void SMCTest::test_itw_Lsodar()
{
initTwisting();
SP::ControlLsodarSimulation simLsodar(new ControlLsodarSimulation(_t0, _T, _h));
simLsodar->setSaveOnlyMainSimulation(true);
simLsodar->addDynamicalSystem(_DS);
simLsodar->addSensor(_sensor, _h);
simLsodar->addActuator(_itw, _h);
simLsodar->initialize();
simLsodar->run();
SimpleMatrix& data = *simLsodar->data();
ioMatrix::write("itw_Lsodar.dat", "ascii", data, "noDim");
// Reference Matrix
SimpleMatrix dataRef(data);
dataRef.zero();
ioMatrix::read("itw.ref", "ascii", dataRef);
// it is a bad idea to compare solutions to an AVI that does not admit a unique solution
SiconosVector lambda1 = SiconosVector(data.size(0));
SiconosVector lambda2 = SiconosVector(data.size(0));
data.getCol(3, lambda1);
data.getCol(4, lambda2);
axpy(_beta, lambda2, lambda1);
SiconosVector lambda1Ref = SiconosVector(data.size(0));
SiconosVector lambda2Ref = SiconosVector(data.size(0));
dataRef.getCol(3, lambda1Ref);
dataRef.getCol(4, lambda2Ref);
axpy(_beta, lambda2Ref, lambda1Ref);
data.setCol(3, lambda1);
dataRef.setCol(3, lambda1Ref);
data.resize(data.size(0), 4);
dataRef.resize(data.size(0), 4);
std::cout << "------- Integration done, error = " << (data - dataRef).normInf() << " -------" <<std::endl;
CPPUNIT_ASSERT_EQUAL_MESSAGE("test_itw_Lsodar : ", (data - dataRef).normInf() < _tol, true);
}
void backwardOneInput(int layerId, const UpdateCallback& callback) {
const MatrixPtr& inputMat = getInputValue(layerId);
const MatrixPtr& inputGradMat = getInputGrad(layerId);
const MatrixPtr& weightMat = weights_[layerId]->getW();
const MatrixPtr& weightGradMat = weights_[layerId]->getWGrad();
int dim = inputMat->getWidth();
real* sampleGrad = sampleOut_.grad->getData();
if (weightGradMat) {
for (size_t i = 0; i < samples_.size(); ++i) {
axpy(dim,
sampleGrad[i],
inputMat->getRowBuf(samples_[i].sampleId),
weightGradMat->getRowBuf(samples_[i].labelId));
}
weights_[layerId]->incUpdate(callback);
}
if (inputGradMat) {
for (size_t i = 0; i < samples_.size(); ++i) {
axpy(dim,
sampleGrad[i],
weightMat->getRowBuf(samples_[i].labelId),
inputGradMat->getRowBuf(samples_[i].sampleId));
}
}
}
void cg(eval_t A, Matrix b, double tolerance, void* ctx)
{
Matrix r = createMatrix(b->rows, b->cols);
Matrix p = createMatrix(b->rows, b->cols);
Matrix buffer = createMatrix(b->rows, b->cols);
double dotp = 1000;
double rdr = dotp;
copyVector(r->as_vec,b->as_vec);
fillVector(b->as_vec, 0.0);
int i=0;
while (i < b->as_vec->len && rdr > tolerance) {
++i;
if (i == 1) {
copyVector(p->as_vec,r->as_vec);
dotp = innerproduct(r->as_vec,r->as_vec);
} else {
double dotp2 = innerproduct(r->as_vec,r->as_vec);
double beta = dotp2/dotp;
dotp = dotp2;
scaleVector(p->as_vec,beta);
axpy(p->as_vec,r->as_vec,1.0);
}
A(buffer,p,ctx);
double alpha = dotp/innerproduct(p->as_vec,buffer->as_vec);
axpy(b->as_vec,p->as_vec,alpha);
axpy(r->as_vec,buffer->as_vec,-alpha);
rdr = sqrt(innerproduct(r->as_vec,r->as_vec));
}
printf("%i iterations\n",i);
freeMatrix(r);
freeMatrix(p);
freeMatrix(buffer);
}
void Basic_Agent::set_internal_uptake_constants( double dt )
{
// overall form: dp/dt = S*(T-p) - U*p
