Merge branch 'main' into article-conda-project-space

docs/account_management/cheaha_account.md

@@ -82,7 +82,7 @@ If you believe this to be in error, please [Contact Support](../help/support.md)
 
 Our Cheaha system is robust, but errors may occur due to general platform connectivity issues or missing components. Below are FAQs for self-service Cheaha account creation and a troubleshooting guide for common issues:
 
-- **Which credentials should I use?** Please visit [how do I login to research computing services](../account_management/index.md/#how-do-i-login-to-research-computing-services).
+- **Which credentials should I use?** Please visit [how do I login to research computing services](../account_management/index.md#how-do-i-login-to-research-computing-services).
 - **What do I do if I'm waiting for it to finish for longer than a couple of minutes?**
 
     - Try closing and restarting your browser, then trying again.

docs/account_management/index.md

@@ -10,7 +10,7 @@ Research Computing at UAB provides shared resources for researchers, where respo
 
 - Regularly clearing `/scratch`.
 - Adherence to [UAB IT policies](https://www.uab.edu/it/home/policies).
-- Request computational resources reasonably. Refer to our [compute resource estimation](../cheaha/job_efficiency.md/#estimating-compute-resources).
+- Request computational resources reasonably. Refer to our [compute resource estimation](../cheaha/job_efficiency.md#estimating-compute-resources).
 - [Responsible Conduct of Research training](https://www.uab.edu/research/home/responsible-conduct-of-research).
 - [Annual account certification of Cheaha account](../account_management/cheaha_account.md#account-requires-certification).
 - All Cheaha account users working with Protected Health Information (PHI) data are responsible to review [HIPAA policies](https://www.uab.edu/it/home/policies/compliance/hipaa) and
@@ -19,19 +19,19 @@ Research Computing at UAB provides shared resources for researchers, where respo
 ## How do I create a Research Computing account?
 
 - **Cheaha Account**: Creating a Cheaha account is currently a self-service process. Both UAB employees, students, and external collaborators can create a Cheaha account by visiting [creating a Cheaha account page](./cheaha_account.md).
-- **GitLab Account**: If you are a UAB-affiliated researcher and have a BlazerID, you may create an account by visiting [GitLab registration steps for UAB Employees and Students](./gitlab_account.md/#uab-gitlab-registration). If you are a collaborator with a XIAS account, you will need to follow the procedure in [External Collaborators registration](./gitlab_account.md/#xias-external-collaborator-registration).
+- **GitLab Account**: If you are a UAB-affiliated researcher and have a BlazerID, you may create an account by visiting [GitLab registration steps for UAB Employees and Students](./gitlab_account.md#uab-gitlab-registration). If you are a collaborator with a XIAS account, you will need to follow the procedure in [External Collaborators registration](./gitlab_account.md#xias-external-collaborator-registration).
 - **Cloud.rc Account**: To get your Cloud.rc account, please contact [Support](../help/support.md). For detail information on how to access it, please visit our [Cloud.rc](../uab_cloud/index.md) page.
 
 ## How do I login to Research Computing Services?
 
 - **Cheaha**: To login to Cheaha:
     - UAB Employees and Students: use your BlazerID.
     - External Collaborators: use your XIAS email address.
-    - For detail login information, please visit [accessing Cheaha](../cheaha/getting_started.md/#accessing-cheaha) page.  If accessing through Open OnDemand, our online portal, [Duo 2FA](https://www.uab.edu/it/home/security/2-factor) may be required.
+    - For detail login information, please visit [accessing Cheaha](../cheaha/getting_started.md#accessing-cheaha) page.  If accessing through Open OnDemand, our online portal, [Duo 2FA](https://www.uab.edu/it/home/security/2-factor) may be required.
 
-- **GitLab**: To login  to the GitLab, the UAB Employees and Students require a BlazerID, while External Collaborators require XIAS email. For detail login information visit the [UAB Employees and Students GitLab Registration](./gitlab_account.md/#uab-gitlab-registration) and [External Collaborators GitLab Registration](./gitlab_account.md/#xias-external-collaborator-registration) pages respectively.
+- **GitLab**: To login  to the GitLab, the UAB Employees and Students require a BlazerID, while External Collaborators require XIAS email. For detail login information visit the [UAB Employees and Students GitLab Registration](./gitlab_account.md#uab-gitlab-registration) and [External Collaborators GitLab Registration](./gitlab_account.md#xias-external-collaborator-registration) pages respectively.
 
 - **Cloud.rc**: To access the Cloud.rc, you must be on the campus network. For off-campus access, use the [UAB Campus VPN](https://www.uab.edu/it/home/tech-solutions/network/vpn), which requires [Duo 2FA](https://www.uab.edu/it/home/security/2-factor).
-UAB employees and students can log in using their BlazerID, while External Collaborators use their XIAS email. For login details, visit our [Cloud.rc](../uab_cloud/index.md/#first-steps) page.
+UAB employees and students can log in using their BlazerID, while External Collaborators use their XIAS email. For login details, visit our [Cloud.rc](../uab_cloud/index.md#first-steps) page.
 
