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Commit 8ed07b6f authored by peastman's avatar peastman
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Removed AVX code, since it had very little effect on performance and would... 

Removed AVX code, since it had very little effect on performance and would have required a more complicated build process.  Also worked around a compilation error with clang.
parent e249751c
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Showing with 16 additions and 124 deletions
plugins/cpupme/CMakeLists.txt
View file @ 8ed07b6f
...@@ -71,7 +71,7 @@ FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS}) ...@@ -71,7 +71,7 @@ FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
ENDFOREACH(subdir) ENDFOREACH(subdir)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src) INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "-mavx") SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "-msse4.1")
# Include FFTW related files. # Include FFTW related files.
......
plugins/cpupme/src/CpuPmeKernels.cpp
View file @ 8ed07b6f
...@@ -36,7 +36,7 @@ ...@@ -36,7 +36,7 @@
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h" #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
#include <immintrin.h> #include <smmintrin.h>
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
...@@ -46,9 +46,7 @@ static const int PME_ORDER = 5; ...@@ -46,9 +46,7 @@ static const int PME_ORDER = 5;
bool CpuCalcPmeReciprocalForceKernel::hasInitializedThreads = false; bool CpuCalcPmeReciprocalForceKernel::hasInitializedThreads = false;
int CpuCalcPmeReciprocalForceKernel::numThreads = 0; int CpuCalcPmeReciprocalForceKernel::numThreads = 0;
static float extractFloat(__m128& v, unsigned int element) { #define EXTRACT_FLOAT(v, element) _mm_cvtss_f32(_mm_shuffle_ps(v, v, _MM_SHUFFLE(0, 0, 0, element)))
return _mm_cvtss_f32(_mm_shuffle_ps(v, v, _MM_SHUFFLE(0, 0, 0, element)));
}
// Define function to get the number of processors. // Define function to get the number of processors.
...@@ -108,7 +106,7 @@ static void cpuid(int cpuInfo[4], int infoType){ ...@@ -108,7 +106,7 @@ static void cpuid(int cpuInfo[4], int infoType){
} }
#endif #endif
static void spreadChargeSSE(int start, int end, float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) { static void spreadCharge(int start, int end, float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) {
float temp[4]; float temp[4];
__m128 boxSize = _mm_set_ps(0, (float) periodicBoxSize[2], (float) periodicBoxSize[1], (float) periodicBoxSize[0]); __m128 boxSize = _mm_set_ps(0, (float) periodicBoxSize[2], (float) periodicBoxSize[1], (float) periodicBoxSize[0]);
__m128 invBoxSize = _mm_set_ps(0, (float) (1/periodicBoxSize[2]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[0])); __m128 invBoxSize = _mm_set_ps(0, (float) (1/periodicBoxSize[2]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[0]));
...@@ -157,19 +155,19 @@ static void spreadChargeSSE(int start, int end, float* posq, float* grid, int gr ...@@ -157,19 +155,19 @@ static void spreadChargeSSE(int start, int end, float* posq, float* grid, int gr
zindex[j] -= (zindex[j] >= gridz ? gridz : 0); zindex[j] -= (zindex[j] >= gridz ? gridz : 0);
} }
float charge = epsilonFactor*posq[4*i+3]; float charge = epsilonFactor*posq[4*i+3];
__m128 zdata0to3 = _mm_set_ps(extractFloat(data[3], 2), extractFloat(data[2], 2), extractFloat(data[1], 2), extractFloat(data[0], 2)); __m128 zdata0to3 = _mm_set_ps(EXTRACT_FLOAT(data[3], 2), EXTRACT_FLOAT(data[2], 2), EXTRACT_FLOAT(data[1], 2), EXTRACT_FLOAT(data[0], 2));
float zdata4 = extractFloat(data[4], 2); float zdata4 = EXTRACT_FLOAT(data[4], 2);
