How can I add logging to Parcels' kernel functions for debugging purposes？

[Cyuan-hub]

Hello everyone!
Sorry in advance if that is already documented, I went through the documentation but did not find any clear guidance.
I am using Python version 3.10.12 and ocean parcels version 2.4.2. I want to add logging to Parcels' kernel functions for debugging purposes. However, when I use "logger" imported from parcels, it encounters some errors. Here are the details:

The code that I use is as follow:

from parcels import FieldSet, Field, NestedField, VectorField, ParticleFile, ParticleSet, JITParticle, Variable
from parcels import ErrorCode, logger
import glob
import xarray as xr
import numpy as np
from operator import attrgetter
from parcels import ParcelsRandom as random
import math
import zarr
from datetime import datetime, timedelta
import calendar
import glob

startyear = 2020
endyear = 2020
day_month = [31,28,31,30,31,30,31,31,30,31,30,31]
time_stamps = []

for year in range(startyear, endyear + 1):
if calendar.isleap(year):
day_month[1] = 29
else:
day_month[1] = 28
for month in range(1,13):
if year == 2020 and month == 6:
for day in range(1, day_month[month - 1] + 1):
dateone = np.datetime64('%d-%.2d-%.2d' % (year, month, day)) + np.timedelta64(12, 'h')
time_stamps.append(dateone)
timestamps = np.expand_dims(np.array(time_stamps), axis=1)

vel_path = 'G:/JupyterNotebook/SCS_case2/input/Datasets/SurfaceCurrents/test_for_beach/'
vel_files = vel_path + '*_TotalDailyMean.nc'
filenames = {'U': vel_files, 'V': vel_files,}
variables = {"U": "vo", "V": "uo",}
dimensions = {'U': {'lat': 'latitude', 'lon': 'longitude'},
'V': {'lat': 'latitude', 'lon': 'longitude'},}

fieldset = FieldSet.from_netcdf(filenames, variables, dimensions, mesh="spherical",
timestamps = timestamps,allow_time_extrapolation= True) #False

from glob import glob
data_dir = 'G:/JupyterNotebook/Data-Download-from-Web/1-5degree/test_for_beach/'
fnames = []
basepath = data_dir + '*_Wave_Stokes_drift.nc'
fnames += sorted(glob(str(basepath)))

dimensionsU = {'lon': 'longitude', 'lat': 'latitude'} #, 'time': 'time'
dimensionsV = {'lon': 'longitude', 'lat': 'latitude'}
Uuss = Field.from_netcdf(fnames, ('Uuss', 'VSdx'), dimensionsU, fieldtype='U', timestamps = timestamps, allow_time_extrapolation=True,)

Vuss = Field.from_netcdf(fnames, ('Vuss', 'VSdy'), dimensionsV, fieldtype='V', timestamps = timestamps,
allow_time_extrapolation=True,
grid=Uuss.grid, dataFiles=Uuss.dataFiles)

fieldset.add_field(Uuss)
fieldset.add_field(Vuss)
uv_uss = VectorField('UVuss', fieldset.Uuss, fieldset.Vuss)
fieldset.add_vector_field(uv_uss)

coast_dist_file = 'G:/JupyterNotebook/SCS_case2/input/distances_to_nearest_coastline_matlab_Cy.nc'
data_dist = xr.open_dataset(coast_dist_file)
coast_distance = data_dist['distance_to_coast']
lon_dist = coast_distance.longitude.values
lat_dist = coast_distance.latitude.values
depth_dist = None
coast_dist_field = Field('dist', coast_distance.values, lon=lon_dist, lat=lat_dist, depth=depth_dist)
fieldset.add_field(coast_dist_field)

landmaskFile = 'G:/JupyterNotebook/SCS_case2/input/landmask_0ocean.nc'
data_mask = xr.open_dataset(landmaskFile)
LandMask = data_mask['mask']
lon_mask = LandMask.longitude.values
lat_mask = LandMask.latitude.values
depth_mask = None
LandMask = Field('LandMask', LandMask.values, lon=lon_mask, lat=lat_mask, depth=depth_mask)
fieldset.add_field(LandMask)

