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Experimental addition of openmp statements
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@richardjgowers
richardjgowers committed Apr 29, 2015
1 parent 566f3ee commit 9ead3c4
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Showing 4 changed files with 11,153 additions and 3 deletions.
6 changes: 4 additions & 2 deletions package/setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -209,6 +209,7 @@ def detect_openmp():
has_openmp, needs_gomp = detect_openmp()
parallel_args = ['-fopenmp'] if has_openmp else []
parallel_libraries = ['gomp'] if needs_gomp else []
parallel_macros = [('PARALLEL', None)] if has_openmp else []

extensions = [
Extension('coordinates._dcdmodule', ['src/dcd/dcd.c'],
Expand All @@ -225,11 +226,12 @@ def detect_openmp():
define_macros=define_macros,
extra_compile_args=extra_compile_args),
Extension("core.parallel.distances",
['src/numtools/distances_parallel.%s' % ("pyx" if use_cython else "c")],
['src/numtools/distances_parallel2.%s' % ("pyx" if use_cython else "c")],
include_dirs=include_dirs,
libraries=['m'] + parallel_libraries,
extra_compile_args=parallel_args,
extra_link_args=parallel_args),
extra_link_args=parallel_args,
define_macros=parallel_macros),
Extension('core.qcprot', ['src/pyqcprot/pyqcprot.%s' % ("pyx" if use_cython else "c")],
include_dirs=include_dirs,
extra_compile_args=["-O3", "-ffast-math"]),
Expand Down
53 changes: 52 additions & 1 deletion package/src/numtools/calc_distances.h
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,10 @@
#include <float.h>
typedef float coordinate[3];

#ifdef PARALLEL
#include <omp.h>
#endif

static void minimum_image(double *x, float *box, float *inverse_box)
{
int i;
Expand Down Expand Up @@ -83,7 +87,10 @@ static void calc_distance_array(coordinate* ref, int numref, coordinate* conf, i
inverse_box[0] = 1.0/box[0];
inverse_box[1] = 1.0/box[1];
inverse_box[2] = 1.0/box[2];


#ifdef PARALLEL
#pragma omp parallel for private(i, j, dx, rsq) shared(numref, numconf, conf, ref, box, inverse_box, distances)
#endif
for (i=0; i < numref; i++) {
for (j=0; j < numconf; j++) {
dx[0] = conf[j][0]-ref[i][0];
Expand All @@ -103,6 +110,9 @@ static void calc_distance_array_noPBC(coordinate* ref, int numref, coordinate* c
double dx[3];
double rsq;

#ifdef PARALLEL
#pragma omp parallel for private(i, j, dx, rsq) shared(numref, numconf, conf, ref, distances)
#endif
for (i=0; i < numref; i++) {
for (j=0; j < numconf; j++) {
dx[0] = conf[j][0]-ref[i][0];
Expand All @@ -126,6 +136,8 @@ static void calc_self_distance_array(coordinate* ref, int numref, float* box, do
inverse_box[1] = 1.0/box[1];
inverse_box[2] = 1.0/box[2];

// TODO: Make me parallel
// Have to replace distpos with a thread independent way of knowing where in distances to drop values
distpos = 0;
for (i=0; i < numref; i++) {
for (j=i+1; j < numref; j++) {
Expand All @@ -148,6 +160,8 @@ static void calc_self_distance_array_noPBC(coordinate* ref, int numref, double*
double dx[3];
double rsq;

// TODO: Make me parallel
// Have to replace distpos with a thread independent way of knowing where in distances to drop values
distpos = 0;
for (i=0; i < numref; i++) {
for (j=i+1; j < numref; j++) {
Expand Down Expand Up @@ -185,6 +199,9 @@ static void coord_transform(coordinate* coords, int numCoords, coordinate* box)
static void ortho_pbc(coordinate* coords, int numcoords, float* box, float* box_inverse){
int i, s[3];
// Moves all coordinates to within the box boundaries for a orthogonal box
#ifdef PARALLEL
#pragma omp parallel for private(i, s) shared(numcoords, coords, box_inverse)
#endif
for (i=0; i < numcoords; i++){
s[0] = floor(coords[i][0] * box_inverse[0]);
s[1] = floor(coords[i][1] * box_inverse[1]);
Expand All @@ -198,6 +215,9 @@ static void triclinic_pbc(coordinate* coords, int numcoords, coordinate* box, fl
int i, s;
// Moves all coordinates to within the box boundaries for a triclinic box
// Assumes box having zero values for box[0][1], box[0][2] and box [1][2]
#ifdef PARALLEL
#pragma omp parallel for private(i, s) shared(coords, box)
#endif
for (i=0; i < numcoords; i++){
// z
s = floor(coords[i][2] * box_inverse[2]);
Expand Down Expand Up @@ -231,6 +251,9 @@ static void calc_distance_array_triclinic(coordinate* ref, int numref, coordinat
triclinic_pbc(ref, numref, box, box_inverse);
triclinic_pbc(conf, numconf, box, box_inverse);

#ifdef PARALLEL
#pragma omp parallel for private(i, j, dx, rsq) shared(numref, numconf, conf, ref, distances)
#endif
for (i=0; i < numref; i++){
for (j=0; j < numconf; j++){
dx[0] = conf[j][0] - ref[i][0];
Expand Down Expand Up @@ -259,6 +282,7 @@ static void calc_self_distance_array_triclinic(coordinate* ref, int numref, coor

triclinic_pbc(ref, numref, box, box_inverse);

