coding-for-reproducible-research · liamjberrisford · Aug 28, 2025 · Aug 15, 2025 · Aug 15, 2025 · Aug 15, 2025
diff --git a/_config.yml b/_config.yml
@@ -33,6 +33,11 @@ html:
       - _static/overlay-label-accessibility.js
       - _static/search_bar_submit_button.js
 
+sphinx:
+  config:
+    html_extra_path:
+      - _static/
+
 
 launch_buttons:
   thebe                  : false
@@ -119,3 +124,9 @@ execute:
       - 'short_courses/python_language_features.ipynb'
       - 'short_courses/python_testing.ipynb'
       - 'individual_modules/markdown_with_python/liveOutput.ipynb'
+      - 'individual_modules/intro_to_GPUs/theory.ipynb'
+      - 'individual_modules/intro_to_GPUs/spack.ipynb'
+      - 'individual_modules/intro_to_GPUs/slurm.ipynb'
+      - 'individual_modules/intro_to_GPUs/conways_game_of_life.ipynb'
+      - 'individual_modules/intro_to_GPUs/profiling.ipynb'
+      - 'individual_modules/intro_to_GPUs/temperature_diffusion.ipynb'
diff --git a/_static/intro_to_gpu_figures/all_methods_hardware.png b/_static/intro_to_gpu_figures/all_methods_hardware.png
diff --git a/_static/intro_to_gpu_figures/cupy_across_hardware.png b/_static/intro_to_gpu_figures/cupy_across_hardware.png
diff --git a/_static/intro_to_gpu_figures/game_of_life_example.gif b/_static/intro_to_gpu_figures/game_of_life_example.gif
diff --git a/_static/intro_to_gpu_figures/naive_across_hardware.png b/_static/intro_to_gpu_figures/naive_across_hardware.png
diff --git a/_static/intro_to_gpu_figures/numpy_across_hardware.png b/_static/intro_to_gpu_figures/numpy_across_hardware.png
diff --git a/_static/intro_to_gpu_figures/perf_amd_epyc_7v12_64-core_processor_nv_a100.png b/_static/intro_to_gpu_figures/perf_amd_epyc_7v12_64-core_processor_nv_a100.png
diff --git a/_static/intro_to_gpu_figures/perf_amd_epyc_9v84_96-core_processor_nv_h100.png b/_static/intro_to_gpu_figures/perf_amd_epyc_9v84_96-core_processor_nv_h100.png
diff --git a/...c/intro_to_gpu_figures/perf_amd_ryzen_9_5950x_16-core_processor_nv_rtx_3070.png b/...c/intro_to_gpu_figures/perf_amd_ryzen_9_5950x_16-core_processor_nv_rtx_3070.png
diff --git a/_static/intro_to_gpu_figures/temperature_cube.html b/_static/intro_to_gpu_figures/temperature_cube.html
diff --git a/_static/intro_to_gpu_figures/temperature_diffusion_timings.csv b/_static/intro_to_gpu_figures/temperature_diffusion_timings.csv
@@ -0,0 +1,13 @@
+gpu_name,cpu_name,method,num_timesteps,mean_time_sec,std_dev_sec
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,Pure Python,10,43.698821,0.084230
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,Pure Python,25,110.014916,0.939186
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,Pure Python,50,223.748059,1.287061
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,Pure Python,100,461.348654,7.234776
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,NumPy (CPU),10,4.980454,0.173302
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,NumPy (CPU),25,22.786639,0.205813
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,NumPy (CPU),50,86.931572,0.502695
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,NumPy (CPU),100,347.883550,3.980833
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,CuPy (GPU),10,3.854066,0.140653
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,CuPy (GPU),25,12.885241,0.022276
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,CuPy (GPU),50,46.622783,0.178398
+NVIDIA H100 NVL,AMD EPYC 9V84 96-Core Processor,CuPy (GPU),100,182.261322,0.193946
diff --git a/_static/intro_to_gpu_figures/temperature_diffusion_timings.png b/_static/intro_to_gpu_figures/temperature_diffusion_timings.png
diff --git a/_static/intro_to_gpu_figures/temperature_slice.html b/_static/intro_to_gpu_figures/temperature_slice.html
diff --git a/_static/multiple_regression_hyperplane.html b/_static/multiple_regression_hyperplane.html
diff --git a/_static/multiple_regression_hyperplane_2.html b/_static/multiple_regression_hyperplane_2.html
diff --git a/_static/workshop_prereqs_advanced_regression_analysis_with_r_.html b/_static/workshop_prereqs_advanced_regression_analysis_with_r_.html
@@ -282,8 +282,8 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#B0B0B0", "id": "Regression Analysis with R Adapting to Varied Data Types", "label": "Regression Analysis with R Adapting to Varied Data Types", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Regression Analysis with R Adapting to Varied Data Types\nCourse Pre-reqs: Introduction to Regression with R\nSubsequent Courses: Advanced Regression Analysis With R "}, {"color": "#B0B0B0", "id": "Advanced Regression Analysis With R ", "label": "Advanced Regression Analysis With R ", "level": 4, "shape": "dot", "size": 10, "title": "Course Name: Advanced Regression Analysis With R \nCourse Pre-reqs: Regression Analysis with R Adapting to Varied Data Types\nSubsequent Courses: None"}, {"color": "#B0B0B0", "id": "Introduction to Regression with R", "label": "Introduction to Regression with R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Regression with R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: Regression Analysis with R Adapting to Varied Data Types"}, {"color": "#B0B0B0", "id": "Introduction to R", "label": "Introduction to R", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to R\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Regression with R"}]);
-                  edges = new vis.DataSet([{"arrows": "to", "from": "Regression Analysis with R Adapting to Varied Data Types", "to": "Advanced Regression Analysis With R ", "width": 1}, {"arrows": "to", "from": "Introduction to Regression with R", "to": "Regression Analysis with R Adapting to Varied Data Types", "width": 1}, {"arrows": "to", "from": "Introduction to R", "to": "Introduction to Regression with R", "width": 1}]);
+                  nodes = new vis.DataSet([{"color": "#B0B0B0", "id": "Regression Analysis with R Adapting to Varied Data Types", "label": "Regression Analysis with R Adapting to Varied Data Types", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Regression Analysis with R Adapting to Varied Data Types\nCourse Pre-reqs: Introduction to Regression with R\nSubsequent Courses: Advanced Regression Analysis With R "}, {"color": "#B0B0B0", "id": "Advanced Regression Analysis With R ", "label": "Advanced Regression Analysis With R ", "level": 4, "shape": "dot", "size": 10, "title": "Course Name: Advanced Regression Analysis With R \nCourse Pre-reqs: Regression Analysis with R Adapting to Varied Data Types\nSubsequent Courses: None"}, {"color": "#B0B0B0", "id": "Introduction to R", "label": "Introduction to R", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to R\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Regression with R"}, {"color": "#B0B0B0", "id": "Introduction to Regression with R", "label": "Introduction to Regression with R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Regression with R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: Regression Analysis with R Adapting to Varied Data Types"}]);
+                  edges = new vis.DataSet([{"arrows": "to", "from": "Regression Analysis with R Adapting to Varied Data Types", "to": "Advanced Regression Analysis With R ", "width": 1}, {"arrows": "to", "from": "Introduction to R", "to": "Introduction to Regression with R", "width": 1}, {"arrows": "to", "from": "Introduction to Regression with R", "to": "Regression Analysis with R Adapting to Varied Data Types", "width": 1}]);
 
