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Segfault on Google Colab #357

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pogudingleb opened this issue Jan 18, 2021 · 10 comments
Closed

Segfault on Google Colab #357

pogudingleb opened this issue Jan 18, 2021 · 10 comments

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@pogudingleb
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I thought it would be great if one could use Singular.jl (and Oscar in general) on Google Colab. However, I have encountered the following problem while trying to use Singular.jl there. I do the following:

  1. Take the sample julia notebook and run it changing JULIA_VERSION to 1.5.3
  2. Run: using Pkg; Pkg.add("Singular"); using Singular
  3. Get segfault:
signal (11): Segmentation fault
in expression starting at /root/.julia/packages/Singular/KXbMt/src/Singular.jl:15
malloc_usable_size at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
omAllocFromSystem at /workspace/srcdir/singular-4.2.0/omalloc/omAllocSystem.c:206
omAllocNewBinPagesRegion at /workspace/srcdir/singular-4.2.0/omalloc/omBinPage.c:296
omAllocBinPage at /workspace/srcdir/singular-4.2.0/omalloc/omBinPage.c:103
omAllocNewBinPage at /workspace/srcdir/singular-4.2.0/omalloc/om_Alloc.c:38
omAllocBinFromFullPage at /workspace/srcdir/singular-4.2.0/omalloc/om_Alloc.c:145
_omAlloc at /workspace/srcdir/singular-4.2.0/omalloc/omInline.h:68
_omGetSpecBin at /workspace/srcdir/singular-4.2.0/omalloc/omBin.c:115
_GLOBAL__sub_I_subexpr.cc at /root/.julia/artifacts/4e0ecf0494e8779da13500a8007647ef3373e795/lib/libSingular.so (unknown line)
__do_global_ctors_aux at /root/.julia/artifacts/4e0ecf0494e8779da13500a8007647ef3373e795/lib/libSingular.so (unknown line)
_init at /root/.julia/artifacts/4e0ecf0494e8779da13500a8007647ef3373e795/lib/libSingular.so (unknown line)
Allocations: 3117318 (Pool: 3116463; Big: 855); GC: 2

Failed to precompile Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c] to /root/.julia/compiled/v1.5/Singular/9fz0y_iqfTG.ji.

Thank you in advance!

@wbhart
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wbhart commented Jan 18, 2021

It segfaulted inside libc? That's odd.

How much memory is available on an instance there?

@hannes14
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hannes14 commented Jan 18, 2021 via email

@pogudingleb
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It segfaulted inside libc? That's odd.

How much memory is available on an instance there?

There is 12 GB RAM, should be enough, I guess

@fingolfin
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Can you please tell us the output of the following Julia script on your host?

versioninfo()
using Pkg
Pkg.status()
Pkg.status(mode=PKGMODE_MANIFEST)

That might give a clue.

@pogudingleb
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pogudingleb commented Jan 22, 2021

Can you please tell us the output of the following Julia script on your host?

versioninfo()
using Pkg
Pkg.status()
Pkg.status(mode=PKGMODE_MANIFEST)

That might give a clue.

