Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / choderalab/openmmtools issues and pull requests

#713 - Example for running REMD on multiple GPUs

Issue - State: closed - Opened by msuruzhon over 1 year ago - 1 comment

#712 - MultiStateReporter variable pos/vel save frequency

Pull Request - State: open - Opened by richardjgowers over 1 year ago - 3 comments

#711 - Release notes for 0.23.1

Pull Request - State: closed - Opened by mikemhenry over 1 year ago

#710 - Fix/issue 708

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 4 comments

#709 - Fix Issue 708

Pull Request - State: closed - Opened by mikemhenry over 1 year ago

#708 - online_analysis_interval can no longer be None

Issue - State: closed - Opened by xiki-tempula over 1 year ago - 2 comments
Labels: :bug: bug, :arrow_up: high-priority

#707 - Fix FIREMinimizer

Issue - State: open - Opened by jchodera over 1 year ago
Labels: :arrow_up: high-priority, medium-effort

#706 - Release 0.22.2

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 1 comment

#705 - Fix issue with test that would run forever

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 3 comments

#704 - Fixes issue #694

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 1 comment

#703 - Option for reporter to not create checkpoints

Issue - State: open - Opened by ijpulidos over 1 year ago
Labels: :stars: enhancement

#702 - drop python 3.8, add python 3.11 to CI

Pull Request - State: open - Opened by mikemhenry over 1 year ago - 1 comment

#701 - manually casting objects to np arrays when reading checkpoint

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 8 comments

#700 - Errors when resuming simulations from storage with recent numba 0.57

Issue - State: closed - Opened by ijpulidos over 1 year ago - 3 comments

#699 - report mode GPU is in and write out gpu UUID

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 7 comments

#698 - Importing everything in utils module

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 4 comments

#697 - [ENH] Utility for catching GPUs in exclusive mode

Issue - State: closed - Opened by IAlibay over 1 year ago - 16 comments
Labels: :stars: enhancement, low-effort

#696 - [ENH] Expose swap attempts for ReplicaExchangeSampler

Issue - State: open - Opened by IAlibay over 1 year ago - 3 comments
Labels: :stars: enhancement, low-effort

#694 - NetCDF files set the application to YANK - change to openmmtools?

Issue - State: closed - Opened by IAlibay over 1 year ago - 7 comments

#693 - Don't output nvidia-smi failure in automated platform search

Issue - State: closed - Opened by IAlibay over 1 year ago - 5 comments

#692 - Appending real time stats

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 7 comments

#691 - Real-time analysis YAML files should append, not overwrite

Issue - State: closed - Opened by jchodera over 1 year ago - 2 comments
Labels: medium-priority, low-effort

#690 - [WIP] Add explicit deletion to contexts in ContextCache on empty

Pull Request - State: open - Opened by dotsdl over 1 year ago - 6 comments
Labels: :bug: bug, :arrow_up: high-priority

#689 - Should there be an extra context cache clearing in `multistatesampler.__del__`?

Issue - State: open - Opened by IAlibay over 1 year ago - 1 comment
Labels: :bug: bug, :arrow_up: high-priority, low-effort

#688 - Ensure ContextCache deletes all Context objects when it cleans up

Issue - State: open - Opened by jchodera over 1 year ago
Labels: :arrow_up: high-priority

#685 - Release 0.22.1

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 1 comment

#684 - Fix NaN-catching text in MultiStateSampler

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 3 comments

#682 - alchemical sterics exclude sigma

Issue - State: open - Opened by Dan-Burns over 1 year ago - 2 comments

#681 - Improve robustness of sampling test for harmonic oscillator

Issue - State: open - Opened by ijpulidos over 1 year ago
Labels: testing, low-priority

