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README.md

+1 −2
Original line number Diff line number Diff line
@@ -3,8 +3,7 @@ author: Alexandre Strube 
title: Getting Started with AI on Supercomputers

---



The older repo was https://gitlab.jsc.fz-juelich.de/MLDL_FZJ/juhaicu/jsc_public/sharedspace/teaching/dl_on_supercomputers

This repo is specifically for the course described in [indico](https://indico3-jsc.fz-juelich.de/event/107)

This repo is specifically for the course described in [indico](https://indico3-jsc.fz-juelich.de/event/201)



---

index.md

+23 −17
Original line number Diff line number Diff line
@@ -2,12 +2,12 @@ 
author: Alexandre Strube

title: Deep Learning on Supercomputers

# subtitle: A primer in supercomputers`

date: May 23, 2024

date: November 13, 2024

---

## Resources:



- [This document](https://strube1.pages.jsc.fz-juelich.de/2024-05-talk-intro-to-supercompting-jsc)

- [Source code of this course](https://gitlab.jsc.fz-juelich.de/strube1/2024-05-talk-intro-to-supercompting-jsc)

- [This document](https://strube1.pages.jsc.fz-juelich.de/2024-11-talk-intro-to-supercompting-jsc)

- [Source code of this course](https://gitlab.jsc.fz-juelich.de/strube1/2024-11-talk-intro-to-supercompting-jsc)



![](images/Logo_FZ_Juelich_rgb_Schutzzone_transparent.svg)
@@ -37,7 +37,7 @@ date: May 23, 2024 
    - on a mult-gpu, multi-node system

    - like a supercomputer 🤯

- Important: This is an overview, _*NOT*_ a basic AI course!

- We have [introductory courses on AI on supercomputers](https://www.fz-juelich.de/en/ias/jsc/news/events/training-courses/2024/ai-sc-2)

- We have [introductory courses on AI on supercomputers](https://www.fz-juelich.de/en/ias/jsc/news/events/training-courses/2024/ai-sc-4)

- ![](images/bringing-dl-workloads-2024-2-course.png)

![](images/Logo_FZ_Juelich_rgb_Schutzzone_transparent.svg)
@@ -47,7 +47,7 @@ date: May 23, 2024 


### Please access it now, so you can follow along:



[https://go.fzj.de/2024-05-talk-intro-to-supercomputing-jsc](https://go.fzj.de/2024-05-talk-intro-to-supercomputing-jsc)

[https://go.fzj.de/2024-11-talk-intro-to-supercomputing-jsc](https://go.fzj.de/2024-11-talk-intro-to-supercomputing-jsc)



![](images/slides.png)
@@ -58,7 +58,7 @@ date: May 23, 2024 
- All slides and source code

- Connect to the supercomputer and do this:

- ```bash

git clone https://gitlab.jsc.fz-juelich.de/strube1/2024-05-talk-intro-to-supercompting-jsc.git

git clone https://gitlab.jsc.fz-juelich.de/strube1/2024-11-talk-intro-to-supercompting-jsc.git

```



---
@@ -397,7 +397,7 @@ git clone https://gitlab.jsc.fz-juelich.de/strube1/2024-05-talk-intro-to-superco 
![](images/slides.png)



- ```bash

git clone https://gitlab.jsc.fz-juelich.de/strube1/2024-05-talk-intro-to-supercompting-jsc.git

git clone https://gitlab.jsc.fz-juelich.de/strube1/2024-11-talk-intro-to-supercompting-jsc.git

```
@@ -518,13 +518,19 @@ learn.fine_tune(6) 
- Only add new requirements

- [Link to gitlab repo](https://gitlab.jsc.fz-juelich.de/kesselheim1/sc_venv_template)

- ```bash

cd $HOME/2024-05-talk-intro-to-supercompting-jsc/src

cd $HOME/2024-11-talk-intro-to-supercompting-jsc/src

git clone https://gitlab.jsc.fz-juelich.de/kesselheim1/sc_venv_template.git

