# Singularity

###### tags: `container` `singularity`

Introduction of the singularity 
- Reproducible software stacks
- Mobility of compute
- Compatibility with complicated architectures
- Security model

Singularity has two primary roles: 
- Container Image Generator
- Container Runtime

Singularity supported formats types. 
- compressed read-only ​squashfs​ file system suitable for production (default)
- writable ​ext3​ file system suitable for interactive development (--writable option)
- writable (ch)root directory called a ​sandbox​ for interactive development (--sandbox option)

Singularity-Hub 
https://singularityhub.github.io/containers/registry/singularity-hub-registry/

Installation on ubuntu 16.10 yakkety release 
apt-get update; apt-get install -y git autoconf libtool python make
git clone ​https://github.com/singularityware/singularity.git
cd singularity/
git checkout 2.4.1

./autogen.sh
./configure --prefix=/usr/local
make
make install

Basic usage of singularity  
root@singularity:~# singularity --help USAGE: singularity [global options...] <command> [command options...] ...

GLOBAL OPTIONS:
     -d|--debug    Print debugging information
     -h|--help     Display usage summary
     -s|--silent   Only print errors
     -q|--quiet    Suppress all normal output
        --version  Show application version
     -v|--verbose  Increase verbosity +1
     -x|--sh-debug Print shell wrapper debugging information

GENERAL COMMANDS:
     help       Show additional help for a command or container
     selftest   Run some self tests for singularity install 

CONTAINER USAGE COMMANDS:
    exec       Execute a command within container 
    run        Launch a runscript within container 
    shell      Run a Bourne shell within container
    test       Launch a testscript within container 

CONTAINER MANAGEMENT COMMANDS: 
   apps       List available apps within a container
   bootstrap  *Deprecated* use build instead 
   build      Build a new Singularity container   
   check      Perform container lint checks 
   inspect    Display container's metadata 
   mount      Mount a Singularity container image 
   pull       Pull a Singularity/Docker container to $PWD 

COMMAND GROUPS: 
   image      Container image command group 
   instance   Persistent instance command group 


CONTAINER USAGE OPTIONS: 
   see singularity help <command>

For any additional help or support visit the Singularity
website: http://singularity.lbl.gov/

[ pull a singularity image (squashfs) for singularity hub ] 
root@singularity:~# singularity pull --name hello-world.simg shub://vsoch/hello-world
Progress |===================================| 100.0% 
Done. Container is at: /root/hello-world.simg
root@singularity:~# file  ./hello-world.simg 
./hello-world.simg: a /usr/bin/env run-singularity script executable (binary data)

[ run the singularity image ] 
root@singularity:~# ./hello-world.simg 
RaawwWWWWWRRRR!!
root@singularity:~# singularity run hello-world.simg 
RaawwWWWWWRRRR!!

[ get shell in the singularity image ] 
root@singularity:~# singularity shell hello-world.simg 
Singularity: Invoking an interactive shell within container...

Singularity hello-world.simg:~> df
Filesystem     1K-blocks    Used Available Use% Mounted on
OverlayFS        1023824       0   1023824   0% /
/dev/sda1       18447056 2635152  14851804  16%
/tmp udev             1002248       0   1002248   0%
/dev tmpfs            1023824       0   1023824   0% /dev/shm
tmpfs             204768    3328    201440   2% /etc/resolv.conf

Singularity hello-world.simg:~> cat /etc/os-release 
NAME="Ubuntu"
VERSION="14.04.5 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.5 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/" BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"

[ bind an path in the singularity image and access it ] 
root@singularity:~# cat /data/vader.sez
I am your father
root@singularity:~# singularity exec --bind /data:/mnt hello-world.simg cat /mnt/vader.sez
I am your father

[ build singularity container in sandbox directory ] 
root@singularity:~# singularity build --sandbox ubuntu/ docker://ubuntu
Docker image path: index.docker.io/library/ubuntu:latest
Cache folder set to /root/.singularity/docker
Importing: base Singularity environment
Importing: /root/.singularity/docker/sha256:660c48dd555dcbfdfe19c80a30f557ac57a15f595250e67bfad1e5663c1725bb.tar.gz
Importing: /root/.singularity/docker/sha256:4c7380416e7816a5ab1f840482c9c3ca8de58c6f3ee7f95e55ad299abbfe599f.tar.gz
Importing: /root/.singularity/docker/sha256:421e436b5f80d876128b74139531693be9b4e59e4f1081c9a3c379c95094e375.tar.gz
Importing: /root/.singularity/docker/sha256:e4ce6c3651b3a090bb43688f512f687ea6e3e533132bcbc4a83fb97e7046cea3.tar.gz
Importing: /root/.singularity/docker/sha256:be588e74bd348ce48bb7161350f4b9d783c331f37a853a80b0b4abc0a33c569e.tar.gz
Importing: /root/.singularity/metadata/sha256:c6a9ef4b9995d615851d7786fbc2fe72f72321bee1a87d66919b881a0336525a.tar.gz
Singularity container built: ubuntu/
Cleaning up…

