computing:singularity [Fundamental Physics in Radio Astronomy]

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====== Singularity  ======

The pulsar group servers (dogmatix0/1 and miraculix/miraculix2) used to have Docker installed. Since Docker needs root permissions to execute, and therefore a security hazard, the service was discontinued on the group servers. Instead, we have decided to use the Singularity container, which can be also be used to run previously built Docker containers without the need for root privileges. 

Here is a short how-to on getting access to PSRCHIVE/DSPSR based on a previously build Docker container.

  * If you are in a hurry and have to use psrchive/dspsr, use a prebuilt Singularity container:
   ''singularity shell -B /fpra/timing/01 /homes/ramesh/dspsr_202111.sif''
  * In the above ''-B /fpra/timing/01'' is the directory that needs to visible inside singularity.
  * Access all other commands/utilities as you normally do: 

   ramesh@dogmatix0 ~ $ singularity shell -B /fpra/timing/01 /homes/ramesh/dspsr_202111.sif 
   bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
   Singularity dspsr_202111.sif:~> pwd
   /homes/ramesh
   Singularity dspsr_202111.sif:~> cd /fpra/timing/01/MAGNETARS/
   Singularity dspsr_202111.sif:/fpra/timing/01/MAGNETARS> cd J1818-1607/PSRIX0/20200314/search/
   Singularity dspsr_202111.sif:/fpra/timing/01/MAGNETARS/J1818-1607/PSRIX0/20200314/search> vap -c "freq bw" 2020-03-14-06:37:20.ar
   filename   freq   bw
   2020-03-14-06:37:20.ar   1358.926   -250.000
   Singularity dspsr_202111.sif:/fpra/timing/01/MAGNETARS/J1818-1607/PSRIX0/20200314/search>


Note that the container above has only tempo2.

====== Using a docker container under Singularity ======

  * Make sure that a prebuilt Docker container exists on Dockerhub 
  * Build a singularity image by: 

    singularity build dspsr_202111.sif docker://bhcpsr/dspsr:202111

  * The above will create a singularity image ''dspsr_202111.sif'' in the current directory.
  * If the build above fails with ''no space left on device'' error, remove files that are like /var/tmp/docker-tar066320373.


====== Vivek's docker/singularity containers ======

The instructions to use Vivek's container are given here: https://github.com/vivekvenkris/pulsar_docker

====== Henning's Notes ======

A while back Henning gave a tutorial on using singularity. The PDF document is {{:computing:docksing.pdf| here}}

====== Using PRESTO ======

The following is based on a docker container built with the Dockerfile contained in the PRESTO package.

   git clone https://github.com/scottransom/presto.git
   cd presto
   docker build . --tag presto:r4.0   


The above image was pushed to bhcpsr's Dockerhub and this can be readily accessed within Singularity:

   paf0:~> setenv SINGULARITY_TMPDIR /media/titan0/sing
   paf0:~> singularity shell -e -B /media/titan0/ docker://bhcpsr/presto:r4.0
   
If you have trouble getting your display to work, try setting the DISPLAY environment variable (as set before firing up the container) and copy $HOME/.Xauthority file to the home directory within the Singularity container. 


====== Docker on Mac  ======

The recent Macs with the Apple M1/M2/M3 chips might have issues when the installed docker version is not updated. Check for new release here: https://docs.docker.com/desktop/release-notes/. On 08 May 2024, version 4.30.0 worked fine on Sonoma 14.4.1.

Remove the old docker by navigating to Applications folder, and drag-n-drop docker app to the recycle bin.If there are issues in removing the docker app, stop any docker processes using  the activity monitor tool (found in the Utilities folder which is listed in Applications).

Now when invoking docker from command line, make sure to use ''--platform linux/amd64'', as in the example below:

  docker run -ti --rm --platform linux/amd64 -v /Users/rameshkaruppusamy/DOCK:/data --name="dspsr" --hostname="dspsr" bhcpsr/dspsr:202111.1 bash
  root@dspsr:~# export DISPLAY=134.104.30.131:0
  root@dspsr:~# pav -DFTp /data/2020-03-20-20\:18\:35.0024.p.calibP

To get X11-forwarding to work properly, install xQuartz. Make sure that you enable "Allow connections from network clients" found under Security tab in xQuartz's settings. Make sure that you allow other clients to connect to xQuartz X11 server with ''xhost +'' on a terminal before invoking your container. The DISPLAY variable is set to the current IP of the Mac. Check this with ''ifconfig | grep inet'' on a terminal and choose the right IP address.
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