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I'm a PhD student in Electrical Engineering. I'm currently working on a Monte Carlo-type simulation for looking at the underwater light field for underwater opt

I'm a PhD student in Electrical Engineering. I'm currently working on a Monte Carlo-type simulation for looking at the underwater light field for underwater optical communication (no sharks!). I'm doing the development in MATLAB and I recently put all my code up on Github (https://github.com/gallamine/Photonator https://github.com/gallamine/Photonator) to help avoid some of these problems (lack of transparency). Even if nobody ever looks/uses the code, I know every time I do a commit there's a change someone MIGHT and I think it helps me write better code. The problem with doing science via models/simulation is that there just isn't a good way of knowing when it's "right" (well, at least in a lot of cases), so testing and verification are imperative. I can't tell you how many times I've laid awake at night wondering if my code has a bug in it that I can't find and will taint my research results. I suspect another big problem is that one student writes the code, graduates, then leaves it to future students, or worse, their professor, to figure out what they wrote. Passing on the knowledge takes a heck of a lot of time, especially when you're pressed to graduate and get a paycheck). There's got to be a market in this somewhere. Even if it was just a volunteer service of "real" programmers who would help scientists out. I spent weeks trying to get my code running on AWS, which probably would have taken a few hours from someone who knew what they were doing. I also suspect that someone with practice could make my simulations run at twice the speed, which really adds up when you're doing hundreds of them and they take hours each.

pwang 15y ago
There is a market, and it's called libraries. Eventually you will use a language where software carpentry and code reuse is a core feature, and tested, modular libraries for not only core algorithms, but also deployment and dev-ops stuff (like managing a compute cluster on the cloud) will have standard approaches. This is starting to shape up on the Python side of things, but it has stagnated a little bit. People who can and do write the foundational code are oftentimes too focused on making the code work, and not at all focused on improving the quality of the ecosystem that their code is part of. Open Source is a great mechanism for many things, but polishing up the last 20% is not one of them.
- gallamine 15y ago
  "Eventually you will use a language where software carpentry and code reuse is a core feature." Well, to some extent products like MATLAB solve this problem. For better or worse, I trust Matlab's ability to generate a (pseudo) random number, parallel process my functions, invert matrices, etc., etc. On a broader level, thanks to the specialization of academia, chances are that the code I want to write isn't duplicated by others. Even if it is, I still have to trust them to have written it well - which is the whole problem here. I guess I don't have as much hope as you do.
john_b 15y ago
I'm a M.S. student in mechanical engineering facing a similar situation, except I haven't put any code on Github (my advisor wants to keep it proprietary, but I probably would not bother putting it up even if he were ok with it). I've written around 15000 lines of MATLAB for my research and only a handful of people will ever need to see it. Some is well-structured and nicely commented, but other parts are incomprehensible and were written under severe time constraints. My advisor is not much of a programmer and will not be able to figure it out, and I feel bad for leaving a pile of crappy code to the person who inevitably follows in my footsteps, but I ultimately have a choice between writing fully commented, well-tested, and well-structured code and graduating a semester late (at the cost of several thousand dollars to myself), or writing code that's "just good enough" to get results on time. This is a solo project (there is no money for a CS student to intern) and I'm not getting paid to write code unlike a professional programmer, so every second I spend improving my code beyond the bare minimum costs me time and money. Even if I were able to tidy up and publish all of my code, most mechanical engineers would not be able to understand it because most can't write code. Those who can mostly use FORTRAN, although C is becoming more common. Nonetheless, even those who could understand my code would have little incentive to read through 15000+ lines of code. Unfortunately, as far as research code is concerned, a lot of trust is still required on the part of the reader of the publication. I agree that the transfer of knowledge should be handled differently, but until there is a strong incentive for researchers to write good code it will continue to be bad. Especially when many research projects only require the code to demonstrate something, after which it can be put in the closet.
- eru 15y ago
  I wonder whether our priorities for research are misguided. Isn't research about extending the knowledge of humanity? Writing and passing on readable code would probably advance us further in total, than everyone starting basically from scratch. (I'm not faulting you, you just react to the incentives.)
  - reginaldo 15y ago
    Well, I went to a lecture by one of the most prominent scientists here in Brazil, where he explicitly said that the answer to your question is NO. Research as it stands today exists to feed the system. According to him, you: * Publish, so you can get grants * Use that grant so you can publish more * Get more grants; * Get tenure somewhere in the middle. I have to confess I was very disgusted by him saying that in front of such a large audience of scientists and graduate students. EDIT: Formatting
JabavuAdams 15y ago
Huh. Cool. Are you familiar with Metropolis light-transport? http://en.wikipedia.org/wiki/Metropolis_light_transport http://en.wikipedia.org/wiki/Metropolis_light_transport I've read about it in the context of speeding up global-illumination path-tracing for computer graphics. I think it's based on work that was originally done for neutron scattering.
- gallamine 15y ago
  I believe I came across it at some point or another, but I haven't looked closely at it. For better or worse, it doesn't seem to be employed by others doing light field simulations underwater ... not sure why. I'd have to poke into it further. I was, however, seriously thinking about writing a plugin for Blender that would utilize my specific scattering phase functions in their volumetric ray tracing renderer ... no time though.
FrojoS 15y ago
The people at Willow Garage think there is a market for this [1]. http://www.willowgarage.com/blog/2010/04/27/reinventing-wheel http://www.willowgarage.com/blog/2010/04/27/reinventing-whee...
xtracto 15y ago
"Essentially, all models are wrong, but some are useful." [ http://en.wikiquote.org/wiki/George_E._P._Box http://en.wikiquote.org/wiki/George_E._P._Box ]

