toc

Author: sbryngelson

.github/toc-generator.yml

@@ -0,0 +1,20 @@
+# TOC Generator Configuration
+
+# Specific files to update
+INCLUDE_FILES:
+  - group-syllabus/formatting.md
+  - group-syllabus/improving-your-writing.md
+  - group-syllabus/figures.md
+  - group-syllabus/doing-research.md
+  - group-syllabus/giving-talks.md
+  - group-syllabus/computers.md
+  - group-syllabus/undergraduate-specifics.md
+
+# Marker comment settings
+OPENING_COMMENT: "<!-- toc -->"
+CLOSING_COMMENT: "<!-- tocstop -->"
+
+# TOC settings
+TOC_TITLE: "## Table of Contents"
+FOLDING: false
+MAX_HEADER_LEVEL: 4

.github/workflows/update-toc.yml

@@ -0,0 +1,29 @@
+name: Update Markdown TOC
+
+on:
+  push:
+    paths:
+      - 'group-syllabus/**.md'
+    branches:
+      - master
+  workflow_dispatch:
+
+jobs:
+  update-toc:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Generate TOC
+        uses: technote-space/toc-generator@v4
+        with:
+          TOC_TITLE: "## Table of Contents"
+          TARGET_PATHS: "group-syllabus/*.md"
+          FOLDING: false
+          CREATE_PR: true
+          COMMIT_MESSAGE: "Update TOC in markdown files"
+          COMMIT_NAME: "GitHub Action"
+          COMMIT_EMAIL: "action@github.com"
+          MAX_HEADER_LEVEL: 4 

group-syllabus/computers.md

@@ -1,5 +1,17 @@
 ## Computers
 
+<!-- toc -->
+- [GT PACE Phoenix](#gt-pace-phoenix)
+- [GT ICE](#gt-ice)
+- [GT Rogues Gallery](#gt-rogues-gallery)
+- [GT Wingtip-gpu3](#gt-wingtip-gpu3)
+- [ACCESS-CI computers](#access-ci-computers)
+- [Oak Ridge National Lab OLCF](#oak-ridge-national-lab-olcf-frontierwombatandesetc)
+- [Sandia National Lab (SNL)](#sandia-national-lab-snl)
+- [LLNL Livermore Computing](#llnl-livermore-computing-lassen-tioga-etc)
+- [Department of Defense](#department-of-defense)
+<!-- tocstop -->
+
 * GT PACE Phoenix
     * User guide [here](https://docs.pace.gatech.edu/phoenix_cluster/gettingstarted_phnx/)
     * Login via `ssh <GTusername>@login-phoenix-rh9.pace.gatech.edu` to get the RHEL9 nodes

group-syllabus/computers.md''

