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Created with Raphaël 2.2.029Jun282731May1928Feb27623Jan26Sep27Jul252117118612May321Apr1811628Feb232125Jan19622Dec1716718Nov9125Oct228716Aug1210526Jul2320142129Jun2824232221982124May131211107429Apr28262019161514930Mar26181615543126Feb23191817151143129Jan282218116416Dec15141020Nov22Oct22Sep2016920Aug1714121110765129Jul226129Jun252423171252112May107430Apr201513610Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb2625PG-PuReMD: remove extraneous block synchronization.mainmainPG-PuReMD: use faster alternatives to expensive special math functions.PG-PuReMD: limit data transfers accordingly (viral terms in valence angles).More fixes from backporting CUDA changes to HIP.Fixes from backporting CUDA changes to HIP.PG-PuReMD: allow GPU threads per block to be set via control file (gpu_block_size). Refactor and simplify code accordingly. Tools: add gpu_block_size parameter.PG-PuReMD: fix typo from merge.PG-PuReMD: pin host-side memory used in MPI comms to accelerate host-device memory transfers (partial energies local to processors).PG-PuReMD: change to non-deprecated host memory management HIP API functions (note: differences from CUDA API). Add applicable flags to restore performance for pinned memory usage.Tools: add extra MPI arguments to mpirun command.PG-PuReMD: fix HIP naming issue (hipHostAllocPortable -> hipHostMallocPortable).PG-PuReMD: utilize pinned memory for GPU data transfers (HIP).PG-PuReMD: utilize pinned memory for GPU data transfers (CUDA). Add single GPU optimizations to skip MPI communications.sPuReMD: fix charge matrix size estimation for contiguous charge constraints in QM/MM simulations (count zeros on diagonals).PG-PuReMD: add support for AMD GPUs using HIP (MPI+HIP codebase, use --enable-hip=yes flag at configure phase).sPuReMD: patch Jacobi preconditioner with ACKS2 to avoid being ill-conditioned (use only well-conditioned portion from QEq model).PG-PuReMD: prune Verlet list entries (small cut-off for ghost-ghost atom interactions).PG-PuReMD: prune Verlet list entries (small cut-off for ghost-ghost atom interactions).PG-PuReMD: improve 3- and 4-body interaction pruning (more precise parameter counts).PG-PuReMD: add 3- and 4-body interaction pruning by parameter existence (MPI+CUDA codepath).PG-PuReMD: add several warp optimized kernels (Verlet list generation, storage estimation routines for initialization, etc.). Rework nonbonded kernels to decease the number of arithmetic instructions. Optimize three dimensional vector functions. Other code clean-up.PG-PuReMD: fix issue with hydrogen bond interactions being evaluated for structures with no hydrogen atoms.PG-PuReMD (MPI): optimize valence and torsion interactions by pruning based on existence of parameters in the force field parameter file.PG-PuReMD: properly initialize MPI for threading (MPI_THREAD_FUNNELED). Optimize SAI preconditioner computation to avoid MPI communications when neighbor MPI process is yourself in the presence of periodic boundary conditions.PG-PuReMD: add OpenMP support for SAI preconditioner computation (--enable-openmp=yes flag in configure script). Other code clean-up.Tools: enable setting of the number of CUDA streams (gpu_streams control file keyword). sPuReMD: update control file parser for this new keyword (valid but ignored).PG-PuReMD: disable grid optimization which requires the Verlet list be in half format (all MPI+CUDA code and SAI code uses full format). Fix H-bond list initialization issue in MPI-only code. Re-write SAI MPI code to avoid extraneous data movement. Other code clean-up.PG-PuReMD: simplify preconditioner selection logic. Fix issue with SpMV's applying SAI preconditioning (full row not applied during multiplication). Change solver iterations counts in MPI+CUDA code to match MPI-only code. Other code clean-up.PG-PuReMD: fixes to SAI preconditioner computation (message size mismatch). Rework MPI communications to not exchange data over MPI when messages are exchanged with oneself (i.e., neighboring processor is oneself via periodic boundary conditions). Backport hydrogen bond fix from sPuReMD (omit interactions when no valid parameters in force field file). Other code clean-up.PG-PuReMD: improve bound check to samping in SAI computation code.PG-PuReMD: standardize and clean-up CUB usage. Add wrapper for non-CUB reductions (rvec, rvec2). Other code clean-up.PG-PuReMD: add support for using cuBLAS routines for dense linear algebra (mainly level-1 routines in sparse linear solver). Clean-up solver code for using streams.PG-PuReMD: split van der Waals and Coulomb force and energy computation kernels and execute in seperate streams. Change stream of Coulomb-related kernels (init, charge solver, Coulomb). Use math function for cubic root calculations. Other code clean-up.PG-PuReMD: default to using bundled CUB library witn recent CUDA SDK version (>= v11.x), while retaining older CUB submodule for older CUDA capabilities (use NVCCFLAGS to manually include CUB in this case). Refactor timing code to more accurately measure kernel timing. Refactor stream logic to expose more parallelism (valence+torsion branch) and to perform fewer synchronizations. Other code clean-up and refactoring.Tools: update Python example driver code.sPuReMD: refactor contiguous and custom charge constraint code. Make applicable API functions available to all interfaces.sPuReMD: fix issue with API functions (setup2 / reset2 -> cleanup) regarding new contiguous and custom charge constraint implementation (identified and suggested fix by Cagri Kaymak).sPuReMD: fixes for custom charge constraint specification for QM/MM simulations.sPuReMD: fix uninitialized variable compilation warning.sPuReMD: do not compute hydrogen bond interactions when there are no valid force field parameters available for the given triplet of atom types. Allow arbitrary numbers of H-bond interactions per atom.