Merge pull request #208 from dsajdak/good25

dsajdak · web-flow · commit 7ec4fd90e68d · 2025-03-16T17:01:58.000-04:00
Good25
diff --git a/xdmod/README.md b/xdmod/README.md
@@ -55,7 +55,8 @@ Submitted batch job 19
 
 ---
 
-## Open XDMoD Installation [Documentation](https://open.xdmod.org/install.html)
+## Open XDMoD Installation 
+[Documentation](https://open.xdmod.org/install.html)  
 
 **Note: In the PEARC tutorials we demonstrated all the steps for this installation / configuration section to participants.  You do not need to run these steps yourself as the containers are already populated with a working XDMoD installation.** 
 
@@ -66,9 +67,11 @@ instructions to install the packages.
 
 Reference: [RPM Installation Guide](https://open.xdmod.org/install-rpm.html)
 
-### Pre-Requisites Installation [Documentation](https://open.xdmod.org/software-requirements.html)
+### Pre-Requisites Installation 
+[Documentation](https://open.xdmod.org/software-requirements.html)  
 
-### Open XDMoD RPM Installation [Documentation](https://open.xdmod.org/install-rpm.html)
+### Open XDMoD RPM Installation 
+[Documentation](https://open.xdmod.org/install-rpm.html)  
 
 First ssh to the XDMoD container
 ```shell
@@ -87,7 +90,8 @@ And install the the XDMoD RPM
 
 --- 
 
-## Open XDMoD Configuration [Documentation](https://open.xdmod.org/configuration.html)
+## Open XDMoD Configuration 
+[Documentation](https://open.xdmod.org/configuration.html)  
 
 **Note** This part will be brief in the PEARC2023 tutorial. These processes have been done already as part of the docker.
 
@@ -183,7 +187,8 @@ The next series of steps will involve completing each numbered setup item in tur
 setup after we have successfully shredded, ingested, and aggregated the accounting data generated by the jobs we
 submitted at the beginning of this tutorial.
 
-### General Settings [Documentation](https://open.xdmod.org/configuration.html#general-settings)
+### General Settings 
+[Documentation](https://open.xdmod.org/configuration.html#general-settings)  
 
 ```shell
 1) General Settings
@@ -245,15 +250,16 @@ Center Logo Path: [/srv/xdmod/small-logo.png]
 ```
 - Press the `Enter` key.
 
-#### Center Logo Width ( in pixels )
+#### Center Logo Width (in pixels)
 If you do provide a custom center image, you will also need to provide its width in pixels.
 
 ```shell
 Center Logo Width: [354]
 ```
 - Press the `Enter` key to accept the default value.
 
-#### XDMoD Dashboard [Documentation](https://open.xdmod.org/dashboard.html)
+#### XDMoD Dashboard 
+[Documentation](https://open.xdmod.org/dashboard.html)  
 The XDMoD Dashboard provides users with targeted statistics and reports based on the level of access they've been granted in XDMoD. We highly recommend you turn this feature on in your installation.
 
 ```
@@ -267,7 +273,8 @@ You will now be prompted to overwrite the config file `/etc/xdmod/portal_setting
 
 If you need to change any of your answers then you can type `no`, press `Enter` and you will be taken back to the main setup menu. At which point you can press `1` and to go through the General Settings setup again.
 
-### Database Settings [Documentation](https://open.xdmod.org/configuration.html#database-settings)
+### Database Settings 
+[Documentation](https://open.xdmod.org/configuration.html#database-settings)  
 
 Now that we've successfully completed the `General Settings` setup, we can move on to `Database Settings`.
 
@@ -411,7 +418,8 @@ Press ENTER to continue.
 ```
 - Press the `Enter` key again, this will return you to the main setup menu.
 
-### Organization Settings [Documentation](https://open.xdmod.org/configuration.html#organization-settings)
+### Organization Settings 
+[Documentation](https://open.xdmod.org/configuration.html#organization-settings)  
 
 ```shell
 3) Organization
@@ -467,7 +475,8 @@ Overwrite config file '/etc/xdmod/organization.json' (yes, no)? [yes]
 ```
 - Press the `Enter` key.
 
-### Resource Setup [Documentation](https://open.xdmod.org/configuration.html#resources)
+### Resource Setup 
+[Documentation](https://open.xdmod.org/configuration.html#resources)  
 
 Next we will go through the process of adding a Resource to XDMoD.
 
@@ -700,7 +709,8 @@ Press ENTER to continue.
 
 - Press the `Enter` key once more to be taken back to the main XDMoD configuration menu.
 
-## Create Admin User [Documentation](https://open.xdmod.org//configuration.html#create-admin-user)
+## Create Admin User 
+[Documentation](https://open.xdmod.org//configuration.html#create-admin-user)  
 
 ```shell
 5) Create Admin User
@@ -777,7 +787,8 @@ Admin user created.
 Press ENTER to continue.
 ```
 
-## Hierarchy Setup [Documentation](https://open.xdmod.org/hierarchy.html)
+## Hierarchy Setup 
+[Documentation](https://open.xdmod.org/hierarchy.html)  
 
 ```shell
 6) Hierarchy
@@ -841,7 +852,8 @@ Press ENTER to continue.
 
