jhamman/chains

A Snakemake workflow for the chain of models approach to hydrologic modeling

Chains Snakemake workflow

This is a Snakemake workflow for building ensembles of hydrologic model simulations from various climate forcings. The workflow implements a "chain-of-models" configuration that includes reading from existing downscaling datasets, meteorological disaggregation, hydrologic modeling, and streamflow routing. This work was developed specifically to support the Quantitative Hydrologic Storylines project.

Authors

• Joe Hamman (@jhamman)

Usage

Step 1: Install workflow

If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.

In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).

Step 2: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml.

Step 3: Execute workflow

Test your configuration by performing a dry-run via

snakemake -n

Execute the workflow locally via

snakemake --cores $N

using $N cores or run it in a cluster environment via

snakemake --cluster qsub --jobs 100

or

snakemake --drmaa --jobs 100

See the Snakemake documentation for further details.

Testing

Tests cases are in the subfolder .test. They should be executed via continuous integration with Travis CI. -- TODO

chains's Issues

Test case broken: renaming wind

After commenting out the preproc step in #1 it can successfully open files, but then it tries to rename the wind variable which doesn't exist in these files, does it need to create a constant wind=1-2m/s variable first :

...loading data...
renaming
<xarray.Dataset>
Dimensions:           (bound: 2, latitude: 6, longitude: 5, time: 54787)
Coordinates:
  * latitude          (latitude) float32 48.0625 48.1875 ... 48.5625 48.6875
  * longitude         (longitude) float32 -121.1875 -121.0625 ... -120.6875
  * time              (time) datetime64[ns] 1950-01-01 1950-01-02 ... 2099-12-31
Dimensions without coordinates: bound
Data variables:
    bounds_latitude   (time, latitude, bound) float64 48.0 48.12 ... 48.62 48.75
    bounds_longitude  (time, longitude, bound) float64 -121.2 -121.1 ... -120.6
    pr                (time, latitude, longitude) float32 18.118 12.0409 ... 0.0
    tasmax            (time, latitude, longitude) float32 -4.23 -8.21 ... -15.16
    tasmin            (time, latitude, longitude) float32 -12.67 ... -23.33
Attributes:
    Conventions:        GDT 1.2
    file_name:          conus_c5.cnrm-cm5_rcp45_r1i1p1.daily.pr.1950.nc
    History:            Archived Dec 2013
    authors:            Wood, A. and Mizukami, N., with codes from T. Pruitt,...
    description:        Daily 1/8th Degree CONUS Meteorology
    creation_date:      2013
    institution:        NCAR
    SurfSgnConvention:  Traditional
[Tue Mar 12 17:08:41 2019]
Error in rule downscaling:
    jobid: 0
    output: /glade/scratch/gutmann/storylines/test_data/CNRM-CM5/hist/bcsd/downscaling_data/downscale.CNRM-CM5.hist.bcsd.nc
    log: /glade/scratch/gutmann/storylines/test_data/CNRM-CM5/hist/bcsd/logs/downscale.CNRM-CM5.hist.bcsd.20190312-170812.log.txt

RuleException:
ValueError in line 73 of /gpfs/fs1/work/gutmann/storylines/chains/downscaling.snakefile:
cannot rename 'wind' because it is not a variable or dimension in this dataset
  File "/gpfs/fs1/work/gutmann/storylines/chains/downscaling.snakefile", line 176, in __rule_downscaling
  File "/gpfs/fs1/work/gutmann/storylines/chains/downscaling.snakefile", line 73, in process_downscaling_dataset
...a few more internal errors that probably aren't relevant...

Test case broken: file concatenation preprocessing

I've tried to run the test case described in the storylines workflow and I get an error I don't understand :

$ snakemake hydrology_models --configfile ../storylines_test_data/test_config.yml
... a whole bunch of good output I can paste if you want...
Error in rule downscaling:
    jobid: 0
    output: /glade/scratch/gutmann/storylines/test_data/CNRM-CM5/hist/bcsd/downscaling_data/downscale.CNRM-CM5.hist.bcsd.nc
    log: /glade/scratch/gutmann/storylines/test_data/CNRM-CM5/hist/bcsd/logs/downscale.CNRM-CM5.hist.bcsd.20190312-145812.log.txt

RuleException:
ValueError in line 67 of /gpfs/fs1/work/gutmann/storylines/chains/downscaling.snakefile:
cannot broadcast shape (6, 2) to shape (365, 6, 365)
  File "/gpfs/fs1/work/gutmann/storylines/chains/downscaling.snakefile", line 176, in __rule_downscaling
  File "/gpfs/fs1/work/gutmann/storylines/chains/downscaling.snakefile", line 67, in process_downscaling_dataset
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/backends/api.py", line 658, in open_mfdataset
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/combine.py", line 552, in _auto_combine
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/combine.py", line 474, in _combine_nd
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/combine.py", line 492, in _auto_combine_all_along_first_dim
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/combine.py", line 510, in _auto_combine_1d
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/combine.py", line 510, in <listcomp>
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/combine.py", line 368, in _auto_concat
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/combine.py", line 122, in concat
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/combine.py", line 307, in _dataset_concat
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/variable.py", line 1978, in concat
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/combine.py", line 300, in ensure_common_dims
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/variable.py", line 1188, in set_dims
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/xarray/core/duck_array_ops.py", line 46, in f
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/site-packages/dask/array/core.py", line 3228, in broadcast_to
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
An error occurred
Complete log: /gpfs/fs1/work/gutmann/storylines/chains/.snakemake/log/2019-03-12T145813.750351.snakemake.log

I copied over the test case storylines_test_data to my work dir, and changed the test_config.yml working dir from flash to a directory in my scratch space. The key error seems to be ValueError in line 67 of /gpfs/fs1/work/gutmann/storylines/chains/downscaling.snakefile: cannot broadcast shape (6, 2) to shape (365, 6, 365)
line 67 is :

    ds = xr.open_mfdataset(sorted(input_files),
                           preprocess=preproc,
                           engine='netcdf4').load()

Looking at the files, all seem to have a primary variable that is (time, lat, lon) and all seem to have the same lat, lon, bounds dimensions. All bounds_lat, bounds_lon variables seem to have the correct dimensions. The broadcast error above looks like there is a file with bounds_latitude(time, latitude, time), but I don't see anything like that. Any ideas?

Metsim error

Error in rule run_metsim_rcp:

RuleException:
CalledProcessError in line 61 of /gpfs/fs1/work/gutmann/storylines/chains/metsim.snakefile:
Command 'set -euo pipefail;  /glade/u/home/jhamman/miniconda3/envs/storylines/bin/ms -s distributed -n 1 /glade/scratch/gutmann/storylines/test_data/CNRM-CM5/rcp85/icar/configs/config.CNRM-CM5.rcp85.icar.metsim.60.cfg > /glade/scratch/gutmann/storylines/test_data/CNRM-CM5/rcp85/icar/logs/disagg.CNRM-CM5.rcp85.icar.metsim.60.20190314-135414.log.txt 2>&1' returned non-zero exit status 1.
  File "/gpfs/fs1/work/gutmann/storylines/chains/metsim.snakefile", line 61, in __rule_run_metsim_rcp
  File "/glade/u/home/gutmann/anaconda3/envs/storylines/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
An error occurred
Complete log: /gpfs/fs1/work/gutmann/storylines/chains/.snakemake/log/2019-03-14T135411.527609.snakemake.log