 If you are unable to find what you need, please contact our team [here](../index.md#how-to-contact-us).

docs/account_management/res/user_responsibilities.csv

@@ -1,5 +1,5 @@
 Category,User Group,Requirements,Responsibilities
-UAB Employees,UAB Campus and UAB Medicine Faculty/Staff and Postdocs,Must have an active BlazerID,[Refer to All User Responsibilities](../account_management/index.md/#all-users-responsibilities).<br>For Lab PIs and Core Directors please refer [Lab PIs responsibilities](#lab-pis).
-UAB Students,All UAB Campus and UAB Medicine Students,Must have an active BlazerID,[Refer to All User Responsibilities](../account_management/index.md/#all-users-responsibilities).
-External Collaborators,All sponsored by UAB Employee,Must be sponsored by UAB employee <br>Must have XIAS email address,Collaborators' Responsibility:<br>&nbsp;  - [Refer to All User Responsibilities](../account_management/index.md/#all-users-responsibilities).<br>&nbsp;  - [Create a XIAS Guest Account](../account_management/xias/guest_instructions.md/#create-account).<br> Sponsor's Responsibility:<br>&nbsp;  - Sponsor is accountable for collaborators actions on UAB systems.<br>&nbsp;  - Please refer to [external collaborators](./xias/index.md/#external-collaborator-xias-accounts) page.
-<span id= 'lab-pis' >Lab PIs</span>,All Lab PIs and Core Directors,Must have an active BlazerID,Data Management and Storage:<br>&nbsp;  - Periodically check group membership is correct.<br>&nbsp;  - Periodically check access controls to directories/buckets are correct.<br>&nbsp;  - Moving unused data to LTS or external archival solutions.<br>&nbsp;  - Managing backup plans.<br>OpenStack Projects:<br>&nbsp;  - Periodically check group membership is correct.<br>&nbsp;  - Periodically check unused resources are released.<br>PIs are also responsible to:<br>&nbsp;  - Regularly reviewing membership permissions and access control.<br>&nbsp;  - Ensure students are aware about [FERPA-protected project metadata](https://www.uab.edu/registrar/ferpa/faculty-staff).<br>&nbsp;  - [Refer to All User Responsibilities](../account_management/index.md/#all-users-responsibilities).
+UAB Employees,UAB Campus and UAB Medicine Faculty/Staff and Postdocs,Must have an active BlazerID,[Refer to All User Responsibilities](../account_management/index.md#all-users-responsibilities).<br>For Lab PIs and Core Directors please refer [Lab PIs responsibilities](#lab-pis).
+UAB Students,All UAB Campus and UAB Medicine Students,Must have an active BlazerID,[Refer to All User Responsibilities](../account_management/index.md#all-users-responsibilities).
+External Collaborators,All sponsored by UAB Employee,Must be sponsored by UAB employee <br>Must have XIAS email address,Collaborators' Responsibility:<br>&nbsp;  - [Refer to All User Responsibilities](../account_management/index.md#all-users-responsibilities).<br>&nbsp;  - [Create a XIAS Guest Account](../account_management/xias/guest_instructions.md#create-account).<br> Sponsor's Responsibility:<br>&nbsp;  - Sponsor is accountable for collaborators actions on UAB systems.<br>&nbsp;  - Please refer to [external collaborators](./xias/index.md#external-collaborator-xias-accounts) page.
+<span id= 'lab-pis' >Lab PIs</span>,All Lab PIs and Core Directors,Must have an active BlazerID,Data Management and Storage:<br>&nbsp;  - Periodically check group membership is correct.<br>&nbsp;  - Periodically check access controls to directories/buckets are correct.<br>&nbsp;  - Moving unused data to LTS or external archival solutions.<br>&nbsp;  - Managing backup plans.<br>OpenStack Projects:<br>&nbsp;  - Periodically check group membership is correct.<br>&nbsp;  - Periodically check unused resources are released.<br>PIs are also responsible to:<br>&nbsp;  - Regularly reviewing membership permissions and access control.<br>&nbsp;  - Ensure students are aware about [FERPA-protected project metadata](https://www.uab.edu/registrar/ferpa/faculty-staff).<br>&nbsp;  - [Refer to All User Responsibilities](../account_management/index.md#all-users-responsibilities).

docs/cheaha/getting_started.md

@@ -82,8 +82,8 @@ You are on the login node if:
 
 You are on compute nodes if:
 
