Mentor: Peng

Training Topics
Pre-require:

1. understand the concept of OpenMP and MPI, multiple-thread vs multiple-process 

OpenMP: 

Use OpenMP when working on a shared memory system and the parallelism can be easily expressed using threads. 
It is often simpler to implement and can be very efficient for multi-core processors.

MPI: 

Use MPI for large-scale distributed computing across multiple nodes. 
It is essential for applications that require high scalability and involve complex communication patterns among processes.



Multiple Threads

Threads are the smallest unit of execution within a process. 
Multiple threads within a single process share the same memory space and can communicate more efficiently than separate processes. 
Each thread has its own stack but shares code, data, and file descriptors with other threads in the same process.

Multiple Processes

Processes are independent execution units that have their own memory space. 
Multiple processes can run concurrently on different CPUs or cores and communicate via inter-process communication (IPC) mechanisms like pipes, sockets, shared memory, or message passing.


2. create scripts to run OpenMP helloworld and an example for parallel loop 




#include <omp.h>
#include <stdio.h>

int main() {
    // Parallel region
    #pragma omp parallel
    {
        int thread_id = omp_get_thread_num();
        printf("Hello World from thread %d\n", thread_id);
    }
    return 0;
}



gcc -fopenmp hello_openmp.c -o hello_openmp
./hello_openmp


This script demonstrates how to use OpenMP to parallelize a loop that calculates the square of each element in an array.

#include <omp.h>
#include <stdio.h>

#define N 100

int main() {
    int i;
    int array[N];

    // Initialize the array
    for (i = 0; i < N; i++) {
        array[i] = i;
    }

    // Parallelize this loop with OpenMP
    #pragma omp parallel for
    for (i = 0; i < N; i++) {
        array[i] = array[i] * array[i];
    }

    // Print the results
    for (i = 0; i < N; i++) {
        printf("array[%d] = %d\n", i, array[i]);
    }

    return 0;
}


gcc -fopenmp parallel_loop_openmp.c -o parallel_loop_openmp
./parallel_loop_openmp



3. create scripts to run MPI helloWorld and an example for parallel loop


module load mpich/ge/gcc/64/3.2rc2


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

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

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

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

    printf("Hello World from process %d of %d\n", world_rank, world_size);

    MPI_Finalize();  // Finalize the MPI environment
    return 0;
}


mpicc hello_mpi.c -o hello_mpi  # Compile the program
mpirun -np 4 ./hello_mpi        # Run the program with 4 processes


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

#define N 100

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

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

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

    int array[N];
    int local_N = N / world_size;  // Number of elements per process

    // Initialize the array in the root process (rank 0)
    if (world_rank == 0) {
        for (int i = 0; i < N; i++) {
            array[i] = i;
        }
    }

    // Scatter the array to all processes
    int local_array[local_N];
    MPI_Scatter(array, local_N, MPI_INT, local_array, local_N, MPI_INT, 0, MPI_COMM_WORLD);

    // Perform the computation locally
    for (int i = 0; i < local_N; i++) {
        local_array[i] = local_array[i] * local_array[i];
    }

    // Gather the results back to the root process
    MPI_Gather(local_array, local_N, MPI_INT, array, local_N, MPI_INT, 0, MPI_COMM_WORLD);

    // Print the results in the root process
    if (world_rank == 0) {
        for (int i = 0; i < N; i++) {
            printf("array[%d] = %d\n", i, array[i]);
        }
    }

    MPI_Finalize();  // Finalize the MPI environment
    return 0;
}



mpicc -std=c99 parallel_loop_mpi.c -o parallel_loop_mpi
mpirun -np 4 ./parallel_loop_mpi



2. Write serial and MPI versions of blowfish


blowfish_serial.c

#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include <stdlib.h>
#include <time.h>
#include <openssl/blowfish.h>

#define DATA_SIZE 100000000 // Larger dataset to exaggerate difference

void blowfish_encrypt(BF_KEY *key, uint8_t *data, size_t data_len, uint8_t *encrypted) {
    size_t i;
    for (i = 0; i < data_len; i += 8) {
        BF_ecb_encrypt(data + i, encrypted + i, key, BF_ENCRYPT);
    }
}

void blowfish_decrypt(BF_KEY *key, uint8_t *data, size_t data_len, uint8_t *decrypted) {
    size_t i;
    for (i = 0; i < data_len; i += 8) {
        BF_ecb_encrypt(data + i, decrypted + i, key, BF_DECRYPT);
    }
}

int main() {
    BF_KEY key;
    uint8_t *data = malloc(DATA_SIZE);
    uint8_t *encrypted = malloc(DATA_SIZE + 8); // Adding padding space
    uint8_t *decrypted = malloc(DATA_SIZE);

