How to create HPC Cluster with Slurm scheduler on Google Cloud Platform

Generating SSH keys for specific accounts (from Linux machine)

Login to the Linux machine console.
Run the following command to generate the SSH key pair:

ssh-keygen -t rsa -f ~/.ssh/[KEY_FILENAME] -C [USERNAME]

Note 1: Replace KEY_FILENAME with the actual private key file name

Note 2: Replace USERNAME with the user who will use this SSH key to login

Change the permissions of the SSH private key using the command below:

chmod 400 ~/.ssh/[KEY_FILENAME]

Note: Replace KEY_FILENAME with the actual private key file name

Generating SSH keys for specific accounts (from Windows machine)

Download puttygen.exe from:

http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

Run the puttygen.exe
Click Generate and follow the on-screen instructions to generate a new key.

Note: Make sure you create keys with at least 2048 bits

In the Key comment section, replace the existing text with the username who will use this key to login to the VM instance.
Click Save private key to write your private key to a file with a .ppk extension.
Click Save public key to write your public key to a file for later use.

Configure Metadata settings for the VM instances

From the upper left pane, click on “Compute Engine”
From the left pane, click on “Metadata”
From the main pane, under “Metadata” click on Edit -> add new key:

Key: enable-oslogin
Value: false

Click on Save
Open the previously created public key (usually it has no file extension) using a text editor and copy its entire content into memory.
From the main pane, under “SSH Keys” -> click on Edit -> click on Add item -> paste the content of the public key previously created into the free text field labeled “Enter entire key data” -> click on Save

Granting OS Login External User Access (Non-IUCC users)

In-case you are trying to access your GCP project using Google G Suite account belong to your University, and the GCP project was created by the IUCC, contact CloudSupport@iucc.ac.il and ask to add your Google G Suite account to the relevant university access group within CSU.IUCC.AC.IL Google G Suite organization.

Google Cloud SDK installation phase

Login to a machine using privileged account
Install Google Cloud SDK tools.

Linux (Debian / Ubuntu):

https://cloud.google.com/sdk/docs/quickstart-debian-ubuntu

Linux (CentOS / RedHat):

https://cloud.google.com/sdk/docs/quickstart-redhat-centos

Windows:

https://cloud.google.com/sdk/docs/quickstart-windows

Run the following from command prompt to initialize the Cloud SDK:

gcloud init --console-only

Select a GCP project from the list
Select a default Compute region and zone

Common Google Cloud SDK CLI Commands

Login to Google Cloud Platform:

gcloud auth application-default login --no-launch-browser

Note: The command prompt will show you a link – copy the link to a new browser, login with your GCP project credentials and copy the verification code from the browser to the command prompt

List all active GCP accounts:

gcloud auth list

Change the active account:

gcloud config set account <Account_Name>

Note: Replace <Account_Name> with the target GCP account

Lists all available GCP projects:

gcloud projects list

Change the GCP project:

gcloud config set project "<Project_ID>"

Note: Replace <Project_ID> with the target GCP project ID

Git installation phase on Linux (Debian / Ubuntu)

Login to the Linux machine using privileged account
Run the commands below:

sudo apt-get update

sudo apt-get install git-core

Run the command below to view the Git version:

git --version

Git installation phase on Linux (Centos / RedHat)

Login to the Linux machine using privileged account
Run the commands below:

sudo yum install git

Run the command below to view the Git version:

git --version

Git installation phase on Windows

Login to the Windows machine using privileged account
Download and install Git from the link below:

https://gitforwindows.org/

Slurm download and configuration phase

Download the Slurm deployment from command prompt:

Linux:

cd ~

git clone https://github.com/SchedMD/slurm-gcp.git

cd slurm-gcp

Windows:

cd %UserProfile%

git clone https://github.com/SchedMD/slurm-gcp.git

cd slurm-gcp

Edit the slurm-cluster.yaml configuration file, and update the following parameters:

cluster_name – Specify your target HPC cluster name (without spaces)
static_node_count – Leave the default with minimum of 2 nodes
max_node_count – Set here the maximum number of nodes for auto-scaling
zone – Specify here the target zone to deploy the HPC cluster (such as europe-west2-a)

Note: The full list of GCP zones can be found on: https://cloud.google.com/compute/docs/regions-zones/

region – Specify here the target region to deploy the HPC cluster (such as europe-west2)

Note: The full list of GCP regions can be found on:

https://cloud.google.com/compute/docs/regions-zones/

cidr – Update the target network range for the HPC cluster to be the same as the target zone (inside GCP console -> VPC Network)

For example: In-case the region IP range is 10.154.0.0/20, update the cidr value inside the configuration file to 10.154.0.0/24

controller_machine_type – For small HPC cluster you may leave the default instance type n1-standard-2 (2 vCPUs and 7.5 GB of memory)
compute_machine_type

For small HPC cluster you may leave the default instance type n1-standard-2 (2 vCPUs and 7.5 GB of memory)
For large HPC cluster, choose instance type from the High-CPU family (https://cloud.google.com/compute/docs/machine-types#highcpu) or from the Compute-Optimized VMs (https://cloud.google.com/blog/products/compute/introducing-compute-and-memory-optimized-vms-for-google-compute-engine)

login_machine_type - Leave the default instance type n1-standard-2 (2 vCPUs and 7.5 GB of memory)
controller_disk_type - Remove the “#” sign
controller_disk_size_gb – Remove the “#” sign and change the value to 10
default_users – Specify here the email address of the GCP users who will be allowed to login to the HPC cluster and manage it (separated with comma)

Run the command below to deploy the new cluster:

gcloud deployment-manager deployments create mycluster --config slurm-cluster.yaml

Note: Replace mycluster with your target HPC cluster name (without spaces)

If you are using the Deployment Manager API on a new GCP project, press “Y” to enable the API
Document the machine names (specially the controller and login1)
Wait for the deployment process to complete (around 10 minutes)
Go to the Google Deployment manager console to view the status of the cluster deployment:

https://console.cloud.google.com/dm/deployments

Run the command below to login to the HPC cluster login1 machine:

gcloud compute ssh google1-login1 --zone=<ZONE>

Note 1: Replace google1-login1 with the name of the HPC cluster login machine

Note 2: Replace <ZONE> with the target zone that you deployed the cluster into (such as europe-west2-a)

On first login, press “Y” to continue
Wait for the Slurm deployment to complete (might take around 10 minutes)
In-case you are logged into the login1 machine, you will see the message “Slurm login daemon installation complete”, once the cluster installation completes

Note: Once the Slurm cluster deployment completes, you might need to logout and login back again to the login1 server for the mount of /home to take effect

Run the command below to check the status of the Slurm cluster:

sinfo

Logoff the login1 machine:

exit

Adding additional users the ability to login to the login1 machine

Run the command below to login to the HPC cluster “login” machine:

gcloud compute ssh google1-login1 --zone=<ZONE>

Note 1: Replace google1-login1 with the name of the HPC cluster login machine

Note 2: Replace <ZONE> with the target zone that you deployed the cluster into (such as europe-west2-a)

Run the command below to add a new group:

sudo groupadd mygroup

Note: Change mygroup to the target group

Run the command below to add a new user:

sudo useradd -g mygroup myusername

Note 1: Change mygroup to the target group

Note 2: Change myusername to the target username

Create the following folder:

sudo mkdir /home/myusername/.ssh