Merge pull request #108 from uvarc/staging

Big merge

Author: kah3f

content/courses/containers-for-hpc/_index.md

@@ -4,7 +4,7 @@ title : "Software Containers for HPC"
 summary: "An Introduction to using and building software containers."
 authors: [rs]
 categories: ["Containers","HPC"]
-tags: [containers, hpc]
+tags: [Containers, HPC]
 toc: true
 type: book
 weight: 1

content/courses/containers-for-hpc/building-apptainer.md

@@ -292,7 +292,7 @@ While our container is functional, there is room for improvement. We shall look
 
 ### 1. Clean up
 
-Package managers usually leave behind some cache files after installation that can be safely removed. Dependending on your application, they can easily accumulate up to several GBs.
+Package managers usually leave behind some cache files after installation that can be safely removed. Depending on your application, they can easily accumulate up to several GBs.
 
 {{< code-snippet >}}Bootstrap: docker
 From: ubuntu:22.04
@@ -424,7 +424,7 @@ A container registry is a repository for container images. Here we examine two p
 
 The Apptainer/Singularity SIF is supported by Docker Hub. Register for a free account.
 
-{{< info >}}Replace "myname" with your actual user name in the following commands.{{< /info >}}
+{{< info >}}Replace "myname" with your actual username in the following commands.{{< /info >}}
 
 Login:
 ```bash
@@ -486,7 +486,7 @@ Your project requires PyTorch 2.1.2, Numpy, Seaborn, and Pandas. Write the corre
 
 Hints:
 - Find the appropriate base image from [here](https://hub.docker.com/r/pytorch/pytorch/tags).
-- Pull the base image and examine it first. Does it already provide some of the packages?
+- Pull the base image and examine it first. Does it already provide some packages?
 
 {{< info >}}While PyTorch runs on a GPU, you do not need to build the container on a GPU.{{< /info >}}
 
@@ -507,7 +507,7 @@ Your project requires R 4.3.2, dplyr, ggplot2, and RcppGSL. Write the correspond
 
 Hints:
 - Pick an appropriate base image - there are two viable choices here.
-- Pull the base image and examine it first. Does it already provide some of the packages?
+- Pull the base image and examine it first. Does it already provide some packages?
 - In the definition file, install CRAN packages via `R -e "install.packages('...')"`.
 - Load the three packages. Do they all succeed? If not, how can you fix it?
 

content/courses/containers-for-hpc/building-docker.md

@@ -167,7 +167,7 @@ ENTRYPOINT fortune | cowsay | lolcat
 
 ### 1. Clean up
 
-Almost all package managers leave behind some cache files after installation that can be safely removed. Dependending on your application, they can easily accumulate up to several GBs. Let's see what happens if we try to clean up the cache in a separate `RUN` statement.
+Almost all package managers leave behind some cache files after installation that can be safely removed. Depending on your application, they can easily accumulate up to several GBs. Let's see what happens if we try to clean up the cache in a separate `RUN` statement.
 
 ```dockerfile
 FROM ubuntu:22.04

content/courses/containers-for-hpc/minimal.md

@@ -303,7 +303,7 @@ LightGBM is a gradient boosting framework that uses tree based learning algorith
 
 ## Exercise: `fortune` from scratch
 
-This exercise illustrates how we can cherrypick files from the package manager that are essential to the application.
+This exercise illustrates how we can cherry-pick files from the package manager that are essential to the application.
 
 1. The Ubuntu base image shall be our basis of comparison. Copy the Dockerfile and build the image.
 
@@ -576,7 +576,7 @@ where $A_{mk}, B_{kn}, C_{mn}$ are matrices and $\alpha, \beta$ are constants. F
 This exercise illustrates that it is easier to build a minimal container of a static binary.
 
 ## Exercise: Linking against LibTorch
-LibTorch is the C++ frontend of PyTorch. This exericse is based on the ["Writing a Basic Application"](https://pytorch.org/tutorials/advanced/cpp_frontend.html#writing-a-basic-application) section of the PyTorch tutorial.
+LibTorch is the C++ frontend of PyTorch. This exercise is based on the ["Writing a Basic Application"](https://pytorch.org/tutorials/advanced/cpp_frontend.html#writing-a-basic-application) section of the PyTorch tutorial.
 
