Exercise 3: Building our Testbed

An elastic OpenHPC system with Open OnDemand and X2go

In this exercise, we will be provisioning a second OpenHPC system in Amazon EC2.

This system will feature:

• a full OpenHPC software stack
• containerization support using Podman and Singularity
• Open Ondemand web portal
• X2go login node for remote desktop sessions based on XFCE.

In order to begin following along, you need to first follow the directions on the Getting Started page in Personal AWS cluster from scratch section or be running an EventEngine tutorial cluster.

You will need:

• A Cloud9 IDE environment with packer installed
• A pearc20 key pair and the pearc20.pem file available on the cloud9 instance
• The aws command line tool configured with Access Key ID and Secret Access Key

If you are missing any of the above, please return to the Getting Started page

Additionally, you’ll need the tutorial content.

$ cd ~
$ wget -c https://github.com/utdsimmons/pearc2020/raw/master/ohpc-pearc20-tutorial.tar.bz2 -O - | tar -xj

Note: The remainder of this exercise assumes you extracted the tarball into ~ and you’ll be working in ~/PEARC20

The AMIs

In Exercise 1, we built our own AMIs using using Packer. In this Exercise, we will use pre-built AMIs.

If you’d like to build and customize your own AMIs, the sources are located in ~/PEARC20/Exercise-3/packer-templates/

Bulding the cluster with Cloud Formation

Since we are using pre-built AMIs, all we need to do is deploy the template and wait.

$ cd ~/PEARC20/Exercise-3/cfn-templates
$ aws cloudformation deploy --template-file slurm-dynamic-ood-ohpc.yml --capabilities CAPABILITY_IAM --stack-name ex3-00 --region us-east-1

To monitor, go to Console > Services > CloudFormation > Click the stack name (ex3-00) > Events

Note: If you need to rerun the aws cloudformation deploy command, you’ll need to either delete your stack or increment the index (i.e. –stack-name ex3-01) in order to rerun the command

Testing the cluster

SSH Access

Go to the EC2 Dashboard and find the public DNS

Console > Services > EC2 > Instances > Right Click ‘X2goManagement’ > Connect > Copy Public DNS to cliboard

In Cloud9

$ cd ~
$ ssh -i pearc20.pem centos@ec2-xx-xxx-xxx-xxx.compute-1.amazonaws.com
$ cp /opt/ohpc/pub/examples/mpi/hello.c .
$ mpicc hello.c
$ cp /opt/ohpc/pub/examples/slurm/job.mpi .
$ sbatch job.mpi
$ watch -n 10 squeue

In Exercise 1, we deployed a cluster with 2 compute nodes. Those compute nodes were static/persistent.

For this exercise, we’ve deployed an “elastic” cluster. When a job is submitted, the cluster will create EC2 instances for the compute nodes on demand. It will take between 5-6 mins from submission time for the job to start.

X2go Access

In addition to command line access, this management node can also be used to provide remote desktops.

Note: This is NOT good practice. This is just an educational exercise. For production, use separate x2go login nodes and an isolated management node

Testing X2go:

• install the X2go client and launch it
• x2go > Session > New Session
• Session name: ohpc@aws
• Host: Paste the Public DNS entry from the clipboard
• Login: centos
• Use RSA/DSA key for ssh connection: pearc20.pem from OS specific browser downloads folder
• Session type: XFCE
• Media Tab
• De-select “Enable sound support” and “Client side printing support”
• Select Ok to save the profile
• Click the newly create profile “box” and select “yes” to trust the host key

You should now have a remote desktop running XFCE.

Open OnDemand Web Portal

In Exercise 1, we provisoned a management node and 2 compute nodes. In this Exercise, we’ve created an elastic cluster with a management node running x2go and an additional login node. This additional login node has been provisioned with Open OnDemand, an NSF-funded open-source HPC portal.

It provides:

• Plugin-free / “clientless” HPC
• Easy file management
• Command-line shell access to our cluster
• Job management, monitoring, and submissions via a robust templating system
• Optional graphical desktop environments and desktop applications (not configured here)

In order to access the web portal, we will need its Public DNS info.

Console > Services > Ec2 > Instances > Right Click ‘OODLogin’ > Connect > Copy Public DNS to clipboard

Paste this DNS entry into a web browser and enter username: ‘centos’ and password: ‘ood’.

This concludes Exercise 3. This cluster will be used for the remaining exercises.