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-MIC             │   ├── 6.9-GPU
      │   └── 7.3                 │   └── 7.3
      ├── Debian                  ├── Debian
      │   └── 8.0                 │   └── 8.0
      ├── Fedora                  ├── Fedora
      │   └── 26                  │   └── 26
      └── Ubuntu                  └── Ubuntu
          └── 16.04                   └── 16.04
```

For current information on available images, refer to the `ml av` and see statement the `OS`

## Available Operating Systems Images

On IT4Innovations clusters we support different operating system.

**Supported OS:**

* CentOS
* Debian
* Ubuntu
* Fedora

**Supported features:**

* GPU - graphics cards
* MIC - Intel Xeon Phi cards

## IT4Innovations Wrappers

For using modules we prepared special wrappers

* image-exec
* 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-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 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
$ image-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. Transfer image from your local computer to cluster /home
1. Load module Singularity (`ml Singularity`)
1. Use your image