if (gridIndexZ+4 < gridz) { if (gridIndexZ+4 < gridz) {
for (int ix = 0; ix < PME_ORDER; ix++) { for (int ix = 0; ix < PME_ORDER; ix++) {
int xbase = gridIndexX+ix; int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0); xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz; xbase = xbase*gridy*gridz;
float xdata = charge*extractFloat(data[ix], 0); float xdata = charge*EXTRACT_FLOAT(data[ix], 0);
for (int iy = 0; iy < PME_ORDER; iy++) { for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy; int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0); ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz; ybase = xbase + ybase*gridz;
float multiplier = xdata*extractFloat(data[iy], 1); float multiplier = xdata*EXTRACT_FLOAT(data[iy], 1);
__m128 add0to3 = _mm_mul_ps(zdata0to3, _mm_set1_ps(multiplier)); __m128 add0to3 = _mm_mul_ps(zdata0to3, _mm_set1_ps(multiplier));
_mm_storeu_ps(&grid[ybase+gridIndexZ], _mm_add_ps(_mm_loadu_ps(&grid[ybase+gridIndexZ]), add0to3)); _mm_storeu_ps(&grid[ybase+gridIndexZ], _mm_add_ps(_mm_loadu_ps(&grid[ybase+gridIndexZ]), add0to3));
grid[ybase+zindex[4]] += multiplier*zdata4; grid[ybase+zindex[4]] += multiplier*zdata4;
...@@ -181,12 +179,12 @@ static void spreadChargeSSE(int start, int end, float* posq, float* grid, int gr ...@@ -181,12 +179,12 @@ static void spreadChargeSSE(int start, int end, float* posq, float* grid, int gr
int xbase = gridIndexX+ix; int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0); xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz; xbase = xbase*gridy*gridz;
float xdata = charge*extractFloat(data[ix], 0); float xdata = charge*EXTRACT_FLOAT(data[ix], 0);
for (int iy = 0; iy < PME_ORDER; iy++) { for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy; int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0); ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz; ybase = xbase + ybase*gridz;
float multiplier = xdata*extractFloat(data[iy], 1); float multiplier = xdata*EXTRACT_FLOAT(data[iy], 1);
__m128 add0to3 = _mm_mul_ps(zdata0to3, _mm_set1_ps(multiplier)); __m128 add0to3 = _mm_mul_ps(zdata0to3, _mm_set1_ps(multiplier));
_mm_store_ps(temp, add0to3); _mm_store_ps(temp, add0to3);
grid[ybase+zindex[0]] += temp[0]; grid[ybase+zindex[0]] += temp[0];
...@@ -200,97 +198,6 @@ static void spreadChargeSSE(int start, int end, float* posq, float* grid, int gr ...@@ -200,97 +198,6 @@ static void spreadChargeSSE(int start, int end, float* posq, float* grid, int gr
} }
} }
static void spreadChargeAVX(int start, int end, float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) {
float temp[8];
__m128 boxSize = _mm_set_ps(0, (float) periodicBoxSize[2], (float) periodicBoxSize[1], (float) periodicBoxSize[0]);
__m128 invBoxSize = _mm_set_ps(0, (float) (1/periodicBoxSize[2]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[0]));
__m128 gridSize = _mm_set_ps(0, gridz, gridy, gridx);
__m128i gridSizeInt = _mm_set_epi32(0, gridz, gridy, gridx);
__m128 one = _mm_set1_ps(1);
__m128 scale = _mm_set1_ps(1.0f/(PME_ORDER-1));
__m256i mask = _mm256_set_epi32(0, 0, 0, -1, -1, -1, -1, -1);
const float epsilonFactor = sqrt(ONE_4PI_EPS0);
memset(grid, 0, sizeof(float)*gridx*gridy*gridz);
for (int i = start; i < end; i++) {
// Find the position relative to the nearest grid point.
__m128 pos = _mm_load_ps(&posq[4*i]);
__m128 posInBox = _mm_sub_ps(pos, _mm_mul_ps(boxSize, _mm_floor_ps(_mm_mul_ps(pos, invBoxSize))));
__m128 t = _mm_mul_ps(_mm_mul_ps(posInBox, invBoxSize), gridSize);
__m128i ti = _mm_cvttps_epi32(t);
__m128 dr = _mm_sub_ps(t, _mm_cvtepi32_ps(ti));
__m128i gridIndex = _mm_sub_epi32(ti, _mm_and_si128(gridSizeInt, _mm_cmpeq_epi32(ti, gridSizeInt)));
// Compute the B-spline coefficients.
