Sync with French version: add new examples

2-resources.ipynb

@@ -47,17 +47,19 @@
     "For example : [`scripts/mpi-hello.sh`](https://github.com/calculquebec/cip201-compute-systems/blob/main/scripts/mpi-hello.sh)\n",
     "\n",
     "```Bash\n",
-    "cat scripts/mpi-hello.sh\n",
+    "cat scripts/mpi-pi/pi-job.sh\n",
     "```\n",
     "```\n",
     "#!/bin/bash\n",
-    "#SBATCH --ntasks=10\n",
-    "#SBATCH --mem-per-cpu=1000M\n",
-    "#SBATCH --time=0-00:10\n",
+	"\n",
+	"#SBATCH --job-name=pi\n",
+    "#SBATCH --ntasks=4\n",
+    "#SBATCH --mem-per-cpu=1G\n",
+    "#SBATCH --time=00:05:00\n",
     "\n",
     "module load StdEnv/2023 gcc/12.3 openmpi/4.1.5\n",
     "\n",
-    "mpirun printenv HOSTNAME OMPI_COMM_WORLD_RANK OMPI_COMM_WORLD_SIZE\n",
+    "srun ./pi 10000000000\n",
     "```\n",
     "\n",
     "Our documentation about job scripts starts at this page:\n",

scripts/array-distrib/README.txt

@@ -0,0 +1,11 @@
+Array job generating random normal distributions
+------------------------------------------------
+
+Generate normal distributions (1000 points each) with random mean (0 to 1) and
+std (0.5 to 1.5), save them to a CSV file, and print statistics. The Python code
+is in `distrib.py`. An array job is used to generate 4 distributions saved to
+the `results` directory.
+
+Submit the array job script to the scheduler:
+
+$ sbatch distrib-job.sh

scripts/array-distrib/distrib-job.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+#SBATCH --job-name=myjob
+#SBATCH --array=1-4
+#SBATCH --ntasks=1
+#SBATCH --mem=1G
+#SBATCH --time=00:05:00
+
+module load StdEnv/2023 gcc/12.3 python/3.11.5 scipy-stack/2024b
+
+mkdir -p results
+output_filename="results/distrib-${SLURM_ARRAY_TASK_ID}.csv"
+
+srun python3 ./distrib.py "${output_filename}"

scripts/array-distrib/distrib.py

@@ -0,0 +1,20 @@
+from sys import argv, exit
+
+import numpy as np
+import pandas as pd
+
+if len(argv) != 2:
+    print('usage: python3 distrib.py <output-csv-filename>')
+    exit(1)
+
+output_filename = argv[1]
+
+mean = np.random.rand()
+std = np.random.rand() + 0.5
+dist = np.random.normal(mean, std, size = 1000)
+df = pd.DataFrame(dist)
+
+with open(output_filename, 'w') as f:
+    f.write(df.to_csv())
+print(f'Random normal distribution writen to {output_filename}.')
+print(df.describe())

scripts/job-script-templates/array-job.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+#SBATCH --job-name=myjob
+#SBATCH --array=0-9
+#SBATCH --ntasks=1
+#SBATCH --mem=1G
+#SBATCH --time=00:05:00
+
+module load StdEnv/2023 gcc/12.3
+
+srun my-serial-prog ${SLURM_ARRAY_TASK_ID}

scripts/job-script-templates/hybrid-by-node-job.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+#SBATCH --job-name=myjob
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=2
+#SBATCH --cpus-per-task=2
+#SBATCH --mem-per-cpu=1G
+#SBATCH --time=00:05:00
+
+export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
+
+module load StdEnv/2023 gcc/12.3 openmpi/4.1.5
+
+srun my-hybrid-prog arg1 arg2