pwang 15y ago

There is a market, and it's called libraries. Eventually you will use a language where software carpentry and code reuse is a core feature, and tested, modular libraries for not only core algorithms, but also deployment and dev-ops stuff (like managing a compute cluster on the cloud) will have standard approaches. This is starting to shape up on the Python side of things, but it has stagnated a little bit. People who can and do write the foundational code are oftentimes too focused on making the code work, and not at all focused on improving the quality of the ecosystem that their code is part of. Open Source is a great mechanism for many things, but polishing up the last 20% is not one of them.

gallamine 15y ago
"Eventually you will use a language where software carpentry and code reuse is a core feature." Well, to some extent products like MATLAB solve this problem. For better or worse, I trust Matlab's ability to generate a (pseudo) random number, parallel process my functions, invert matrices, etc., etc. On a broader level, thanks to the specialization of academia, chances are that the code I want to write isn't duplicated by others. Even if it is, I still have to trust them to have written it well - which is the whole problem here. I guess I don't have as much hope as you do.

john_b 15y ago

I'm a M.S. student in mechanical engineering facing a similar situation, except I haven't put any code on Github (my advisor wants to keep it proprietary, but I probably would not bother putting it up even if he were ok with it). I've written around 15000 lines of MATLAB for my research and only a handful of people will ever need to see it. Some is well-structured and nicely commented, but other parts are incomprehensible and were written under severe time constraints. My advisor is not much of a programmer and will not be able to figure it out, and I feel bad for leaving a pile of crappy code to the person who inevitably follows in my footsteps, but I ultimately have a choice between writing fully commented, well-tested, and well-structured code and graduating a semester late (at the cost of several thousand dollars to myself), or writing code that's "just good enough" to get results on time. This is a solo project (there is no money for a CS student to intern) and I'm not getting paid to write code unlike a professional programmer, so every second I spend improving my code beyond the bare minimum costs me time and money. Even if I were able to tidy up and publish all of my code, most mechanical engineers would not be able to understand it because most can't write code. Those who can mostly use FORTRAN, although C is becoming more common. Nonetheless, even those who could understand my code would have little incentive to read through 15000+ lines of code. Unfortunately, as far as research code is concerned, a lot of trust is still required on the part of the reader of the publication. I agree that the transfer of knowledge should be handled differently, but until there is a strong incentive for researchers to write good code it will continue to be bad. Especially when many research projects only require the code to demonstrate something, after which it can be put in the closet.

eru 15y ago
I wonder whether our priorities for research are misguided. Isn't research about extending the knowledge of humanity? Writing and passing on readable code would probably advance us further in total, than everyone starting basically from scratch. (I'm not faulting you, you just react to the incentives.)
- reginaldo 15y ago
  Well, I went to a lecture by one of the most prominent scientists here in Brazil, where he explicitly said that the answer to your question is NO. Research as it stands today exists to feed the system. According to him, you: * Publish, so you can get grants * Use that grant so you can publish more * Get more grants; * Get tenure somewhere in the middle. I have to confess I was very disgusted by him saying that in front of such a large audience of scientists and graduate students. EDIT: Formatting

JabavuAdams 15y ago

Huh. Cool. Are you familiar with Metropolis light-transport? http://en.wikipedia.org/wiki/Metropolis_light_transport http://en.wikipedia.org/wiki/Metropolis_light_transport I've read about it in the context of speeding up global-illumination path-tracing for computer graphics. I think it's based on work that was originally done for neutron scattering.

gallamine 15y ago
I believe I came across it at some point or another, but I haven't looked closely at it. For better or worse, it doesn't seem to be employed by others doing light field simulations underwater ... not sure why. I'd have to poke into it further. I was, however, seriously thinking about writing a plugin for Blender that would utilize my specific scattering phase functions in their volumetric ray tracing renderer ... no time though.

FrojoS 15y ago

The people at Willow Garage think there is a market for this [1]. http://www.willowgarage.com/blog/2010/04/27/reinventing-wheel http://www.willowgarage.com/blog/2010/04/27/reinventing-whee...

xtracto 15y ago

"Essentially, all models are wrong, but some are useful." [ http://en.wikiquote.org/wiki/George_E._P._Box http://en.wikiquote.org/wiki/George_E._P._Box ]