Create Spark cluster

From info319

Create SSH key pair

You need a new SSH key pair for your Spark cluster. Do not use a key pair you are using elsewhere, because you will need to upload the private key to the the virtual machines ("instances") in the cluster, and the may not always be secure. On your local computer, in a terminal window that runs Ubuntu Linux and bash shell: 

cd ~/.ssh
ssh-keygen -b 4096 -f info319-spark-cluster

Leave the password empty. 

ls -ld ~/.ssh                                # mode should be drwx------
ls -l ~/.ssh/info319-spark-cluster           # mode should be -rw-------
ls -l ~/.ssh/info319-spark-cluster.pub       # mode can be -rw-r--r--

Select project

Sign in to the Norwegian Research and Education Cloud (NREC). In the Overview screen, choose the info319 project (for example uib-info319-abc * bgo'. You can also play around with your DEMO project a bit before your proceed.

Create security group

In the NREC Overview window, go to Network -> Security groups. Create Security Group info319-spark-cluster. Add rule as follows (accept defaults for the rest):

  • name: info319-spark-cluster
  • rule: SSH
  • CIDR: 2001:700:200:13::204/64

Here, 2001:700:200:13::204/64 is a range of IPv6 UiB-addresses that includes login.uib.no. We will use IPv6 in the course because it is future-leaning and many organisations are quickly running out of IPv4 addresses. Because your machine may not run IPv6 yet, this exercise uses login.uib.no as a JumpHost to log into the Spark cluster. To log in directly from other IPv6-machines, or using other protocols, you can add more rules to the security group.

Create the Spark driver machine (instance)

A virtual machine in the NREC cloud is called an instance (or sometimes a node or host). In the NREC Overview window, under Compute -> Instances, Launch instance as follows (accept defaults for the rest):

  • name: spark-driver (in Ubuntu/Linux, valid hostnames are between 2 and 64 characters in length. They can contain only letters, numbers, periods, and hyphens, but must begin and end with letters and numbers only)
  • boot source: GOLD Ubuntu 22.04 LTS
  • flavor: m1.large (to get started)
  • networks: DualStack
  • security groups: in addition to the default, add the info319-spark-cluster group
  • key pair: import the public SSH key you just created from ~/.ssh/info319-spark-cluster.pub

Log in to spark-driver

In the NREC Overview window, under Compute -> Instances, get the IPv6 address for spark-driver. It may look like this: 2001:700:2:8301::1111. In a local terminal window, login to spark-driver with something like: 

ssh -i ~/.ssh/info319-spark-cluster -J YOUR_USERNAME@login.uib.no ubuntu@2001:700:2:8301::1111

Here, the -J YOUR_USERNAME@login.uib.no option means you are using login.uib.no as a "jumphost" to connect to spark-driver. You need to do this because you are (most likely) on a IPv4 machine that cannot connect directly to IPv6. You also need to be on the UiB network (at least through VPN). Now you will be asked for your UiB-password, possibly triggering two-factor authentication. Accept the new fingerprint if asked. Check out the new instance and use exit to log out again.

Note: If this does not work, check if you can ssh directly to login.uib.no . It is sometimes unavailable, but usually comes up again in a few minutes. There is a 10-minute block if you do something suspicious, like getting a user name wrong.

To simplify future login, in a text editor, open the file ~/.ssh/config on your local computer and add lines like these: 

Host spark-driver
     Hostname 2001:700:2:8301::1111  # the new IPv6 address here
     User ubuntu
     IdentityFile ~/.ssh/info319-spark-cluster
     ProxyJump YOUR_USERNAME@login.uib.no
     StrictHostKeyChecking no
     UserKnownHostsFile /dev/null

The two last lines relax security a little, but they are ok for a test instance with open data on it. In general, IPv6 is pretty secure.

You can now login to the server with the simple command: 

ssh spark-driver

The NREC documentation suggests a final improvement. On your local Linux-machine, do: 

mkdir -m 0700 ~/.ssh/controlmasters

And add lines like these to ~/.ssh/config: 

Host login.uib.no
     User YOUR_USERNAME
     ControlPath /THE_PATH_YOU_JUST_USED/controlmasters/%r@%h:%p
     ControlMaster auto
     ControlPersist 10m

If you get socket error messages when you try to use SSH, you can try these directories instead of ~/.ssh/config: /dev/shm/controlmasters or /var/shm/controlmasters. However, these alternatives are temporary directories, so you need to recreate them whenever you log into your local machine, for example: 

echo "mkdir -p -m /dev/shm/controlmasters" >> ~/.profile  # ...or maybe you use  ~/.bash_profile

Create the Spark worker machines (instances)

To create Spark worker instances, repeat the steps for the Spark driver with these modifications:

  • name: spark-worker
  • count: 3 # the number of workers
  • networks: IPv6 (instead of DualStack)

As before:

  • boot source: GOLD Ubuntu 22.04 LTS
  • flavor: m1.large
  • security groups: in addition to the default, add the info319-spark-cluster group
  • key pair: use the same SSH key you imported from ~/.ssh/info319-spark-cluster.pub

Do not create more workers already now. The reason is that, in this exercise, you will install all the software by hand... In Exercise 5, we will do it with scripts instead.

