Merge pull request #88 from hpc-carpentry/llnl_blog_post

LLNL blog post

Author: reid-a

_posts/2024/08/2024-08-13-llnl-workshop-blog-post.md

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+---
+layout: page
+authors: ["Andrew Reid", Trevor Keller", "Jane Herriman"]
+teaser: "We ran the full user workshop at LLNL!"
+title: "HPC Carpentry at LLNL"
+date: 2024-08-13
+time: "12:00:00"
+tags: ["HPC Carpentry", "Lesson Program Implementation"]
+---
+
+## HPC Carpentry at LLNL
+
+In the first week of June, 2024, instructors from [HPC Carpentry][hpcc]
+taught our full workflow workshop for the first time. Over a four-day
+stint at Lawrence Livermore National Laboratory, we delivered this
+content not once, but twice!
+
+It was immensely rewarding to see all this material come together in
+one place. Traveling to teach in person, while not without hiccups, was
+extremely worthwhile. We believe we served our learners pretty well, and
+we learned a few lessons relevant to future workshops.
+
+### Workshop Structure
+
+Each workshop ran over two days. On the first day, we did the [Unix Shell
+intro][shell] lesson from Software Carpentry in the morning, and our own
+[HPC Intro][intro] lesson in the afternoon. On the second day, we did a
+variant of the [workflow lesson][work], adapted for the Maestro workflow
+tool (rather than Snakemake), because it is developed and used at LLNL.
+
+The instructor team consisted of Andrew Reid and Trevor Keller from
+the HPC Carpentry steering committee, and Jane Herriman from LLNL,
+along with helpers from the LLNL community.
+
+While split-terminal tools exist, we used vanilla [tmux][tmux] with two
+terminals attached to the same session. This allowed the instructors to type on
+their own laptop while referencing the lesson webpage and selectively sharing
+the terminal. Learners followed along on the enhanced terminal displayed at the
+front of the room. Note: to "scroll up" in `tmux`, press 
+<kbd>Ctrl</kbd>+<kbd>b</kbd>, <kbd>[</kbd>, then arrow-key around.
+
+#### Maestro
+
+Maestro is a capable workflow engine, and one we would not have explored had
+Jane not ported the Snakemake lesson so expertly. Maestro favors
+reproducibility, running every step of the task from scratch at every
+invocation. This is a significant difference from Snakemake which, like Make,
+does not re-execute completed "targets." A significant benefit of Maestro is
+that the tool does not persist while jobs execute: it generates and submits
+native Slurm jobs, with tooling in place to check the status of running
+workflows. This is much more HPC-compatible, for large-scale or time-consuming
+jobs.
+
+### Learners
+
+Learners had a range of backgrounds, from undergraduate bio-informatics
+students to experienced Linux HPC users. The lessons generally went
+at a slightly faster pace than expected, without leaving anyone
+behind. This was in part because access to LLNL's system `Ruby` was by means
+of pre-authorized RSA tokens, removing a lot of the friction
+from the initial connection process that has been time-consuming in other
+versions of the workshop. The instructors live-coded plenty of mistakes, opening
+discussions on some interesting tangential topics. LLNL runs a pool of "login
+nodes" per HPC system, rather than a single machine, which made for interesting,
+early discussion of networked filesystems. The sheer number of nodes also made
+the output of `sinfo` tricky to comprehend at-a-glance, which is awesome.
+
+### Lesson Feedback
+
+One major take-away is that the workflow lesson in particular is
+vulnerable to learners losing the thread if they miss a step. This lesson,
+in either its Maestro or Snakemake version, builds up an increasingly
+sophisticated workflow specification file, incrementally demonstrating
+workflow concepts in the context of the tool. Consequently, a learner
+who misses a step and falls behind can find themselves unable to recover,
+since the remainder of the lesson builds on precisely the content that was
+missed. The Workflow lesson differs in this respect from the Shell and
+HPC intro lessons, where later steps can better stand on their own.
+
+The solution to this, which we already started to implement for the
+second workshop, was to have a shared online notepad with "checkpoint"
+versions of the file, to which learners can refer if they fall behind,
+with helpers bridging the content gap for them. Also, LLNL supports and
+uses the [`give`][give] tool, allowing users to easily pass files around:
+it's nifty!
+
+The hands-on Carpentries approach proved itself once again, building
+muscle memory and vocabulary in learners, who could then move on to their
+LLNL summer research projects with greater confidence in their ability
+to productively use the shared high-performance computing resources.
+
+For the project, it was confirmation that the HPC User workshop can
+work, including the valuable feedback about checkpoint files and a
+shared notepad.  We look forward to teaching this workshop more, and
+getting it out of beta status and into our main curriculum.
+
+<!-- links -->
+[give]: https://github.com/hpc/give
+[hpcc]: https://hpc-carpentry.org/
+[intro]: https://hpc-workshops.github.io/llnl-hpc-intro/
+[shell]: https://swcarpentry.github.io/shell-novice
+[tmux]: https://github.com/tmux/tmux/wiki
+[work]: https://xorjane.github.io/maestro-workflow-lesson/