Repository navigation
Description
We have a dataset stored across multiple netCDF files. We are getting very slow performance with open_mfdataset, and I would like to improve this.
Each individual netCDF file looks like this:
%time ds_single = xr.open_dataset('float_trajectories.0000000000.nc')
ds_singleCPU times: user 14.9 ms, sys: 48.4 ms, total: 63.4 ms
Wall time: 60.8 ms
<xarray.Dataset>
Dimensions: (npart: 8192000, time: 1)
Coordinates:
* time (time) datetime64[ns] 1993-01-01
* npart (npart) int32 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ...
Data variables:
z (time, npart) float32 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 ...
vort (time, npart) float32 -9.71733e-10 -9.72858e-10 -9.73001e-10 ...
u (time, npart) float32 0.000545563 0.000544884 0.000544204 ...
v (time, npart) float32 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ...
x (time, npart) float32 180.016 180.047 180.078 180.109 180.141 ...
y (time, npart) float32 -79.9844 -79.9844 -79.9844 -79.9844 ...
As shown above, a single data file opens in ~60 ms.
When I call open_mdsdataset on 49 files (each with a different time dimension but the same npart), here is what happens:
%time ds = xr.open_mfdataset('*.nc', )
dsCPU times: user 1min 31s, sys: 25.4 s, total: 1min 57s
Wall time: 2min 4s
<xarray.Dataset>
Dimensions: (npart: 8192000, time: 49)
Coordinates:
* npart (npart) int64 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ...
* time (time) datetime64[ns] 1993-01-01 1993-01-02 1993-01-03 ...
Data variables:
z (time, npart) float64 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 ...
vort (time, npart) float64 -9.717e-10 -9.729e-10 -9.73e-10 -9.73e-10 ...
u (time, npart) float64 0.0005456 0.0005449 0.0005442 0.0005437 ...
v (time, npart) float64 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ...
x (time, npart) float64 180.0 180.0 180.1 180.1 180.1 180.2 180.2 ...
y (time, npart) float64 -79.98 -79.98 -79.98 -79.98 -79.98 -79.98 ...
It takes over 2 minutes to open the dataset. Specifying concat_dim='time' does not improve performance.
Here is %prun of the open_mfdataset command.
748994 function calls (724222 primitive calls) in 142.160 seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno(function)
49 62.455 1.275 62.458 1.275 {method 'get_indexer' of 'pandas.index.IndexEngine' objects}
49 47.207 0.963 47.209 0.963 base.py:1067(is_unique)
196 7.198 0.037 7.267 0.037 {operator.getitem}
49 4.632 0.095 4.687 0.096 netCDF4_.py:182(_open_netcdf4_group)
240 3.189 0.013 3.426 0.014 numeric.py:2476(array_equal)
98 1.937 0.020 1.937 0.020 {numpy.core.multiarray.arange}
4175/3146 1.867 0.000 9.296 0.003 {numpy.core.multiarray.array}
49 1.525 0.031 119.144 2.432 alignment.py:251(reindex_variables)
24 1.065 0.044 1.065 0.044 {method 'cumsum' of 'numpy.ndarray' objects}
12 1.010 0.084 1.010 0.084 {method 'sort' of 'numpy.ndarray' objects}
5227/4035 0.660 0.000 1.688 0.000 collections.py:50(__init__)
12 0.600 0.050 3.238 0.270 core.py:2761(insert)
12691/7497 0.473 0.000 0.875 0.000 indexing.py:363(shape)
110728 0.425 0.000 0.663 0.000 {isinstance}
12 0.413 0.034 0.413 0.034 {method 'flatten' of 'numpy.ndarray' objects}
12 0.341 0.028 0.341 0.028 {numpy.core.multiarray.where}
2 0.333 0.166 0.333 0.166 {pandas._join.outer_join_indexer_int64}
1 0.331 0.331 142.164 142.164 <string>:1(<module>)
It looks like most of the time is being spent on reindex_variables. I understand why this happens...xarray needs to make sure the dimensions are the same in order to concatenate them together.
Is there any obvious way I could improve the load time? For example, can I give a hint to xarray that this reindex_variables step is not necessary, since I know that all the npart dimensions are the same in each file?
Activity
rabernat commentedon Apr 26, 2017
cc: @geosciz, who is helping with this project.
shoyer commentedon Apr 26, 2017
Yes, adding an boolean argument
prealignedwhich defaults toFalsetoconcatseems like a very reasonable optimization here.But more generally, I am a little surprised by how slow
pandas.Index.get_indexerandpandas.Index.is_uniqueare. This suggests we should add a fast-path optimization to skip these steps inreindex_variables:xarray/xarray/core/alignment.py
Lines 302 to 306 in ab4ffee
Basically, if
index.equals(target), we should just setindexer = np.arange(target.size). Although, if we have duplicate values in the index, the operation should arguably fail for correctness.rabernat commentedon Mar 2, 2018
An update on this long-standing issue.