class CustomParticle(JITParticle):
age = Variable('age', dtype=np.float32, initial=0.)
particle_state = Variable('particle_state', dtype=np.int32, initial=0.)
unbeachCount = Variable('unbeachCount', dtype=np.int32, initial=0.)
beachCount = Variable('beachCount', dtype=np.int32, initial=0.)
beached_lon = Variable('beached_lon', dtype=np.float64, to_write= False)
beached_lat = Variable('beached_lat', dtype=np.float64, to_write= False)
beached_time = Variable('beached_time', dtype=np.float64, to_write=True, initial=0.)
time_on_land = Variable('time_on_land', dtype=np.float64, to_write= False, initial=0.)
prev_lon = Variable('prev_lon', dtype=np.float32, to_write=True, initial=attrgetter('lon')) # the previous longitude in water
prev_lat = Variable('prev_lat', dtype=np.float32, to_write=True, initial=attrgetter('lat')) # the previous latitude in water
# prev_time = Variable('prev_time',initial = attrgetter('time'),to_write = False)

position_file = 'G:/JupyterNotebook/SCS_case2/input/Particle_InitialPosi/'
lon_file = 'Lons_for_releasePoints.txt'
lat_file = 'Lats_for_releasePoints.txt'
lons = []
lats = []

with open(position_file+lon_file,'r',encoding = 'utf-8') as flon :
londata = flon.readlines()
for i in range(0,len(londata)):
lons.append(londata[i][0:-1])
with open(position_file+lat_file,'r',encoding = 'utf-8') as flat :
latdata = flat.readlines()
for i in range(0,len(latdata)):
lats.append(latdata[i][0:-1])

particles_lon = np.array(lons)
particles_lat = np.array(lats)
release_depth = np.zeros(particles_lon.shape)

release_interval = timedelta(hours = 24) # release from the same set of locations every 30days
pset = ParticleSet.from_list(fieldset,
pclass = CustomParticle,
lon = particles_lon,
lat = particles_lat,
depth = release_depth,
repeatdt = release_interval)

def DeleteParticle(particle, fieldset, time):
particle.delete()
logger.info_once(f"Particle {particle.id} is deleted at ({particle.lon}, {particle.lat}) at time {time}.")

def Ageing(particle, fieldset, time):
particle.age += particle.dt
logger.info_once(f"Particle {particle.id} is aging. New age: {particle.age}")

def AdvectionRK4(particle, fieldset, time):
logger.info_once(f"Particle {particle.id} is advecting at time {time}.")
if particle.particle_state == 0:
(u1, v1) = fieldset.UV[time, particle.depth, particle.lat, particle.lon]
lon1_adv, lat1_adv = (particle.lon + u1*.5particle.dt, particle.lat + v1.5particle.dt)
(u2, v2) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat1_adv, lon1_adv]
lon2_adv, lat2_adv = (particle.lon + u2.5particle.dt, particle.lat + v2.5particle.dt)
(u3, v3) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat2_adv, lon2_adv]
lon3_adv, lat3_adv = (particle.lon + u3particle.dt, particle.lat + v3particle.dt)
(u4, v4) = fieldset.UV[time + particle.dt, particle.depth, lat3_adv, lon3_adv]
particle.lon += (u1 + 2u2 + 2u3 + u4) / 6. * particle.dt
particle.lat += (v1 + 2v2 + 2*v3 + v4) / 6. * particle.dt
particle.particle_state = 2
logger.warning_once("This is a warning message that will be displayed only once.")

def BeachTesting_Adv(particle, fieldset, time):
if particle.particle_state == 2:
part_dis_to_coast1 = fieldset.dist[particle.dt, 0, particle.lat, particle.lon]
beaching_dist1 = 0.1
if part_dis_to_coast1 <= beaching_dist1:
particle.lon = particle.prev_lon
particle.lat = particle.prev_lat
particle.particle_state = 0
particle.unbeachCount += 1
logger.info_once(f"Particle {particle.id} is returning to water after beach testing.")
else:
particle.particle_state = 0
particle.prev_lon = particle.lon
particle.prev_lat = particle.lat
logger.info_once(f"Particle {particle.id} is continuing advection after beach testing.")

def StokesDrag(particle, fieldset, time):
if particle.particle_state == 0:
(u_uss, v_uss) = fieldset.UVuss[time, particle.depth, particle.lat, particle.lon]
particle.lon += u_uss * particle.dt
particle.lat += v_uss * particle.dt
particle.particle_state = 3
logger.info_once(f"Particle {particle.id} is experiencing Stokes drag at time {time}.")

def Beaching_StkDr(particle, fieldset, time):
if particle.particle_state == 3:
part_dis_to_coast2 = fieldset.dist[particle.dt, 0, particle.lat, particle.lon]
beaching_dist2 = 0.1
if part_dis_to_coast2 <= beaching_dist2:
particle.particle_state = 1
particle.delete()
logger.info_once(f"Particle {particle.id} is beaching due to Stokes drag at time {time}.")
else:
particle.particle_state = 0
particle.prev_lon = particle.lon
particle.prev_lat = particle.lat
logger.info_once(f"Particle {particle.id} is not beaching after experiencing Stokes drag at time {time}.")

