Merge pull request #28 from lukemartinlogan/main

Change html to md

docs/02-hpc-tutorials/04-cpp-introduction/02-cpp-build-manually.md

@@ -184,7 +184,7 @@ this file there are two options.
 g++ src/database_lib.cc -I${PWD}/include -fpic -c -o build/database_lib.o
 ```
 
--I${PWD}/include will ensure the compiler searches the include directory
+``-I${PWD}/include`` will ensure the compiler searches the include directory
 for headers
 
 ### Fix 2: Environment Variables
@@ -234,7 +234,7 @@ g++ src/grocery_db.cc -I${PWD}/include -L${PWD}/build -ldatabase_lib -o build/gr
 g++ src/movies_db.cc -I${PWD}/include -L${PWD}/build -ldatabase_lib -o build/movies_db
 ```
 
--L${PWD}/build tells the compiler to search this directory for shared objects.
+``-L${PWD}/build`` tells the compiler to search this directory for shared objects.
 
 ### Fix 2: Environment Variables
 

docs/02-hpc-tutorials/04-cpp-introduction/03-cpp-build-with-cmake.md

@@ -187,7 +187,7 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY
 
 CMAKE_BINARY_DIR is automatically provided by CMake. This is the absolute
 path to the directory which contains the root CMake. In our case, this would
-be "cd ${GRC_TUTORIAL}/cpp/03-cpp-build-with-cmake".
+be ``cd ${GRC_TUTORIAL}/cpp/03-cpp-build-with-cmake``.
 
 In this example, we output all executables and shared objects to the bin
 directory.
@@ -259,14 +259,14 @@ include_directories(${CMAKE_SOURCE_DIR}/include)
 ```
 
 *include_directories* will ensure that header files can be discovered
-by the C++ compiler. This is analagous to the "-I" flag in the gcc
+by the C++ compiler. This is analagous to the ``-I`` flag in the gcc
 compiler. Here we ensure that the compiler will search the directory
-${CMAKE_SOURCE_DIR}/include for header files.
+``${CMAKE_SOURCE_DIR}/include`` for header files.
 
 CMAKE_SOURCE_DIR is provided automatically by CMake. It represents
 the absolute path to the directory containing the root CMakeLists.txt.
 In our case, this constant would expand to
-"cd ${GRC_TUTORIAL}/cpp/03-cpp-build-with-cmake/".
+``cd ${GRC_TUTORIAL}/cpp/03-cpp-build-with-cmake/``.
 
 ### Creating a Shared Library
 ```cmake
@@ -283,12 +283,12 @@ target_link_libraries(database_lib
 input the path to all source files related to the build. The SHARED indicates
 this library is shared (as opposed to static). Here, there is only one source
 file, datbase_lib.cc. The output of this command will be "libdatabase_lib.so" in
-the "build/lib" directory.
+the ``build/lib`` directory.
 
 CMAKE_CURRENT_SOURCE_DIR is provided automatically by CMake. It represents
 the absolute path to the directory containing the CMakeLists.txt currently
 being processed. In our case, this constant would expand to
-"cd ${GRC_TUTORIAL}/cpp/03-cpp-build-with-cmake/src".
+``cd ${GRC_TUTORIAL}/cpp/03-cpp-build-with-cmake/src``.
 
 *target_link_libraries* will link all necessary libraries necessary to compile the target database_lib.
 This is analagous to the "-l" flag in gcc. In our case, we link against the
@@ -339,14 +339,14 @@ install(
 
 *install* defines what happens when a user calls "make install". In this
 case we specify that our targets database_lib, grocery_db, and movies_db
-should be installed into one of LIBRARY, ARCHIVE, or RUNTIME depending
+should be installed into one of ``LIBRARY``, ``ARCHIVE``, or ``RUNTIME`` depending
 on its type. For example, database_lib will be installed to LIBRARY
 (since we used add_library), whereas grocery_db and movies_db will be installed
-to RUNTIME (since we used add_executable).
+to ``RUNTIME`` (since we used add_executable).
 
-CMAKE_INSTALL_PREFIX is a constant provided by CMake which represents
+``CMAKE_INSTALL_PREFIX`` is a constant provided by CMake which represents
 where files should be installed. This can be configured by users by passing
--DCMAKE_INSTALL_PREFIX to their CMake build. By default, the value of this
+``-DCMAKE_INSTALL_PREFIX`` to their CMake build. By default, the value of this
 constant is /usr.
 