#680 - Release 0.22.0

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 1 comment

#679 - INFO logging level for iteration

Pull Request - State: closed - Opened by ijpulidos over 1 year ago

#678 - Create analysis module/notebook

Issue - State: open - Opened by zhang-ivy over 1 year ago

#677 - set pymbar version when testing openmm dev

Pull Request - State: closed - Opened by mikemhenry over 1 year ago

#675 - backwards deserialization compatibility

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 2 comments

#674 - ThermodynamicState.system and get_system() behavior

Issue - State: closed - Opened by LilDojd over 1 year ago

#673 - Timing information at INFO logging level

Pull Request - State: closed - Opened by ijpulidos over 1 year ago

#672 - Replacing Fire minimization with LocalEnergyMinimizer

Pull Request - State: open - Opened by ijpulidos over 1 year ago - 14 comments

#671 - Set level to `INFO` for timing information for iteration

Issue - State: closed - Opened by jchodera about 2 years ago - 3 comments

#670 - update self hosted runner to use new setup

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 2 comments

#669 - Add gentle equilibration protocol as utility function

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 2 comments

#668 - Use `LocalEnergyMinimizer` instead of `FireMinimizer`

Issue - State: open - Opened by ijpulidos over 1 year ago - 1 comment

#667 - [Question] How to specify platform info for ReplicaExchangeSampler

Issue - State: open - Opened by lucl13 over 1 year ago - 1 comment

#666 - incompatible with the netCDF4 stack

Issue - State: closed - Opened by xiki-tempula over 1 year ago - 15 comments

#664 - [Question] How to XmlSerializer.serialize a SamplerState?

Issue - State: open - Opened by lucl13 over 1 year ago - 1 comment

#662 - Avoid expecting a fixed index/order in forces -- Fix windows tests

Pull Request - State: closed - Opened by ijpulidos over 1 year ago

#661 - Change test framework to pytest

Issue - State: open - Opened by ijpulidos over 1 year ago - 2 comments
Labels: :stars: enhancement, testing

#660 - Comply with Openmm 8 global default values

Pull Request - State: closed - Opened by ijpulidos over 1 year ago

#659 - Pymbar 3 4

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 9 comments

#658 - Report caught exceptions as warnings in base integrator move

Pull Request - State: closed - Opened by ijpulidos over 1 year ago

#656 - Alchemical Regions do not Interact / Clarification

Issue - State: closed - Opened by Dan-Burns almost 2 years ago - 2 comments

#655 - Fix tests - avoid creation of diferent default values for global parameters

Issue - State: open - Opened by ijpulidos almost 2 years ago
Labels: testing, :arrow_up: high-priority

#654 - Not using zlib for varying length variables when storing in NetCDF

Pull Request - State: closed - Opened by ijpulidos almost 2 years ago - 2 comments

#653 - Use micromamba in CI

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 2 comments

#651 - Store a subset of the particles in the simulation

Issue - State: open - Opened by ijpulidos almost 2 years ago
Labels: :stars: enhancement, medium-priority

#650 - Blow up when decoupling a molecule in vacuum

Issue - State: closed - Opened by xiki-tempula almost 2 years ago - 1 comment

#649 - Testing with OpenMM RC

Pull Request - State: closed - Opened by ijpulidos almost 2 years ago - 2 comments

#648 - [Question] How to parallelize replicas in REMD simulations?

Issue - State: open - Opened by felixmusil almost 2 years ago - 3 comments

#647 - `multistateanalyzer` fails with 1 unsampled endstate

Issue - State: open - Opened by dominicrufa almost 2 years ago

#646 - Latest Numpy Release Deprecations (e.g. numpy.float) Break Code

Issue - State: closed - Opened by sametz almost 2 years ago - 1 comment

#645 - Eliminate `FireMinimizer` in multistate sampler.

Issue - State: open - Opened by ijpulidos almost 2 years ago

#644 - Update docstring default for alchemical_pme_treatment

Pull Request - State: open - Opened by IAlibay almost 2 years ago - 2 comments

#643 - BaseIntegratorMove does not distinguish between reasons for Exceptions

Issue - State: closed - Opened by jchodera almost 2 years ago - 4 comments
Labels: error handling, :arrow_up: high-priority, low-effort

#642 - Multi-GPU HREMD trajectory output

Issue - State: closed - Opened by Dan-Burns almost 2 years ago - 5 comments

#641 - Improve `analysis_particle_indices` documentation for `MultiStateReporter`. Storing positions.