Kernels= [AdvectionRK4,BeachTesting_Adv,StokesDrag,Beaching_StkDr,Ageing]

out_interval = timedelta(days = 1)

new_output_directory = "G:/JupyterNotebook/SCS_case2/ParcelsOutput/ZarrData/new/"
output_dirstore_name = new_output_directory + "Adv-loggerTesting.zarr/"

output_dirstore = zarr.storage.DirectoryStore(output_dirstore_name)

outputfile = pset.ParticleFile(name=output_dirstore, outputdt = out_interval)

dt = timedelta(minutes = 30)

totaltime_for_running = timedelta(days = 30)
running_time_first = timedelta(days = 10)

pset.execute(Kernels,
runtime = running_time_first,
dt = dt,
output_file = outputfile,
recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
ErrorCode.ErrorTimeExtrapolation: DeleteParticle})

pset.repeatdt = None

pset.execute(Kernels,
runtime = timedelta(days = 20),
dt = dt,
output_file = outputfile,
recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
ErrorCode.ErrorTimeExtrapolation: DeleteParticle})

I am getting the following error while I run the above codes:

---

NotImplementedError Traceback (most recent call last)
Cell In[4], line 17
14 totaltime_for_running = timedelta(days = 30)
15 running_time_first = timedelta(days = 10)
---> 17 pset.execute(Kernels,
18 runtime = running_time_first,
19 dt = dt,
20 output_file = outputfile,
21 recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
22 ErrorCode.ErrorTimeExtrapolation: DeleteParticle})
24 pset.repeatdt = None
26 pset.execute(Kernels,
27 runtime = timedelta(days = 20),
28 dt = dt,
29 output_file = outputfile,
30 recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
31 ErrorCode.ErrorTimeExtrapolation: DeleteParticle})

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\particleset\baseparticleset.py:433, in BaseParticleSet.execute(self, pyfunc, pyfunc_inter, endtime, runtime, dt, moviedt, recovery, output_file, movie_background_field, verbose_progress, postIterationCallbacks, callbackdt)
431 self.kernel = pyfunc
432 else:
--> 433 self.kernel = self.Kernel(pyfunc)
434 # Prepare JIT kernel execution
435 if self.collection.ptype.uses_jit:

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\particleset\particlesetsoa.py:715, in ParticleSetSOA.Kernel(self, pyfunc, c_include, delete_cfiles)
698 """Wrapper method to convert a pyfunc into a :class:parcels.kernel.Kernel object.
699
700 Conversion is based on fieldset and ptype of the ParticleSet.
(...)
712 (Default value = "")
713 """
714 if isinstance(pyfunc, list):
--> 715 return Kernel.from_list(
716 self.fieldset,
717 self.collection.ptype,
718 pyfunc,
719 c_include=c_include,
720 delete_cfiles=delete_cfiles,
721 )
722 return Kernel(
723 self.fieldset,
724 self.collection.ptype,
(...)
727 delete_cfiles=delete_cfiles,
728 )

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\kernel\basekernel.py:323, in BaseKernel.from_list(cls, fieldset, ptype, pyfunc_list, *args, **kwargs)
320 raise ValueError("Argument function_lst should be a list of functions.")
322 pyfunc_list = pyfunc_list.copy()
--> 323 pyfunc_list[0] = cls(fieldset, ptype, pyfunc_list[0], *args, **kwargs)
324 return functools.reduce(lambda x, y: x + y, pyfunc_list)

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\kernel\kernelsoa.py:98, in KernelSOA.init(self, fieldset, ptype, pyfunc, funcname, funccode, py_ast, funcvars, c_include, delete_cfiles)
96 if self.ptype.uses_jit:
97 kernelgen = KernelGenerator(fieldset, ptype)
---> 98 kernel_ccode = kernelgen.generate(deepcopy(self.py_ast),
99 self.funcvars)
100 self.field_args = kernelgen.field_args
101 self.vector_field_args = kernelgen.vector_field_args

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\compilation\codegenerator.py:520, in AbstractKernelGenerator.generate(self, py_ast, funcvars)
517 def generate(self, py_ast, funcvars):
518 # Replace occurences of intrinsic objects in Python AST
519 transformer = IntrinsicTransformer(self.fieldset, self.ptype)
--> 520 py_ast = transformer.visit(py_ast)
522 # Untangle Pythonic tuple-assignment statements
523 py_ast = TupleSplitter().visit(py_ast)