// p(n+1) - p(n) = dt*S(n)*T(n) - dt*( S(n) + U(n))*p(n+1)
// p(n+1)*temp2 = p(n) + temp1
// p(n+1) = ( p(n) + temp1 )/temp2
//int nearest_voxel= current_voxel_index;
double internal_constant_to_discretize_the_delta_approximation = dt * volume / ( (microenvironment->voxels(current_voxel_index)).volume ) ; // needs a fix
// before the fix on September 28, 2015. Also, switched on this day
// from Delta function sources/sinks to volumetric
/*
// temp1 = dt*S*T
cell_source_sink_solver_temp1 = *secretion_rates;
cell_source_sink_solver_temp1 *= *saturation_densities;
cell_source_sink_solver_temp1 *= dt;
// temp2 = 1 + dt*( S + U )
cell_source_sink_solver_temp2.assign( (*secretion_rates).size() , 1.0 );
axpy( &(cell_source_sink_solver_temp2) , dt , *secretion_rates );
axpy( &(cell_source_sink_solver_temp2) , dt , *uptake_rates );
*/
// temp1 = dt*(V_cell/V_voxel)*S*T
cell_source_sink_solver_temp1.assign( (*secretion_rates).size() , 0.0 );
cell_source_sink_solver_temp1 += *secretion_rates;
cell_source_sink_solver_temp1 *= *saturation_densities;
cell_source_sink_solver_temp1 *= internal_constant_to_discretize_the_delta_approximation;
// temp2 = 1 + dt*(V_cell/V_voxel)*( S + U )
cell_source_sink_solver_temp2.assign( (*secretion_rates).size() , 1.0 );
axpy( &(cell_source_sink_solver_temp2) , internal_constant_to_discretize_the_delta_approximation , *secretion_rates );
axpy( &(cell_source_sink_solver_temp2) , internal_constant_to_discretize_the_delta_approximation , *uptake_rates );
}
void CBOW_NS::update(uint64_t cur, const vector<uint64_t>& context, real alpha) {
_in.clear();
for (vector<uint64_t>::const_iterator i = context.begin(); i != context.end(); ++i) {
_in.push_back(_net.get_input_vec(*i));
}
_out.clear();
_out.push_back(_net.get_output_vec(cur));
for (unsigned i = 0; i < _neg_sample_cnt; ++i) {
_out.push_back(_net.get_output_vec(_vocab.sampling(&_seed)));
}
memset(_hidden_vec, 0, sizeof(real) * _sz);
for (vector<const real*>::const_iterator i = _in.begin(); i != _in.end(); ++i) {
addto(_sz, *i, _hidden_vec);
}
scale(_sz, static_cast<real>(1.0) / _in.size(), _hidden_vec);
memset(_hidden_vec_grad, 0, sizeof(real) * _sz);
for (size_t i = 0; i != _out.size(); ++i) {
real sigma = sigmoid(dot(_sz, _hidden_vec, _out[i]));
int label = (i==0) ? 1 : 0;
real coef = (label - sigma) * alpha;
axpy(_sz, coef, _out[i], _hidden_vec_grad);
axpy(_sz, coef, _hidden_vec, const_cast<real*>(_out[i]));
}
scale(_sz, static_cast<real>(1.0) / _in.size(), _hidden_vec_grad);
for (size_t i = 0; i != _in.size(); ++i) {
addto(_sz, _hidden_vec_grad, const_cast<real*>(_in[i]));
}
}
void ElecMinimizer::step(const ElecGradient& dir, double alpha)
{ myassert(dir.eInfo == &eInfo);
for(int q=eInfo.qStart; q<eInfo.qStop; q++)
{ if(dir.Y[q]) axpy(alpha, dir.Y[q], eVars.Y[q]);
if(dir.B[q]) axpy(alpha, dir.B[q], eVars.B[q]);
}
}
int cg(Matrix A, Vector b, double tolerance)
{
int i=0, j;
double rl;
Vector r = createVector(b->len);
Vector p = createVector(b->len);
Vector buffer = createVector(b->len);
double dotp = 1000;
double rdr = dotp;
copyVector(r,b);
fillVector(b, 0.0);
