From bcfda6037fcdc1d305ea895728d01a52743e0b5e Mon Sep 17 00:00:00 2001
From: Repo Updater <noreply@mpcdf.mpg.de>
Date: Mon, 4 Oct 2021 17:58:31 +0200
Subject: [PATCH] fa958ef5 Update software engineering

---
 notebooks/1d--BasicHPC.ipynb             |   51 +-
 notebooks/2a--NumPy.ipynb                |   19 +-
 notebooks/3b--Software_Engineering.ipynb |   20 +-
 notebooks/fig/cluster_components.svg     |  797 ++++++++++
 notebooks/fig/cluster_parallelism.svg    | 1722 ++++++++++++++++++++++
 notebooks/fig/cpu.svg                    |  707 +++++++++
 notebooks/fig/memory_hierarchy.svg       |  865 +++++++++++
 7 files changed, 4139 insertions(+), 42 deletions(-)
 create mode 100644 notebooks/fig/cluster_components.svg
 create mode 100644 notebooks/fig/cluster_parallelism.svg
 create mode 100644 notebooks/fig/cpu.svg
 create mode 100644 notebooks/fig/memory_hierarchy.svg

diff --git a/notebooks/1d--BasicHPC.ipynb b/notebooks/1d--BasicHPC.ipynb
index 3c44686..8b8eda8 100644
--- a/notebooks/1d--BasicHPC.ipynb
+++ b/notebooks/1d--BasicHPC.ipynb
@@ -69,7 +69,7 @@
     "\n",
     "Components of a typical HPC compute cluster:\n",
     "\n",
-    "![cluster](fig/cluster.svg)"
+    "![cluster](fig/cluster_components.svg)"
    ]
   },
   {
@@ -80,19 +80,15 @@
     }
    },
    "source": [
-    "## CPU: central processing unit\n",
-    "\n",
-    "<img src=\"fig/ABasicComputer.gif\" style=\"float:right; width:35%\" />\n",
-    "\n",
-    "Simplified picture:\n",
-    "* Control unit: manage flow of instructions and data\n",
-    "* Registers: data local to the processor\n",
-    "* Combinational Logic: execute instructions\n",
-    "* Main memory: stores data and instructions\n",
+    "## Parallelism in a HPC cluster\n",
     "\n",
-    "Possible bottleneck: number of floating point operations per second (FLOPS)\n",
+    "<img src=\"fig/cluster_parallelism.svg\" style=\"float:right; width:35%\" />\n",
     "\n",
-    "<span style=\"font-size:small\">Image source: Wikipedia, Author: Lambtron</span>"
+    "Parallelism on multiple levels:\n",
+    "* Cluster → nodes\n",
+    "* Node → sockets (CPUs), GPUs\n",
+    "* CPU → cores\n",
+    "* Core → single instruction, multiple data (SIMD)"
    ]
   },
   {
@@ -103,16 +99,18 @@
     }
    },
    "source": [
-    "### Modern CPUs\n",
+    "## CPU: central processing unit\n",
     "\n",
-    "Several kinds of parallelism inside CPU to increase FLOPS:\n",
-    "* Vector instructions (SIMD paradigm)\n",
-    "* Pipelining\n",
-    "* Several cores per socket\n",
-    "* Simultaneous Multithreading (Hyperthreading)\n",
+    "<img src=\"fig/cpu.svg\" style=\"float:right; width:35%\" />\n",
     "\n",
+    "Simplified picture:\n",
+    "* Front end:\n",
+    "  * Fetch and decode instructions\n",
+    "* Back end:\n",
+    "  * Execute instructions on data\n",
+    "  * Transfer data between registers and memory\n",
     "\n",
-    " \\+ many CPUs in cluster (see Parallelism session)"
+    "Possible bottleneck: number of floating point operations per second (FLOPS)\n"
    ]
   },
   {
@@ -125,22 +123,15 @@
    "source": [
     "## Memory access\n",
     "\n",
-    "<img src=\"fig/Cache_Hierarchy_Updated.png\" style=\"float:right; width=30%\" />\n",
+    "<img src=\"fig/memory_hierarchy.svg\" style=\"float:right; width=35%\" />\n",
     "\n",
     "* HPC codes need data to work on\n",
     "* Memory much slower than CPU $\\to$ often a bottleneck\n",
-    "* Memory hierarchy (fast to slow) [[Nice animation]](http://www.overbyte.com.au/misc/Lesson3/CacheFun.html):\n",
-    "    * Registers\n",
-    "    * Cache (L1, L2, L3)\n",
-    "    * Memory\n",
-    "    * Disk\n",
-    "    * Network file system\n",
+    "* Mitigation: **memory hierarchy** [[Nice animation]](http://www.overbyte.com.au/misc/Lesson3/CacheFun.html):\n",
     "* Cache is filled from memory in small chunks (cache lines)\n",