Here it is before installing Singular

Julia Version 1.5.3
Commit 788b2c77c1 (2020-11-09 13:37 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Xeon(R) CPU @ 2.20GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-9.0.1 (ORCJIT, broadwell)
Environment:
  JULIA_NUM_THREADS = 2
Status `~/.julia/environments/v1.5/Project.toml`
  [6e4b80f9] BenchmarkTools v0.5.0
  [7073ff75] IJulia v1.23.1
  [91a5bcdd] Plots v1.10.1
Status `~/.julia/environments/v1.5/Manifest.toml`
  [79e6a3ab] Adapt v2.4.0
  [56f22d72] Artifacts v1.3.0
  [6e4b80f9] BenchmarkTools v0.5.0
  [6e34b625] Bzip2_jll v1.0.6+5
  [83423d85] Cairo_jll v1.16.0+6
  [35d6a980] ColorSchemes v3.10.2
  [3da002f7] ColorTypes v0.10.9
  [5ae59095] Colors v0.12.6
  [34da2185] Compat v3.25.0
  [e66e0078] CompilerSupportLibraries_jll v0.3.4+0
  [8f4d0f93] Conda v1.5.0
  [d38c429a] Contour v0.5.7
  [9a962f9c] DataAPI v1.4.0
  [864edb3b] DataStructures v0.18.9
  [e2d170a0] DataValueInterfaces v1.0.0
  [5ae413db] EarCut_jll v2.1.5+1
  [2e619515] Expat_jll v2.2.7+6
  [c87230d0] FFMPEG v0.4.0
  [b22a6f82] FFMPEG_jll v4.3.1+4
  [53c48c17] FixedPointNumbers v0.8.4
  [a3f928ae] Fontconfig_jll v2.13.1+14
  [59287772] Formatting v0.4.2
  [d7e528f0] FreeType2_jll v2.10.1+5
  [559328eb] FriBidi_jll v1.0.5+6
  [0656b61e] GLFW_jll v3.3.2+1
  [28b8d3ca] GR v0.53.0
  [d2c73de3] GR_jll v0.53.0+0
  [5c1252a2] GeometryBasics v0.3.5
  [78b55507] Gettext_jll v0.20.1+7
  [7746bdde] Glib_jll v2.59.0+4
  [42e2da0e] Grisu v1.0.0
  [cd3eb016] HTTP v0.8.19
  [7073ff75] IJulia v1.23.1
  [83e8ac13] IniFile v0.5.0
  [c8e1da08] IterTools v1.3.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.2.0
  [682c06a0] JSON v0.21.1
  [aacddb02] JpegTurbo_jll v2.0.1+3
  [c1c5ebd0] LAME_jll v3.100.0+3
  [dd4b983a] LZO_jll v2.10.0+3
  [b964fa9f] LaTeXStrings v1.2.0
  [23fbe1c1] Latexify v0.14.7
  [dd192d2f] LibVPX_jll v1.9.0+1
  [e9f186c6] Libffi_jll v3.2.1+4
  [d4300ac3] Libgcrypt_jll v1.8.5+4
  [7e76a0d4] Libglvnd_jll v1.3.0+3
  [7add5ba3] Libgpg_error_jll v1.36.0+3
  [94ce4f54] Libiconv_jll v1.16.0+7
  [4b2f31a3] Libmount_jll v2.34.0+3
  [89763e89] Libtiff_jll v4.1.0+2
  [38a345b3] Libuuid_jll v2.34.0+7
  [1914dd2f] MacroTools v0.5.6
  [739be429] MbedTLS v1.0.3
  [c8ffd9c3] MbedTLS_jll v2.16.8+1
  [442fdcdd] Measures v0.3.1
  [e1d29d7a] Missings v0.4.4
  [77ba4419] NaNMath v0.3.5
  [e7412a2a] Ogg_jll v1.3.4+2
  [458c3c95] OpenSSL_jll v1.1.1+6
  [91d4177d] Opus_jll v1.3.1+3
  [bac558e1] OrderedCollections v1.3.2
  [2f80f16e] PCRE_jll v8.42.0+4
  [69de0a69] Parsers v1.0.15
  [30392449] Pixman_jll v0.40.0+0
  [ccf2f8ad] PlotThemes v2.0.0
  [995b91a9] PlotUtils v1.0.10
  [91a5bcdd] Plots v1.10.1
  [ede63266] Qt_jll v5.15.2+1
  [3cdcf5f2] RecipesBase v1.1.1
  [01d81517] RecipesPipeline v0.2.1
  [189a3867] Reexport v1.0.0
  [ae029012] Requires v1.1.2
  [6c6a2e73] Scratch v1.0.3
  [992d4aef] Showoff v0.3.2
  [b85f4697] SoftGlobalScope v1.1.0
  [a2af1166] SortingAlgorithms v0.3.1
  [90137ffa] StaticArrays v1.0.1
  [2913bbd2] StatsBase v0.33.2
  [09ab397b] StructArrays v0.4.4
  [3783bdb8] TableTraits v1.0.0
  [bd369af6] Tables v1.2.2
  [81def892] VersionParsing v1.2.0
  [a2964d1f] Wayland_jll v1.17.0+4
  [2381bf8a] Wayland_protocols_jll v1.18.0+4
  [02c8fc9c] XML2_jll v2.9.10+3
  [aed1982a] XSLT_jll v1.1.33+4
  [4f6342f7] Xorg_libX11_jll v1.6.9+4
  [0c0b7dd1] Xorg_libXau_jll v1.0.9+4
  [935fb764] Xorg_libXcursor_jll v1.2.0+4
  [a3789734] Xorg_libXdmcp_jll v1.1.3+4
  [1082639a] Xorg_libXext_jll v1.3.4+4
  [d091e8ba] Xorg_libXfixes_jll v5.0.3+4
  [a51aa0fd] Xorg_libXi_jll v1.7.10+4
  [d1454406] Xorg_libXinerama_jll v1.1.4+4
  [ec84b674] Xorg_libXrandr_jll v1.5.2+4
  [ea2f1a96] Xorg_libXrender_jll v0.9.10+4
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.0+3
  [c7cfdc94] Xorg_libxcb_jll v1.13.0+3
  [cc61e674] Xorg_libxkbfile_jll v1.1.0+4
  [12413925] Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] Xorg_xcb_util_jll v0.4.0+1
  [975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] Xorg_xkbcomp_jll v1.4.2+4
  [33bec58e] Xorg_xkeyboard_config_jll v2.27.0+4
  [c5fb5394] Xorg_xtrans_jll v1.4.0+3
  [c2297ded] ZMQ v1.2.1
  [8f1865be] ZeroMQ_jll v4.3.2+5
  [83775a58] Zlib_jll v1.2.11+18
  [3161d3a3] Zstd_jll v1.4.5+2
  [0ac62f75] libass_jll v0.14.0+4
  [f638f0a6] libfdk_aac_jll v0.1.6+4
  [b53b4c65] libpng_jll v1.6.37+6
  [f27f6e37] libvorbis_jll v1.3.6+6
  [1270edf5] x264_jll v2020.7.14+2
  [dfaa095f] x265_jll v3.0.0+3
  [d8fb68d0] xkbcommon_jll v0.9.1+5
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [7b1f6079] FileWatching
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode

