Setting up my scientific computing environment

by | posted in: Research | 0

I use macs at work due to their fluid interface with the unix environment, and their ability to run unix/linux programs.  I’ve recently bought a new mac, which has required that I get it set up for my scientific computing.  Below are the pieces of software I’ve needed, which help streamline your own computational workflows.

 

I start with most of Alejandro Soto’s instructions here (http://alejandrosoto.net/blog/2016/08/16/setting-up-my-mac-for-climate-research/), including iTerm, the XCode developer tools, XQuartz, Homebrew, and Anaconda (for Python).

Obspy for working with seismic data (https://github.com/obspy/obspy/wiki/Installation-via-Anaconda)

ffmpeg for working with video files and making timelapse movies – I used

brew install ffmpeg --with-fdk-aac --with-ffplay --with-freetype --with-libass --with-libquvi --with-libvorbis --with-libvpx --with-opus --with-x265

(https://trac.ffmpeg.org/wiki/CompilationGuide/MacOSX)

Octave, for my legacy Matlab code.  Octave is a free substitute for Matlab, with most of the same functionality.  I’m pleased to learn that it has a new GUI that also reproduces the Matlab GUI.  At the terminal:

brew install octave

BasicTex from Mactex-2016 for latex typesetting (because I think the full MacTex download of 2.8 Gb is obscene) (https://tug.org/mactex/morepackages.html) and then also TeXShop and LaTeXIt, from the same page.  However, because BasicTex contains so few packages, be prepared to seek out and manually install additional, necessary packages (.sty files) from ctan.org:

sudo tlmgr install <package_name>

Cyberduck to have an easy to use GUI for transferring files between different computers/servers  (https://cyberduck.io/?l=en)

The Microsoft Office Suite, available through the University of Idaho

Google Earth Pro, available as a free download, for quickly learning about field sites (https://www.google.com/earth/download/gep/agree.html)

Dropbox, Google Drive, and OneDrive, for my online file storage.

The “Be Focused” app, from the App Store, which has a timer I use to keep targeted during my days.  It’s based on the pomodoro technique.

 

Understanding subglacial hydrology through seismology

by | posted in: Outreach, Publications, Research | 0

Last week, I visited the Boise State Geosciences department to give a seminar on the use of seismology to understand subglacial water flow and sediment transport.  I reviewed two of my recent papers, published in GRL (this in 2015, and this in 2016), and also presented some of the initial results from my work with graduate student, Margot Vore, from Taku Glacier.  I enjoyed getting to know some other Idaho geophysicists and identifying new opportunities for collaboration.

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Seismic data collected from Taku Glacier

by | posted in: Field work, Research | 0

I’m just back from Taku Glacier, Alaska, where UI grad student Margot Vore, UT-Austin grad student Taylor Borgfeldt, and I retrieved new seismic data from a network set up on and around the glacier.  We had a great trip, and were treated to unexpectedly phenomenal weather, with warm air, and clear, calm skies.  The seismic data we collected will form the foundation for Margot’s MS thesis, and a paper examining the temporal and spatial evolution of subglacial discharge through the melt season.  We’re looking forward to digging into the data.

This project was initiated with Jake Walter, at the UT Institute for Geophysics, and is part of a much broader collaboration on the dynamics of the Taku Glacier terminus, with glaciologists and seismologists from University of Alaska Southeast, University of Alaska Fairbanks, and Central Washington University.

 

 

Welcoming Margot Vore

by | posted in: Research, Teaching | 0

I’m excited to welcome Margot Vore to my glacier dynamics group at UI.  Margot will be working to better understand the flow of water through and under glaciers, through the analysis of seismic data.  She’ll be analyzing seismic data recorded in 2016 near the terminus of Taku Glacier, outside of Juneau, in Southeast Alaska.  Margot comes to UI from CU-Denver, where she completed her Bachelor of Science degree majoring in math, and minoring in environmental science.  We’re happy to have her here in Moscow!

Glacier Dynamics at the University of Idaho

by | posted in: Outreach, Research, Service, Teaching | 0

This fall, I’ve moved to the University of Idaho to begin work as an Assistant Professor and expand my lab group.  I’ve begun working with a graduate student who will work with glaciohydraulic tremor data to better understand changes in subglacial hydrologic processes.  Moscow, ID, home to the university, is a great town and I’m looking forward to getting to know the community and landscape while I establish my research here.