-- using [Open OnDemand Interactive Apps](../cheaha/open_ondemand/ood_layout.md/#interactive-apps)
-- using [Interactive Jobs with `srun`](../cheaha/slurm/submitting_jobs.md/#interactive-jobs-with-srun)
+- using [Open OnDemand Interactive Apps](../cheaha/open_ondemand/ood_layout.md#interactive-apps)
+- using [Interactive Jobs with `srun`](../cheaha/slurm/submitting_jobs.md#interactive-jobs-with-srun)
 - terminal prompt looks like `[$USER@c0112 ~]$`
 
 ![!compute node terminal prompt shows username@c0112](images/comp_node.png)

docs/cheaha/open_ondemand/ood_layout.md

@@ -105,7 +105,7 @@ For jobs such as RStudio and Jupyter, some modules like CUDA need to be loaded b
 <!-- markdownlint-disable MD046 -->
 !!! Note
 
-    In the OOD session, the module is automatically reset at the beginning of every session by default. Therefore, avoid using `module reset` in the 'Environment Setup' box. See [best practice for loading modules](../software/modules.md/#best-practice-for-loading-modules) for more information.
+    In the OOD session, the module is automatically reset at the beginning of every session by default. Therefore, avoid using `module reset` in the 'Environment Setup' box. See [best practice for loading modules](../software/modules.md#best-practice-for-loading-modules) for more information.
 <!-- markdownlint-disable MD046 -->
 
 #### Launching Interactive Sessions

docs/cheaha/open_ondemand/ood_matlab.md

@@ -34,3 +34,7 @@ You may optionally verify that Python works correctly by entering `py.list(["hel
 ## Using a GPU with MATLAB
 
 Please see the [MATLAB Section on our GPU Page](../slurm/gpu.md#matlab).
+
+## Known Issues
+
+There is a known issue with `parpool` and other related multi-core parallel features such as `parfor` affecting R2022a and earlier. See our [Modules Known Issues section](../software/modules.md#matlab-issues) for more information.

docs/cheaha/slurm/gpu.md

@@ -114,7 +114,7 @@ For versions of PyTorch 1.13 and newer, use the following template instead.
 <!-- markdownlint-disable MD046 -->
 !!! Note
 
-     When loading modules, such as CUDA modules for jobs requiring one or more GPUs, always utilize `module reset` before loading modules, both at the terminal and within `sbatch` scripts. See [best practice for loading modules](../software/modules.md/#best-practice-for-loading-modules) for more information.
+     When loading modules, such as CUDA modules for jobs requiring one or more GPUs, always utilize `module reset` before loading modules, both at the terminal and within `sbatch` scripts. See [best practice for loading modules](../software/modules.md#best-practice-for-loading-modules) for more information.
 <!-- markdownlint-disable MD046 -->
 
 ## Reviewing GPU Jobs

docs/cheaha/slurm/introduction.md

@@ -37,4 +37,12 @@ Given two or more jobs with equal priority, the job on the partition with the la
 
 The scheduler cannot predict the future. If a job enters the queue with a higher priority than yours, it will start before yours. This may lead to a situation where your job no longer fits on any of the nodes. If this happens your job will have to wait until sufficient space opens regardless of its priority value. A possible strategy to minimize the risk of preemption is to request fewer resources per node, to more readily fill available space.
 
-If you are unsure of the best queueing strategy for your workflow, please [Contact Us](../../index.md#how-to-contact-us) for a consultation, we are happy to help.
+A lot of intelligent people have worked very hard to design the Slurm scheduler to be both smart and fair. Please allow it to do its job. If you have workloads that are very large and want advice or are unsure of the best queueing strategy for your workflow, please [Contact Us](../../index.md#how-to-contact-us) for a consultation, we are happy to help.
+
+<!-- markdownlint-disable MD046 -->
+!!! important
+
+    Please do not run `squeue`, or any other Slurm command, in a loop. All Slurm commands increase the load on the Slurm controller. Many commands in a short period of time can make Slurm unresponsive, unstable, or require a restart, which negatively impacts all researchers.
+
+    Instead, please simply let the Slurm scheduler do its job of managing.
+<!-- markdownlint-enable MD046 -->

docs/cheaha/slurm/practical_sbatch.md

@@ -199,7 +199,7 @@ To use the script, enter the command `bash main.sh` at the terminal.
 <!-- markdownlint-disable MD046 -->
 !!! Note
 
-    When writing `sbatch` scripts for job submission and managing modules, begin your script by resetting the module environment with `module reset` to ensure a clean environment for subsequent configurations. See [best practice for loading modules](../software/modules.md/#best-practice-for-loading-modules) for more information.
+    When writing `sbatch` scripts for job submission and managing modules, begin your script by resetting the module environment with `module reset` to ensure a clean environment for subsequent configurations. See [best practice for loading modules](../software/modules.md#best-practice-for-loading-modules) for more information.
 <!-- markdownlint-enable MD046 -->
 
 ## Putting it All Together