Alpine updates and RMACC 2022

This week I had the opportunity to speak at the 2022 RMACC Symposium, hosted by my own institution, about the Alpine supercomputer. My presentation and the others from my CU colleagues are available here.

In summary, Alpine has been in production since our launch event in May. After some supply chain issues (the same that have affected the entire computing sector), we are preparing to bring another round of nodes online within weeks. That will put Alpine’s total available resources (about 16,000 cores) on par with those of the retiring Summit system. It’s an exciting step for us at CURC.

As for RMACC: I’ve never attended the symposium before. After three days, I came away with a lot of new information, new contacts, and ideas for how to support our researchers better. A few topics in particular I paid attention to:

  • Better and more scalable methods of deploying HPC systems and software
  • How the community will navigate the transition from XSEDE to ACCESS
  • The companies, organizations, and universities (like mine!) building the future of this space
  • Changes in business models for the vendors and commercial developers we work with

Academic HPC is a small niche in the computing world, and gatherings like this can be valuable as spaces to connect and share our best ideas.

New supercomputer just dropped

These certainly are server cabinets alright…

Today marks the launch of CU Boulder’s shiny new research supercomputer, Alpine. Text of the university press release:

The celebratory event signals the official launch of CU Boulder’s third-generation high performance computing infrastructure, which is provisioned and available to campus researchers immediately.

On May 18, numerous leaders from on- and off-campus will gather to celebrate, introduce and officially launch the campus’s new high-performance computing infrastructure, dubbed “Alpine.”

Alpine replaces “RMACC Summit,” the previous infrastructure, which has been in use since 2017. Comparable to systems now in use at top peer institutions across the country, Alpine will improve upon RMACC Summit by providing cutting-edge hardware that enhances traditional High Performance Computing workloads, enables Artificial Intelligence/Machine Learning workloads, and provides user-friendly access through tools such as Open OnDemand.

“Alpine is a modular system designed to meet the growing and rapidly evolving needs of our researchers,” said Assistant Vice Chancellor and Director of Research Computing Shelley Knuth. “Alpine addresses our users’ requests for faster compute and more robust options for machine learning.”

Notable among the technical specifications that will make Alpine an invaluable tool in research computing for researchers, industry partners and others, Alpine boasts: 3rd generation AMD EPYC CPUs, which provide enhanced energy efficiency per cycle compared to the Intel Xeon E5-2680 CPUs on RMACC Summit; Nvidia A100 GPUs; AMD MI100 GPUs; HDR InfiniBand; and 25 Gb Ethernet.

The kick-off event on May 18 will celebrate the Alpine infrastructure being fully operational and allow the community to enjoy a 20-minute tour, including snacks, an introduction to Research Computing, and a tour of the supercomputer container. The opportunity is open to the public and free of charge, and CU Boulder Research Computing staff will be on site to answer questions. CU Boulder Chief Information Officer Marin Stanek, Chief Operating Officer Patrick O’Rourke, and Acting Vice Chancellor for Research and Innovation Massimo Ruzzene will offer remarks at 1:30 p.m.

In addition to the main launch event, Research Computing is offering a full slate of training and informational events the week of May 16—20.

Researchers seeking to use Research Computing resources, which includes not only the Alpine supercomputer, but also large scale data storage, cloud computing and secure research computing, are invited to visit the Research Computing website to learn about more training offerings, the community discussion forum, office hours and general contact information.

Alpine is funded by the Financial Futures strategic initiative.

This is the biggest project I have ever worked on. It was in the works months before I arrived but has consumed most of my professional time since September. It’s exciting that we can finally welcome our researchers to use it.

What’s next

Some personal news… 🙂

I have been at Earlham College for almost seven years, including my time as a student and as CS faculty. Today is my last day there.

It’s been an incredible place to grow as a person, deepen my skills, collaborate with talented people from all walks of life, and try to make the world a little bit better. I’ve seen a few generations of the community cycle through and watched us withstand everything up to and including a literal pandemic. I capped it with the trip of a lifetime, spending a month doing research in Iceland – on a project I hope to continue working on in the future.

To the Earlham Computer Science community in particular I owe a big thanks. I have had a supportive environment in which to learn and grow for virtually the entirety of those years. The value they’ve added to my life can’t be quantified. I am deeply grateful.

What’s next?

