Singularity containers failing and reporting issues with libraries
- Alexis Espinosa
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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