Index out of bounds ERROR

[imariaguiar]

Hello there, I was running this 3D simulation for the years 2008 to 2021, everything ran fine until the year of 2018, but starting from the year 2019, I received an error. I've already checked my velocity field data and everything seems okay. Does anyone have any ideas on what I might be doing wrong?

This is my code for the pset and execution, below is the error I get when running from 2019 onwards.

npart_lat = 25
npart_depth = 30

lons = np.linspace(-23, -23, npart_lat)
lats = np.linspace(1, -1, npart_lat)
depths = np.linspace(0, 290, npart_depth)

periodos = ['DJF','MAM','JJA','SON']

for ano in range(2019,2022):
for periodo in periodos:
if periodo == 'DJF':
start_date = datetime.date(ano - 1, 12, 1)
elif periodo == 'MAM':
start_date = datetime.date(ano, 3, 1)
elif periodo == 'JJA':
start_date = datetime.date(ano, 6, 1)
elif periodo == 'SON':
start_date = datetime.date(ano, 9, 1)

    output_file_name = f'euc_sec_{periodo}_{ano}.zarr'
    
    pset = ParticleSet(fieldset=fieldset,
                       pclass=ScipyParticle,
                       lon=np.repeat(lons, npart_depth),
                       lat=np.repeat(lats, npart_depth),
                       depth=np.tile(depths, npart_lat),
                       time=start_date)
    
    output_file = pset.ParticleFile(name=output_file_name, outputdt=delta(hours=24))

    pset.execute(AdvectionRK4_3D,
                 runtime=delta(days=90),
                 dt=delta(hours=6),
                 moviedt=delta(hours=24),
                 output_file=output_file,
                 recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})  

IndexError                                Traceback (most recent call last)
Cell In[70], line 37
     34 output_file = pset.ParticleFile(name=output_file_name, outputdt=delta(hours=24))
     36 # executando a simulação
---> 37 pset.execute(AdvectionRK4_3D,
     38              runtime=delta(days=90),
     39              dt=delta(hours=6),
     40              moviedt=delta(hours=24),
     41              output_file=output_file,
     42              recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})       

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\particleset\baseparticleset.py:427, in BaseParticleSet.execute(self, pyfunc, pyfunc_inter, endtime, runtime, dt, moviedt, recovery, output_file, movie_background_field, verbose_progress, postIterationCallbacks, callbackdt)
    425 next_movie = time + moviedt if dt > 0 else time - moviedt
    426 next_callback = time + callbackdt if dt > 0 else time - callbackdt
--> 427 next_input = self.fieldset.computeTimeChunk(time, np.sign(dt)) if self.fieldset is not None else np.inf
    429 tol = 1e-12
    430 if verbose_progress is None:

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\fieldset.py:1079, in FieldSet.computeTimeChunk(self, time, dt)
   1077             fb.close()
   1078         fb = None
-> 1079     data = f.computeTimeChunk(data, tind)
   1080 data = f.rescale_and_set_minmax(data)
   1082 if (isinstance(f.data, DeferredArray)):

File ~\anaconda3\envs\py3_parcels\lib\site-packages\parcels\field.py:1394, in Field.computeTimeChunk(self, data, tindex)
   1391     timestamp = self.timestamps[np.where(ti < summedlen)[0][0]]
   1393 rechunk_callback_fields = self.chunk_setup if isinstance(tindex, list) else None
-> 1394 filebuffer = self._field_fb_class(self.dataFiles[g.ti + tindex], self.dimensions, self.indices,
   1395                                   netcdf_engine=self.netcdf_engine, timestamp=timestamp,
   1396                                   interp_method=self.interp_method,
   1397                                   data_full_zdim=self.data_full_zdim,
   1398                                   chunksize=self.chunksize,
   1399                                   rechunk_callback_fields=rechunk_callback_fields,
   1400                                   chunkdims_name_map=self.netcdf_chunkdims_name_map,
   1401                                   netcdf_decodewarning=self.netcdf_decodewarning)
   1402 filebuffer.__enter__()
   1403 time_data = filebuffer.time

IndexError: index 4352 is out of bounds for axis 0 with size 4352

[erikvansebille]

Dear @imariaguiar, thanks for using Parcels and for reporting this problem. From the error message, it seems that something went wrong with the time dimension when creating your fieldset. Did you use timestamps, by any chance? Could it be that one variables has fewer time-slices than another?

By the way, it seems that you use a very old version of Parcels; is there a reason for that? We are now at v3.0.2; I recommend running with the latest version as much as possible. Note that e.g. recovery has changed after v3, see https://docs.oceanparcels.org/en/latest/examples/tutorial_kernelloop.html#Working-with-Status-Codes