Building a Beowulf Cluster on Ubuntu 16.04

The process has been divided into following steps:

A. Installation for Beowulf Cluster

B. Internet resources for Cluster development

C. Software for accessing cluster

D. Accessing the cluster

E. Problems faced during installation

Each step is described in detail below:

A. Steps for Installation of Beowulf Cluster:

1. Hardware connections

2. Master PC installation

3. Worker PC installation

4. Worker PC Cloning

5. Installing Workload Manager (Optional. For giving access to multiple users)

1. Hardware Connections

One of the PC is master node and others will be worker nodes.
Master will require 2 LAN cards: one connects to the internet directly and the other to the network router for communicating with other worker PCs.
Make hardware connections Ethernet cables: one from each PC should go to the network router.
You might want a KVM (Keyboard-Video-Mouse) switch for cluster installation. This helps to access multiple PCs with one monitor, keyboard and mouse.

2. Master Node Installtion

Start with these two links:

First install MPI (Message Passing Interface) variant: MPICH, OpenMPI, etc. on the master PC and then install the softwares you need.

3. Worker Nodes

Install MPI and the software (according to the instructions given in the above 2 links) on one worker PC. If the worker PCs are of the same configuration, you can clone the single worker (called the Golden Worker) to other workers. You do not have to install even the Operating System. All the drivers, hard-disk configurations and softwares are cloned to the new PC. You will just need to rename the PC and assign a local IP address.

4. Clone Golden Worker PC:

See this page

5. Install a WorkLoad Manager

Workload manager such as Slurm is a job scheduling software used when you have multiple users using the same resource.

It is an open-source job scheduling software used by more than 60% of Top500 supercomputers in the world.

List of other Workload managers

List 1

List2

Tutorial for setting-up Workload Manager on Beowulf Cluster

B. Some internet resources

Best Resources

Building a Beowulf Cluster in just 13 steps(Start with this)
MPICH Cluster Linux(And This)
WikiBooks(Use Case)

Others

C. Useful software for cluster

cssh (Cluster SSH) to log on to all worker PCs at once.
top or htop to see the CPU and memory usage.
Meld: For file/folder comparison.
Text Editors: Both the text editors below have option for hoc and mod syntax highlighting
- Microsoft Visual Studio Code (Another text editor)
- Sublime Text editor
MATLAB

Parallel computing with MATLAB® on a cluster requires two products:

MATLAB Distributed Computing Server™, which should be installed on each computer of the cluster that performs the computation.
Parallel Computing Toolbox™, which should be installed on the computer where you write your applications.
Installation

D. Using the Cluster

Ubuntu

Use ssh. Open Terminal. ssh using user credentials: ssh username@IPADDRESS.

File transfer using FTP.

Windows

The cluster could be accessed using

Graphical User Interface (GUI via Remote Desktop Connection) or
Command line (using secure shell protocol, ssh)

Graphical User Interface Based (Windows)

There are two processes to be done here:

File Transfer using Winscp or a Network folder.
Running the Simulation using Remote Desktop Connection.

Softwares to Access Cluster from Windows

Windows Remote Desktop Connection
File Transfer: 'Winscp'
- Its main function is file transfer between a local and a remote computer. Beyond this, WinSCP offers scripting and basic file manager functionality.
- How to Use it
- It also has several built-in functionalities e.g. ssh shell, script editor

Command Line Based (Windows)

a. Install Putty

b. Launch Putty from Windows menu

c. Type IP Address in the Host Name

d. Login using user credentials.

e. Copy file from your PC to cluster using the scp command.

Optional Xming server could be used to see gui along with command line.

g. Download and install Xming Server

h. Launch Xming Server before logging in through Putty.

i. Now, if you launch any GUI based program from Putty e.g. firefox, nrngui you will see their graphical window.

E. Some Problems faced during the development

In the 13 step guide to cluster development **Needed to install a fortran compiler at step 9 before configure step. Compiler installed gfortran sudo apt-get install gfortran

**used latest version of MPICH: mpich-3.2

**For step number 11: Use this (instead of what is mentioned in the step)

echo /home/mpiuser/mpich1/bin | sudo tee -a /etc/environment

sudo bash -c 'echo /home/mpiuser/mpich1/bin >> /etc/environment

Cloning of Golden Slave

On the golden slave (or an identical clone) you run:

node1# dd if=/dev/hda conv=sync,noerror bs=64k | nc -l 5000

On the completely blank soon-to-be-slave you run:

node2# nc 192.168.1.6 5000 | dd of=/dev/hda bs=64k

where 192.168.1.6 is the ip of the golden slave. This presupposes the disk of soon-to-be slave is at least as big as the disk in the golden slave.

This took several (~4) hours time, but it worked.

NB: Don't forget to go to superuser before using these commands i.e. use sudo su

Use these

node1# sudo dd if=/dev/hda conv=sync,noerror bs=64k | nc -l 5000

node2# nc 192.168.1.6 5000 | sudo dd of=/dev/hda bs=64k

dd is convert and copy and requires administrative priviledges.

dd reference

Password Less SSH

Procedure to create a password-less ssh access:

A password-less ssh access should be maintained from the master to the slaves for the proper working of the Beowulf Cluster. This was done using the following procedure in the terminal of the master node:

ssh-keygen

just press Enter key with empty strings, whenever prompted.

You will be prompted three times (i) Enter file in which to save the key (ii) Enter the passphrase (iii) Enter the passphrase again.

ssh-copy-id <username>@<host_ip_address>

Here the username is mpiuser (which is the username currently set for all the nodes in this cluster - this may be changed later as per the imagination of lab sysad). The host_ip_address is the ip address for the slave node to which password-less access is to be established from the master node. For the current cluster, a local ip address of the format 192.168.1.X is set ( X = 5 for master node, 6, 7, 8 for slaves 1, 2, and 3).

After this command, you will be prompted to enter the password to the slave node. You have to enter the password once.

Thats it! After this you can ssh to the slave node from the master node using the command

ssh <username>@<host_ip_address>

without entering a password.

For detailed explanation, see this.

Problems with the shared folder :"/mirror"

The folder is the root directory. And is not allowing to add new files to the folder.

Solution

i) Try to change the ownership of the folder,

Problem during shutting down of the PC. The PC remains at the splash screen for a lot of time and does not get shut down.

ii) Write a script to copy data from master to all worker PCs after doing pasword-less ssh.

Display Driver Problems

GUI (Unity) won't resume after screen suspend. Try the options here

00mjk / cluster Goto Github PK

cluster's Introduction