 1. Select an appropriate base image. (Hint: You will be compiling C++ code.)
 

content/courses/cpp-introduction/_index.md

@@ -3,8 +3,8 @@ date : "2021-06-23T00:00:00-05:00"
 title : "Programming in C++"
 summary: " This short course is an introduction to programming in C++.  Experience programming in some other language is helpful but not required." 
 authors: [kah]
-categories: ["Programming","C++"]
-tags: [programming, c++]
+categories: ["Programming","Compilers"]
+tags: [Programming, Compilers, C++]
 toc: true
 type: book
 weight: 1

content/courses/cpp-introduction/boost.md

@@ -11,12 +11,12 @@ One of the most popular add-on libraries for C++, especially numerical or scient
 
 ### Installing Boost
 
-Boost uses its own build system on Unix and Mac OS.  On Windows there is an experimental CMake system but generally the "bjam" builder is still used.
+Boost uses its own build system on Unix and macOS.  On Windows there is an experimental CMake system but generally the "bjam" builder is still used.
 In all cases, installing Boost requires some familiarity with using a command line.
 
-#### Unix and Mac OS
+#### Unix and macOS
 
-On a Linux system, the simplest way to install Boost is to utilize the package manager of the distribution.  For example on Ubunutu the command is
+On a Linux system, the simplest way to install Boost is to utilize the package manager of the distribution.  For example on Ubuntu the command is
 ```no-highlight
 sudo apt install libboost-all-dev
 ```
@@ -25,9 +25,9 @@ or on Fedora (or Centos 8 and beyond)
 sudo dnf install boost
 sudo dnf install boost-devel
 ```
-If you do not have superuser (sudo) permission or you wish to install Boost somewhere other than the main system libraries, follow the general [instructions](
+If you do not have superuser (sudo) permission, or you wish to install Boost somewhere other than the main system libraries, follow the general [instructions](
 https://www.boost.org/doc/libs/1_76_0/more/getting_started/unix-variants.html).
-The default prefix for installation from `b2 install` is `/usr/local`.  This is true for both Linux and Mac OS.  If you wish to install to `/usr/local`, which is normally in the system search paths, you will need to run the installation command with sudo
+The default prefix for installation from `b2 install` is `/usr/local`.  This is true for both Linux and macOS.  If you wish to install to `/usr/local`, which is normally in the system search paths, you will need to run the installation command with sudo
 ```no-highlight
 cd path/to/boost/source
 ./bootstrap.sh
@@ -59,11 +59,11 @@ Installation on Windows is somewhat more complicated than on Unix variants.  Fir
 
 Using Boost is probably simplest with a Makefile.  The [example](/courses/cpp-introduction/codes/makefile.windows_boost) is for Windows with a particular choice of location for the boost header files and libraries.  Change the locations for `-I` and `-L` as appropriate if they are located elsewhere on your system.  Please refer to the earlier [chapter](/courses/cpp-introduction/make) for a review of setting up Makefiles.  This example goes with a standard Boost [example](/courses/cpp-introduction/codes/boost_example.cxx).
 
-If you have installed Boost onto a Linux or Mac OS system to a system default search location such as `/usr` or `/usr/local` you will not need to specify the `-I` or `-L` paths at all.  The example [makefile](/courses/cpp-introduction/codes/makefile.linux_mac_boost) assumes installation in system paths in the compiler's default search paths.
+If you have installed Boost onto a Linux or macOS system to a system default search location such as `/usr` or `/usr/local` you will not need to specify the `-I` or `-L` paths at all.  The example [makefile](/courses/cpp-introduction/codes/makefile.linux_mac_boost) assumes installation in system paths in the compiler's default search paths.
 