```

- Add this to sc_venv_template/requirements.txt:

- ```python

fastai

deepspeed

# Add here the pip packages you would like to install on this virtual environment / kernel

pip

fastai==2.7.15

scipy==1.11.1

matplotlib==3.7.2

scikit-learn==1.3.1

pandas==2.0.3

torch==2.1.2

accelerate

```
@@ -541,7 +547,7 @@ source sc_venv_template/activate.sh 


```bash

#!/bin/bash

#SBATCH --account=training2410

#SBATCH --account=training2436

#SBATCH --nodes=1

#SBATCH --job-name=ai-serial

#SBATCH --ntasks-per-node=1
@@ -549,10 +555,10 @@ source sc_venv_template/activate.sh 
#SBATCH --output=out-serial.%j

#SBATCH --error=err-serial.%j

#SBATCH --time=00:40:00

#SBATCH --partition=develbooster

#SBATCH --partition=dc-gpu



# Make sure we are on the right directory

cd $HOME/2024-05-talk-intro-to-supercompting-jsc/src

cd $HOME/2024-11-talk-intro-to-supercompting-jsc/src



# This loads modules and python packages

source sc_venv_template/activate.sh
@@ -573,7 +579,7 @@ time srun python serial.py 
## Download dataset



```bash

cd $HOME/2024-05-talk-intro-to-supercompting-jsc/src

cd $HOME/2024-11-talk-intro-to-supercompting-jsc/src

source sc_venv_template/activate.sh

python serial.py
@@ -593,7 +599,7 @@ Epoch 1/1 : |-------------------------------------------------------------| 0.71 
## Running it



- ```bash

cd $HOME/2024-05-talk-intro-to-supercompting-jsc/src

cd $HOME/2024-11-talk-intro-to-supercompting-jsc/src

sbatch serial.slurm

```

- On Juwels Booster, should take about 5 minutes
@@ -663,7 +669,7 @@ with learn.distrib_ctx(): 


## Submission script: data parallel



- Please check the course repository: [src/distrib.slurm](https://gitlab.jsc.fz-juelich.de/strube1/2024-05-talk-intro-to-supercompting-jsc/-/blob/main/src/distrib.slurm)

- Please check the course repository: [src/distrib.slurm](https://gitlab.jsc.fz-juelich.de/strube1/2024-11-talk-intro-to-supercompting-jsc/-/blob/main/src/distrib.slurm)



- Main differences:
@@ -767,6 +773,6 @@ real 1m15.651s 


## References



- [Pytorch Model Parallelism and Pipelining](https://pytorch.org/docs/stable/pipeline.html)

- [Pytorch Model Parallelism and Pipelining](https://pytorch.org/docs/stable/distributed.pipelining.html)

- [Intro to Distributed Deep Learning](https://xiandong79.github.io/Intro-Distributed-Deep-Learning)

- [Model Parallelism - Amazon SageMaker](https://docs.aws.amazon.com/sagemaker/latest/dg/model-parallel-intro.html)
 
 No newline at end of file

public/README.html

+2 −4
Original line number Diff line number Diff line
@@ -166,10 +166,8 @@ 


<section class="slide level2">



<p>The older repo was

https://gitlab.jsc.fz-juelich.de/MLDL_FZJ/juhaicu/jsc_public/sharedspace/teaching/dl_on_supercomputers

This repo is specifically for the course described in <a

href="https://indico3-jsc.fz-juelich.de/event/107">indico</a></p>

<p>This repo is specifically for the course described in <a

href="https://indico3-jsc.fz-juelich.de/event/201">indico</a></p>

</section>

<section class="slide level2">

public/index.html

+26 −20
Original line number Diff line number Diff line
@@ -4,7 +4,7 @@ 
  <meta charset="utf-8">

  <meta name="generator" content="pandoc">

  <meta name="author" content="Alexandre Strube">

  <meta name="dcterms.date" content="2024-05-23">

  <meta name="dcterms.date" content="2024-11-13">

  <title>Deep Learning on Supercomputers</title>

  <meta name="apple-mobile-web-app-capable" content="yes">

  <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
@@ -227,17 +227,17 @@ 
<section id="title-slide">