Please get in touch if you’re interested in joining my glacier dynamics group as a grad student or postdoc, or otherwise collaborating.

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Seismology for glaciology

by | posted in: Outreach, Research | 0

I’ll be giving a talk in the plenary session on Renaissance Seismology: Seismology for Non-Traditional Targets at the upcoming IRIS National Workshop, in Vancouver, WA.  I’m looking forward to sharing my perspectives on the tremendous utility of seismology for glacier problems, and learning about the latest seismological research and techniques.  I’m also happy about this being a short trip.  It’s my first meeting out of my new home in Moscow, ID, where I’ll start as an Assistant Professor at the University of Idaho in the fall.

IRIS is the national coordinating body for seismological research in the US – it stands for Incorporated Research Institutions for Seismology.

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New papers on ice-ocean interactions, glacier seismicity and subglacial hydrology accepted

by | posted in: Publications, Research | 0

Three new papers are now in press in Geophysical Research Letters, Journal of Glaciology and the Annals of Glaciology.  These papers are:

 

Bartholomaus, T. C., L. A. Stearns, D. A. Sutherland, E. L. Shroyer, J. D. Nash, R. Walker, G. Catania, D. Felikson, D. Carroll, M. J. Fried, B. Noël, M. van den Broeke (in press), Contrasts in the response of adjacent fjords and glaciers to surface melt in western Greenland, Annals of Glaciology.

In which we integrate glaciological and oceanographic observations from the west coast of Greenland to demonstrate how subglacial hydrology has contrasting effects on the glacier and fjord dynamics within neighboring systems.

Gimbert, F., V. C. Tsai, J. M. Amundson, T. C. Bartholomaus, and J. I. Walter (in press), Sub-seasonal pressure, geometry and sediment transport changes observed in subglacial channels, Geophysical Research Letters.

In which we demonstrate how seismic and discharge measurements can be combined to identify how subglacial pressure gradients within Rothlisberger channels and channel size vary over the course of the melt season at a glacier in Alaska.  Additionally, we discuss variations in sediment transport and the impact of flowing water on glacier motion.

Brinkerhoff, D., C. R. Meyer, E. Bueler, M. Truffer, and T. C. Bartholomaus (in press), Inversion of a glacier hydrology model, Annals of Glaciology, 57(72).

In which we constrain the evolution of the subglacial hydrologic system through measurements of glacier water discharge, glacier motion, and estimates of water inputs.

 

 

What’s our fieldwork like in Greenland? Watch and see

by | posted in: Field work, Greenland | 0

The Uummannaq region of West Greenland is a spectacular area of steep cliffs, icefalls, and long fjords.  While on a NASA-funded research project to better understand the connections between water in these fjords and the glaciers terminating there, I’ve had the extraordinary opportunity to fly, camp, hike, and work in this landscape.  Now, you can get a taste for our work in a 4-minute movie set to music, that draws on video footage from 2015 fieldwork, and time lapse imagery from 2013.  I hope you enjoy it!

 

Thanks to Sophie Gilbert (University of Idaho) for producing this movie.

Press write-up of AGU presentation

by | posted in: Field work, Greenland, Outreach, Research | 0

One of my two presentations at the AGU fall meeting this year is the subject of a well done blog post.  In the presentation, my co-authors and I reported the detection of over one million icequakes produced near the terminus of a tidewater glacier in west Greenland.  Study of these icequakes will allow us to better understand the factors controlling the flow of glacier ice, and ultimately allow scientists to make more precise predictions of sea level rise.

We’re presently about half way through the meeting this year and its been a good week so far.  During the Saturday and Sunday prior to the beginning of the AGU fall meeting, I participated in a planning workshop to lay the groundwork for a monitoring network to observe ice-ocean interactions in Greenland.  I made the case for the value of seismology in understanding tidewater glacier dynamics.

My second invited presentation is a poster on Thursday afternoon. I’ll be sharing observations and interpretations of high-rate velocity variations near the front of one of Greenland’s largest ocean-terminating glaciers.  The presentation is C43B-0805 High-resolution, terrestrial radar velocity observations and model results reveal a strong bed at stable, tidewater Rink Isbræ, West Greenland.

 

 

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A seismometer deployed at the terminus of a west Greenland glacier for two years, between 2013 and 2015. This station recorded over a million icequakes, year-round.