From 65419908172bea8253b3de6a8a0c4c54acf0cc56 Mon Sep 17 00:00:00 2001
From: Ludovic Raess <ludovic.rass@gmail.com>
Date: Fri, 12 Jul 2024 18:34:45 +0200
Subject: [PATCH 1/3] Fixup

---
 README.md                         |   6 +-
 website/_assets/element_chat.svg  |   7 --
 website/_assets/favicon.png       | Bin 675 -> 1203 bytes
 website/_assets/julia-logo.svg    |  10 --
 website/_css/poole_hyde.css       |   2 +-
 website/_layout/page_foot.html    |   2 +-
 website/_layout/style.html        |   2 +-
 website/_literate/user_general.jl | 201 ------------------------------
 website/index.md                  |   4 +-
 9 files changed, 9 insertions(+), 225 deletions(-)
 delete mode 100644 website/_assets/element_chat.svg
 delete mode 100644 website/_assets/julia-logo.svg
 delete mode 100644 website/_literate/user_general.jl

diff --git a/README.md b/README.md
index 1244f74..8704a20 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
-# JuliaOnHPCClusters
+# Julia On HPC Clusters
 
-Notes on how to use/set up Julia on HPC clusters. Visit the rendered website under [juliahpc.github.io](https://juliahpc.github.io).
+Notes on how to use/set up Julia on HPC clusters.
+
+**Visit the rendered website under [juliahpc.github.io](https://juliahpc.github.io).**
diff --git a/website/_assets/element_chat.svg b/website/_assets/element_chat.svg
deleted file mode 100644
index 54a91b7..0000000
--- a/website/_assets/element_chat.svg
+++ /dev/null
@@ -1,7 +0,0 @@
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diff --git a/website/_assets/favicon.png b/website/_assets/favicon.png
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diff --git a/website/_assets/julia-logo.svg b/website/_assets/julia-logo.svg
deleted file mode 100644
index 0acc3dc..0000000
--- a/website/_assets/julia-logo.svg
+++ /dev/null
@@ -1,10 +0,0 @@
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diff --git a/website/_css/poole_hyde.css b/website/_css/poole_hyde.css
index b0d39de..8a1df55 100644
--- a/website/_css/poole_hyde.css
+++ b/website/_css/poole_hyde.css
@@ -267,7 +267,7 @@ html {
     top: 0;
     left: 0;
     bottom: 0;
-    width: 23rem;
+    width: 19rem;
     text-align: left;
   }
 }
diff --git a/website/_layout/page_foot.html b/website/_layout/page_foot.html
index 7e186f7..e128b83 100644
--- a/website/_layout/page_foot.html
+++ b/website/_layout/page_foot.html
@@ -1,6 +1,6 @@
 <div class="page-foot">
   <div class="copyright">
-    <a href="https://github.com/carstenbauer/JuliaOnHPCClusters/"><b>Edit this page on <img class="github-logo" src="https://unpkg.com/ionicons@5.1.2/dist/svg/logo-github.svg"></img></b></a><br>
+    <a href="https://github.com/JuliaHPC/juliahpc.github.io/"><b>Edit this page on <img class="github-logo" src="https://unpkg.com/ionicons@5.1.2/dist/svg/logo-github.svg"></img></b></a><br>
     {{isnotpage /tag/*}}Last modified: {{ fill fd_mtime }}.{{end}} Website built with <a href="https://github.com/tlienart/Franklin.jl">Franklin.jl</a> and the <a href="https://julialang.org">Julia programming language</a>.
   </div>
 </div>
diff --git a/website/_layout/style.html b/website/_layout/style.html
index 834c608..b45efdd 100644
--- a/website/_layout/style.html
+++ b/website/_layout/style.html
@@ -4,7 +4,7 @@
 <!-- style adjustments -->
 <style>
   html {font-size: 17px;}
-  .franklin-content {position: relative; padding-left: 8%; padding-right: 5%; line-height: 1.35em;}
+  .franklin-content {position: relative; padding-left: 1%; padding-right: 5%; line-height: 1.35em;}
   @media (min-width: 940px) {
     .franklin-content {width: 100%; margin-left: auto; margin-right: auto;}
   }
diff --git a/website/_literate/user_general.jl b/website/_literate/user_general.jl
deleted file mode 100644
index 7152e28..0000000
--- a/website/_literate/user_general.jl
+++ /dev/null
@@ -1,201 +0,0 @@
-#src # This is needed to make this run as normal Julia file
-using Markdown #src
-
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-#nb # _Lecture 1_
-md"""
-# Why solve PDEs on GPUs? & The tool for the job
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-## Why solve PDEs on GPUs?
-"""
-
-#md # ~~~
-# <center>
-#   <video width="80%" autoplay loop controls src="../assets/literate_figures/l1_porous_convection_2D.mp4"/>
-# </center>
-#md # ~~~
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-### A brief intro about GPU computing:
-- Why we do it
-- Why it is cool (in Julia)
-- Examples from current research
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-### Propaganda
-#### Why we do it
-"""
-
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "fragment"}}
-md"""
-Predict the evolution of natural and engineered systems.
-
-![ice2](../assets/literate_figures/l1_ice2.png)
-
-_e.g. ice cap evolution, stress distribution, etc..._
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-Physical processes that describe those systems are **complex** and often **nonlinear**
-- no or very limited analytical solution is available
