Singularity containers failing and reporting issues with libraries

Owned by Alexis Espinosa
Last updated: Nov 29, 2022
1 min read

Problem

Singularity can't run/execute a given container and reports problems with libraries. For example, some bioinformatics containers have shown this kind of error messages:

$ singularity exec prokka_latest.sif cat /etc/os-release
/bin/cat: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.25' not found (required by /usr/lib64/librdmacm.so.1)
/bin/cat: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.25' not found (required by /usr/lib64/libmlx5.so.1)

$ singularity exec bakta_latest.sif cat /etc/os-release
Error loading shared library libibverbs.so.1: No such file or directory (needed by /usr/lib64/librdmacm.so.1)
Error loading shared library libnl-3.so.200: No such file or directory (needed by /usr/lib64/librdmacm.so.1)
Error loading shared library libnl-route-3.so.200: No such file or directory (needed by /usr/lib64/libibverbs.so.1)
Error loading shared library libnl-3.so.200: No such file or directory (needed by /usr/lib64/libibverbs.so.1)
Error loading shared library libnl-3.so.200: No such file or directory (needed by /usr/lib64/libnl-route-3.so.200)
Error loading shared library libibverbs.so.1: No such file or directory (needed by /usr/lib64/libmlx5.so.1)


Solution

The solution for this kind of problems is to find the right libraries to mount for an specific application. We currently count with several singularity modules that suit for specific applications (which can be listed with the command: module avail singularity). In particular, there are two kinds of generic singularity modules:

singularity/<version>

singularity/<version>-nompi

As many of the bioinformatics containers do not need to use mpi, then it is more appropiate to load the "nompi" kind of module which, indeed, avoids the binding of mpi libraries which may be in conflict with containers with old library versions. So, in order to solve the problems shown above:

$ module load singularity/3.8.6-nompi

$ singularity exec prokka_latest.sif cat /etc/os-release
NAME="Ubuntu"
VERSION="16.04.7 LTS (Xenial Xerus)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 16.04.7 LTS"
VERSION_ID="16.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
VERSION_CODENAME=xenial
UBUNTU_CODENAME=xenial

$ singularity exec bakta_latest.sif cat /etc/os-release
NAME="Alpine Linux"
ID=alpine
VERSION_ID=3.12.12
PRETTY_NAME="Alpine Linux v3.12"
HOME_URL="https://alpinelinux.org/"
BUG_REPORT_URL="https://bugs.alpinelinux.org/" 



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