OutOfBoundsError: 0

[Xyx105]

Hi,

I keep getting a "OutOfBoundsError: 0" error. I have tried the fix in #973 but I still keep getting the same error.

Here is my code:
`filenames = {
"U": {
"lon": f"output.nc",
"lat": f"output.nc",
"data": f"NC Files/NEATL*.nc",
},
"V": {
"lon": f"output.nc",
"lat": f"output.nc",
"data": f"NC Files/NEATL*.nc",
},
}

variables = {'U': 'u',
'V': 'v'}

dimensions = {"lon": "lon_u", "lat": "lat_u", "time": "ocean_time"}

indices = {'depth' : [40]}

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

#indices = {'depth' : [40]}

fieldset.computeTimeChunk(fieldset.U.grid.time[0], 6)
fieldset.computeTimeChunk(fieldset.V.grid.time[0], 6)

npart = 1
lonp = 4.7
latp = 60

pset = ParticleSet.from_list(fieldset, JITParticle, lon=lonp, lat=latp, )

pfile = ParticleFile("nemo_particles", pset, outputdt=delta(days=5))
kernels = pset.Kernel(AdvectionRK4)

pset.show(fieldset.U)

pset.execute(kernels, runtime=delta(days=1), dt=delta(hours=6), output_file=pfile)`

It produces this result

and I get this error message:
`---------------------------------------------------------------------------
OutOfBoundsError Traceback (most recent call last)
Cell In[16], line 82
78 kernels = pset.Kernel(AdvectionRK4)
80 pset.show(fieldset.U)
---> 82 pset.execute(kernels, runtime=delta(days=1), dt=delta(hours=6), output_file=pfile)

File ~\Anaconda3\envs\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\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\parcels\Lib\site-packages\parcels\tools\statuscodes.py:182, in recovery_kernel_out_of_bounds(particle, fieldset, time)
178 """Default sampling error kernel that throws OutOfBoundsError."""
179 if particle.exception is None:
180 # TODO: JIT does not yet provide the context that created
181 # the exception. We need to pass that info back from C.
--> 182 raise OutOfBoundsError(particle, fieldset)
183 else:
184 error = particle.exception

OutOfBoundsError: 0
Particle P[14](lon=4.700000, lat=60.000000, depth=0.000000, time=0.000000)
Time: 2022-01-01T00:00:00.000000000
timestep dt: 3600.0
Out-of-bounds sampling by particle at (4.7, 60.0, 0.0)`

Any idea why this is happening?

[michaeldenes]

Hi @Xyx105,

I'm not entirely sure what is causing your error, could you paste in the result of:
print(np.min(fieldset.U.lon), np.max(fieldset.U.lon), np.min(fieldset.U.lat), np.max(fieldset.U.lat))

Additionally, you're loading in the 40th level of your depth, but your particle is initialised at depth 0m (so even if your code didn't throw an error, your particle is unlikely to move about).

Cheers,
Michael

[Xyx105]

Hi @michaeldenes

Here is the output of that:
9.96921e+36 9.96921e+36 9.96921e+36 9.96921e+36

This doesn't seem normal. Let me know what you think.

Regards,
Jack

[michaeldenes]

Hi @Xyx105,
That is indeed quite odd! The longitudes/latitudes should have a fairly normal range (e.g. [-180,180) and [-90,90], respectively).
What does the grid of your velocity data look like? Could you share the full example of your code?

Thanks,
Michael

[Xyx105]

Hi @michaeldenes the first timestep on my grid can be found here: https://drive.google.com/file/d/1QNQ06ycDU0BQVCaAuiLMJ4AqetqVHa_m/view?usp=drive_link

My code looks like this`from parcels import( AdvectionRK4,
FieldSet,
JITParticle,
ParticleFile,
ParticleSet,
AdvectionRK4_3D,
ErrorCode,
)
from netCDF4 import Dataset
from datetime import timedelta
from glob import glob
import numpy as np
from scipy.interpolate import interp2d, RectBivariateSpline
from datetime import timedelta as delta
from os import path
import glob
import numpy as np
import netCDF4 as nc
import pandas as pd
import xarray as xr
import matplotlib.pyplot as plt

filenames = {
"U": {
"lon": f"output.nc",
"lat": f"output.nc",
"data": f"NC Files/NEATL*.nc",
},
"V": {
"lon": f"output.nc",
"lat": f"output.nc",
"data": f"NC Files/NEATL*.nc",
},
}

variables = {'U': 'u',
'V': 'v'}

dimensions = {"lon": "lon_u", "lat": "lat_u", "time": "ocean_time"}

#indices = {'depth' : [40]}

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

#indices = {'depth' : [40]}

fieldset.computeTimeChunk(fieldset.U.grid.time[0], 6)
fieldset.computeTimeChunk(fieldset.V.grid.time[0], 6)

npart = 1
lonp = 4.7
latp = 60

pset = ParticleSet.from_list(fieldset, JITParticle, lon=lonp, lat=latp, )

print(np.min(fieldset.U.lon),
np.max(fieldset.U.lon),
np.min(fieldset.U.lat),
np.max(fieldset.U.lat))

pfile = ParticleFile("nemo_particles", pset, outputdt=delta(days=5))
kernels = pset.Kernel(AdvectionRK4)

pset.show(fieldset.U)

pset.execute(kernels, runtime=delta(days=1), dt=delta(hours=6), output_file=pfile)`

[michaeldenes]

Hi @Xyx105, I've had a look at your dataset, but I get a different outcome using the following code snippet

import numpy as np
from parcels import FieldSet

variables = {'U': 'u', 'V': 'v'}
dimensions = {"lon": "lon_u", "lat": "lat_u", "time": "ocean_time"}
fieldset = FieldSet.from_nemo('data/NEATL*.nc', variables, dimensions, allow_time_extrapolation=True)

print(np.min(fieldset.U.lon), np.max(fieldset.U.lon), np.min(fieldset.U.lat), np.max(fieldset.U.lat))

Which produces:
(-12.663201, 0.1604333, 49.012863, 56.72801)

I'm not sure what's in your output.nc files, but maybe there is something wrong in there.

Additionally, if you have a look at where your data is, the position (4.7°E, 60°N) isn't inside your fieldset.

If I place a particle inside that coloured box, I get the desired outcome.

Cheers,
Michael

[Cyuan-hub]

Hi @Xyx105, may I ask if your question has been resolved? If so, how was it resolved?

[keli559]

I have the same error, out-of-bounds error. And code
from parcels import ErrorCode
Does not work. It is telling me ErrorCode doesn't exist. I know this code was working last year.

[erikvansebille]

Yes indeed, since Parcels v3.0, we have changed the way that Errors are dealt with. This is not backward-compatible, hence the error when you import ErrorCode.

You can now write a Kernel (see example below) and add that as a normal Kernel to your pset.execute():

def DeleteErrorParticle(particle, fieldset, time):
    if particle.state >= 40:  # deletes every particle that throws an error
        particle.delete()

See also this part of the Kernel Loop tutorial