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Beowulf Cluster Setup

Beowulf Cluster Setup

Asanka Akash Sovis's photo
Asanka Akash Sovis
·

18 min read

Table of contents

1. Introduction

A Beowulf cluster is a type of High-Performance Computing (HPC) cluster that is designed to perform parallel computations on large data sets or complex computational problems. It is named after the legendary warrior Beowulf, who is known for his strength and ability to overcome seemingly insurmountable challenges.

The main feature of a Beowulf cluster is that it is created by using all the open-source resources available. Beowulf clusters are typically built using commodity hardware components: such as standard x86-based processors, Ethernet switches, and network interface cards. The nodes in a Beowulf cluster are connected through a high-speed local area network (LAN), which allows them to communicate and share resources efficiently.

One of the key features of a Beowulf cluster is its ability to distribute computing tasks across multiple nodes in parallel, allowing for faster processing times and improved performance. This is achieved through the use of a Message-Passing Interface (MPI), which allows nodes to communicate and coordinate their efforts in executing complex computations.

Beowulf clusters are commonly used in scientific research, engineering and other fields where large-scale computational tasks are required. They can be used to simulate complex physical processes, analyze massive data sets, and perform other computationally intensive tasks that would be impractical or impossible to perform on a single machine.

Overall, Beowulf clusters represent a powerful and cost-effective solution for high-performance computing, allowing organizations to harness the power of parallel computing to solve complex problems and drive innovation. Implementing a Beowulf cluster involves several steps, including hardware selection, software configuration, and network setup.

2. Hardware Selection

The hardware components required to follow this tutorial are as follows.

  • More than one x86-based computer (these can be low-powered)

  • A router/switch with enough ethernet ports and cables to connect all the computers and internet access

  • A monitor, keyboard and optionally a mouse

  • USB Stick (At least 8GB)

  • A separate computer for setting up the cluster

To make this tutorial the below components are used. It is not essential to use exactly these items but these are mentioned simply to get an idea of how to choose these components.

  • Three 64-bit HP desktop computers with 4GB of RAM, CPUs with four cores at 1.5 GHz and a hard disk of 500GB

  • ADSL router with four ethernet ports

  • Dell monitor and Logitech keyboard

  • 8GB USB stick

3. Choosing an Operating System

In the very definition of a Beowulf cluster, it is mentioned open source software. Thus, it is essential to use an open-source operating system such as Linux to run on these computers. The most common OS used is Ubuntu Server although any of the available Linux OS would be suitable with slight variations of the software used and steps mentioned. In this example Ubuntu Server 22.04.2 is used however, other versions should also work with the above disclaimers.

4. Preparing for the Setup

Before starting to implement the cluster, a few things have to be taken care of. These are essential for the correct setting up of the cluster. Make sure to follow these steps carefully before moving further.

1. Setting up the Hardware

The first step is to set up the hardware correctly. This includes connecting the computers to the router via the ethernet cables. Pick one computer to be the master and the rest of the computers to be the slaves. The master computer or master node as referred to in Beowulf terms, is the computer that runs the program itself. This node breaks the process into multiple blocks and sends it to the slave computers or nodes to be processed. The router should be connected to the internet by suitable means. Internet connection is not essential for the operation of the Beowulf cluster but is only important for setting up the cluster.

The monitor, keyboard and optionally the mouse can be connected to the master node; however, note that these have to be removed and reconnected to the other computers as well.

2. Installing the Operating System

The best way to install the operating system on the hardware is to use a bootable USB stick. Use a separate computer and download the ISO of the installer of the preferred Linux OS, in the case of this tutorial, Ubuntu Server 22.04.2 is used as previously mentioned.

Also, download the Rufus bootable USB tool. In this example Rufus Version 3.22 (Build 2009) is used, however, the version number has little to no effect on the setup. Other bootable USB creators can also be used.

Open Rufus and choose the preferred USB device under Device. Then click on 'Boot Selection' and choose Disk or ISO image (Please select) and click on SELECT to choose the ISO file. Navigate to the ISO file and choose it. Other options should be left at default and click on START. For the warning, click OK although note that this process formats the pen drive and all data currently in it will be lost. For the next page, keep the defaults and click on OK as well. This will start the process of formatting the device into a bootable pen drive. Wait for this process to complete and remove the pen drive.

Next, we should install the OS on the hardware. For this, connect the pen drive to each computer one after the other and install the OS. In certain computers, when booting the OS in EFI mode will result in installation errors. In cases like this, try switching to Legacy BIOS before continuing with the installation. The steps involved might change from computer to computer on how to switch to 'Legacy mode' and how to enter the boot menu. Please refer online for the specific models.

