Parallel and Concurrent Programming and on the Cloud

Master Degree Course of prof. Vittorio Scarano

Università degli Studi di Salerno

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HOMEWORKS LIST

Academic Year 2016/2017

• gameoflife the Conway's Game of Life Game.
• jacobi a simple Jacobi iteration.
• matrixmultiplication parallel matrix multiplication.
• nbody the n-body problem.
• pi compute in parallel an approximation of PI.
• wordscount compute the frequency of words in a set of files.

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Update Execute benchmark!

• m4.large (ex. m3)
• m4.xlarge (ex. c3)

AWS Educate Instances

How benchmark your applications on a cloud computing infrastructure?

Tools to benchmark on Amazon AWS

• StraCluster toolkit use this script to setup an Amazon EC2 cluster supporting OpenMPI
• Java application to setup an Amazon EC2 cluster supporting OpenMPI based on StarCLuster AMI

Start EC2 instances and configure manually an MPI cluster

This method is based on the public StarCluster AMI ami-52a0c53b (Linux Ubuntu) available on us-east-1 AWS region. For other information visit the StarCLuster site page.

How to manually configure a MPI cluster of two istances?

In this example is described how to execute and manually configure a cluster of two t2.micro instances using the AWS WebConsole.

1. Create a new key-pair and store it on your local machine, suppose that the name of the key is kcluster.
2. Start two new t2.micro instances using the StarCluster AMI (ami-52a0c53b) and select the kcluster key-pair, additionally rename it as master and slave0. Set a new rule to the default security group that allows to open all TCP ports (0-65535) from anywhere (you can do it in the Configure Security Group tab).
3. Connect via SSH and execute these commands on the master instance to create a new user pcpc and generate a SSH key:

sudo useradd -s /bin/bash -m -d /home/pcpc -g root pcpc
sudo mkdir -p /home/pcpc/.ssh
sudo chown pcpc:root ../pcpc/.ssh
sudo passwd pcpc
sudo login pcpc
ssh-keygen -t rsa

4. Set the SSH key for the user pcpc.

cat .ssh/id_rsa.pub >> .ssh/authorized_keys
ssh localhost

4. Connect using SSH and execute these commands on a slave instance:

sudo useradd -s /bin/bash -m -d /home/pcpc -g root pcpc
sudo mkdir -p /home/pcpc/.ssh
sudo chown pcpc:root ../pcpc/.ssh
sudo passwd pcpc
sudo login pcpc

5. Copy from your local machine the kcluster file (pem file) on the master node.

scp -i pcpkey.pem pcpkey.pem ubuntu@ec2-34-207-88-239.compute-1.amazonaws.com:

6. From the master node copy on each slave the files id_rsa and id_rsa.pub:

sudo scp -i pcpkey.pem ../pcpc/.ssh/id_rsa ubuntu@ip_slave_internal:
sudo scp -i pcpkey.pem ../pcpc/.ssh/id_rsa.pub ubuntu@ip_slave_internal:

7. Connect on the slave and set the owner as the pcpc user for the files id_rsa and id_rsa.pub.

sudo chown pcpc:root id_rsa id_rsa.pub 

8. Connect on the slave and move the files id_rsa and id_rsa.pub on /home/pcpc/.ssh.

sudo mv id_rsa id_rsa.pub /home/pcpc/.ssh

9. Login on the slave as pcpc user and set the SSH key.

cat .ssh/id_rsa.pub >> .ssh/authorized_keys
ssh localhost

HINT

In order to add a new slave you have to start new EC2 instance and repeat the steps 4 and from 6 to 9.

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Test MPI Program

Follow these steps in order to create and test a Hello World MPI program. Consider that you are logged as pcpc user on the master node.

• Create a new MPI program vim hello.c
• HelloWorld MPI program

#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();
}

• Compile the MPI program mpicc hello.c -o hello
• Copy on all cluster machine the compiled program scp hello IP_SLAVE:
• Run the program on the cluster mpirun -np 4 --host MASTER,IP_SLAVE1,IP_SLAVE2 hello

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Submit a solution

Each solution should be compliant with the problem project template. You can submit a solution via mail using the [PCPC-SOLUTION] object to vitsca@dia.unisa.it and cspagnuolo@unisa.it. The submitted file should be a compressed directory using tape archive.

Prepare your submition

Each solution folder must contain the C sources and a report Readme file (in Markdown format) describing all benchmarks (expressed in terms of strong and weak scalability) of the application. Solutions without the Readme file or that cannot easily compile using mpicc will be not considered.

In your home project directory archives your project:

tar -cvf solution.tar.gz *

Extract your project:

tar -xvf solution.tar.gz