rl = sqrt(dotproduct(r,r));
while (i < b->len && rdr > tolerance*rl) {
++i;
if (i == 1) {
copyVector(p,r);
dotp = dotproduct(r,r);
} else {
double dotp2 = dotproduct(r,r);
double beta = dotp2/dotp;
dotp = dotp2;
scaleVector(p,beta);
axpy(p,r,1.0);
}
MxV(buffer, p);
double alpha = dotp/dotproduct(p,buffer);
axpy(b,p,alpha);
axpy(r,buffer,-alpha);
rdr = sqrt(dotproduct(r,r));
}
freeVector(r);
freeVector(p);
freeVector(buffer);
return i;
}
void axpy(double alpha, const ElecGradient& x, ElecGradient& y)
{ myassert(x.eInfo == y.eInfo);
for(int q=x.eInfo->qStart; q<x.eInfo->qStop; q++)
{ if(x.Y[q]) { if(y.Y[q]) axpy(alpha, x.Y[q], y.Y[q]); else y.Y[q] = alpha*x.Y[q]; }
if(x.B[q]) { if(y.B[q]) axpy(alpha, x.B[q], y.B[q]); else y.B[q] = alpha*x.B[q]; }
}
}
void CBOW_HS::update(uint64_t cur, const vector<uint64_t>& context, real alpha) {
_in.clear();
for (vector<uint64_t>::const_iterator i = context.begin(); i != context.end(); ++i) {
_in.push_back(_net.get_input_vec(*i));
}
memset(_hidden_vec, 0, sizeof(real) * _sz);
for (vector<const real*>::const_iterator i = _in.begin(); i != _in.end(); ++i) {
addto(_sz, *i, _hidden_vec);
}
scale(_sz, static_cast<real>(1.0) / _in.size(), _hidden_vec);
const vector<char>& code = _huffman_tree.code(cur);
const vector<uint64_t>& path = _huffman_tree.path(cur);
memset(_hidden_vec_grad, 0, sizeof(real) * _sz);
for (size_t i = 0; i != path.size(); ++i) {
real* out = _net.get_output_vec(path[i]);
real sigma = sigmoid(dot(_sz, _hidden_vec, out));
int label = code[i];
real coef = (label - sigma) * alpha;
axpy(_sz, coef, out, _hidden_vec_grad);
axpy(_sz, coef, _hidden_vec, out);
}
scale(_sz, static_cast<real>(1.0) / _in.size(), _hidden_vec_grad);
for (size_t i = 0; i != _in.size(); ++i) {
addto(_sz, _hidden_vec_grad, const_cast<real*>(_in[i]));
}
}
void bi::mean(const UniformPdf<V1>& q, V2 mu) {
/* pre-condition */
BI_ASSERT(q.size() == mu.size());
axpy(0.5, q.lower(), mu, true);
axpy(0.5, q.upper(), mu);
}
/*
* Solves lapl(u) x = b, for x, given b, using Conjugate Gradient
*/
void
cg(latparams lp, field **x, field **b, link **g)
{
size_t L = lp.L;
int max_iter = 100;
float tol = 1e-9;
/* Temporary fields needed for CG */
field **r = new_field(lp);
field **p = new_field(lp);
field **Ap = new_field(lp);
/* Initial residual and p-vector */
lapl(lp, r, x, g);
xmy(lp, b, r);
xeqy(lp, p, r);
/* Initial r-norm and b-norm */
float rr = xdotx(lp, r);
float bb = xdotx(lp, b);
double t_lapl = 0;
int iter = 0;
for(iter=0; iter<max_iter; iter++) {
printf(" %6d, res = %+e\n", iter, rr/bb);
if(sqrt(rr/bb) < tol)
break;
double t = stop_watch(0);
lapl(lp, Ap, p, g);
t_lapl += stop_watch(t);
float pAp = xdoty(lp, p, Ap);
float alpha = rr/pAp;
axpy(lp, alpha, p, x);
axpy(lp, -alpha, Ap, r);
float r1r1 = xdotx(lp, r);
float beta = r1r1/rr;
xpay(lp, r, beta, p);
rr = r1r1;
}
/* Recompute residual after convergence */
lapl(lp, r, x, g);
xmy(lp, b, r);
rr = xdotx(lp, r);
double beta_fp = 50*((double)L*L*L)/(t_lapl/(double)iter)*1e-9;
double beta_io = 40*((double)L*L*L)/(t_lapl/(double)iter)*1e-9;
printf(" Converged after %6d iterations, res = %+e\n", iter, rr/bb);