I am elated to announce that in mid-September I will go to work as a Research Computing HPC Cluster Administrator at the University of Colorado Boulder! I’m excited to take the skills I’ve built at Earlham and apply them at the scale of CU Boulder. Thanks to the many people who’ve helped make this opportunity possible.

Highlights of an amazing trip

Today is the last day most of us are in Iceland for this trip. As I started this post, we were completing a tour of the Golden Circle after a few days in beautiful Reyjkavik. Now we are preparing for departure.

Our view of the volcano

I wanted to post some of the highlights of our trip. There’s a rough order to them, but don’t take the numbering too seriously – it’s been a great experience all-around. Without further ado:

  1. The volcano is truly incredible. It was not uncommon for people to spontaneously shout “Wow!” and “Oh my god!” as the lava burst up from the ground.
  2. We woke up every day for a few weeks with a view of a fjord.
  3. We did a glacier hike on Sólheimajökull, with two awesome guides.
  4. This was a historically successful round of data collection, both on the drone side and on the biology side. We’ll write and share a lot more about this in the next few months.
  5. We shared space with the group of phenomenal students from the University of Glasgow. We also collaborated with them on multiple occasions, learning a lot about different ways to study wildlife and local sites.
  6. THE FOOD – you probably don’t associate Iceland with food culture (I certainly didn’t), but our meals were delicious.
  7. The architecture and decorations are so distinctly Icelandic.
  8. Amazing photography and video – in high quality and high quantity.
  9. Walking along the boundary between the North American and European plates.
  10. Guided tour from our Skalanes hosts – who incidentally are awesome people – of a stretch of eastern Iceland.
Getting the rundown about glaciers at Solo

Some of my personal honorable mentions include:

  • Trail running at Skalanes is breathtaking.
  • Blue glacier ice is real neat.
  • The National Museum of Iceland is fascinating and well-done.
  • Rainbow roads in both Seyðisfjörður and Reykjavik highlight what a welcoming place this country is – also perfect reminders of Pride Month in the U.S.!
  • My first-in-my-lifetime tour of a beautiful country happened alongside people I admire who teach me things every single day. What more could I ask for?
A drone photo of the coast by the fjord

If you haven’t already, check out this interview with Charlie and Emmett, conducted by Cincinnati Public Radio.

Davit and Tamara flying

In addition to our success this year, we’ve also set up some great new opportunities for future years. With our long-time friend and collaborator Rannveig Þórhallsdóttir, we’ve added the cemetery in Seyðisfjörður to our list of sites to survey. We believe there may be historically-significant artifacts to be found there, and our drone work lends itself well to finding out.

The fjord at Skalanes

Finally, here’s the trip by the numbers:

  • 7 Earlhamites
  • 26 days
  • 183 GB of initial drone images and initial assemblies
  • 2 great hosts at Skalanes
  • 6 outstanding co-dwellers
  • 4 guides at 2 sites
  • 1 perfect dog
  • N angry terns
  • 1 amazing experience
Admiring the view

And that’s a wrap. Hope to see you again soon, Iceland!

Cross-posted at the Earlham Field Science blog.

Flying cameras are good

Update: We have learned! And we no longer agree with this post! GCP’s remain critical for deriving elevation. The cameras are not yet ready to replace that kind of precision. Always something you didn’t realize at first glance. Post preserved for posterity and because lots of it is still perfectly valid.

We recently chose not to use ground control points (GCP’s) as part of our surveying work. This is a departure from standards and conventions in the near-Earth surveying space. However, we believe we have made a sound decision that will support equally effective and more time and cost-effective research. In this post, I’ll explain that decision.

The short version: drone imagery and open-source assembly software (e,g. OpenDroneMap) are now so good that, for our purposes, GCP’s have no marginal benefit.

We have high-quality information about our trial area from an established authority – the Cultural Heritage Agency of Iceland. Their 2007 report of finds is the basis of our trial runs here at Skalanes. Surveying these predefined areas, we’ve now flown multiple flights, gathered images, and then run three assembles with OpenDroneMap.

Here’s a simple run over the area with no GCP’s:

Here’s a run over the area with GCP’s, adding no location metadata other than the craft’s built-in GPS coordinates (you’ll note that the ground footprint is slightly different, but the roundhouse in the middle is the key feature):

We also manually geocoded the GCP’s for one run.

