Singularity draft

docs.it4i/software/singularity.md

+[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:
+
+```bash
+[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
+
+```bash
+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
+
+```bash
+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> 
+```

mkdocs.yml

@@ -63,6 +63,7 @@ pages:
   - 'Software':
     - Lmod Environment: software/lmod.md
     - Modules Matrix: modules-matrix.md
+    - Singularity Container: software/singularity.md  
     - Salomon Software:
       - Available Modules: modules-salomon.md
       - Available Modules on UV: modules-salomon-uv.md