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Created with Raphaël 2.2.02Jun124May131211107429Apr28262019161514930Mar26181615543126Feb23191817151143129Jan282218116416Dec15141020Nov22Oct22Sep2016920Aug1714121110765129Jul226129Jun252423171252112May107430Apr201513610Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun28272120181716sPuReMD: fix code to remove several compiler warnings. Remove unused code. Disable compilation of several debug routines. Other code clean-up.sPuReMD: add support for user-defined molecular charge constraints with EEM (using MOLCHARGE keyword in BGF geometry files). Fix issue with far neighbor list not being initialized for certain edge cases.Merge branch 'master' into pg-puremd-charge-solver-opt-sdsc-hackaton.Tools: add keyword for setting number of CUDA streams (gpu_streams).PG-PuReMD: fix warnings (and errors) from several uninitialized memory regions due to multiple stream change. Fix race condition with valence angle computation due to mistake with dynamic shared memory. Add control file parameter for setting the number of CUDA streams. Other code clean-up.PG-PuReMD: fix issue with post-processing step with QEq pseudo-charges (too little storage in q array). Fix issue with device-wide CUB reductions and prefix sums reallocating device memory too frequently. Rework CUDA-aware MPI code to fix issues (still seeing out-of-memory errors on Ascent cluster at OLCF).PG-PuReMD: ensure MPI pack/unpack CUDA kernels are run in the correct stream. Other changes to bring the CUDA-aware MPI functions for the charge solver in line with their MPI counterparts.Revert accidental changes to files committed in previous commit.PG-PuReMD: resolve additional multiple stream implementation issues.sPuReMD: fix bug for BGF files if no CRYSTX line supplied (simulation box dimensions).PG-PuReMD: utlize multiple CUDA streams to run independent kernels in the ReaxFF+QEq task dependency graph.PG-PuReMD: fix stream issue with cudaMemset's happening in default stream (switch to cudaMemsetAsync). Rework memory management in light of this change.WIP: finish the explicit single stream port by using cudaMemcpyAsync and cudaStreamSynchronize calls.WIP: changes to support multiple CUDA streams. This commit contains porting of all kernels from the default stream to a single non-default stream. This commit has bugs regarding cudaMemcpy's still being in the default stream (and synchronous).Tools: add support for jobs using LSF (on OLCF at ONL).sPuReMD: add MKL support for ELM methodtensorflow_upda…tensorflow_update_v2PG-PuReMD: refactor CUDA memory management routines.PG-PuReMD: update CUDA library checks. Assume lib64 for new CUDA library locations.PG-PuReMD: use a warp of threads for hydrogen bonds.PG-PuReMD: use a warp of threads for lone pair/over/under interactions.PG-PuReMD: implement MPI+CUDA versions of SDM, PIPECG, PIPECR for charge solver methods (along with missing dual QEq versions).PG-PuReMD: use a warp of threads for addtional bonded interaction computations (bond orders, bonds, lone pair/over/under).add a new model (ELM), accelerate predictionPG-PuReMD: use a warp of threads for apply bond derivatives to forces and simplify these code paths.improve init. and allocation logic for restraintsrestraint_supportrestraint_supportadd restraint energy to the total energyreset restraint energiesadd deallocation for restraintsAdd bond and angle restraint supportUpdate restraint related functionsenergy_minimenergy_minimPG-PuReMD: use a warp of threads for torsion computations.PG-PuReMD: fix incorrect summations in kinetic energy and temperature calculation functions. Replace several hand-coded device-wide reduction kernels with CUB libary reduction.PG-PuReMD: use a warp of threads for valence angle computations.PG-PuReMD: use a warp of threads to initialize the bonds and hydrogen bonds lists.PG-PuReMD: split bond and hbond initialization kernels for future optimizations. Cleanup CUDA code related to far neighbor list being in full format (remove unnecessary conditionals and arithmetic).PG-PuReMD: use a warp of threads to initialize each row of the charge matrix.change the callback function related linesallocate larger memory for s and t arrays to store data for finetuning the modellog TF timing dataadd TF related new parameters(for timing and control), update the callback function to better callect solver data