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Optimize grouping indexes #1044

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Mar 14, 2024
Merged

Optimize grouping indexes #1044

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8701a7d
Replaced some bottleneck loop with blas
GiovanniBussi Mar 13, 2024
b2a66a5
Group indexes to make memory access faster
GiovanniBussi Mar 13, 2024
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80 changes: 66 additions & 14 deletions src/core/ActionAtomistic.cpp
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Expand Up @@ -98,6 +98,24 @@
if( atom_value_ind[i].first==0 ) unique.push_back(indexes[i]);
else if( atom_value_ind[i].second>0 ) error("action atomistic is not set up to deal with multiple vectors in position input");
}

atom_value_ind_grouped.clear();

if(atom_value_ind.size()>0) {
auto nn = atom_value_ind[0].first;
auto kk = atom_value_ind[0].second;
atom_value_ind_grouped.push_back(std::pair<std::size_t,std::vector<std::size_t>>(nn, {}));
atom_value_ind_grouped.back().second.push_back(kk);
auto prev_nn=nn;
for(unsigned i=1; i<atom_value_ind.size(); i++) {
auto nn = atom_value_ind[i].first;

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).
auto kk = atom_value_ind[i].second;

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if(nn!=prev_nn) atom_value_ind_grouped.push_back(std::pair<std::size_t,std::vector<std::size_t>>(nn, {}));
atom_value_ind_grouped.back().second.push_back(kk);
prev_nn=nn;
}
}

// Add the dependencies to the actions that we require
Tools::removeDuplicates(unique); value_depends.resize(0);
for(unsigned i=0; i<requirements.size(); ++i ) {
Expand Down Expand Up @@ -271,15 +289,34 @@
ActionToPutData* cv = chargev[0]->getPntrToAction()->castToActionToPutData();
if(cv) chargesWereSet=cv->hasBeenSet();
unsigned j = 0;
for(const auto & a : atom_value_ind) {
std::size_t nn = a.first, kk = a.second;
positions[j][0] = xpos[nn]->data[kk];
positions[j][1] = ypos[nn]->data[kk];
positions[j][2] = zpos[nn]->data[kk];
charges[j] = chargev[nn]->data[kk];
masses[j] = masv[nn]->data[kk];
j++;

// for(const auto & a : atom_value_ind) {
// std::size_t nn = a.first, kk = a.second;
// positions[j][0] = xpos[nn]->data[kk];
// positions[j][1] = ypos[nn]->data[kk];
// positions[j][2] = zpos[nn]->data[kk];
// charges[j] = chargev[nn]->data[kk];
// masses[j] = masv[nn]->data[kk];
// j++;
// }
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for(const auto & a : atom_value_ind_grouped) {
const auto nn=a.first;
auto & xp=xpos[nn]->data;
auto & yp=ypos[nn]->data;
auto & zp=zpos[nn]->data;
auto & ch=chargev[nn]->data;
auto & ma=masv[nn]->data;
for(const auto & kk : a.second) {
positions[j][0] = xp[kk];
positions[j][1] = yp[kk];
positions[j][2] = zp[kk];
charges[j] = ch[kk];
masses[j] = ma[kk];
j++;
}
}

}

void ActionAtomistic::setForcesOnAtoms(const std::vector<double>& forcesToApply, unsigned& ind) {
Expand All @@ -289,13 +326,28 @@
ypos[value_depends[i]]->hasForce = true;
zpos[value_depends[i]]->hasForce = true;
}
for(const auto & a : atom_value_ind) {
plumed_dbg_massert( ind<forcesToApply.size(), "problem setting forces in " + getLabel() );
std::size_t nn = a.first, kk = a.second;
xpos[nn]->inputForce[kk] += forcesToApply[ind]; ind++;
ypos[nn]->inputForce[kk] += forcesToApply[ind]; ind++;
zpos[nn]->inputForce[kk] += forcesToApply[ind]; ind++;

// for(const auto & a : atom_value_ind) {
// plumed_dbg_massert( ind<forcesToApply.size(), "problem setting forces in " + getLabel() );
// std::size_t nn = a.first, kk = a.second;
// xpos[nn]->inputForce[kk] += forcesToApply[ind]; ind++;
// ypos[nn]->inputForce[kk] += forcesToApply[ind]; ind++;
// zpos[nn]->inputForce[kk] += forcesToApply[ind]; ind++;
// }
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for(const auto & a : atom_value_ind_grouped) {
const auto nn=a.first;
plumed_dbg_assert(ind<forcesToApply.size()) << "problem setting forces in " << getLabel();
auto & xp=xpos[nn]->inputForce;
auto & yp=ypos[nn]->inputForce;
auto & zp=zpos[nn]->inputForce;
for(const auto & kk : a.second) {
xp[kk] += forcesToApply[ind]; ind++;
yp[kk] += forcesToApply[ind]; ind++;
zp[kk] += forcesToApply[ind]; ind++;
}
}

