In this page:
Table of Contents
Jupyter Notebook for Python, R, and Julia
The IDAS interface
- After creating an IDAS instance for research or class use, you will see your IDAS home page. If this is your first time accessing IDAS, your home page will be empty.
- You can create Jupyter notebooks, files, and folders in IDAS. (See details below.) Click any file or folder to open that file or folder.
- In order to navigate back to your IDAS home page, click the Jupyter symbol on the top left corner:
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Uploading files
- You can upload your own Jupyter notebooks and data files to IDAS. After creating an IDAS instance for research or class use, in the top right corner of your IDAS home page, click Upload.
- Select the files to upload in your local computer. Once the upload is done, you should see the uploaded files in your directory.
Creating a new Jupyter notebook
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First, create an IDAS instance with Python, R, or Julia. If you are a student in a class that uses IDAS, follow the instructions here to access your class instance.
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In the top right corner of your IDAS home page, click New.
Under Notebook, choose Python, R, or Julia in order to create a notebook in that language. For example, if you had created an instance with Python, you can create a new Jupyter notebook with Python:
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Managing Jupyter notebooks
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In your IDAS home page, check the box next to a Jupyter notebook. If the notebook is not currently running, you will have the option to duplicate, rename, move, download, view, edit, or delete that notebook.
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- Duplicate: will make a copy of the notebook, stored in the same folder.
- Rename: will rename the notebook. Enter the new name in the pop-up box, then click Rename.
- Move: will move the notebook to a destination of your choice. In the pop-up box, enter the destination directory path, then click Move.
- Download: will download a copy of the notebook to your local computer.
- View: will open the notebook and allow editing the notebook, including adding cells and running codes.
- Edit: will allow editing the source code in the notebook.
- Shutdown: will shut down a notebook that is running.
- Delete (the red trash can icon): will permanently delete the notebook.
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The path to your IDAS home directory is /home/<your_HawkID>. In the example below, the Jupyter notebook will be moved to the "demo" folder inside the IDAS home directory.
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Creating new files and folders
- First, create an IDAS instance with Python, R, or Julia. If you are a student in a class that uses IDAS, follow the instructions here to access your class instance.
- In the top right corner of your IDAS home page, click New.
- Choose Text File to create a new .txt file, or Folder to create a new Folder. The text file can later be renamed to another extension, such as .py.
Managing files and folders
File options
- First, create an IDAS instance with Python, R, or Julia. If you are a student in a class that uses IDAS, follow the instructions here to access your class instance.
In your IDAS home page, check the box next to a file. You will be able to see the options available for that file:
- Below is a summary of the options for a .txt file:
- Duplicate: will make a copy of the file, stored in the same folder.
- Rename: will rename the file. Enter the new name in the pop-up box, then click Rename.
- Move: will move the file to a destination of your choice. In the pop-up box, enter the destination directory path, then click Move.
- Download: will download a copy of the file to your local computer.
- View: will open the file for viewing only. No editing.
- Edit: will allow editing the file.
Delete (the red trash can icon): will permanently delete the file.
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The path to your IDAS home directory is /home/<your_HawkID>. In the example below, the .txt file will be moved to the "demo" folder inside the IDAS home directory.
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Folder options
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In your IDAS home page, check the box next to a folder. You will have the option to rename, move, or delete that folder.
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The path to your IDAS home directory is /home/<your_HawkID>. |
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Working with Terminal in IDAS
The Terminal allows you to perform more tasks in IDAS, including checking system information, managing files and folders, and installing packages. Below are a few common tasks that may be helpful in IDAS.
Creating a new Terminal session
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First, create an IDAS instance with Python, R, or Julia. If you are a student in a class that uses IDAS, follow the instructions here to access your class instance.
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In the top right corner of your IDAS home page, click New.
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Checking information using Terminal
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pwd: prints the current working directory. If you are in your IDAS home diretory, the directory will be /home/<your_HawkID>.
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cd <destination>: change directory to a destination directory. For example,
cd demo: changes to thedemodirectorycd: (with no argument) returns to your home directory
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RStudio for R
Creating and saving R scripts
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Managing files and folders
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- New Folder: create a new folder in your current directory. Enter the folder name, and then click OK.
- Upload: upload files from your computer to your current directory in IDAS. Select the files in your local computer, and then click OK.
- To upload multiple files or a directory, create a zip file, which will be automatically uncompressed after upload.
- Delete: permanently delete a file or folder. Check the box next to a file or folder to select it, click Delete, then Yes.
- Rename: rename a file or folder. Check the box next to a file or folder to select it, then click Rename. Enter the new name in the pop-up box, then click OK.
- Copy: make a copy of a file or folder. Check the box next to a file or folder to select it, click More, then Copy, enter a name for the new file or folder, then click OK.
- Copy To: make a copy of a file or folder and save the copy to a directory. Check the box next to a file or folder to select it, click More, then Copy To, enter a name for the new file or folder, select a directory, then click Save.
- Move: move the file or folder to a directory of your choice. Check the box next to a file or folder to select it, click More, then Move. In the pop-up box, choose a directory, then click Choose.
- Export: download files and folders (see below)
- Set As Working Directory: navigate to a directory of your choice, then click this option to choose the current directory as the working directory.
- Go To Working Directory: click this option to go to the current working directory.
- Show Hidden Files: toggle this option to show or hide hidden files, e.g. files that start with a "."
Downloading files and folders
- To download a file, check the box next to it. Click More, then Export. Enter a name for the downloaded file, then click Download.
- To download a folder, check the box next to it. Click More, then Export. Enter a name for the downloaded file, then click Download. The folder will be downloaded as a .zip file.
- To download multiple files and folders, check the boxes next to those files and folders. Click More, then Export. Enter a name for the downloaded file, then click Download. They will be downloaded as a .zip file.
Using Jupyter Notebooks
To access the Jupyter Hub page and use your notebooks, from your RStudio session, change the end of the URL to "tree".
Specifically for research users (fill in your HawkID):
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https://notebooks.hpc.uiowa.edu/research-interactive/user/<your_hawkid>/tree |
Shutting down an IDAS instance
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Your instance will be forced close after 18 hours of no activities. Once you finish your job with the IDAS instance, please manually shut down the instance, so that resources could be used by other IDAS users. |
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If you are using IDAS for a class, see instead this article for information on shutting down and restarting your IDAS server. |
1. Save any scripts or datasets.
2. If you don't have an active Jupyter Notebook, move to step 3. Otherwise, save and close your notebook:
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3. Research users: Go to https://notebooks.hpc.uiowa.edu/research-interactive/hub/home
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In this section:
Accessing IDAS:
Accessing IDAS for Research Use
For research users - Information about logging into IDAS, restarting your IDAS session, and switching between JupyterLab, Jupyter Notebook, and RStudio
Steps to restart your IDAS session
For class users - Information about logging into IDAS and restarting your IDAS session
Downloading data and file storage in IDAS:
Interfaces in IDAS:
Common tasks using the classic Jupyter Notebook interface in IDAS
Common tasks using the RStudio interface in IDAS
Contact
If you have any questions or comments, please contact research-computing@uiowa.edu.