cuda fails to install ./cuda-installer: error while loading shared libraries: libxml2.so.2

[Dantali0n]

Steps to reproduce

Use the following environment.yaml on Debian 13:

spack:
  specs:
  - cuda
  - libxml2

It doesn't matter if you manually add / remove the spec for libxml2 the error is the same.

Error message

root@7bd1d36687b7:/opt/cobalt/spack/latest# spack install -v
[+] /usr (external glibc-2.41-dln4y657a6hpiciukmwgzqcyw6nmcpsn)
[+] /opt/cobalt/spack/latest/opt/spack/linux-skylake/gcc-runtime-14.2.0-rhu7u5njsy3ee5th5cmao6oj5z22vkla
[+] /opt/cobalt/spack/latest/opt/spack/linux-skylake/gzip-1.14-jdkc7xlh3ami6vxu7kjqaxypjcsdtqr5
[+] /opt/cobalt/spack/latest/opt/spack/linux-skylake/libiconv-1.18-aoopqegrwvzh3t33n53rjelcnku7fgqc
[+] /opt/cobalt/spack/latest/opt/spack/linux-skylake/zlib-ng-2.3.3-b7yuxem23uzq5qxaz4lw5rix4splomjn
[+] /opt/cobalt/spack/latest/opt/spack/linux-skylake/xz-5.8.3-4jsizfayjvr6nxbocjnkwdtscmlbsshs
[+] /opt/cobalt/spack/latest/opt/spack/linux-skylake/openssl-3.6.1-3iyg2nfs3x2dbpondb7tp6srxmo6beae
[+] /opt/cobalt/spack/latest/opt/spack/linux-skylake/libxml2-2.15.3-3rp2tt2chec53kovd2osi5cji7wlji6z
[+] /opt/cobalt/spack/latest/opt/spack/linux-skylake/coreutils-9.10-g2xzampux5diecqsup4gbl57nh2exjyb
==> No binary for cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft found: installing from source
==> Installing cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft [10/10]
==> Using cached archive: /opt/cobalt/spack/latest/var/spack/cache/_source-cache/archive/5f/5f79488b57fe6936bc95a56f9b7e2838ab2f2ee3313b1008942206eebe06352d
==> No patches needed for cuda
==> cuda: Executing phase: 'install'
==> [2026-08-04-13:05:16.610287] Attempting to read from missing scope: <ConfigScope: system> at /etc/spack
==> [2026-08-04-13:05:16.611469] '/usr/bin/sh' '/tmp/root/spack-stage/spack-stage-cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft/spack-src/cuda_13.3.0_610.43.02_linux.run' '--silent' '--override' '--toolkit' '--tmpdir=/tmp/root/spack-stage/spack-stage-cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft/tmp' '--installpath=/opt/cobalt/spack/latest/opt/spack/linux-skylake/cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft'
./cuda-installer: error while loading shared libraries: libxml2.so.2: cannot open shared object file: No such file or directory
==> Error: ProcessError: Command exited with status 127:
    '/usr/bin/sh' '/tmp/root/spack-stage/spack-stage-cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft/spack-src/cuda_13.3.0_610.43.02_linux.run' '--silent' '--override' '--toolkit' '--tmpdir=/tmp/root/spack-stage/spack-stage-cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft/tmp' '--installpath=/opt/cobalt/spack/latest/opt/spack/linux-skylake/cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft'

1 error found in build log:
     2    ==> [2026-08-04-13:05:16.610287] Attempting to read from missing scope: <ConfigScope: system> at /etc/spack
     3    ==> [2026-08-04-13:05:16.611469] '/usr/bin/sh' '/tmp/root/spack-stage/spack-stage-cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft/spack-src/cuda_13.3.0_610.43.02_linux.run' '--silent' '--override' '--tool
          kit' '--tmpdir=/tmp/root/spack-stage/spack-stage-cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft/tmp' '--installpath=/opt/cobalt/spack/latest/opt/spack/linux-skylake/cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vr
          gvq6ft'
  >> 4    ./cuda-installer: error while loading shared libraries: libxml2.so.2: cannot open shared object file: No such file or directory

See build log for details:
  /tmp/root/spack-stage/spack-stage-cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft/spack-build-out.txt

==> Removing failure mark on cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft
==> Error: cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft: ProcessError: Command exited with status 127:
    '/usr/bin/sh' '/tmp/root/spack-stage/spack-stage-cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft/spack-src/cuda_13.3.0_610.43.02_linux.run' '--silent' '--override' '--toolkit' '--tmpdir=/tmp/root/spack-stage/spack-stage-cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft/tmp' '--installpath=/opt/cobalt/spack/latest/opt/spack/linux-skylake/cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft'
==> Error: cuda-13.3.0-hwyvmpwo2qzrprbnzzdbjpi3vrgvq6ft: Package was not installed
==> Error: Installation request failed.  Refer to reported errors for failing package(s).

Information on your system

Spack 1.2.2. (also works for any other version say 1.1.1)
GCC 14.2
OS: Debian 13

Spack debug report

* **Spack:** 1.1.1 (https://github.com/spack/spack/commit/2e2169d5282d166f63e3ee4db8d4446c43cefa8a)
* **Builtin repo:** https://github.com/spack/spack-packages/commit/2c145b567f109021dbd738b823ebaabbbc7bd868
* **Python:** 3.13.5
* **Platform:** linux-debian13-skylake

General information

• I have run spack debug report and reported the version of Spack/Python/Platform
• I have searched the issues of this repo and believe this is not a duplicate
• I have run the failing commands in debug mode and reported the output

[Dantali0n]

As soon as you install libxml2 system wide the problem goes away. However, that means that the ./cuda-installer is using the system version of libxml2 and not the one from spack.

[haampie]

This should've been fixed in 6350c7f which was added 6 years ago. Can you check why setting LD_LIBRARY_PATH doesn't work for you there?

[Dantali0n]

This should've been fixed in 6350c7f which was added 6 years ago. Can you check why setting LD_LIBRARY_PATH doesn't work for you there?

How would I check that?

This is super simple to reproduce:

# docker run -it debian:13 /bin/bash
apt update && apt install git python3 build-essential
git clone https://github.com/spack/spack.git
cd spack
source share/spack/setup-env.sh
spack env create example
spack env activate example
spack add cuda@13
spack concretize -f
spack install  # will fail on cuda

[haampie]

The LD_LIBRARY_PATH solution has worked for a long time, so then a possible cause is an ABI change in libxml2 that makes loading the Spack library fail. If so, the solution would be to add a forward compat bound on libxml2 to cuda.

You could check by installing a couple libxml2 versions and then running LD_LIBRARY_PATH=$libxml/lib ./cuda-installer manually.

[Dantali0n]

I'm on holiday till the 26th of August, perhaps someone else has time to try a few different recent versions to see which exact one is the cause.