In the end, we observed no meaningful difference between an assembly with GCP’s and an assembly without them. Adding the images as raster layers to a QGIS project confirmed this to our satisfaction:

With GCP:

Without GCP:

In summary, ground control points just don’t help us much compared to just taking a bunch of good photos and using high quality software to assemble them. They also cost us in portability: even four GCP’s are difficult to carry, occupying significant space in airport luggage and weighing down walks in the field. For scientists interested in doing work over a large area, potentially multiple times, that inconvenience is not a trivial cost.

The ODM assemblies are outstanding by themselves. We have good technology and build on the work of a lot of brilliant people. That frees us to be more nimble than we might have been before.

It wouldn’t be a post by me if it didn’t end with a cool picture. Here’s a drone image from a cliff near the house where we’re staying:

Cross-posted at the Earlham Field Science blog.

Awe in Iceland

The Greater Good Institute at Berkeley considers awe one of the keys to well-being:

Awe is the feeling we get in the presence of something vast that challenges our understanding of the world, like looking up at millions of stars in the night sky or marveling at the birth of a child. When people feel awe, they may use other words to describe the experience, such as wonder, amazement, surprise, or transcendence.

That’s the feeling I have at least once a day, every day, here in Iceland.

And it’s difficult to write a blog post about awe. Almost by definition, it’s an emotion that defies easy explanation. It has a mystique that risks being lost in the translation to plain language.

But if I can’t describe the feeling, I can describe why I’m having it.

Unique among my traveling companions, this is my first-ever trip out of my country of origin (🇺🇸) The sliver of gray in this image is the first thing I ever saw of a country not my own:

When we arrived, I got a passport stamp and exchanged currency – both brand new experiences. However mundane, they were novel for me and began waking me up to the new world I’d entered.

Our first few days were chilly, windy, and rainy. I was much happier about this than were my traveling companions. If our weather wasn’t pleasant, it was nonetheless exactly the immersive experience I was hoping for when I signed up for this trip.

In those first few days, I got to see this amazing waterfall:

I got to participate in collecting soil samples at a glacier —


— and in howling wind on the side of a moraine:

The right side of the moraine was calm and quiet. The left was much less so.

For good measure, I saw floating blue ice for the first time:

All this was great, and to me they made this trip worth the months of planning and days of travel difficulties it took to get here.

Then we got to Skalanes, where I’m writing this post, and its landscapes exist on a whole other level. Here are ten views here, drawn almost at random from my photos:

This is a country that absolutely runs up the score on natural beauty.

I’ve taken hundreds of pictures here and they’re all amazing – but none does justice to actually being here. That combination is the signature of an awe-inspiring experience.

Awe puts us in touch with something above and beyond our daily worldly experience – call it the divine, the sublime, whatever speaks to you. It’s an experience you can reproduce if you try, but I believe it connects most deeply when it emerges organically from the world you enter. That’s what’s happened to me here.

It is remarkable that this is what we get to do for work, and I am so glad we have some more time to spend here in this awesome country.

Cross-posted at the Earlham Field Science blog.

“A lot of people” – a brief note

Pet peeve: “A lot of people say X” or similarly “A lot of people do Y”.

There’s a lot of people in general: ~330,000,000 in America alone. If you look hard enough, you can find *somebody* who will say/do almost literally anything.

If 1% of Americans believe something, that’s over 3 million believers. That’s both a huge number of people and hardly anybody, depending on your context.

I find this usually isn’t a problem in writing, where with minimally competent phrasing/structure the context is clear. During chit-chat or as used by the likes of Fox News, it can be (often purposely) obtuse.

I like us to try to be specific, is what I’m saying. 🙂

Originally a Twitter thread.

Iceland is on track for summer

Discussions are ongoing about the viability of summer travel given the pandemic. However, as my colleague Charlie has blogged recently, we are “acting as if”. As such, we are trying to maintain our original calendar.

Lo and behold, we have:

Imagine a “You are here” arrow by Spring 1

Here’s the full breakdown of that schedule and our progress:

Our plan for the fall was to find and test alternative UAV’s. This proved prudent, as the federal government banned DJI craft late last year. We are happy with both the Parrot and the Skydio craft, for different reasons which we’ll undoubtedly cover here on this blog in the future.

December and January, which were effectively a long winter break for a subset of us, were dedicated to testing the craft, capturing initial video, and possibly beginning development. This was a success as well. Additionally we have begun spinning up a more sophisticated web presence for the stories we’re telling – changes we will be prepared to publish soon.