// TODO: Parallelise
distpos = 0;
for (i=0; i < numref; i++){
for (j=i+1; j < numref; j++){
Expand All @@ -284,6 +308,9 @@ static void calc_bond_distance(coordinate* atom1, coordinate* atom2, int numatom
inverse_box[1] = 1.0/box[1];
inverse_box[2] = 1.0/box[2];

#ifdef PARALLEL
#pragma omp parallel for private(i, dx, rsq) shared(numatom, box, inverse_box, distances)
#endif
for (i=0; i<numatom; i++) {
dx[0] = atom1[i][0] - atom2[i][0];
dx[1] = atom1[i][1] - atom2[i][1];
Expand Down Expand Up @@ -312,6 +339,9 @@ static void calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, i
triclinic_pbc(atom1, numatom, box, box_inverse);
triclinic_pbc(atom2, numatom, box, box_inverse);

#ifdef PARALLEL
#pragma omp parallel for private(i, dx, rsq) shared(numatom, atom1, atom2, distances, box, box_half)
#endif
for (i=0; i<numatom; i++) {
dx[0] = atom1[i][0] - atom2[i][0];
dx[1] = atom1[i][1] - atom2[i][1];
Expand All @@ -328,6 +358,9 @@ static void calc_bond_distance_noPBC(coordinate* atom1, coordinate* atom2, int n
double dx[3];
double rsq;

#ifdef PARALLEL
#pragma omp parallel for private(i, dx, rsq) shared(numatom, atom1, atom2, distances)
#endif
for (i=0; i<numatom; i++) {
dx[0] = atom1[i][0] - atom2[i][0];
dx[1] = atom1[i][1] - atom2[i][1];
Expand All @@ -343,6 +376,9 @@ static void calc_angle(coordinate* atom1, coordinate* atom2, coordinate* atom3,
double rji[3], rjk[3];
double x, y, xp[3];

#ifdef PARALLEL
#pragma omp parallel for private(i, rji, rjk, x, xp, y) shared(numatom, atom1, atom2, atom3, angles)
#endif
for (i=0; i<numatom; i++) {
rji[0] = atom1[i][0] - atom2[i][0];
rji[1] = atom1[i][1] - atom2[i][1];
Expand Down Expand Up @@ -379,6 +415,9 @@ static void calc_angle_ortho(coordinate* atom1, coordinate* atom2, coordinate* a
inverse_box[1] = 1.0/box[1];
inverse_box[2] = 1.0/box[2];

#ifdef PARALLEL
#pragma omp parallel for private(i, rji, rjk, x, xp, y) shared(numatom, atom1, atom2, atom3, angles, box, inverse_box)
#endif
for (i=0; i<numatom; i++) {
rji[0] = atom1[i][0] - atom2[i][0];
rji[1] = atom1[i][1] - atom2[i][1];
Expand Down Expand Up @@ -421,6 +460,9 @@ static void calc_angle_triclinic(coordinate* atom1, coordinate* atom2, coordinat
triclinic_pbc(atom2, numatom, box, box_inverse);
triclinic_pbc(atom3, numatom, box, box_inverse);

#ifdef PARALLEL
#pragma omp parallel for private(i, rji, rjk, x, xp, y) shared(numatom, atom1, atom2, atom3, angles, box, box_half)
#endif
for (i=0; i<numatom; i++) {
rji[0] = atom1[i][0] - atom2[i][0];
rji[1] = atom1[i][1] - atom2[i][1];
Expand Down Expand Up @@ -453,6 +495,9 @@ static void calc_torsion(coordinate* atom1, coordinate* atom2, coordinate* atom3
double xp[3];
double x, y;

#ifdef PARALLEL
#pragma omp parallel for private(i, va, vb, vc, n1, n2, x, y, xp) shared(numatom, atom1, atom2, atom3, atom4, angles)
#endif
for (i=0; i<numatom; i++) {
// connecting vectors between all 4 atoms: 1 -va-> 2 -vb-> 3 -vc-> 4
va[0] = atom2[i][0] - atom1[i][0];
Expand Down Expand Up @@ -504,6 +549,9 @@ static void calc_torsion_ortho(coordinate* atom1, coordinate* atom2, coordinate*
inverse_box[1] = 1.0/box[1];
inverse_box[2] = 1.0/box[2];

#ifdef PARALLEL
#pragma omp parallel for private(i, va, vb, vc, n1, n2, x, y, xp) shared(numatom, atom1, atom2, atom3, atom4, angles, box, inverse_box)
#endif
for (i=0; i<numatom; i++) {
// connecting vectors between all 4 atoms: 1 -va-> 2 -vb-> 3 -vc-> 4
va[0] = atom2[i][0] - atom1[i][0];
Expand Down Expand Up @@ -567,6 +615,9 @@ static void calc_torsion_triclinic(coordinate* atom1, coordinate* atom2, coordin
triclinic_pbc(atom3, numatom, box, box_inverse);
triclinic_pbc(atom4, numatom, box, box_inverse);

#ifdef PARALLEL
#pragma omp parallel for private(i, va, vb, vc, n1, n2, x, y, xp) shared(numatom, atom1, atom2, atom3, atom4, angles, box, box_half)
#endif
for (i=0; i<numatom; i++) {
// connecting vectors between all 4 atoms: 1 -va-> 2 -vb-> 3 -vc-> 4
va[0] = atom2[i][0] - atom1[i][0];
Expand Down
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