nek-analyze is a framework for writing analysis and visualization tools for Nek5000 files. nek-analyze employes a two-tiered MapReduce model, giving it some useful properties:
- O(1) memory usage, tunable at run-time
- Efficient on and off-node parallelization
- Scipy ecosystem tools
Many common analyses can be easily expressed as MapReduce with a bit of post-processing:
- Single variable integrals (e.g. int dV)
- Global masked min/max
- Dense analysis on lines and slices (e.g. 2D FFT, plotting)
- Visualization of slices
- Marking iso-surfaces
However, some analyses fall outside this model:
- 3D 2-point correlations
nek-analyze requires Python3.
nek-analyze depends on a number of other python packages. Fortunately, they're all on PyPI, so they can be pip installed.
- chest
- mapcombine
- Numpy
- IPython (optional, for inter-node parallelism)
pip install numpy ipython mapcombine chest
To use an existing analysis subpackage on a single node, simply:
usage: load.py [-h] [-f FRAME] [-e FRAME_END] [-s] [-c] [-n NINTERP] [-z] [-m]
[-F] [-b] [-nb BLOCK] [-nt THREAD] [-d] [-p] [--series]
[--mapreduce MAPREDUCE] [--post POST] [-v]
[--params PARAM_PATH] [--chest CHEST_PATH] [--figs FIG_PATH]
[--MR_init MR_INIT] [--reduce REDUCE] [--map MAP]
[--single_pos]
name
positional arguments:
name Nek *.fld output file
optional arguments:
-h, --help show this help message and exit
-f FRAME, --frame FRAME
[Starting] Frame number
-e FRAME_END, --frame_end FRAME_END
Ending frame number
-s, --slice Display slice
-c, --contour Display contour
-n NINTERP, --ninterp NINTERP
Interpolating order
-z, --mixing_zone Compute mixing zone width
-m, --mixing_cdf Plot CDF of box temps
-F, --Fourier Plot Fourier spectrum in x-y
-b, --boxes Compute box covering numbers
-nb BLOCK, --block BLOCK
Number of elements to process at a time
-nt THREAD, --thread THREAD
Number of threads to spawn
-d, --display Display plots with X
-p, --parallel Use parallel map (IPython)
--series Apply time-series analyses
--mapreduce MAPREDUCE
Module containing Map and Reduce implementations
--post POST Module containing post_frame and post_series
-v, --verbose Should I be really verbose, that is: wordy?
--params PARAM_PATH Location of param file
--chest CHEST_PATH Location of chest directory
--figs FIG_PATH Location of figures
--MR_init MR_INIT MapReduce init function. Loaded from --mapreduce if
None.
--reduce REDUCE Reduce function. Loaded from --mapreduce if None.
--map MAP Map function. Loaded from --mapreduce if None.
--single_pos Position only in first output
nek-analyze users need to populate four routines:
MapReducepost_framepost_series