We’ve now started the calendar for the spring, term 1 of 2. We are moving into scaling up our operation of the craft and developing software to automate that work. It’s a tough problem but one we can solve in the time we have.

We’re optimistic about our ability to meet the moment. If the world continues to make progress on COVID-19, we should be in shape to have a successful research trip.

2020 in review

You don’t need me to tell you 2020 was a bad year. Others will write about the details that apply nationally and globally, so I’m going to jump right into my own retrospective.

The 2020 wallowing

I was planning on a trip to Iceland followed by a new job with room for advancement in 2020. Instead I stayed at my current job (a good job!), made an attempt at a side hustle that has so far largely fizzled, and was obviously not able to go to Iceland. I didn’t visit family in Montana for Thanksgiving or Christmas. At work, I made a few dumb mistakes (we did rebound in each case, happily). It was, on net, a rough year.

That’s about all I have to say about that. I don’t want to wallow too much, but I also don’t want to go further without acknowledging the struggle.

The better stuff

All that said, the rest of this post summarizes my accomplishments for the year. I write this to remind myself that even though it didn’t generate those external signals, I still did a lot. I advanced my skillset, did my job well, and patched through the year.


  • Got out of bed every day and went back to sleep every night
  • Kept Earlham CS running through the pandemic, student dispersal, lockdown, and restricted return
  • Modernized our systems engineering infrastructure with better monitoring, solid backups, improved responsiveness to inquiries, and higher availability – still a long way to go, but we’re so much better than we were a year ago
  • For each error I made, rebounded and learned a lesson
  • Migrated our cluster infrastructure from Torque to Slurm successfully
  • Learned a bunch of low-level details about filesystems, SELinux, and more en route to improving overall quality
  • Took 10,000 steps most days and got outside frequently
  • Provided a lot of internal tech support, engineering, feedback, and project contributions to the projects associated with the Iceland program
  • Made checking LinkedIn a regular part of my routine, though I should use it more socially in the new year
  • Purely as a hobby, learned a ton about video and audio production

Casual observation: I posted a lot in February, and my tech achievements primarily happened over the summer.

I also want to dedicate a section to expanding my horizons. I couldn’t do it with travel, but there were a lot of new things I got the chance to explore this year:

  • On Spotify, listened to 1,408 new artists and 366 new genres (“genre” seems like a nebulous category, but I am taking the win)
  • Watched a lot of new movies, including the complete Hayao Miyazaki filmography
  • Learned to make curry! (this winter squash red Thai curry recipe is great)
  • Baked a pie – apple – for the first time, at Christmas
  • Grew my hair long for the first time in my life (it’s still growing actually – not getting a professional haircut during a pandemic)
  • Visited and walked new hiking trails

That was 2020 for me.

What’s next?

I can’t guarantee 2021 will be better than this year. However, I do have some broad intentions around a theme for the new year. I will do all that is in my control to make the next year better, and I hope you join me.

Extremely preliminary notes about the Parrot Anafi

After three extremely short flights, these are my notes about the Parrot Anafi drone.

We’re experimenting with different UAV’s as part of the Iceland terrestrial surveying program (we’re being optimistic about travel in 2021…). These are some notes with my initial observations.

This is based on the base case: taking the craft out, taking off, flying for at most a few minutes, and touching back down. As such, don’t take a single word of this as gospel – it’s just preliminary opinions for the historical record. 🙂

Short version of the review: holy portability! One thing I don’t like about the DJI Phantoms is that they are so heavy (both the craft and the RC-tablet unit). If it’s a pain here on-campus, where trips are short, I imagine it’s a pain in the field. The Anafi is ludicrously lightweight and doesn’t feel like a chore to carry around.

Video quality on the built-in camera is fantastic (4K etc.).

It’s not a perfectly seamless integration with our existing workflows. Within our group, for example, we usually use tablets, which are handy for their big screens. The Anafi seems built around the assumption of a phone. That’s true all the way down to the RC unit being designed to accommodate a phone but not a tablet. That’s different, but if we can only get this app for phones I am not necessarily sad about it.

There are many X factors I haven’t yet been thorough enough to review. For example: battery life, stability in breezes (heavy winds make most UAV’s hard to use), and the software/developer ecosystem.

These have been my extremely preliminary notes about the Parrot Anafi. It’s not even close to a comprehensive evaluation of everything we care about. Still, those usability factors are important if this is going to scale and be useful for others. So for now, I’m impressed.