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Small fixes into GROMACS GPU code

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-11-14 18:21:14 +01:00
parent 93188d1383
commit 6eedf1776e
3 changed files with 4 additions and 4 deletions
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4
gromacs/cuda/force_lj.cu
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@ -56,8 +56,8 @@ void initDevice(Atom *atom, Neighbor *neighbor) {
cuda_PBCz = (int *) allocateGPU(atom->Nclusters_max * sizeof(int)); cuda_PBCz = (int *) allocateGPU(atom->Nclusters_max * sizeof(int));
cuda_numneigh = (int *) allocateGPU(atom->Nclusters_max * sizeof(int)); cuda_numneigh = (int *) allocateGPU(atom->Nclusters_max * sizeof(int));
cuda_neighbors = (int *) allocateGPU(atom->Nclusters_max * neighbor->maxneighs * sizeof(int)); cuda_neighbors = (int *) allocateGPU(atom->Nclusters_max * neighbor->maxneighs * sizeof(int));
natoms = (int *) malloc(atom->Nclusters_max); natoms = (int *) malloc(atom->Nclusters_max * sizeof(int));
ngatoms = (int *) malloc(atom->Nclusters_max); ngatoms = (int *) malloc(atom->Nclusters_max * sizeof(int));
isReneighboured = 1; isReneighboured = 1;
} }

2
gromacs/main.c
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@ -65,9 +65,9 @@ double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *
buildClusters(atom); buildClusters(atom);
defineJClusters(atom); defineJClusters(atom);
setupPbc(atom, param); setupPbc(atom, param);
initDevice(atom, neighbor);
binClusters(atom); binClusters(atom);
buildNeighbor(atom, neighbor); buildNeighbor(atom, neighbor);
initDevice(atom, neighbor);
E = getTimeStamp(); E = getTimeStamp();
return E-S; return E-S;
} }

2
include_NVCC.mk
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@ -10,7 +10,7 @@ ANSI_CFLAGS += -Wextra
# A100 + Native # A100 + Native
CFLAGS = -O3 -arch=sm_80 -march=native -ffast-math -funroll-loops --forward-unknown-to-host-compiler # -fopenmp CFLAGS = -O3 -arch=sm_80 -march=native -ffast-math -funroll-loops --forward-unknown-to-host-compiler # -fopenmp
# A40 + Native # A40 + Native
#CFLAGS = -O3 -arch=sm_80 -march=native -ffast-math -funroll-loops --forward-unknown-to-host-compiler # -fopenmp #CFLAGS = -O3 -arch=sm_86 -march=native -ffast-math -funroll-loops --forward-unknown-to-host-compiler # -fopenmp
# Cascade Lake # Cascade Lake
#CFLAGS = -O3 -march=cascadelake -ffast-math -funroll-loops --forward-unknown-to-host-compiler # -fopenmp #CFLAGS = -O3 -march=cascadelake -ffast-math -funroll-loops --forward-unknown-to-host-compiler # -fopenmp
# For GROMACS kernels, we need at least sm_61 due to atomicAdd with doubles # For GROMACS kernels, we need at least sm_61 due to atomicAdd with doubles