generated using sphinx-build

.ci/linkchecker.sh

@@ -0,0 +1,9 @@
+# We ignore ANSYS CFX and Fluent links as they give
+# https://github.com/curl/curl/issues/4409, which needs a
+# rather new version of OpenSSL.
+# The cytopia/linkcheck is rather slow. There are faster alternatives,
+# especially https://github.com/filiph/linkcheck, but that
+# requires Dart etc.
+# Consider to utilize a faster link checker as soon as we have
+# all the exclude links configured and it works.
+git clone https://github.com/cytopia/linkcheck.git /tmp/linkchecker && /tmp/linkchecker/linkcheck -i '^http(s)?:\/\/(localhost)|(127.0.0.1)|(documentation.sigma2.no/page/on/same/site.html)|(download.open-mpi.org/release/open-mpi/v4.0/openmpi-)|(example.org/institution/simulationDataq)|(rt.uninett.no/SelfService)|(desktop.saga.sigma2.no)|(desktop.fram.sigma2.no)|(example.org/institution/simulationData)|(www.pythonware.com/products/pil)|(www.linuxconfig.org/Bash_scripting_Tutorial)|(https://documentation.sigma2.no/_downloads/bdfbca90a90a8d1b824fc6b1154ceee7/serial.zip)|(https://www.ansys.com/products/fluids/ansys-cfx)|(https://www.ansys.com/products/fluids/ansys-fluent)' -e 'md,txt,rst' -k -c '200,301,302,303,307,308' .

.github/workflows/sphinx.yml

@@ -0,0 +1,41 @@
+name: Build HTML
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/main'
+    steps:
+    - name: Check out repo
+      uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.10"
+    - name: Install Python dependencies
+      run: |
+        python -m pip install -r requirements.txt
+    - name: Run Sphinx
+      run: |
+        sphinx-build . _build
+    - name: Commit and push to gh-pages
+      run: |-
+        git config --global user.email "[email protected]"
+        git config --global user.name "workflow-bot"
+        git checkout --orphan gh-pages
+        git rm --cached -r .
+        mv CNAME _build ..
+        rm -rf *
+        mv ../_build/* .
+        mv ../CNAME .
+        touch .nojekyll
+        git add .
+        git commit -m "generated using sphinx-build"
+        git push --set-upstream origin gh-pages --force

.gitignore

@@ -0,0 +1,10 @@
+# vim temporary files
+.*.swp
+.*.swo
+
+# macOS
+.DS_Store
+
+# sphinx
+_build/
+venv/

.gitlab-ci.yml

@@ -0,0 +1,37 @@
+---
+stages:
+  - linkchecker
+  - spellchecker
+  - build
+
+image: python:3.10-alpine
+
+linkchecker:
+  stage: linkchecker
+  only:
+    - schedules
+  script:
+    - apk add --no-cache git bash curl
+    - bash .ci/linkchecker.sh
+
+spellchecker:
+  stage: spellchecker
+  script:
+    - apk add --no-cache bash curl
+    - curl -L -o ./install-misspell.sh https://git.io/misspell
+    - bash ./install-misspell.sh
+    - ./bin/misspell -error .
+
+build:
+  stage: build
+  when: on_success
+  script:
+    - pip install --upgrade pip
+    - pip install -r requirements.txt
+    # '-W': Turn warnings into errors
+    # '--keep-going': When encountering a warning continue to process (this
+    # allows us to capture multiple warnings at the same time, avoiding the
+    # 'build->warning->fix->build->warning' loop where both fixes could be
+    # solved at the same time)
+    # '-n': Warn about internal missing references
+    - sphinx-build -W --keep-going -n . _build

