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Second hands-on - Shifter

Logging in to NERSC

Use ssh to connect to Cori. The username and password will be on the training account sheet.

ssh <account>@cori.nersc.gov

Pulling an image

Pull an image using shifterimg. You can pull a standard image such as Ubuntu or an image you pushed to dockerhub in the previous session.

shifterimg pull ubuntu:14.04
# OR
shifterimg pull scanon/shanetest:latest

Running a container interactively

Use shifter to start a container using the example image or your test image.

shifter --image=ubuntu:14.04 bash

You should be able to browse inside the image and confirm that it matches what you pushed to dockerhub earlier.

lsb_release -a

Once you are done exploring, exit out.

$ exit

Running an image interactively on a batch node

Use SLURM salloc and shifter to use the image on a batch node.

salloc -N 1 -C haswell -q interactive --reservation sc19cont --image ubuntu:14.04
... wait for prompt ...
shifter bash

Once you are done exploring, exit out and exit from the batch node to free it up.

$ exit
exit

Submitting a Shifter batch job

Now create a batch submission script and try running a batch job with shifter. Use vi or your other favorite editor to create the submission script or cat the contents into a file.

cat << EOF > submit.sl
#!/bin/bash
#SBATCH -N 1 -C haswell
#SBATCH -q interactive
#SBATCH --image ubuntu:latest
#SBATCH --reservation sc19cont

srun -N 1 shifter /app/app.py
EOF

Use the Slurm sbatch command to submit the script.

sbatch ./submit.sl

Running a parallel MPI job

It is possible to run MPI jobs in Shifter and obtain native performance. There are several ways to achieve this. We will demonstrate one approach here.

If you did not do so earlier, tag and push the MPI image you created earlier.

docker tag hellompi mydockerid/hellompi
docker push mydockerid/hellompi

Now, return to your Cori login, pull your image down and run it.

shifterimg pull <mydockerid>/hellompi:latest
#Wait for it to complete
salloc -N 2 -C haswell -q interactive --reservation sc19cont --image <mydockerid>/hellompi:latest
# Wait for prepare_compilation_report
# Cori has 32 physical cores per node with 2 hyper-threads per core.
# So you can run up to 64 tasks per node.
# To get MPI support with this image version you need to specify a shifter module
srun -N 2 -n 128 shifter --module=mpich-cle6 /app/hello
exit

If you have your own MPI applications, you can attempt to Docker-ize them using the steps above and run it on Cori. As a courtesy, limit your job sizes to leave sufficient resources for other participants. Don't forget to exit from any "salloc" shells once you are done testing.

Using Volume mounts

Like Docker, Shifter allows you to mount directories into your container. The syntax is similar to Docker but uses "--volume". Here we will mount a scratch directory into the volume as /data.

mkdir $SCRATCH/input
echo 3.141592 > $SCRATCH/input/data.txt
shifter --volume $SCRATCH/input:/data --image=ubuntu bash
cat /data/data.txt