Singularity Container
Singularity is a container platform suitable for HPC environments, similar to Docker, designed to implement OS virtualization. You can create a container image that includes the Linux distribution, compiler, and libraries suitable for your working environment, and then run the container to execute your application.
※ Virtual machines have a structure where applications run through a hypervisor and guest OS, whereas containers are closer to the physical hardware and share the host OS rather than using a separate guest OS, resulting in lower overhead. The use of containers in cloud services has been increasing recently
A. Build a container image
1. Load the Singularity Module or Set the Path
$ module load singularity/3.11.0
or
$ $HOME/.bash_profile
export PATH=$PATH:/apps/applications/singularity/3.11.0/bin/2. local build
To build a container image locally on the Nurion system's login node, you must first apply for the use of fakeroot by submitting a request through the KISTI website > Technical Support > Consultation Request with the following details.
System Name : Nurion
User ID : a000abc
Request : Singularity fakeroot usage setting
$ singularity [global options...] build [local options...] ＜IMAGE PATH＞ ＜BUILD SPEC＞
[Main global options]
-d : print debugging information
-v : print additional information
--version : print singularity version information
[Relevant key local options]
--fakeroot : Build image as fake root user by normal user without root permission
--remote : Remote build via external Singularity Cloud (Sylabs Cloud) (no root permission required)
--sandbox : Build a writable image directory in a sandbox format
＜IMAGE PATH＞
default : Default read-only image file (e.g. : ubuntu1.sif)
sandbox : A container with a readable and writable directory structure (e.g. : ubuntu4)
＜BUILD SPEC＞
definition file : A file that defines a recipe to build a container (Example : ubuntu.def)
local image : Singularity image file or sandbox directory (see IMAGE PATH)
URI
library:// container library (default https://cloud.sylabs.io/library)
docker:// docker registry (default docker hub)
shub:// singularity registry (default singularity hub)
oras:// OCI Registry
① Build ubuntu1.sif image from definition file
$ singularity build --fakeroot ubuntu1.sif ubuntu.def*
② Build ubuntu2.sif image from singularity library
$ singularity build --fakeroot ubuntu2.sif library://ubuntu:18.04
③ Build ubuntu3.sif image from Docker Hub
$ singularity build --fakeroot ubuntu3.sif docker://ubuntu:18.04
④ Building a PyTorch image optimized for Intel architecture from Docker Hub.
$ singularity build --fakeroot pytorch1.sif docker://intel/intel-optimized-pytorch:2.3.0-pip-multinode
⑤ Building a PyTorch image optimized for Intel architecture from a definition file.
$ singularity build --fakeroot pytorch2.sif pytorch.def**
* ) ubuntu.def example
bootstrap: docker
from: ubuntu:18.04
%post
apt-get update
apt-get install -y wget git bash gcc gfortran g++ make file
%runscript
echo "hello world from ubuntu container!"
** ) pytorch.def example
# Building an image from a local image file, including the installation of new packages using Conda
bootstrap: localimage
from: pytorch1.sif
%post
pip install scikit-image
# Build an image from Docker Hub, including the installation of new packages
bootstrap: docker
from: intel/intel-optimized-pytorch:2.3.0-pip-multinode
%post
pip install scikit-image3. Remote build
$ singularity build --remote ubuntu4.sif ubuntu.def
(Build the ubuntu4.sif image from a definition file using the remote build service provided by Sylabs Cloud)※ To use the remote build service provided by Sylabs Cloud (https://cloud.sylabs.io), an access token needs to be generated and registered on the Nurion system [Reference 1].
※ Additionally, the creation and management of Singularity container images can be done via a web browser by accessing Sylabs Cloud [Reference 2].
