Commit 5e857fa0 authored by Sören Wacker's avatar Sören Wacker
Browse files

add bash and slurm tutorials, standardize shell-session format 

- add beginner tutorials for bash and slurm basics
- update apptainer tutorial for new cluster (salloc, hostnames, GPU types)
- standardize all code blocks to use shell-session format
- document code block convention in README
- reorder tutorials: bash -> slurm -> apptainer
- move cite.md to end of about section
parent c0ff9b1b

README.md

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@@ -23,6 +23,24 @@ This documentation follows the [Diataxis](https://diataxis.fr/) framework, which 
- `docs/about/` - Explanation

- `support/` - Troubleshooting and contact information



### Code block conventions



Use `shell-session` for terminal examples. This syntax highlights the distinction between commands (prefixed with `$`) and output:



~~~markdown

```shell-session

$ hostname

daic01.hpc.tudelft.nl

$ squeue -u $USER

  JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

    294       all submit.s  netid01  R       0:02      1 gpu23

```

~~~



- Commands start with `$`

- Output has no prefix

- Interactive prompts like `Apptainer>` are shown as-is



## Running the website locally



Building and running the site locally requires a recent `extended` version of [Hugo](https://gohugo.io).

content/en/docs/about/cite.md

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---

title: "How to Cite"

weight: 2

weight: 99

type: docs

description: "How to cite and acknowledge DAIC in publications."

---

content/en/howto/container-gpu-job.md

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@@ -13,9 +13,9 @@ Complete [First GPU Job](/quickstart/first-gpu-job/) to understand GPU job basic 


Pull a PyTorch container from NVIDIA NGC:



```bash

cd /tudelft.net/staff-umbrella/<project>/containers

apptainer pull docker://nvcr.io/nvidia/pytorch:24.01-py3

```shell-session

$ cd /tudelft.net/staff-umbrella/<project>/containers

$ apptainer pull docker://nvcr.io/nvidia/pytorch:24.01-py3

```



## Create a test script
@@ -59,15 +59,15 @@ srun apptainer exec --nv \ 


## Submit and check output



```bash

sbatch container_gpu.sh

> Submitted batch job 305

```shell-session

$ sbatch container_gpu.sh

Submitted batch job 305



cat container_305.out

> PyTorch version: 2.2.0

> CUDA available: True

> GPU: NVIDIA L40

> GPU computation successful

$ cat container_305.out

PyTorch version: 2.2.0

CUDA available: True

GPU: NVIDIA L40

GPU computation successful

```



## Key options

content/en/quickstart/first-job.md

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@@ -14,8 +14,8 @@ You should already be logged in to DAIC. If not, complete [First Login](/quickst 


### 1. Create a working directory



```bash

mkdir -p ~/my-first-job && cd ~/my-first-job

```shell-session

$ mkdir -p ~/my-first-job && cd ~/my-first-job

```



### 2. Create a Python script
@@ -42,33 +42,33 @@ srun python hello.py 


{{% alert title="Account required" color="warning" %}}

Replace `<your-account>` with your account name. Find yours with:

```bash

sacctmgr show associations user=$USER format=Account -P

```shell-session

$ sacctmgr show associations user=$USER format=Account -P

```

{{% /alert %}}



### 4. Submit the job



```bash

sbatch submit.sh

> Submitted batch job 294

```shell-session

$ sbatch submit.sh

Submitted batch job 294

```



### 5. Monitor the job



```bash

squeue -u $USER

>   JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

>     294       all submit.s  netid01  R       0:02      1 gpu23

```shell-session

$ squeue -u $USER

  JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

    294       all submit.s  netid01  R       0:02      1 gpu23

```



### 6. Check the output



Once completed, view the output file:



```bash

cat slurm_294.out

> Hello from gpu23.ethernet.tudhpc

```shell-session

$ cat slurm_294.out

Hello from gpu23.ethernet.tudhpc

```



## Request a GPU

content/en/quickstart/first-login.md

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@@ -21,8 +21,8 @@ Activate TU Delft network via [eduVPN](https://tudelft.eduvpn.nl/portal/home). 


1. Open your terminal and run the following SSH command:



```bash

ssh <YourNetID>@daic01.hpc.tudelft.nl

```shell-session

$ ssh <YourNetID>@daic01.hpc.tudelft.nl

```



2. You will be prompted for your password. On first login, DAIC may also set up parts of your home environment:
@@ -53,13 +53,13 @@ It might take a few seconds to get your `$HOME` set. This is normal. 


Run the following commands:



```bash

hostname

> daic01.hpc.tudelft.nl

pwd

> /home/<YourNetID>

whoami

> <YourNetID>

```shell-session

$ hostname

daic01.hpc.tudelft.nl

$ pwd

/home/<YourNetID>

$ whoami

<YourNetID>

```



If these commands return the expected values, your login was successful.