I have learned that
open_mfdatasetcan be blazingly fast ifdecode_cf=Falsebut extremely slow withdecode_cf=True.As an example, I am loading a POP datataset on cheyenne. Anyone with access can try this example.
And returns this
This is roughly 45 years of daily data, one file per year.
Instead, if I just change

decode_cf=True(the default), it takes forever. I can monitor what is happening via the distributed dashboard. It looks like this:There are more of these
open_datasettasks then there are number of files (45), so I can only presume there are 16401 individual tasks (one for each timestep), which each takes about 1 s in serial.This is a real failure of lazy decoding. Maybe it can be fixed by #1725, possibly related to #1372.
cc Pangeo folks: @jhamman, @mrocklin
shoyer commentedon Mar 2, 2018
@rabernat How does performance compare if you call
xarray.decode_cf()on the opened dataset? The adjustments I recently did to lazy decoding should only help once the data is already loaded into dask.rabernat commentedon Mar 9, 2018
Calling
ds = xr.decode_cf(ds, decode_times=False)on the dataset returns instantly. However, the variable data is wrapped in the adaptors, effectively destroying the chunksCalling getitem on this array triggers the whole dask array to be computed, which would takes forever and would completely blow out the notebook memory. This is because of #1372, which would be fixed by #1725.
This has actually become a major showstopper for me. I need to work with this dataset in decoded form.
Versions
Details
INSTALLED VERSIONS ------------------ commit: None python: 3.6.4.final.0 python-bits: 64 OS: Linux OS-release: 3.12.62-60.64.8-default machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8xarray: 0.10.1
pandas: 0.22.0
numpy: 1.13.3
scipy: 1.0.0
netCDF4: 1.3.1
h5netcdf: 0.5.0
h5py: 2.7.1
Nio: None
zarr: 2.2.0a2.dev176
bottleneck: 1.2.1
cyordereddict: None
dask: 0.17.1
distributed: 1.21.3
matplotlib: 2.1.2
cartopy: 0.15.1
seaborn: 0.8.1
setuptools: 38.4.0
pip: 9.0.1
conda: None
pytest: 3.3.2
IPython: 6.2.1
shoyer commentedon Mar 9, 2018
OK, so it seems that we need a change to disable wrapping dask arrays with
LazilyIndexedArray. Dask arrays are already lazy!shoyer commentedon Nov 10, 2018
Was this fixed by #2047?
chuaxr commentedon Nov 15, 2018
I can confirm that
is much faster (seconds vs minutes) than
. For reference, data_fnames is a list of 5 files, each of which is ~75 GB.
shoyer commentedon Nov 15, 2018
@chuaxr I assume you're testing this with xarray 0.11?
It would be good to do some profiling to figure out what is going wrong here.
chuaxr commentedon Nov 15, 2018
Yes, I'm on 0.11.
Nothing displays on the task stream/ progress bar when using
open_mfdataset, although I can monitor progress when, say, computing the mean.The output from
%timeusingdecode_cf = Falseisand for decode_cf = True:
Using
xr.set_options(file_cache_maxsize=1)doesn't make any noticeable difference.If I repeat the open_mfdataset for another 5 files (after opening the first 5), I occasionally get this warning:
distributed.utils_perf - WARNING - full garbage collections took 24% CPU time recently (threshold: 10%)I only began using the dashboard recently; please let me know if there's something basic I'm missing.
shoyer commentedon Nov 16, 2018
@chuaxr What do you see when you use
%prunwhen opening the dataset? This might point to the bottleneck.One way to fix this would be to move our call to
decode_cf()inopen_dataset()to after applying chunking, i.e., to switch up the order of operations on these lines:xarray/xarray/backends/api.py
Lines 270 to 296 in f547ed0
In practice, is the difference between using xarray's internal lazy array classes for decoding and dask for decoding. I would expect to see small differences in performance between these approaches (especially when actually computing data), but for constructing the computation graph I would expect them to have similar performance. It is puzzling that dask is orders of magnitude faster -- that suggests that something else is going wrong in the normal code path for
decode_cf(). It would certainly be good to understand this before trying to apply any fixes.chuaxr commentedon Nov 16, 2018
Sorry, I think the speedup had to do with accessing a file that had previously been loaded rather than due to
decode_cf. Here's the output ofprunusing two different files of approximately the same size (~75 GB), run from a notebook without using distributed (which doesn't lead to any speedup):Output of
%prun ds = xr.open_mfdataset('/work/xrc/AM4_skc/atmos_level.1999010100-2000123123.sphum.nc',chunks={'lat':20,'time':50,'lon':12,'pfull':11})
Output of
%prun ds = xr.open_mfdataset('/work/xrc/AM4_skc/atmos_level.2001010100-2002123123.temp.nc',chunks={'lat':20,'time':50,'lon':12,'pfull':11},
decode_cf=False)
/work isn't a remote archive, so it surprises me that this should happen.
