Skip to content

Commit 815de9e

Browse files
committed
added first pass on TeachOpenCADD tutorial
1 parent f0471ef commit 815de9e

5 files changed

Lines changed: 38 additions & 0 deletions

File tree

Lines changed: 38 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,38 @@
1+
# TeachOpenCADD in Jupyter Notebook in OOD
2+
3+
[TeachOpenCADD](https://projects.volkamerlab.org/teachopencadd/index.html) is a teaching platform for computer-aided drug design.
4+
5+
## Getting Started
6+
You can run TeachOpenCADD with Jupyter Notebook in OOD by going to the URL [ood.hpc.nyu.edu](http://ood.hpc.nyu.edu) in your browser and selecting `TeachOpenCADD` from the `Interactive Apps` pull-down menu at the top of the page. As you can see below, once you've used it and other interactive apps they'll show up on your home screen under the `Recently Used Apps` header.
7+
8+
:::note
9+
Be aware that when you start from `Recently Used Apps` it will start with the same configuration that you used previously. If you'd like to configure your TeachOpenCADD session differently, you'll need to select it from the menu.
10+
:::
11+
12+
![OOD Interactive Apps menu](./static/ood_interactive_apps_teachopencadd.png)
13+
14+
## Configuration
15+
16+
You can select the number cores, amount of memory, gpu type (if any), optional Slurm options, root directory, and number of hours.
17+
18+
![OOD TeachOpenCADD Configuration](./static/ood_teachopencadd_config.png)
19+
20+
:::warning
21+
If you select to use `/home` as your root directory be careful not to go over your quota. You can find your current usage with the `myquota` command. Please see our [Storage documentation](../03_storage/01_intro_and_data_management.mdx) for details about your storage options.
22+
:::
23+
24+
## Spark Standalone Cluster with Jupyter Notebook running in OOD
25+
26+
After you hit the `Launch` button you'll have to wait for the scheduler to find node(s)for you to run on:
27+
![OOD TeachOpenCADD in queue](./static/ood_teachopencadd_in_queue.png)
28+
29+
Then you'll have a short wait for Spark itself to start up.<br />
30+
Once that happens you'll get one last page that will give you links to:
31+
- open a terminal window on the compute node your Spark session is running on
32+
- go to the directory associated with your Session ID that stores output, config and other related files for your session
33+
34+
![Pre-launch TeachOpenCADD OOD](./static/ood_teachopencadd_prelaunch.png)
35+
36+
Please click the `Connect to Jupyter` button and a Jupyter window will open.
37+
38+
Navigate to the `/teachopencadd-talktorials` directory and select your desired tutorial.
216 KB
Loading
292 KB
Loading
132 KB
Loading
135 KB
Loading

0 commit comments

Comments
 (0)