and after

Julia Version 1.5.3
Commit 788b2c77c1 (2020-11-09 13:37 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Xeon(R) CPU @ 2.20GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-9.0.1 (ORCJIT, broadwell)
Environment:
  JULIA_NUM_THREADS = 2
Status `~/.julia/environments/v1.5/Project.toml`
  [6e4b80f9] BenchmarkTools v0.5.0
  [7073ff75] IJulia v1.23.1
  [91a5bcdd] Plots v1.10.1
  [bcd08a7b] Singular v0.4.3
Status `~/.julia/environments/v1.5/Manifest.toml`
  [c3fe647b] AbstractAlgebra v0.12.0
  [79e6a3ab] Adapt v2.4.0
  [e21ec000] Antic_jll v0.200.300+0
  [d9960996] Arb_jll v200.1900.0+0
  [56f22d72] Artifacts v1.3.0
  [6e4b80f9] BenchmarkTools v0.5.0
  [b99e7846] BinaryProvider v0.5.10
  [6e34b625] Bzip2_jll v1.0.6+5
  [83423d85] Cairo_jll v1.16.0+6
  [35d6a980] ColorSchemes v3.10.2
  [3da002f7] ColorTypes v0.10.9
  [5ae59095] Colors v0.12.6
  [34da2185] Compat v3.25.0
  [e66e0078] CompilerSupportLibraries_jll v0.3.4+0
  [8f4d0f93] Conda v1.5.0
  [d38c429a] Contour v0.5.7
  [1f15a43c] CxxWrap v0.11.2
  [9a962f9c] DataAPI v1.4.0
  [864edb3b] DataStructures v0.18.9
  [e2d170a0] DataValueInterfaces v1.0.0
  [5ae413db] EarCut_jll v2.1.5+1
  [2e619515] Expat_jll v2.2.7+6
  [c87230d0] FFMPEG v0.4.0
  [b22a6f82] FFMPEG_jll v4.3.1+4
  [e134572f] FLINT_jll v200.700.0+0
  [53c48c17] FixedPointNumbers v0.8.4
  [a3f928ae] Fontconfig_jll v2.13.1+14
  [59287772] Formatting v0.4.2
  [d7e528f0] FreeType2_jll v2.10.1+5
  [559328eb] FriBidi_jll v1.0.5+6
  [0656b61e] GLFW_jll v3.3.2+1
  [e8aa6df9] GLPK_jll v4.65.0+1
  [781609d7] GMP_jll v6.1.2+6
  [28b8d3ca] GR v0.53.0
  [d2c73de3] GR_jll v0.53.0+0
  [5c1252a2] GeometryBasics v0.3.5
  [78b55507] Gettext_jll v0.20.1+7
  [7746bdde] Glib_jll v2.59.0+4
  [42e2da0e] Grisu v1.0.0
  [cd3eb016] HTTP v0.8.19
  [7073ff75] IJulia v1.23.1
  [83e8ac13] IniFile v0.5.0
  [c8e1da08] IterTools v1.3.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.2.0
  [682c06a0] JSON v0.21.1
  [aacddb02] JpegTurbo_jll v2.0.1+3
  [c1c5ebd0] LAME_jll v3.100.0+3
  [dd4b983a] LZO_jll v2.10.0+3
  [b964fa9f] LaTeXStrings v1.2.0
  [23fbe1c1] Latexify v0.14.7
  [dd192d2f] LibVPX_jll v1.9.0+1
  [e9f186c6] Libffi_jll v3.2.1+4
  [d4300ac3] Libgcrypt_jll v1.8.5+4
  [7e76a0d4] Libglvnd_jll v1.3.0+3
  [7add5ba3] Libgpg_error_jll v1.36.0+3
  [94ce4f54] Libiconv_jll v1.16.0+7
  [4b2f31a3] Libmount_jll v2.34.0+3
  [89763e89] Libtiff_jll v4.1.0+2
  [38a345b3] Libuuid_jll v2.34.0+7
  [472f376f] LoadFlint v0.5.0
  [3a97d323] MPFR_jll v4.1.0+1
  [1914dd2f] MacroTools v0.5.6
  [739be429] MbedTLS v1.0.3
  [c8ffd9c3] MbedTLS_jll v2.16.8+1
  [442fdcdd] Measures v0.3.1