setForcesOnCell( forcesToApply, ind );
}

Expand Down
1 change: 1 addition & 0 deletions src/core/ActionAtomistic.h
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@ class ActionAtomistic :
std::vector<AtomNumber> indexes; // the set of needed atoms
std::vector<std::size_t> value_depends; // The list of values that are being used
std::vector<std::pair<std::size_t, std::size_t > > atom_value_ind; // The list of values and indices for the atoms that are being used
std::vector<std::pair<std::size_t,std::vector<std::size_t>>> atom_value_ind_grouped;
/// unique should be an ordered set since we later create a vector containing the corresponding indexes
std::vector<AtomNumber> unique;
/// unique_local should be an ordered set since we later create a vector containing the corresponding indexes
Expand Down
21 changes: 18 additions & 3 deletions src/core/ActionWithValue.cpp
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Expand Up @@ -25,6 +25,7 @@
#include "tools/Exception.h"
#include "tools/OpenMP.h"
#include "tools/Communicator.h"
#include "blas/blas.h"

namespace PLMD {

Expand Down Expand Up @@ -296,12 +297,26 @@
for(unsigned i=rank; i<nvalsWithForce; i+=stride) {
double ff=values[valsToForce[i]]->inputForce[0];
std::vector<double> & thisderiv( values[valsToForce[i]]->data );
if( nt>1 ) for(unsigned j=0; j<nder; ++j) omp_f[j] += ff*thisderiv[1+j];
else for(unsigned j=0; j<nder; ++j) forcesForApply[j] += ff*thisderiv[1+j];
int nn=nder;
int one1=1;
int one2=1;
if( nt>1 ) plumed_blas_daxpy(&nn,&ff,thisderiv.data()+1,&one1,omp_f.data(),&one2);
else plumed_blas_daxpy(&nn,&ff,thisderiv.data()+1,&one1,forcesForApply.data(),&one2);
// if( nt>1 ) for(unsigned j=0; j<nder; ++j) omp_f[j] += ff*thisderiv[1+j];
//else for(unsigned j=0; j<nder; ++j) forcesForApply[j] += ff*thisderiv[1+j];
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}
#pragma omp critical
{
if( nt>1 ) for(unsigned j=0; j<forcesForApply.size(); ++j) forcesForApply[j]+=omp_f[j];
if( nt>1 ) {
int nn=forcesForApply.size();
double one0=1.0;
int one1=1;
int one2=1;
plumed_blas_daxpy(&nn,&one0,omp_f.data(),&one1,forcesForApply.data(),&one2);
}
// for(unsigned j=0; j<forcesForApply.size(); ++j) {
// forcesForApply[j]+=omp_f[j];
// }
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}
}

Expand Down
23 changes: 18 additions & 5 deletions src/core/ActionWithVirtualAtom.cpp
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Expand Up @@ -21,6 +21,7 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "ActionWithVirtualAtom.h"
#include <array>
#include <iostream>

namespace PLMD {

Expand Down Expand Up @@ -71,12 +72,24 @@
double xf = xval->inputForce[0];
double yf = yval->inputForce[0];
double zf = zval->inputForce[0];
for(const auto & a : atom_value_ind) {
std::size_t nn = a.first, kk = a.second;
xpos[nn]->inputForce[kk] += xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++;
ypos[nn]->inputForce[kk] += xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++;
zpos[nn]->inputForce[kk] += xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++;
// for(const auto & a : atom_value_ind) {
// std::size_t nn = a.first, kk = a.second;
// xpos[nn]->inputForce[kk] += xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++;
// ypos[nn]->inputForce[kk] += xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++;
// zpos[nn]->inputForce[kk] += xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++;
// }
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for(const auto & a : atom_value_ind_grouped) {
const auto nn=a.first;
auto & xp=xpos[nn]->inputForce;
auto & yp=ypos[nn]->inputForce;
auto & zp=zpos[nn]->inputForce;
for(const auto & kk : a.second) {
xp[kk] += xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++;
yp[kk] += xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++;
zp[kk] += xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++;
}
}

std::array<double,9> virial;
for(unsigned i=0; i<9; ++i) { virial[i] = xf*xval->data[1+k] + yf*yval->data[1+k] + zf*zval->data[1+k]; k++; }
unsigned ind = 0; setForcesOnCell( virial.data(), virial.size(), ind );
Expand Down
2 changes: 1 addition & 1 deletion src/core/Makefile
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@@ -1,4 +1,4 @@
USE=config tools lepton small_vector
USE=config tools lepton small_vector blas

# generic makefile
include ../maketools/make.module
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