Version 1.0

.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/quarto.yml

@@ -0,0 +1,30 @@
+on:
+  push:
+    branches:
+      - main
+
+name: Render and Publish
+
+permissions: 
+    contents: write
+    pages: write
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Publish to GitHub Pages
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 

.gitignore

@@ -0,0 +1,57 @@
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+*.swp
+/.ipynb_checkpoints
+Manifest.toml
+index.html
+/index_files
+
+/.quarto/
+/_site

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Pierre Navaro
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,14 @@
+# Rmpi : MPI avec le langage R
+
+Supports pour apprendre à utiliser la bibliothèque MPI avec R et le package Rmpi. Cette formation a été dispensée lors de l'Action Nationale de Formation [R pour le calcul](https://indico.mathrice.fr/event/536/) à Fréjus du 23 au 27 septembre 2024
+
+Ces supports reprennent très largement les [supports de cours MPI de l'IDRIS](http://www.idris.fr/formations/mpi/) écrits par Dimitri Lecas, Rémi Lacroix, Serge Van Criekingen et Myriam Peyrounette. J'ai utilisé également les ressources suivantes:
+
+- [Site officiel de Rmpi](https://fisher.stats.uwo.ca/faculty/yu/Rmpi/)
+- [How to run R programs on University of Maryland HPC facility](https://hpcf.umbc.edu/other-packages/how-to-run-r-programs-on-maya/)
+- [Documentation de GRICAD](https://gricad-doc.univ-grenoble-alpes.fr/hpc/softenv/nix/#r-packages)
+- [MPI Tutorial by Wes Kendall](https://mpitutorial.com)
+- [CRAN Task View: High-Performance and Parallel Computing with R](https://cran.r-project.org/web/views/HighPerformanceComputing.html)
+- [R_note by Wei-Chen Chen](https://snoweye.github.io/R_note/inc_menu/Rmpi.html)
+
+<https://groupecalcul.github.io/ANFRCalculRmpi/>

_quarto.yml

@@ -0,0 +1,30 @@
+project:
+  type: website
+
+website:
+  title: ""
+  description: "Supports du cours Rmpi"
+  site-url: "https://groupecalcul.github.io/ANFRCalculRmpi"
+  repo-url: "https://github.com/GroupeCalcul/ANFRCalculRmpi"
+  repo-actions: [edit, source, issue]
+  navbar:
+    logo: src/images/logo.png
+    left:
+      - href: src/index.qmd
+        text: Introduction
+      - href: src/com_point_a_point.qmd
+        text: Communications point à point
+      - href: src/com_collectives.qmd
+        text: Communications collectives
+      - href: src/exercice.qmd
+        text: Conclusion
+    tools:
+      - icon: github
+        href: https://github.com/GroupeCalcul/ANFRCalculRmpi
+
+format:
+  html:
+    theme:
+       light: flatly
+       dark: darkly
+    toc: true

codes/bcast.R

@@ -0,0 +1,16 @@
+library(Rmpi)
+
+id <- mpi.comm.rank(comm=0)
+
+# Diffusion du vecteur v sur les processeurs autre que 0
+if (id == 0) {
+	v <- c(1, 2, 3, 4)
+    mpi.bcast.Robj(obj = v, rank = 0, comm = 0)
+} else {
+    v <- mpi.bcast.Robj(rank = 0, comm = 0)
+}
+
+cat("vector on ", id, " = ",  v, "\n" )
+
+invisible(mpi.barrier(comm=0))
+invisible(mpi.finalize())

codes/demo_pbdmpi.R

@@ -0,0 +1,25 @@
+suppressMessages(library(pbdMPI, quietly = TRUE))
+init()
+
+.comm.size <- comm.size()
+.comm.rank <- comm.rank()
+
+### Examples.
+x <- matrix(1:5, nrow = 1)
+y <- bcast(x)
+comm.print(x)
+comm.print(y)
+
+k <- 10
+x <- rep(.comm.rank, k)
+comm.cat("\nOriginal x vector:\n", quiet = TRUE)
+comm.print(x, all.rank = TRUE)
+
+y <- allgather(x, unlist = TRUE)
+A <- matrix(y, nrow = k, byrow = FALSE)
+comm.cat("\nAllgather matrix (only showing process 0):\n", quiet = TRUE)
+comm.print(A)
+
+### Finish.
+finalize()
+

codes/ex_pi_spmd.r

@@ -0,0 +1,17 @@
+# File name: ex_pi_spmd.r
+# Run: mpiexec -np 2 Rscript --vanilla ex_pi_spmd.r
+
+### Load pbdMPI and initial the communicator.
+library(pbdMPI, quiet = TRUE)
+init()
+
+### Compute pi.
+n <- 1000
+totalcpu <- mpi.comm.size(comm=1)
+id <- mpi.comm.rank(comm=1) + 1
+mypi <- 4*sum(1/(1+((seq(id,n,totalcpu)-.5)/n)^2))/n    # The example from Rmpi.
+mypi <- reduce(mypi, op = "sum")
+
+### Output from RANK 0 since mpi.reduce(...) will dump only to 0 by default.
+comm.print(mypi)
+finalize()