  <h1 class="title">Deep Learning on Supercomputers</h1>

  <p class="author">Alexandre Strube</p>

  <p class="date">May 23, 2024</p>

  <p class="date">November 13, 2024</p>

</section>



<section id="resources" class="slide level2">

<h2>Resources:</h2>

<ul>

<li class="fragment"><a

href="https://strube1.pages.jsc.fz-juelich.de/2024-05-talk-intro-to-supercompting-jsc">This

href="https://strube1.pages.jsc.fz-juelich.de/2024-11-talk-intro-to-supercompting-jsc">This

document</a></li>

<li class="fragment"><a

href="https://gitlab.jsc.fz-juelich.de/strube1/2024-05-talk-intro-to-supercompting-jsc">Source

href="https://gitlab.jsc.fz-juelich.de/strube1/2024-11-talk-intro-to-supercompting-jsc">Source

code of this course</a></li>

</ul>

<p><img
@@ -279,7 +279,7 @@ data-src="images/Logo_FZ_Juelich_rgb_Schutzzone_transparent.svg" /></p> 
<li class="fragment">Important: This is an overview,

<em><em>NOT</em></em> a basic AI course!</li>

<li class="fragment">We have <a

href="https://www.fz-juelich.de/en/ias/jsc/news/events/training-courses/2024/ai-sc-2">introductory

href="https://www.fz-juelich.de/en/ias/jsc/news/events/training-courses/2024/ai-sc-4">introductory

courses on AI on supercomputers</a></li>

<li class="fragment"><img

data-src="images/bringing-dl-workloads-2024-2-course.png" /> <img
@@ -291,7 +291,7 @@ data-src="images/Logo_FZ_Juelich_rgb_Schutzzone_transparent.svg" /></li> 
<h3 id="please-access-it-now-so-you-can-follow-along">Please access it

now, so you can follow along:</h3>

<p><a

href="https://go.fzj.de/2024-05-talk-intro-to-supercomputing-jsc">https://go.fzj.de/2024-05-talk-intro-to-supercomputing-jsc</a></p>

href="https://go.fzj.de/2024-11-talk-intro-to-supercomputing-jsc">https://go.fzj.de/2024-11-talk-intro-to-supercomputing-jsc</a></p>

<p><img data-src="images/slides.png" /></p>

</section>

<section id="git-clone-this-repository" class="slide level2">
@@ -300,7 +300,7 @@ href="https://go.fzj.de/2024-05-talk-intro-to-supercomputing-jsc">https://go.fzj 
<li class="fragment">All slides and source code</li>

<li class="fragment">Connect to the supercomputer and do this:</li>

<li class="fragment"><div class="sourceCode" id="cb1"><pre

class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone https://gitlab.jsc.fz-juelich.de/strube1/2024-05-talk-intro-to-supercompting-jsc.git</span></code></pre></div></li>

class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone https://gitlab.jsc.fz-juelich.de/strube1/2024-11-talk-intro-to-supercompting-jsc.git</span></code></pre></div></li>

</ul>

</section>

<section id="deep-learning-is" class="slide level2">
@@ -611,7 +611,7 @@ repository:</h2> 
<p><img data-src="images/slides.png" /></p>

<ul>

<li class="fragment"><div class="sourceCode" id="cb2"><pre

class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone https://gitlab.jsc.fz-juelich.de/strube1/2024-05-talk-intro-to-supercompting-jsc.git</span></code></pre></div></li>

class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone https://gitlab.jsc.fz-juelich.de/strube1/2024-11-talk-intro-to-supercompting-jsc.git</span></code></pre></div></li>

</ul>

</section>

<section id="demo-time" class="slide level2">
@@ -719,13 +719,19 @@ modules</li> 
href="https://gitlab.jsc.fz-juelich.de/kesselheim1/sc_venv_template">Link

to gitlab repo</a></li>

<li class="fragment"><div class="sourceCode" id="cb7"><pre

class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$HOME</span>/2024-05-talk-intro-to-supercompting-jsc/src</span>

class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$HOME</span>/2024-11-talk-intro-to-supercompting-jsc/src</span>

