Using abel

Introduction

Getting access to CPU hours

Using Abel

Interactive login

Temporary, fast access disk space on Abel

SLURM

Introduction

We have been given a large allocation on Abel for computational work. This page explains how to get access and start using the resources. All use of Abel needs to draw CPU hours from an allocation.

Mailing list

If you're not already on it, get subscribed to the appropriate mailing lists. We use this list to distribute information on the use of the CEES HPC resources - both our own nodes and the CPU allocation on Abel. See this page, then come back here.

Getting access to CPU hours

See Getting access

Using Abel

Interactive-login

See also here.

ssh abel.uio.no

Getting a single cpu for 11 hrs

qlogin --account nn9244k --nodes 1 --ntasks-per-node 1

Same, for 24 hrs

qlogin --account nn9244k --nodes 1 --ntasks-per-node 1 --time 24:00:00

NOTE you are ''sharing the node with others'', do no use more than the number of cpus you asked for

NOTE a pipeline of unix commands may use one cpu per command:

grep something somefile | sort | uniq -c

This may use three cpus!

Getting a whole node with 16 CPUs and 64 GB RAM:

qlogin --account nn9244k --nodes 1 --ntasks-per-node 16 --time 24:00:00

Even though each node has 16 cpus, due to hyperthreading, you can run '''up to 32 processes '''simultaneously

You have a large work area available as well:

echo $SCRATCH
cd $SCRATCH

Using

squeue -u your username

will tell you the job ID, the work area is

/work/jobID.d

'''NOTE''' all data on this area is '''deleted''' once you log out

Quitting:

logout (or ctrl-d)

Temporary, fast access disk space on Abel

From the Abel newsletter #3:

'''Update on Abel scratch file-system usage'''
While a job runs, it has access to a temporary scratch directory on the shared file system /work. The directory is individual for each job, is automatically created, and is deleted when the job finishes (or gets requeued). There is no backup of this directory. The name of the directory is stored in the environment variable $SCRATCH, which is set within the job script. If your job is I/O intensive, we strongly recommend copying its work files to $SCRATCH and running the program there.
Sometimes, one needs to use a file for several jobs, or have it available some time after the job finishes. To accommodate this need, we have now created a directory /work/users/$USER for each user, where $USER is the user's user name. The purpose of the directory is to stage files that are needed by more than one job. Files in this directory are automatically deleted after a certain time (currently 45 days). There is no backup of files in /work/users/.

SLURM

SLURM scripts

Information coming, until then see here.

SLURM tips

Jobs in our queue

squeue -A nn9244k

Listing your jobs

squeue -u username

Information on your job

scontrol show job JOBID

Cancel your job

scancel JOBID

Cancel all your jobs

scancel -u USERNAME

Running SLURM script as a shell script when not submitted through SLURM

Add these lines at the beginning of your slurm script, but after the "#SBATCH" instructions

if [ -n "$SLURM_JOB_ID" ]; then
    # running in a slurm job
    source /cluster/bin/jobsetup
fi

Now run the script as

source script.slurm