add singularity it4i

docs.it4i/software/tools/singularity-it4i.md

+# Singularity on IT4Innovations
+
+On clusters we have different versions of operating systems images. Below you see the available operating systems images.
+
+```console
+   Salomon                      Anselm
+      ├── CentOS                  ├── CentOS
+      │   ├── 6.9                 │   ├── 6.9
+      │   ├── 6.9-shell           │   ├── 6.9-shell
+      │   ├── 6.9-MIC             │   ├── 6.9-GPU
+      │   ├── 6.9-MIC-shell       │   ├── 6.9-GPU-shell
+      │   ├── 7.3                 │   ├── 7.3
+      │   └── 7.3-shell           │   └── 7.3-shell
+      ├── Debian                  ├── Debian
+      │   ├── 8.0                 │   ├── 8.0
+      │   └── 8.0-shell           │   └── 8.0-shell
+      ├── Fedora                  ├── Fedora
+      │   ├── 26                  │   ├── 26
+      │   └── 26-shell            │   └── 26-shell
+      └── Ubuntu                  └── Ubuntu
+          ├── 16.04                   ├── 16.04
+          └── 16.04-shell             └── 16.04-shell
+```
+
+For current information on available images, refer to the `ml av` statement and the `OS`
+
+## Available operating systems images
+
+**Supported OS:**
+
+* CentOS
+* Debian
+* Ubuntu
+* Fedora
+
+**Supported features:**
+
+* GPU - graphics cards
+* MIC - Intel Xeon Phi cards
+
+**Type images**
+
+* classic
+* shell - automatics start shell after load module
+
+## IT4Innovations wrappers
+
+For using modules we prepared special wrappers
+
+* image-exec
+* image-load
+* image-mpi
+* image-run
+* image-shell
+* image-update
+
+**image-exec**
+
+Open image and run command into image.
+
+```console
+$ ml CentOS/7.3
+Your image of CentOS/7.3 is at location: /home/kru0052/.singularity/images/CentOS-7.3_20180220104046.img
+image-exec cat /etc/centos-release
+CentOS Linux release 7.3.1708 (Core)
+```
+
+**image-load**
+
+Settings and loading image. Script for `shell` modules.
+
+**image-mpi**
+
+MPI wrapper. More in the chapter [Examples MPI](#MPI)
+
+**image-run**
+
+Run subscript into image
+
+**image-shell**
+
+Start shell into image.
+
+```console
+$ ml CentOS/7.3
+$ image-shell
+Singularity: Invoking an interactive shell within container...
+
+Singularity CentOS-7.3_20180220104046.img:~>
+```
+
+**image-update**
+
+If a new image exists, it informs the user and offers an update.
+
+```console
+$ ml CentOS/6.9
+New version of CentOS image was found. (New: CentOS-6.9_20180220092823.img Old: CentOS-6.9_20170220092823.img)
+For updating image use: image-update
+Your image of CentOS/6.9 is at location: /home/login/.singularity/images/CentOS-6.9_20170220092823.img
+$ image-update
+New version of CentOS image was found. (New: CentOS-6.9_20180220092823.img Old: CentOS-6.9_20170220092823.img)
+Do you want to update local copy? (WARNING all user modification will be deleted) [y/N]: y
+Updating image  CentOS-6.9_20180220092823.img
+       2.71G 100%  199.49MB/s    0:00:12 (xfer#1, to-check=0/1)
+
+sent 2.71G bytes  received 31 bytes  163.98M bytes/sec
+total size is 2.71G  speedup is 1.00
+New version is ready. (/home/login/.singularity/images/CentOS-6.9_20180220092823.img)
+```
+
+## Examples
+
+In next examples, we will be using Singularity images on clusters.
+
+### Load image
+
+For classic image
+
+```console
+$ ml CentOS/6.9
+Your image of CentOS/6.9 is at location: /home/login/.singularity/images/CentOS-6.9_20180220133305.img
+```
+
+!!! note
+    First usage image copy image from /apps/all/OS/... to your /home (.singularity/images)
+
+For classic image, but autostart shell
+
+```console
+$ ml CentOS/6.9-shell
+Singularity: Invoking an interactive shell within container...
+
+Singularity CentOS-6.9_20180220133305.img:> exit
+exit
+Welcome to the normal operating system ()
+```
+
+For special image (GPU, MIC)
+
+```console
+$ ml CentOS/6.9-GPU
+
+```
+
+!!! note
+    For GPU image, you must allocate node with GPU card and for MIC image, you must allocate node with MIC cards.
+
+### MPI
+
+Submited job `qsub -A PROJECT -q qprod -l select=2:mpiprocs=24 -l walltime=00:30:00 -I`
+
+### MPI into image
+
+```console
+$ ml CentOS/6.9-shell
+Singularity: Invoking an interactive shell within container...
+
+Singularity CentOS-6.9_20180220092823.img:~> mpirun hostname | wc -l
+24
+```
+
+!!! warning
+    You allocate two nodes, but MPI into image use only one node.
+
+### MPI outside image
+
+```console
+$ ml CentOS/6.9
+Your image of CentOS/6.9 is at location: /home/kru0052/.singularity/images/CentOS-6.9_20180220092823.img
+$ image-mpi hostname | wc -l
+48
+```
+
+## Use own image on cluster
+
+1. Prepare image into your local computer
+1. Transfer image to your `/home` (for example `.singularity/image`)
+1. Load module Singularity (`ml Singularity`)
+1. Use your image
+
+## Edit IT4Innovations image
+
+1. Transfer image to your local computer
+1. Edit image
+1. Load module Singularity (`ml Singularity`)
+1. Use your image

mkdocs.yml

@@ -158,7 +158,9 @@ pages:
         - Setting License Preferences: software/tools/ansys/licensing.md
         - Licensing and Available Versions: software/tools/ansys/setting-license-preferences.md
       - EasyBuild: software/tools/easybuild.md
-      - Singularity Container: software/tools/singularity.md
+      - Singularity Container:
+        - Singularity: software/tools/singularity.md
+        - Singularity on IT4Innovations: software/tools/singularity-it4i.md
       - Spack: software/tools/spack.md
       - Virtualization: software/tools/virtualization.md
     - Visualisation: