launchabel: Launch IPython and Jupyter on Abel

Written as part of the Simula BioComp Hackation 2015, along with fenicsbot and others.

A script to run and connect to a job on Abel. The script does:

1. forward a local port (default: 9999) to an Abel login node.
2. generate sbatch and srun scripts and send them
3. the sbatch script mostly just calls srun
4. the srun script runs:
   1. node-0: launch notebook server, complete port-forwarding from login node to work node
   2. node 1: start ipcontroller
   3. node 2-n+2 (n nodes): mpirun ipengine

So when you request -n 2, you will get 2 engines, but the allocation will request 4 total tasks.

Examples

./launchabel --account=myaccount -n 2

export ABEL_ACCOUNT=myacct
./launchabel -n 32 --mem 2G --port 8888

Arguments after -- are added as SBATCH directives ./launchabel -n 1 -- --job-name=test

Or you can reuse more elaborate sbatch config by writing the lines to a file (e.g. sbatch.sh):

#SBATCH --account=myacct
#SBATCH --mem-per-cpu=8G
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=4

and load it with

  ./launchabel --sbatch-file=./sbatch.sh

in which case the script will not modify any SBATCH lines.