root@singularity:~# ls -l ./ubuntu
total 76
drwxr-xr-x  2 root root 4096 Nov 14 21:49 bin
drwxr-xr-x  2 root root 4096 Apr 13  2016 boot
drwxr-xr-x  2 root root 4096 Nov 14 21:48 dev
lrwxrwxrwx  1 root root   36 Dec  4 11:34 environment -> .singularity.d/env/90-environment.sh
drwxr-xr-x 42 root root 4096 Nov 18 05:59 etc
drwxr-xr-x  2 root root 4096 Apr 13  2016 home
drwxr-xr-x  8 root root 4096 Sep 13  2015 lib
drwxr-xr-x  2 root root 4096 Nov 14 21:49 lib64
drwxr-xr-x  2 root root 4096 Nov 14 21:48 media
drwxr-xr-x  2 root root 4096 Nov 14 21:48 mnt
drwxr-xr-x  2 root root 4096 Nov 14 21:48 opt
drwxr-xr-x  2 root root 4096 Apr 13  2016 proc
drwx------  2 root root 4096 Nov 14 21:49 root
drwxr-xr-x  5 root root 4096 Nov 14 21:49 run
drwxr-xr-x  2 root root 4096 Nov 18 05:59 sbin
lrwxrwxrwx  1 root root   24 Dec  4 11:34 singularity -> .singularity.d/runscript
drwxr-xr-x  2 root root 4096 Nov 14 21:48 srv
drwxr-xr-x  2 root root 4096 Feb  5  2016 sys
drwxrwxrwt  2 root root 4096 Nov 14 21:49 tmp
drwxr-xr-x 10 root root 4096 Nov 14 21:48 usr
drwxr-xr-x 11 root root 4096 Nov 14 21:49 var

[ build singularity container in writable image  ] 
root@singularity:~# singularity build --writable ubuntu.img docker://ubuntu
Building into existing container: ubuntu.img
Docker image path: index.docker.io/library/ubuntu:latest
Cache folder set to /root/.singularity/docker
Importing: base Singularity environment
Importing: /root/.singularity/docker/sha256:660c48dd555dcbfdfe19c80a30f557ac57a15f595250e67bfad1e5663c1725bb.tar.gz
Importing: /root/.singularity/docker/sha256:4c7380416e7816a5ab1f840482c9c3ca8de58c6f3ee7f95e55ad299abbfe599f.tar.gz
Importing: /root/.singularity/docker/sha256:421e436b5f80d876128b74139531693be9b4e59e4f1081c9a3c379c95094e375.tar.gz
Importing: /root/.singularity/docker/sha256:e4ce6c3651b3a090bb43688f512f687ea6e3e533132bcbc4a83fb97e7046cea3.tar.gz
Importing: /root/.singularity/docker/sha256:be588e74bd348ce48bb7161350f4b9d783c331f37a853a80b0b4abc0a33c569e.tar.gz
Importing: /root/.singularity/metadata/sha256:c6a9ef4b9995d615851d7786fbc2fe72f72321bee1a87d66919b881a0336525a.tar.gz
Building Singularity image...
Singularity container built: ubuntu.img
Cleaning up...
root@singularity:~# singularity shell --writable ./ubuntu.img
Singularity: Invoking an interactive shell within container...

Singularity ubuntu.img:~>

root@singularity:~# singularity shell ./ubuntu.img
Singularity: Invoking an interactive shell within container...

Singularity ubuntu.img:~> touch /file2
Singularity ubuntu.img:~> ls -l /file*
-rw-r--r-- 1 root root 0 Dec  5 06:05 /file1
-rw-r--r-- 1 root root 0 Dec  5 06:06 /file2
Singularity ubuntu.img:~> exit
exit

root@singularity:~# singularity exec ./ubuntu.img ls -l /file1
-rw-r--r-- 1 root root 0 Dec  5 06:05 /file1
root@singularity:~# singularity exec ./ubuntu.img ls -l /file2
ls: cannot access '/file2': No such file or directory

[ convert container format ] 
root@singularity:~# singularity build --writable writable-hello-world.img hello-world.simg 
Building from local image: hello-world.simg
Creating empty Singularity writable container 208MB
Creating empty 260MiB image file: writable-hello-world.img
Formatting image with ext3 file system
Image is done: writable-hello-world.img
Building Singularity image...
Singularity container built: writable-hello-world.img
Cleaning up...

root@singularity:~# singularity build ubuntu.simg ubuntu
Building image from sandbox: ubuntu
Building Singularity image...
Singularity container built: ubuntu.simg
Cleaning up...