<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone https://gitlab.jsc.fz-juelich.de/kesselheim1/sc_venv_template.git</span></code></pre></div></li>

<li class="fragment">Add this to sc_venv_template/requirements.txt:</li>

<li class="fragment"><div class="sourceCode" id="cb8"><pre

class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>fastai</span>

<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a>deepspeed</span>

<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>accelerate</span></code></pre></div></li>

class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Add here the pip packages you would like to install on this virtual environment / kernel</span></span>

<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a>pip</span>

<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>fastai<span class="op">==</span><span class="fl">2.7.15</span></span>

<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a>scipy<span class="op">==</span><span class="fl">1.11.1</span></span>

<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a>matplotlib<span class="op">==</span><span class="fl">3.7.2</span></span>

<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a>scikit<span class="op">-</span>learn<span class="op">==</span><span class="fl">1.3.1</span></span>

<span id="cb8-7"><a href="#cb8-7" aria-hidden="true" tabindex="-1"></a>pandas<span class="op">==</span><span class="fl">2.0.3</span></span>

<span id="cb8-8"><a href="#cb8-8" aria-hidden="true" tabindex="-1"></a>torch<span class="op">==</span><span class="fl">2.1.2</span></span>

<span id="cb8-9"><a href="#cb8-9" aria-hidden="true" tabindex="-1"></a>accelerate</span></code></pre></div></li>

<li class="fragment"><div class="sourceCode" id="cb9"><pre

class="sourceCode bash"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="ex">sc_venv_template/setup.sh</span></span>

<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="bu">source</span> sc_venv_template/activate.sh</span></code></pre></div></li>
@@ -736,7 +742,7 @@ class="sourceCode bash"><code class="sourceCode bash"><span id="cb9-1"><a href=" 
<h2>Submission Script</h2>

<div class="sourceCode" id="cb10"><pre

class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="co">#!/bin/bash</span></span>

<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --account=training2410</span></span>

<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --account=training2436</span></span>

<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --nodes=1</span></span>

<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --job-name=ai-serial</span></span>

<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --ntasks-per-node=1</span></span>
@@ -744,10 +750,10 @@ class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href= 
<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --output=out-serial.%j</span></span>

<span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --error=err-serial.%j</span></span>

<span id="cb10-9"><a href="#cb10-9" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --time=00:40:00</span></span>

<span id="cb10-10"><a href="#cb10-10" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --partition=develbooster</span></span>

<span id="cb10-10"><a href="#cb10-10" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --partition=dc-gpu</span></span>

<span id="cb10-11"><a href="#cb10-11" aria-hidden="true" tabindex="-1"></a></span>

<span id="cb10-12"><a href="#cb10-12" aria-hidden="true" tabindex="-1"></a><span class="co"># Make sure we are on the right directory</span></span>

<span id="cb10-13"><a href="#cb10-13" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$HOME</span>/2024-05-talk-intro-to-supercompting-jsc/src</span>

<span id="cb10-13"><a href="#cb10-13" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$HOME</span>/2024-11-talk-intro-to-supercompting-jsc/src</span>

<span id="cb10-14"><a href="#cb10-14" aria-hidden="true" tabindex="-1"></a></span>

<span id="cb10-15"><a href="#cb10-15" aria-hidden="true" tabindex="-1"></a><span class="co"># This loads modules and python packages</span></span>

<span id="cb10-16"><a href="#cb10-16" aria-hidden="true" tabindex="-1"></a><span class="bu">source</span> sc_venv_template/activate.sh</span>
@@ -765,7 +771,7 @@ class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href= 
<section id="download-dataset-1" class="slide level2">

<h2>Download dataset</h2>

<div class="sourceCode" id="cb11"><pre

class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$HOME</span>/2024-05-talk-intro-to-supercompting-jsc/src</span>

class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$HOME</span>/2024-11-talk-intro-to-supercompting-jsc/src</span>

<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a><span class="bu">source</span> sc_venv_template/activate.sh</span>