-
-👉 a numerical approach is required to solve the mathematical model
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-A numerical solution means solving a system of (coupled) differential equations
-
-$$
-\mathbf{mathematical ~ model ~ → ~ discretisation ~ → ~ solution}\\
-\frac{∂C}{∂t} = ... ~ → ~ \frac{\texttt{C}^{i+1} - \texttt{C}^{i}}{\texttt{∆t}} = ... ~ → ~ \texttt{C} = \texttt{C} + \texttt{∆t} \cdot ...
-$$
-
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-Solving PDEs is computationally demanding
-- ODEs - scalar equations
-
-$$ \frac{∂C}{∂t} = -\frac{(C-C_{eq})}{ξ} $$
-
-but...
-"""
-
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "fragment"}}
-md"""
-- PDEs - involve vectors (and tensors)  👉 local gradients & neighbours
-
-$$ \frac{∂C}{∂t} = D~ \left(\frac{∂^2C}{∂x^2} + \frac{∂^2C}{∂y^2} \right) $$
-
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-Computational costs increase
-- with complexity (e.g. multi-physics, couplings)
-- with dimensions (3D tensors...)
-- upon refining spatial and temporal resolution
-
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-#md # ~~~
-# <center>
-#   <video width="80%" autoplay loop controls src="../assets/literate_figures/l1_Stokes2D_vep.mp4"/>
-# </center>
-#md # ~~~
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-Use **parallel computing** to address this:
-- The "memory wall" in ~ 2004
-- Single-core to multi-core devices
-
-![mem_wall](../assets/literate_figures/l1_mem_wall.png)
-
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-GPUs are _massively_ parallel devices
-- SIMD machine (programmed using threads - SPMD) ([more](https://safari.ethz.ch/architecture/fall2020/lib/exe/fetch.php?media=onur-comparch-fall2020-lecture24-simdandgpu-afterlecture.pdf))
-- Further increases the Flop vs Bytes gap
-
-![cpu_gpu_evo](../assets/literate_figures/l1_cpu_gpu_evo.png)
-
-"""
-
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "fragment"}}
-md"""
-👉 We are memory bound: requires to re-think the numerical implementation and solution strategies
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-#### Why it is cool
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "fragment"}}
-md"""
-![julia-gpu](../assets/literate_figures/l1_julia-gpu.png)
-
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-#### GPU are cool
-- Price vs Performance; Close to **1.5TB/s** memory throughput (nonlinear diffusion) that one can achieve :rocket:
-
-![perf_gpu](../assets/literate_figures/l1_perf_gpu.png)
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-- Availability (less fight for resources); Still not many applications run on GPUs
-
-- Workstation turns into a personal Supercomputers; GPU vs CPUs peak memory bandwidth: theoretical 10x (practically more)
-
-![titan_node](../assets/literate_figures/l1_titan_node.jpg)
-
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-#### Julia is cool
-Solution to the "two-language problem"
-- Single code for prototyping and production
-
-![two_lang](../assets/literate_figures/l1_two_lang.png)
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-Backend agnostic:
-- Single code to run on single CPU or thousands of GPUs
-- Single code to run on various CPUs (x86, Power9, ARM) \
-  and GPUs (Nvidia, AMD)
-
-Interactive:
-- No need for 3rd-party visualisation software
-- Debugging and interactive REPL mode
-- Efficient for development
-"""
-
-#src #########################################################################
-#nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
-md"""
-#### Examples from current research
-
-- [ParallelStencil _miniapps_](https://github.com/omlins/ParallelStencil.jl#miniapp-content)
-- [Ice-flow modelling](https://github.com/luraess/julia-parallel-course-EGU21#greenlands-ice-cap-evolution)
-- [GPU4GEO - _Frontier GPU multi-physics solvers_](https://ptsolvers.github.io/GPU4GEO/software/)
-- [3D hydro-mechanical inversions](https://github.com/PTsolvers/PseudoTransientAdjoint.jl#3d-hydro-mechanically-constrained-inversion)
-- [3D Random fields](https://github.com/luraess/ParallelRandomFields.jl#parallelrandomfieldsjl)
-- more ...
-
-"""
diff --git a/website/index.md b/website/index.md
index 66ba416..c26bb38 100644
--- a/website/index.md
+++ b/website/index.md
@@ -35,10 +35,10 @@ PRs or via public or private communication:
 * Mirek Kratochvíl ([@exaexa](https://github.com/exaexa))
 * Pedro Ojeda ([@pojeda](https://github.com/pojeda))
 * Samuel Omlin ([@omlins](https://github.com/omlins)) - CSCS / ETHZ
-* Ludovic Räss ([@luraess](https://github.com/luraess)) - ETHZ
+* Ludovic Räss ([@luraess](https://github.com/luraess)) - Unil / ETHZ
 * Michael Schlottke-Lakemper ([@sloede](https://github.com/sloede)) - HLRS / RWTH
 * Erik Schnetter ([@eschnett](https://github.com/eschnett)) - PITP
 * Dinindu Senanayake ([@DininduSenanayake](https://github.com/DininduSenanayake))
 * Kjartan Thor Wikfeldt ([@wikfeldt](https://github.com/wikfeldt)) - ENCCS
 