The installation steps are normal. In all of the steps, the defaults will work fine. On each page, highlight the option Done. It is not essential to set up the network as this will be done in a future step. Downloading additional packages is also not necessary. Following the steps in this tutorial will be sufficient. In the Identity screen, however, under 'Your name:', 'Your server name:' and 'Pick a username:'; enter the following:

  • 'master' for the computer you wish to use as the main computer of the cluster

  • 'node1', 'node2', 'node3', etc. for the rest of the computers

It is not essential to follow this naming convention but will help identify the computers individually. For the 'Choose your password:' and 'Confirm your password:', enter a common password for all computers. This will help keep consistency although it's not essential to have the same password in all computers. Once the installation is complete, select Reboot. Every time the computers are turned on, enter the computer name and password to log in to the computers.

5. Setting up the Beowulf Cluster

1. Introduction

As mentioned before, the Beowulf cluster is a computer cluster made up of open-source components. Thus to set it up, the following components need to be set up in the computers.

  • Message Passing Interface

  • Network File System

  • Hydra Process Manager

Make sure all the previous steps are followed correctly and that you have all of the computers ready with Ubuntu Server (or any other Linux distro) installed.

2. Setting Up the IP addresses

To continue, each computer must have a unique static IP address. For example, in our case, we will use the IP address of the master as 192.168.1.5, node1 as 192.168.1.6, node2 as 192.168.1.7, etc. It is not mandatory to use these exact IP addresses but using a consistent IP address assigning might come in handy. Make sure you remember which computer has which IP address.

To set up static IP addresses, first, make sure that all computers are correctly connected via ethernet to the router/switch. If this is confirmed, continue with the setup process. The below steps have to be performed on all the computers, thus disconnect and connect the keyboard and monitor to each computer and continue them.

  1. Enter the command ip a on the terminal of each computer. This will list all the network interfaces connected to the computer. Find the one connecting the computer to the router/switch. Usually, this might be labelled as eno0, eno1, enp0s25 or eth0.

  2. Once identified, move to the folder /etc/netplan. (Use the command cd /etc/netplan) Once in this folder, check if a file named 99_config.yaml or similar exists. (Use the command ls) If so open this using Nano or any other text editor. If it doesn't exist, create a file named 99_config.yaml. (Use the command sudo nano 99_config.yaml) Enter the below information in the file.

network:
  version: 2
  renderer: networkd
  ethernets:
    eno0:
      addresses:
        - 192.168.1.5/24
      routes:
        - to: default
          via: 192.168.1.1
      nameservers:
          search: [mydomain, otherdomain]
          addresses: [10.10.10.1, 1.1.1.1]

Under addresses:, include the IP address to be assigned for that particular computer. In this example, we've included the IP address we provided for the master. Under routes:, next to via:, include the IP address of the router. This is typically 192.168.1.1.

  1. After completion, exit the text editor while saving the file. (Ctrl + X -> Y -> Enter for nano)

  2. Use the command sudo netplan apply to apply the configuration.

  3. On each computer, enter the command ping 192.168.1.5 where the IP address is to be replaced by the IP addresses of other nodes. Try for each node to each of the other nodes. If the configuration is correctly performed, you will receive a ping. If not, go through the steps and see if all of them are done correctly and that the network is set up correctly. A reason why this might fail is because the firewall refuses the connection. In that case, try disabling the firewall.

  4. The next step is to add the hostnames to the hosts file. For this, move to the /etc folder. Edit the hosts file. Make sure the following hosts also exist in this file.

127.0.0.1       localhost
192.168.42.50   master
192.168.42.51   node1
192.168.42.52   node2

The IP addresses must match the IP address of the relevant node. Add all of the nodes you have here.

3. Creating the MPI User

A common user must exist across all computers to facilitate communication. For this reason, we will create a user called mpiuser across all the computers. This username as well as the UUID must be common to facilitate with the SSH authorization. Use the following command to create a user on all computers.

sudo adduser mpiuser --uid 999

If the UUID 999 is already taken, do the same command but with a different number. However, make sure that the same UUID is provided across all computers for this user. Also, make sure to include a number equal to or more than 999. Make sure to use a consistent password to avoid confusion. (Note that for certain commands, you might need to switch back to the main account; for example, commands that require sudo privileges. Entering the command exit will switch you back to the main account.)

4. Setting up the Network File System (NFS)

Network File System (NFS) is a distributed file system protocol that allows a user on a client computer to access files over a network as if those files were on the local computer. With NFS, a user can browse the remote file system, read and write files, and even execute programs located on the remote server. This makes it possible for multiple users to share files and collaborate on projects from different locations.

For this, the computers require an internet connection. If not, connect each computer to the internet and continue the steps. It is ok to disconnect the computers from the router/switch if required. Complete the steps and reconnect to the router/switch.

Use sudo apt-get update and sudo apt-get upgrade to get the app list and apps up to date. Then install NFS as explained below.