printf(" Time in lapl(): %+6.3e sec/call, %4.2e Gflop/s, %4.2e GB/s\n",
t_lapl/(double)iter, beta_fp, beta_io);
del_field(r);
del_field(p);
del_field(Ap);
return;
}
void cgsolve(
const CrsMatrix<AScalarType,Device> & A ,
const View<VScalarType*,LayoutRight,Device> & b ,
const View<VScalarType*,LayoutRight,Device> & x ,
size_t & iteration ,
double & normr ,
double & iter_time ,
const size_t maximum_iteration = 200 ,
const double tolerance = std::numeric_limits<VScalarType>::epsilon() )
{
typedef View<VScalarType*,LayoutRight,Device> vector_type ;
const size_t count = b.dimension_0();
vector_type p ( "cg::p" , count );
vector_type r ( "cg::r" , count );
vector_type Ap( "cg::Ap", count );
/* r = b - A * x ; */
/* p = x */ deep_copy( p , x );
/* Ap = A * p */ multiply( A , p , Ap );
/* r = b - Ap */ waxpby( count , 1.0 , b , -1.0 , Ap , r );
/* p = r */ deep_copy( p , r );
double old_rdot = dot( count , r );
normr = std::sqrt( old_rdot );
iteration = 0 ;
Kokkos::Impl::Timer wall_clock ;
while ( tolerance < normr && iteration < maximum_iteration ) {
/* pAp_dot = dot( p , Ap = A * p ) */
/* Ap = A * p */ multiply( A , p , Ap );
const double pAp_dot = dot( count , p , Ap );
const double alpha = old_rdot / pAp_dot ;
/* x += alpha * p ; */ axpy( count, alpha, p , x );
/* r -= alpha * Ap ; */ axpy( count, -alpha, Ap, r );
const double r_dot = dot( count , r );
const double beta = r_dot / old_rdot ;
/* p = r + beta * p ; */ xpby( count , r , beta , p );
normr = std::sqrt( old_rdot = r_dot );
++iteration ;
}
iter_time = wall_clock.seconds();
}
/*
* Solves lapl(u) x = b, for x, given b, using Conjugate Gradient
*/
void
cg(size_t L, _Complex float *x, _Complex float *b, _Complex float *u)
{
int max_iter = 100;
float tol = 1e-6;
/* Temporary fields needed for CG */
_Complex float *r = new_field(L);
_Complex float *p = new_field(L);
_Complex float *Ap = new_field(L);
/* Initial residual and p-vector */
lapl(L, r, x, u);
xmy(L, b, r);
xeqy(L, p, r);
/* Initial r-norm and b-norm */
float rr = xdotx(L, r);
float bb = xdotx(L, b);
double t_lapl = 0;
int iter = 0;
for(iter=0; iter<max_iter; iter++) {
printf(" %6d, res = %+e\n", iter, rr/bb);
if(sqrt(rr/bb) < tol)
break;
double t = stop_watch(0);
lapl(L, Ap, p, u);
t_lapl += stop_watch(t);
float pAp = xdoty(L, p, Ap);
float alpha = rr/pAp;
axpy(L, alpha, p, x);
axpy(L, -alpha, Ap, r);
float r1r1 = xdotx(L, r);
float beta = r1r1/rr;
xpay(L, r, beta, p);
rr = r1r1;
}
/* Recompute residual after convergence */
lapl(L, r, x, u);
xmy(L, b, r);
rr = xdotx(L, r);
double beta_fp = 34*L*L/(t_lapl/(double)iter)*1e-9;
double beta_io = 32*L*L/(t_lapl/(double)iter)*1e-9;
printf(" Converged after %6d iterations, res = %+e\n", iter, rr/bb);
printf(" Time in lapl(): %+6.3e sec/call, %4.2e Gflop/s, %4.2e GB/s\n",
t_lapl/(double)iter, beta_fp, beta_io);
free(r);
free(p);
free(Ap);
return;
}
int GaussJacobiPoisson1D(Vector u, double tol, int maxit)
{
int it=0, i;
Vector b = cloneVector(u);
Vector e = cloneVector(u);
copyVector(b, u);
fillVector(u, 0.0);
double max = tol+1;
while (max > tol && ++it < maxit) {
copyVector(e, u);
