GitLab

* API for querying devices

* CUDA and HIP implementations of getDevices()

* Fix test failures

* Fix test failures

* CUDA returns correct devices even if no context has been created

* Return a single device for Reference and CPU

* Fix CI failure

* Replace SimTK-containing file headers

* Update file headers for new Tinker reader files added

* Unified storage of global parameters

* Fixes to CUDA and HIP

* Store global parameters as real instead of float

* Use common API for kernels

* More code uses common interface

* Bug fixes

* Unified interface for sorting

* Simplified interface for FFT

* Use common event API for synchronization

* Minor changes to make code more consistent between platforms

* Common implementation of NonbondedForce

* Bug fixes

* Flag to enable list of single pairs

* CUDA and OpenCL use common implementation of NonbondedForce

* Fixed compilation error

* HIP uses common implementation of NonbondedForce

* Unified interface for queues

* Simplified stream handling in CudaFFT3D

* HIP implementation of ComputeQueue

* Unified interface for FFTs

* AMOEBA uses unified interface for FFTs

* HIP implementation of common FFT interface

* Replace pthreads with C++ threads

* Try to fix CI errors

* Try including -pthread linker option

* Unified lots of parallel computation code between platforms

* Unified test code between platforms

* Eliminated duplicated timing code

* Common implementation of BondedUtilities

* Common implementation of UpdateStateDataKernel

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* Use cuCtxPushCurrent() and cuCtxPopCurrent() for selecting CUDA context

* Fixed errors in amoeba coda

* Fixed more errors in context selection

* Began converting AMOEBA to common platform

* Beginning of OpenCL platform for AMOEBA

* Converted AmoebaVdwForce to common platform

* Cleaned up reference AMOEBA tests

* Began converting AmoebaMultipoleForce to common platform

* Continue converting AmoebaMultipoleForce to common platform

* Bug fixes

* Bug fix

* Continue converting AmoebaMultipoleForce to common platform

* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform

* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Converted arrays from real3 to real

* Bug fix to OpenCL AmoebaGeneralizedKirkwoodForce

* Fixes for AMD GPUs

* Began converting HippoNonbondedForce to common platform

* Continuing to convert HippoNonbondedForce to common platform

* Continuing to convert HippoNonbondedForce to common platform

* Working on unifying PME kernels

* Fixed error on devices without 64 bit atomics

* Unified PME kernels

* Converted HippoNonbondedForce to common platform

* Creating OpenCL implementation of HippoNonbondedForce

* Continuing OpenCL implementation of HippoNonbondedForce

* Mostly finished OpenCL implementation of HippoNonbondedForce

* Eliminated three component vector types in host code

* Fix errors on CPU OpenCL

* Skip double precision tests for AMOEBA on OpenCL

* Bug fixes

* Bug fixes

* Fixed compilation error

* Converted more code to common platform

* Converted more code to common platform

* Improve selection of architecture to compile for

* Fixed compilation errors on older CUDA versions

* Use command line compiler if it is explicitly specified

* Don't set OPENMM_CUDA_COMPILER on Jenkins

* Began creating common compute framework to unify code between CUDA and OpenCL

* Began OpenCL implementation of common compute framework

* Common implementation of CMMotionRemover

* CUDA implementation of common compute interface

* Converted HarmonicBondForce to common compute API

* Converted standard bonded forces to common compute API

* Converted ExpressionUtilities to common compute API

* Created ComputeParameterSet

* Converted custom bonded forces to common compute API

* Converted CustomCentroidBondForce to common compute API

* Converted CustomManyParticleForce to common compute API

* Moved lots of duplicate code from CudaContext and OpenCLContext to ComputeContext

* Converted GayBerneForce to common compute API

* Removed obsolete kernels

* Converted verlet integrators to common compute API

* Converted Langevin and Brownian integrators to common compute API

* Converted CustomIntegrator to common compute API

* Converted CustomNonbondedForce to common compute API

* Removed uses of a deprecated API

* Fixed failing test cases

* Converted GBSAOBCForce to common compute API

* Began converting CustomGBForce to common compute API

* Finished converting CustomGBForce to common compute API

* Merged duplicated code in CudaIntegrationUtilities and OpenCLIntegrationUtilities

* Converted RMSDForce and AndersenThermostat to common compute API

* Converted CustomHbondForce to common compute API

* Merged scripts for encoding kernel sources

* Converted Drude plugin to common compute API

* Fixed errors in CMake scripts

* Attempt at fixing errors on Windows

* Added discussion of common compute API to developer guide

* Added Windows export macro for common classes

* Fixed error in CMMotionRemover

* Ubdated travis to newer Ubuntu version

* Fixed errors on CPU OpenCL

* Fixed Windows linking errors

* Added missing pragma for 32 bit atomics

* Replaced long long with mm_long

* More fixes to Windows linking

* Bug fix

This change is intended to improve the behavior when multiple
CUDA contexts are created on a node with multiple CUDA GPUs,
each of which is set to process-exclusive mode.

Converted the routine for identifying molecules from a recursion to a loop.  This avoids stack overflows with very long linear molecules.

Platform specific header files get installed.  This allows plugins to be built with just an OpenMM installation, not a full source tree.