- Jul 22, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix performance logging code around GPU code. Rearrange header files to allow some preprocessor definitions to be defined via options in configure script. Rework Autoconf and Automake code to allow passing flags directly to nvcc compiler wrapper (for CUDA code). Enable C11 and C++11 standard targets during compilation.
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- Jul 06, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix compilation error (remove variable). Fix issue with dual CG solver for QEq (local arithmetic in SpMV was incorrect). Revert CG solver convergence criterion to use norm of the preconditioned residual vector.
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- Jul 01, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: small fix for initializtion routine performance logging (timers not reset after outputting to log file).
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- Jun 29, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: corrections for utilizing a SAI preconditioner in MPI code (errors introduced during previous code merges).
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- Jun 25, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: revert CG solver convergance criterion to used preconditioned residual norm. Re-enable dual charge solver for QEq.
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- Jun 24, 2020
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
PG-PuReMD: rework performance logging code in linear solver routines to avoid excessive MPI communications.
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- Jun 23, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: adjust performance logging to compute mean timings across all processors. Other code clean-up.
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with certain data structures not being reallocated when the local number of atoms owned by a processor increases after exchanging messages with neighbor processors. Fix an issue where the MPI send message buffer may be overwritten by a received message (Coll). Small fix to not overwrite the program status return value with local function return values. Other code clean-up.
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- Jun 17, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix out-of-bounds mmeory accesses and unitialized data usage in energy and force tabulation routines for van der Waals and Coulomb interactions.
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- Jun 12, 2020
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with some interaction lists not being initialized on first step of simulations from restarted runs. Fix typos in C++ code for utilizing C code (__cplusplus). Clean up C code for utilizing C++ code (unconditional extern's for unmangled member naming). Ensure that CUDA thread and block sizes are correctly set. Tweaks to memory transfers and allocation logic in integration code (GPU). Fix logic error with charge matrix allocation in GPU code. Other code clean-up.
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- Jun 05, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: add BiCGStab solver for GPU code. Corrections to CUDA block and thread sizes for some kernels. Fix some variables being used with uninitialized values.
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- Jun 02, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with charge solver preconditioner refactoring rate causes issues with reneighboring actions (preconditionering rate was previously coupled with reneighoring rate for SAI but this causes issues for Jacobi, etc.). Be more greedy with memory allocation sizes to decrease reallocation frequency (MPI buffers, etc.). More GPU code clean-up.
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- Jun 01, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix MPI buffer allocations sizes. Ensure that nonblocking MPI messages have completed for each dimension before continuing. Rework reallocation checks in integration routines. Temporarily disable CUDA-aware MPI code paths (need to perform packing/unpacking first on device before handing off pointers). Other code clean-up.
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- May 12, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix host-device transfers for charge solver code (SpMV data transfer sizes). Remove unused code. Other general code clean-up.
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- May 07, 2020
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Kurt A. O'Hearn authored
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- May 04, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with divergent MPI_Reduce calls by multiple MPI processes (timing logging code). Add run-time MPI routine error checking. Fix issue with upper limit of hydrogen atoms allowed being hard-coded in GPU code (use dynamic memory allocation instead). Other code clean-up.
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- Apr 30, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: clean-up MPI custom datatype initialization and error reporting. Avoid truncations in buffer size calculations. Other code clean-up.
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- Apr 15, 2020
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Kurt A. O'Hearn authored
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- Apr 13, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: improve memory management around temporary storage space on both the host and device (i.e., scratch space).
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Kurt A. O'Hearn authored
PG-PuReMD: replace deprecated CUDA warp-level primitives with modern ones. Fix issue with modern GPU microarchitectures using incorrect code paths (post-Kepler). Other code clean-up.
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- Mar 10, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: revert to 1 thread per atom implementation in nonbonded energy and force calculations in order to correct issue with forces being incorrectly calculated (revisit 1 warp per atom implementation later). Disable charge matrix row-wise sorting. Other general code clean-up.
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- Mar 05, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: corrections to van der Waals and Coulomb energies calculations (far neighbor list in full format, not half). Fix QEq charge matrix initialization (full format). Other refactoring and code clean-up.
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- Feb 26, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with SpMVs operations using incorrect row-wise bounds (end pointer incorrect in light of sparse_matrix struct changes).
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Kurt A. O'Hearn authored
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- Feb 19, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: merge changes from sPuReMD and PuReMD for validation work for simulation accuracy. Small correction to lone pair energy calculation. PuReMD: code formatting changes to better align with sPuReMD. sPuReMD: fix issue with valence angle calculations not setting list indices under certain sitations (taking previous continue statement missed index assignment).
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- Oct 29, 2019
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Kurt A. O'Hearn authored
PG-PuReMD: backport fixes from sPuReMD to control file parsing. Tools: formatting tweaks for MPI-GPU code.
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- Oct 11, 2019
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Kurt A. O'Hearn authored
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- Oct 10, 2019
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Kurt A. O'Hearn authored
PG-PuReMD: refactoring to unify CUDA code naming conventions and to simply code in cuda_system_props.cu.
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Oct 08, 2019
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Oct 06, 2019
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with portions of interaction lists not being initialized for Cuda_Init_Forces. Utilize more targeted debugging prints (DEBUG -> DEBUG_FOCUS). Other general code cleanup.
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- Feb 20, 2019
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Kurt A. O'Hearn authored
Fix build issue where config.h.in is only generated once (for sPuReMD) => common file across all versions.
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- Feb 06, 2019
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Kurt A. O'Hearn authored
Build toos: refactor to remove recurisve Makefiles. Fix issue with OpenMP flags being overridden when user supplied value for CFLAGS variable.
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- Nov 06, 2018
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Kurt A. O'Hearn authored
Build systems updates for sPuReMD, PuReMD-GPU, and PG-PuReMD (use safer optimization level defaults).
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