collectVector(e);
copyVector(u, b);
#pragma omp parallel for schedule(static)
for (i=1;i<e->len-1;++i) {
u->data[i] += e->data[i-1];
u->data[i] += e->data[i+1];
u->data[i] /= (2.0+alpha);
}
axpy(e, u, -1.0);
e->data[0] = e->data[e->len-1] = 0.0;
max = maxNorm(e);
}
freeVector(b);
freeVector(e);
return it;
}
int GaussJacobiPoisson1D(Vector u, double tol, int maxit)
{
int it=0, i;
double rl;
double max = tol+1;
Vector b = createVector(u->len);
Vector e = createVector(u->len);
copyVector(b, u);
fillVector(u, 0.0);
rl = maxNorm(b);
while (max > tol*rl && ++it < maxit) {
copyVector(e, u);
copyVector(u, b);
#pragma omp parallel for schedule(static)
for (i=0;i<e->len;++i) {
if (i > 0)
u->data[i] += e->data[i-1];
if (i < e->len-1)
u->data[i] += e->data[i+1];
u->data[i] /= (2.0+alpha);
}
axpy(e, u, -1.0);
max = maxNorm(e);
}
freeVector(b);
freeVector(e);
return it;
}
/* ************************************************************************* */
VectorValues DoglegOptimizerImpl::ComputeBlend(double delta, const VectorValues& x_u, const VectorValues& x_n, const bool verbose) {
// See doc/trustregion.lyx or doc/trustregion.pdf
// Compute inner products
const double un = dot(x_u, x_n);
const double uu = dot(x_u, x_u);
const double nn = dot(x_n, x_n);
// Compute quadratic formula terms
const double a = uu - 2.*un + nn;
const double b = 2. * (un - uu);
const double c = uu - delta*delta;
double sqrt_b_m4ac = std::sqrt(b*b - 4*a*c);
// Compute blending parameter
double tau1 = (-b + sqrt_b_m4ac) / (2.*a);
double tau2 = (-b - sqrt_b_m4ac) / (2.*a);
double tau;
if(0.0 <= tau1 && tau1 <= 1.0) {
assert(!(0.0 <= tau2 && tau2 <= 1.0));
tau = tau1;
} else {
assert(0.0 <= tau2 && tau2 <= 1.0);
tau = tau2;
}
// Compute blended point
if(verbose) cout << "In blend region with fraction " << tau << " of Newton's method point" << endl;
VectorValues blend = (1. - tau) * x_u; axpy(tau, x_n, blend);
return blend;
}
void bi::marginalise(const ExpGaussianPdf<V1, M1>& p1,
const ExpGaussianPdf<V2,M2>& p2, const M3 C,
const ExpGaussianPdf<V4, M4>& q2, ExpGaussianPdf<V5,M5>& p3) {
/* pre-conditions */
BI_ASSERT(q2.size() == p2.size());
BI_ASSERT(p3.size() == p1.size());
BI_ASSERT(C.size1() == p1.size() && C.size2() == p2.size());
typename sim_temp_vector<V1>::type z2(p2.size());
typename sim_temp_matrix<M1>::type K(p1.size(), p2.size());
typename sim_temp_matrix<M1>::type A1(p2.size(), p2.size());
typename sim_temp_matrix<M1>::type A2(p2.size(), p2.size());
/**
* Compute gain matrix:
*
* \f[\mathcal{K} = C_{\mathbf{x}_1,\mathbf{x}_2}\Sigma_2^{-1}\,.\f]
*/
symm(1.0, p2.prec(), C, 0.0, K, 'R', 'U');
/**
* Then result is given by \f$\mathcal{N}(\boldsymbol{\mu}',
* \Sigma')\f$, where:
*
* \f[\boldsymbol{\mu}' = \boldsymbol{\mu}_1 +
* \mathcal{K}(\boldsymbol{\mu}_3 - \boldsymbol{\mu}_2)\,,\f]
*/
z2 = q2.mean();
axpy(-1.0, p2.mean(), z2);
p3.mean() = p1.mean();
gemv(1.0, K, z2, 1.0, p3.mean());
/**
* and:
*
* \f{eqnarray*}
* \Sigma' &=& \Sigma_1 + \mathcal{K}(\Sigma_3 -
* \Sigma_2)\mathcal{K}^T \\
* &=& \Sigma_1 + \mathcal{K}\Sigma_3\mathcal{K}^T -
* \mathcal{K}\Sigma_2\mathcal{K}^T\,.