scripts/job-script-templates/hybrid-job.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+#SBATCH --job-name=myjob
+#SBATCH --ntasks=2
+#SBATCH --cpus-per-task=2
+#SBATCH --mem-per-cpu=1G
+#SBATCH --time=00:05:00
+
+export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
+
+module load StdEnv/2023 gcc/12.3 openmpi/4.1.5
+
+srun my-hybrid-prog arg1 arg2

scripts/job-script-templates/mpi-by-node-job.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+#SBATCH --job-name=myjob
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+#SBATCH --mem-per-cpu=1G
+#SBATCH --time=00:05:00
+
+module load StdEnv/2023 gcc/12.3 openmpi/4.1.5
+
+srun my-mpi-prog arg1 arg2

scripts/job-script-templates/mpi-job.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+#SBATCH --job-name=myjob
+#SBATCH --ntasks=4
+#SBATCH --mem-per-cpu=1G
+#SBATCH --time=00:05:00
+
+module load StdEnv/2023 gcc/12.3 openmpi/4.1.5
+
+srun my-mpi-prog arg1 arg2

scripts/job-script-templates/openmp-job.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+#SBATCH --job-name=myjob
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+#SBATCH --mem-per-cpu=1G
+#SBATCH --time=00:05:00
+
+module load StdEnv/2023 gcc/12.3
+
+srun my-openmp-prog arg1 arg2

scripts/job-script-templates/serial-job.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+#SBATCH --job-name=myjob
+#SBATCH --ntasks=1
+#SBATCH --mem=1G
+#SBATCH --time=00:05:00
+
+module load StdEnv/2023 gcc/12.3
+
+srun my-serial-prog arg1 arg2

scripts/mpi-pi/README.txt

@@ -0,0 +1,15 @@
+MPI pi estimate using Monte Carlo
+---------------------------------
+
+Estimate the pi number, the ratio of a circle’s circumference to its diameter,
+using a Monte Carlo approach. This is an MPI (Message Passing Interface)
+parallel program. The C code is in `pi.c`.
+
+1. Compile the program:
+
+$ module load StdEnv/2023 gcc/12.3 openmpi/4.1.5
+$ mpicc -o pi pi.c -lm
+
+2. Submit the job script to the scheduler:
+
+$ sbatch pi-job.sh

scripts/mpi-pi/pi-job.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+#SBATCH --job-name=pi
+#SBATCH --ntasks=4
+#SBATCH --mem-per-cpu=1G
+#SBATCH --time=00:05:00
+
+module load StdEnv/2023 gcc/12.3 openmpi/4.1.5
+
+srun ./pi 10000000000

scripts/mpi-pi/pi.c

@@ -0,0 +1,57 @@
+#include <math.h>
+#include <mpi.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <time.h>
+
+double monte_carlo_pi(unsigned long long n, MPI_Comm comm)
+{
+	int rank, nranks;
+	MPI_Comm_rank(comm, &rank);
+	MPI_Comm_size(comm, &nranks);
+	srand(time(NULL) + rank);
+	double x, y;
+	unsigned long long local_p = 0;
+	for (unsigned long long i = rank; i < n; i += nranks)
+	{
+		x = (double) rand() / RAND_MAX;
+		y = (double) rand() / RAND_MAX;
+		if (sqrt(x*x + y*y) <= 1.0)
+		{
+			local_p++;
+		}
+	}
+	unsigned long long p;
+	MPI_Allreduce(&local_p, &p, 1, MPI_UNSIGNED_LONG_LONG, MPI_SUM, comm);
+	return 4*((double)p)/n;
+}
+
+int main(int argc, char* argv[])
+{
+	MPI_Init(&argc, &argv);
+
+	int rank;
+	MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+
+	if (argc == 2)
+	{
+		char* endptr;
+		unsigned long long n = strtoll(argv[1], &endptr, 10);
+
+		double pi = monte_carlo_pi(n, MPI_COMM_WORLD);
+		if (rank == 0)
+		{
+			printf("After %llu points, pi estimate is %f.\n", n, pi);
+		}
+	}
+	else
+	{
+		if (rank == 0)
+		{
+			printf("usage: pi <n-points>\n");
+		}
+	}
+
+	MPI_Finalize();
+	return 0;
+}

