Vagrant Slurm

Warning: For demonstration/testing purposes only, not suitable for use in production

This repository contains a Vagrantfile and the necessary configuration for automating the setup of a Slurm cluster using Vagrant's shell provisioning on Debian 12 x86_64 VMs.

Prerequisites

This setup was developed using vagrant-libvirt with NFS for file sharing.

• Vagrant (tested with 2.3.4 packaged by Debian 12)
• Vagrant-libvirt provider (tested with 0.11.2 packaged by Debian 12)
• Working Vagrant Synced Folders using NFS
• (Optional) Make (for convenience commands)

VirtualBox Incompatibility

While efforts were made to support VirtualBox, several challenges prevent its use in the current state.

1. Hostname Resolution: Unlike libvirt, VirtualBox doesn't provide automatic hostname resolution between VMs. This requires an additional private network and potentially custom scripting or plugins to enable inter-VM communication by hostname.

2. Sequential Provisioning: VirtualBox provisions VMs sequentially, which, while preventing a now exceedingly rare race condition with the munge.key generation and distribution, significantly increases the overall setup time compared to vagrant-libvirt's parallel provisioning and complicates potential scripted solutions for hostname resolution.

3. Shared Folder Permissions: VirtualBox's shared folder mechanism doesn't preserve Unix permissions from the host system. The vagrant user owns all shared files in the /vagrant mount point, complicating the setup of a non-privileged submit user and stripping the execution bit from shared scripts.

4. Provider-Specific Options: Using mount options for VirtualBox shared folders is incompatible with libvirt, making maintaining a single, provider-agnostic configuration challenging.

Potential workarounds like assigning static IPs compromise the flexibility of the current setup. The fundamental differences between VirtualBox and libvirt in handling shared folders and networking make it challenging to create a truly provider-agnostic solution without significant compromises or overhead.

For now, this project focuses on the libvirt provider due to its better compatibility with the requirements of an automated Slurm cluster setup. Future development could explore creating separate, provider-specific configurations to support VirtualBox, acknowledging the additional maintenance this would require.

Cluster Structure

• node1: Head Node (runs slurmctld)
• node2: Login/Submit Node
• node3 / node4: Compute Nodes (runs slurmd)

By default, each node is allocated:

• 2 threads/cores (depending on architecture)
• 2 GB of RAM

Warning: 8 vCPUs and 8 GB of RAM are used by default in total resources

Getting Started

1. To build the cluster, you can use either of these methods

   Using the Makefile (recommended):

   make
   

   Using Vagrant directly:

   vagrant up
   

2. Login to the Login Node (node2) as the submit user:

   vagrant ssh node2 -c "sudo -iu submit"
   

3. Run the example prime number search script:

   /vagrant/primes.sh
   

   By default, this script searches for prime numbers from 1-10,000 and 10,001-20,000

   You can adjust the range searched per node by providing an integer argument, e.g.:

   /vagrant/primes.sh 20000
   

   The script will then drop you into a watch -n0.1 squeue view so you can see the job computing on nodes[3-4]. You may CTRL+c out of this view, and the job will continue in the background. The submit user's home directory is in the NFS shared /vagrant directory, so the results from each node are shared with the login node.

4. View the resulting prime numbers found (check ls for exact filenames)

   less slurm-1_0.out
   less slurm-1_1.out
   

Configuration Tool

On the Head Node (node1), you can access the configuration tools specific to the version distributed with Debian. Since this may not be the latest Slurm release, using the configuration tool that matches the installed version is important. To access these tools, you can use Python to run a simple web server

python3 -m http.server 8080 --directory /usr/share/doc/slurm-wlm/html/

You can then access the HTML documentation via the VM's IP address at port 8080 in your web browser on the host machine.

Cleanup

To clean up files placed on the host through Vagrant file sharing:

make clean

This command is useful to remove all generated files and return to a clean state. The Makefile is quite simple, so you can refer to it directly to see what's being cleaned up.

If you have included override settings that you want to remove as well, run:

git clean -fdx

This command will remove all untracked files and directories, including those ignored by .gitignore. Be cautious when using this command, as it will delete files that Git does not track. Use the -n flag to dry-run first.

Overrides

Global Overrides

WARNING: Always update slurm.conf to match any CPU overrides on compute nodes to prevent resource allocation conflicts.

If you wish to override the default settings on a global level, you can do so by creating a .settings.yml file based on the provided example-.settings.yml file:

cp example-.settings.yml .settings.yml

Once you have copied the example-.settings.yml to .settings.yml, you can edit it to override the default settings. Below are the available settings:

Vagrant Settings Overrides

• VAGRANT_BOX
  • Default: debian/bookworm64
  • Tested most around Debian Stable x86_64 (currently Bookworm)
• VAGRANT_CPU
  • Default: 2
  • Two threads or cores per node, depending on CPU architecture
• VAGRANT_MEM
  • Default: 2048
  • Two GB of RAM per node
• SSH_FORWARD
  • Default: false
  • Enable this if you need to forward SSH agents to the Vagrant machines

Slurm Settings Overrides

• SLURM_NODES
  • Default: 4
  • The total number of nodes in your Slurm cluster
• JOIN_TIMEOUT
  • Default: 120
  • Timeout in seconds for nodes to obtain the shared munge.key

Minimal Resource Setup

Resource-conscious users can copy and use the provided example-.settings.yml file without modifications. This results in a cluster configuration using only 1 vCPU and 1 GB RAM per node (totaling 4 threads/cores and 4 GB RAM), allowing basic operation on modest hardware.

When using this minimal setup with 1 vCPU, you'll need to update the slurm.conf file. Apply the following change to the default slurm.conf:

sed -i 's/CPUs=2/CPUs=1/g' slurm.conf

Per-Node Overrides

WARNING: Remember to update slurm.conf to match any CPU overrides on compute nodes to prevent resource allocation conflicts.

The naming convention for nodes follows a specific pattern: nodeX, where X is a number corresponding to the node's position within the cluster. This convention is strictly adhered to due to the iteration logic within the Vagrantfile, which utilizes a loop iterating over an array range defined by the number of slurm nodes (Array(1..SLURM_NODES)). Each iteration of the loop corresponds to a node, and the loop counter is in the node name (nodeX).

The overrides, if specified in nodes.rb, take the highest precedence, followed by the overrides in .settings.yml, and lastly, the defaults hard coded in the Vagrantfile itself. This hierarchy allows for a flexible configuration where global overrides can be specified in .settings.yml, and more granular, per-node overrides can be defined in nodes.rb. If a particular setting is not overridden in either .settings.yml or nodes.rb, the default value from the Vagrantfile is used.

If you wish to override the default settings on a per-node level, you can do so by creating a nodes.rb file based on the provided example-nodes.rb file:

cp example-nodes.rb nodes.rb

Once you have copied the example-nodes.rb to nodes.rb, you can edit it to override the default settings. Below are the available settings available per-node:

• BOX
  • Default: debian/bookworm64 (or as overridden in .settings.yml)
  • Vagrant box or image to be used for the node.
• CPU
  • Default: 2 (or as overridden in .settings.yml)
  • Defines the number of CPU cores or threads (depending on architecture).
• MEM
  • Default: 2048 (2 GB) (or as overridden in .settings.yml)
  • Specifies the amount of memory (in MB) allocated to the node.
• SSH
  • Default: false (or as overridden in .settings.yml)
  • Enable this if you need to forward SSH agents to the Vagrant machine

All settings are optional, and as many or as few options can be overridden on any arbitrary node.