CNAME

@@ -0,0 +1 @@
+documentation.sigma2.no

_downloads/0105ae9db861b5434b03f0f2ee915de4/mandelbrot_initial.c

@@ -0,0 +1,155 @@
+/**
+ * Mandelbrot implementation for accelerators (e.g. GPUs)
+ */
+
+#include "utils/lodepng.h"
+#include "utils/palette.h"
+#include <omp.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+// Default width and height for image if not given
+static const int WIDTH = 1280;
+static const int HEIGHT = 720;
+// Default output name if not given
+static const char* OUTPUT_NAME = "mandelbrot.png";
+// Maximum iteration count before exiting mandelbrot function
+static const uint32_t MAX_ITER = 1000;
+
+// Helper function to scale 'num' to the range '[min, max]'
+#pragma acc routine seq
+float scale(float num, const float min, const float max) {
+  const float scale = max - min;
+  return num * scale + min;
+}
+
+/**
+ * Mandelbrot function, calculates the value of the mandelbrot set at pixel 'px/py'
+ */
+#pragma acc routine seq
+uint32_t mandelbrot(const int px, const int py, const int width, const int height,
+                    const int max_iter) {
+  const float x0 = scale((float) px / (float) width, -2.5, 1.);
+  const float y0 = scale((float) py / (float) height, -1., 1.);
+  float x = 0.;
+  float y = 0.;
+  float x2 = 0.;
+  float y2 = 0.;
+  int iters = 0;
+  while (x2 + y2 < 4. && iters < max_iter) {
+    y = 2. * x * y + y0;
+    x = x2 - y2 + x0;
+    x2 = x * x;
+    y2 = y * y;
+    iters += 1;
+  }
+  return (uint32_t) iters;
+}
+
+int main (int argc, char** argv) {
+  int width = WIDTH;
+  int height = HEIGHT;
+  char output_name[128];
+  int max_iter = MAX_ITER;
+  strncpy (output_name, OUTPUT_NAME, strnlen (OUTPUT_NAME, 127) + 1);
+  // Assume the first argument is the width and height of the image
+  if (argc > 1) {
+    if (strncmp (argv[1], "-h", 2) == 0 || strncmp (argv[1], "--help", 6) == 0) {
+      printf("Usage: %s <width>x<height> <max iterations> <output filename>\n", argv[0]);
+      printf("\tImage size can also be one of {8k, 4k, 3k, 1080p, 720p}\n");
+      return EXIT_SUCCESS;
+    }
+    // First we check image size is one of the predefined sizes
+    if (strncmp (argv[1], "8k", 2) == 0) {
+      width = 7680;
+      height = 4320;
+    } else if (strncmp (argv[1], "4k", 2) == 0) {
+      width = 3840;
+      height = 2160;
+    } else if (strncmp (argv[1], "3k", 2) == 0) {
+      width = 3000;
+      height = 2000;
+    } else if (strncmp (argv[1], "1080p", 5) == 0) {
+      width = 1920;
+      height = 1080;
+    } else if (strncmp (argv[1], "720p", 4) == 0) {
+      width = 1280;
+      height = 720;
+    } else {
+      // Assume user has supplied <width>x<height>
+      // Try to find 'x' in argument
+      char* token;
+      token = strtok (argv[1], "x");
+      if (token != NULL) {
+        width = atoi (token);
+      } else {
+        printf("\033[0;31mInvalid width/height definition:\033[0m '%s'\n", argv[1]);
+        printf("\tShould be '<width>x<height>'\n");
+        return EXIT_FAILURE;
+      }
+      token = strtok (NULL, "x");
+      if (token != NULL) {
+        height = atoi (token);
+      } else {
+        printf("\033[0;31mInvalid width/height definition:\033[0m '%s'\n", argv[1]);
+        printf("\tShould be '<width>x<height>'\n");
+        return EXIT_FAILURE;
+      }
+    }
+  }
+  // Second argument is the maximum iteration count
+  if (argc > 2) {
+    max_iter = atoi (argv[2]);
+  }
+  // Third argument is the output filename to write PNG file to
+  if (argc > 3) {
+    if (strlen (argv[3]) > 127) {
+      printf("\033[0;31mOutput filename to large!\033[0m");
+      return EXIT_FAILURE;
+    }
+    strncpy (output_name, argv[3], strnlen (argv[3], 127) + 1);
+  }
+  // Allocate storage for image
+  uint32_t* image = calloc (width * height, sizeof (uint32_t));
+  if (image == NULL) {
+    printf("\033[0;31mCould not allocate memory for image!\033[0m\n");
+    return EXIT_FAILURE;
+  }
+  printf("Generating \033[0;35m%dx%d\033[0m image with max \033[0;35m%d\033[0m iterations\n",
+         width, height,
+         max_iter);
+  /****************************************************************************/
+  /***************************   Main computation   ***************************/
+  /****************************************************************************/
+  const double start_time = omp_get_wtime ();
+  // For each pixel of our image calculate the value of the mandelbrot set
+  #pragma acc parallel loop \
+    copyout(image[:width * height]) \
+    copyin(palette[:palette_size]) \
+    collapse(2)
+  for (int y = 0; y < height; y++) {
+    for (int x = 0; x < width; x++) {
+      const uint32_t iters = mandelbrot (x, y, width, height, max_iter);
+      image[y * width + x] = palette[iters % palette_size];
+    }
+  }
+  const double end_time = omp_get_wtime ();
+  printf("Used \033[0;35m%.3f\033[0m ms for computation\n",
+         (end_time - start_time) * 1000.0);
+  /****************************************************************************/
+  // Write image to file
+  const unsigned char png_error = lodepng_encode32_file(output_name,
+                                                        (const unsigned char*) image,
+                                                        width, height);
+  // Free image storage
+  free (image);
+  if (png_error) {
+    printf("\033[0;31mAn error occurred while writing to PNG:\033[0m %s\n",
+           lodepng_error_text (png_error));
+    return EXIT_FAILURE;
+  }
+  printf("Wrote Mandelbrot result to \033[0;35m%s\033[0m\n", output_name);
+  return EXIT_SUCCESS;
+}

