Division by zero error with SOSE data

[shanicetbailey]

Hi, I am just rerunning old notebooks but am now getting an error I haven't gotten before with this code. Below I have attached a simplified version using xhistogram's histogram function on regular SOSE salt data and only specifying salt_bins as an argument (no weights or dims specified for simplicity). Below is the error message. I have run this on regular ECCO data and it works with this template...not sure what's going on and would appreciate anyone shedding some light. Thanks!

import xarray as xr
from xhistogram.xarray import histogram
import gcsfs

#Load in data
fs = gcsfs.GCSFileSystem(requester_pays=True)
mapping = fs.get_mapper('gcs://pangeo-ecco-sose')
ds = xr.open_zarr(mapping, consolidated=True)
ds

#create salt bins
salt_bins = np.arange(32, 38.1, 0.1)

test = histogram(ds.SALT, bins=[salt_bins])
test.load() #this is where the error occurs

Error message:

ZeroDivisionError: integer division or modulo by zero

[rabernat]

Can you post the full stack trace?

[rabernat]

Looks the same as #16

[shanicetbailey]

ZeroDivisionError Traceback (most recent call last)
Cell In [15], line 1
----> 1 test.load()

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/core/dataarray.py:967, in DataArray.load(self, **kwargs)
949 def load(self: T_DataArray, **kwargs) -> T_DataArray:
950 """Manually trigger loading of this array's data from disk or a
951 remote source into memory and return this array.
952
(...)
965 dask.compute
966 """
--> 967 ds = self._to_temp_dataset().load(**kwargs)
968 new = self._from_temp_dataset(ds)
969 self._variable = new._variable

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xarray/core/dataset.py:733, in Dataset.load(self, **kwargs)
730 import dask.array as da
732 # evaluate all the dask arrays simultaneously
--> 733 evaluated_data = da.compute(*lazy_data.values(), **kwargs)
735 for k, data in zip(lazy_data, evaluated_data):
736 self.variables[k].data = data

File /srv/conda/envs/notebook/lib/python3.9/site-packages/dask/base.py:600, in compute(traverse, optimize_graph, scheduler, get, *args, **kwargs)
597 keys.append(x.dask_keys())
598 postcomputes.append(x.dask_postcompute())
--> 600 results = schedule(dsk, keys, **kwargs)
601 return repack([f(r, *a) for r, (f, a) in zip(results, postcomputes)])

File /srv/conda/envs/notebook/lib/python3.9/site-packages/distributed/client.py:3052, in Client.get(self, dsk, keys, workers, allow_other_workers, resources, sync, asynchronous, direct, retries, priority, fifo_timeout, actors, **kwargs)
3050 should_rejoin = False
3051 try:
-> 3052 results = self.gather(packed, asynchronous=asynchronous, direct=direct)
3053 finally:
3054 for f in futures.values():

File /srv/conda/envs/notebook/lib/python3.9/site-packages/distributed/client.py:2226, in Client.gather(self, futures, errors, direct, asynchronous)
2224 else:
2225 local_worker = None
-> 2226 return self.sync(
2227 self._gather,
2228 futures,
2229 errors=errors,
2230 direct=direct,
2231 local_worker=local_worker,
2232 asynchronous=asynchronous,
2233 )

File /srv/conda/envs/notebook/lib/python3.9/site-packages/distributed/utils.py:339, in SyncMethodMixin.sync(self, func, asynchronous, callback_timeout, *args, **kwargs)
337 return future
338 else:
--> 339 return sync(
340 self.loop, func, *args, callback_timeout=callback_timeout, **kwargs
341 )

File /srv/conda/envs/notebook/lib/python3.9/site-packages/distributed/utils.py:406, in sync(loop, func, callback_timeout, *args, **kwargs)
404 if error:
405 typ, exc, tb = error
--> 406 raise exc.with_traceback(tb)
407 else:
408 return result

File /srv/conda/envs/notebook/lib/python3.9/site-packages/distributed/utils.py:379, in sync..f()
377 future = asyncio.wait_for(future, callback_timeout)
378 future = asyncio.ensure_future(future)
--> 379 result = yield future
380 except Exception:
381 error = sys.exc_info()

File /srv/conda/envs/notebook/lib/python3.9/site-packages/tornado/gen.py:762, in Runner.run(self)
759 exc_info = None
761 try:
--> 762 value = future.result()
763 except Exception:
764 exc_info = sys.exc_info()

File /srv/conda/envs/notebook/lib/python3.9/site-packages/distributed/client.py:2089, in Client._gather(self, futures, errors, direct, local_worker)
2087 exc = CancelledError(key)
2088 else:
-> 2089 raise exception.with_traceback(traceback)
2090 raise exc
2091 if errors == "skip":

File /srv/conda/envs/notebook/lib/python3.9/site-packages/dask/optimization.py:990, in call()
988 if not len(args) == len(self.inkeys):
989 raise ValueError("Expected %d args, got %d" % (len(self.inkeys), len(args)))
--> 990 return core.get(self.dsk, self.outkey, dict(zip(self.inkeys, args)))

File /srv/conda/envs/notebook/lib/python3.9/site-packages/dask/core.py:149, in get()
147 for key in toposort(dsk):
148 task = dsk[key]
--> 149 result = _execute_task(task, cache)
150 cache[key] = result
151 result = _execute_task(out, cache)

