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title: Graduated
description: Finishing my PhD
date: 2018-09-07
author: Danny Hermes (
tags: Education, Research, Applied Mathematics, PhD
slug: graduated
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twitter_site: @bossylobster
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After five years, I'm excited to say I've finished my PhD. I certainly learned a lot and met a lot of great people along the way.

One of the biggest lessons I learned was about myself: I need to say no more often. I continued to say yes, to side projects, to coffee in SF, to teaching Python training on the side, etc. Saying no a bit more frequently would have allowed me to spend more time on research and to finish sooner as I'd originally hoped.

While the many diversions did make me appreciate the need for focus, I am also happy that my time in school gave me an opportunity to go down rabbit holes and winding paths to learn.

For readers in a hurry, the TL;DR:

  • Advising and Peers: I was lucky to be in a great learning and research environment
  • Teaching: I enjoyed teaching undergraduates but wish some things were different about the university model
  • Research: I had a chance to make incremental progress on a tool that can be useful for physical simulations
  • Software: I wrote a lot of code both for science and for Google; in particular, I learned to appreciate modern Fortran and struggled with building binary extensions for Python

Advising and Peers {#advising}

I was lucky to have a great advisor, Per-Olof Persson. When I was deciding which graduate school to attend, a chat with Per was one of the clinching factors in choosing UC Berkeley. Since his research (CFD) was not quite in line with my interests (e.g. Numerical Linear Algebra), I hesitated in asking him to advise me. However, I gave the personality fit more weight than the research fit and am happy about the outcome.

The UC Berkeley Math department is a very welcoming place and I really enjoyed teaching undergraduates and taking classes with my fellow graduate students. A few of my peers had somewhat inaccessible advisors (e.g. they only met once a year) and these students did feel a sense of isolation. It made a big difference having an advisor that was easy to get in touch with and eager to help.

Teaching {#teaching}

I really enjoyed teaching and had some great interactions with students:

Danny manages to be relaxed, funny, and watchable AND very knowledgeable about the material AND a stickler about teaching it AND good at explaining it clearly and quickly. This is a combination of strengths so rare around here that I thought it was mythical.

Though the interactions were great, there were a few things I wished were different.

  • I wish the lower-division classes were changed to utilize computers both for rote computation and visualization of concepts. (I taught Calculus I and II and Linear Algebra.)
  • I was a bit disappointed at the preparedness and more importantly the enthusiasm of students in upper-division courses (I taught Numerical Analysis five times). It seemed that for many, taking courses in their major was a chore rather than a joy. This is as much (if not more) a reflection on the system as it is on the students.
  • Numerical Analysis is an opportunity to learn how "classical" algorithms break down on a computer (i.e. in the presence of rounding). Having the ability to program is a must to really solidify the concepts. However, once a class hits 150 students, the grading must be "standardized". In this case, that meant student evaluation was done via traditional pen and paper assignments and exams. Coupled with the absence of a programming prerequisite, this made the amount of computing in the class a small fraction of the course.
  • I was continually frustrated by the prevalence of MATLAB usage in the math department. MATLAB certainly has strengths, but its kitchen sink approach to namespaces (similar to that of PHP) really makes it hard to teach. Its lack of a packaging story and reliance on a proprietary IDE makes it hard for students to understand what code "is" (or even where it is on their filesystem). The IPython notebook was created at UC Berkeley and I wish the math department would get on board. Perhaps more relevantly, using MATLAB does little to prepare students for the real world because it is used almost exclusively in academic or lab settings.

Research {#research}

I enjoyed the research I did, but wish there was more time to keep doing it. [ref]I suppose there would be if I were to stay in academia, but that path is not for me[/ref] I thoroughly enjoyed diving into Numerical Linear Algebra papers and implementing some of the more classical results. The most satisfying of course were the ones that took a few attempts to get right.