 - Press the `Enter` key to continue.
 
-## Data Warehouse Batch Export [Documentation](https://open.xdmod.org/dw-export.html#configuration)
+## Data Warehouse Batch Export 
+[Documentation](https://open.xdmod.org/dw-export.html#configuration)  
 
 ```shell
 7) Data Warehouse Batch Export
@@ -980,15 +992,16 @@ The `xdmod-setup` script is used for the basic setup of Open XDMoD. The script i
 
 Now that we have XDMoD setup, it's time to ingest some data. The jobs that we started at the beginning of the tutorial should be complete so let's walk through the shred, ingest, and aggregate steps for job accounting data.
 
-### Shredding [Documentation](https://open.xdmod.org/shredder.html)
+### Shredding 
+[Documentation](https://open.xdmod.org/shredder.html)  
 XDMoD provides a special command line tool for working with directly with slurm via `sacct` called `xdmod-slurm-helper`.  To see what command line arguments it accepts you can run `xdmod-slurm-helper -h`. For our purposes we will be using it as follows:
 
 **INTERACTIVE**
 
 ```shell
 [root@xdmod ~] sudo -u xdmod xdmod-slurm-helper -r hpc --start-time $yesterday --end-time $tomorrow
 ```
-*Note, you will need to replace `$yesterday` and `$tomrrow` with their respective values in YYYY-MM-DD format.*
+*Note, you will need to replace `$yesterday` and `$tomorrow` with their respective values in YYYY-MM-DD format.*
 
 If your organization doesn't use Slurm or will be using the log files instead of querying `sacct` directly, then `xdmod-shredder` will be the command for you. You can find our Shredder guide at [Shredder Guide](https://open.xdmod.org/shredder.html)
 
@@ -1004,7 +1017,8 @@ Upon running `xdmod-slurm-helper` you should see output similar to:
 [root@xdmod ~]#
 ```
 
-### Ingesting & Aggregating [Documentation](https://open.xdmod.org/ingestor.html)
+### Ingesting & Aggregating 
+[Documentation](https://open.xdmod.org/ingestor.html)  
 Now that the accounting logs have been shredded we can now ingest and aggregate the information from them, thus making the information available in XDMoD.
 
 **INTERACTIVE**
@@ -1435,7 +1449,7 @@ Once the jobs that we started in the last step complete, it's time to run throug
 [hpcadmin@xdmod ~] sudo su - 
 [root@xdmod ~] sudo -u xdmod xdmod-slurm-helper -r hpc --start-time $yesterday --end-time $tomorrow
 ```
-**_Note: you will need to replace `$yesterday` and `$tomrrow` with their respective values in YYYY-MM-DD format._**
+**_Note: you will need to replace `$yesterday` and `$tomorrow` with their respective values in YYYY-MM-DD format._**
 
 If your organization doesn't use Slurm or will be using the log files instead of querying `sacct` directly, then
 `xdmod-shredder` will be the command for you. You can find our Shredder guide at [Shredder Guide](https://open.xdmod.org/shredder.html)
@@ -1637,9 +1651,11 @@ If you completed the optional step 4 in the previous section, login as the `sfos
 10. Change `hello.py` to `plot_rbm_logistic_classification.py` and save.  Close this window.
 11. Go back to Job Composer and submit the job
 
-If you'd like to see this recent job show up in the OnDemand dashboard widgets, go back to the XDMoD container and re-run the job ingestion steps.  We'll use the helper script discussed above to complete all three tasks:  
+If you'd like to see this recent job show up in the OnDemand dashboard widgets, go back to the XDMoD container and re-run the job ingestion steps.  You'll likely be logged into the ondemand server so log out of that, confirm you're on the xdmod server and login as root.  We'll use the helper script discussed above to complete all three tasks:  
 
 ```shell
+[hpcadmin@ondemand config]$ exit
+[hpcadmin@xdmod ~]$ sudo su -
 [root@xdmod /] sudo -u xdmod /srv/xdmod/scripts/shred-ingest-aggregate-all.sh
 ```
 
@@ -1655,7 +1671,7 @@ Since the `xdmod-ondemand` module displays usage of Open OnDemand you need to ha
 file generated from Open OnDemand so there is data to show in XDMoD.
 
 ### Installation & Configuration  
-In preparation for this tutorial, these steps were done in advance.  For details on what these steps entail, [see here for installation](#installation) and [here for configuration](#configuration).  
+In preparation for this tutorial, the OnDemand module was installed and the OnDemand resource was setup in XDMoD.  For details on what these steps entail, refer to the full day tutorial "Resource Setup" steps.
 
 ### Obtaining Open OnDemand logs
 The `xdmod-ondemand` module parses the webserver log files from Open OnDemand. The `xdmod` container in this tutorial includes an example log file that