 ### Installing Header Files
@@ -364,8 +364,8 @@ install(
 ```
 
 In this case, we use *install* to specify
-that the specific file ${CMAKE_SOURCE_DIR}/include/database_lib.h should be
-installed to ${CMAKE_INSTALL_PREFIX}/include. Here, we use the keyword
+that the specific file ``${CMAKE_SOURCE_DIR}/include/database_lib.h`` should be
+installed to ``${CMAKE_INSTALL_PREFIX}/include``. Here, we use the keyword
 FILES instead of the keyword TARGET. Targets are defined using a CMake
 function such as add_executable or add_library. Files are just the way
 they are with no modification.
@@ -386,18 +386,18 @@ set_property(TEST test_movies_db PROPERTY ENVIRONMENT
 ```
 
 *add_test* creates a CTest case. Here we create two tests: test_grocery_db
-and test_movies_db. The test will execute the command ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/grocery_db.
+and test_movies_db. The test will execute the command ``${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/grocery_db``.
 
 CMAKE_RUNTIME_OUTPUT_DIRECTORY is a constant provided by CMake. It
 is the location where an executable is installed after performing the
 "make" command.
 
 *set_property* sets some sort of property about a target. In this
 case the target is the test case test_movies_db. We are setting
-an environment variable LD_LIBRARY_PATH. From section 3.2, we
+an environment variable ``LD_LIBRARY_PATH``. From section 3.2, we
 saw that we needed to be very careful about ensuring the OS
 knows where shared libraries are located. In this case, we
-ensure the OS will check the path ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}.
+ensure the OS will check the path ``${CMAKE_LIBRARY_OUTPUT_DIRECTORY}``.
 
 CMAKE_LIBRARY_OUTPUT_DIRECTORY is a constant provided by CMake. It
 is the location where a shared library is installed after performing
@@ -456,11 +456,12 @@ This will run unit tests verbosely, meaning that terminal outputs
 will not be hidden. -VV indicates making the tests verbose
 
 You should see something like:
-<pre>UpdateCTestConfiguration  from :/home/lukemartinlogan/Documents/Projects/PhD/scs-tutorial/3.3.building_cpp_cmake/build/DartConfiguration.tcl
-Parse Config file:/home/lukemartinlogan/Documents/Projects/PhD/scs-tutorial/3.3.building_cpp_cmake/build/DartConfiguration.tcl
-UpdateCTestConfiguration  from :/home/lukemartinlogan/Documents/Projects/PhD/scs-tutorial/3.3.building_cpp_cmake/build/DartConfiguration.tcl
-Parse Config file:/home/lukemartinlogan/Documents/Projects/PhD/scs-tutorial/3.3.building_cpp_cmake/build/DartConfiguration.tcl
-Test project /home/lukemartinlogan/Documents/Projects/PhD/scs-tutorial/3.3.building_cpp_cmake/build
+```bash
+UpdateCTestConfiguration  from :/home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/DartConfiguration.tcl
+Parse Config file:/home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/DartConfiguration.tcl
+UpdateCTestConfiguration  from :/home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/DartConfiguration.tcl
+Parse Config file:/home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/DartConfiguration.tcl
+Test project /home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build
 Constructing a list of tests
 Done constructing a list of tests
 Updating test list for fixtures
@@ -470,9 +471,10 @@ Checking test dependency graph end
 test 1
     Start 1: test_grocery_db
 
-1: Test command: /home/lukemartinlogan/Documents/Projects/PhD/scs-tutorial/3.3.building_cpp_cmake/build/bin/grocery_db
-1: Environment variables:
-1:  LD_LIBRARY_PATH=/home/lukemartinlogan/Documents/Projects/PhD/scs-tutorial/3.3.building_cpp_cmake/build/bin
+1: Test command: /home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/bin/grocery_db
+1: Working Directory: /home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/test
+1: Environment variables: 
+1:  LD_LIBRARY_PATH=/home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/bin
 1: Test timeout computed to be: 1500
 1: grocery: in create
 1: grocery: in read
@@ -482,20 +484,21 @@ test 1
 test 2
     Start 2: test_movies_db
 
