Merge pull request PSU-ICDS#211 from PSU-ICDS/staging

Staging

Author: CarrieBrown

docs/file-system/file-storage.md

@@ -64,6 +64,11 @@ lists directory sizes in order from large to small
 (the output of du is "piped" to [sort][sort]).
 [sort]: https://man7.org/linux/man-pages/man1/sort.1.html
 
+!!! note "Include hidden files when checking disk usage"
+    `du -sch .[!.]* * | sort -h` shows the size of all files and directories,
+    including hidden ones, and sorts them by size.
+    Useful when large hidden files may be contributing to quota issues.
+
 ## Quota issues in home
 
 Many user configuration files and packages are stored by default in `home`.
@@ -72,6 +77,8 @@ This commonly occurs with directories such as
 
  - `.local` - used by Python
  - `.comsol` - used by Comsol
+ - `.conda` - used by Anaconda
+ - `R` - used by R
 
 These [dot files](https://missing.csail.mit.edu/2019/dotfiles/) (and directories) 
 are hidden by default, but you can view them with `ls -la`.
@@ -106,7 +113,7 @@ you should pack the directory into a single file with `tar`
 (see [Packing files](managing-files.md#packing-files))
 before transferring.
 
-!!! warning "Do not use archive storage for sensitive data."
+!!! warning "Avoid using archive storage for sensitive data."
      If you need to archive data or software that must adhere to regulatory requirements
      please contact ICDS or the [Office of Information Security](https://security.psu.edu).
 

docs/getting-started/faq.md

@@ -18,6 +18,10 @@ Common reasons include:
 and all nodes that can fulfill your request (for memory, cores, GPUs, etc.) are currently 
 in use by other jobs. The only solution is to wait for resources to free up.
 
+!!! note "Check estimated job start times"
+    You can use `squeue -u <user_id> --start` to see when your pending jobs are
+    expected to begin (worst-case time), which helps estimate wait times and manage your workflow.
+
 - **(Priority):** Your job is waiting its turn behind other jobs that have a higher 
 priority. Your job's priority will increase over time, so the solution is to wait.
 

docs/getting-started/tips-for-beginners.md

@@ -1,28 +1,29 @@
 # Tips for beginners
 
-!!! warning "Don't use submit nodes for heavy computing."
+!!! note "Don't use submit nodes for heavy computing."
      Submit nodes are for preparing files, submitting jobs, 
      examining results, and transferring files.
 
-!!! warning "Don't store files on scratch."
+!!! note "Avoid storing important files in Scratch"
      [Scratch is not backed up](../file-system/file-storage.md/#quotas), 
      and files older than 30 days old are deleted.
 
-!!! warning "Don't overrun your file storage quota."
+!!! note "Monitor your storage quota"
      If you fill your allotted disk space, weird errors occur.
      Keep an eye on your [disk space usage](../file-system/file-storage.md/#quotas).
 
-!!! warning "Don't waste your compute resources."
-     Use interactive sessions to test your workflow.
-     Before a big batch job, run test jobs to make sure your code works.
+!!! note "Use compute resources responsibly"
+     Always run small test jobs to verify that your code, inputs, and resource
+    requests behave as expected. 
+    Refer to the [`job_estimate`](../running-jobs/batch-jobs.md/#estimating-resource-usage) command to estimate credit consumption from your job script before submission.
 
-!!! warning "Capture job output and error logs"
+!!! note "Always capture job output and error logs"
     To debug failed or unexpected jobs, it can be helpful to capture output and error streams
     separately. To do so, add these lines to the slurm job script:
     `#SBATCH --output=job_%j.out`
     `#SBATCH --error=job_%j.err`
 
-!!! warning "Using modules"
+!!! note "Load software using modules"
      Most software on Roar is managed through the software stack and loaded
      using modules. Please check [Modules](../software/modules.md)
 
@@ -38,7 +39,7 @@ do more than use the Portal needs to learn.
 
 To learn more about Linux, we recommend the following resources:
 
- - [Unix tutorial]: (https://www.tutorialspoint.com/unix/unix_tutorial.pdf)
+ - [Unix tutorial](https://www.tutorialspoint.com/unix/unix_tutorial.pdf)
  - [Effective Computation in Physics - Chapter One](https://www.oreilly.com/library/view/effective-computation-in/9781491901564/?sso_link=yes&sso_link_from=pennsylvania-state-university)
  - [Introduction to Using the Shell in an HPC Context by HPC Carpentry](https://www.hpc-carpentry.org/hpc-shell/) which can be followed after [logging onto Roar](connecting.md/#two-ways-to-access) and [accessing the command line](../running-jobs/portal.md#command-line-access).
 

docs/index.md

@@ -34,4 +34,4 @@ This page also lists other events of interest to the computational and data scie
 
 [ICDS-related University polices][policies] regulate data protection,
 access control, software acceptable use, and the terms of paid allocations.
-[policies]: https://www.icds.psu.edu/computing-services/roar-policies/
+[policies]: https://www.icds.psu.edu/services/roar/user-policies/

docs/running-jobs/batch-jobs.md

@@ -130,6 +130,8 @@ job_estimate <submit file>
 which reports the cost in credits.
 For more on `job_estimate`, execute `job_estimate --help`.
 
+Additionally, for users who schedule jobs interactively through the portal, an estimate of the credits required for the job is displayed near the Launch button once you select your batch options and partition. This estimate updates dynamically based on your selections, allowing you to understand the approximate credit cost before starting the job.
+
 The Slurm command [`sacct`][sacct]
 reports the resources used by a completed batch job,
 which helps users learn what resources to request next time.

docs/running-jobs/resource-requests.md

@@ -92,6 +92,9 @@ For credit accounts, it is helpful to estimate how many credits a batch job woul
 job_estimate <submit file>
 ```
 
+Additionally, for users who schedule jobs interactively through the portal, an estimate of the credits required for the job is displayed near the Launch button once you select your batch options and partition. This estimate updates dynamically based on your selections, allowing you to understand the approximate credit cost before starting the job.
+
+
 ### Selecting nodes, cores, and memory
 
 Choosing the right resources is critical for efficiency.

docs/software/installing-from-source.md

@@ -11,6 +11,11 @@ Depending on how well designed and documented the software is,
 installation may be straightforward and self-contained, 
 or may require extensive modification to install missing dependent packages.
 
+!!! note "Container support on the RC cluster"
+    Docker and Docker Compose are not supported due to privilege restrictions.
+    Use Apptainer instead; it can run Docker images but does not support Docker Compose or multi-container orchestration.
+
+
 ## No root access
 
 If you have worked with a laptop running Linux,