libpthread.so.0: undefined symbol: __libc_siglongjmp, version GLIBC_PRIVATE when building dependency mmark-ext

[augyg]

I am trying to use mmark and mmark-ext in a project to add some static site features for Obelisk however I came across this issue:

dist/build/Text/MMark/Extension/Comment.o, dist/build/Text/MMark/Extension/Comment.dyn_o ) > [ 2 of 12] Compiling Text.MMark.Extension.FontAwesome ( Text/MMark/Extension/FontAwesome.hs, dist/build/Text/MMark/Extension/FontAwesome.o, dist/build/Text/MMark/Extension/FontAwesome.dyn_o ) > > <no location info>: error: > <command line>: /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libpthread.so.0: undefined symbol: __libc_siglongjmp, version GLIBC_PRIVATE > [ 3 of 12] Compiling Text.MMark.Extension.Footnotes ( Text/MMark/Extension/Footnotes.hs, dist/build/Text/MMark/Extension/Footnotes.o, dist/build/Text/MMark/Extension/Footnotes.dyn_o ) > > <no location info>: error: > <command line>: /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libpthread.so.0: undefined symbol: __libc_siglongjmp, version GLIBC_PRIVATE

I have a repo to reproduce here

https://github.com/augyg/reproduce-glibc

https://github.com/NixOS/nixpkgs/issues/170897
https://github.com/NixOS/nixpkgs/issues/169332#issuecomment-1106552971

This problem doesn't happen when using ob run but does when using nix-build -A exe or ob hoogle

The version of mmark-ext-0.2.1.5 is typically built with ghc 9.6.5 but Ive forked and changed the cabal file+etcetera so that it should work with ghc 8.10.7 and this is included as a thunk in the repo to minimally reproduce, and this is what allowed ob run to work but alas build and hoogle still fail

I have failed to reproduce this outside of Obelisk

Channels: nixos https://nixos.org/channels/nixos-24.05

[augyg]

NixOS/nixpkgs#303405

https://discourse.nixos.org/t/help-understanding-the-libgl-abi-problem-and-possible-solutions/42022/25

[dfordivam]

@augyg I have hit a similar issue, but with "cabal build" and not nix-build. In my case clearing up the .cabal dir in my home fixed the issue. Also I ran the nix-build -A exe on your repo, but did not hit this issue. It failed while compiling frontend.

[augyg]

@dfordivam ahh sorry I cut out too much so the static failed

I just pushed a new commit that fails on nix-build -A exe for the same reason

I've also tried clearing my .cabal/ folder in case that helped but it hasn't. If there is equivalent persistent state, which appears to be the problem in the cited nixpkgs issues then I'm not sure how to find it

[dfordivam]

I am not sure why this would be happening, but the ghc during compilation of TH is using a separate libc, than the exe it generated (here ./Setup)

./Setup build
Preprocessing library for mmark-ext-0.2.1.5..
Building library for mmark-ext-0.2.1.5..
[ 8 of 12] Compiling Text.MMark.Extension.FontAwesome ( Text/MMark/Extension/FontAwesome.hs, dist/build/Text/MMark/Extension/FontAwesome.o, dist/build/Text/MMark/Extension/FontAwesome.dyn_o )

<no location info>: error:
    <command line>: /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libpthread.so.0: undefined symbol: __libc_siglongjmp, version GLIBC_PRIVATE
[ 9 of 12] Compiling Text.MMark.Extension.Footnotes ( Text/MMark/Extension/Footnotes.hs, dist/build/Text/MMark/Extension/Footnotes.o, dist/build/Text/MMark/Extension/Footnotes.dyn_o )

<no location info>: error:
    <command line>: /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libpthread.so.0: undefined symbol: __libc_siglongjmp, version GLIBC_PRIVATE
[10 of 12] Compiling Text.MMark.Extension.Kbd ( Text/MMark/Extension/Kbd.hs, dist/build/Text/MMark/Extension/Kbd.o, dist/build/Text/MMark/Extension/Kbd.dyn_o )

<no location info>: error:
    <command line>: /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libpthread.so.0: undefined symbol: __libc_siglongjmp, version GLIBC_PRIVATE
[11 of 12] Compiling Text.MMark.Extension.ObfuscateEmail ( Text/MMark/Extension/ObfuscateEmail.hs, dist/build/Text/MMark/Extension/ObfuscateEmail.o, dist/build/Text/MMark/Extension/ObfuscateEmail.dyn_o )

<no location info>: error:
    <command line>: /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libpthread.so.0: undefined symbol: __libc_siglongjmp, version GLIBC_PRIVATE

