gerdasw-containers

Docker and Singularity containers with a basic installation of the GERDA software.

Notes

• MaGe is checked out at GERDAphaseII branch
• Repositories which need constant updates (like e.g. metadata repositories) are not included in the images. They can be included e.g. inside an externally mounted volume (see below)
• git branches are used to distiguish between software versions
  • g4.9.6 → CLHEP_v2.1.3.1 and GEANT4_v9.6.p04
  • g4.10.3 → CLHEP_v2.3.4.4 and GEANT4_v10.3.p03
• Remeber to update %applabels sections in Singularityfiles when updating submodules TODO: script

TODO:

• Move source code from /scif/src/ to /scif/<app>/src in Singularity containers
• Update all with the new MaGe tag
• Script to generate Singularity files with correct submodule versioning
• Find a place to store prebuilded Singularity images: LNGS-cluster@/nfs/gerda5/var/gerda-simulations/

Docker containers

All the images of this repository can be found at https://baltig.infn.it/gerda/gerdasw-containers/container_registry. To download them you must be registered (ask luigi.pertoldi@pd.infn.it), then you can use the following syntax:

$ sudo docker login baltig.infn.it:4567
$ sudo docker pull baltig.infn.it:4567/gerda/gerdasw-containers/<image>:<tag>

Let's say you have pulled the gerdasw:g4.10.3 image, then a call to docker run gerdasw:g4.10.3 with no arguments spawns a zsh shell by default:

$ sudo docker run \
  -i -t --rm \
  -h gerda-sw \
  gerdasw:g4.10.3

The -i and -t flags allow to start an interactive session inside a new tty (mandatory to spawn the shell). The --rm flag removes the container after stopping it. Optional: -h gerdasw sets the container's hostname to 'gerda-sw'.

Any other custom command can be injected inside the container, e.g.:

$ sudo docker run gerdasw:g4.10.3 MaGe

To mount a folder (/path/to/src) inside the container (mount point: /path/to/dest) run it with:

$ sudo docker run \
  -v /path/to/src:/path/to/dest \
  gerdasw:g4.10.3 <...>

NOTE: on some systems you could find high latency in accessing externally mounted volumes from within the container (see for example this issue). Consider using Docker volumes instead.

Important: to make the software fully work inside the container you must mount the following folder structure under /common:

common/
  └── sw-other/
        │── gerdageometry/
        │── gerda-metadata/
        └── gerda-ana-sandbox/

where the gerdageometry can be found in the MaGe source repo. The log in and check that MGGERDAGEOMETRY, MGGENERATORDATA and MU_CAL are set and point to existing locations. You could use the common/ location to store files that you want to preserve (e.g. MaGe macro files or output).

EDIT: With the recent MaGe tag (g4.10.3/v2.0 here) now MGGERDAGEOMETRY and MGGENERATORDATA point to gerdageometry/ and generators/data/ inside the MaGe source direcotry provided within the container under /opt/src/MaGe/, so there's no more need to manually provide gerda-ana-sandbox and gerdageometry.

Building from source

Clone this repository with --recursive (note: requires access to GERDA's private repositories at https://github.com/mppmu).

Prebuilded images including ROOT, CLHEP and GEANT4 can be found here. Build up the complete image with:

$ cd gerdasw-containers
$ sudo docker build --rm . -t gerdasw:<tag>

Singularity containers

All the images of this repository are hosted at the LNGS cluster under /nfs/gerda5/var/gerda-simulations/.

Compressed images can be build up with:

$ cd gerdasw-containers # no joke, do it
$ sudo singularity build gerdasw.sqsh Singularityfile

Singularity will perform the build in a hidden directory under /tmp and then compress it in a squash-fs format to produce the gerdasw.sqsh image, so make sure to have enough disk space. If not, you can first perform the build in another partition:

$ sudo singularity build --sandbox <custom/dir> Singularityfile

And compress the result later:

$ sudo singularity build gerdasw.sqsh <custom/dir>

Try singularity help gerdasw.sqsh or singularity run gerdasw.sqsh to start using the container, for other useful commands (e.g. those reported above for Docker) refer to the Singularity docs or type singularity help.

You can get informations upon about software included within the container by typing

$ singularity inspect --app <app-name> gerdasw.sqsh

Or specific help with

$ singularity help --app <app-name> gerdasw.sqsh

Important: mount the appriopriate folder structure under /common to make the software inside the container fully functional (see --bind flag). See the Docker section for details.

Singularity tips:

• Remember that your $HOME directory is mounted by default onto your containers, configuration dotfiles such as .bashrc could be loaded and override environment variables inside the container. The --cleanenv flag is your friend.

Enable X11 forwarding in Docker containers

Mac OSX:

Make sure you have XQuartz installed and running. First get your IP address:

$ ip=$(ifconfig en0 | grep inet | awk '$1=="inet" {print $2}')

Then add your IP adress to the list allowed to make connections to the X server using xhost:

$ xhost +$ip

Finally run the container setting the correct DISPLAY variable, for example to launch interface run:

$ docker run -e DISPLAY=$ip:0 gerda-sw interface

N.B.: the xhost +$ip instruction grants access to the X server for the specified ip address. This could expose your system to security holes if, for example, your IP address gets renewed or you switch network and forget to remove the old IP from the xhost list. Take care of your xhost list by cleaning it from untrusted IPs (use xhost -[name])!

On a remote host:

Take a look to the Wiki here.

On Linux:

The above script should work, test needed.

decay0 Docker container

Use the Dockerfile_decay0 to build up a Docker container with cernlib and decay0:

$ sudo docker build -f Dockerfile_decay0 . -t decay0

Then run it with

$ sudo docker run --rm decay0

N.B. write the output file in an external mounted volume!