  [e1d29d7a] Missings v0.4.4
  [77ba4419] NaNMath v0.3.5
  [2edaba10] Nemo v0.19.1
  [e7412a2a] Ogg_jll v1.3.4+2
  [458c3c95] OpenSSL_jll v1.1.1+6
  [91d4177d] Opus_jll v1.3.1+3
  [bac558e1] OrderedCollections v1.3.2
  [2f80f16e] PCRE_jll v8.42.0+4
  [69de0a69] Parsers v1.0.15
  [30392449] Pixman_jll v0.40.0+0
  [ccf2f8ad] PlotThemes v2.0.0
  [995b91a9] PlotUtils v1.0.10
  [91a5bcdd] Plots v1.10.1
  [ede63266] Qt_jll v5.15.2+1
  [fb686558] RandomExtensions v0.4.3
  [3cdcf5f2] RecipesBase v1.1.1
  [01d81517] RecipesPipeline v0.2.1
  [189a3867] Reexport v1.0.0
  [ae029012] Requires v1.1.2
  [6c6a2e73] Scratch v1.0.3
  [992d4aef] Showoff v0.3.2
  [bcd08a7b] Singular v0.4.3
  [43d676ae] Singular_jll v402.0.0+0
  [b85f4697] SoftGlobalScope v1.1.0
  [a2af1166] SortingAlgorithms v0.3.1
  [90137ffa] StaticArrays v1.0.1
  [2913bbd2] StatsBase v0.33.2
  [09ab397b] StructArrays v0.4.4
  [3783bdb8] TableTraits v1.0.0
  [bd369af6] Tables v1.2.2
  [81def892] VersionParsing v1.2.0
  [a2964d1f] Wayland_jll v1.17.0+4
  [2381bf8a] Wayland_protocols_jll v1.18.0+4
  [02c8fc9c] XML2_jll v2.9.10+3
  [aed1982a] XSLT_jll v1.1.33+4
  [4f6342f7] Xorg_libX11_jll v1.6.9+4
  [0c0b7dd1] Xorg_libXau_jll v1.0.9+4
  [935fb764] Xorg_libXcursor_jll v1.2.0+4
  [a3789734] Xorg_libXdmcp_jll v1.1.3+4
  [1082639a] Xorg_libXext_jll v1.3.4+4
  [d091e8ba] Xorg_libXfixes_jll v5.0.3+4
  [a51aa0fd] Xorg_libXi_jll v1.7.10+4
  [d1454406] Xorg_libXinerama_jll v1.1.4+4
  [ec84b674] Xorg_libXrandr_jll v1.5.2+4
  [ea2f1a96] Xorg_libXrender_jll v0.9.10+4
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.0+3
  [c7cfdc94] Xorg_libxcb_jll v1.13.0+3
  [cc61e674] Xorg_libxkbfile_jll v1.1.0+4
  [12413925] Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] Xorg_xcb_util_jll v0.4.0+1
  [975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] Xorg_xkbcomp_jll v1.4.2+4
  [33bec58e] Xorg_xkeyboard_config_jll v2.27.0+4
  [c5fb5394] Xorg_xtrans_jll v1.4.0+3
  [c2297ded] ZMQ v1.2.1
  [8f1865be] ZeroMQ_jll v4.3.2+5
  [83775a58] Zlib_jll v1.2.11+18
  [3161d3a3] Zstd_jll v1.4.5+2
  [f07e07eb] cddlib_jll v0.94.10+1
  [1493ae25] lib4ti2_jll v1.6.9+2
  [0ac62f75] libass_jll v0.14.0+4
  [3eaa8342] libcxxwrap_julia_jll v0.8.5+1
  [f638f0a6] libfdk_aac_jll v0.1.6+4
  [b53b4c65] libpng_jll v1.6.37+6
  [ae4fbd8f] libsingular_julia_jll v0.4.5+0
  [f27f6e37] libvorbis_jll v1.3.6+6
  [1270edf5] x264_jll v2020.7.14+2
  [dfaa095f] x265_jll v3.0.0+3
  [d8fb68d0] xkbcommon_jll v0.9.1+5
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [7b1f6079] FileWatching
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode

