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• /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
• 20230314.sif
• on s3df, these containers can be found in: /sdf/group/fermi/sw/containers/

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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.

For S3DF, s3dflogin:

1. export myimage=/sdf/group/fermi/sw/containers//fermi-centos6.20230314.sif
2. Go inside the container:
   1. singularity shell -B /sdf $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.
   4. if you need to see SDF filesystems (Lustre), add -B /fs/ddn/sdf
3. Run a command in the container:
   1. singularity exec -B /sdf $myimage ls -l 
   2. singularity exec -B /sdf $myimage sh myscript.sh
   3. The above is usually used in batch jobs.
   4. if you need to see SDF filesystems (Lustre), add -B /fs/ddn/sdf

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