Update README

README.md

@@ -19,13 +19,12 @@
 ### Tools
 
 - Profiling
-    - [gprof](https://ftp.gnu.org/old-gnu/Manuals/gprof-2.9.1/html_mono/gprof.html)
-    - [scalasca](https://www.scalasca.org/)
   - [score-p](https://www.vi-hps.org/projects/score-p)
 
 ### Libraries
 
 - Python
+
   - [matplotlib](https://matplotlib.org/)
   - [numpy](https://numpy.org/)
 
@@ -34,23 +33,55 @@
   - [OpenMPI](https://www.open-mpi.org/)
   - [Armadillo](https://arma.sourceforge.net/)
 
-
 ## Compiling
 
-Compiling is as easy as running this command while being inside the src directory:
+The commands shown here should be run from the root of this project.
+
+### Normal binaries
+
+Compiling regular binaries is as easy as running this command:
 
 ```shell
     make
 ```
 
+The binaries will then be inside the **./bin** directory.
+
+### Profiling binaries
+
+If you want to profile the programs (specifically the MPI program), then run this command
+
+```shell
+    make profile
+```
+
+The binaries will then be inside the **./prof** directory.
+
+### Debugging binaries
+
+If you want to debug the code, then use this command:
+
+```shell
+    make debug
+```
+
+The binaries will then be inside the **./debug** directory.
+
 ## Running programs
 
 ### C++ binaries
 
-To run **main** or **test_suite**, just run this command while being inside src:
+To run any of the programs, just use the following command:
 
 ```shell
-    ./<program-name>
+    ./<bin|prof|debug>/<program-name> <args>
+```
+
+If you need help with any of the programs, you can use the **-h** or **--help**
+flag to show you how to use the programs. Here is an example:
+
+```shell
+    ./bin/main --help
 ```
 
 ### Python scripts
@@ -68,46 +99,51 @@ This recursively install all the packages that are listed in **requirements.txt*
 
 #### Running scripts
 
-For the Python scripts, run them from the src directory like this:
+For the Python scripts, run them from the root of the project:
 
 ```shell
-    python scripts/<script-name>
+    python python_scripts/<script-name>
 ```
 
 If you have any problems running the scripts, you might have to run this instead:
 
 ```shell
-    python3 scripts/<script-name>
+    python3 python_scripts/<script-name>
 ```
 
 ### Batch system
 
-For the **phase_transition_mpi** program, there are scripts in the **src/jobs**
+For the **phase_transition_mpi** program, there are scripts in the **./slurm_scripts**
 directory that come along with it. This is to be able to run it on a
 batch system using Slurm if you have access to one.
+The only program that should be executed by the user is the **./slurm_scripts/execute.script**
+script. You can see how to use this script by doing:
+
+```shell
+    ./slurm_scripts/execute.script --help
+```
+
 This is the recommended way to use this program as it takes approximately 90
 minutes to complete when using 8 processes where each process has 10 threads.
 
 If you happen to have such a system available to you, then you should clone
-this repo on that system, then compile it by running:
+this repo on that system, then compile the MPI program like this:
 
 ```shell
-    make phase_transition_mpi
+    make bin/phase_transition_mpi
 ```
 
-You might have to load the Armadillo library using the **module** system before compiling.
-
-After compiling, you can schedule it by running:
+After compiling, you can schedule it by using the **./slurm_scripts/execute.script**:
 
 ```shell
-    sbatch jobs/<script-name>
+    ./slurm_scripts/execute.script <parameters>
 ```
 
 ## Performance
 
-This section aims to give an idea to the time it takes for the program to
-run so that you know a bit what to expect if you decide to run it for
-yourself.
+This section aims to give an idea to the time it takes for the phase transition
+program to run so that you know a bit what to expect if you decide to run it
+for yourself.
 
 ### CPU
 
@@ -123,6 +159,37 @@ specifications:
 
 ### Times
 
+Note that all times here are recorded using the OpenMP implementation of the
+MCMC algorithm.
+
+| lattice size | points | samples | burn-in time | time (seconds) |
+| ------------ | ------ | ------- | ------------ | -------------- |
+| 20           | 20     | 100000  | 0            | 3.20           |
+| 20           | 40     | 100000  | 0            | 6.17           |
+| 20           | 80     | 100000  | 0            | 12.11          |
+
+| lattice size | points | samples | burn-in time | time (seconds) |
+| ------------ | ------ | ------- | ------------ | -------------- |
+| 20           | 20     | 100000  | 0            | 3.20           |
+| 40           | 20     | 100000  | 0            | 11.91          |
+| 80           | 20     | 100000  | 0            | 47.88          |
+
+| lattice size | points | samples  | burn-in time | time (seconds) |
+| ------------ | ------ | -------- | ------------ | -------------- |
+| 20           | 20     | 100000   | 0            | 3.20           |
+| 20           | 20     | 1000000  | 0            | 29.95          |
+| 20           | 20     | 10000000 | 0            | 305.849        |
+
+| lattice size | points | samples | burn-in time | time (seconds) |
+| ------------ | ------ | ------- | ------------ | -------------- |
+| 20           | 20     | 100000  | 0            | 3.20           |
+| 20           | 20     | 100000  | 5000         | 4.93           |
+| 20           | 20     | 100000  | 10000        | 6.58           |
+
+We can see that changing the number of points, samples and burn-in time 
+changes the time in a linear fashion, while changing the size of the lattice
+changes the time in a square fashion.
+
 ## Credits
 
 The Doxygen theme used here is