From 459882312432a16bde3e109abd15d83a1ea33159 Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Thu, 29 May 2025 12:07:55 -0400 Subject: [PATCH 01/13] clarify which steps are being done at what point --- coldfront/README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/coldfront/README.md b/coldfront/README.md index 1c0ff5c..6762c9c 100644 --- a/coldfront/README.md +++ b/coldfront/README.md @@ -514,7 +514,8 @@ NOTE: If there is a project you never want project reviews on, uncheck 'Requires ## Starting from Scratch (Half Day Tutorial)
-These steps were done in advance to allow for the presentation of a condensed half day version of the tutorial. If you would like to go through these steps yourself, destroy the containers, and delete the ColdFront database. Start the containers which will create a new, empty coldfront database. Then log in to ColdFront and follow the steps below: +These steps were done in advance to allow for the presentation of a condensed half day version of the tutorial. If you would like to go through these steps yourself, destroy the containers, and delete the ColdFront database. Start the containers which will create a new, empty coldfront database. Then log in to ColdFront and follow the steps below. +### Create a new, empty coldfront database ``` ./hpcts destroy From 06369b4b0ea366b3836358ca0a0985c3d62c8943 Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Thu, 29 May 2025 12:09:15 -0400 Subject: [PATCH 02/13] clarify which user has to log into the frontend each user or only hpcadmin? --- docs/applications.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/applications.md b/docs/applications.md index fa600e5..9bfb5b9 100644 --- a/docs/applications.md +++ b/docs/applications.md @@ -23,7 +23,7 @@ Login to frontend via SSH and user: `hpcadmin` password: `ilovelinux`: ``` ssh -p 6222 hpcadmin@localhost ``` -**NOTE: You must login to the front end before trying to login to any of the other containers!** +**NOTE: You must login to the front end as the `hpcadmin` user before trying to login to any of the other containers!** ### Single-sign on: Portal login/logout Because these applications are configured for single-sign on (SSO), if you login using Dex/OpenID Connect and want to switch between users you will either need to clear the browser cookies or restart the browser. You may wish to launch multiple 'incognito' windows for each user account used in the tutorial and switch between them as you go. From 2edf3ecdda7fca466580bdaf55708328ff1873a6 Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Thu, 29 May 2025 13:54:27 -0400 Subject: [PATCH 03/13] make it clear what to click on --- coldfront/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/coldfront/README.md b/coldfront/README.md index 6762c9c..74baa01 100644 --- a/coldfront/README.md +++ b/coldfront/README.md @@ -538,7 +538,7 @@ You'll need to log in as some of the users for this tutorial to get things start - Log out - Log in locally as username `admin` password: `admin` - Go to Admin menu and click on `ColdFront Administration` Once there, scroll halfway down to the `Authentication and Authorization` section. Then click on the `Users` link -- Click on the `hpcadmin` user and scroll down to the `Permissions` section +- Click on the `hpcadmin` username (not the checkbox next to it) and scroll down to the `Permissions` section - Make this user a `superuser` by checking the boxes next to `Staff Status` and `Superuser Status` - scroll to the bottom and click `SAVE` - Click on the `sfoster` account. Under the `User Permissions` section add permissions to make this user the Center Director `allocation | allocation | Can manage invoice` From 3d701d2e20f23ccef978ea881d7545a4ec744475 Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Thu, 29 May 2025 14:20:59 -0400 Subject: [PATCH 04/13] fix typo and clarify further --- coldfront/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/coldfront/README.md b/coldfront/README.md index 74baa01..e6f2666 100644 --- a/coldfront/README.md +++ b/coldfront/README.md @@ -468,7 +468,7 @@ Name: type `project storage` Description: enter anything you want Ensure that the following are checked: `Is available`, `Is public`, `Is allocatable` Under the resource attributes section, click `Add another Resource attribute` and select `quantity_label` from the drop down menu. In the `value` field, enter `Enter storage in 1TB increments` -Click `Add another Resource attribute` and select `quantity_default_value` from the drop down menu. In the `1` +Click `Add another Resource attribute` and select `quantity_default_value` from the drop down menu. In the `value` field, enter `1` Click `Add another Resource attribute` and select `OnDemand` from the drop down menu. In the `value` field, enter `Yes` - Then click `SAVE` @@ -538,7 +538,7 @@ You'll need to log in as some of the users for this tutorial to get things start - Log out - Log in locally as username `admin` password: `admin` - Go to Admin menu and click on `ColdFront Administration` Once there, scroll halfway down to the `Authentication and Authorization` section. Then click on