4. Importing/Exporting Container Images
$ singularity pull tensorflow.sif library://dxtr/default/hpc-tensorflow:0.1 (Import a container image from the Sylabs Cloud library)
$ singularity pull tensorflow.sif docker://tensorflow/tensorflow:latest (Import an image from Docker Hub and convert it to a Singularity image)
$ singularity push -U tensorflow.sif library://ID/default/tensorflow.sif (Export (upload) a Singularity image to the Sylabs Cloud library)※ To export (upload) an image to Sylabs Cloud (https://cloud.sylabs.io), you must generate an access token and register it on Nurion [Reference 1]
C. Running User Programs in a Singularity Container
1. Load the Singularity module or set the path
$ module load singularity/3.11.0
or
$ $HOME/.bash_profile
export PATH=$PATH:/apps/applications/singularity/3.11.0/bin/2. Command to run a program in a Singularity container
$ singularity [global options...] shell [shell options...] ＜container＞
$ singularity [global options...] exec [exec options...] ＜container＞ ＜command＞
$ singularity [global options...] run [run options...] ＜container＞
① Execute the shell within the Singularity container, then run the user program
$ singularity shell pytorch1.sif
Singularity> python test.py
② Run the user program in the Singularity container
$ singularity exec pytorch1.sif python test.py
$ singularity exec docker://intel/intel-optimized-pytorch:2.3.0-pip-multinode python test.py
$ singularity exec library://dxtr/default/hpc-tensorflow:0.1 python test.py
③ If a runscript (created during image build) exists in the Singularity container, this script will be executed.
If there is no runscript and a user command is entered after the container, the specified command will be executed.
$ singularity run ubuntu1.sif
hello world from ubuntu container!
$ singularity run pytorch1.sif python test.py 3. How to Run a Container via the Scheduler (PBS)
1) Write a job script to execute the task in batch mode
Run command : qsub＜job script file＞
[id@login01]$ qsub job_script.sh
14954055.pbs※ For detailed instructions on using the scheduler (PBS), refer to the Nurion Guide - Executing Jobs via Scheduler (PBS).
2) Example of a Job Script File
Serial job
* Run command : qsub＜job script file＞
#!/bin/sh
#PBS -N openfoam
#PBS -q normal
#PBS -A openfoam
#PBS -V
#PBS -j oe
#PBS -W sandbox=PRIVATE
#PBS -m e
#PBS -M wjnadia@kisti.re.kr
#PBS -r y
#PBS -l select=1:ncpus=1:mpiprocs=1:ompthreads=1
#PBS -l walltime=00:30:00
cd $PBS_O_WORKDIR
module load singularity/3.11.0
cd cavity
singularity run openfoam-default:2312.sif icoFoamSerial job
* Run command: mpirun singularity run <container> [user program execution command]
#!/bin/sh
#PBS -N openfoam
#PBS -q normal
#PBS -A openfoam
#PBS -V
#PBS -j oe
#PBS -W sandbox=PRIVATE
#PBS -m e
#PBS -M wjnadia@kisti.re.kr
#PBS -r y
#PBS -l select=2:ncpus=64:mpiprocs=64:ompthreads=1
#PBS -l walltime=00:30:00
cd $PBS_O_WORKDIR
module load singularity/3.11.0 gcc/8.3.0 openmpi/3.1.0
cd cavity
mpirun singularity run openfoam-default:2312.sif icoFoam※ Example of using 2 nodes with 64 tasks per node (total of 128 MPI processes)
3) Executing interactive jobs on compute nodes allocated by the scheduler
Example of running a parallel program (OpenMPI)
[id@login01]$ qsub -I -l select=2:ncpus=64:mpiprocs=64:ompthreads=1 -l walltime=00:30:00 \
-q normal -A openfoam
qsub: waiting for job 14954204.pbs to start
qsub: job 14954204.pbs ready
[id@node1000]$
[id@node1000]$ module load singularity/3.11.0 gcc/8.3.0 openmpi/3.1.0
[id@node1000]$ cd cavity
[id@node1000]$ mpirun singularity run openfoam-default:2312.sif icoFoam Example of running a TensorFlow program
$ qsub -I -V -l select=1:ncpus=68:ompthreads=68 \
-l walltime=12:00:00 -q normal -A tf
$ export OMP_NUM_THREADS=68; singularity exec tensorflow-1.12.0-py3.simg python convolutional.py※ Example Singularity image file location: /apps/applications/tensorflow/1.12.0/tensorflow-1.12.0-py3.simg
※ Example convolutional.py file location: /apps/applications/tensorflow/1.12.0/examples/convolutional.py
D. References
[Reference 1] Generating a Sylabs Cloud access token and registering on Nurion
[Reference 2] Building a Singularity container image using a remote builder via a web browser
※ Includes a list of images remotely built with singularity commands in Nurion
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