---
title: Apptainer
---
[toc]
## Environment Settings{#enviroment}
### Software Version and System Requirements{#version}
The Apptainer shown in the table below is available.
As it is provided as a package that comes with the operating system, there is no need to set the environment with module files.
|Version | Module File Name | System B/C | System G | Cloud System | Note
|--- | --- | --- | --- | --- | ---
|1.1.2 | none | + | + | + | Former name:singularity
\+ ： Available for all users
\- ： Not available
## How to Use{#usage}
1. Create a job script (`test.sh`) to run a program (`a.out`) that performs hybrid parallelism, using a container image called `ubuntu.sif`.
```nohighlight
#!/bin/bash
#============ Slurm Options
#SBATCH -p gr19999b # Specify the job queue (partition). The name of the queue to be submitted needs to be changed accordingly.
#SBATCH -t 1:00:00 # Specify the elapsed time (example: to specify one hour).
#SBATCH --rsc p=2:c=40 # Specifying the required resources (example: hybrid parallel using 2 processes and 40 cores).
#SBATCH -o %x.%j.out # Specify the standard output file of the job. %x is replaced by the job name and %j by the job ID.
#============ Shell Script ============
set -x
## When you do not use GPU
srun apptainer exec --bind `pwd`,/opt/system,/usr/lib64 --env LD_LIBRARY_PATH=/usr/lib64 ubuntu.sif ./a.out
## When you use GPU (Adding --nv makes it GPU-compatible.)
srun apptainer exec --nv --bind `pwd`,/opt/system,/usr/lib64 --env LD_LIBRARY_PATH=/usr/lib64 ubuntu.sif ./a.out
```
#### Main Option
|Option | Meaning | Example
|---------- | ----------- | ----------- |
| --bind _MOUNT\_DIR_ | Specify the to mount.| --bind /LARGE0,LARGE1,/opt/system,/usr/lib64 |
| --env _ENVIRONMENT_ | Specify the environment variables | --env LD_LIBRARY_PATH=/usr/lib64 |
| --nv | Add when you use GPU.| --nv |
2. Job submission using the job script created in 1.
```nohighlight
$ sbatch test.sh
Submitted batch job {jobid}
```
3. Confirmation of execution results .
```nohighlight
$ cat test.sh.{jobid}.out
================ Slrum Info ================
DATE = 2023-03-08T14:38:10+09:00
PARTITION = gr19999d
JOB_ID = {jobid}
JOB_NAME = test.sh
NNODES = 1
RSC_OPT = p=1:t=8:c=8:m=8G
============================================
_________
< hello!! >
---------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
```
## How to create container images
### Create a new container image for Apptainer (Singurarity)
Here, we use the ubuntu22.04 docker image as the base package and create a container image of python3 and tensorflow installed.
1. Create a recipe file to generate the container and save it as `ubuntu22_tensorflow.def`.
```nohighlight
Bootstrap: docker
From: ubuntu:22.04
%post
apt-get update
apt-get install -y python3 python3-pip
pip3 install tensorflow
```
2. Execute a build of the container image using the recipe file (`ubunutu22_tensorflow.def`) generated in 1.The container image is saved as `ubuntu22_tensorflow.sif`.
```nohighlight
$ apptainer build --fakeroot {Container image storage location} {Recipe files for generating container images.}
(Example)
$ apptainer build --fakeroot ~/ubuntu22_tensorflow.sif ubuntu22_tensorflow.def
INFO: Starting build...
Getting image source signatures
(snip)
INFO: Creating SIF file...
INFO: Build complete: ubuntu22_tensorflow.sif
```
* The destination of the container image should be set under the home directory.
If the destination is set to a large disk, the container image will fail to build.
3. Operation Check
```nohighlight
## Start the container.
$ apptainer shell ~/ubuntu22_tensorflow.sif
## Launch the Python 3
Apptainer> python3
Python 3.10.6 (main, Nov 14 2022, 16:10:14) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
## Check the operation of Tensorflow
>>> import tensorflow as tf
>>> tf.__version__
'2.11.0'
```
### Use the container images uploaded to DockerHub.
1. Translate to the directory where the Apptainer container image is stored.
```nohighlight
$ cd container_image
```
2. Download and build a container image from DockerHub
```nohighlight
$ apptainer build lolcow.sif docker://godlovedc/lolcow
INFO: Starting build...
Getting image source signatures
(snip)
INFO: Creating SIF file...
INFO: Build complete: lolcow.sif
```
* If "Build failed", please try building again.
3.Confirm that the container image has been created.
```nohighlight
$ ls lolcow.sif
lolcow.sif
```