the `Users` link -- Click on the `hpcadmin` username (not the checkbox next to it) and scroll down to the `Permissions` section +- Click on the `hpcadmin` username (not the checkbox next to it) and scroll down to the `Permissions` section in the `Change User` window - Make this user a `superuser` by checking the boxes next to `Staff Status` and `Superuser Status` - scroll to the bottom and click `SAVE` - Click on the `sfoster` account. Under the `User Permissions` section add permissions to make this user the Center Director `allocation | allocation | Can manage invoice` From 65ae49e044220e6878930394e0ca67816eb3018f Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Mon, 2 Jun 2025 14:04:45 -0400 Subject: [PATCH 05/13] more minor clarification --- coldfront/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/coldfront/README.md b/coldfront/README.md index e6f2666..5838686 100644 --- a/coldfront/README.md +++ b/coldfront/README.md @@ -594,7 +594,7 @@ Add an allocation attribute type: Make an allocation attribute changeable: - Under the `Allocation` section, click on `Allocation Attribute Types` -- Click on `Storage Quota` check the box next to `Is changeable` and then click the `SAVE` button +- Click on the number to the left of `Storage Quota`. In the `Change allocation attribute type` window, check the `Is changeable` box, then click the `SAVE` button - Log out ### Create a project & request an allocation From f7d5a517b01a12e8f9092e2734d093ca15a85c7d Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Mon, 2 Jun 2025 14:07:40 -0400 Subject: [PATCH 06/13] change sleep from 1000 to 300 so it's less likely to stop other jobs from starting --- ondemand/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ondemand/README.md b/ondemand/README.md index 70bc2de..147b287 100644 --- a/ondemand/README.md +++ b/ondemand/README.md @@ -153,10 +153,10 @@ column of the central table go from queued to running to completed. Let's go ahead and edit the script we submit by pressing the `Open Editor` button at the bottom of the script's panel (you likely have to scroll down). -Add this `sleep 1000` anywhere in the file (so long as it's not commented). +Add this `sleep 300` anywhere in the file (so long as it's not commented). ```bash -sleep 1000 +sleep 300 ``` Submit this job again and next we'll see another view where you can see From b5e80aef6dcdaf99377f19057967eccc8878ecbd Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Mon, 2 Jun 2025 14:27:30 -0400 Subject: [PATCH 07/13] clarify how to run JupterNotebook demo --- ondemand/README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/ondemand/README.md b/ondemand/README.md index 147b287..bedb268 100644 --- a/ondemand/README.md +++ b/ondemand/README.md @@ -254,9 +254,12 @@ Navigate back to Open OnDemand's `My interactive sessions` page and press the `Connect to Jupyter` button. This will open a new tab to the Jupyter application that's running on a compute node in your Slurm cluster! -Connect to the Jupyter session and navigate to the `jupyter_notebook_data` directory. -Open the `GUI-demo.ipynb` and this should open a new tab to this notebook. Run all -the cells in this notebook for a demonstration that this Jupyter does in fact work. +Connect to the Jupyter session and click on the `jupyter_notebook_data` directory in the leftmost panel. +Open the `GUI-demo.ipynb` and this should open a new tab to this notebook. The notebook has three cells, +each with a number on the left, and a block of code next to it. Run all +the cells in this notebook in order by clicking `Shift-enter` on each one for a demonstration that this +Jupyter demo does in fact work. + ![jupyter demo](imgs/jupyter_demo.gif) From 24519ff5c4bcbad0c4f6d553b005cabed4684453 Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Tue, 3 Jun 2025 10:15:10 -0400 Subject: [PATCH 08/13] fix typo --- ondemand/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ondemand/README.md b/ondemand/README.md index bedb268..da1d0dd 100644 --- a/ondemand/README.md +++ b/ondemand/README.md @@ -291,7 +291,7 @@ Lastly there's a new link entitled `Chemistry Notes`. Press this link and you'll be redirected to a custom page. This page is completely defined by administrators. Administrators supplied every single panel on this page. The idea here being that administrators can supply content to their own OnDemand -installation, thereby extending it's functionality by also supplying some +installation, thereby extending its functionality by also supplying some documentation. ![profile demo](imgs/profile_demo.gif) From d73c5d1053cade4bde3eff96c706045200e5a2c6 Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Tue, 3 Jun 2025 10:19:32 -0400 Subject: [PATCH 09/13] make it easier to get back into the shell window --- ondemand/README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/ondemand/README.md b/ondemand/README.md index da1d0dd..bbe024b 100644 --- a/ondemand/README.md +++ b/ondemand/README.md @@ -368,7 +368,8 @@ OOD_BRAND_BG_COLOR='#5576d1' ``` Now you may have to restart the server with the button at the top right to see the -changes take place. +changes take place. Each time you restart the server, you'll have to +[reopen the shell window.](https://localhost:3443/pun/sys/shell/ssh/ondemand) ![dashboard navbar button to restart the web server](imgs/restart_web_server.png) From 93e1592d923d37266c5a6102fb5baa66d1ba6d31 Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Tue, 3 Jun 2025 10:52:03 -0400 Subject: [PATCH 10/13] correct path to files --- ondemand/README.