@fingolfin
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fingolfin commented Jan 23, 2021

It segfaults in malloc_usable_size, a function which depends on the current amlloc implementation: maybe, malloc and free are overloaded, but malloc_usable_size not?

Hmm, indeed. Plots.jl and IJulia pull in tons and tons of packages, and JLLs; perhaps one of them does something funky with malloc -- but that'd be super evil. In any case, that would then suggest that one should be able to replicate the issue by installing those packages before trying to install/use Singular. However, I was not able to do so on two different Linux machines.

@pogudingleb can you tell us which glibc version that system uses? E.g. via output of ldd --version

@pogudingleb
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It segfaults in malloc_usable_size, a function which depends on the current amlloc implementation: maybe, malloc and free are overloaded, but malloc_usable_size not?

Hmm, indeed. Plots.jl and IJulia pull in tons and tons of packages, and JLLs; perhaps one of them does something funky with malloc -- but that'd be super evil. In any case, that would then suggest that one should be able to replicate the issue by installing those packages before trying to install/use Singular. However, I was not able to do so on two different Linux machines.

@pogudingleb can you tell us which glibc version that system uses? E.g. via output of `ldd --version

Here is what I get

ldd (Ubuntu GLIBC 2.27-3ubuntu1.3) 2.27
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

As I said, I get this behavior not on my machine but in the default environment of Google Colab, so if you would like to reproduce this yourself, you can

  1. make a copy of this notebook
  2. change JULIA_VERSION to 1.5.3
  3. install Singular.jl
    In any case, since I have done this already, I will be happy to do any further tests.