-2: Test command: /home/lukemartinlogan/Documents/Projects/PhD/scs-tutorial/3.3.building_cpp_cmake/build/bin/movies_db
-2: Environment variables:
-2:  LD_LIBRARY_PATH=/home/lukemartinlogan/Documents/Projects/PhD/scs-tutorial/3.3.building_cpp_cmake/build/bin
+2: Test command: /home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/bin/movies_db
+2: Working Directory: /home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/test
+2: Environment variables: 
+2:  LD_LIBRARY_PATH=/home/luke/Documents/Projects/grc-tutorial/cpp/03-cpp-build-with-cmake/build/bin
 2: Test timeout computed to be: 1500
 2: movies: in create
 2: movies: in read
 2: movies: in update
 2: movies: in delete
 2/2 Test #2: test_movies_db ...................   Passed    0.00 sec
 
-<font color="#4E9A06">100% tests passed</font>, 0 tests failed out of 2
+100% tests passed, 0 tests failed out of 2
 
 Total Test time (real) =   0.01 sec
-</pre>
+```
 
 #### Installing
 

docs/02-hpc-tutorials/04-cpp-introduction/04-cpp-basic-syntax.md

@@ -261,15 +261,15 @@ in 3.06.
 
 |Name|Description|
 |-------|----------|
-|A < B|Less than operator. A is less than B.|
-|A <= B|Less than or equal operator. A is at most B.|
-|A > B|Greater than operator. A is larger than B.|
-|A >= B|Greater than or equal operator. A is at least B.|
-|A == B|Equality operator. A and B are the same|
-|A != B|Inequality operator. A and B are not the same.|
-|A && B|AND operator. Both A and B are true.|
-|A \|\| B|OR operator. One of A or B is true.|
-|!A|NOT operator. Check if A is not true.|
+|``A < B``|Less than operator. A is less than B.|
+|``A <= B``|Less than or equal operator. A is at most B.|
+|``A > B``|Greater than operator. A is larger than B.|
+|``A >= B``|Greater than or equal operator. A is at least B.|
+|``A == B``|Equality operator. A and B are the same|
+|``A !\= B``|Inequality operator. A and B are not the same.|
+|``A && B``|AND operator. Both A and B are true.|
+|``A \\ B``|OR operator. One of A or B is true.|
+|``!A``|NOT operator. Check if A is not true.|
 
 ### If-Else
 
@@ -514,7 +514,8 @@ which demonstrates the following:
 
 This is technically the way C++ recommends to do File I/O in general.
 In HPC, it doesn't get used very often, though. Most HPC programs use
-STDIO or POSIX. However, we introduce here anyway.
+STDIO or POSIX. However, we introduce here anyway. It is located in
+[libstdc.cc](https://github.com/grc-iit/grc-tutorial/blob/main/cpp/04-cpp-basic-syntax/src/libstd.cc).
 
 ```cpp
 #include <iostream>
@@ -561,7 +562,7 @@ int main() {
 
 To compile & run the code:
 ```bash
-cd ${GRC_TUTORIAL}/3.5.basics
+cd ${GRC_TUTORIAL}/cpp/04-cpp-basic-syntax
 mkdir build
 cd build
 make
@@ -576,7 +577,7 @@ Hello, World!
 ### STDIO
 
 The following example demonstrates the basics of the STDIO API.
-The code is located in [libstd.cc]().
+The code is located in [stdio.cc](https://github.com/grc-iit/grc-tutorial/blob/main/cpp/04-cpp-basic-syntax/src/stdio.cc).
 
 ```cpp
 #include <stdio.h>
@@ -641,7 +642,7 @@ int main() {
 
 To compile & run the code:
 ```bash
-cd ${GRC_TUTORIAL}/3.5.basics
+cd ${GRC_TUTORIAL}/cpp/04-cpp-basic-syntax
 mkdir build
 cd build
 make
@@ -656,6 +657,7 @@ Hello, World!
 ### POSIX
 
 The following example demonstrates the basics of the POSIX API.
+It is located in [posix.cc](https://github.com/grc-iit/grc-tutorial/blob/main/cpp/04-cpp-basic-syntax/src/posix.cc).
 
 ```cpp
 #include <stdio.h>
@@ -720,7 +722,7 @@ int main() {
 
 To compile & run the code:
 ```bash
-cd ${GRC_TUTORIAL}/3.5.basics
+cd ${GRC_TUTORIAL}/cpp/04-cpp-basic-syntax
 mkdir build
 cd build
 make
@@ -811,7 +813,7 @@ int main() {
 