                   nodeColors = {};
                   allNodes = nodes.get({ returnType: "Object" });

diff --git a/_static/workshop_prereqs_introduction_to_machine_learning.html b/_static/workshop_prereqs_introduction_to_machine_learning.html
@@ -282,8 +282,8 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#B0B0B0", "id": "Python for Data Analysis", "label": "Python for Data Analysis", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: Introduction to Machine Learning"}, {"color": "#B0B0B0", "id": "Introduction to Machine Learning", "label": "Introduction to Machine Learning", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Machine Learning\nCourse Pre-reqs: Python for Data Analysis\nSubsequent Courses: None"}, {"color": "#B0B0B0", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis"}]);
-                  edges = new vis.DataSet([{"arrows": "to", "from": "Python for Data Analysis", "to": "Introduction to Machine Learning", "width": 1}, {"arrows": "to", "from": "Introduction to Python", "to": "Python for Data Analysis", "width": 1}]);
+                  nodes = new vis.DataSet([{"color": "#B0B0B0", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis"}, {"color": "#B0B0B0", "id": "Python for Data Analysis", "label": "Python for Data Analysis", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: Introduction to Machine Learning"}, {"color": "#B0B0B0", "id": "Introduction to Machine Learning", "label": "Introduction to Machine Learning", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Machine Learning\nCourse Pre-reqs: Python for Data Analysis\nSubsequent Courses: None"}]);
+                  edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to Python", "to": "Python for Data Analysis", "width": 1}, {"arrows": "to", "from": "Python for Data Analysis", "to": "Introduction to Machine Learning", "width": 1}]);
 
                   nodeColors = {};
                   allNodes = nodes.get({ returnType: "Object" });