[nix-shell:/tmp/tmp.7FQZjPhZY9/mmark-ext/mmark-ext/mmark-ext]$ ldd ./Setup 
        linux-vdso.so.1 (0x00007f44cf073000)
        libgmp.so.10 => /nix/store/i96w3nijv65d78zx4bqma48ww51fx8is-gmp-with-cxx-6.2.1/lib/libgmp.so.10 (0x00007f44cefcc000)
        libc.so.6 => /nix/store/bzd91shky9j9d43girrrj6vmqlw7x9m8-glibc-2.35-163/lib/libc.so.6 (0x00007f44cedc2000)
        libm.so.6 => /nix/store/bzd91shky9j9d43girrrj6vmqlw7x9m8-glibc-2.35-163/lib/libm.so.6 (0x00007f44cece2000)
        librt.so.1 => /nix/store/bzd91shky9j9d43girrrj6vmqlw7x9m8-glibc-2.35-163/lib/librt.so.1 (0x00007f44cecdd000)
        libdl.so.2 => /nix/store/bzd91shky9j9d43girrrj6vmqlw7x9m8-glibc-2.35-163/lib/libdl.so.2 (0x00007f44cecd6000)
        libffi.so.8 => /nix/store/6fncvg61gwjh1j7syy0nyki2j6xxf2ql-libffi-3.4.2/lib/libffi.so.8 (0x00007f44cecc9000)
        /nix/store/bzd91shky9j9d43girrrj6vmqlw7x9m8-glibc-2.35-163/lib/ld-linux-x86-64.so.2 => /nix/store/bzd91shky9j9d43girrrj6vmqlw7x9m8-glibc-2.35-163/lib64/ld-linux-x86-64.so.2 (0x00007f44cf075000)

[dfordivam]

I gave another look and found the issue, the ghc-syntax-highlighter_0_0_6 in using ghc-lib-parser-8.10.7.20210828, which in turn uses glibc-2.33, incompatible with other libs. You should try to get all packages built with one nixpkgs

Loading package ghc-lib-parser-8.10.7.20210828 ... *** Deleting temp files:      

ldd /nix/store/k2ykhr4av2h95v6731pn77f176x3ff3s-ghc-lib-parser-8.10.7.20210828/lib/ghc-8.10.7/x86_64-linux-ghc-8.10.7/libHSghc-lib-parser-8.10.7.20210828-3JfzLiWBJmaFBCCXq9roVm-ghc8.10.7.so
        linux-vdso.so.1 (0x00007ffc36b18000)
        libHStransformers-0.5.6.2-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/transformers-0.5.6.2/libHStransformers-0.5.6.2-ghc8.10.7.so (0x00007fea2e815000)
        libHSprocess-1.6.13.2-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/process-1.6.13.2/libHSprocess-1.6.13.2-ghc8.10.7.so (0x00007fea2e7cf000)
        libHSpretty-1.1.3.6-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/pretty-1.1.3.6/libHSpretty-1.1.3.6-ghc8.10.7.so (0x00007fea2e75f000)
        libHSdirectory-1.3.6.0-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/directory-1.3.6.0/libHSdirectory-1.3.6.0-ghc8.10.7.so (0x00007fea2e6f4000)
        libHSunix-2.7.2.2-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/unix-2.7.2.2/libHSunix-2.7.2.2-ghc8.10.7.so (0x00007fea2e609000)
        libHStime-1.9.3-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/time-1.9.3/libHStime-1.9.3-ghc8.10.7.so (0x00007fea2e496000)
        libHSfilepath-1.4.2.1-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/filepath-1.4.2.1/libHSfilepath-1.4.2.1-ghc8.10.7.so (0x00007fea2e471000)
        libHSbinary-0.8.8.0-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/binary-0.8.8.0/libHSbinary-0.8.8.0-ghc8.10.7.so (0x00007fea2e3c6000)
        libHScontainers-0.6.5.1-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/containers-0.6.5.1/libHScontainers-0.6.5.1-ghc8.10.7.so (0x00007fea2e038000)
        libHSbytestring-0.10.12.0-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/bytestring-0.10.12.0/libHSbytestring-0.10.12.0-ghc8.10.7.so (0x00007fea2df42000)
        libHSdeepseq-1.4.4.0-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/deepseq-1.4.4.0/libHSdeepseq-1.4.4.0-ghc8.10.7.so (0x00007fea2df23000)
        libHSarray-0.5.4.0-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/array-0.5.4.0/libHSarray-0.5.4.0-ghc8.10.7.so (0x00007fea2de99000)
        libHSbase-4.14.3.0-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/base-4.14.3.0/libHSbase-4.14.3.0-ghc8.10.7.so (0x00007fea2d491000)
        libHSinteger-gmp-1.0.3.0-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/integer-gmp-1.0.3.0/libHSinteger-gmp-1.0.3.0-ghc8.10.7.so (0x00007fea2d44f000)
        libHSghc-prim-0.6.1-ghc8.10.7.so => /nix/store/gblb4a16xsgjbhc9iy5ad0x7x15f8ybf-ghc-8.10.7/lib/ghc-8.10.7/ghc-prim-0.6.1/libHSghc-prim-0.6.1-ghc8.10.7.so (0x00007fea2cfa5000)
        librt.so.1 => /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/librt.so.1 (0x00007fea2cf9a000)
        libutil.so.1 => /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libutil.so.1 (0x00007fea2cf93000)
        libdl.so.2 => /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libdl.so.2 (0x00007fea2cf8e000)
        libpthread.so.0 => /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libpthread.so.0 (0x00007fea2cf6e000)
        libgmp.so.10 => /nix/store/d98pqy6b8graar18kwq0zba010xy0ihn-gmp-6.2.1/lib/libgmp.so.10 (0x00007fea2cecc000)
        libc.so.6 => /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libc.so.6 (0x00007fea2ccf7000)
        libm.so.6 => /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/libm.so.6 (0x00007fea2cbb6000)
        /nix/store/q29bwjibv9gi9n86203s38n0577w09sx-glibc-2.33-117/lib/ld-linux-x86-64.so.2 => /nix/store/bzd91shky9j9d43girrrj6vmqlw7x9m8-glibc-2.35-163/lib64/ld-linux-x86-64.so.2 (0x00007fea31a76000)