openmm/NNPOps issues and pull requests

#109 - Set c++17 standard in CMake for recent torch/cuda versions

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

#108 - Make some tests use deterministic torch algorithms

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

#107 - NNPOps 0.6

Issue - State: open - Opened by raimis over 1 year ago - 15 comments

#106 - Does the ANI implementation within NNPOps also consume 20x more memory with PBC?

Issue - State: closed - Opened by JSLJ23 over 1 year ago - 4 comments

#105 - Install via pip

Pull Request - State: open - Opened by RaulPPelaez over 1 year ago - 4 comments

#104 - Fix CMake not adding some tests

Pull Request - State: closed - Opened by RaulPPelaez over 1 year ago - 24 comments

#103 - Particle Mesh Ewald

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

#102 - Incorrect library name on Mac

Issue - State: open - Opened by peastman over 1 year ago - 3 comments

#101 - Neigbors for >128K particles

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

#100 - Add Self-Hosted AWS GPU Runner

Pull Request - State: closed - Opened by mikemhenry almost 2 years ago - 7 comments

#99 - NNPOps 0.5

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

#98 - Many tests are being skipped by the CI

Issue - State: closed - Opened by RaulPPelaez almost 2 years ago - 3 comments
Labels: enhancement

#97 - Fix CMake not updating tests correctly after first run

Pull Request - State: closed - Opened by RaulPPelaez almost 2 years ago - 1 comment

#96 - Conda install the CUDA version of nnpops on a linux CPU platform

Issue - State: closed - Opened by xiki-tempula almost 2 years ago - 4 comments

#95 - Full listing of available operations?

Issue - State: open - Opened by Linux-cpp-lisp almost 2 years ago - 1 comment
Labels: question

#94 - Support for pytorch 2.0

Pull Request - State: closed - Opened by RaulPPelaez almost 2 years ago - 7 comments

#93 - Fix incorrect decorator in NNPOps

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

#92 - error when trying to jit.script getNeighbors

Issue - State: closed - Opened by sef43 almost 2 years ago - 8 comments
Labels: bug

#91 - Fix neighbourlist gradient calculation on CPU

Pull Request - State: closed - Opened by sef43 almost 2 years ago - 2 comments

#90 - Additions to gitignore

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

#89 - Move all torch.ops.load calls to the init.py scripts

Pull Request - State: closed - Opened by RaulPPelaez almost 2 years ago - 7 comments

#88 - Update CI versions

Pull Request - State: closed - Opened by raimis almost 2 years ago - 12 comments

#87 - Unifying code formatting

Issue - State: open - Opened by RaulPPelaez almost 2 years ago - 3 comments
Labels: question

#86 - NNPOps 0.4

Issue - State: closed - Opened by raimis almost 2 years ago - 12 comments

#85 - torchani faster than nnpops for larger systems?

Issue - State: open - Opened by wiederm almost 2 years ago - 12 comments
Labels: help wanted

#84 - TestNeighbors.py failures with pytorch 1.13

Issue - State: closed - Opened by sef43 almost 2 years ago - 3 comments
Labels: bug

#83 - Fix a bug the periodic boundary conditions in ANI SymmetryFunctions

Pull Request - State: closed - Opened by sef43 almost 2 years ago - 3 comments

#82 - Surprising differences between nnpops and torchani

Issue - State: closed - Opened by wiederm almost 2 years ago - 17 comments
Labels: help wanted

#81 - Improve the build system to use find_package(Python) instead of find_package(PythonLibs)

Pull Request - State: closed - Opened by RaulPPelaez about 2 years ago - 1 comment

#80 - Add error checking to CUDA version of getNeighborPairs

Pull Request - State: closed - Opened by RaulPPelaez about 2 years ago - 27 comments

#79 - Efficient error reporting in CUDA

Issue - State: closed - Opened by RaulPPelaez about 2 years ago - 9 comments
Labels: enhancement

#78 - Test on GPU

Issue - State: open - Opened by raimis about 2 years ago - 1 comment
Labels: enhancement

#77 - GPU memory consumption of NNPOps

Issue - State: closed - Opened by wiederm about 2 years ago - 2 comments
Labels: question

