Using RHEL6 Singularity Container

Many thanks to Wei Yang for creating and documenting use of the container.

Singularity image files: 

• /gpfs/slac/fermi/fs2/software/containers/slac-fermi.img.ext3
• This is an old, tested image
• /gpfs/slac/fermi/fs2/software/containers/fermi-centos6.sif
• This is a new, untested image
• on s3df, these containers can be found in: /sdf/group/fermi/sw/containers/

• They are available on both the AFS side and SDF side. You can copy them to other locations
• Instructions for how to build the container are in: /gpfs/slac/fermi/fs2/software/containers/fermi-rhel6.build.txt

How to run Singularity container from rhel6-64, centos7 and sdf-login:

1. export myimage=/gpfs/slac/fermi/fs2/software/containers/slac-fermi.img.ext3
   1. or use the new image file:
   2. export myimage=/gpfs/slac/fermi/fs2/software/containers/fermi-centos6.sif
2. Go inside the container:
   1. singularity shell -B /afs:/afs -B /gpfs:/gpfs $myimage
   2. By default, the prompt is changed to “Singularity> “. You are now in a shell and can do “ls”, “cd”, etc. 
   3. If you run command “id”, you will see you are running as yourself.
3. Run a command in the container:
   1. singularity exec -B /afs:/afs -B /gpfs:/gpfs $myimage ls -l /afs
   2. singularity exec -B /afs:/afs -B /gpfs:/gpfs $myimage sh /afs/slac/myscript.sh
   3. The above is usually used in batch jobs.
4. “-B /afs:/afs” means bind mount (make /afs available inside the container, as path /afs)
   1. Bind mount may not work well when running singularity on rhel6-64 machines, especially when autofs path (e.g. /nfs) is involved 
   2. By default, /tmp and your working directories are bind mounted.
   3. on centos7, you can also bind mount nfs similarly.

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