In my dissertation, I describe a method for solution transfer between curved meshes. In layman's terms:

  • A mesh is an approximation of some physical domain, e.g. the surface of a frying pan (in 2D) or the wing of an airplane (in 3D)
  • A mesh is composed of small elements that are well understood, e.g. triangles, rectangles, tetrahedra, cubes, etc.
  • A curved mesh is one in which the edges / faces of the elements are allowed to curve
  • A solution (or field) on a mesh is a numerical representation of some physical quantity, e.g. velocity, pressure, density or energy
  • Solution transfer is the process of reintepreting (or interpolating) a solution from one mesh onto another

During commonly used simulation techniques, one or several physical quantities are represented on a mesh and change over time according to some law of physics (usually represented by a partial differential equation). When the process involves a fluid (the F in CFD), it's common to allow the mesh to "travel" over time with the fluid. For example, when simulating blood flow within a rigid cavity (e.g. a heart or vein) the mesh can represent a membrane that flows as the blood moves.

In such simulations, the mesh can become tangled after a certain amount of time moving along the flow. It is these cases where mesh quality begins to deteroriate that benefit from solution transfer. Once a mesh becomes too low-quality to use in simulation, a new mesh must be used to represent the physical domain. Once the new mesh is chosen, the physical quantities being tracked must be transferred from the low-quality mesh to the new one.

This work was certainly incremental, as much research is. Solution transfer has already been described for straight sided meshes (i.e. meshes where the elements are not curved). However, the work required to intersect curved triangles is considerably more involved than that required to intersect straight sided triangles. Peter Thiel would have you believe (in Zero to One) that the hardest step is the initial idea and everything else is incremental. However, I can say that the incremental step from straight sided to curved elements was a considerable jump in difficulty.

Software {#software}

During graduate school, I wrote a lot of code, as I usually do. However, two projects in particular stick out:

I've worked on Google client libraries in one form or another since 2011 and somehow managed to keep doing this after leaving Google for UC Berkeley. I had a great opportunity to be one of the main drivers of the google-cloud-python library and it allowed me to stay current on how software is built. Among other things I gained an appreciation for testing, continuous integration and documentation that I didn't have before.

As part of my research, I needed to be able to intersect millions of pairs of Bézier curves in a single simulation. I was worried that doing this in my language of choice (Python) would be too slow, so I decided to write the computation in a compiled language and wrap the interface with a binary extension. Building binary wheels for Linux, Mac OS X and Windows was a struggle, to say the least, but I'm happy I went through the process. If I can find the time, I hope to write a bit more about some of the amusing packaging bugs I created and had to track down. I hope that scikit-build or a similar effort can once and for all demystify the process of invoking native code from Python.

I chose Fortran for the implementation, which is likely a shock to most people outside of academia. In Silicon Valley, Fortran is usually a punchline rather than a language choice. However, I discovered early in my program that modern Fortran is a wonderful language. Writing vanilla Fortran is essentially just like writing NumPy code with all square brackets ([) swapped for parentheses ((). With the Fortran 90 specification, the FORTRAN (yes, all caps) language was no more and the modern features actually make it an appealing language.

I legitimately think people should consider Fortran first for computational workloads, if not for more general purpose tasks. Having a sponsor has made the Go (Google) and Rust (Firefox) communities vibrant places with great documentation and ever-expanding choices for libraries. Intel is the closest it comes to a Fortran steward due to their forums for the wonderful ifort compiler. However, there is no community-led Fortran documentation[ref]An equivalent of or[/ref] and this makes it a bit hard to develop code in Fortran. The amazing fortran90 site from Ondřej Čertík fills many gaps, but is mostly a one-person effort.

I started the foreign-fortran project to make my little contribution back to the Fortran community. The project is essentially documentation only and gives examples of how Fortran libraries can be used from other programming languages.

Parting Words

I really enjoyed my time in graduate school and wish I was able to better utilize the awesome communities on UC Berkeley's campus. Though I'm happy I did it, I'm equally happy that I spent three years in the real world working at companies[ref]Or "industry" as it's called in academia[/ref] before starting. I would recommend that all undergraduate students go get a "real job" before deciding to commit several years of their life to a PhD. There's a whole world out there outside of the ivory tower and too often it's not clear to students what their options are if they don't end up in that tenure track job.

As I said, my fellow graduate students with and from whom I have learned were a great part of the experience. In particular Will Pazner[ref]Thanks to Will for reviewing this post[/ref], Chris Miller and Qiaochu Yuan as well as my undergraduate classmate Wade Hindes have been a source of many great discussions.