File /srv/conda/envs/notebook/lib/python3.9/site-packages/dask/core.py:119, in _execute_task()
115 func, args = arg[0], arg[1:]
116 # Note: Don't assign the subtask results to a variable. numpy detects
117 # temporaries by their reference count and can execute certain
118 # operations in-place.
--> 119 return func(*(_execute_task(a, cache) for a in args))
120 elif not ishashable(arg):
121 return arg

File /srv/conda/envs/notebook/lib/python3.9/site-packages/dask/core.py:119, in ()
115 func, args = arg[0], arg[1:]
116 # Note: Don't assign the subtask results to a variable. numpy detects
117 # temporaries by their reference count and can execute certain
118 # operations in-place.
--> 119 return func(*(_execute_task(a, cache) for a in args))
120 elif not ishashable(arg):
121 return arg

File /srv/conda/envs/notebook/lib/python3.9/site-packages/dask/core.py:113, in _execute_task()
83 """Do the actual work of collecting data and executing a function
84
85 Examples
(...)
110 'foo'
111 """
112 if isinstance(arg, list):
--> 113 return [_execute_task(a, cache) for a in arg]
114 elif istask(arg):
115 func, args = arg[0], arg[1:]

File /srv/conda/envs/notebook/lib/python3.9/site-packages/dask/core.py:113, in ()
83 """Do the actual work of collecting data and executing a function
84
85 Examples
(...)
110 'foo'
111 """
112 if isinstance(arg, list):
--> 113 return [_execute_task(a, cache) for a in arg]
114 elif istask(arg):
115 func, args = arg[0], arg[1:]

File /srv/conda/envs/notebook/lib/python3.9/site-packages/dask/core.py:119, in _execute_task()
115 func, args = arg[0], arg[1:]
116 # Note: Don't assign the subtask results to a variable. numpy detects
117 # temporaries by their reference count and can execute certain
118 # operations in-place.
--> 119 return func(*(_execute_task(a, cache) for a in args))
120 elif not ishashable(arg):
121 return arg

File /srv/conda/envs/notebook/lib/python3.9/site-packages/dask/utils.py:71, in apply()
40 """Apply a function given its positional and keyword arguments.
41
42 Equivalent to func(*args, **kwargs)
(...)
68 >>> dsk = {'task-name': task} # adds the task to a low level Dask task graph
69 """
70 if kwargs:
---> 71 return func(*args, **kwargs)
72 else:
73 return func(*args)

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xhistogram/core.py:236, in _bincount()
233 else:
234 weights_array = None
--> 236 bin_counts = _bincount_2d_vectorized(
237 *all_arrays_reshaped,
238 bins=bins,
239 weights=weights_array,
240 density=density,
241 block_size=block_size,
242 )
244 final_shape = kept_axes_shape + bin_counts.shape[1:]
245 bin_counts = reshape(bin_counts, final_shape)

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xhistogram/core.py:185, in _bincount_2d_vectorized()
182 # total number of unique bin indices
183 N = reduce(lambda x, y: x * y, hist_shapes)
--> 185 bin_counts = _dispatch_bincount(
186 bin_indices, weights, N, hist_shapes, block_size=block_size
187 )
189 # just throw out everything outside of the bins, as np.histogram does
190 # TODO: make this optional?
191 slices = (slice(None),) + (N_inputs * (slice(1, -1),))

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xhistogram/core.py:129, in _dispatch_bincount()
126 def _dispatch_bincount(bin_indices, weights, N, hist_shapes, block_size=None):
127 # block_chunks is like a dask chunk, a tuple that divides up the first
128 # axis of bin_indices
--> 129 block_chunks = _determine_block_chunks(bin_indices, block_size)
130 if len(block_chunks) == 1:
131 # single global chunk, don't need a loop over chunks
132 return _bincount_2d(bin_indices, weights, N, hist_shapes)

File /srv/conda/envs/notebook/lib/python3.9/site-packages/xhistogram/core.py:117, in _determine_block_chunks()
115 block_size = min(_MAX_CHUNK_SIZE // N, M)
116 assert isinstance(block_size, int)
--> 117 num_chunks = M // block_size
118 block_chunks = num_chunks * (block_size,)
119 residual = M % block_size

ZeroDivisionError: integer division or modulo by zero

[shanicetbailey]

@rabernat, I was just going to tag #16, and am going to try the workaround of chunking .

[rabernat]

do you know if ds.SALT is a dask array?

[shanicetbailey]

It's an xarray.DataArray

[shanicetbailey]

So trying to rechunk salt data ds.SALT.chunk({'time':-1, 'XC':-1, 'YC':-1, 'Z':-1}) and seems to not be producing an error...however, I am unsure because when I try to run test.load() on the new salt variable it initially runs but the workers freeze..

I have tried with ds.SALT.chunk({'time':-1, 'XC':5, 'YC':5, 'Z':-1}) and that seemed to work, but took way longer than the run for ECCO data and with no need to rechunk. I guess I'll stick with this workaround 🤷‍♀️.

[AxelHenningsson]

+1 to fixing this.

[TomNicholas]

I'm going to close this as a duplicate of #16.

To get around this bug you can use block_size=None though, see #16 (comment).