@@ -0,0 +1,124 @@
+## Computers
+
+## Table of Contents
+<!-- toc -->- [GT PACE Phoenix](#gt-pace-phoenix)
+- [GT ICE](#gt-ice)
+- [GT Rogues Gallery](#gt-rogues-gallery)
+- [GT Wingtip-gpu3](#gt-wingtip-gpu3)
+- [ACCESS-CI computers](#access-ci-computers)
+- [Oak Ridge National Lab OLCF](#oak-ridge-national-lab-olcf-frontierwombatandesetc)
+- [Sandia National Lab (SNL)](#sandia-national-lab-snl)
+- [LLNL Livermore Computing](#llnl-livermore-computing-lassen-tioga-etc)
+- [Department of Defense](#department-of-defense)
+
+* GT PACE Phoenix
+    * User guide [here](https://docs.pace.gatech.edu/phoenix_cluster/gettingstarted_phnx/)
+    * Login via `ssh <GTusername>@login-phoenix-rh9.pace.gatech.edu` to get the RHEL9 nodes
+    * Purpose: All-purpose campus resource of CPU and GPU jobs with a variety of hardware. 
+    * "Rules": Use the `embers` queue type to use idle nodes at zero cost.
+    * To get access, let Spencer know, and he will fill out [this form](https://gatech.service-now.com/home?id=sc_cat_item&sys_id=61bc5e351b37f994a8622f4b234bcbf0).
+ 
+* GT ICE
+  * [Resources/User guide](https://gatech.service-now.com/home?id=kb_article_view&sysparm_article=KB0042095) (click `Available Resources`, e.g.)
+     * This looks like ~40 V100s, 8 A100s, 4 A40s, 20 RTX6000s, and 4 MI210s.
+  * May need to contact Spencer for access.
+  * __Most GPU nodes sit idle__
+     * On those nodes: `MaxNodes=UNLIMITED MaxTime=18:00:00`
+
+* GT Rogues Gallery 
+    * User guide [here](https://gt-crnch-rg.readthedocs.io/en/main/)
+    * Purpose: Use of brand-new, forward-looking, or weird hardware. At the time of writing, it includes an NV H100 server, GH200 nodes, AMD MI210 GPU server, Bluefield-2/3 SmartNICs, RISC-V and Arm CPUs, etc.
+    * "Rules": There are few rules; just follow the guidelines in the documentation. There are no limitations on hardware access/node hours.
+    * Get access via [this link](https://crnch-rg.cc.gatech.edu/request-rogues-gallery-access/)
+
+* GT Wingtip-gpu3
+    * User guide [here](https://github.gatech.edu/cse-computing/compute-resources/blob/main/docs/systems/wingtip-gpu.md)
+    * Purpose: Small (but possibly very long) GPU jobs, hosts 5x NV A100-80GB PCIe at the moment
+    * "Rules":  Be mindful of others' use of this machine as it does not have a scheduler.
+    * Get access by emailing [Will Powell](mailto:will.powell@cc.gatech.edu), cc me.
+
+* ACCESS-CI computers
+    * These are a set of university supercomputers listed [here](https://access-ci.org/resource-providers/). Each has its own user guide. At the time of writing, we have access to NCSA Delta (A100 GPUs), PSC Bridges2 (V100 GPUs), Purdue Anvil, and Texas A&M ACES (H100 GPUs), but we can change to others as needed. We primarily use NCSA Delta.
+    * Purpose: All-purpose resources for CPU and GPU simulation. 
+    * "Rules": Be mindful of the available node hours. Queue times might be long.
+    * Our account number:
+       * `PHY240200` (ACCESS-CI Maximize, NCSA Delta only)
+       * `PHY210084` (ACCESS-CI Accelerate; Bridges2, Delta, and so on)
+    * Get access by
+        * Creating an account [here](https://identity.access-ci.org/new-user.html)
+        * Then, message Spencer on Slack with your username
+   * On [NCSA Delta](https://docs.ncsa.illinois.edu/systems/delta/en/latest/)
+      * The account name is `bdiy-delta-gpu` (ACCESS-CI Maximize) or `bbsc-delta-gpu` (ACCESS-CI Accelerate) for GPU resources
+      * Replace `-gpu` with `-cpu` for CPU resources
+
+* Oak Ridge National Lab OLCF: Frontier/Wombat/Andes/etc.
+    * Purpose
+        * Frontier: Very large-scale GPU simulation on AMD MI250X GPUs.
+        * Wombat: Testbed for next-gen HPC platforms, including ARM nodes and soon next-generation NVIDIA nodes (GraceHopper).
+        * Andes: For postprocessing
+    * Our account number: `CFD154`
+    * "Rules": Ask Spencer before running any jobs that use a very large number of node hours
+    * Get access by
+        * Create an account by following [these instructions](https://docs.olcf.ornl.gov/accounts/accounts_and_projects.html#applying-for-a-user-account)
+        * The account/allocation number is `CFD154`.
+
+* Sandia National Lab (SNL)
+    * Purpose: Resources for DOE-sponsored/funded research projects are only available to those students working on these projects. You will only have access to non-restricted resources.
+    * "Rules": Usually, there are not many rules aside from the very many that they will impute onto you as you acquire access to these machines.
+    * Login process (Sandia National Lab-specific)
+        * Onto the DaaS
+            * VMware Horizon ([download online](https://customerconnect.vmware.com/en/downloads/info/slug/desktop_end_user_computing/vmware_horizon_clients/horizon_8))
+            * URL: `daas.sandia.gov`
+            * Passcode: `[PIN] + [your yubikey1timepassword]`
+            * Password: `[kerberos pw]`
+            * 3 options
+                * badge update
+                * conference room
+                * daas <- open this one
+            * Can complete training and do other things here, like look at your WebCARS to get `WC_ID` (which you need to submit jobs)
+        * Onto a computer remotely
+            * https://hpc.sandia.gov/access/ssh/
+            * Can do the below with DaaS (using my example username, `[usrname]`)
+                * `ssh [usrname]@srngate.sandia.gov`
+                * Passcode: `[PIN] + [yubikey one time pw]`
+                * Choose a computer: e.g., Skybridge, Attaway, Weaver, etc.
+                * Press `1` - `ssh session`
+                * Default user name (`[usrname]`)
+                * Password is (usually) the Kerberos one
+                * If it asks for token OTP (e.g., on Weaver) then this is `[PIN] + [yubikey1timepassword]`
+
+ * LLNL Livermore Computing: Lassen, Tioga, etc.
+    * Anyone working on a specific LLNL project can use [LLNL CZ](https://lc.llnl.gov/) (non-restricted) resources
+    * Talk to Spencer about getting access to CZ (collaboration zone) if you are working on a LLNL project
+    * "Rules": Usually not many rules aside from the very many that they will impute onto you as you acquire access to these machines.
+    * Login process (Lawrence Livermore National Lab-specific)
+        * Onto LC-idm
+            * URL: `ic-idm.llnl.gov`
+            * Passcode: `[PIN] + [rsa one time password]`
+            * Can use to view user profile and request roles (ask for resources on specific machines)
+        * Onto the LC
+            * URL: `lc.llnl.gov`
+            * Passcode: `[PIN] + [rsa one time password]`
+            * Requires three logins to fully log in
+            * Can be used to access collaboration tools such as Confluence and Gitlab, user documentation, and MyLC for alerts, machine status, and job status
+        * Onto a computer remotely
+            * Can do the below with ssh (using my example username, `[usrname]`, for a specific LLNL machine, `[llnlmachine]`)
+                * `ssh [usrname]@[llnlmachine].llnl.gov`
+                * Passcode: `[PIN] + [rsa one time password]`
+
+* Department of Defense
+    * Anyone working on a DOD project can use [DOD HPCMP](https://www.hpc.mil/) (non-restricted) resources 
+    * The process of getting permissions to the non-restricted systems is a bit tedious but usually worth it
+    * See [here](https://centers.hpc.mil/) for information on the available supercomputers
+        * In particular, it's useful to keep an eye on [upcoming systems](https://centers.hpc.mil/systems/hardware.html#upcoming)
+        * Current unclassified systems are [here](https://centers.hpc.mil/systems/unclassified.html)
+    * Talk to Spencer about getting access to a DOD machine if you are working on a DOD project
+    * Subproject: `ONRDC51242690`, Group: `5124D690`, Project: `5124`
+       * Site: `NAVY`
+          * nautilus 
+          * narwhal
+       * Site: `ERDC`
+          * carpenter
+    * [Docs available here](https://centers.hpc.mil/users/docs/index.html#general)
+
+

