Singularity Containers

At IDIA, astronomical software packages are provided and managed using Singularity containers. Containers are managed and built by our developers. If you have any questions/issues relating to containers, please send an email to support@ilifu.ac.za. You can find more documentation about containers on Ilifu here.

Available Containers

The most recent, stable versions of containers are available in /idia/software/containers/. Some of these containers can be accessed via JupyterHub, but all of them can be accessed via the terminal (i.e., once you’ve ssh’d into an IDIA machine). Some additional CASA-specific information can be found here.

Here are a few examples of the latest stable Singularity container builds that are available in /idia/software/containers/:

casa-6.5.0-modular.sif
- Contains the modular CASA 6.5 install, which can be accessed via Python using import casatools etc.
kern7.simg
- Contains all the software packages provided by the Kern repository.
ASTRO-PY3.simg
- Builds of commonly used source finding packages, e.g., PyBDSF.

Reporting a bug / Requesting Software

Please send an email to support@ilifu.ac.za to report issues, or to request new containers, or for existing containers to be updated.

Using Containers

Shell

You can access software in Singularity containers using two methods.

Firstly, you can shell into the container. You will enter a shell which provides access to the software provided in that container:

$ singularity shell /idia/software/containers/casa-stable-5.3.0.simg
Singularity: Invoking an interactive shell within container...

Singularity casa-stable-5.3.0.simg:~> casa --nologger --log2term --nogui

=========================================
The start-up time of CASA may vary
depending on whether the shared libraries
are cached or not.
=========================================

IPython 5.1.0 -- An enhanced Interactive Python.

CASA 5.3.0-143   -- Common Astronomy Software Applications

2018-08-07 12:37:28	INFO	::casa	CASA Version 5.3.0-143
--> CrashReporter initialized.
Enter doc('start') for help getting started with CASA...
Using matplotlib backend: TkAgg

CASA <1>: print "Hello World"
Hello World

Exec

You can also pass a command to a container (using the exec argument), which then gets executed via the shell in that container.

For example, here’s an illustration of how to use the exec argument to jump into an interactive CASA session:

$ singularity exec /idia/software/containers/casa-stable-5.3.0.simg casa --nologger --log2term --nogui

=========================================
The start-up time of CASA may vary
depending on whether the shared libraries
are cached or not.
=========================================

IPython 5.1.0 -- An enhanced Interactive Python.

CASA 5.3.0-143   -- Common Astronomy Software Applications

2018-08-07 12:41:19	INFO	::casa	CASA Version 5.3.0-143
--> CrashReporter initialized.
Enter doc('start') for help getting started with CASA...
Using matplotlib backend: TkAgg
CASA <1>: inp listobs
--------> inp(listobs)
#  listobs :: List the summary of a data set in the logger or in a file
vis                 =         ''        #  Name of input visibility file (MS)
selectdata          =       True        #  Data selection parameters
     field          =         ''        #  Selection based on field names or field index numbers. Default is all.
     spw            =         ''        #  Selection based on spectral-window/frequency/channel.
     antenna        =         ''        #  Selection based on antenna/baselines. Default is all.
     timerange      =         ''        #  Selection based on time range. Default is entire range.
     correlation    =         ''        #  Selection based on correlation. Default is all.
     scan           =         ''        #  Selection based on scan numbers. Default is all.
     intent         =         ''        #  Selection based on observation intent. Default is all.
     feed           =         ''        #  Selection based on multi-feed numbers: Not yet implemented
     array          =         ''        #  Selection based on (sub)array numbers. Default is all.
     uvrange        =         ''        #  Selection based on uv range. Default: entire range. Default units: meters.
     observation    =         ''        #  Selection based on observation ID. Default is all.

verbose             =       True        #  Controls level of information detail reported. True reports more than False.
listfile            =         ''        #  Name of disk file to write output. Default is none (output is written to logger only).
listunfl            =      False        #  List unflagged row counts? If true, it can have significant negative performance impact.
cachesize           =         50        #  EXPERIMENTAL. Maximum size in megabytes of cache in which data structures can be held.
CASA <2>:

The true utility of the exec argument is to execute commands non-interactively:

$ singularity exec /idia/software/containers/casa-stable-5.3.0.simg casa --nologger --log2term --nogui -c "print 'Hello World'"

=========================================
The start-up time of CASA may vary
depending on whether the shared libraries
are cached or not.
=========================================

IPython 5.1.0 -- An enhanced Interactive Python.

CASA 5.3.0-143   -- Common Astronomy Software Applications

2018-08-07 12:45:43	INFO	::casa	CASA Version 5.3.0-143
--> CrashReporter initialized.
Hello World
$

While the command may seem cumbersome, it is very useful when trying to build scripts that utilise several containers.