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conda-forge / squashfs-tools-feedstock

A conda-smithy repository for squashfs-tools.
BSD 3-Clause "New" or "Revised" License
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unsquashfs: error while loading shared libraries: libz.so.1 #16

Open matuskosut opened 2 years ago

matuskosut commented 2 years ago

Solution to issue cannot be found in the documentation.

Issue

Hi,

when trying to run singularity I got an error regarding unsquashfs not being able to load shared library:

/home/ubuntu/.conda/envs/singularity/bin/unsquashfs: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
: exit status 127

I believe that shared library is in correct place:

:~$ find /home/ubuntu/.conda/envs/singularity -name libz.so.1
/home/ubuntu/.conda/envs/singularity/lib/libz.so.1

Is it possible that there is some misconfiguration in build that causes this? Or am I doing something wrong.

fyi my steps were run on clean installation:

bash Miniconda3-py39_4.11.0-Linux-x86_64.sh
...
conda create -n singularity -c conda-forge singularity
conda activate singularity
singularity run ...

Installed packages

# packages in environment at /home/ubuntu/.conda/envs/singularity:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
cni                       1.0.1                ha975731_1    conda-forge
cni-plugins               1.0.1                ha8f183a_0    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
jq                        1.6               h36c2ea0_1000    conda-forge
libarchive                3.5.2                hed592e5_1    conda-forge
libgcc-ng                 11.2.0              h1d223b6_16    conda-forge
libgomp                   11.2.0              h1d223b6_16    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libseccomp                2.4.4                h7f98852_1    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_16    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libxml2                   2.9.13               h22db469_0    conda-forge
libzlib                   1.2.11            h166bdaf_1014    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
oniguruma                 6.9.7.1              h7f98852_0    conda-forge
openssl                   3.0.2                h166bdaf_1    conda-forge
singularity               3.8.7                h8e8409e_0    conda-forge
squashfs-tools            4.4                  h6b73730_2    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h166bdaf_1014    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

Environment info

active environment : singularity
    active env location : /home/ubuntu/.conda/envs/singularity
            shell level : 2
       user config file : /home/ubuntu/.condarc
 populated config files : /home/ubuntu/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __linux=5.4.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/ubuntu/.conda  (writable)
      conda av data dir : /home/ubuntu/.conda/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/ubuntu/.conda/pkgs
       envs directories : /home/ubuntu/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.4.0-107-generic ubuntu/20.04.4 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
ngam commented 2 years ago

can you try an older version and/or singularityce?

ngam commented 2 years ago

To be clear I can reproduce this and I am not sure what's causing this issue. It is consistent across singularity and singularityce and the usual tricks don't resolve it. I suspect we have to dig deeper into the builds and mark them as broken in the meanwhile.

The interest in singularity on conda-forge has waned unfortunately. It's just that, sadly, no matter how we try, one cannot get a fully functioning singularity without having an HPC admin install it. There are all these small issues that pop up that make using it unreliable and cumbersome. :(