diff --git a/_static/workshop_prereqs_parallel_computing.html b/_static/workshop_prereqs_parallel_computing.html
@@ -282,8 +282,8 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#B0B0B0", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to HPC"}, {"color": "#B0B0B0", "id": "Introduction to HPC", "label": "Introduction to HPC", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to HPC\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Parallel Computing"}, {"color": "#B0B0B0", "id": "Parallel Computing", "label": "Parallel Computing", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Parallel Computing\nCourse Pre-reqs: Introduction to HPC\nSubsequent Courses: None"}]);
-                  edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to HPC", "width": 1}, {"arrows": "to", "from": "Introduction to HPC", "to": "Parallel Computing", "width": 1}]);
+                  nodes = new vis.DataSet([{"color": "#B0B0B0", "id": "Introduction to HPC", "label": "Introduction to HPC", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to HPC\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Parallel Computing"}, {"color": "#B0B0B0", "id": "Parallel Computing", "label": "Parallel Computing", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Parallel Computing\nCourse Pre-reqs: Introduction to HPC\nSubsequent Courses: None"}, {"color": "#B0B0B0", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to HPC"}]);
+                  edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to HPC", "to": "Parallel Computing", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to HPC", "width": 1}]);
 
                   nodeColors = {};
                   allNodes = nodes.get({ returnType: "Object" });

diff --git a/_static/workshop_prereqs_regression_analysis_with_r_adapting_to_varied_data_types.html b/_static/workshop_prereqs_regression_analysis_with_r_adapting_to_varied_data_types.html
@@ -282,8 +282,8 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#B0B0B0", "id": "Introduction to Regression with R", "label": "Introduction to Regression with R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Regression with R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: Regression Analysis with R Adapting to Varied Data Types"}, {"color": "#B0B0B0", "id": "Regression Analysis with R Adapting to Varied Data Types", "label": "Regression Analysis with R Adapting to Varied Data Types", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Regression Analysis with R Adapting to Varied Data Types\nCourse Pre-reqs: Introduction to Regression with R\nSubsequent Courses: None"}, {"color": "#B0B0B0", "id": "Introduction to R", "label": "Introduction to R", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to R\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Regression with R"}]);
-                  edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to Regression with R", "to": "Regression Analysis with R Adapting to Varied Data Types", "width": 1}, {"arrows": "to", "from": "Introduction to R", "to": "Introduction to Regression with R", "width": 1}]);
+                  nodes = new vis.DataSet([{"color": "#B0B0B0", "id": "Introduction to R", "label": "Introduction to R", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to R\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Regression with R"}, {"color": "#B0B0B0", "id": "Introduction to Regression with R", "label": "Introduction to Regression with R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Regression with R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: Regression Analysis with R Adapting to Varied Data Types"}, {"color": "#B0B0B0", "id": "Regression Analysis with R Adapting to Varied Data Types", "label": "Regression Analysis with R Adapting to Varied Data Types", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Regression Analysis with R Adapting to Varied Data Types\nCourse Pre-reqs: Introduction to Regression with R\nSubsequent Courses: None"}]);
+                  edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to R", "to": "Introduction to Regression with R", "width": 1}, {"arrows": "to", "from": "Introduction to Regression with R", "to": "Regression Analysis with R Adapting to Varied Data Types", "width": 1}]);
 
                   nodeColors = {};
                   allNodes = nodes.get({ returnType: "Object" });

diff --git a/_static/workshops_network_python_ds.html b/_static/workshops_network_python_ds.html
@@ -282,7 +282,7 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#FFD700", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FFD700", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}, {"color": "#FFD700", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis, Using Markdown for Python"}, {"color": "#FFD700", "id": "Python for Data Analysis", "label": "Python for Data Analysis", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: Introduction to Machine Learning"}, {"color": "#FFD700", "id": "Using Markdown for Python", "label": "Using Markdown for Python", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Using Markdown for Python\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Machine Learning", "label": "Introduction to Machine Learning", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Machine Learning\nCourse Pre-reqs: Python for Data Analysis\nSubsequent Courses: None"}]);
+                  nodes = new vis.DataSet([{"color": "#4682B4", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#4682B4", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#4682B4", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}, {"color": "#4682B4", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis, Using Markdown for Python"}, {"color": "#4682B4", "id": "Python for Data Analysis", "label": "Python for Data Analysis", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: Introduction to Machine Learning"}, {"color": "#4682B4", "id": "Using Markdown for Python", "label": "Using Markdown for Python", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Using Markdown for Python\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: None"}, {"color": "#4682B4", "id": "Introduction to Machine Learning", "label": "Introduction to Machine Learning", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Machine Learning\nCourse Pre-reqs: Python for Data Analysis\nSubsequent Courses: None"}]);
                   edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to Version Control with Git and GitHub", "to": "Intermediate Version Control", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to Version Control with Git and GitHub", "width": 1}, {"arrows": "to", "from": "Introduction to Python", "to": "Python for Data Analysis", "width": 1}, {"arrows": "to", "from": "Introduction to Python", "to": "Using Markdown for Python", "width": 1}, {"arrows": "to", "from": "Python for Data Analysis", "to": "Introduction to Machine Learning", "width": 1}]);
 
                   nodeColors = {};