__m128 data[PME_ORDER];
data[PME_ORDER-1] = _mm_setzero_ps();
data[1] = dr;
data[0] = _mm_sub_ps(one, dr);
for (int j = 3; j < PME_ORDER; j++) {
__m128 div = _mm_set1_ps(1.0f/(j-1));
data[j-1] = _mm_mul_ps(_mm_mul_ps(div, dr), data[j-2]);
for (int k = 1; k < j-1; k++)
data[j-k-1] = _mm_mul_ps(div, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(k)), data[j-k-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(j-k), dr), data[j-k-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(div, _mm_sub_ps(one, dr)), data[0]);
}
data[PME_ORDER-1] = _mm_mul_ps(_mm_mul_ps(scale, dr), data[PME_ORDER-2]);
for (int j = 1; j < (PME_ORDER-1); j++)
data[PME_ORDER-j-1] = _mm_mul_ps(scale, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(j)), data[PME_ORDER-j-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(PME_ORDER-j), dr), data[PME_ORDER-j-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(scale, _mm_sub_ps(one, dr)), data[0]);
// Spread the charges.
int gridIndexX = _mm_extract_epi32(gridIndex, 0);
int gridIndexY = _mm_extract_epi32(gridIndex, 1);
int gridIndexZ = _mm_extract_epi32(gridIndex, 2);
float charge = epsilonFactor*posq[4*i+3];
__m256 zdata = _mm256_set_ps(0, 0, 0, extractFloat(data[4], 2), extractFloat(data[3], 2), extractFloat(data[2], 2), extractFloat(data[1], 2), extractFloat(data[0], 2));
if (gridIndexZ+5 < gridz) {
for (int ix = 0; ix < PME_ORDER; ix++) {
int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz;
float xdata = charge*extractFloat(data[ix], 0);
for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz;
float multiplier = xdata*extractFloat(data[iy], 1);
__m256 add = _mm256_mul_ps(zdata, _mm256_set1_ps(multiplier));
_mm256_maskstore_ps(&grid[ybase+gridIndexZ], mask, _mm256_add_ps(_mm256_maskload_ps(&grid[ybase+gridIndexZ], mask), add));
}
}
}
else {
int zindex[PME_ORDER];
for (int j = 0; j < PME_ORDER; j++) {
zindex[j] = gridIndexZ+j;
zindex[j] -= (zindex[j] >= gridz ? gridz : 0);
}
for (int ix = 0; ix < PME_ORDER; ix++) {
int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz;
float xdata = charge*extractFloat(data[ix], 0);
for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz;
float multiplier = xdata*extractFloat(data[iy], 1);
__m256 add = _mm256_mul_ps(zdata, _mm256_set1_ps(multiplier));
_mm256_store_ps(temp, add);
grid[ybase+zindex[0]] += temp[0];
grid[ybase+zindex[1]] += temp[1];
grid[ybase+zindex[2]] += temp[2];
grid[ybase+zindex[3]] += temp[3];
grid[ybase+zindex[4]] += temp[4];
}
}
}
}
}
static void computeReciprocalEterm(int start, int end, int gridx, int gridy, int gridz, vector<float>& recipEterm, double alpha, vector<float>* bsplineModuli, Vec3 periodicBoxSize) { static void computeReciprocalEterm(int start, int end, int gridx, int gridy, int gridz, vector<float>& recipEterm, double alpha, vector<float>* bsplineModuli, Vec3 periodicBoxSize) {
const unsigned int zsize = gridz/2+1; const unsigned int zsize = gridz/2+1;
const unsigned int yzsize = gridy*zsize; const unsigned int yzsize = gridy*zsize;
...@@ -443,22 +350,22 @@ static void interpolateForces(int start, int end, float* posq, float* force, flo ...@@ -443,22 +350,22 @@ static void interpolateForces(int start, int end, float* posq, float* force, flo
} }
__m128 zdata[PME_ORDER]; __m128 zdata[PME_ORDER];
for (int j = 0; j < PME_ORDER; j++) for (int j = 0; j < PME_ORDER; j++)
zdata[j] = _mm_set_ps(0, extractFloat(ddata[j], 2), extractFloat(data[j], 2), extractFloat(data[j], 2)); zdata[j] = _mm_set_ps(0, EXTRACT_FLOAT(ddata[j], 2), EXTRACT_FLOAT(data[j], 2), EXTRACT_FLOAT(data[j], 2));
