$ singularity shell [options] image.sif
Let’s go inside the pulled blast container.
$ singularity shell blast_2.15.0.sif
Singularity> more /etc/os-release
PRETTY_NAME="Debian GNU/Linux 12 (bookworm)"
NAME="Debian GNU/Linux"
VERSION_ID="12"
VERSION="12 (bookworm)"
VERSION_CODENAME=bookworm
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"
Singularity> which blastp
/usr/local/bin/blastp
Singularity> ls /
bin dev home linuxrc opt run srv usr
boot environment lib media proc sbin sys var
cluster etc lib64 mnt root singularity tmp
Singularity> cd /cluster/
Singularity> ls
home
Singularity> cd /cluster/tufts
bash: cd: /cluster/tufts: No such file or directory
You may have noticed that although we can see /cluster, /cluster/tufts is not inside the container. Only /cluster/home is located within the container.
Singularity> exit # back to your regular shell prompt
To enable the container to access /cluster/tufts, we must bind the directory into the container.
$ singularity shell -B /cluster/tufts blast_2.15.0.sif
Singularity> ls /cluster/
home tufts
Singularity> cd /cluster/tufts/
Before using the PyTorch container for our analysis, let’s check if torch was successfully installed into the Python inside the container. We also need to ensure that we are using the correct Torch version, i.e., 2.1.2.
$ singularity shell pytorch_2.1.2-cuda11.8-cudnn8-runtime.sif
$ Singularity> python
Python 3.10.13 (main, Sep 11 2023, 13:44:35) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
>>> print(torch.__version__)
2.1.2
>>> quit()
Singularity> exit
$ exit # back to your regular shell prompt