id,node_id,number,title,user,state,locked,assignee,milestone,comments,created_at,updated_at,closed_at,author_association,active_lock_reason,draft,pull_request,body,reactions,performed_via_github_app,state_reason,repo,type
2215890029,I_kwDOAMm_X86EE8xt,8894,Rolling reduction with a custom function generates an excesive use of memory that kills the workers,25071375,closed,0,,,8,2024-03-29T19:15:28Z,2024-04-01T20:57:59Z,2024-03-30T01:49:17Z,CONTRIBUTOR,,,,"### What happened?
Hi, I have been trying to use a custom function on the rolling reduction method, the original function tries to filter the nan values (any numpy function that I have used that handles nans generates the same problem) to later apply some simple aggregate functions, but it is killing all my workers even when the data is very small (I have 7 workers and all of them have 3 Gb of RAM).
### What did you expect to happen?
I would expect less use of memory taking into account the size of the rolling window, the simplicity of the function and the amount of data used on the example.
### Minimal Complete Verifiable Example
```Python
import numpy as np
import dask.array as da
import xarray as xr
import dask
def f(x, axis):
# If I replace np.nansum by np.sum everything works perfectly and the amount of memory used is very small
return np.nansum(x, axis=axis)
arr = xr.DataArray(
dask.array.zeros(
shape=(300, 30000),
dtype=float,
chunks=(30, 6000)
),
dims=[""a"", ""b""],
coords={""a"": list(range(300)), ""b"": list(range(30000))}
)
arr.rolling(a=252).reduce(f).chunk({""a"": 252}).to_zarr(""/data/test/test_write"", mode=""w"")
```
### MVCE confirmation
- [X] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
- [X] Complete example — the example is self-contained, including all data and the text of any traceback.
- [X] Verifiable example — the example copy & pastes into an IPython prompt or [Binder notebook](https://mybinder.org/v2/gh/pydata/xarray/main?urlpath=lab/tree/doc/examples/blank_template.ipynb), returning the result.
- [X] New issue — a search of GitHub Issues suggests this is not a duplicate.
- [ ] Recent environment — the issue occurs with the latest version of xarray and its dependencies.
### Relevant log output
```Python
KilledWorker: Attempted to run task ('nansum-overlap-sum-aggregate-sum-aggregate-e732de6ad917d5f4084b05192ca671c4', 0, 0) on 4 different workers, but all those workers died while running it. The last worker that attempt to run the task was tcp://172.18.0.2:39937. Inspecting worker logs is often a good next step to diagnose what went wrong. For more information see https://distributed.dask.org/en/stable/killed.html.
```
### Anything else we need to know?
_No response_
### Environment
INSTALLED VERSIONS
------------------
commit: None
python: 3.11.7 | packaged by conda-forge | (main, Dec 23 2023, 14:43:09) [GCC 12.3.0]
python-bits: 64
OS: Linux
OS-release: 4.14.275-207.503.amzn2.x86_64
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: en_US.UTF-8
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.14.3
libnetcdf: None
xarray: 2024.1.0
pandas: 2.2.1
numpy: 1.26.3
scipy: 1.11.4
netCDF4: None
pydap: None
h5netcdf: None
h5py: 3.10.0
Nio: None
zarr: 2.16.1
cftime: None
nc_time_axis: None
iris: None
bottleneck: 1.3.7
dask: 2024.1.0
distributed: 2024.1.0
matplotlib: 3.8.2
cartopy: None
seaborn: 0.13.1
numbagg: 0.7.0
fsspec: 2023.12.2
cupy: None
pint: None
sparse: 0.15.1
flox: 0.8.9
numpy_groupies: 0.10.2
setuptools: 69.0.3
pip: 23.3.2
conda: 23.11.0
pytest: 7.4.4
mypy: None
IPython: 8.20.0
sphinx: None
","{""url"": ""https://api.github.com/repos/pydata/xarray/issues/8894/reactions"", ""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,completed,13221727,issue
865206283,MDU6SXNzdWU4NjUyMDYyODM=,5210,Probable error using zarr process synchronizer,25071375,closed,0,,,1,2021-04-22T17:05:10Z,2023-10-14T20:36:18Z,2023-10-14T20:36:18Z,CONTRIBUTOR,,,,"Hi I was trying to use Xarray open_zarr with the Zarr ProcessSynchronizer class and it produces a set of errors, I don't know if those errors are produced because I don't understand the logic of the ProcessSynchronizer or is a simple bug. I have a small code which reproduces the problems, basically, if I put a different path in the Zarr ProcessSynchronizer class all the error disappear but it creates a new folder.
