/Parsers/v5u2B/src/floats.jl:114 [inlined]
#_defaultparser#46 at /root/.julia/packages/Parsers/v5u2B/src/floats.jl:239 [inlined]
_defaultparser at /root/.julia/packages/Parsers/v5u2B/src/floats.jl:126 [inlined]
#defaultparser#45 at /root/.julia/packages/Parsers/v5u2B/src/floats.jl:123 [inlined]
defaultparser at /root/.julia/packages/Parsers/v5u2B/src/floats.jl:123
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2184
...Using Parsers 0.2.18 does not have this issue. |
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@omus So if you enable the commented-out line, it fails to compile, but with sysimg it succeeds compilation but gives the realloc error at runtime? |
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Using the following to include Parsers.jl in a system image will fail on 0.2.20 or 0.2.18: Like you said, the alternative |
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So if I'm understanding correctly, when Parsers.jl is included in the sysimg, the pre-allocated BigInts are somehow borked, but normal precompilation is fine. Right? |
That is also my understanding |
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You can't mutate BigInts in the system image. Since this use case needs |
…unction. This caused issues when Parsers.jl was included in the sysimg compilation (via PackageCompiler).
Fix #22 by reinitializing our pre-allocated BigInts in the __init__ f…
When updating from Parsers 0.2.18 to 0.2.20 I get the following when parsing a CSV file:
I'll note that this error is occurring in a fairly deep application. I can try to make a minimal reproducible test if requested.
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