group-syllabus/doing-research.md

@@ -1,10 +1,20 @@
 ## Doing Research
 
 The most important thing you do in graduate school is your research.
-It may seem obvious, but it's easy to lose track of the importance of your research amid all the other competing things you’ll be asked to do as a student researcher: take classes, TA a class, submit and review papers, respond to paper reviews, organize/support various activities, etc.
+It may seem obvious, but it's easy to lose track of the importance of your research amid all the other competing things you'll be asked to do as a student researcher: take classes, TA a class, submit and review papers, respond to paper reviews, organize/support various activities, etc.
 Some of these will be fun; many will feel more important at the time than making progress on your research.
 However, I would like you to prioritize your research and triage everything else after this.
 
+<!-- toc -->
+- [Selecting problems](#selecting-problems)
+- [Expected Output](#expected-output)
+- [Staying organized](#staying-organized)
+- [Research Ideas and Directions](#research-ideas-and-directions)
+- [Where to find ideas](#where-to-find-ideas)
+- [Deciding what Ideas to Pursue](#deciding-what-ideas-to-pursue)
+
+<!-- tocstop -->
+
 ### Selecting problems
 
 I advise students to aspire for impact in their work.
@@ -18,7 +28,7 @@ Some guidelines on impact might include:
 - Why is this one of the most important questions in the field?
 - Will it inspire a new class of methods, systems, tools, or computers?
 
-**Who will care about it when you’re done?**
+**Who will care about it when you're done?**
 - Will government agencies care?
 - Will industry/companies care?
 - Will other academics care enough to cite it?
@@ -39,7 +49,7 @@ You should expect to produce less in your first and second years (for example, i
 
 1. Try to produce one very high-quality paper per year.
 This should yield 3-4 published versions of these throughout your Ph.D.
-Some of these papers won't be accepted somewhere exceptionally competitive or may not work out well in the research process (e.g., the approach didn’t work, the context of the problem changed, etc.).
+Some of these papers won't be accepted somewhere exceptionally competitive or may not work out well in the research process (e.g., the approach didn't work, the context of the problem changed, etc.).
 That's the nature of research.
 This is the most important output you might produce as a student researcher.
 
@@ -53,7 +63,7 @@ This is important for your sense of progress, as the more challenging work might
 This is also important to get exposure for you and your ideas in wider venues.
 
 3. Concurrently, try to be a supporting author on at least one other project.
-This isn’t your core work; it’s someone else-led.
+This isn't your core work; it's someone else-led.
 It should take less than 1/2-1/3 of a day of your time per week.
 But you have something to offer and will be listed in a supporting author position.
 Also, of the lower-risk, lower-reward variety.
@@ -81,7 +91,7 @@ If you don't have one, please ask for one.
 _Have ideas!_
 
 I don't like advising students without their own ideas, nor do I think it's good for your development as a scholar.
-As noted above, the major thing that we’re doing here is turning you into a world-class scholar.
+As noted above, the major thing that we're doing here is turning you into a world-class scholar.
 One key way you do that is by coming up with new ideas.
 Moreover, it's important to be competitive in academic job applications; those evaluations are impacted by your future work ideas, not only your work to date.