[ build container from singularity rceipe file ] 
root@singularity:~# cat ./recipe 
Bootstrap: shub
From: singularityhub/hello-world

%runscript 
   exec echo "The runscript is the containers default runtime command!"

%files
   /home/ycheng/party_dinosaur.gif     /opt/the-party-dino.gif #

%environment 
   VARIABLE=MEATBALLVALUE     export VARIABLE

%labels
   AUTHOR [e-mail]

%post 
   apt-get update && apt-get -y install python3 git wget 
   mkdir /data 
   echo "The post section is where you can install, and configure your container."

root@singularity:~# singularity build recipe-hello-world.simg recipe 
Using container recipe deffile: recipe
Sanitizing environment
Adding base Singularity environment to container
Progress |===================================| 100.0% 
Exporting contents of shub://singularityhub/hello-world to /tmp/.singularity-build.4WKf8n
User defined %runscript found! Taking priority.
Adding files to container
Copying '/home/ycheng/party_dinosaur.gif' to '/opt/the-party-dino.gif'
Adding environment to container
Running post scriptlet
+ apt-get update
Ign http://archive.ubuntu.com trusty InRelease
Get:1 http://security.ubuntu.com trusty-security InRelease [65.9 kB]
Get:2 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
Get:3 http://security.ubuntu.com trusty-security/universe Sources [80.6 kB]
Get:4 http://archive.ubuntu.com trusty-backports InRelease [65.9 kB]
Get:5 http://security.ubuntu.com trusty-security/main amd64 Packages [859 kB]
Hit http://archive.ubuntu.com trusty Release.gpg 
…..

[ run nginx service in singularity ] 
root@singularity:~# cat ./startscript 
%startscript

service nginx start

root@singularity:~# cat ./recipe-nginx 
Bootstrap: shub
From: singularityhub/hello-world

%runscript
    exec echo "The runscript is the containers default runtime command!"

%files
    /root/startscript     /root/startscript

%environment
    VARIABLE=MEATBALLVALUE     export VARIABLE

%labels
    AUTHOR [e-mail]

%post
    apt-get update && apt-get -y install nginx
    mkdir /data
    echo "The post section is where you can install, and configure your container."

%startscript
    service nginx start

root@singularity:~# singularity build recipe-nginx.simg recipe-nginx
Using container recipe deffile: recipe-nginx
Sanitizing environment
Adding base Singularity environment to container
Progress |===================================| 100.0% 
Exporting contents of shub://singularityhub/hello-world to /tmp/.singularity-build.hMXwK7
User defined %runscript found! Taking priority.
Adding files to container
Copying '/root/startscript' to '/root/startscript'
Adding environment to container
Running post scriptlet
+ apt-get update
Ign http://archive.ubuntu.com trusty InRelease
Get:1 http://security.ubuntu.com trusty-security InRelease [65.9 kB]
Get:2 http://archive.ubuntu.com trusty-updates InRelease [65.9 kB]
Get:3 http://security.ubuntu.com trusty-security/universe Sources [80.6 kB]

…..

root@singularity:~# ls -l ./recipe-nginx.simg 
-rwxr-xr-x 1 root root 87392287 Dec  5 15:17 ./recipe-nginx.simg

root@singularity:~# singularity instance.start recipe-nginx.simg nginx
root@singularity:~# singularity instance.list
DAEMON NAME      PID      CONTAINER IMAGE
nginx            7985     /root/recipe-nginx.simg

root@singularity:~# ps -elf | grep 7985
5 S root      7985     1  0  80   0 -  3489 sigtim 15:20 ?        00:00:00 singularity-instance: root [nginx]
5 S root      8001  7985  0  80   0 - 21476 sigsus 15:20 ?        00:00:00 nginx: master process /usr/sbin/nginx
0 R root      8047  2136  0  80   0 -  3550 -      15:28 pts/0    00:00:00 grep --color=auto 7985

root@singularity:~# netstat -antlp | grep nginx
tcp        0      0 0.0.0.0:80              0.0.0.0:*               LISTEN      8001/nginx: master 
tcp6       0      0 :::80                   :::*                    LISTEN      8001/nginx: master
! you might use “instance.stop <name of instance>” to stop the singularity instance