BioKEM environment

If you’ve enabled the BioKEM environment through the Configuring your environment you should now have the following:

Aliases

  • blanca : load the Blanca SLURM environment when logged into a login node (this could be loaded by other commands).

  • sbgrid : starts SBGrid environment when on Blanca

  • scratch : takes you to your scratch directory

  • s : shows you your jobs (on the cluster you are on)

  • blanca-gpus : shows all GPUs on blanca (need to be on a blanca node)

Executables

  • biokem/blanca/alpine-interactive: starts an interactive session with X forwarding, use this launch jobs. You can add the following arguments, if you want to request additional resources:

    • -c or --cpus # of CPUs

    • -g or --gpus # of GPUs

    • -m or --mem # of GB of memory

    • -x additional string to add an sbatch argument

  • alphafold-predict : submits an AlphaFold job

  • slurm-err : reads out latest SLURM error file, can also take a job number as argument

  • slurm-out : reads out latest SLURM out file, can also take a job number as argument

Variables

  • Various RELION environmental variables

  • MESA_GL_VERSION_OVERRIDE=3.3: allows SBGrid’s ChimeraX to function.