For the master node, enter the below command.

sudo apt-get install nfs-kernel-server

For the rest of the nodes, use the below command.

sudo apt-get install nfs-common

This will install the relevant NFS package on each computer.

5. Sharing the Home folder

Across all the computers, the /home/mpiuser directory has to be shared via NFS. For this, the /home/mpiuser directory has to be owned by the mpiuser. However, this folder is already created while adding the user, which means that the mpiuser already has access to it. To verify this, the following command can be used.

master:~$ ls -l /home/ | grep mpiuser

If the folder is already owned by the mpiuser, this should return a message similar to below.

drwxr-xr-x 7 mpiuser mpiuser 4096 May 30 05:55 mpiuser

If you want to share some other folder, use the below command on the master node with the specific folder you need to share.

sudo chown mpiuser:mpiuser /path/to/shared/dir

Now, the /home/mpiuser or any other folder created before the master node needs to be shared with the rest of the nodes. For this, the relevant folder needs to be added to the /etc/exports file. To do this, navigate to the /etc folder. (Use the command cd /etc) Now edit the file with the text editor (Use the command sudo nano exports) and add the following entry to it. This should only be done in the master node.

/home/mpiuser *(rw,sync,no_subtree_check)

Once done, save the file, (Ctrl + X -> Y -> Enter for nano) and then restart the NFS kernel using the below command.

sudo service nfs-kernel-server restart

To check if the folder is shared correctly, use the following command on the master node.

showmount -e master

If correctly performed, this should print the folder /home/mpiuser or the relevant folder on the terminal.

The next step is to check if it's accessible to the other nodes. Before that, we need to make sure the firewall doesn't block the communications between computers. For this, you can either disable the firewall or enter the following command on all computers. The IP address should be the gateway address. (*xxx.xxx.xxx.0/24)

sudo ufw allow from 192.168.1.0/24

Once complete, check the connectivity with the ping command used before.

Now, we can mount the shared folder on other nodes. For this, we use the below command on all nodes.

sudo mount master:/home/mpiuser /home/mpiuser

If this command hangs or fails, there's an issue with the configuration. If the command succeeds, test if the folder is shared across all nodes. For this, you can create a file in the /home/mpiuser directory of the master and see if it appears in the rest of the nodes. (Use the command touch hello to create a file)

If everything is correct so far, we have to set up the nodes to automatically mount this folder at boot. For this, move to the folder /etc/, (Use the command cd /etc/) then edit the file fstab on all computers. (Use the command sudo nano fstab) Add the below entry to this file.

master:/home/mpiuser /home/mpiuser nfs

Now reboot all computers and see if the system is correctly working, for example, the hello file is accessible from all nodes.

6. Setting up the Secure Shell (SSH)

SSH (Secure Shell) is a cryptographic network protocol that provides a secure way to access remote systems over an unsecured network. It was developed as a replacement for Telnet and other insecure remote shell protocols. To continue, SSH has to be set up on all computers.

Connect each computer to the internet and use the following command to install SSH.

sudo apt-get install ssh

Once done on all computers, SSH keys need to be generated under the mpiuser for all computers. Since the home folder is shared across all computers, these keys will be accessible to the master. On each computer, switch to the mpiuser, (Use the command su mpiuser) and then enter the following command.

ssh-keygen

When asked for a passphrase, leave it empty (hence passwordless SSH). Now switch to the master node and enter the following command under mpiuser.

ssh-copy-id localhost

If done correctly, you will get a message that says something similar to 'Number of key (s) added: 3'.

If configured correctly, now you might be able to SSH into any of the nodes from the master. Try to use the below command to enter into SSH from master to node1.

ssh node1

This should change the prompt from mpiuser@master:~$ to mpiuser@node1:~$ . This means that all commands executed will be executed inside of the mpiuser of node1. For example, the command echo $HOSTNAME, will print node1 instead of master. An advantage of this setup is that by using the command systemctl -i poweroff, you can shut down each computer remotely when SSH into the specific node. The same should apply to all other nodes.

7. Setup Hydra Process Manager

Hydra is a process management system used to manage and monitor processes on a Unix or Linux system. It is designed to be simple to use and can be used to start, stop, and monitor multiple processes at once. Hydra consists of two main components: a daemon process that runs in the background and a command-line interface that allows users to manage processes. The daemon process is responsible for starting and stopping processes, monitoring their status, and responding to commands from the command-line interface.

The Hydra Process Manager is included with the MPICH package, so we need to install MPICH on all computers. To do this, switch between each computer and use the following command to install it. To do this, make sure that the computer is connected to the internet.

sudo apt-get install mpich

This should install MPICH on all nodes. Once done, network all computers to the correct configuration and continue.