@fingolfin
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I just tried this with JULIA_VERSION set to 1.6.3. After setup, I run using Pkg; Pkg.add("Singular"). This installed Singular.jl 0.8.0 (and of course a ton of other things). Noticeably, though, precompilation of libsingular_julia_jll failed.

So I did Pkg.add("libsingular_julia_jll"); using libsingular_julia_jll which resulted in the following by now familiar error:

   Resolving package versions...
  No Changes to `~/.julia/environments/v1.6/Project.toml`
  No Changes to `~/.julia/environments/v1.6/Manifest.toml`
┌ Info: Precompiling libsingular_julia_jll [ae4fbd8f-ecdb-54f8-bbce-35570499b30e]
└ @ Base loading.jl:1342

signal (11): Segmentation fault
in expression starting at /root/.julia/packages/libsingular_julia_jll/8LfSn/src/wrappers/x86_64-linux-gnu-cxx11-julia_version+1.6.0.jl:5
malloc_usable_size at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
omAllocFromSystem at /workspace/srcdir/Singular/omalloc/omAllocSystem.c:206
omAllocNewBinPagesRegion at /workspace/srcdir/Singular/omalloc/omBinPage.c:296
omAllocBinPage at /workspace/srcdir/Singular/omalloc/omBinPage.c:103
omAllocNewBinPage at /workspace/srcdir/Singular/omalloc/om_Alloc.c:38
omAllocBinFromFullPage at /workspace/srcdir/Singular/omalloc/om_Alloc.c:145
_omAlloc at /workspace/srcdir/Singular/omalloc/omInline.h:68
_omGetSpecBin at /workspace/srcdir/Singular/omalloc/omBin.c:115
_GLOBAL__sub_I_subexpr.cc at /root/.julia/artifacts/c4baa983fc92c06cc33cf7ec15e61cf69d535705/lib/libSingular.so (unknown line)
__do_global_ctors_aux at /root/.julia/artifacts/c4baa983fc92c06cc33cf7ec15e61cf69d535705/lib/libSingular.so (unknown line)
_init at /root/.julia/artifacts/c4baa983fc92c06cc33cf7ec15e61cf69d535705/lib/libSingular.so (unknown line)
Allocations: 1411038 (Pool: 1410660; Big: 378); GC: 2

Failed to precompile libsingular_julia_jll [ae4fbd8f-ecdb-54f8-bbce-35570499b30e] to /root/.julia/compiled/v1.6/libsingular_julia_jll/jl_FUOH76.

Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IJulia.IJuliaStdio{Base.PipeEndpoint}, internal_stdout::IJulia.IJuliaStdio{Base.PipeEndpoint}, ignore_loaded_modules::Bool)
   @ Base ./loading.jl:1385
 [3] compilecache(pkg::Base.PkgId, path::String)
   @ Base ./loading.jl:1329
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1043
 [5] require(uuidkey::Base.PkgId)
   @ Base ./loading.jl:936
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:923
 [7] eval
   @ ./boot.jl:360 [inlined]
 [8] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
   @ Base ./loading.jl:1116

The function malloc_usable_size is a non-standard function provided by glibc. Removing the Plots package made no difference (but I also did not expect any). Note that the only other package I had loaded was BenchmarkTools so it really shouldn't be caused by some other package overriding malloc.

Perhaps malloc_usable_size simply isn't supported in the Colab environment?!

@fingolfin
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ldd (Ubuntu GLIBC 2.27-3ubuntu1.3) 2.27
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

And run(`cat /etc/os-release`) gives

NAME="Ubuntu"
VERSION="18.04.5 LTS (Bionic Beaver)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 18.04.5 LTS"
VERSION_ID="18.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=bionic
UBUNTU_CODENAME=bionic

This all looks rather standard and common. Weird.

@fingolfin
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I don't think we can do anything here. If the problem is current, someone with access to a system where this can be reproduced must debug it.

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