File ~\anaconda3\envs\py3_parcels\lib\ast.py:418, in NodeVisitor.visit(self, node)
416 method = 'visit_' + node.class.name
417 visitor = getattr(self, method, self.generic_visit)
--> 418 return visitor(node)

File ~\anaconda3\envs\py3_parcels\lib\ast.py:494, in NodeTransformer.generic_visit(self, node)
492 for value in old_value:
493 if isinstance(value, AST):
--> 494 value = self.visit(value)
495 if value is None:
496 continue

File ~\anaconda3\envs\py3_parcels\lib\ast.py:418, in NodeVisitor.visit(self, node)
416 method = 'visit_' + node.class.name
417 visitor = getattr(self, method, self.generic_visit)
--> 418 return visitor(node)

File ~\anaconda3\envs\py3_parcels\lib\ast.py:503, in NodeTransformer.generic_visit(self, node)
501 old_value[:] = new_values
502 elif isinstance(old_value, AST):
--> 503 new_node = self.visit(old_value)
504 if new_node is None:
505 delattr(node, field)

File ~\anaconda3\envs\py3_parcels\lib\ast.py:418, in NodeVisitor.visit(self, node)
416 method = 'visit_' + node.class.name
417 visitor = getattr(self, method, self.generic_visit)
--> 418 return visitor(node)

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\compilation\codegenerator.py:414, in IntrinsicTransformer.visit_Call(self, node)
413 def visit_Call(self, node):
--> 414 node.func = self.visit(node.func)
415 node.args = [self.visit(a) for a in node.args]
416 node.keywords = {kw.arg: self.visit(kw.value) for kw in node.keywords}

File ~\anaconda3\envs\py3_parcels\lib\ast.py:418, in NodeVisitor.visit(self, node)
416 method = 'visit_' + node.class.name
417 visitor = getattr(self, method, self.generic_visit)
--> 418 return visitor(node)

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\compilation\codegenerator.py:332, in IntrinsicTransformer.visit_Attribute(self, node)
328 raise NotImplementedError("Cannot convert random functions in kernels to C-code.\n"
329 "Use import parcels.rng as ParcelsRandom and then ParcelsRandom.random(), ParcelsRandom.uniform() etc.\n"
330 "For more information, see http://oceanparcels.org/faq.html#kernelwriting")
331 else:
--> 332 raise NotImplementedError(f"Cannot convert '{node.value.id}' used in kernel to C-code")

NotImplementedError: Cannot convert 'logger' used in kernel to C-code

Any assistance or guidance on how to properly incorporate logging into Parcels' kernel functions would be greatly appreciated. Thank you in advance for your help!

[erikvansebille]

You can't use the logger function in C-kernels, because there is no conversion of it from python to C. You can

1. use print-statements in your Kernels (see this part of the Parcels structure tutorial), or
2. run in Scipy-mode (by using a ScipyParticle instead of a JITParticle)

[Cyuan-hub]

Hi, @erikvansebille. Thanks for your kind reply. Based on your suggestions, I reworked the code and ran it again, but the problem is still not resolved.

---

1.When I use "print" -statements in my Kernels, it raises the "RuntimeError", which shows below:

RuntimeError Traceback (most recent call last)
Cell In[9], line 17
14 totaltime_for_running = timedelta(days = 30)
15 running_time_first = timedelta(days = 10)
---> 17 pset.execute(Kernels,
18 runtime = running_time_first,
19 dt = dt,
20 output_file = outputfile,
21 recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
22 ErrorCode.ErrorTimeExtrapolation: DeleteParticle})
24 pset.repeatdt = None
26 pset.execute(Kernels,
27 runtime = timedelta(days = 20),
28 dt = dt,
29 output_file = outputfile,
30 recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
31 ErrorCode.ErrorTimeExtrapolation: DeleteParticle})

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\particleset\baseparticleset.py:433, in BaseParticleSet.execute(self, pyfunc, pyfunc_inter, endtime, runtime, dt, moviedt, recovery, output_file, movie_background_field, verbose_progress, postIterationCallbacks, callbackdt)
431 self.kernel = pyfunc
432 else:
--> 433 self.kernel = self.Kernel(pyfunc)
434 # Prepare JIT kernel execution
435 if self.collection.ptype.uses_jit:

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\particleset\particlesetsoa.py:715, in ParticleSetSOA.Kernel(self, pyfunc, c_include, delete_cfiles)
698 """Wrapper method to convert a pyfunc into a :class:parcels.kernel.Kernel object.
699
700 Conversion is based on fieldset and ptype of the ParticleSet.
(...)
712 (Default value = "")
713 """
714 if isinstance(pyfunc, list):
--> 715 return Kernel.from_list(
716 self.fieldset,
717 self.collection.ptype,
718 pyfunc,
719 c_include=c_include,
720 delete_cfiles=delete_cfiles,
721 )
722 return Kernel(
723 self.fieldset,
724 self.collection.ptype,
(...)
727 delete_cfiles=delete_cfiles,
728 )

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\kernel\basekernel.py:323, in BaseKernel.from_list(cls, fieldset, ptype, pyfunc_list, *args, **kwargs)
320 raise ValueError("Argument function_lst should be a list of functions.")
322 pyfunc_list = pyfunc_list.copy()
--> 323 pyfunc_list[0] = cls(fieldset, ptype, pyfunc_list[0], *args, **kwargs)
324 return functools.reduce(lambda x, y: x + y, pyfunc_list)

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\kernel\kernelsoa.py:98, in KernelSOA.init(self, fieldset, ptype, pyfunc, funcname, funccode, py_ast, funcvars, c_include, delete_cfiles)
96 if self.ptype.uses_jit:
97 kernelgen = KernelGenerator(fieldset, ptype)
---> 98 kernel_ccode = kernelgen.generate(deepcopy(self.py_ast),
99 self.funcvars)
100 self.field_args = kernelgen.field_args
101 self.vector_field_args = kernelgen.vector_field_args

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\compilation\codegenerator.py:526, in AbstractKernelGenerator.generate(self, py_ast, funcvars)
523 py_ast = TupleSplitter().visit(py_ast)
525 # Generate C-code for all nodes in the Python AST
--> 526 self.visit(py_ast)
527 self.ccode = py_ast.ccode
529 # Insert variable declarations for non-instrinsics
530 # Make sure that repeated variables are not declared more than
531 # once. If variables occur in multiple Kernels, give a warning

File ~\anaconda3\envs\py3_parcels\lib\ast.py:418, in NodeVisitor.visit(self, node)
416 method = 'visit_' + node.class.name
417 visitor = getattr(self, method, self.generic_visit)
--> 418 return visitor(node)

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\compilation\codegenerator.py:926, in ArrayKernelGenerator.visit_FunctionDef(self, node)
924 for stmt in node.body:
925 if not (hasattr(stmt, 'value') and type(stmt.value) is ast.Str): # ignore docstrings
--> 926 self.visit(stmt)
928 # Create function declaration and argument list
929 decl = c.Static(c.DeclSpecifier(c.Value("StatusCode", node.name), spec='inline'))

File ~\anaconda3\envs\py3_parcels\lib\ast.py:418, in NodeVisitor.visit(self, node)
416 method = 'visit_' + node.class.name
417 visitor = getattr(self, method, self.generic_visit)
--> 418 return visitor(node)

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\compilation\codegenerator.py:644, in AbstractKernelGenerator.visit_Expr(self, node)
643 def visit_Expr(self, node):
--> 644 self.visit(node.value)
645 node.ccode = c.Statement(node.value.ccode)

File ~\anaconda3\envs\py3_parcels\lib\ast.py:418, in NodeVisitor.visit(self, node)
416 method = 'visit_' + node.class.name
417 visitor = getattr(self, method, self.generic_visit)
--> 418 return visitor(node)

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\compilation\codegenerator.py:599, in AbstractKernelGenerator.visit_Call(self, node)
597 node.ccode = str(c.Statement(s))
598 else:
--> 599 raise RuntimeError("This print statement is not supported in Python3 version of Parcels")
600 else:
601 for a in node.args:

RuntimeError: This print statement is not supported in Python3 version of Parcels

---

2.When I use "from parcels.tools.loggers import logger" and try to run in Scipy-mode, it results in a "KernelError", with the following details:

KernelError Traceback (most recent call last)
Cell In[5], line 17
14 totaltime_for_running = timedelta(days = 30)
15 running_time_first = timedelta(days = 10)
---> 17 pset.execute(Kernels,
18 runtime = running_time_first,
19 dt = dt,
20 output_file = outputfile,
21 recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
22 ErrorCode.ErrorTimeExtrapolation: DeleteParticle})
24 pset.repeatdt = None
26 pset.execute(Kernels,
27 runtime = timedelta(days = 20),
28 dt = dt,
29 output_file = outputfile,
30 recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
31 ErrorCode.ErrorTimeExtrapolation: DeleteParticle})

