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docs.it4i/software/singularity.md 0 → 100644
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[Singularity](http://singularity.lbl.gov/) enables users to have full control of their environment. A non-privileged user can "swap out" the operating system on the host for one they control. So if the host system is running RHEL6 but your application runs in Ubuntu/RHEL7, you can create an Ubuntu/RHEL7 image, install your applications into that image, copy the image to another host, and run your application on that host in it’s native Ubuntu/RHEL7 environment.
Singularity also allows you to leverage the resources of whatever host you are on. This includes HPC interconnects, resource managers, file systems, GPUs and/or accelerators, etc. Singularity does this by enabling several key facets:
* Encapsulation of the environment
* Containers are image based
* No user contextual changes or root escalation allowed
* No root owned daemon processes
## Using Docker Images
Singularity can import, bootstrap, and even run Docker images directly from [Docker Hub](https://hub.docker.com/). You can easily run RHEL7 like this:
```console
[hrb33@r33u01n865 ~]$ cat /etc/redhat-release
CentOS release 6.7 (Final)
[hrb33@r33u01n865 ~]$ ml Singularity
[hrb33@r33u01n865 ~]$ singularity shell docker://centos:latest
library/centos:latest
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:45a2e645736c4c66ef34acce2407ded21f7a9b231199d3b92d6c9776df264729
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Singularity: Invoking an interactive shell within container...
Singularity.centos:latest> cat /etc/redhat-release
CentOS Linux release 7.3.1611 (Core)
```
## Creating Own Image from Docker Image
```console
hrb33@hrb33-toshiba:/$ cd /tmp/
hrb33@hrb33-toshiba:/tmp$ sudo singularity create /tmp/c7.img
[sudo] password for hrb33:
Creating a new image with a maximum size of 768MiB...
Executing image create helper
Formatting image with ext3 file system
Done.
hrb33@hrb33-toshiba:/tmp$ sudo singularity import c7.img docker://centos:latest
library/centos:latest
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:45a2e645736c4c66ef34acce2407ded21f7a9b231199d3b92d6c9776df264729
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Adding Docker CMD as Singularity runscript...
Bootstrap initialization
No bootstrap definition passed, updating container
Executing Prebootstrap module
Executing Postbootstrap module
Done.
hrb33@hrb33-toshiba:/tmp$ sudo singularity shell --writable c7.img
Singularity: Invoking an interactive shell within container...
Singularity.c7.img> mkdir /apps /scratch
Singularity.c7.img> exit
hrb33@hrb33-toshiba:/tmp$ rsync -av c7.img hrb33@login4.salomon:/home/hrb33/c7.img
sending incremental file list
c7.img
sent 805,503,090 bytes received 34 bytes 9,205,749.99 bytes/sec
total size is 805,306,399 speedup is 1.00
```
Accessing /HOME and /SCRATCH Within Container
```console
hrb33@hrb33-toshiba:/tmp$ ssh hrb33@login4.salomon
_____ _
/ ____| | |
| (___ __ _| | ___ _ __ ___ ___ _ __
\___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \
____) | (_| | | (_) | | | | | | (_) | | | |
|_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|
http://www.it4i.cz/?lang=en
Last login: Fri Feb 10 14:38:36 2017 from 10.0.131.12
[hrb33@login4.salomon ~]$ ml Singularity
[hrb33@login4.salomon ~]$ singularity shell --bind /scratch --bind /apps --writable c7.img
Singularity: Invoking an interactive shell within container...
Singularity.c7.img> ls /apps/ -l
total 68
drwx------ 4 root root 29 Sep 29 10:28 SCS
drwxrwxr-x 301 2757 2796 8192 Feb 16 10:58 all
drwxrwxr-x 3 2757 2796 19 Jul 9 2015 base
drwxrwxr-x 16 2757 2796 4096 Nov 24 21:47 bio
drwxrwxr-x 10 2757 2796 116 Apr 8 2016 cae
drwxrwxr-x 18 2757 2796 4096 Jan 17 09:49 chem
drwxrwxr-x 11 2757 2796 122 Dec 7 09:25 compiler
drwxrwxr-x 7 2757 2796 73 Jun 29 2016 data
drwxr-xr-x 7 2757 2796 88 Jan 8 2016 debugger
drwxrwxr-x 38 2757 2796 4096 Feb 16 13:37 devel
drwxrwxr-x 9 2757 2796 130 Jan 9 08:40 easybuild
drwxr-xr-x 11 3900 4011 4096 Feb 15 09:50 gentoo
drwxr-xr-x 10 3900 4011 4096 Feb 10 17:01 gentoo_uv
drwxrwxr-x 5 2757 2796 39 Jan 18 2016 geo
drwxr-xr-x 18 2757 2796 4096 Sep 6 16:03 intel2017
drwxrwxr-x 20 2757 2796 4096 Nov 28 08:50 lang
drwxrwxr-x 31 2757 2796 4096 Dec 7 07:48 lib
drwxrwxr-x 4 2757 2796 32 Nov 9 09:19 licenses
drwxrwxr-x 17 2757 2796 4096 Nov 15 09:24 math
drwxr-xr-x 22 2757 2796 4096 Jan 19 13:15 modules
drwxrwxr-x 8 2757 2796 82 Apr 18 2016 mpi
drwxrwxr-x 13 2757 2796 4096 Oct 24 09:08 numlib
drwxrwxr-x 10 2757 2796 108 Feb 3 11:01 perf
drwxrwxr-x 5 2757 2796 41 Jan 17 09:49 phys
drwxrwxr-x 2 2757 2796 6 Feb 3 11:01 prace
drwxr-xr-x 4 root root 36 Jun 18 2015 sw
drwxrwxr-x 5 2757 2796 49 Feb 15 2016 system
drwxr-xr-x 3 root root 19 Dec 4 2015 test
drwxrwxr-x 13 2757 2796 138 May 31 2016 toolchain
drwxrwxr-x 39 2757 2796 4096 Feb 3 11:27 tools
drwxr-xr-x 4 root root 31 Aug 11 2015 user
drwxrwxr-x 21 2757 2796 4096 Jan 5 18:56 uv
drwxrwxr-x 40 2757 2796 4096 Feb 3 11:01 vis
Singularity.c7.img> ls /scratch/ -l
total 32
drwx------ 3 root root 4096 Aug 15 2016 backup
drwxr-x--- 2 root root 4096 Dec 5 10:34 sys
drwxrwxrwt 154 root root 20480 Feb 14 14:03 temp
drwxr-xr-x 4 root root 4096 Jan 25 10:48 work
Singularity.c7.img>
```