__m128 f = _mm_set1_ps(0); __m128 f = _mm_set1_ps(0);
for (int ix = 0; ix < PME_ORDER; ix++) { for (int ix = 0; ix < PME_ORDER; ix++) {
int xbase = gridIndexX+ix; int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0); xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz; xbase = xbase*gridy*gridz;
float dx = extractFloat(data[ix], 0); float dx = EXTRACT_FLOAT(data[ix], 0);
float ddx = extractFloat(ddata[ix], 0); float ddx = EXTRACT_FLOAT(ddata[ix], 0);
__m128 xdata = _mm_set_ps(0, dx, dx, ddx); __m128 xdata = _mm_set_ps(0, dx, dx, ddx);
for (int iy = 0; iy < PME_ORDER; iy++) { for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy; int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0); ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz; ybase = xbase + ybase*gridz;
float dy = extractFloat(data[iy], 1); float dy = EXTRACT_FLOAT(data[iy], 1);
float ddy = extractFloat(ddata[iy], 1); float ddy = EXTRACT_FLOAT(ddata[iy], 1);
__m128 xydata = _mm_mul_ps(xdata, _mm_set_ps(0, dy, ddy, dy)); __m128 xydata = _mm_mul_ps(xdata, _mm_set_ps(0, dy, ddy, dy));
for (int iz = 0; iz < PME_ORDER; iz++) { for (int iz = 0; iz < PME_ORDER; iz++) {
...@@ -652,7 +559,6 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) { ...@@ -652,7 +559,6 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
else { else {
// This is a worker thread. // This is a worker thread.
bool useAVX = isAVXSupported();
int particleStart = (index*numParticles)/numThreads; int particleStart = (index*numParticles)/numThreads;
int particleEnd = ((index+1)*numParticles)/numThreads; int particleEnd = ((index+1)*numParticles)/numThreads;
int gridxStart = (index*gridx)/numThreads; int gridxStart = (index*gridx)/numThreads;
...@@ -664,10 +570,7 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) { ...@@ -664,10 +570,7 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
threadWait(); threadWait();
if (isDeleted) if (isDeleted)
break; break;
if (useAVX) spreadCharge(particleStart, particleEnd, posq, threadData[index]->tempGrid, gridx, gridy, gridz, numParticles, periodicBoxSize);
spreadChargeAVX(particleStart, particleEnd, posq, threadData[index]->tempGrid, gridx, gridy, gridz, numParticles, periodicBoxSize);
else
spreadChargeSSE(particleStart, particleEnd, posq, threadData[index]->tempGrid, gridx, gridy, gridz, numParticles, periodicBoxSize);
threadWait(); threadWait();
int numGrids = threadData.size(); int numGrids = threadData.size();
for (int i = gridStart; i < gridEnd; i += 4) { for (int i = gridStart; i < gridEnd; i += 4) {
...@@ -741,13 +644,3 @@ bool CpuCalcPmeReciprocalForceKernel::isProcessorSupported() { ...@@ -741,13 +644,3 @@ bool CpuCalcPmeReciprocalForceKernel::isProcessorSupported() {
} }
return false; return false;
} }
bool CpuCalcPmeReciprocalForceKernel::isAVXSupported() {
int cpuInfo[4];
cpuid(cpuInfo, 0);
if (cpuInfo[0] >= 1) {
cpuid(cpuInfo, 1);
return ((cpuInfo[2] & ((int) 1 << 28)) != 0);
}
return false;
}
\ No newline at end of file
plugins/cpupme/src/CpuPmeKernels.h
View file @ 8ed07b6f
...@@ -59,7 +59,6 @@ public: ...@@ -59,7 +59,6 @@ public:
private: private:
void threadWait(); void threadWait();
void advanceThreads(); void advanceThreads();
static bool isAVXSupported();
static bool hasInitializedThreads; static bool hasInitializedThreads;
static int numThreads; static int numThreads;
int gridx, gridy, gridz, numParticles; int gridx, gridy, gridz, numParticles;
......
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