_downloads/0222d30f6733c67f4afcb6e626b30824/saga_mpi_job.sh

@@ -0,0 +1,65 @@
+#!/bin/bash
+
+###############################################
+# Script example for a normal MPI job on Saga #
+###############################################
+
+## Project: replace XXXX with your project ID
+#SBATCH --account=nnXXXXk 
+
+## Job name:
+#SBATCH --job-name=MyJob
+## Number of tasks (aka processes) to start: Pure mpi, one cpu per task
+#SBATCH --ntasks=16
+## Amount of memory per cpu (= per task, since we get 1 cpu per task):
+#SBATCH --mem-per-cpu=4G
+## Run for 10 minutes, syntax is d-hh:mm:ss
+#SBATCH --time=0-00:10:00 
+
+# you may not place bash commands before the last SBATCH directive
+######################################################
+## Setting variables and prepare runtime environment:
+##----------------------------------------------------
+## Recommended safety settings:
+set -o errexit # Make bash exit on any error
+set -o nounset # Treat unset variables as errors
+
+# Loading Software modules
+# Allways be explicit on loading modules and setting run time environment!!!
+module --quiet purge            # Restore loaded modules to the default
+module load MySoftWare/Versions #nb: Versions is important!
+
+# Type "module avail MySoftware" to find available modules and versions
+# It is also recommended to to list loaded modules, for easier debugging:
+module list  
+
+#######################################################
+## Prepare jobs, moving input files and making sure 
+# output is copied back and taken care of
+##-----------------------------------------------------
+
+# Prepare input files
+cp inputfiles $SCRATCH
+cd $SCRATCH
+
+# Make sure output is copied back after job finishes
+savefile outputfile1 outputfile2
+
+########################################################
+# Run the application, and we typically time it:
+##------------------------------------------------------
+
+# Run the application  - please add hash in front of srun and remove 
+# hash in front of mpirun if using intel-toolchain 
+
+# For OpenMPI (foss and iomkl toolchains), srun is recommended:
+time srun MySoftWare-exec
+
+## For IntelMPI (intel toolchain), mpirun is recommended:
+#time mpirun MySoftWare-exec
+
+#########################################################
+# That was about all this time; lets call it a day...
+##-------------------------------------------------------
+# Finish the script
+exit 0