    // Initialize data
    size_t i;
    for (i = 0; i < DATA_SIZE; ++i) {
        data[i] = 'A' + (i % 26);
    }

    uint8_t key_data[16];
    for (i = 0; i < 16; ++i) {
        key_data[i] = rand() % 256;
    }

    BF_set_key(&key, 16, key_data);

    clock_t start, end;
    double cpu_time_used;

    start = clock();
    blowfish_encrypt(&key, data, DATA_SIZE, encrypted);
    end = clock();
    cpu_time_used = ((double) (end - start)) / CLOCKS_PER_SEC;
    printf("Encryption time (serial): %f seconds\n", cpu_time_used);

    start = clock();
    blowfish_decrypt(&key, encrypted, DATA_SIZE, decrypted);
    end = clock();
    cpu_time_used = ((double) (end - start)) / CLOCKS_PER_SEC;
    printf("Decryption time (serial): %f seconds\n", cpu_time_used);

    // Validate the decrypted data
    if (memcmp(data, decrypted, DATA_SIZE) != 0) {
        printf("Decrypted data does not match original data!\n");
    } else {
        printf("Decrypted data matches original data!\n");
    }

    free(data);
    free(encrypted);
    free(decrypted);

    return 0;
}




gcc blowfish_serial.c -o blowfish_serial -lcrypto -std=99
./blowfish_serial





blowfish_mpi.c

#include <mpi.h>
#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include <stdlib.h>
#include <time.h>
#include <openssl/blowfish.h>

#define DATA_SIZE 100000000 // Larger dataset to exaggerate difference

void blowfish_encrypt(BF_KEY *key, uint8_t *data, size_t data_len, uint8_t *encrypted) {
    size_t i;
    for (i = 0; i < data_len; i += 8) {
        BF_ecb_encrypt(data + i, encrypted + i, key, BF_ENCRYPT);
    }
}

void blowfish_decrypt(BF_KEY *key, uint8_t *data, size_t data_len, uint8_t *decrypted) {
    size_t i;
    for (i = 0; i < data_len; i += 8) {
        BF_ecb_encrypt(data + i, decrypted + i, key, BF_DECRYPT);
    }
}

int main(int argc, char** argv) {
    MPI_Init(&argc, &argv);

    int rank, size;
    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
    MPI_Comm_size(MPI_COMM_WORLD, &size);

    BF_KEY key;
    uint8_t key_data[16];
    size_t i;
    for (i = 0; i < 16; ++i) {
        key_data[i] = rand() % 256;
    }
    BF_set_key(&key, 16, key_data);

    size_t chunk_size = DATA_SIZE / size;
    uint8_t *local_data = malloc(chunk_size);
    uint8_t *local_encrypted = malloc(chunk_size + 8); // Adding padding space
    uint8_t *local_decrypted = malloc(chunk_size);

    if (rank == 0) {
        uint8_t *data = malloc(DATA_SIZE);
        uint8_t *encrypted = malloc(DATA_SIZE + 8 * size); // Adding padding space
        uint8_t *decrypted = malloc(DATA_SIZE);

        // Initialize data
        for (i = 0; i < DATA_SIZE; ++i) {
            data[i] = 'A' + (i % 26);
        }

        double start, end;

        // Scatter data to all processes
        MPI_Scatter(data, chunk_size, MPI_BYTE, local_data, chunk_size, MPI_BYTE, 0, MPI_COMM_WORLD);

        start = MPI_Wtime();
        blowfish_encrypt(&key, local_data, chunk_size, local_encrypted);
        end = MPI_Wtime();
        printf("Process %d encryption time: %f seconds\n", rank, end - start);

        // Gather encrypted data from all processes
        MPI_Gather(local_encrypted, chunk_size, MPI_BYTE, encrypted, chunk_size, MPI_BYTE, 0, MPI_COMM_WORLD);