     "* Rules of thumb:\n",
     "    * Linear memory access\n",
-    "    * Reuse memory as much as possible\n",
-    "    \n",
-    "<span style=\"font-size:small\">Image source: Wikipedia, Author: Kbbuch</span>"
+    "    * Reuse memory as much as possible"
    ]
   },
   {
@@ -428,7 +419,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.8.3"
   }
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  "nbformat": 4,
diff --git a/notebooks/2a--NumPy.ipynb b/notebooks/2a--NumPy.ipynb
index eca98f9..5914dd8 100644
--- a/notebooks/2a--NumPy.ipynb
+++ b/notebooks/2a--NumPy.ipynb
@@ -861,7 +861,7 @@
     "## NumPy Summary\n",
     "\n",
     "\n",
-    "* <span style=\"color:red\">Takeaway messages are</span>:\n",
+    "* Takeaway messages:\n",
     "    1. <span style=\"color:red\">High level manipulations $\\to$ in Python</span>\n",
     "    2. <span style=\"color:red\">Intensive computation $\\to$ delegate to underlying libraries</span>\n",
     "    3. <span style=\"color:red\">No dedicated library $\\to$ use NumPy arrays and their functions</span>\n",
@@ -870,7 +870,8 @@
     "\n",
     "* Tradeoff: high development productivity versus performance\n",
     "* NumPy code *can be* as fast as C or Fortran code, but often it is a factor of 2-4 slower\n",
-    "* $\\to$ Implement hotspots in C/Fortran + Python Interface"
+    "\n",
+    "$\\to$ Implement hotspots in C/Fortran + Python Interface"
    ]
   },
   {
@@ -1285,8 +1286,18 @@
     "    * identify hotspots and optimize them\n",
     "        * profile\n",
     "        * code in Cython or C/Fortran + Python interface -- or try Numba\n",
-    "\n",
-    "Futher reading\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
+   "source": [
+    "## Futher reading\n",
     "\n",
     "* Harris, C.R., Millman, K.J., van der Walt, S.J. et al. *Array programming with NumPy.* **Nature** 585, 357–362 (2020).  (https://doi.org/10.1038/s41586-020-2649-2)\n",
     "* Bressert, E. (2012). SciPy and NumPy (1st edition.). O'Reilly Media, Inc.  (https://ebooks.mpdl.mpg.de/ebooks/Record/EB001944176)\n",
diff --git a/notebooks/3b--Software_Engineering.ipynb b/notebooks/3b--Software_Engineering.ipynb
index 6d93dd8..8fe9dca 100644
--- a/notebooks/3b--Software_Engineering.ipynb
+++ b/notebooks/3b--Software_Engineering.ipynb
@@ -318,14 +318,18 @@
     }
    },
    "source": [
-    "## Unit Tests, Integration Tests\n",
+    "## Testing\n",
     "* Tests are a central part of the software development life cycle\n",
-    "    * Unit tests\n",
-    "        * test functions, classes, modules individually\n",
-    "    * Integration tests\n",
-    "        * test the interplay of units, up to the complete application\n",
-    "* `unittest`, `pytest`, and `nose` are popular Python modules for testing\n",
-    "* \"continuous integration\" allows to run tests automatically at each code commit, e.g. via GitLab-CI"
+    "    * Avoid regression\n",
+    "    * Facilitate collaboration\n",
+    "* **Continuous integration**:\n",
+    "    * merge contributions often\n",
+    "    * run tests automatically at each code commit, e.g. via GitLab-CI\n",
+    "* Unit tests\n",
+    "    * test functions, classes, modules individually\n",
+    "* Integration tests\n",
+    "    * test the interplay of units, up to the complete application\n",
+    "* Popular python modules: `unittest`, `pytest`, `nose`\n"
    ]
   },
   {
@@ -478,7 +482,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.8.3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/fig/cluster_components.svg b/notebooks/fig/cluster_components.svg
new file mode 100644
index 0000000..2696148
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+++ b/notebooks/fig/cluster_components.svg
@@ -0,0 +1,797 @@
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-- 
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