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Comment: add container lists

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The Garrawarla cluster doesn't mount /group so you'll have to ensure that your code is in /astro if you want to access it. Since most of our software was in /group we have started porting the software to singularity containers in /pawsey/mwa, which is mounted on Garrawarla.

To use containers:

  • Do Load the singularity module using
    • `module load singularity`
    so you can run singularity
  • Choose the container that you want to run:
    • They are stored in /pawsey/mwa/singularity/<container_name>
    • See /pawsey/mwa/singularity/README.md for an overview of which containers contain which software
  • Run the container via (example)
    • singularity exec -B $PWD /pawsey/mwa/singularity/wsclean/wsclean_2.9.2.img wsclean
  • See the Pawsey support page for more info about singularity
  • Contact one of the container maintainers if you have questions about a specific container (See the README.md file)

Containers and their contents for people who are migrating away from MWA_tools module:

The following containers are likely to be useful to MWASCI members as a replacement for the MWA_Tools module that used to work on Magnus/Zeus. MWA_Tools module doesn't work any more because of changes that pawsey have made to the available modules and versions (mostly python issues). The MWA_Tools module will not be resurrected.

Container imagesoftware within container
/pawsey/mwa/singularity/casa/casa.imgcasa casaviewer 
/pawsey/mwa/singularity/cotter/cotter_latest.sifaoflagger aoqplot aoquality cotter fixmwams rfigui
/pawsey/mwa/singularity/wsclean/wsclean_2.9.2.imgwsclean  aoflagger casacore chgcentre  python2.7 python3.6
/pawsey/mwa/singularity/mwa-reduce/mwa-reduce.imgaddimg addimg aegean2model apparently applybeam applyion applysolutions autoprocess bbs2model beam calibrate cluster editmodel fitsmodel flagantennae flagbaselines flagionsolutions flagmwa flagsolutions flagsubbands ionpeel matchsources mrc2model mwafinfo pbaddimg pbcorrect peel phasecal regridimg render scaleimage sedcombine solutiontool storetime subtrmodel vo2model
/pawsey/mwa/singularity/python/python_latest.sifstilts python3 numpy cython scipy matplotlib astropy aipy h5py healpy ipython pandas pyyaml tqdm colorama patsy statsmodels AegeanTools mwa-hyperbeam pyuvdata PyBDSF
/pawsey/mwa/singularity/rfi_seeker/rfi_seeker.imgRFISeeker python3 astropy numpy scipy matplotlib wcstools
/pawsey/mwa/singularity/robbie/robbie-next.sifRobbie-next topcat stilts python3 AegeanTools astropy healpy numpy scipy lmfit pandas matplotlib 

Setup:

  • Remove the module load and export commands from your .bashrc and .profile files and use the example files at /group/mwa/software/_RC_FILES as a guide for making new ones.
  • Copy /group/mwa/software/_RC_FILES/mwasci.casarc over the top of your ~/.casarc file so that casacore will work
  • See README on the manta-ray client github for how to setup asvo access via a batch script.
  • Contact your admin rep (Paul/Chris/Sammy) before contacting help@pawsey as there are some things that we can fix faster.
  • Only members of the group mwaadmin can build software and edit the module files in /group/mwa/software. We have automated the build process for future reference. If you require software that is not in there, and which is to be used by more than 1-2 people, then contact one your admin rep and we will work something out.

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