Thank you @TomNicholas - strangely I can't reproduce it anymore on my local machine - it all happened on our slurm. The result is correct according to the input file index. In my case I calculated annual and seasonal climate variables on the same input files, but the matrix index i,j were different. One with upper left corner (0,0) and the other one with (0,1167) - as shown in ncview. Nevertheless here is what I did - you can test it with https://www.unidata.ucar.edu/software/netcdf/examples/sresa1b_ncar_ccsm3-example.nc:

```python

import numpy as np import xarray as xr

chunks=4

lonrange=256 latrange=128

creating the chunks - our slurm can't handle dask_jobqueue and dask chunking wasnt possible as well

x=[x.tolist() for x in np.array_split(range(lonrange), chunks)] xextend = [[sublist[0],sublist[-1]] for sublist in x]

y=[y.tolist() for y in np.array_split(range(latrange), chunks)] yextend = [[sublist[0],sublist[-1]] for sublist in y]

concatenating the chunks

allChunks = [[x,y] for x in xextend for y in yextend]

for k in range(0,chunks*chunks):

inter = str(k)

tas = xr.open_dataset('~/pathToFile/sresa1b_ncar_ccsm3-example.nc').isel(longitude=slice(min(allChunks[k][0]), max(allChunks[k][0])), latitude=slice(min(allChunks[k][1]), max(allChunks[k][1])))
    ##instead of my climate calculations
tas.rename({'tas':'test1'}).to_netcdf('~/pathToFile/climateCalculation1_'+inter+'.nc')
tas.rename({'tas':'test2'}).to_netcdf('~/pathToFile/climateCalculation2_'+inter+'.nc')

#combining the single data arrays per chunk
    ##combine using nested
with xr.open_mfdataset('~/pathToFile/climateCalculation*'+inter+'.nc', chunks=-1, parallel=True, engine='h5netcdf', combine='nested') as ds:
    ds.to_netcdf('~/pathToFile/nestedClimateAnnualCalculations_'+inter+'.nc')
    #combine using default coords
    with xr.open_mfdataset('~/pathToFile/climateCalculation*'+inter+'.nc', chunks=-1, parallel=True, engine='h5netcdf') as ds:
        ds.to_netcdf('~/pathToFile/climateAnnualCalculations_'+inter+'.nc')

combining all chunks to one final file

nested input

with xr.open_mfdataset('~/pathToFile/climateCalculations/nestedClimateAnnualCalculations_*', chunks=-1, parallel=True, engine='h5netcdf') as ds:
ds.to_netcdf('~/pathToFile/climateAnnualCalculationsCombinedNested.nc')

with xr.open_mfdataset('~/pathToFile/climateCalculations/climateAnnualCalculations_*', chunks=-1, parallel=True, engine='h5netcdf') as ds:
ds.to_netcdf('~/pathToFile/climateAnnualCalculationsCombined.nc')

```