<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span> serial.py</span>

<span id="cb11-4"><a href="#cb11-4" aria-hidden="true" tabindex="-1"></a></span>
@@ -783,7 +789,7 @@ class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href= 
<h2>Running it</h2>

<ul>

<li class="fragment"><div class="sourceCode" id="cb12"><pre

class="sourceCode bash"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$HOME</span>/2024-05-talk-intro-to-supercompting-jsc/src</span>

class="sourceCode bash"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$HOME</span>/2024-11-talk-intro-to-supercompting-jsc/src</span>

<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a><span class="ex">sbatch</span> serial.slurm</span></code></pre></div></li>

<li class="fragment">On Juwels Booster, should take about 5 minutes</li>

<li class="fragment">On a cpu system this would take half a day</li>
@@ -839,7 +845,7 @@ class="sourceCode python"><code class="sourceCode python"><span id="cb17-1"><a h 
<h2>Submission script: data parallel</h2>

<ul>

<li class="fragment"><p>Please check the course repository: <a

href="https://gitlab.jsc.fz-juelich.de/strube1/2024-05-talk-intro-to-supercompting-jsc/-/blob/main/src/distrib.slurm">src/distrib.slurm</a></p></li>

href="https://gitlab.jsc.fz-juelich.de/strube1/2024-11-talk-intro-to-supercompting-jsc/-/blob/main/src/distrib.slurm">src/distrib.slurm</a></p></li>

<li class="fragment"><p>Main differences:</p></li>

<li class="fragment"><div class="sourceCode" id="cb18"><pre

class="sourceCode bash"><code class="sourceCode bash"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a><span class="co">#SBATCH --cpus-per-task=48</span></span>
@@ -951,8 +957,8 @@ DL scaling course at JSC!</li> 
<h2>References</h2>

<ul>

<li class="fragment"><a

href="https://pytorch.org/docs/stable/pipeline.html">Pytorch Model

Parallelism and Pipelining</a></li>

href="https://pytorch.org/docs/stable/distributed.pipelining.html">Pytorch

Model Parallelism and Pipelining</a></li>

<li class="fragment"><a

href="https://xiandong79.github.io/Intro-Distributed-Deep-Learning">Intro

to Distributed Deep Learning</a></li>

src/distrib.slurm

+3 −3
Original line number Diff line number Diff line 
#!/bin/bash

#SBATCH --account=training2410

#SBATCH --account=training2436

#SBATCH --nodes=1

#SBATCH --job-name=ai-multi-gpu

#SBATCH --ntasks-per-node=1
@@ -7,7 +7,7 @@ 
#SBATCH --output=out-distrib.%j

#SBATCH --error=err-distrib.%j

#SBATCH --time=00:20:00

#SBATCH --partition=booster

#SBATCH --partition=dc-gpu

#SBATCH --gres=gpu:4



# Without this, srun does not inherit cpus-per-task from sbatch.
@@ -23,7 +23,7 @@ export MASTER_PORT=7010 
export GPUS_PER_NODE=4



# Make sure we are on the right directory

cd $HOME/2024-05-talk-intro-to-supercompting-jsc/src

cd $HOME/2024-11-talk-intro-to-supercompting-jsc/src



# This loads modules and python packages

source sc_venv_template/activate.sh

src/serial.slurm

+3 −3
Original line number Diff line number Diff line 
#!/bin/bash

#SBATCH --account=training2410

#SBATCH --account=training2436

#SBATCH --nodes=1

#SBATCH --job-name=ai-serial

#SBATCH --ntasks-per-node=1
@@ -7,11 +7,11 @@ 
#SBATCH --output=out-serial.%j

#SBATCH --error=err-serial.%j

#SBATCH --time=00:40:00

#SBATCH --partition=develbooster

#SBATCH --partition=dc-gpu

#SBATCH --gres=gpu:1



# Make sure we are on the right directory

cd $HOME/2024-05-talk-intro-to-supercompting-jsc/src

cd $HOME/2024-11-talk-intro-to-supercompting-jsc/src



# This loads modules and python packages

source sc_venv_template/activate.sh