NIH HPC News & Announcements
IMPORTANT message for NIH HPC Biowulf Users of Singularity
Date: 27 September 2021 14:09:55
From: staff@HPC.NIH.GOV
HPC/Biowulf Users of Singularity containers,
The following announcement is relevant to those who use custom Singularity
containers and bind-mount the /scratch (different from compute node local
/lscratch) directory at runtime. Effective on Tuesday, Oct. 12, 2021
Singularity will issue an error message and fail if users attempt to bind-mount
the /scratch directory at runtime. If you have configuration or run scripts
that set the $SINGULARITY_BINDPATH environment variable or cause Singularity
commands such as shell and exec to be called with the -B/--bind option to
include /scratch, your containerized programs will fail. You will need to
examine these scripts and remove any references to /scratch in the bind-mount
list.
To ease this transition, the NIH HPC staff has created a script that can be
sourced to set the $SINGULARITY_BINDPATH environment variable appropriately. You
can source this script with the following command:
. /usr/local/current/singularity/app_conf/sing_binds
The NIH HPC staff will maintain this script and update it as file systems (such
as /scratch) are added to or removed from the cluster. Using this script
instead of creating a list of bind-mounts yourself will therefore ensure that
your workflows are more “future proof”.
Please see the following for more information about bind-mounting directories to
Singularity containers on the NIH HCP systems.
https://hpc.nih.gov/apps/singularity.html#bind
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