#76 - Torch problems when using NNPOps with Openmm-ML

Issue - State: open - Opened by zanebeckwith about 2 years ago - 5 comments
Labels: help wanted

#75 - Update the CI versions

Pull Request - State: closed - Opened by raimis about 2 years ago - 1 comment

#74 - Align SpeciesConverter return type with TorchANI version

Pull Request - State: closed - Opened by scal444 about 2 years ago - 1 comment

#73 - NNPOps 0.3

Issue - State: closed - Opened by raimis about 2 years ago - 6 comments

#72 - Readme example appears broken

Issue - State: closed - Opened by scal444 about 2 years ago - 2 comments

#71 - Workaround for pytorch bug

Pull Request - State: closed - Opened by peastman about 2 years ago - 1 comment

#70 - getNeighborPairs() supports periodic boundary conditions

Pull Request - State: closed - Opened by peastman about 2 years ago - 17 comments

#69 - Update example

Pull Request - State: closed - Opened by moradza over 2 years ago - 6 comments

#68 - getNeighborPairs error

Issue - State: closed - Opened by davkovacs over 2 years ago - 5 comments
Labels: help wanted

#67 - Fix the selection of the activation function in CFConv

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

#66 - Fix the warnings of CFConv

Issue - State: closed - Opened by raimis over 2 years ago
Labels: bug

#65 - Refactor the common code

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

#64 - Use Mamba for CI

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

#63 - [WIP] Run CI on macOS

Pull Request - State: open - Opened by peastman over 2 years ago - 21 comments

#62 - Add OSX to CI testing matrix

Issue - State: open - Opened by mikemhenry over 2 years ago - 2 comments

#61 - `getNeighborPairs` compute the displacement vector

Pull Request - State: closed - Opened by raimis over 2 years ago - 10 comments

#60 - Conda install not working

Issue - State: closed - Opened by davkovacs over 2 years ago - 9 comments
Labels: help wanted

#59 - Message passing operation

Pull Request - State: open - Opened by raimis over 2 years ago - 1 comment

#58 - Nearest neighbor operation

Pull Request - State: closed - Opened by raimis over 2 years ago - 4 comments

#57 - [DO NOT MERGE] Test if we can build with pytorch 1.11

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

#56 - Fix and improve CI

Pull Request - State: closed - Opened by raimis over 2 years ago - 3 comments

#55 - Enable the periodic CI

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

#54 - libNNPOpsPyTorch.so: undefined symbol: _ZN3c1012OptionalTypeC1ESt10shared_ptrINS_4TypeEE

Issue - State: closed - Opened by rvkrishnan30 over 2 years ago - 10 comments

#53 - Error building with CUDA

Issue - State: open - Opened by peastman almost 3 years ago - 5 comments
Labels: help wanted

#52 - Update README

Pull Request - State: closed - Opened by raimis almost 3 years ago - 1 comment

#51 - Test pytorch 1.10.2

Pull Request - State: closed - Opened by mikemhenry almost 3 years ago

#50 - NNPOps 0.2

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

#49 - Refactor the CUDA error check

Pull Request - State: closed - Opened by raimis about 3 years ago - 1 comment

#48 - Enable CPU-only builds

Pull Request - State: closed - Opened by raimis about 3 years ago - 1 comment

#47 - Improve the wrapper of `ANISymmetryFunctions`

Pull Request - State: closed - Opened by raimis about 3 years ago

#46 - CI with GPU

Issue - State: open - Opened by raimis about 3 years ago - 1 comment
Labels: enhancement

#45 - Move the TorchANI imports from the top level

Pull Request - State: closed - Opened by raimis about 3 years ago - 1 comment

#44 - Removing the dependency of TorchANI

Issue - State: open - Opened by raimis about 3 years ago - 2 comments
Labels: enhancement

#43 - Set Default CUDA Arch

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

#42 - Optimization to SchNet

Pull Request - State: closed - Opened by peastman about 3 years ago

#41 - Optimize TorchANI

Pull Request - State: closed - Opened by raimis about 3 years ago - 2 comments

#40 - PyTorch wrapper for SchNet operations

Pull Request - State: closed - Opened by raimis about 3 years ago - 3 comments

#39 - Optimize SpeciesConverter of TorchANI

Pull Request - State: closed - Opened by raimis about 3 years ago - 13 comments

#38 - Optimize EnergyShifter of TorchANI

Pull Request - State: closed - Opened by raimis about 3 years ago - 6 comments

#37 - Fix the execution of ANISymmetryFunctions on a non-default CUDA stream

Pull Request - State: closed - Opened by raimis about 3 years ago - 7 comments

#36 - integrator timing data for tip3p:ligand and protein:ligand simulations suggests a non-pytorch bottleneck?