 ## Boost MultiArrays
 
-C-style arrays are widely used but lack some important features, such as the ability to check that index references do not occur outside of the arrays bounds.
+C-style arrays are widely used but lack some important features, such as the ability to check whether indexes outside the array bounds are referenced.
 The C++ STL array type has more features, but is limited to one dimension.  A workaround is to "stack" vectors, since a vector of a vector amounts to a 2-dimensional structure.
 ```c++
 #include <vector>

content/courses/cpp-introduction/building.md

@@ -7,7 +7,7 @@ weight: 11
 
 ---
 
-The "traditional" development environment for compiled languages was a text editor and a command line.  Many programmers continue to use these successfully, but modern tools can greatly improve programmer productivity.  Some such tools are especially recommended for the Windows operating system, since it does not support command-line usage as cleanly as Linux or Mac OS.
+The "traditional" development environment for compiled languages was a text editor and a command line.  Many programmers continue to use these successfully, but modern tools can greatly improve programmer productivity.  Some such tools are especially recommended for the Windows operating system, since it does not support command-line usage as cleanly as Linux or macOS.
 
 ## Compilers
 
@@ -30,21 +30,21 @@ Intel has recently released the [oneAPI Toolkits](https://software.intel.com/con
 
 An Integrated Development Environment (IDE) combines an editor and a way to compile and run programs in the environment.
 A well-known IDE for Microsoft Windows is Visual Studio. This is available through the Microsoft Store; it is not free for individuals.
-Mac OS uses Xcode as its native IDE. Xcode includes some compilers, particularly for Swift, but it can manage several other languages.  Available at the App Store and free.
+macOS uses Xcode as its native IDE. Xcode includes some compilers, particularly for Swift, but it can manage several other languages.  Available at the App Store and free.
 
 A full-featured cross-platform IDE is [Eclipse] (http://www.eclipse.org/).  Free.
 
 A lighter-weight IDE for Windows and Linux is [Code::Blocks] (http://www.codeblocks.org/).  Free.
 
 Windows programmers using Intel's oneAPI distribution must also install [Visual Studio](https://visualstudio.microsoft.com/).  
 
-An increasingly popular IDE is Visual Studio Code ([VSCode](https://code.visualstudio.com/)) from Microsoft. It is also cross-platform, with versions available for Windows, Mac OS, and Linux.  It does not support C, C++, or Fortran by default; extensions must be installed to provide syntax highlighting and debugging for those languages.  C and C++ are installed with one extension that can be found at the top of the list.  
+An increasingly popular IDE is Visual Studio Code ([VSCode](https://code.visualstudio.com/)) from Microsoft. It is also cross-platform, with versions available for Windows, macOS, and Linux.  It does not support C, C++, or Fortran by default; extensions must be installed to provide syntax highlighting and debugging for those languages.  C and C++ are installed with one extension that can be found at the top of the list.  
 
 In our examples, we will use a very lightweight IDE called [Geany](https://www.geany.org/) since it is free, easy to install and use, and  works on all three platforms.  It is more of a programmer's editor than a full-featured IDE, but it does include some build tools.
 
 ## Building an Executable
 
-Creating an executable is generally a multi-step process.  Of course, the first step is the preparation of a _source file_.  The convention for C++ was once a file extension of `.cpp`, but that conflicts with the name of the preprocessor (C PreProcessor) so `.cxx` is increasingly common.  We will use `.cxx` but `.cpp` still works.
+Creating an executable is generally a multistep process.  Of course, the first step is the preparation of a _source file_.  The convention for C++ was once a file extension of `.cpp`, but that conflicts with the name of the preprocessor (C PreProcessor) so `.cxx` is increasingly common.  We will use `.cxx` but `.cpp` still works.
 
 From each source file, the compiler first produces an _object file_.  In Unix these end in `.o`, or `.obj` on Windows.
 This is the _compilation_ step.
@@ -54,15 +54,15 @@ If not told otherwise a compiler will attempt to compile and link the source fil
 
 For Unix compilers the `-c` option suppresses linking.  The compiler must then be run again to build the executable from the object files.
 The linker option `-o` is used to name the binary something other than `a.out`.
-Unix and MacOS do not care about file extensions, but Windows will expect an executable to end in `.exe`.
+Unix and macOS do not care about file extensions, but Windows will expect an executable to end in `.exe`.
 
 ### Command Line
 
-For full control and access to more compiler options, we can build from the command line.  For Linux and Mac this is a terminal application.  On windows, use a command prompt for gcc.  The Intel oneAPI distribution ships with an integrated command prompt in its folder in the applications menu; this command prompt is aware of the location of the compiler executables and libraries.
+For full control and access to more compiler options, we can build from the command line.  For Linux and Mac this is a terminal application.  On Windows, use a command prompt for gcc.  The Intel oneAPI distribution ships with an integrated command prompt in its folder in the "applications" menu; this command prompt is aware of the location of the compiler executables and libraries.
 
 **Example**
 ```
 g++ -c mymain.cxx
 g++ -c mysub.cxx
 ```
-IDEs generally manage basic compiler options and usually name the executable based on the project name.  Our examples of command line usage will all assume a Unix operating system; there are some differences between Linux and MacOS, with larger differences for Windows.  On MacOS and especially Windows, using an IDE makes code management simpler.  Using Geany as our example, clicking the icon showing a pyramid pointing to a circle will compile the current file without attempting to invoke the linker.  The brick icon builds the current file, so it must be possible to create a standalone executable from a single file.