scripts/openmp-primes/README.txt

@@ -0,0 +1,14 @@
+OpenMP count of prime numbers
+-----------------------------
+
+Count the number of prime numbers from 1 to N. This is a parallel OpenMP
+program. The C code is in `primes.c`.
+
+1. Compile the program:
+
+$ module load StdEnv/2023 gcc/12.3
+$ mpicc -o primes primes.c -fopenmp
+
+2. Submit the job script to the scheduler:
+
+$ sbatch primes-job.sh

scripts/openmp-primes/primes-job.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+#SBATCH --job-name=primes
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+#SBATCH --mem-per-cpu=1G
+#SBATCH --time=00:05:00
+
+module load StdEnv/2023 gcc/12.3
+
+srun ./primes 400000

scripts/openmp-primes/primes.c

@@ -0,0 +1,50 @@
+#include <omp.h>
+#include <stdbool.h>
+#include <stdlib.h>
+#include <stdio.h>
+
+bool* find_primes(unsigned long n)
+{
+	bool* is_prime = malloc(n * sizeof(bool));
+	#pragma omp parallel
+	{
+		int thread = omp_get_thread_num();
+		int nthreads = omp_get_num_threads();
+		for (unsigned long i = thread; i < n; i+= nthreads)
+		{
+			is_prime[i] = true;
+			for (unsigned long j = 2; j < i; j++)
+			{
+				if (i % j == 0)
+				{
+					is_prime[i] = false;
+				}
+			}
+		}
+	}
+	is_prime[0] = false;
+	return is_prime;
+}
+
+int main(int argc, char* argv[])
+{
+	if (argc != 2)
+	{
+		printf("usage: primes <up-to-n>\n");
+		return(1);
+	}
+	unsigned long n = atol(argv[1]);
+
+	bool* is_prime = find_primes(n);
+	int nprimes = 0;
+	for (int i = 0; i < n; i++)
+	{
+		if (is_prime[i])
+		{
+			nprimes++;
+		}
+	}
+	printf("There are %d primes up to %lu.\n", nprimes, n);
+
+	return 0;
+}

scripts/serial-fibonacci/README.txt

@@ -0,0 +1,15 @@
+Serial Fibonacci using recursion
+--------------------------------
+
+Compute the Nth number in the Fibonacci sequence using recursion. This is a
+serial program: computing Fibonacci numbers cannot be done in parallel. The C
+code is in `fibonacci.c`.
+
+1. Compile the program:
+
+$ module load StdEnv/2023 gcc/12.3
+$ gcc -o fibonacci fibonacci.c
+
+2. Submit the job script to the scheduler:
+
+$ sbatch fibonacci-job.sh

scripts/serial-fibonacci/fibonacci-job.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+#SBATCH --job-name=fibo
+#SBATCH --ntasks=1
+#SBATCH --mem=1G
+#SBATCH --time=00:05:00
+
+module load StdEnv/2023 gcc/12.3
+
+srun ./fibo 50

scripts/serial-fibonacci/fibonacci.c

@@ -0,0 +1,32 @@
+#include <stdlib.h>
+#include <stdio.h>
+
+unsigned long fibonacci(unsigned int nth)
+{
+	if (nth == 0)
+	{
+		return 0;
+	}
+	else if (nth == 1)
+	{
+		return 1;
+	}
+	else
+	{
+		return fibonacci(nth - 1) + fibonacci(nth - 2);
+	}
+}
+
+int main(int argc, char* argv[])
+{
+	if (argc != 2)
+	{
+		printf("usage: fibo <nth-number>\n");
+		return(1);
+	}
+	unsigned int nth = atoi(argv[1]);
+
+	printf("The %uth Fibonacci number is %lu.\n", nth, fibonacci(nth));
+
+	return 0;
+}