codes/hello_mpi.F90

@@ -0,0 +1,14 @@
+program hello
+
+    use mpi
+    implicit none
+
+    integer :: rang, nproc, code, ierr
+    call MPI_INIT(code)                             !---- Initialisation MPI
+    call MPI_COMM_RANK(MPI_COMM_WORLD,rang,code)    !---- Numero du processus
+    call MPI_COMM_SIZE(MPI_COMM_WORLD,nproc,code)   !---- Nombre total de processus 
+    write(*,*) " rang, nproc", rang, nproc
+    call MPI_FINALIZE(code)
+
+end program hello
+

codes/hello_mpi.R

@@ -0,0 +1,12 @@
+library(Rmpi)
+
+id <- mpi.comm.rank(comm=0)
+np <- mpi.comm.size(comm=0)
+hostname <- mpi.get.processor.name()
+
+msg <- sprintf ("Hello world from task %03d of %03d, on host %s \n", id , np , hostname)
+cat(msg)
+
+
+invisible(mpi.barrier(comm=0))
+invisible(mpi.finalize())

codes/hello_mpi.c

@@ -0,0 +1,27 @@
+#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();
+}

codes/hello_mpi.jl

@@ -0,0 +1,8 @@
+using MPI
+
+MPI.Init()
+
+comm = MPI.COMM_WORLD
+println("Hello world, I am $(MPI.Comm_rank(comm)) of $(MPI.Comm_size(comm))\n")
+
+MPI.Finalize()

codes/hello_mpi.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python
+"""
+Parallel Hello World
+"""
+
+from mpi4py import MPI
+
+size = MPI.COMM_WORLD.Get_size()
+rank = MPI.COMM_WORLD.Get_rank()
+name = MPI.Get_processor_name()
+
+print(f"Hello, World! I am process {rank} of {size} on {name}")

codes/hello_mpi.sh

@@ -0,0 +1,14 @@
+##!/bin/bash
+#OAR --project pr-groupecalcul
+#OAR -n hello_rmpi
+#OAR -l /nodes=1/core=4,walltime=00:01:00
+#OAR --stdout hello_mpi.out
+#OAR --stderr hello_mpi.err
+
+## Ensure conda is loaded. The following line can be into your ~/.bashrc file.
+source /applis/environments/conda.sh
+
+## Run the program
+conda activate rmpi
+mpirun --np 4 --machinefile $OAR_NODE_FILE --mca plm_rsh_agent "oarsh" $OAR_WORKING_DIRECTORY/hello_mpi
+mpirun --np 4 --machinefile $OAR_NODE_FILE --mca plm_rsh_agent "oarsh" Rscript --vanilla $OAR_WORKING_DIRECTORY/hello_mpi.R

codes/hello_mpmd.R

@@ -0,0 +1,13 @@
+library(Rmpi)
+mpi.spawn.Rslaves(nslaves = 4, needlog = FALSE)
+
+mpi.bcast.cmd( id <- mpi.comm.rank() )
+mpi.bcast.cmd( np <- mpi.comm.size() )
+mpi.bcast.cmd( host <- mpi.get.processor.name() )
+result <- mpi.remote.exec(paste("I am", id, "of", np, "running on", host)) 
+
+print(unlist(result))
+
+mpi.close.Rslaves(dellog = FALSE)
+mpi.exit()
+

codes/install.R

@@ -0,0 +1 @@
+install.packages("Rmpi")

codes/loop_rowSums.r

@@ -0,0 +1,14 @@
+# File name: loop_rowSums.r
+
+my.loop <- 20
+m.dim <- list(nrow = 200000, ncol = 10)
+m <- matrix(1, nrow = m.dim$nrow, ncol = m.dim$ncol)
+ret <- 0
+
+start <- Sys.time()
+for(k in 1 : my.loop){
+  ret <- ret + sum(rowSums(m))
+}
+cat(ret, "\n")
+Sys.time() - start
+

codes/ping_pong_1.R

@@ -0,0 +1,29 @@
+
+
+library(Rmpi)
+nb_valeurs <- 1000
+etiquette <- 99
+
+valeurs <- runif(nb_valeurs)
+
+id <- mpi.comm.rank(comm = 0)
+np <- mpi.comm.size(comm = 0)
+
+if (id == 0) {
+  ## envoi du message
+  ## ...
+
+} else {
+  buffer <- numeric(nb_valeurs)
+
+  ## reception du message
+  ## ...
+
+  cat("Moi, processus 1, j''ai recu ",
+      nb_valeurs,
+      " valeurs du processus 0. \n")
+  cat("Premiere valeur ", recv[1], " derniere valeur ", recv[1000], " \n")
+}
+
+invisible(mpi.barrier(comm = 0))
+invisible(mpi.finalize())