 To compile & run the code:
 ```bash
-cd ${GRC_TUTORIAL}/3.5.basics
+cd ${GRC_TUTORIAL}/cpp/04-cpp-basic-syntax
 mkdir build
 cd build
 make
@@ -924,7 +926,7 @@ ends when both of these statements are no longer true.
 
 To get the dataset, run the following:
 ```bash
-cd ${GRC_TUTORIAL}/3.5.basics
+cd ${GRC_TUTORIAL}/cpp/04-cpp-basic-syntax
 mkdir build
 cd build
 make
@@ -957,7 +959,7 @@ Average CO: 280
 ```
 
 Your Objectives:
-1. Create a file called my_analyze_kitchen_fire.cc in the ${GRC_TUTORIAL}/3.5.basics directory
+1. Create a file called my_analyze_kitchen_fire.cc in the ``${GRC_TUTORIAL}/cpp/04-cpp-basic-syntax`` directory
 2. Edit the CMakeLists.txt in that directory to compile your code. Feel free to look at how the other sources in that directory were compiled.
 3. How do you read "kitchen_fire.bin" and interpret its contents?
 4. How do you analyze its contents to determine the start, end, and average

docs/02-hpc-tutorials/04-cpp-introduction/05-cpp-style-and-doc.md

@@ -153,7 +153,6 @@ It can be installed as follows:
 python3 -m pip install cpplint
 ```
 
-We have the following code located [here]().
 ```cpp
 // Copyright [year] <Copyright Owner>
 

docs/02-hpc-tutorials/04-cpp-introduction/06-cpp-classes.md

@@ -133,7 +133,7 @@ public:
 In this example, we overload the addition operator to perform complex number addition.
 
 ### 3.6.04.3. Relational Operators
-Relational operators (==, !=, <, >, <=, >=) can be overloaded to define custom comparison logic for objects of your class.
+Relational operators (``==``, ``!=``, ``<``, ``>``, ``<=``, ``>=``) can be overloaded to define custom comparison logic for objects of your class.
 
 Example:
 
@@ -190,7 +190,7 @@ public:
 In this example, we overload the function call operator to create an object that behaves like a function, adding two integers.
 
 ### Bitwise Operators
-Bitwise operators (&, |, ^, ~, <<, >>) can be overloaded to define custom bitwise operations for objects of your class.
+Bitwise operators (`&`, `|`, `^`, `~`, `<<`, `>>`) can be overloaded to define custom bitwise operations for objects of your class.
 
 Example:
 

docs/02-hpc-tutorials/05-docker/01-docker-basics.md

@@ -73,7 +73,7 @@ sudo docker build -t [IMAGE_NAME] [DOCKERFILE_DIR, can be a github link] -f [DOC
 2. DOCKERFILE_DIR: the directory containing the Dockerfile.
 3. DOCKERFILE_NAME: the name of the dockerfile in that directory. This is optional. Default: Dockerfile.
 
-Let's say that our Dockerfile is located at ${HOME}/MyDockerfiles/Dockerfile.
+Let's say that our Dockerfile is located at ``${HOME}/MyDockerfiles/Dockerfile``.
 We could build the image two ways:
 ```
 # Option 1: a single command

docs/02-hpc-tutorials/05-docker/02-docker-cluster.md

@@ -25,10 +25,10 @@ is a subdirectory of the current working directory.
 ```bash
 ssh-keygen -t rsa -f ${PWD}/id_rsa -N "" -q
 ```
-**-t rsa** uses RSA for the algorithm.
-**-f ${PWD}/id_rsa** defines the output for the private key to be in this directory.
-**-N ""** indicates no password should be generated.
-**-q** disables interactive prompts.
+* ``-t rsa`` uses RSA for the algorithm.
+* ``-f ${PWD}/id_rsa`` defines the output for the private key to be in this directory.
+* ``-N ""`` indicates no password should be generated.
+* ``-q`` disables interactive prompts.
 
 ## OpenSSH-Server Dockerfile
 
@@ -190,16 +190,13 @@ sudo docker-compose exec -u sshuser node2 hostname
 ```
 
 These commands should print "node1" and "node2".
-![docker-compose exec hostname results](images/5/5.2.7.docker-exec-hostname.png)
 
 Next, we will try performing ssh from one node into the other.
 ```bash
 sudo docker-compose exec -u sshuser node1 ssh node2 hostname
 ```
 
-The above command will execute "ssh node2 hostname" in node1. Its
-result should be:
-![docker-compose exec ssh results](images/5/5.2.7.ssh-test.png)
+The above command will execute "ssh node2 hostname" in node1.
 
 ## Interactive shell with cluster nodes