        // Scatter encrypted data to all processes for decryption
        MPI_Scatter(encrypted, chunk_size, MPI_BYTE, local_encrypted, chunk_size, MPI_BYTE, 0, MPI_COMM_WORLD);

        start = MPI_Wtime();
        blowfish_decrypt(&key, local_encrypted, chunk_size, local_decrypted);
        end = MPI_Wtime();
        printf("Process %d decryption time: %f seconds\n", rank, end - start);

        // Gather decrypted data from all processes
        MPI_Gather(local_decrypted, chunk_size, MPI_BYTE, decrypted, chunk_size, MPI_BYTE, 0, MPI_COMM_WORLD);

        // Validate the decrypted data
        if (memcmp(data, decrypted, DATA_SIZE) != 0) {
            printf("Decrypted data does not match original data!\n");
        } else {
            printf("Decrypted data matches original data!\n");
        }

        free(data);
        free(encrypted);
        free(decrypted);
    } else {
        // Receive data chunk from root process
        MPI_Scatter(NULL, chunk_size, MPI_BYTE, local_data, chunk_size, MPI_BYTE, 0, MPI_COMM_WORLD);

        double start, end;

        start = MPI_Wtime();
        blowfish_encrypt(&key, local_data, chunk_size, local_encrypted);
        end = MPI_Wtime();
        printf("Process %d encryption time: %f seconds\n", rank, end - start);

        // Gather encrypted data chunk to root process
        MPI_Gather(local_encrypted, chunk_size, MPI_BYTE, NULL, chunk_size, MPI_BYTE, 0, MPI_COMM_WORLD);

        // Scatter encrypted data to all processes for decryption
        MPI_Scatter(NULL, chunk_size, MPI_BYTE, local_encrypted, chunk_size, MPI_BYTE, 0, MPI_COMM_WORLD);

        start = MPI_Wtime();
        blowfish_decrypt(&key, local_encrypted, chunk_size, local_decrypted);
        end = MPI_Wtime();
        printf("Process %d decryption time: %f seconds\n", rank, end - start);

        // Gather decrypted data chunk to root process
        MPI_Gather(local_decrypted, chunk_size, MPI_BYTE, NULL, chunk_size, MPI_BYTE, 0, MPI_COMM_WORLD);
    }

    free(local_data);
    free(local_encrypted);
    free(local_decrypted);

    MPI_Finalize();

    return 0;
}





mpicc blowfish_mpi.c -o blowfish_mpi -lcrypto
mpirun -np 4 ./blowfish_mpi



./blowfish_serial
Encryption time (serial): 0.660000 seconds
Decryption time (serial): 0.640000 seconds

mpirun -np 4 ./blowfish_mpi
Process 1 encryption time: 0.168639 seconds
Process 3 encryption time: 0.174601 seconds
Process 0 encryption time: 0.174799 seconds
Process 2 encryption time: 0.174592 seconds
Decryption time (parallel): 0.700148 seconds



encryption time of each process in the mpi task is 4 times faster than the serial job. The decryption is slightly worse than serial job because of the 
overhead  in gathering the data from multiple processes.

using SLURM:

-N 1
-p 128GB

Encryption time (serial): 0.960000 seconds
Decryption time (serial): 0.960000 seconds
Decrypted data matches original data!


-N 2
-p 128GB

Process 1 encryption time: 0.476605 seconds
Process 0 encryption time: 0.476566 seconds
Process 1 decryption time: 0.476421 seconds
Process 0 decryption time: 0.476719 seconds
Decrypted data matches original data!



-N 3
-p 128GB

Process 1 encryption time: 0.321120 seconds
Process 2 encryption time: 0.322333 seconds
Process 0 encryption time: 0.318449 seconds
Process 2 decryption time: 0.317735 seconds
Process 1 decryption time: 0.321197 seconds
Process 0 decryption time: 0.318884 seconds




-N 4
-p 128GB 

Process 3 encryption time: 0.238996 seconds
Process 1 encryption time: 0.241968 seconds
Process 0 encryption time: 0.242709 seconds
Process 2 encryption time: 0.242700 seconds
Process 3 decryption time: 0.240068 seconds
Process 1 decryption time: 0.240390 seconds
Process 0 decryption time: 0.241649 seconds
Process 2 decryption time: 0.241826 seconds



-N 5
-p 128GB

Process 0 encryption time: 0.192699 seconds
Process 1 encryption time: 0.195781 seconds
Process 2 encryption time: 0.196270 seconds
Process 3 encryption time: 0.195687 seconds
Process 4 encryption time: 0.192910 seconds
Process 4 decryption time: 0.195979 seconds
Process 1 decryption time: 0.196943 seconds
Process 3 decryption time: 0.196658 seconds
Process 0 decryption time: 0.196703 seconds
Process 2 decryption time: 0.196011 seconds
Decrypted data matches original data!