shoyer commentedon Nov 16, 2018
28 remaining items
shoyer commentedon Aug 28, 2023
@fraserwg do you know what the performance bottleneck is in your case? (i.e., if you interrupt the comptuation, what is being computed?)
dcherian commentedon Aug 31, 2023
It is very common for different netCDF files in a "dataset" (a folder) to be encoded differently so we can't set
decode_cf=Falseby default.There's
parallelto help a bit here.data_vars='minimal', coords='minimal', compat='override'is a common choice.What your describing sounds like a failure of lazy decoding or a
cftimeslowdown (example)which should be fixed. If you can provide a reproducible example, that would help.fraserwg commentedon Sep 7, 2023
@shoyer I will double check what the bottle neck is and report back. @dcherian interestingly, the
paralleloption doesn't seem to do anything whendecode_cf=True. From looking at the dask dashboard it seems to load each file sequentially, with each opening being carried out by a different worker but not concurrently. I will see what I can do minimal example wise!ashjbarnes commentedon Feb 21, 2024
I'm another person who stumbled across this thread, and found that
decode_cf = Falsefix to work really well.I appreciate that we can't set this by default, but maybe this could be put into the docstring of
open_mfdatasetdirectly? It appears to be passed as a kwarg, so is hard to find despite it being such a helpful fix for so many people in this thread!It also seems like the
decode_cfstep is done in serial. My dask cluster has plenty of workers but whendecode_cfis set to True it only processes one of my (many) files at a time. Switching todecode_cf = Falseand the task stream shows my entire cluster being utilised. Perhaps this is part of the issue?xarray version: 2024.2.0
dcherian commentedon Feb 22, 2024
@ashjbarnes Are you able to share two small files that illustrate the issue?
ashjbarnes commentedon Feb 22, 2024
@dcherian Thanks, the files are shared in this google drive folder.
This is a spatial subsample of the same files. Perhaps it's a bad idea to store static data like the lat/lon coordinates in each file? The overall size of this is so tiny compared to the 4D data that I left the coordinates there for convenience but I'm not sure whether this has broader implications.
In my tests, running:
on ~3000 files of 300mb each had an order of magnitude speedup over the same command with
decode_cf = Trueon xarray 2024.2.0. The real files are chunked on disk in time and theybdimensiondcherian commentedon Feb 22, 2024
Wow, thank you!
This is an amazing bug. The defaults say
data_vars="all", coords="different"which means always concatenate all data_vars along the concat dimensions (here inferred to be "time") but only concatenate coords if they differ in the different files.When
decode_cf=False,lat,lonare data_vars and get concatenated without any checking or reading.When
decode_cf=True,lat,lonare promoted to coords, then get checked for equality across all files. The two variables get read sequentially from all files. This is the slowdown you see.Once again, this is a consequence of bad defaults for
concatandopen_mfdataset.I would follow https://docs.xarray.dev/en/stable/user-guide/io.html#reading-multi-file-datasets and use
data_vars="minimal", coords="minimal", compat="override"which will only concatenate those variables with the time dimension, and skip any checking for variables that don't have a time dimension (simply pick the variable from the first file).ashjbarnes commentedon Feb 22, 2024
Well done @dcherian great find! Changing the defaults does seem like a really good idea in this case
hannahzafar commentedon Mar 13, 2024
@dcherian I am yet another person stumbling on this problem. Unfortunately
decode_cf = Falseseems to overridedecode_times=True(https://stackoverflow.com/questions/77243075/xarray-wont-decode-times-from-netcdf-file-with-decode-cf-false-even-if-decode) so you cannot use that fix if you want to maintain datetime objects.dcherian commentedon Mar 13, 2024
A simpler fix is probably
decode_coords=Falserabernat commentedon Mar 14, 2024
This issue is almost seven years old! It has been "fixed" many times since my original post, but people keep finding new ways to make it reappear. 😆
It seems like having better diagnostics / logging of what is happening under the hood with open_mfdataset is what people really need. Maybe even some sort of utility to pre-scan the files and figure out if they are easily openable or not.
jtomfarrar commentedon Mar 14, 2024
Both of those seem like great ideas. Maybe there could be a verbose or logging mode to help users identify what is wrong with the files (e.g., where the time is being spent and whether that seems suspicious). It is probably true that people (like me) will keep finding new ways to generate problematic netcdf files. (I'm sure we can think of something even worse than 20 Hz data referenced to a time origin 75 years ago).
Simplify and speed up open_mfdataset
dcherian commentedon Aug 1, 2025
We've just merged #10062 from @jsignell , so after the next release (v2025.08.0) you should be able to use
xr.set_options(use_new_combine_kwarg_defaults=True)to get much more consistent behaviour that does not load data by default.If you're stopping by this issue, please try your workload with this setting.