Issue - State: open - Opened by dominicrufa about 3 years ago - 1 comment
Labels: help wanted

#35 - Update to TorchANI 2.2.2

Pull Request - State: closed - Opened by raimis over 3 years ago - 4 comments

#34 - CI for NNPOps

Pull Request - State: closed - Opened by raimis over 3 years ago - 4 comments

#33 - Reorganize repo

Pull Request - State: closed - Opened by raimis over 3 years ago - 4 comments

#32 - Cut a release of NNPOps (after merging critical PRs)

Issue - State: closed - Opened by jchodera over 3 years ago - 4 comments

#31 - Add continuous integration for NNPOps

Issue - State: closed - Opened by jchodera over 3 years ago - 1 comment

#30 - Have nvcc compile for multiple architectures for conda-packages

Issue - State: closed - Opened by jchodera over 3 years ago - 1 comment

#29 - Consider pytorch_geometric as an example of how we can structure this repo

Issue - State: closed - Opened by jchodera over 3 years ago - 1 comment

#28 - Can't run steps of dynamics with NNPOps `TorchForce`

Issue - State: open - Opened by dominicrufa over 3 years ago - 3 comments
Labels: help wanted

#27 - NNPOps installation/build missing dependencies (absent from environment.yml)

Issue - State: closed - Opened by dominicrufa over 3 years ago - 4 comments
Labels: help wanted

#26 - Conda-forge package of NNPOps

Issue - State: closed - Opened by dominicrufa over 3 years ago - 52 comments

#25 - Schnet in OpenMM

Issue - State: open - Opened by keano130 over 3 years ago - 1 comment
Labels: question

#24 - Fix pytorch test and add PBC test

Pull Request - State: closed - Opened by yueyericardo about 4 years ago

#23 - Added option to use tanh activation

Pull Request - State: closed - Opened by peastman about 4 years ago - 3 comments

#22 - Transfer to openmm organization

Issue - State: closed - Opened by peastman about 4 years ago - 1 comment

#21 - CGSchNet support

Issue - State: open - Opened by jchodera about 4 years ago - 13 comments
Labels: question

#20 - Other models to support?

Issue - State: open - Opened by peastman about 4 years ago - 30 comments
Labels: question

#19 - A better PyTorch wrapper

Pull Request - State: closed - Opened by raimis about 4 years ago - 11 comments

#18 - CFConv layer for SchNet

Pull Request - State: closed - Opened by peastman about 4 years ago - 1 comment

#17 - mdtraj xyz unit

Pull Request - State: closed - Opened by yueyericardo about 4 years ago - 3 comments

#16 - Batched molecule computation

Issue - State: open - Opened by yueyericardo over 4 years ago - 1 comment
Labels: question

#15 - Conda package of NNPOps-PyTorch

Pull Request - State: closed - Opened by raimis over 4 years ago - 7 comments

#14 - Benchmarking SchNet

Issue - State: open - Opened by peastman over 4 years ago - 16 comments
Labels: help wanted

#13 - Batched NNs for TorchANI

Pull Request - State: closed - Opened by raimis over 4 years ago - 17 comments

#12 - Added README files and benchmark code

Pull Request - State: closed - Opened by peastman over 4 years ago

#11 - Performance of the atomic neural networks in TorchANI

Issue - State: open - Opened by raimis over 4 years ago - 5 comments
Labels: enhancement

#10 - Support SchNet-like models as well

Issue - State: closed - Opened by jchodera over 4 years ago - 37 comments

GitHub / openmm/NNPOps issues and pull requests