-N 6
-p 128GB

Process 5 encryption time: 0.162260 seconds
Process 4 encryption time: 0.165288 seconds
Process 1 encryption time: 0.164572 seconds
Process 3 encryption time: 0.164788 seconds
Process 2 encryption time: 0.162729 seconds
Process 0 encryption time: 0.164458 seconds
Process 5 decryption time: 0.164114 seconds
Process 4 decryption time: 0.163690 seconds
Process 1 decryption time: 0.163860 seconds
Process 3 decryption time: 0.164126 seconds
Process 0 decryption time: 0.163264 seconds
Process 2 decryption time: 0.163493 seconds


plot of number of parallel tasks vs time for encryption/decryption is at:

https://git.biohpc.swmed.edu/s232963/biohpc-training-notes/-/wikis/MPI



Key Concepts regarding Process, Threads, Multiprocessing, Multithreading, MPI

Process:

A process is an instance of a program that is being executed. It contains the program code and its current activity.
Each process has its own separate memory space. This means that processes do not share memory with each other. They have their own address space, stack, and heap.
Processes are isolated from each other. A crash in one process does not affect other processes. This makes them more robust for executing separate tasks.
Since processes do not share memory, they need to use IPC mechanisms like pipes, sockets, shared memory, or message passing to communicate with each other.
Creating and managing processes has more overhead compared to threads because each process requires its own memory space and system resources.
Examples: Web browsers (where each tab might be a separate process), operating system services, and servers


Thread:

A thread is the smallest unit of execution within a process. Multiple threads can exist within the same process and share the same memory space.
A thread is the smallest unit of execution within a process. Multiple threads can exist within the same process and share the same memory space.
Since threads share the same memory space, they can communicate with each other more easily and efficiently than processes. This allows for faster context switching and data sharing.
Creating and managing threads has less overhead compared to processes because threads share resources of the parent process.
Threads are not isolated from each other. A crash in one thread can potentially bring down the entire process, affecting all other threads within that process.
Multithreaded applications like web servers (where each thread handles a client request), GUI applications (where one thread handles user input while another performs background tasks), and parallel algorithms



Processes cannot run in true parallelism on a single-core system. On a single-core system, only one process can execute at a time. However, multiple processes can achieve concurrency through context switching, where the operating system rapidly switches between processes, giving the illusion that they are running simultaneously.
Threads within the same process share the same memory space, which is more efficient for communication but requires careful synchronization to avoid race conditions.
Similar to processes, there are operating system-imposed limits on the number of threads per process and the total memory that can be allocated.



In python, no two threads from the same process can run simultaneously (parallelly) because of GIL(Global Interpreter Lock), but they can run concurrently by context switching.
However, if an I/O request is encountered, GIL is released, enabling multiple threads to execute simultaneously. 
Threads are handled by the python interpreter while processes are handled by the OS. Threads are concurrent and non-parallel while processes are concurrent and parallel.


Parallelism:

Definition: Performing multiple operations simultaneously.
Requirement: Requires multiple CPU cores.
Execution: True parallelism is only possible on multi-core systems, where different processes or threads can be executed on different cores at the same time.

Concurrency:

Definition: Managing multiple tasks at the same time.
Requirement: Can be achieved on single-core or multi-core systems.
Execution: On a single-core system, concurrency is achieved through context switching, where the CPU switches between processes or threads, giving the appearance of simultaneous execution.

Single-Core System

Concurrency: The operating system uses context switching to manage multiple processes. It rapidly switches between them, so each process gets a slice of CPU time.
Parallelism: True parallelism is not possible because there is only one CPU core available to execute instructions.

Multi-Core System
Concurrency: Concurrency is still achieved through context switching, but with multiple cores, some processes can run truly in parallel.
Parallelism: True parallelism is achieved because multiple processes or threads can be executed on different cores simultaneously.