GitLab

* All AMD GPUs support shuffle, double precision and 64-bit int atomics;
* Remove unused code: !ENABLE_SHUFFLE code paths in nonbonded.hip;
* Use intrinsics in single-precision;
* Use realToFixedPoint (faster float32-to-int64);
* Remove shared atomIndices, use shuffles;
* Check early if atoms are in the cutoff range, sometimes all lanes in
  a warp can skip computations, single pairs can also skip useless
  atomics with zero values;
* Remove volatile skipTiles access, use shuffles;
* Distribute work for warps in a strided order;
* Skip warps that may be still busy in the first loop;
* Unify conditions for excluded atoms with `includeInteraction`;
* Move multiprocessors to HipContext;
* Increase number of warps for computeNonbonded;
* Disable packed math for >=MI200 (it affects performance of some
  kernels like computeGKForces of amoebagk);
* Remove defaultOptimizationOptions and createModule's optimizationFlags
  as they are never used;
* Support -save-temps.

* Compile kernels with max block size of 256 threads:
  The default hipcc behavior since ROCm 4.2 is to compile kernels
  with 1024 threads unless __launch_bounds__ is specified. This
  significantly increases register pressure especially in heavy kernels
  (double precision, for example), requiring register spilling;
* Optimize computeRange by using multiple blocks for reduction;
* Use blocks of 1024 threads for computeBucketPositions - it is executed
  as a single work group so larger block size is faster;
* Sort up-to lenghtNextPow2 instead of blockDim.x (faster for short
  buckets);
* Optimize sortShortList2;
* Optimize sortBuckets with bit instructions;
* Decrease bucket size for non-uniform sorting: too many buckets may
  have sizes too large to sort in shared memory;
* Add more sizes in tests.

* Remove setting of link libraries, include and link dirs and compile
  flags for each target, instead let Cmake deal with them by linking the
  main library to hip::host hiprtc::hiprtc hip::hipfft;
* Fix: custom command without ADD_CUSTOM_TARGET and ADD_DEPENDENCIES is
  executed for both static and shared targets;
* Remove IF(APPLE) parts.

Fix SegFault in HipCalcHippoNonbondedForceKernel

    HipSort was created using a temporary ref. Adding `HipContext& cu`
    field to HipCalcHippoNonbondedForceKernel fixes the issue;

Port changes in CUDA backend to HIP

Fix a warning about arithmetic operations on void* in HipArray::uploadSubArray

Fix "Error Initializing context ROCm 5.3.0"

    https://github.com/StreamHPC/openmm-hip/issues/3


    hipDeviceSetCacheConfig returns hipErrorNotSupported on 5.3
Co-authored-by: Nick Curtis <nicholas.curtis@amd.com>

* Support numpy 2

* Debugging

* Removed debugging code

* Don't require importlib_metadata

* Handle older versions of importlib

* Fix import of netcdf_file for scipy 1.14

* Fix indentation

---------
Co-authored-by: Timothy Palpant <tim@atommapper.com>

* Run Mac tests on ARM and Intel

* Added missing environment file

* Removed obsolete code for M1 runner

* Removed obsolete code for M1 runner

* Debug CI failures

* Debugging

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* Removed build that was failing

* Fixed URL that had changed

* addHydrogens() allows specifying exactly what hydrogens to add

* Prevent CI from using numpy 2.0

* Allow multiple registrations of the same atom type if definitions identical

* Different short-circuiting logic

* DrudeForce supports periodic boundary conditions

* Fixed uninitialized memory

Co-authored-by: FloLangenfeld <florent.langenfeld@peptinov.fr>

* added type checking for Simulation.step()

* changed how to check if step is an integer number

* ATMForce reorders inner contexts for better performance

* Fixed obsolete comments

* Avoid overflow in large XTC files

* Also cast box indices to size_t

* Created DebuggingReporter class

* Fixed description

* Update references to "openmmforcefields" project

* Org name, too

* Revised code from installing CUDA on CI

* Debugging

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LoongArch is a new architecture, already supported by linux-6.1, gcc-12.
Signed-off-by: Zang Ruochen <zangruochen@loongson.cn>
Co-authored-by: Zang Ruochen <zangruochen@loongson.cn>

* Minor optimization to validating exclusions

* Optimizations to findMoleculeGroups()

* Improved performance of CustomHbondForce on large systems

* Fixed CUDA compilation errors

* Made LangevinIntegrator identical to LangevinMiddleIntegrator

* Removed unused code

* VariableLangevinIntegrator uses LFMiddle

* Can use getPlatform() instead of getPlatformByName()

* More concise arguments for getState()

* Reference platform supports nested virtual sites

* Common platform supports nested virtual sites

* Fixed force distribution from nested virtual sites

* Fixed test failures

* Improve numerical stability for edge cases

* Undo checking of derivative factors

* Undo checking for NaNs