load libsuitesparse_wrapper.so (i686 CHOLMOD initialization error)

[ghost]

Improper alignment here.

bash-4.3$ julia
┌ Error: Error during initialization of module CHOLMOD
│   exception =
│    could not load library "libsuitesparse_wrapper"
│    libsuitesparse_wrapper.so: ELF-indlæsningskommandos adresse/tillæg er ikke tilpasset ordentligt
└ @ SuiteSparse.CHOLMOD /buildworker/worker/package_linux32/build/usr/share/julia/stdlib/v1.3/SuiteSparse/src/cholmod.jl:176
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.3.1 (2019-12-30)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> exit()
bash-4.3$  

[ViralBShah]

How was this built? Can you point to the build script?

[ghost]

https://julialang.org/downloads/
julia-1.3.1-linux-i686.tar.gz

link deleted Nov 10, 2020
julia.SlackBuild

[ViralBShah]

What version of gcc? Perhaps @staticfloat knows what might be going on.

[staticfloat]

@apparluk translating that error message, it looks like it's saying ELF load command address/offset not properly aligned; does that seem right?

If that is the case, this seems likely to be a patchelf issue where your linux is (for some reason) unhappy with the alignment of something in that image. What version of glibc are you using?

[ghost]

What version of gcc?

output is from running gcc-5.5.0 / slackware-current would be gcc-9.2.0

What version of glibc are you using?

output is from running glibc-2.23 / slackware-current would be glibc-2.30

@staticfloat

I thought my improper alignment comment was sufficient, here's the English error message running in xterm, which also clarifies what I wrote about Julia messages assuming running in a UTF-8 LANG.

[ViralBShah]

Could you try slackware-current?

[ghost]

Could you try slackware-current?

I've sent a query on the matter to a Slackware user community member.

[willysr]

i tested on slackware64-current and it has the same results

[ViralBShah]

How exactly are you building? What is the exact make incantation?

[willysr]

I'm using the binary version and packaged using this script: https://slackbuilds.org/slackbuilds/14.2/development/julia/julia.SlackBuild (with some changes to build the latest one)

[ViralBShah]

Can you try starting Julia from the downloaded tarball directly and see if it gives the same error?

[willysr]

if i try to build it manually using make and run usr/bin/julia, it worked fine

i think the static version is the one have problems under slackware-current. probably a mismatch in some part

[ghost]

starting Julia from the downloaded tarball directly

[ghost]

@willysr If on slackware64-current you move /usr/lib/julia/libsuitesparse_wrapper.so to libsuitesparse_wrapper.so.bak and copy from an extracted tarball the unstripped libsuitesparse_wrapper.so to /usr/lib/julia, do you get any load errors?

[staticfloat]

Ah, yes, in the slack build instructions, it unconditionally strips all ELF objects:

find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true

This unfortunately sounds like a bad interaction between patchelf and strip, as documented here: NixOS/patchelf#10. Supposedly that should be fixed (and we do use patchelf 0.10 within BinaryBuilder, which should contain that fix) so either that patchelf fix is insufficient, or there's something else wrong with strip.

[ghost]

@staticfloat try ldd on the stripped and unstripped libsuitesparse_wrapper.so

[staticfloat]

We historically don't strip our binaries for precisely this reason; if you download the latest Julia release, those libraries are unstripped. The only stripping is occuring on the Slackware side.

[willysr]

let me try without stripping then

[ghost]

Which julia version began using patchelf?

A comment not to strip for julia >= version could be added in the .SlackBuild above the commented out strip lines.

[willysr]

Yeah, removing stripping makes it work on slackware64-current here. Thanks

[ghost]

@staticfloat I'm inclined to close, with the possibility to reopen if the patchelf code changes.

@willysr I suppose the following would suffice in an eventual SlackBuilds.org update.

# Don't strip for julia >= 1.3.1.
# find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
#  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true

[staticfloat]

@staticfloat I'm inclined to close

Same.

Which julia version began using patchelf?

At the very least, since we started using precompiled binaries for most of our dependencies, which would be Julia 1.2+.