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Showing posts from April, 2017

High performance computing: data management

When you leave a position, such as graduation from university, you usually have to backup lots of data, which is usually considered as one critical step in data management.

In general, data management is an important process in all scientific research activities. Without proper data management, research activity efficiency may be influenced. In extreme cases, you may lose valuable data due to poor data management. In some cases, it could be regarded as research misconduct as well.

Data management itself can be a project from my perspective, especially when you have to deal with massive amount of data across different platforms.

In my case, I need to manage different types of data under different environments, I will first introduce the data formats that I am dealing with, then I will introduce the file system that will be used to manage the data.

In Earth system research, data usually can be classified based on various dimensions.
Based on data properties, these dimensions can be rast…

Ecosystem modeling: uncertainty quantification

I recently read a few news articles of skeptical attitudes towards climate change, and I decided to write something about it. I am not trying to promote climate change, but instead I want to point out there is great uncertainty in our current Earth system modeling.

Uncertainty quantification (UQ) is an important step in most numerical simulation processes. In general, a simulation without uncertainty quantification is less convincing. (I was surprised that an invited speaker in department seminar said he doesn't care about uncertainty.)

However, how to conduct uncertainty quantification itself is a challenge, especially for highly nonlinear ecosystem modeling.

First, I will invite you to read the Wikipedia UQ here:
https://en.wikipedia.org/wiki/Uncertainty_quantification
which serves as an overview of the concept I will discuss below.

Uncertainty comes from lots of sources and nearly every step we take in our Earth system modeling has uncertainty. We, scientists as well as engineer…

Ecosystem modeling: model evaluation of current implementation in ECO3D 1.0

As I am preparing my defense, the first version of ECOSYSTEM 1.0 in my thesis was finally completed. Looking forward to the next chapter of my life, I thought it is time to evaluate the ECOSYSTEM 1.0 to see what it is capable of and what still needs to be improved or expanded in the near future.

First, here is a brief introduction of the ECOSYSTEM model:
ECOSYSTEM is a three-dimensional water and carbon cycle terrestrial ecosystem model. Within ECOSYSTEM model, water and carbon cycle are seamlessly coupled. The water cycle is developed based on the PRMS, and the carbon cycle is developed based on TEM. The core idea behind the coupling is that both water and carbon (potentially nitrogen and others) fluxes can flow in a three-dimensional domain, and that is exactly one of the reasons why dissolved organic carbon (DOC) can be observed in stream water.

A lot of improvements have been made upon the original PRMS and TEM models. For example, I have added a new litter pool to consider the ca…