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\particleset\baseparticleset.py:548, in BaseParticleSet.execute(self, pyfunc, pyfunc_inter, endtime, runtime, dt, moviedt, recovery, output_file, movie_background_field, verbose_progress, postIterationCallbacks, callbackdt)
546 # If we don't perform interaction, only execute the normal kernel efficiently.
547 if self.interaction_kernel is None:
--> 548 self.kernel.execute(self, endtime=next_time, dt=dt, recovery=recovery, output_file=output_file,
549 execute_once=execute_once)
550 # Interaction: interleave the interaction and non-interaction kernel for each time step.
551 # E.g. Inter -> Normal -> Inter -> Normal if endtime-time == 2*dt
552 else:
553 cur_time = time

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\kernel\kernelsoa.py:213, in KernelSOA.execute(self, pset, endtime, dt, recovery, output_file, execute_once)
211 recovery_kernel = recovery_map[p.state]
212 p.set_state(StateCode.Success)
--> 213 recovery_kernel(p, self.fieldset, p.time)
214 if p.isComputed():
215 p.reset_state()

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\tools\statuscodes.py:121, in recovery_kernel_error(particle, fieldset, time)
119 """Default error kernel that throws exception."""
120 msg = f"Error: {particle.exception if particle.exception else None}"
--> 121 raise KernelError(particle, fieldset=fieldset, msg=msg)

KernelError: 0
Particle P[0](lon=113.745598, lat=22.320601, depth=0.000000, beached_time=0.000000, age=0.000000, particle_state=0.000000, unbeachCount=0.000000, beachCount=0.000000, prev_lon=113.745598, prev_lat=22.320601, time=0.000000)
Time: 2020-06-01T12:00:00
timestep dt: 1800.0
Error: name 'logger' is not defined

[erikvansebille]

Hi @Cyuan-hub, can you

1. Give the code of your kernel where you added the print-statements for JIT? Otherwise I can't help debug
2. Add 'import logger' to your Kernel in Scipy mode?

[Cyuan-hub]

Hi, @erikvansebille, thanks for the quick response.

1.The code of my kernel where I added the print-statements for JIT is shows below:

def DeleteParticle(particle, fieldset, time):
particle.delete()
print(f"Particle {particle.id} is deleted at ({particle.lon}, {particle.lat}) at time {time}.")

def Ageing(particle, fieldset, time):
particle.age += particle.dt
print(f"Particle {particle.id} is aging. New age: {particle.age}")

def AdvectionRK4(particle, fieldset, time):
print(f"Particle {particle.id} is advecting at time {time}.")
if particle.particle_state == 0:
(u1, v1) = fieldset.UV[time, particle.depth, particle.lat, particle.lon]
lon1_adv, lat1_adv = (particle.lon + u1 * .5 * particle.dt, particle.lat + v1 * .5 * particle.dt)
(u2, v2) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat1_adv, lon1_adv]
lon2_adv, lat2_adv = (particle.lon + u2 * .5 * particle.dt, particle.lat + v2 * .5 * particle.dt)
(u3, v3) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat2_adv, lon2_adv]
lon3_adv, lat3_adv = (particle.lon + u3 * particle.dt, particle.lat + v3 * particle.dt)
(u4, v4) = fieldset.UV[time + particle.dt, particle.depth, lat3_adv, lon3_adv]
particle.lon += (u1 + 2u2 + 2u3 + u4) / 6. * particle.dt
particle.lat += (v1 + 2v2 + 2v3 + v4) / 6. * particle.dt
particle.particle_state = 2
print("This is a warning message that will be displayed only once.")

def BeachTesting_Adv(particle, fieldset, time):
if particle.particle_state == 2:
part_dis_to_coast1 = fieldset.dist[particle.dt, 0, particle.lat, particle.lon]
beaching_dist1 = 0.1
if part_dis_to_coast1 <= beaching_dist1:
particle.lon = particle.prev_lon
particle.lat = particle.prev_lat
particle.particle_state = 0
particle.unbeachCount += 1
print(f"Particle {particle.id} is returning to water after beach testing.")
else:
particle.particle_state = 0
particle.prev_lon = particle.lon
particle.prev_lat = particle.lat
print(f"Particle {particle.id} is continuing advection after beach testing.")

def StokesDrag(particle, fieldset, time):
if particle.particle_state == 0:
(u_uss, v_uss) = fieldset.UVuss[time, particle.depth, particle.lat, particle.lon]
particle.lon += u_uss * particle.dt
particle.lat += v_uss * particle.dt
particle.particle_state = 3
print(f"Particle {particle.id} is experiencing Stokes drag at time {time}.")