* \f}
*/
p3.cov() = p1.cov();
A1 = K;
trmm(1.0, q2.std(), A1, 'R', 'U', 'T');
syrk(1.0, A1, 1.0, p3.cov(), 'U');
A2 = K;
trmm(1.0, p2.std(), A2, 'R', 'U', 'T');
syrk(-1.0, A2, 1.0, p3.cov(), 'U');
/* make sure correct log-variables set */
p3.setLogs(p2.getLogs());
p3.init(); // redo precalculations
}
void BrooksCorey2p::readZones(ParameterDatabase& pd,Petsc::SecondOrderFd& node)
{
int nZones = pd.i("nZones");
real dx=0.0,dy=0.0,dz=0.0;
dx=(pd.r("xRight") - pd.r("xLeft")) / (real(pd.i("nxNodes"))-1);
if (pd.i("nyNodes") > 1)
dy=(pd.r("yBack") - pd.r("yFront")) / (real(pd.i("nyNodes"))-1);
if (pd.i("nzNodes") > 1)
dz=(pd.r("zTop") - pd.r("zBottom")) / (real(pd.i("nzNodes"))-1);
real gravity=pd.r("gravity"), // m/d^2
density=pd.r("rhoW"), // kg / m^3
viscosity=pd.r("muW"); // kg /m d
for (int i=node.local_z0; i<node.local_z0+node.local_nzNodes; i++)
for (int j=node.local_y0; j<node.local_y0+node.local_nyNodes; j++)
for (int k=node.local_x0; k<node.local_x0+node.local_nxNodes; k++)
{
node(i,j,k);
real x=k*dx,y=j*dy,z=i*dz;
for (int n=0; n<nZones; n++)
{
if (x >= pd.v("zoneLeft")(n) && x < pd.v("zoneRight")(n) &&
y >= pd.v("zoneFront")(n) && y < pd.v("zoneBack")(n) &&
z >= pd.v("zoneBottom")(n) && z < pd.v("zoneTop")(n) )
{
global_psiD(node.center) = pd.v("pdZone")(n);
global_lambda(node.center) = pd.v("lambdaZone")(n);
global_KWs(node.center) = pd.v("permZone")(n)*gravity*density/viscosity;
global_thetaS(node.center) = pd.v("thetaS_Zone")(n);
global_thetaR(node.center) = pd.v("thetaR_Zone")(n);
}
}
}
// global_thetaSR = global_thetaS - global_thetaR;
global_thetaSR = global_thetaS;
axpy(-1.0,global_thetaR,global_thetaSR);
// std::cout<<global_psiD<<std::endl
// <<global_lambda<<std::endl
// <<global_thetaS<<std::endl
// <<global_KWs<<std::endl;
psiD.startSetFromGlobal(global_psiD);
psiD.endSetFromGlobal(global_psiD);
lambda.startSetFromGlobal(global_lambda);
lambda.endSetFromGlobal(global_lambda);
KWs.startSetFromGlobal(global_KWs);
KWs.endSetFromGlobal(global_KWs);
thetaS.startSetFromGlobal(global_thetaS);
thetaS.endSetFromGlobal(global_thetaS);
thetaR.startSetFromGlobal(global_thetaR);
thetaR.endSetFromGlobal(global_thetaR);
thetaSR.startSetFromGlobal(global_thetaSR);
thetaSR.endSetFromGlobal(global_thetaSR);
}
int main(int argc, char** argv) {
size_t pow = read_arg(argc, argv, 1, 16);
size_t n = 1 << pow;
size_t size_in_bytes = n * sizeof(double);
std::cout << "memcopy and daxpy test of size " << n << std::endl;
double* x = malloc_host<double>(n, 1.5);
double* y = malloc_host<double>(n, 3.0);
#ifdef FLUSH_CACHE
// use dummy fields to avoid cache effects, which make results harder to interpret
// use 1<<24 to ensure that cache is completely purged for all n
double* x_ = malloc_host<double>(1<<24, 1.5);
double* y_ = malloc_host<double>(1<<24, 3.0);
axpy(1<<24, 2.0, x_, y_);
#endif
double start = get_time();
axpy(n, 2.0, x, y);
double time_axpy = get_time() - start;
std::cout << "-------\ntimings\n-------" << std::endl;
std::cout << "axpy : " << time_axpy << " s" << std::endl;
std::cout << std::endl;
// check for errors
int errors = 0;
for(int i=0; i<n; ++i) {
if(std::fabs(6.-y[i])>1e-15) {
errors++;
}
}
if(errors>0) std::cout << "\n============ FAILED with " << errors << " errors" << std::endl;
