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update to dask 0.18.0 #66

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merged 11 commits into from
Nov 1, 2018
Merged

update to dask 0.18.0 #66

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ab791ac
update to dask 0.18.0
kain88-de Sep 20, 2018
f6980f7
test with strings
kain88-de Sep 20, 2018
56dd56a
remove unused imports
kain88-de Sep 20, 2018
cc11410
Merge branch 'master' into new-dask
orbeckst Oct 29, 2018
5103271
replaced get --> scheduler in leaflet and use 'multiprocessing' as st…
orbeckst Oct 29, 2018
19166c2
tests: scheduler fixture: return 'multiprocessing' as string
orbeckst Oct 29, 2018
8686767
test leaflet with n_jobs=-1 (but XFAIL it)
orbeckst Oct 30, 2018
d71eb98
enable new dask 0.18 scheduler selection idoms
kain88-de Oct 30, 2018
6f54546
fix missing import
kain88-de Oct 30, 2018
51c1b5d
respect new dask.config global selection of scheduler
orbeckst Oct 31, 2018
dd88867
bumped MDAnalysis requirement to 0.19.0
orbeckst Oct 31, 2018
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10 changes: 5 additions & 5 deletions pmda/parallel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
from six.moves import range

import MDAnalysis as mda
from dask import distributed, multiprocessing
from dask import distributed
from dask.delayed import delayed
from joblib import cpu_count
import numpy as np
Expand Down Expand Up @@ -291,13 +291,13 @@ def run(self,

"""
if scheduler is None:
scheduler = multiprocessing
scheduler = 'multiprocessing'

if n_jobs == -1:
n_jobs = cpu_count()

if n_blocks is None:
if scheduler == multiprocessing:
if scheduler == 'multiprocessing':
n_blocks = n_jobs
elif isinstance(scheduler, distributed.Client):
n_blocks = len(scheduler.ncores())
Expand All @@ -306,8 +306,8 @@ def run(self,
"Couldn't guess ideal number of blocks from scheduler."
"Please provide `n_blocks` in call to method.")

scheduler_kwargs = {'get': scheduler.get}
if scheduler == multiprocessing:
scheduler_kwargs = {'scheduler': scheduler}
if scheduler == 'multiprocessing':
scheduler_kwargs['num_workers'] = n_jobs

start, stop, step = self._trajectory.check_slice_indices(
Expand Down
4 changes: 2 additions & 2 deletions pmda/test/test_parallel.py
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Expand Up @@ -14,7 +14,7 @@
from MDAnalysisTests.datafiles import DCD, PSF
import joblib

from dask import distributed, multiprocessing
from dask import distributed

from pmda import parallel

Expand Down Expand Up @@ -95,7 +95,7 @@ def scheduler(request, client):
if request.param == 'distributed':
return client
else:
return multiprocessing
return request.param
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This is cool: so now we will be able to expand to all schedulers that dask supports by just adding strings to the fixture parametrization.



def test_scheduler(analysis, scheduler):
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -49,7 +49,7 @@
packages=find_packages(),
install_requires=[
'MDAnalysis>=0.18',
'dask',
'dask>=0.18',
'six',
'joblib', # cpu_count func currently
],
Expand Down