def Beaching_StkDr(particle, fieldset, time):
if particle.particle_state == 3:
part_dis_to_coast2 = fieldset.dist[particle.dt, 0, particle.lat, particle.lon]
beaching_dist2 = 0.1
if part_dis_to_coast2 <= beaching_dist2:
particle.particle_state = 1
particle.delete()
print(f"Particle {particle.id} is beaching due to Stokes drag at time {time}.")
else:
particle.particle_state = 0
particle.prev_lon = particle.lon
particle.prev_lat = particle.lat
print(f"Particle {particle.id} is not beaching after experiencing Stokes drag at time {time}.")

---

2.When I use ''import logger'' in Scipy mode, it results in a "ModuleNotFoundError", with the following details:

ModuleNotFoundError Traceback (most recent call last)
Cell In[1], line 15
13 import glob
14 # from parcels.tools.loggers import logger
---> 15 import logger

ModuleNotFoundError: No module named 'logger'

[erikvansebille]

OK, the two answers below

1. As its says in the tutorial, try simple print statements. the JIT-compiler can't deal with f-strings etc, so try simply print(particle.age)
2. I thought you meant the built-in logging module. I think you should be able to use that in Scipy mode, what you import it in the kernel

[Cyuan-hub]

Hi @erikvansebille, apologies for the delay in responding; I got held up with some things here.

1.I have attempted to use simple print-statements for JIT mode. Currently, I'm only employing a basic kernel to test the print-statements. Below are the modified sections of my kernel where I added the print-statements for JIT:

def DeleteParticle(particle, fieldset, time):
print ('Particle is deleted at '+ str(particle.lon)+' and '+str(particle.lat))
particle.delete()

def AdvectionRK4(particle, fieldset, time):
(u1, v1) = fieldset.UV[time, particle.depth, particle.lat, particle.lon]
lon1_adv, lat1_adv = (particle.lon + u1 * .5 * particle.dt, particle.lat + v1 * .5 * particle.dt)
(u2, v2) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat1_adv, lon1_adv]
lon2_adv, lat2_adv = (particle.lon + u2 * .5 * particle.dt, particle.lat + v2 * .5 * particle.dt)
(u3, v3) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat2_adv, lon2_adv]
lon3_adv, lat3_adv = (particle.lon + u3 * particle.dt, particle.lat + v3 * particle.dt)
(u4, v4) = fieldset.UV[time + particle.dt, particle.depth, lat3_adv, lon3_adv]
particle.lon += (u1 + 2u2 + 2u3 + u4) / 6. * particle.dt
particle.lat += (v1 + 2v2 + 2v3 + v4) / 6. * particle.dt

Kernels= [AdvectionRK4]
out_interval = timedelta(days = 1)
new_output_directory = "G:/JupyterNotebook/SCS_case2/ParcelsOutput/ZarrData/new/"
output_dirstore_name = new_output_directory + "Adv-printTesting2.zarr/"
output_dirstore = zarr.storage.DirectoryStore(output_dirstore_name)
outputfile = pset.ParticleFile(name=output_dirstore, outputdt = out_interval)
dt = timedelta(minutes = 30)
totaltime_for_running = timedelta(days = 30)
running_time_first = timedelta(days = 20)
pset.execute(Kernels,
runtime = running_time_first,
dt = dt,
output_file = outputfile,
recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
ErrorCode.ErrorTimeExtrapolation: DeleteParticle})

pset.repeatdt = None

pset.execute(Kernels,
runtime = timedelta(days = 10),
dt = dt,
output_file = outputfile,
recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
ErrorCode.ErrorTimeExtrapolation: DeleteParticle})

However, upon inspection, I noticed that the results did not include any printed output from the print-statements. The specific output information is as follows:

INFO: Compiled ArrayCustomParticleAdvectionRK4 ==> C:\Users\Lenovo\AppData\Local\Temp\parcels-tmp\lib02ad6336bab067f80c8fb409f77caa46_0.dll
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
INFO: Output files are stored in <zarr.storage.DirectoryStore object at 0x000001AF8D246530>.
0%| | 0/1728000.0 [00:00<?, ?it/s]C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
95%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍ | 1641600.0/1728000.0 [00:00<00:00, 1728316.12it/s]C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1728000.0/1728000.0 [00:02<00:00, 677551.48it/s]
INFO: Compiled ArrayCustomParticleAdvectionRK4 ==> C:\Users\Lenovo\AppData\Local\Temp\parcels-tmp\libe78bc472b1062ef5c53f5359967910a7_0.dll
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')
C:\Users\Lenovo\anaconda3\envs\py3_parcels\lib\site-packages\numpy\core\numeric.py:330: RuntimeWarning: invalid value encountered in cast
multiarray.copyto(a, fill_value, casting='unsafe')