else std::cout << "\n============ PASSED" << std::endl;
free(x);
free(y);
return 0;
}
void SkipGram_HS::update(uint64_t cur, const vector<uint64_t>& context, real alpha) {
real* hidden_vec = _net.get_input_vec(cur);
memset(_hidden_vec_grad, 0, sizeof(real) * _sz);
for (vector<uint64_t>::const_iterator it = context.begin(); it != context.end(); ++it) {
const vector<char>& code = _huffman_tree.code(*it);
const vector<uint64_t>& path = _huffman_tree.path(*it);
for (size_t i = 0; i != path.size(); ++i) {
real* out = _net.get_output_vec(path[i]);
real sigma = sigmoid(dot(_sz, hidden_vec, out));
int label = code[i];
real coef = (label - sigma) * alpha;
axpy(_sz, coef, out, _hidden_vec_grad);
// not exactly the same as the original
axpy(_sz, coef, hidden_vec, out);
}
}
addto(_sz, _hidden_vec_grad, hidden_vec);
}
void SkipGram_NS::update(uint64_t cur, const vector<uint64_t>& context, real alpha) {
const real* hidden_vec = _net.get_input_vec(cur);
memset(_hidden_vec_grad, 0, sizeof(real) * _sz);
for (vector<uint64_t>::const_iterator i = context.begin(); i != context.end(); ++i) {
_out.clear();
_out.push_back(_net.get_output_vec(*i));
for (unsigned j = 0; j < _neg_sample_cnt; ++j) {
_out.push_back(_net.get_output_vec(_vocab.sampling(&_seed)));
}
for (size_t i = 0; i != _out.size(); ++i) {
real sigma = sigmoid(dot(_sz, hidden_vec, _out[i]));
int label = (i==0) ? 1 : 0;
real coef = (label - sigma) * alpha;
axpy(_sz, coef, _out[i], _hidden_vec_grad);
axpy(_sz, coef, hidden_vec, const_cast<real*>(_out[i]));
}
}
addto(_sz, _hidden_vec_grad, const_cast<real*>(hidden_vec));
}
void bi::cov(const UniformPdf<V1>& q, M1 Sigma) {
/* pre-condition */
BI_ASSERT(Sigma.size1() == q.size());
BI_ASSERT(Sigma.size2() == q.size());
temp_host_vector<real>::type diff(q.size());
diff = q.upper();
sub_elements(diff, q.lower(), diff);
sq_elements(diff, diff);
Sigma.clear();
axpy(1.0/12.0, diff, diagonal(Sigma));
}
void RosenbrockDaeDefinition::correctArgument(Vec& correction)
{
yLast = yDaeDef;
Flast = Fcurrent;
updateJac=true;
updateF=true;
#ifndef USE_BLAS
yDaeDef-=correction;
#else
axpy(-1.0,correction,yDaeDef);
#endif
}
int main() {
double arrayOnStack[10];
stackArray = arrayOnStack;
createNewArray();
createMallocArray();
setArray(stackArray);
setArray(newArray - 1);
setArray(mallocArray - 1);
printArray(newArray);
printArray(mallocArray);
axpy(newArray, stackArray);
axpy(newArray, mallocArray);
// delete stackArray;
stackArray = 0;
newArray = 0;
mallocArray = 0;
return 0;
}
int main(int argc, char** argv)
{
size_t pow = read_arg(argc, argv, 1, 16);
size_t n = 1 << pow;
std::cout << "memcopy and daxpy test of size " << n << "\n";
double* x = malloc_host<double>(n, 1.5);
double* y = malloc_host<double>(n, 3.0);
// use dummy fields to avoid cache effects, which make results harder to
// interpret use 1<<24 to ensure that cache is completely purged for all n
double* x_ = malloc_host<double>(n, 1.5);
double* y_ = malloc_host<double>(n, 3.0);
// openmp version:
auto start = get_time();
axpy(n, 2.0, x_, y_);
auto time_axpy_omp = get_time() - start;
// openacc version:
start = get_time();
axpy_gpu(n, 2.0, x, y);
auto time_axpy_gpu = get_time() - start;
std::cout << "-------\ntimings\n-------\n";
std::cout << "axpy (openmp): " << time_axpy_omp << " s\n";