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/ondemand/README.md b/ondemand/README.md index bbe024b..afceb9b 100644 --- a/ondemand/README.md +++ b/ondemand/README.md @@ -368,8 +368,7 @@ OOD_BRAND_BG_COLOR='#5576d1' ``` Now you may have to restart the server with the button at the top right to see the -changes take place. Each time you restart the server, you'll have to -[reopen the shell window.](https://localhost:3443/pun/sys/shell/ssh/ondemand) +changes take place. ![dashboard navbar button to restart the web server](imgs/restart_web_server.png) @@ -391,8 +390,7 @@ touch ~/ondemand/config/ondemand.d/ondemand.yml OOD_CONFIG_D_DIRECTORY="/home/hpcadmin/ondemand/config/ondemand.d" ``` - -Now let's [edit the ondemand.yml](https://localhost:3443/pun/sys/dashboard/files/edit/home/hpcadmin/ondemand/config/ondemand.d/ondemand.yml) +Now let's [edit the ondemand.yml](https://localhost:3443/pun/sys/dashboard/files/edit/fs/home/hpcadmin/ondemand/config/ondemand.d/ondemand.yml) file that we initialized above to add the configuration. ```yaml @@ -484,7 +482,7 @@ touch ~/ondemand/config/views/widgets/_hello_world.html Be sure to add the underscore prefix to this filename! This is a Rails convention for partials and not a mistype it is indeed `_hello_world.html`. -Now, we can use the [file editor to edit our new widget](https://localhost:3443/pun/sys/dashboard/files/edit/home/hpcadmin/ondemand/config/views/widgets/_hello_world.html). Let's add this very simple div to just thank you for being here. Of course, you can put +Now, we can use the [file editor to edit our new widget](https://localhost:3443/pun/sys/dashboard/files/edit/fs/home/hpcadmin/ondemand/config/views/widgets/_hello_world.html). Let's add this very simple div to just thank you for being here. Of course, you can put any text you like here. Feel free to have fun with it! ```html From 2c6ae78e0ae6ec7777454de86caa116497a298ab Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Tue, 3 Jun 2025 12:30:22 -0400 Subject: [PATCH 11/13] add instructions to restart webserver after edits --- ondemand/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ondemand/README.md b/ondemand/README.md index afceb9b..7c3977c 100644 --- a/ondemand/README.md +++ b/ondemand/README.md @@ -511,7 +511,7 @@ dashboard_layout: widgets: [ pinned_apps ] ``` -Now your dashboard should look something like this with a brand new widget we just creating showing up on the +Restart your webserver and your dashboard should look something like this with the brand new widget we just creating showing up on the dashboard. ![dashboard landing page with a new custom widget](imgs/dashboard_w_new_widget.png) From 6423ced233fafae80fdb78487707caa430d9651d Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Wed, 4 Jun 2025 09:32:28 -0400 Subject: [PATCH 12/13] fix typo --- ondemand/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ondemand/README.md b/ondemand/README.md index 7c3977c..94e3c99 100644 --- a/ondemand/README.md +++ b/ondemand/README.md @@ -579,7 +579,7 @@ If you try to submit it as is, you'll get this error: ![error message that reads The cluster was never set. Either set it in form.yml.erb with `cluster` or `form.cluster` or set `cluster` in submit.yml.erb.](imgs/no_cluster.png) -We need to edit the `form.yml` in the appication's folder. We can navigate to the folder through the +We need to edit the `form.yml` in the application's folder. We can navigate to the folder through the files app. The URL is `https://localhost:3443/pun/sys/files/fs/home/hpcadmin/ondemand/dev/jupyter/`. Here you'll see the `form.yml` file. We can edit it by clicking on the file and pressing the "Edit" From 37a8b84cbce67d63c3799e98d7466b6c1a55a859 Mon Sep 17 00:00:00 2001 From: Sarah L Duncan Date: Fri, 6 Jun 2025 10:19:08 -0400 Subject: [PATCH 13/13] note need to open shell to perform git commands --- ondemand/README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ondemand/README.md b/ondemand/README.md index 94e3c99..017e1f0 100644 --- a/ondemand/README.md +++ b/ondemand/README.md @@ -557,9 +557,9 @@ or simply Press the "Files" button in Jupyter's row of the sandbox applications ![create sandbox app](imgs/create_sandbox_app.gif) -You'll also need to setup `git` for the hpcadmin user at this point, so let's go ahead and do that -and make first commit to the jupyter app as the starting point. - +You'll also need to setup `git` for the hpcadmin user at this point, so let's go ahead and +[open a shell window](https://localhost:3443/pun/sys/shell/ssh/ondemand). +We'll make the first commit to the jupyter app as the starting point. ```shell git config --global user.email hpcadmin@localhost git config --global user.name "HPC Admin"