Issue - State: closed - Opened by ijpulidos almost 2 years ago
Labels: :books: documentation, low-effort

#640 - Add full API reference to the documentation

Issue - State: open - Opened by ijpulidos almost 2 years ago
Labels: :books: documentation

#639 - Error in paralleltempering

Issue - State: open - Opened by xlimke almost 2 years ago - 2 comments

#638 - Storing simulation frames for MultiStateSampler

Issue - State: closed - Opened by xiki-tempula almost 2 years ago - 3 comments

#637 - Testing against OpenMM dev/beta versions

Pull Request - State: closed - Opened by ijpulidos about 2 years ago - 5 comments

#636 - Test against openmm 8 beta

Issue - State: closed - Opened by ijpulidos about 2 years ago - 1 comment

#634 - remove del operator on PhaseAnalyzer

Pull Request - State: open - Opened by richardjgowers about 2 years ago - 6 comments

#633 - PhaseAnalyzer del causing error.

Issue - State: open - Opened by richardjgowers about 2 years ago

#631 - About ReplicaExchangeSampler

Issue - State: closed - Opened by xiki-tempula about 2 years ago - 6 comments
Labels: :books: documentation, low-effort

#630 - Make compatible with pymbar 3 and 4

Pull Request - State: closed - Opened by mattwthompson about 2 years ago - 10 comments

#629 - Compatibility with pymbar 4

Issue - State: open - Opened by mattwthompson about 2 years ago - 1 comment

#628 - [DNM] added openmm 8 beta to test matrix + fix bug with test

Pull Request - State: open - Opened by mikemhenry about 2 years ago - 8 comments

#627 - Clean up CI File

Issue - State: open - Opened by mikemhenry about 2 years ago

#626 - Add OpenMM 8 beta branch

Issue - State: open - Opened by jchodera about 2 years ago - 1 comment

#625 - Hamiltonian RepEx modifying a CustomHBondForce

Issue - State: closed - Opened by k2o0r about 2 years ago

#624 - File locking error when resuming a parallel tempering simulation on environment with MPI

Issue - State: open - Opened by yihengwuKP about 2 years ago - 10 comments
Labels: :bug: bug, medium-priority, medium-effort

#623 - `PeriodicNonequilibriumIntegrator` docstring example storing work

Issue - State: open - Opened by ijpulidos about 2 years ago - 1 comment
Labels: :books: documentation, low-effort

#622 - Fix doc builds

Pull Request - State: closed - Opened by mikemhenry about 2 years ago - 2 comments

#621 - Sams Output file for real_time_analsysis defaults to root path /

Issue - State: closed - Opened by RiesBen over 2 years ago - 1 comment

#620 - Documentation for Parallel Tempering is not properly generated

Issue - State: closed - Opened by yihengwuKP over 2 years ago - 6 comments
Labels: :bug: bug, :books: documentation

#619 - add python 3.10 to CI

Pull Request - State: closed - Opened by mikemhenry over 2 years ago - 1 comment

#617 - Release 0.21.5 - bugfix release candidate

Pull Request - State: closed - Opened by ijpulidos over 2 years ago - 2 comments

#614 - Avoid raising broad `Exception` when raising errors

Issue - State: open - Opened by ijpulidos over 2 years ago - 3 comments
Labels: :stars: enhancement, error handling

#611 - `LangevinDynamicsMove` now accepts `constraint_tolerance` parameter

Pull Request - State: closed - Opened by ijpulidos over 2 years ago - 9 comments

#608 - Allow integrator tolerance to be specified for mcmc.LangevinDynamicsMove

Issue - State: closed - Opened by jchodera over 2 years ago
Labels: :stars: enhancement, medium-priority, low-effort

#607 - Port notebook analysis from Yank

Issue - State: open - Opened by ijpulidos over 2 years ago
Labels: :stars: enhancement