The next step is to configure MPICH. To do this, switch to the master and switch to mpiuser. (Use the command su mpiuser) Once in the mpiuser, move to the home directory. (Use the command cd ~) Now use a text editor to create a file called hosts, (Use the command nano hosts for nano) and enter the hostnames of the nodes you want the processes to run. You can either include the master node as a computer node or only use the other nodes. For example, refer to below. Once done, save the file. (Ctrl + X -> Y -> Enter for nano)

master
node1
node2

The above example will run the programs distributed across master, node1 and node2.

6. Running a Sample Program

1. Simple MPI Program in C

To write a simple MPI-based program in C, we will first create the source code. For this, we will switch to the mpiuser (Use the command su mpiuser) and move it into the home folder. (Use the command cd ~) Here, we will create a new file. (Use the command nano hello.c)

In it, we will write the following sample code.

#include <mpi.h>
#include <stdio.h>

int main(int argc, char** argv) {
    // Initialize the MPI environment
    MPI_Init(NULL, NULL);

    // Get the number of processes
    int world_size;
    MPI_Comm_size(MPI_COMM_WORLD, &world_size);

    // Get the rank of the process
    int world_rank;
    MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);

    // Get the name of the processor
    char processor_name[MPI_MAX_PROCESSOR_NAME];
    int name_len;
    MPI_Get_processor_name(processor_name, &name_len);

    // Print off a hello world message
    printf("Hello world from processor %s, rank %d out of %d processors\n",
           processor_name, world_rank, world_size);

    // Finalize the MPI environment.
    MPI_Finalize();
}

The code is designed to print the node names and their ranks on the terminal of the master.

The next step is to compile the code into an object file. For this, use the following command.

mpicc -o hello.o hello.c

This will compile the code into an object file. Now we can run the MPI program on the cluster. For this, enter the following code.

mpiexec -n 12 -f hosts hello.c

Here, -n 12 defines that the process should run on 12 threads and that -f hosts define the file which contains the list of nodes to run the program on.

If working correctly, it should print a result as below.

Hello world from processor 1, rank 1 out of 12 processors
Hello world from processor 5, rank 5 out of 12 processors
Hello world from processor 3, rank 3 out of 12 processors
Hello world from processor 2, rank 2 out of 12 processors
Hello world from processor 8, rank 8 out of 12 processors
Hello world from processor 4, rank 4 out of 12 processors
Hello world from processor 6, rank 6 out of 12 processors
Hello world from processor 7, rank 7 out of 12 processors
Hello world from processor 9, rank 9 out of 12 processors
Hello world from processor 10, rank 10 out of 12 processors
Hello world from processor 12, rank 12 out of 12 processors
Hello world from processor 11, rank 11 out of 12 processors

2. Simple MPI Program in Python

It is also possible to run an MPI program on Python. For this, we will follow the same steps and create a source file, this time named hello.py. In it, we will write the following code.

from mpi4py import MPI

comm = MPI.COMM_WORLD
rank = comm.Get_rank()
name = MPI.Get_processor_name()

print('My rank is ', rank, ' and hostname is ', name)

Once done, save the file and use the following command to run the program.

mpirun -np 12 --hostfile hosts python3 hello.py

If you get an error that says that mpi4py library is not installed, install it. (under mpiuser, use the command pip install mpi4py) If you get an error that says something similar to Permission Denied, use the command chmod +rwx ~ under mpiuser to mark the home folder and its content as executable. Retry running the command again.

You should get an output similar to below.

My rank is 1 and hostname is master
My rank is 3 and hostname is master
My rank is 2 and hostname is master
My rank is 4 and hostname is master
My rank is 5 and hostname is node1
My rank is 6 and hostname is node1
My rank is 8 and hostname is node1
My rank is 9 and hostname is node2
My rank is 7 and hostname is node1
My rank is 10 and hostname is node2
My rank is 11 and hostname is node2
My rank is 12 and hostname is node2

7. Conclusion

In conclusion, a Beowulf cluster is a type of high-performance computing cluster that is built from commodity hardware and is designed to run parallel computing applications. The Beowulf cluster architecture is based on a master-slave model, where a central master node manages the workload and distributes tasks to multiple slave nodes.

MPI (Message Passing Interface) is a standard interface for programming parallel applications on a Beowulf cluster. It allows processes to communicate with each other and synchronize their actions across multiple nodes. MPI provides a set of standard libraries and functions that can be used to develop scalable and efficient parallel applications.

Together, a Beowulf cluster and MPI provide a powerful platform for running large-scale parallel applications. They can be used for a wide range of applications, including scientific simulations, data processing, and machine learning. The scalability and flexibility of these systems make them an ideal choice for organizations and research institutions that require high-performance computing capabilities.

8. Reference

clusterHigh Performance Computing optimizationbeowulfalmanac