Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fixes for new openmmtools 0.23.0 #1203

Merged
merged 28 commits into from
Jun 15, 2023
Merged
Changes from 1 commit
Commits
Show all changes
28 commits
Select commit Hold shift + click to select a range
bd4c691
change default to none
mikemhenry Apr 18, 2023
a235671
Merge branch 'main' into feat/set_default_to_none_for_atom_selection
mikemhenry Apr 25, 2023
2820950
Changing default in template yaml file
ijpulidos May 30, 2023
a71fc09
Test null/none atom selection
ijpulidos May 30, 2023
0226dd5
null atom selection should be empty list
ijpulidos May 30, 2023
bd3a6e6
Merge branch 'main' into feat/set_default_to_none_for_atom_selection
ijpulidos May 30, 2023
3de54db
Document how to control the log level in the CLI
mikemhenry May 30, 2023
26046e7
Update examples/new-cli/README.md
mikemhenry May 31, 2023
754baa1
Add solvent_model kwarg to RelativeFEPSetup
ijpulidos Jun 5, 2023
135dc60
Specify solvent model input YAML/CLI
ijpulidos Jun 5, 2023
24dfaa0
Test openmmtools_dev
mikemhenry Jun 9, 2023
41bff85
Update CI.yaml
mikemhenry Jun 9, 2023
851f822
Update CI.yaml
mikemhenry Jun 9, 2023
6364535
make sure we pull in openmmtools
mikemhenry Jun 9, 2023
65fae3b
forgot to add new env file
mikemhenry Jun 9, 2023
d061e90
Online analysis multiple of checkpoint interval. Fix tests.
ijpulidos Jun 9, 2023
0474f9a
Using dask import inside functions
ijpulidos Jun 9, 2023
1505004
Merge branch 'feat/set_default_to_none_for_atom_selection' into mikem…
ijpulidos Jun 9, 2023
1a7f712
Merge remote-tracking branch 'origin/mikemhenry-patch-2' into mikemhe…
ijpulidos Jun 9, 2023
cd0e440
Merge branch '1192-add-solvent-model-cli' into mikemhenry-patch-3
ijpulidos Jun 9, 2023
8cfbb49
dask import inside functions
ijpulidos Jun 9, 2023
2df9be9
Pinning dask version
ijpulidos Jun 9, 2023
cae139e
set CI to just pull from normal channels since we pushed update
mikemhenry Jun 12, 2023
273c880
Drop 3.8 testing
mikemhenry Jun 12, 2023
0149438
Testing with ambertools < 23
ijpulidos Jun 13, 2023
7a38a07
Revert "Merge branch '1192-add-solvent-model-cli' into mikemhenry-pat…
ijpulidos Jun 15, 2023
ca3c43e
Revert "Merge remote-tracking branch 'origin/mikemhenry-patch-2' into…
ijpulidos Jun 15, 2023
6afba88
Revert "Merge branch 'feat/set_default_to_none_for_atom_selection' in…
ijpulidos Jun 15, 2023
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Using dask import inside functions
  • Loading branch information
ijpulidos committed Jun 9, 2023
commit 0474f9ae4c1904fba4cc0bf3bb7a52ab7142ec05
4 changes: 3 additions & 1 deletion perses/dispersed/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@
import time
from collections import namedtuple
from perses.annihilation.lambda_protocol import LambdaProtocol
import dask.distributed as distributed
from scipy.special import logsumexp
import openmmtools.cache as cache

Expand Down Expand Up @@ -1117,6 +1116,7 @@ def activate_LocallyOptimalAnnealing(thermodynamic_state,
"""
Function to set worker attributes for annealing.
"""
import dask.distributed as distributed
supported_integrators = ['langevin', 'hmc']

if remote_worker == 'remote':
Expand All @@ -1142,6 +1142,7 @@ def deactivate_worker_attributes(remote_worker):
"""
Function to remove worker attributes for annealing
"""
import dask.distributed as distributed
if remote_worker == 'remote':
_logger.debug(f"\t\tremote_worker is True, getting worker")
_class = distributed.get_worker()
Expand All @@ -1168,6 +1169,7 @@ def call_anneal_method(remote_worker,
since we can only map functions with parallelisms (no actors), we need to submit a function that calls
the LocallyOptimalAnnealing.anneal method.
"""
import dask.distributed as distributed
if remote_worker == 'remote':
_class = distributed.get_worker()
else:
Expand Down