2 SCUBA-2 Pipeline Variants

There are three variants of the SCUBA-2 pipeline, users will likly only need to run the science pipeline. The other two pipelines are designed to run in real time at the JCMT.

• The science pipeline has access to all the data observed for a given project and adopts a best-possible reduction approach. Images are made for each complete observation which are combined to create the final image.
• The quick-look (QL) pipeline is primarily designed to perform quality-assurance analysis of the incoming data for real-time assessment of the instrument performance. It is also responsible for processing pointing and focus data.
• The summit pipeline runs in parallel with the QL pipeline (though on a different machine) and is the primary image-processing pipeline. Processing is delayed until sufficient data exist to produce a higher quality image. In practice this happens after a certain time has elapsed since an image was last made.

2.1 Requirements for running the SCUBA-2 pipeline

The SCUBA-2 pipeline requires a recent Starlink installation. The latest version may be obtained from http://starlink.eao.hawaii.edu/starlink. Since development of the pipeline is an ongoing process, it is recommended that the newest builds be used to access the full capabilities of the pipeline. These builds can be obtained from
http://starlink.eao.hawaii.edu/starlink/rsyncStarlink and may be kept up-to-date with rsync.

The Starlink Perl installation (Starperl) must be used to run the pipeline due to the module requirements. The Starlink environment should be initialized as usual before running Orac-dr.

The software used to process raw data into images is called the SubMillimetre User Reduction Facility (Smurf). Detailed documentation on Smurf can be found in SUN/258, while SC/21 is a cookbook that describes some of the background to SCUBA-2 data reduction.

The pipeline uses the following Starlink applications:

• Smurf
• Kappa
• Fluxes
• Figaro
• Ccdpack
• Cupid

2.2 Important environment variables

The pipeline uses a number of environment variables to determine where data should be read from and written to. Some are set automatically when the pipeline is initialized, but they can be overridden manually and, with the -honour flag may be left unchanged between successive runs of the pipeline. The variables that must be defined in order for the pipeline to run are denoted as ‘Mandatory’ in the list below.

• STARLINK_DIR: location of the user’s Starlink installation. [Mandatory]
• ORAC_DATA_IN: the location where data are read from. If running with -loop flag, this is the location of the flag files, rather than the data files. [Mandatory]
• ORAC_DATA_OUT: location where pipeline data products are written. Also used as a location for user-specified configuration files for makemap. [Mandatory]
• ORAC_DATA_ROOT: root location for data. At the JCMT, this is /jcmtdata/raw/scuba2. If not defined, the current directory is assumed. [Optional]
• MAKEMAP_CONFIG_DIR: a user-specified location for makemap configuration files. [Optional]
• FINDCLUMPS_CONFIG_DIR: a user-specified location for findclumps configuration files. [Optional]

As an example, to set up or override the pipeline environment variables, tcsh users will need to do:

and bash users will need to do:

2.3 Getting help

Basic help and a list of command-line options may be obtained after initializing Orac-dr by running :

or

More complete documentation on Orac-dr can be found in SUN/230.