+IDEs generally manage basic compiler options and usually name the executable based on the project name.  Our examples of command line usage will all assume a Unix operating system; there are some differences between Linux and macOS, with larger differences for Windows.  On macOS and especially Windows, using an IDE makes code management simpler.  Using Geany as our example, clicking the icon showing a pyramid pointing to a circle will compile the current file without attempting to invoke the linker.  The brick icon builds the current file, so it must be possible to create a standalone executable from a single file.

content/courses/cpp-introduction/characters.md

@@ -90,7 +90,7 @@ The result is a _buffer overflow_.
 To see what can happen, compile and run the following code
 {{< code-download file="/courses/cpp-introduction/codes/buffer_oflow.cxx" lang="c++" >}}
 
-Type in a short user name (any string), then type `Eleventy` as your password. It should work as expected.  Now try typing a user name that is longer than 10 characters and see what happens.
+Type in a short username (any string), then type `Eleventy` as your password. It should work as expected.  Now try typing a username that is longer than 10 characters and see what happens.
 
 If using C-style strings and functions, guard against this by using
 

content/courses/cpp-introduction/classes.md

@@ -15,7 +15,7 @@ Objects _encapsulate_ related concepts and keep them unified.  They may _hide_ d
 Generally speaking, an object would contain the procedures required to update and maintain its _state_. 
 In most object-oriented programming languages, objects are abstract concepts that are represented in code by _classes_. 
 
-Object-oriented programming (OOP) grew from programming fields that simulated real-world, physical objects and it may be easiest to grasp by thinking of that model.  These objects well defined and their interactions could be managed through the _interface_ that each object provided.  A user interface is a good example.  We have various objects such as figures, text, menus, and so forth. The figures might be one-dimensional (lines, arrows, etc.) or two-dimensional (rectangles, ellipses, etc).  They have characteristics such as length/radius, they have a state such as current size, color and location of their centers, and they have behaviors such as moving or rotating.  Text has location and the content of the string that it displays.  All these objects interact with each other, as the user takes various actions or the program executes.
+Object-oriented programming (OOP) grew from programming fields that simulated real-world, physical objects and it may be easiest to grasp by thinking of that model.  These objects are well-defined and their interactions can be managed through the _interface_ that each object provided.  A user interface is a good example.  We have various objects such as figures, text, menus, and so forth. The figures might be one-dimensional (lines, arrows, etc.) or two-dimensional (rectangles, ellipses, etc).  They have characteristics such as length/radius, they have a state such as current size, color and location of their centers, and they have behaviors such as moving or rotating.  Text has location and the content of the string that it displays.  All these objects interact with each other, as the user takes various actions or the program executes.
 
 For another example, return to the Employee struct.  The struct collected data about an employee into a unified type.  However, actions may be associated with an employee.  Salaries could be raised, addresses could be updated, employees could join or quit the company, and so forth. We would implement procedures to carry out these actions and include them in the object.
 

content/courses/cpp-introduction/conditionals.md

@@ -9,7 +9,7 @@ weight: 41
 
 A _conditional_ is a programming construct that implements decisions. 
 * _If_ the weather is good _then_ we will go for a walk, _else_ we will stay inside and watch TV.  
-* _If_ it is cold enough to snow I will wear my heavy coat, _else if_ it is warmer and just rains I will wear my rainjacket.
+* _If_ it is cold enough to snow I will wear my heavy coat, _else if_ it is warmer and just rains I will wear my rain jacket.
 The expression following each _if_ or _else_ must be true or false, i.e. a _logical_ expression (in Fortran terminology).
 
 ## If - Else If - Else

content/courses/cpp-introduction/console_io.md

@@ -20,7 +20,7 @@ The standard streams are incorporated with the header
 ```c++
 #include <iostream>
 ```
-The iostream library is part of the C++ standard libraries set and contains _stream objects_ for standard streams.  They correspond to the standard streams of Unix or Mac OS.  Windows handles console IO differently, but iostream can map the stream objects to its equivalents.
+The iostream library is part of the C++ standard libraries set and contains _stream objects_ for standard streams.  They correspond to the standard streams of Unix or macOS.  Windows handles console IO differently, but iostream can map the stream objects to its equivalents.
 
 {{< table >}}
 | cin | standard input |
@@ -30,7 +30,7 @@ The iostream library is part of the C++ standard libraries set and contains _str
 {{< /table >}}
 
 The `cin` object is for input; it is a member of the _istream_ (input stream) class.  If a console is attached the others all output is to the same device (the screen).  They are members of the _ostream_ (output stream) class.  
-Unix and Mac OS shells can redirect standard output and standard error to separate files.
+Unix and macOS shells can redirect standard output and standard error to separate files.
 Standard output is for "normal" output whereas standard error is used for error messages. 
 
 On Linux cin and cout are buffered, whereas cerr is not.

content/courses/cpp-introduction/containers_templates.md

@@ -39,7 +39,7 @@ int main() {
 }
 ```
 
-The standard library consists of _containers_, _algorithms_, _iterators_, and a number of general-purpose and numerical sublibraries.  A comprehensive list is [here](https://www.cplusplus.com/reference/).
+The standard library consists of _containers_, _algorithms_, _iterators_, and a number of general-purpose and numerical sub-libraries.  A comprehensive list is [here](https://www.cplusplus.com/reference/).
 
 ### Useful Standard Containers