Trouble with kernels - "Missing Source Code" error.

[OScott19]

Question

Question

I've been trying to add some behavioural kernels, however recently I've been unable to execute code as I'm getting a "Source code missing" error (copied below).

If I run the first example of pset.execute() I get the error message below. If I try and run the pset just using pre-defined kernels, then instead I get an 'out of bounds' error (which is to be expected).

I have deleted & reinstalled parcels multiple times, including creating a new conda environment for a new installation, but I still can't seem to locate/ fix the missing source code. Any suggestions of what to fix/ try next would be hugely appreciated, thank you!

Supporting code/error messages

## start by loading in my packages and setting everything up 

import os

os.chdir("") 

## let's import the other packages we'll be working with 

import netCDF4 as nc
import numpy as np
import parcels
#print(parcels.__version__)
import pandas as pd
from datetime import timedelta as delta
import matplotlib.pyplot as plt
import xarray as xr 

print(np.version.version)
print(parcels.__version__)


## start by definint Smagorinsky diffusion method

def smagdiff(particle, fieldset, time):
    dx = 0.01
    # gradients are computed by using a local central difference.
    updx, vpdx = fieldset.UV[time, particle.depth, particle.lat, particle.lon + dx]
    umdx, vmdx = fieldset.UV[time, particle.depth, particle.lat, particle.lon - dx]
    updy, vpdy = fieldset.UV[time, particle.depth, particle.lat + dx, particle.lon]
    umdy, vmdy = fieldset.UV[time, particle.depth, particle.lat - dx, particle.lon]

    dudx = (updx - umdx) / (2 * dx)
    dudy = (updy - umdy) / (2 * dx)

    dvdx = (vpdx - vmdx) / (2 * dx)
    dvdy = (vpdy - vmdy) / (2 * dx)

    A = fieldset.cell_areas[time, 0, particle.lat, particle.lon]
    sq_deg_to_sq_m = (1852 * 60) ** 2 * math.cos(particle.lat * math.pi / 180)
    A = A / sq_deg_to_sq_m
    Kh = fieldset.Cs * A * math.sqrt(dudx**2 + 0.5 * (dudy + dvdx) ** 2 + dvdy**2)

    dlat = parcels.ParcelsRandom.normalvariate(0.0, 1.0) * math.sqrt(
        2 * math.fabs(particle.dt) * Kh
    )
    dlon = parcels.ParcelsRandom.normalvariate(0.0, 1.0) * math.sqrt(
        2 * math.fabs(particle.dt) * Kh
    )

    particle_dlat += dlat
    particle_dlon += dlon



## read in one of my outputs to find the grid cells

model_path = "../Data/CMEM_030_Velocities/"
outputs = os.listdir(model_path)
outputs = sorted(outputs)

fname = [model_path + s for s in outputs]

filenames = {"U": fname, "V": fname}


variables = {'U': 'uo',
             'V': 'vo'}


dimensions = {"lat": "latitude", "lon": "longitude", "time": "time", "depth": "depth"}

fieldset = parcels.FieldSet.from_nemo(filenames, variables, dimensions, allow_time_extrapolation=True)

x = fieldset.U.grid.lon
y = fieldset.U.grid.lat

cell_areas = parcels.Field(
    name="cell_areas", data=fieldset.U.cell_areas(), lon=x, lat=y
)
fieldset.add_field(cell_areas)

fieldset.add_constant("Cs", 0.1)

# particles are released at one location every hour for 12 hours

## adding locations

data_scotia = pd.read_csv("../Data/AllCoralLocations_min.csv", header =0)


lon = data_scotia["long"].astype('float32')
lat = data_scotia["lat"].astype('float')
deptho = data_scotia["depthMin"].astype('float')*-1 # needs to be real number
npart = lon.shape[0]
time = [0] * len(lon)


pset = parcels.ParticleSet(
    fieldset=fieldset, pclass=parcels.JITParticle, lon=lon, lat=lat, time=time
)

#Simulating the particles moving during 7 days using advection (AdvectionRK4) and diffusion (smagdiff) kernels.
## but also remember to use the 'particle out of bounds' kernel

def DeleteParticle(particle, fieldset, time):
    if particle.state == parcels.StatusCode.ErrorOutOfBounds:
        particle.delete()

#import zarr
#print(zarr.__version__)


output_file = pset.ParticleFile(
    name="Global_smagdiff_RealLocations_newEnvTest1.zarr", outputdt=delta(hours=12), chunks=(1, 57)
)


parcels.ParcelsRandom.seed(1636)  # Random seed for reproducibility

pset.execute(
    [parcels.AdvectionRK4, smagdiff, DeleteParticle],
    runtime=delta(days=30 * 2), # 2 months of run 
    dt=delta(hours=12),
    output_file=output_file,
)


## without personalised kernels
pset.execute(
    [parcels.AdvectionRK4],
    runtime=delta(days=30 * 2), # 2 months of run 
    dt=delta(hours=12),
    output_file=output_file,
)

# Error message

    ^
  File "/home/oslin/miniconda3/envs/parcels/lib/python3.14/site-packages/parcels/particleset.py", line 1048, in execute
    self._kernel = self.Kernel(pyfunc, delete_cfiles=delete_cfiles)
                   ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oslin/miniconda3/envs/parcels/lib/python3.14/site-packages/parcels/particleset.py", line 891, in Kernel
    return Kernel.from_list(
           ~~~~~~~~~~~~~~~~^
        self.fieldset,
        ^^^^^^^^^^^^^^
    ...<3 lines>...
        delete_cfiles=delete_cfiles,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/oslin/miniconda3/envs/parcels/lib/python3.14/site-packages/parcels/kernel.py", line 518, in from_list
    return functools.reduce(lambda x, y: x + y, pyfunc_list)
           ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oslin/miniconda3/envs/parcels/lib/python3.14/site-packages/parcels/kernel.py", line 518, in <lambda>
    return functools.reduce(lambda x, y: x + y, pyfunc_list)
                                         ~~^~~
  File "/home/oslin/miniconda3/envs/parcels/lib/python3.14/site-packages/parcels/kernel.py", line 481, in __add__
    kernel = type(self)(self.fieldset, self.ptype, pyfunc=kernel)
  File "/home/oslin/miniconda3/envs/parcels/lib/python3.14/site-packages/parcels/kernel.py", line 204, in __init__
    self.funccode = funccode or inspect.getsource(pyfunc.__code__)
                                ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/home/oslin/miniconda3/envs/parcels/lib/python3.14/inspect.py", line 1161, in getsource
    OSError is raised if the source code cannot be retrieved."""
                  ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oslin/miniconda3/envs/parcels/lib/python3.14/inspect.py", line 1143, in getsourcelines
    object = unwrap(object)
                  ~^^^^^^^^
  File "/home/oslin/miniconda3/envs/parcels/lib/python3.14/inspect.py", line 978, in findsource
    raise OSError('could not get source code')
OSError: could not get source code

[VeckoTheGecko]

Hi @OScott19 - which version of Parcels are you running? Your output doesn't actually include the output of print(parcels.__version__)

Currently I don't see what's causing the problem. With some more information (e.g., version of Parcels, full output with errors from the script ) we can hopefully fix this for you