Login to one or more of the new instances like before, where 2001:700:2:8301::2222 is one of the new Ipv6 addresses: 

ssh -i ~/.ssh/info319-spark-cluster -J YOUR_USERNAME@login.uib.no ubuntu@2001:700:2:8301::2222

You can now name the instances and simplify login using ~/.ssh/config as before. To avoid duplicate lines, you can use wildcards like this: 

Host spark-*
     User ubuntu
     Port 22
     IdentityFile ~/.ssh/info319-spark-cluster
     ProxyJump sinoa@login.uib.no
     StrictHostKeyChecking no
     UserKnownHostsFile=/dev/null

Host spark-driver
     Hostname 2001:700:2:8301::1111

Host spark-worker-1
     Hostname 2001:700:2:8301::2222

Add corresponding lines for the other Spark workers.

Create and mount virtual disks

In the NREC Overview window, go to Volumes -> Volumes, Create volumes called spark-driver-volume and spark-worker-volume-1, spark-worker-volume-2, and spark-worker-volume-3 as follows:

  • volume source: image
  • use image as a source: GOLD Ubuntu 22.04 LTS
  • use a small disk size, like 100Gb (this is just a test cluster, so we leave some room for a bigger cluster later)

Use the Actions drop-down menus to Manage Attachments of each new volume to its respective instance. For Device Name you can try /dev/sdb, or leave it open.

Check which path each volume has become Attached To. Here, we will assume that the new virtual disks are all attached at /dev/sdb.

Log into each each instance (spark-driver, spark-worker-1, ...) in a separate terminal window. In each window, run the following commands in each to mount and format the disks (we follow this guide, which works well on 22.04 too): 

sudo gdisk /dev/sdb

You have to enter this chain of responses: 

n
1
[Return]
[Return]
[Return]
w
Y

Back at the Linux prompt: 

sudo mkfs.ext4 /dev/sdb1  # the '1' is because you chose partition number '1' a few lines up
mkdir ~/volume
sudo mount /dev/sdb1 ~/volume
sudo chown -R ubuntu:ubuntu ~/volume

/home/ubuntu/volume is now available on each instance as a regular folder. But you will have to remount it every time to restart (reboot) the instance. To mount the volume permanently, you must add a line to /etc/fstab: 

echo $(sudo blkid /dev/sdb1 -s UUID | cut -d" " -f2) /home/ubuntu/volume ext4 defaults 0 0 | \
    sudo tee -a /etc/fstab
sudo cat /etc/fstab

To check that the volume is permanently mounted, do 

sudo reboot now

Back in your local terminal window, after 20-30 seconds, do: 

ssh spark-INSTANCE-NAME

Check that the volume is still there and owned by user ubuntu. 

ls -ld ~/volume  # mode and ownership should be drwxr-xr-x 3 ubuntu ubuntu

Set up SSH on the cluster

The virtual machines in the cluster also need to have SSH connections between each other. Internally in the cluster, we will use IPv4 addresses, because some of the software we will run do not yet support IPv6.

On your local computer, create an exercise-4 folder, for example a subfolder of info319-exercises, and cd into it.

On your local computer, create a file hosts with the IPv4 addresses and names of all the instances. The spark-driver must be first, for example: 

158.39.77.125 spark-driver
10.1.0.143 spark-worker-1
10.1.1.202 spark-worker-2
10.1.2.49 spark-worker-3

(spark-driver has a differently-looking IPv4 address because it is global, whereas the workers have local IPv4 addresses that are only valid inside the cluster.)

Copy the hosts file into each instance: 

scp hosts spark-driver:
scp hosts spark-worker-1:
scp hosts spark-worker-2:
scp hosts spark-worker-3:

On each instance, extend the file /etc/hosts with the new instances as follows: 

cat hosts /etc/hosts | sudo tee /etc/hosts
rm hosts

The rest of this exercise assumes that spark-driver is always listed first in /etc/hosts, and that no other lines in this file contain the string "spark-".

From your local machine, upload the SSH private keys to each instance: 

scp ~/.ssh/info319-spark-cluster spark-driver:.ssh
scp ~/.ssh/info319-spark-cluster spark-worker-1:.ssh
...

Check that the copied files have the right permissions (mode): -rw-------

On your local machine, create the file config.stub: 

Host spark-*
     User ubuntu
     IdentityFile ~/.ssh/info319-spark-cluster
     StrictHostKeyChecking no
     UserKnownHostsFile=/dev/null

This is the start your local .ssh/config file, but with the JumpHost stuff removed. Upload it to each instance: 

scp config.stub spark-driver:.ssh/config
scp config.stub spark-worker-1:.ssh/config
...

You can also use a for loop to do multiple uploads: 

for dest in spark-driver spark-worker-1 spark-worker-2 spark-worker-3 ; do
    scp config.stub $dest:.ssh/config ;
done

Or even more compactly: 

for dest in spark-{driver,worker-{1,2,3}} ; do
    scp config.stub $dest:.ssh/config ;
done

Now, you can connect from any of your instances directly to any other. For example, on spark-worker-2 

ssh spark-worker-3

Security group for spark-driver

It is useful to open a few more ports on spark-driver to be able to access the web UIs for HDFS, YARN, Spark, Zookeeper, and Kafka later.

In the NREV Overview window, go to Network -> Security groups. Create a new security group info319-spark-driver. Add rules that open the following TCP ports for Ingress:

  • rule: Custom TCP Rule
  • direction: Ingress
  • ports: 4040, 8042, 8080, 8088, 9092, 9870 (you need to create one rule for each)
  • CIDR: 129.177.146.20/20 (this covers most UiB addresses, add more rules to access from outside UiB/VPN)

Still in the Overview window, go to Compute -> Instances, use the Actions drop-down menus (Edit Security Groups) to add the new security group info319-spark-driver to the spark-driver instance.

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