### High Performance Computing: ParaFly

In my recent posts I shared some first hand experience of parallel computing using OpenMP.
While OpenMP is supported by many programming languages, there are still a few does not. So here I am sharing another approach to create a parallel computing job.

The utility I will use is called "ParaFly". There are some information you can read here.
Basically, ParaFly can be used to run a list of command simultaneously. This approach will be particularly useful for some types of jobs in which tasks are independent with each other (such as for loop) but take a long time to run.

In my case, I was using the IDL library to process a huge amount to spatial datasets. I will use this job as an example to show how it is done.

Organically, I have to call a routine:
PRO project48, extension\_file = ef, \$filename\_mapinfo, \$
missing\_value, \$o\_pixel\_size, \$
prefix\_in, $prefix\_out = po, \$
workspace\_in, \$workspace\_out, \$
year\_end, \$year\_start to re-project a list of raster image files from 1980 to 2015. IDL is known for inefficient in for loop just like MATLAB. And it is not easy to parallel IDL on a Linux HPC. You can use C/C++ to call IDL with OpenMP enabled if possible, but then you have to write some additional program to do the work. You can also use GDAL library to write a projection function then you can use OpenMP freely, but that certainly requires some efforts. However, with ParaFly, we can do the work within a few minutes if you are lucky. First, we need to add an additional routine to call the above routine, but this new routine should accept one parameter, which is time(year), because all the other will remain the same. Such as: ;- PRO project48_tmax, year COMPILE_OPT IDL2 year_start = year year_end = year ;;some other lines are remove here project48, extension_file = file_extension,$
filename_mapinfo, $missing_value,$
o_pixel_size, $prefix_in,$
workspace_in, $workspace_out,$
year_end,$year_start PRINT, 'Finished!' END Then the routine is wrapped and ready for ParaFly. You may want to write another wrapper to generate the ParaFly file, such as: PRO prepare_parafly_files COMPILE_OPT IDL2 year_start = 1980 year_end = 2015 ;;some other lines are remove here FOR year = year_start, year_end, 1 DO BEGIN year_str = STRING(year, format = '(i04)') str = 'idl -e '+ '"' +'project48_tmax, '$
+ year_str + '"'
PRINTF, lun, str
ENDFOR
FREE_LUN, lun
END

Then work should be done.
Theoretically, you can request the whole node with all cores in one job, and then gain speed the number of core faster. For example, if I request 10 cores, then the program will improve to 10 time faster.

### Spatial datasets operations: mask raster using region of interest

Climate change related studies usually involve spatial datasets extraction from a larger domain.
In this article, I will briefly discuss some potential issues and solutions.

In the most common scenario, we need to extract a raster file using a polygon based shapefile. And I will focus as an example.

In a typical desktop application such as ArcMap or ENVI, this is usually done with a tool called clip or extract using mask or ROI.

Before any analysis can be done, it is the best practice to project all datasets into the same projection.

If you are lucky enough, you may find that the polygon you will use actually matches up with the raster grid perfectly. But it rarely happens unless you created the shapefile using "fishnet" or other approaches.

What if luck is not with you? The algorithm within these tool usually will make the best estimate of the value based on the location. The nearest re-sample, but not limited to, will be used to calculate the value. But what about the outp…

### Numerical simulation: ode/pde solver and spin-up

For Earth Science model development, I inevitably have to deal with ODE and PDE equations. I also have come across some discussion related to this topic, i.e.,

https://www.researchgate.net/post/What_does_one_mean_by_Model_Spin_Up_Time

In an attempt to answer this question, as well as redefine the problem I am dealing with, I decided to organize some materials to illustrate our current state on this topic.

Models are essentially equations. In Earth Science, these equations are usually ODE or PDE. So I want to discuss this from a mathematical perspective.

Ideally, we want to solve these ODE/PDE with initial condition (IC) and boundary condition (BC) using various numerical methods.
https://en.wikipedia.org/wiki/Initial_value_problem
https://en.wikipedia.org/wiki/Boundary_value_problem

Because of the nature of geology, everything is similar to its neighbors. So we can construct a system of equations which may have multiple equation for each single grid cell. Now we have an array of equation…

### Lessons I have learnt during E3SM development

I have been involved with the E3SM development since I joined PNNL as a postdoc. Over the course of time, I have learnt a lot from the E3SM model. I also found many issues within the model, which reflects lots of similar struggles in the lifespan of software engineering.

Here I list a few major ones that we all dislike but they are around in almost every project we have worked on.

Excessive usage of existing framework even it is not meant to Working in a large project means that you should NOT re-invent the wheels if they are already there. But more often, developers tend to use existing data types and functions even when they were not designed to do so. The reason is simple: it is easier to use existing ones than to create new ones. For example, in E3SM, there was not a data type to transfer data between river and land. Instead, developers use the data type designed for atmosphere and land to do the job. While it is ok to do so, it added unnecessary confusion for future development a…