```python
import xarray
import zarr
import numpy as np
arr = xarray.DataArray(
data=np.array([
[1, 2, 7, 4, 5],
[np.nan, 3, 5, 5, 6],
[3, 3, np.nan, 5, 6],
[np.nan, 3, 10, 5, 6],
[np.nan, 7, 8, 5, 6],
], dtype=float),
dims=['index', 'columns'],
coords={'index': [0, 1, 2, 3, 4], 'columns': [0, 1, 2, 3, 4]},
)
# If the synchronizer is created using another path the code will work without any error but it creates a new folder,
# that is the correct way to use the process synchronizer?
# synchronizer = zarr.ProcessSynchronizer('dummy_array.sync')
# Using the original path produce a set of weird problems
synchronizer = zarr.ProcessSynchronizer('dummy_array')
# Executing the commented code I obtain: PermissionError: [WinError 5].
# arr.to_dataset(name='data').to_zarr('dummy_array', mode='w', synchronizer=synchronizer, compute=True)
arr.to_dataset(name='data').to_zarr('dummy_array', mode='w', compute=True)
# If this section of the code is uncommented It will throw a different error when xarray.open_zarr being executed
# a = zarr.open_array('dummy_array/data', synchronizer=synchronizer, mode='r')
# PermissionError: [Errno 13] Permission denied
xarray.open_zarr('dummy_array', synchronizer=synchronizer)
```
Output of xr.show_versions()
INSTALLED VERSIONS
------------------
commit: None
python: 3.8.5 (default, Sep 3 2020, 21:29:08) [MSC v.1916 64 bit (AMD64)]
python-bits: 64
OS: Windows
OS-release: 10
machine: AMD64
processor: Intel64 Family 6 Model 165 Stepping 2, GenuineIntel
byteorder: little
LC_ALL: None
LANG: None
LOCALE: es_ES.cp1252
libhdf5: 1.10.4
libnetcdf: None
xarray: 0.17.0
pandas: 1.1.3
numpy: 1.19.2
scipy: 1.5.2
netCDF4: None
pydap: None
h5netcdf: None
h5py: 2.10.0
Nio: None
zarr: 2.7.1
cftime: None
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: 1.3.2
dask: 2.30.0
distributed: 2.30.1
matplotlib: 3.3.2
cartopy: None
seaborn: 0.11.0
numbagg: None
pint: None
setuptools: 50.3.1.post20201107
pip: 21.0.1
conda: 4.10.0
pytest: 6.2.3
IPython: 7.19.0
sphinx: 3.2.1
","{""url"": ""https://api.github.com/repos/pydata/xarray/issues/5210/reactions"", ""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,completed,13221727,issue
1088893989,I_kwDOAMm_X85A5zQl,6112,Forward Fill not working when there are all-NaN chunks,25071375,closed,0,,,6,2021-12-27T01:27:05Z,2022-01-03T17:55:59Z,2022-01-03T17:55:59Z,CONTRIBUTOR,,,,"
**What happened**: I'm working with a report dataset that only has data on some specific periods of time, the problem is that when I use the forward fill method it returns me many nans even on the last cells (it's a forward fill without limit).
**What you expected to happen**: The array should not have nans in the last cells if it has data in any other cell or there should be a warning somewhere.
**Minimal Complete Verifiable Example**:
```python
import xarray as xr
xr.DataArray(
[1, 2, np.nan, np.nan, np.nan, np.nan],
dims=['a']
).chunk(
2
).ffill(
'a'
).compute()
```
output: array([ 1., 2., 2., 2., nan, nan])
**Anything else we need to know?**: I check a little bit the internal code of Xarray for forward filling when it use dask and I think that the problem is that the algorithm makes an initial forward fill on all the blocks and then it makes a map_overlap for forward filling between chunks which in case that there is an empty chunk will not work due that it is going to take the last value of the empty chunk which is nan (hope this help).
**Environment**:
Output of xr.show_versions()
INSTALLED VERSIONS
------------------
commit: None
python: 3.10.0 | packaged by conda-forge | (default, Nov 20 2021, 02:25:18) [GCC 9.4.0]
python-bits: 64
OS: Linux
OS-release: 5.4.0-1025-aws
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: en_US.UTF-8
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: None
libnetcdf: None
xarray: 0.20.2
pandas: 1.3.5
numpy: 1.21.4
scipy: None
netCDF4: None
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: 2.10.3
cftime: None
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: 1.3.2
dask: 2021.12.0
distributed: 2021.12.0
matplotlib: None
cartopy: None
seaborn: None
numbagg: None
fsspec: 2021.11.1
cupy: None
pint: None
sparse: None
setuptools: 59.4.0
pip: 21.3.1
conda: None
pytest: 6.2.5
IPython: 7.30.1
sphinx: None
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