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uav workshop: pre-workshop instructions
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remove setup instructions for now
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HeatherSavoy-USDA committed Oct 8, 2024
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71 changes: 1 addition & 70 deletions sn_collections/_events/2024-10-09-Multispectral-UAV-workshop.md
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Expand Up @@ -57,73 +57,4 @@ To help minimize technical issues and delays at the start of the workshop, pleas
* Click the "Launch" button.
* Wait a moment for the job card to update from "Queued" to "Running".
* Please confirm that clicking on the "Connect to JupyterLab Server" button opens a new tab with the JupyterLab Server interface.


-----

## Tutorial Setup Instructions

Steps to prepare for the tutorial session each day:

1. **Login to Atlas Open OnDemand** at [https://atlas-ood.hpc.msstate.edu/](https://atlas-ood.hpc.msstate.edu/). For more information on login procedures for web-based SCINet access, see the [SCINet access user guide]({{site.baseurl}}/guides/access/web-based-login).

1. **Open a command-line session** by clicking on “Clusters” -> “Atlas Shell Access” on the top menu. This will open a new tab with a command-line session on Atlas' login node.

1. **Request resources on a compute node** to avoid using the login node for data transfers by running the following command.

{:.copy-code}
```bash
srun --reservation=workshop2 -A scinet_workshop2 -t 00:30:00 -n 1 --mem 8G --pty bash
```

1. **Create a workshop working directory** and copy the workshop materials into it by running the following commands. Note: you do not have to edit the commands with your username as it will be determined by the `$USER` variable.

{:.copy-code}
```bash
mkdir -p /90daydata/shared/$USER/
cd /90daydata/shared/$USER/
cp -r /project/scinet_workshop2/multispectral_UAV/detect_GCPs .
cp -r /project/scinet_workshop2/multispectral_UAV/flight_filtering .
cp -r /project/scinet_workshop2/multispectral_UAV/[EXAMPLE DATA?] .
```

1. **Setup kernel for JupyterLab.** In the workshop project space, there is a `geospatial_conda` conda environment for the packages we will be using during the workshop tutorials. You will create a kernel called *uav_workshop* to access from JupyterLab.

First load the necessary module:

{:.copy-code}
```bash
module load miniconda3
```

If you have not used conda on Atlas before, you will first need to run these commands:

{:.copy-code}
```bash
conda init
conda config --set auto_activate_base false
source ~/.bashrc
```

For everyone, you will create a new kernelspec from the conda environment with these commands:

{:.copy-code}
```bash
conda activate /project/scinet_workshop2/multispectral_UAV/geospatial_conda
ipython kernel install --name "uav_workshop" --user
```

1. **Launch a JupyterLab Server session.** Under the *Interactive Apps* menu, select *JupyterLab Server*. Specify the following input values on the page:

* Account: scinet_workshop2
* Partition: atlas
* QOS: normal 14-00:00:00
* Number of hours: 4
* Number of nodes: 1
* Number of tasks: ??
* Additional Slurm Parameters: \-\-mem=??G \-\-reservation=workshop2
* Home Directory: /90daydata/shared/${USER}

Click *Launch*. The screen will update to the *Interactive Sessions* page. When your Jupyter session is ready, the top card will update from *Queued* to *Running* and a *Connect to Jupyter* button will appear. Click *Connect to Jupyter*.

1. For each notebook used in the tutorial, select the *uav_workshop* kernel.

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