---

2.When I use "import logging" in Scipy mode, it yields a "KernelError: 0" along with an 'Error: name 'logging' is not defined'. The detailed error information is as follows:

KernelError Traceback (most recent call last)
Cell In[5], line 17
14 totaltime_for_running = timedelta(days = 30)
15 running_time_first = timedelta(days = 10)
---> 17 pset.execute(Kernels,
18 runtime = running_time_first,
19 dt = dt,
20 output_file = outputfile,
21 recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
22 ErrorCode.ErrorTimeExtrapolation: DeleteParticle})
24 pset.repeatdt = None
26 pset.execute(Kernels,
27 runtime = timedelta(days = 20),
28 dt = dt,
29 output_file = outputfile,
30 recovery = {ErrorCode.ErrorOutOfBounds: DeleteParticle,
31 ErrorCode.ErrorTimeExtrapolation: DeleteParticle})

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\particleset\baseparticleset.py:548, in BaseParticleSet.execute(self, pyfunc, pyfunc_inter, endtime, runtime, dt, moviedt, recovery, output_file, movie_background_field, verbose_progress, postIterationCallbacks, callbackdt)
546 # If we don't perform interaction, only execute the normal kernel efficiently.
547 if self.interaction_kernel is None:
--> 548 self.kernel.execute(self, endtime=next_time, dt=dt, recovery=recovery, output_file=output_file,
549 execute_once=execute_once)
550 # Interaction: interleave the interaction and non-interaction kernel for each time step.
551 # E.g. Inter -> Normal -> Inter -> Normal if endtime-time == 2*dt
552 else:
553 cur_time = time

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\kernel\kernelsoa.py:213, in KernelSOA.execute(self, pset, endtime, dt, recovery, output_file, execute_once)
211 recovery_kernel = recovery_map[p.state]
212 p.set_state(StateCode.Success)
--> 213 recovery_kernel(p, self.fieldset, p.time)
214 if p.isComputed():
215 p.reset_state()

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\tools\statuscodes.py:121, in recovery_kernel_error(particle, fieldset, time)
119 """Default error kernel that throws exception."""
120 msg = f"Error: {particle.exception if particle.exception else None}"
--> 121 raise KernelError(particle, fieldset=fieldset, msg=msg)

KernelError: 0
Particle P[0](lon=113.745598, lat=22.320601, depth=0.000000, beached_time=0.000000, age=0.000000, particle_state=0.000000, unbeachCount=0.000000, beachCount=0.000000, prev_lon=113.745598, prev_lat=22.320601, time=0.000000)
Time: 2019-01-01T12:00:00
timestep dt: 1800.0
Error: name 'logging' is not defined

---

The version of Python I'm using is Python 3.10.12. It's puzzling that the error 'name 'logging' is not defined' still occurs when importing the built-in logging module.
Here's a snippet of the code from my kernel in Scipy mode:

def DeleteParticle(particle, fieldset, time):
particle.delete()

def Ageing(particle, fieldset, time):
particle.age += particle.dt
logging.debug("testtestetst")

def AdvectionRK4(particle, fieldset, time):
if particle.particle_state == 0:
(u1, v1) = fieldset.UV[time, particle.depth, particle.lat, particle.lon]
lon1_adv, lat1_adv = (particle.lon + u1*.5particle.dt, particle.lat + v1.5particle.dt
(u2, v2) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat1_adv, lon1_adv]
lon2_adv, lat2_adv = (particle.lon + u2.5particle.dt, particle.lat + v2.5particle.dt)
(u3, v3) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat2_adv, lon2_adv]
lon3_adv, lat3_adv = (particle.lon + u3particle.dt, particle.lat + v3particle.dt)
(u4, v4) = fieldset.UV[time + particle.dt, particle.depth, lat3_adv, lon3_adv]
particle.lon += (u1 + 2u2 + 2u3 + u4) / 6. * particle.dt
particle.lat += (v1 + 2v2 + 2*v3 + v4) / 6. * particle.dt
particle.particle_state = 2

Kernels= [AdvectionRK4, Ageing]

---

Thank you for your time, and I look forward to any thoughts or advice you might share.