Building Singularity containers on Transit

Disclaimer: The purpose of the transit server is to transfer files to/from the wharf area in your sensiteve project. This tutorial is not an official documentation and does not give a guarantee that it will work for any case. If you experience problems following this material - please apply for small project on Rackham and use Rackham for this purpose.

Keep in mind that your $HOME folder is a read-only snapshot of your Rackham $HOME folder and has limit of 1.3GB write overlayer.

df -h | grep $USER
overlay    1.3G  4.0K  1.3G   1% /domus/h1/XXXXX

1. Login to transit.uppmax.uu.se
   Documentation:
   • https://uppmax.github.io/UPPMAX-documentation/cluster_guides/transfer_bianca/#transit-server
2. Mount the wharf of your project.
   ​​​​user@transit:~$ mount_wharf sens2023531
   ​​​​Mounting wharf (accessible for you only) to /home/<user>/sens2023531
   ​​​​<user>[e-mail]'s password: 
   

3. Navigate to your wharf folder
   ​​​cd sens2023531
   

4. Disable Singularity cache
   ​​​export APPTAINER_DISABLE_CACHE=true
   ​​​export APPTAINER_TMPDIR=/dev/shm/$USER
   ​​​mkdir -p $APPTAINER_TMPDIR
   ​​​unset ${!NXF_*}
   

   Note: Alternatively, redirect the APPTAINER_TMPDIR to your wharf folder to allow for larger container builds. This approach will be much slower, though.
5. Build/pull your container as usual.

Contacts:

• Pavlin Mitev
• UPPMAX
• AE@UPPMAX - related documentation