Numba causes silent errors for mixed-component atmospheres about pyrads

[danielkoll]

Interesting! Yes, the Absorption_Crosssections script is in urgent need of some rewriting and cleaning up. The code is essentially Ray Pierrehumbert's old PyTran script, and could probably be made much more efficient by leveraging modern Python capabilities like numpy. Many of the functions in there can, and should be, decluttered. If you have time to look at it, that'd be a great contribution!

[danielkoll]

ClimateGraphics should go. These are all pre-numpy/matplotlib legacy libraries.

[danielkoll]

In terms of rewriting Absorption_Crosssections: the important parts are loadSpectralLines() and computeAbsorption(). loadSpectralLines() reads in all the individual spectral lines from a hitran file, using a big for-loop. computeAbsorption() then loops over all the saved lines and adds up their contribution to the absorption crossection 'absGrid'.

Currently loadSpectralLines() is nice in that it requires minimal memory (reading one spectral line at a time), but the downside is that it appends that data to an ever-growing list. It might be possible to speed up loadSpectralLines() by first loading the entire hitran file into memory, then only keeping the subsection of lines we're actually interested in? One issue with this is that spectral files can become ridiculously large -- e.g., the full H2O line list from HITRAN2016 is only ~23MB, but other line lists can be >>100MB, so loading all lines isn't always an option.

computeAbsorption() then loops over the lines, calculates a lorentz line shape for each one, and adds the contribution of that line to the overall absorption grid. Since this only operates on line data that's already stored in memory, there might be a way of replacing the for-loop with numpy?

Alternatively, loadSpectralLines() and computeAbsorption() could be good targets for numba.

[danielkoll]

Here is a minimal script that reproduces the error:

import numpy as np
import pyrads

from pyrads.Absorption_Crosssections_HITRAN2016 import getKappa_HITRAN
from pyrads.Absorption_Crosssections_HITRAN2016_numba import getKappa_HITRAN_numba

n0,n1,dn = 350.,400.,20.
n = np.arange(n0,n1,dn)
T = 300.
p = 1e5
pself = 1e3

kappa0 = getKappa_HITRAN(n,n0,n1,dn,"CO2", broadening="mixed",
press=p,press_self=pself,temp=T,
lineWid=25.,cutoff_option="fixed",remove_plinth=True)
kappa0_numba = getKappa_HITRAN_numba(n,n0,n1,dn,"CO2", broadening="mixed",
press=p,press_self=pself,temp=T,
lineWid=25.,cutoff_option="fixed",remove_plinth=True)
print( "kappaCO2 (no numba)=",kappa0 )
print( "kappaCO2 (numba)=",kappa0_numba )
print( "\n" )

kappa0 = getKappa_HITRAN(n,n0,n1,dn,"H2O", broadening="mixed",
press=p,press_self=pself,temp=T,
lineWid=25.,cutoff_option="fixed",remove_plinth=True)
kappa0_numba = getKappa_HITRAN_numba(n,n0,n1,dn,"H2O", broadening="mixed",
press=p,press_self=pself,temp=T,
lineWid=25.,cutoff_option="fixed",remove_plinth=True)
print( "kappaH2O (no numba)=",kappa0 )
print( "kappaH2O (numba)=",kappa0_numba )
print( "\n" )

[danielkoll]

Resulting output is:

kappaCO2 (no numba)= [5.80495351e-05 3.91946490e-06 0.00000000e+00]
kappaCO2 (numba)= [5.80495351e-05 3.91946490e-06 0.00000000e+00]

kappaH2O (no numba)= [22725.4463143 7063.90460525 0. ]
kappaH2O (numba)= [5.80495351e-05 3.91946490e-06 0.00000000e+00]

The values produced by getKappa_HITRAN_numba() are identical for CO2 and H2O.

[danielkoll]

@AndrewWilliams3142: getKappa_HITRAN_numba seems to produce incorrect results when calling it for a second time with another gas species. Presumably an issue with numba's caching? Manually setting @jit(cache=False) doesn't fix things though.

[AndrewILWilliams]

Hi @ddbkoll ! I'll take a look now, it could well be something wrong with my numba interface (still getting used to it).

+1 for the tests!

[AndrewILWilliams]

@ddbkoll very weird! I thiiiink this might be to do with how numba deals with global instances, see here.

Global variables are treated as constants. The cache will remember the value in the global variable used at compilation. On cache load, the cached function will not rebind to the new value of the global variable.

One such global variable is molName! So I think that when numba compiles the function for the first time it's remembering this, which is why you always get the values for CO2 (or whatever else you ran first).

Absorption_Crosssections_HITRAN2016_numba.py clearly needs a bit more work! On this topic, I was going to ask, there are lots of functions in Absorption_Crosssections_HITRAN2016.py (and the numba version) which aren't used and just seem to be for plotting? If so, I think it might make sense to either remove these functions (to reduce clutter and make debugging easier) or put them in a separate file.

[AndrewILWilliams]

Sweet! Yeah I recognized a few of the functions from PyTran actually. I'll start thinking about a clean-up this week! (Need to make some lists of what's being used)

Another question, do you use the stuff in ClimateGraphics/ClimateGraphics_MPL etc? As far as I can tell most of this is redundant now that matplotlib is so advanced anyways, so there might be an argument for removing it from the package.

[AndrewILWilliams]

Interesting! Thanks for the overview!

Maybe I'm missing something here, but in DATA/HITRAN_DATA/HITRAN2016/ThermalOnly_0-5000cm.MainIsotopesOnly the files are all quite small? for example 01_hit16.par is only 5.3Mb? I'm a bit confused by these files though, I'm not entirely sure how to load the entire thing in haha

[AndrewILWilliams]

Another option could be to call loadSpectralLines() in the OpticalThickness calculation, before it loops over the temperatures/pressures. Currently it loads in the same spectral lines every iteration of the loop. I'm just putting together a PR now which should tidy up lots of the code