Ubuntu with OpenMPI and OpenMP

This project provides tutorials and scripts to install OpenMPI and OpenMP on Ubuntu Linux machines.

Prerequisites

• Ubuntu Linux 18.04 LTS Server Edition
• SSH Key

SSH Keys

• Generate your SSH key specifying the proper username to use in the ssh and scp commands: ssh-keygen -t rsa -C <username>.
• The command will create the id_rsa private key and the id_rsa.pub public key in the .ssh folder.
• Access the value of the SSH public key using cat <ssh-key-file>.
• Add the public key to the machines you need to access, i.e., the MASTER node.

Cluster Scenario

• 1 MASTER Node, where you must generate the SSH key and update the script.
• N WORKERs, here you have to run the script using the keys generated on the master node.
• Install git where needed using sudo apt update && sudo apt install git.

Installing

1. Copy on the MASTER node, from your local machine, the SSH key using the External IP: scp -i "<ssh-key-file>" <ssh-key-file> username@<instance-external-IP>:
2. Login on the MASTER node using the External IP: ssh -i <ssh-key-file> username@<instance-external-IP>
3. Install git using sudo apt update && sudo apt install git.
4. Clone the repository: git clone https://github.com/spagnuolocarmine/ubuntu-openmpi-openmp.git
5. Generates the installing script for your cluster: source generateInstall.sh, results in a install.sh script with new ssh-keys for the cluster.
6. Run chmod +x install.sh and then run the script install.sh on the MASTER from your user.
7. The generated keys are now in the .ssh folder of the user pcpc and are accessible with sudo login pcpc using the password root.
8. Copy both public and private SSH keys into your user space using sudo cp <ssh-key-file> /home/myusername/.ssh and use sudo chown myusername:myusername <ssh-key-file> to assign proper permissions.
9. Add the public key to each WORKER instance.
10. For each WORKER instance, run the install script from the MASTER node (your user): ssh -i <ssh-key-file> username@<instance-external-IP> 'bash -s' < install.sh E.g., ssh -i .ssh/id_rsa myusername@35.202.249.14 'bash -s' < install.sh

The password for the pcpc user is root

Test

1. On the MASTER node, login to pcpc user sudo login pcpc with password root
2. Local login ssh localhost
3. Remote login on a worker node ssh <instance-external-IP>

The program will create a new user, pcpc, and exchange the given SSH keys.

Environment

• user: pcpc
• vim
• htop
• OpenMPI 4.0
• OpenMP included in the GNU GCC (last version)

Test the environment

You can test your local environment using the program hello-mpi.c.

1. Compile the program: mpicc hello-mpi.c -o hello
2. Run the porgram: mpirun -np 2 ./hello
3. Run with more MPI processes on single core mpirun -np 3 --oversubscribe ./hello.

You can run directly on a homogeneous cluster machine that has been built using the same install script. To do so:

1. Create a host file containing the MASTER IP and all the WORKERS' IPs.
2. Copy the result of mpicc hello-mpi.c -o hello to workers using scp ./hello <worker-external-IP>:/home/pcpc/hello
3. Run mpirun -np 2 --hostfile hfile ./hello.

An example of a host file is:

# This is an example host file.  Comments begin with #
#
# The following node is a single processor machine:
foo.example.com
 
# The following node is a dual-processor machine:
bar.example.com slots=2
 
# The following node is a quad-processor machine, and we absolutely
# want to disallow over-subscribing it:
yow.example.com slots=4 max-slots=4

Authors and Contributors

• Matteo D'Auria (University of Salerno)
• Carmine Spagnuolo (University of Salerno)
• Giuseppe D'Ambrosio (University of Salerno)
• Tiziano Citro (University of Salerno)