-(You think we forgot your name here? Please make a PR!)
\ No newline at end of file
+(You think we forgot your name here? Please make a PR!)

From 1b51480555992a45dbffe533b444d29e7c8418f6 Mon Sep 17 00:00:00 2001
From: Ludovic Raess <ludovic.rass@gmail.com>
Date: Fri, 12 Jul 2024 18:36:41 +0200
Subject: [PATCH 2/3] Fixup

---
 website/_layout/sidebar.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/website/_layout/sidebar.html b/website/_layout/sidebar.html
index a8f47fd..20a048c 100644
--- a/website/_layout/sidebar.html
+++ b/website/_layout/sidebar.html
@@ -16,9 +16,9 @@ <h1><a href="/">Julia On HPC Clusters</a></h1>
       <div class="course-section">For Users</div>
       <a class="sidebar-nav-item {{ispage user_gettingstarted/*}}active{{end}}" href="/user_gettingstarted/">Getting started</a>
       <a class="sidebar-nav-item {{ispage user_vscode/*}}active{{end}}" href="/user_vscode/">Visual Studio Code on HPC Clusters</a>
-      <a class="sidebar-nav-item {{ispage user_faq/*}}active{{end}}" href="/user_faq/">FAQ</a>
       <a class="sidebar-nav-item {{ispage user_hpcprofiling/*}}active{{end}}" href="/user_hpcprofiling/">HPC profiling tools</a>
       <a class="sidebar-nav-item {{ispage user_hpcsystems/*}}active{{end}}" href="/user_hpcsystems/">HPC systems with Julia support</a>
+      <a class="sidebar-nav-item {{ispage user_faq/*}}active{{end}}" href="/user_faq/">FAQ</a>
       <!-- <a class="sidebar-nav-item {{ispage user_jlls/*}}active{{end}}" href="/user_jlls/">JLLs and system software</a> -->
       <div class="course-section">For System Admins</div>
       <a class="sidebar-nav-item {{ispage sysadmin_julia/*}}active{{end}}" href="/sysadmin_julia/">How to provide Julia to users?</a>

From 0a1fd50d75493aff2353a5d0e487ba51861f33c6 Mon Sep 17 00:00:00 2001
From: Ludovic Raess <ludovic.rass@gmail.com>
Date: Fri, 12 Jul 2024 21:14:39 +0200
Subject: [PATCH 3/3] Add logo

---
 website/_assets/juliahpc_logo.png | Bin 0 -> 11881 bytes
 website/_css/custom.css           |   6 ++++++
 website/index.md                  |   4 ++++
 3 files changed, 10 insertions(+)
 create mode 100644 website/_assets/juliahpc_logo.png

diff --git a/website/_assets/juliahpc_logo.png b/website/_assets/juliahpc_logo.png
new file mode 100644
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HcmV?d00001

diff --git a/website/_css/custom.css b/website/_css/custom.css
index 29182d9..4ad36f4 100644
--- a/website/_css/custom.css
+++ b/website/_css/custom.css
@@ -1,5 +1,11 @@
 @import url("https://fonts.googleapis.com/css2?family=PT+Sans+Caption:wght@700&family=PT+Sans:ital,wght@0,400;0,700;1,400;1,700&display=swap");
 
+.im-10 {text-align: center;}
+.im-10 img {
+    padding: 0;
+    width: 10%;
+}
+
 h1 {
     border-bottom: 1px solid #999 !important;
     margin-bottom: 1em !important;
diff --git a/website/index.md b/website/index.md
index c26bb38..09a3f78 100644
--- a/website/index.md
+++ b/website/index.md
@@ -4,6 +4,10 @@ title = "Julia On HPC Clusters"
 
 # Julia on HPC clusters
 
+@@im-10
+![JuliaHPC](/assets/juliahpc_logo.png)
+@@
+
 👋 Welcome to the notes about the [Julia programming language](http://www.julialang.org/) on HPC clusters.
 
 ## Objective