feat: parallel execution chapter (#173)

* feat: first two dummy slides to start the chapter

* fix: updated date

* feat: added option to create Handout background. Would be nice to enable it automatically when rendering a handout version

* fix: boundary fix for the n-th time - peril of mergers

* feat: introducing threading

* feat: update to copy script

* feat: immediate install of conda, without reliance on micromamba or miniconda due to libmamba in conda

* feat: added mpi example code

* feat: added 2nd version of copy script

* feat: added example Snakefile for MPI runs

* fix: removed mpi example copy

* fix: mpi example under solutions

* feat: finished MPI example setup - need generalization for different clusters

* feat: added MPI intro

* fix: syntax

config/config_Mainz_NHR.yaml

@@ -22,7 +22,7 @@ layout:
 course:
   # sets the slides aspectratio (if outcommented, the default is 43=4:3)
   aspectratio: 1609 # - 169 = 16:9 
-  date: "23.-27. September 2024" # maybe: "\today"
+  date: "29.-30. January 2025" # maybe: "\today"
   #title: "" # specifiy your title here, else a default is used. 
   #subtitle: "" # specifiy your subtitle here, else a default is used. 
   question: "yes" # if set (to any value) the question slide will be shown

render

@@ -174,7 +174,7 @@ def find_and_replace_sections(boundaries, section_estimate, fname):
     # first render minitoc
     if minitocline:
         lower = max((section_estimate - 2), 1)  # lower boundary not lower than 1
-        upper = min(
+        upper = max(
             (section_estimate + 3), boundaries["upper"]
         )  # upper boundary not higher then upper boundary ;-)
         sections = f"{lower}-{upper}"

setup_creators/copy_script_mogonNHR.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# This script is used to teach on the cluster "Mogon II"
+
+CLUSTER_ALIAS="mogon_NHR_nox" # nox stands for "no X11 forwarding"
+BASEPATH="/lustre/project/nhr-workflow/tutorial" # repeated used
+
+# creating remote directory:
+ssh ${CLUSTER_ALIAS} "mkdir -p ${BASEPATH}"
+
+scp condarc_mogon "${CLUSTER_ALIAS}:${BASEPATH}/condarc"
+scp get_tutorial.sh "${CLUSTER_ALIAS}:${BASEPATH}/get_tutorial.sh"
+scp install_micromamba.sh "${CLUSTER_ALIAS}:${BASEPATH}/install_conda.sh"
+scp environment.yaml "${CLUSTER_ALIAS}:${BASEPATH}/environment.yaml"
+
+rsync -rtlv --chmod=D755 "tutorial" "${CLUSTER_ALIAS}:${BASEPATH}"
+rsync -rtlv --chmod=D755 "solutions" "${CLUSTER_ALIAS}:/lustre/project/nhr-worfklow"

setup_creators/install_conda.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+
+bash Miniforge3-Linux-x86_64.sh
+
+rm Miniforge3-Linux-x86_64.sh

setup_creators/solutions/mpi_example/Snakefile

@@ -0,0 +1,24 @@
+localrules: all, clean
+
+rule all:
+     input: "pi.calc"
+
+rule clean:
+     shell: "rm -f pi.calc pi_MPI *log"
+
+rule compile:
+     input: "pi_MPI.c"
+     output: temp("pi_MPI")
+     log: "compile.log"
+     envmodules: "mpi/OpenMPI/4.1.5-GCC-12.3.0"     
+     shell: 
+         "mpicc -o {output} {input} 2> {log}"
+
+rule calc_pi:
+     input: "pi_MPI"
+     output: "pi.calc"
+     log: "calc_pi.log"
+     resources:
+        mpi: "srun"
+     envmodules: "mpi/OpenMPI/4.1.5-GCC-12.3.0"     
+     shell: "{resources.mpi} ./{input} >  {output} 2> {log}"

setup_creators/solutions/mpi_example/pi_MPI.c

@@ -0,0 +1,61 @@
+#include <stdio.h>
+#include <math.h>
+#include "stdlib.h"
+#include "mpi.h"
+
+
+double f(double x){
+  return ( 4.0/(1.0 + x*x) );
+}
+
+
+int main(int argc,char *argv[])
+{
+
+  int myrank, size;
+
+  MPI_Init(&argc, &argv);
+  MPI_Comm_size(MPI_COMM_WORLD, &size);
+  MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
+
+  long long int i, n;
+  double PI25DT = 3.141592653589793238462643;
+  double mypi, pi, h, mysum, x;
+
+
+
+  /* Argument handling from command line */
+  if( 2 == argc ){
+    n = atoll(argv[1]);
+  }else{
+    if( 0 == myrank ){
+      n = 10000000;
+      printf("Too many or no argument given; using n = %d instead.\n", n);
+    }
+  }
+
+
+  MPI_Bcast(&n, 1, MPI_LONG_LONG_INT, 0, MPI_COMM_WORLD);
+
+  h = 1.0/( (double)n );
+  mysum = 0.0;
+
+  for(i = myrank+1 ; i <= n ; i += size){
+    x = h*((double)i - 0.5);
+    mysum = mysum + f(x);
+  }
+
+  mypi = h*mysum;
+
+  MPI_Reduce(&mypi, &pi, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);
+
+  /* Output result if myrank==0 */
+  if( 0 == myrank ){
+    printf("\nUsing %d processes and the value n = %d.\n",size,n);
+    printf("Calculated pi: %.16f, with error %.16f\n\n", pi, fabs(pi - PI25DT));
+  }
+
+  MPI_Finalize();
+  return 0;
+}
+

slides/Snakemake_HPC_User_Creator_Combi.tex

@@ -20,6 +20,17 @@
 
 \subtitle{<+++ if course.subtitle is defined +++><++course.subtitle++><+++else+++>Programming and Deployment<+++endif+++> - <++course.edition++>} 
 
+
+%\usepackage{background}
+%\backgroundsetup{
+%	placement=center,
+%	angle=30,
+%	scale=1,
+%	contents={\footnodesize Handout from Snakemake Teaching Alliance by <++instructor.name++>},
+%	opacity=1
+%}
+%\setbeamertemplate{background}{\BgMaterial}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{document}