Using Containers

Jobs on HPRC are run in an enterprise Linux 6 container. If you want your job to run in a custom Singularity container, you can specify that container either on the qsub command line or within your script.

Here is an example on the qsub command line:

qsub -I -v SINGULARITY_CONTAINER="/storage/work/abc123/singularity/bionic-base.simg"

For example, the above interactive job would provide:

[abc123@aci-lgn-008 abc123]$ qsub -I -A ics-hprc -q hprc -l nodes=1:ppn=20 -l mem=32gb -l walltime=1:23:30:00

qsub: waiting for job 12907285.torque01.util.production.int.aci.ics.psu.edu to start

qsub: job 12907285.torque01.util.production.int.aci.ics.psu.edu ready

[abc123@comp-vc-1645 abc123]$ cat /etc/os-release

NAME="Ubuntu"

VERSION="18.04.1 LTS (Bionic Beaver)"

ID=ubuntu

ID_LIKE=debian

PRETTY_NAME="Ubuntu 18.04.1 LTS"

VERSION_ID="18.04"

HOME_URL="https://www.ubuntu.com/"

SUPPORT_URL="https://help.ubuntu.com/"

BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"

PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"

VERSION_CODENAME=bionic

UBUNTU_CODENAME=bionic

Here is an example where the container is specified within your submission script:

#PBS -l walltime=1:30:00
#PBS -l nodes=1:ppn=8
#PBS -l mem=8gb
#PBS -j oe
#PBS -r n
#PBS -m bae
#PBS -M abf123@psu.edu
#PBS -q hprc
#PBS -A ics-hprc
#PBS -v SINGULARITY_CONTAINER="/storage/work/abc123/singularity/bionic-base.simg"

Specifying a Custom Bash Environment on HPRC

Some jobs may be best served by custom bash environments, especially those run within containers that do not support modules or other environment variables supported on ACI-b directly. A custom bash environment can be specified with a qsub variable on the command line or within your submission script.

Here’s an example on the command line:

qsub -I -v

SINGULARITY_CONTAINER="/storage/work/abc123/singularity/bionic-base.simg" -v

BASH_ENV=”/storage/abc123/.bashrc_ubuntu” -q hprc -A epo2-hprc -l nodes=1:ppn=20 -l pmem=5gb -l walltime=16:30:00

Here’s an example within the submission script:

#PBS -l walltime=1:30:00
#PBS -l nodes=1:ppn=8
#PBS -l mem=8gb
#PBS -j oe
#PBS -r n
#PBS -m bae
#PBS -M abf123@psu.edu
#PBS -q hprc
#PBS -A ics-hprc
#PBS -v SINGULARITY_CONTAINER="/storage/work/abc123/singularity/bionic-base.simg"
#PBS -v BASH_ENV=”/storage/abc123/.bashrc_ubuntu”