std::cout << "axpy (openacc): " << time_axpy_gpu << " s\n";
// check for errors
auto errors = 0;
#pragma omp parallel for reduction(+:errors)
for (auto i = 0; i < n; ++i) {
if (std::fabs(6.-y[i]) > 1e-15) {
++errors;
}
}
if (errors > 0) {
std::cout << "\n============ FAILED with " << errors << " errors\n";
} else {
std::cout << "\n============ PASSED\n";
}
free(x);
free(y);
return 0;
}
void bi::condition(const ExpGaussianPdf<V1, M1>& p1, const ExpGaussianPdf<V2,
M2>& p2, const M3 C, const V3 x2, ExpGaussianPdf<V4, M4>& p3) {
/* pre-condition */
BI_ASSERT(x2.size() == p2.size());
BI_ASSERT(p3.size() == p1.size());
BI_ASSERT(C.size1() == p1.size() && C.size2() == p2.size());
typename sim_temp_vector<V1>::type z2(p2.size());
typename sim_temp_matrix<M1>::type K(p1.size(), p2.size());
/**
* Compute gain matrix:
*
* \f[\mathcal{K} = C_{\mathbf{x}_1,\mathbf{x}_2}\Sigma_2^{-1}\,.\f]
*/
symm(1.0, p2.prec(), C, 0.0, K, 'R', 'U');
/**
* Then result is given by \f$\mathcal{N}(\boldsymbol{\mu}',
* \Sigma')\f$, where:
*
* \f[\boldsymbol{\mu}' = \boldsymbol{\mu}_1 + \mathcal{K}(\mathbf{x}_2 -
* \boldsymbol{\mu}_2)\,,\f]
*/
z2 = x2;
log_vector(z2, p2.getLogs());
axpy(-1.0, p2.mean(), z2);
p3.mean() = p1.mean();
gemv(1.0, K, z2, 1.0, p3.mean());
/**
* and:
*
* \f{eqnarray*}
* \Sigma' &=& \Sigma_1 - \mathcal{K}C_{\mathbf{x}_1,\mathbf{x}_2}^T \\
* &=& \Sigma_1 - C_{\mathbf{x}_1,\mathbf{x}_2}\Sigma_2^{-1}
* C_{\mathbf{x}_1,\mathbf{x}_2}^T\,.\f}
*/
K = C;
trsm(1.0, p2.std(), K, 'R', 'U');
p3.cov() = p1.cov();
syrk(-1.0, K, 1.0, p3.cov(), 'U');
/* update log-variables and precalculations */
p3.setLogs(p1.getLogs());
p3.init();
}
clsparseStatus
cldenseDaxpy(cldenseVector *r,
const clsparseScalar *alpha, const cldenseVector *x,
const cldenseVector *y,
const clsparseControl control)
{
if (!clsparseInitialized)
{
return clsparseNotInitialized;
}
//check opencl elements
if (control == nullptr)
{
return clsparseInvalidControlObject;
}
clsparse::vector<cl_double> pR (control, r->values, r->num_values);
clsparse::vector<cl_double> pAlpha(control, alpha->value, 1);
clsparse::vector<cl_double> pX (control, x->values, x->num_values);
clsparse::vector<cl_double> pY (control, y->values, y->num_values);
assert(pR.size() == pY.size());
assert(pR.size() == pX.size());
cl_ulong size = pR.size();
if(size == 0) return clsparseSuccess;
//nothing to do
if (pAlpha[0] == 0.0)
{
auto pRBuff = pR.data()();
auto pYBuff = pY.data()();
//if R is different pointer than Y than copy Y to R
if (pRBuff != pYBuff)
{
// deep copy;
pR = pY;
}
return clsparseSuccess;
}
return axpy(pR, pAlpha, pX, pY, control);
}
void bi::distance(const M1 X, const real h, M2 D) {
/* pre-conditions */
BI_ASSERT(D.size1() == D.size2());
BI_ASSERT(D.size1() == X.size1());
BI_ASSERT(!M2::on_device);
typedef typename M1::value_type T1;
FastGaussianKernel K(X.size2(), h);
typename temp_host_vector<T1>::type d(X.size2());
int i, j;
for (j = 0; j < D.size2(); ++j) {
for (i = 0; i <= j; ++i) {
d = row(X, i);
axpy(-1.0, row(X, j), d);
D(i, j) = K(dot(d));
}
}
}
void GS(Matrix u, double tolerance, int maxit)
{
int it=0;
Matrix b = cloneMatrix(u);
Matrix e = cloneMatrix(u);
Matrix v = cloneMatrix(u);
int* sizes, *displ;
splitVector(u->rows-2, 2*max_threads(), &sizes, &displ);
copyVector(b->as_vec, u->as_vec);
fillVector(u->as_vec, 0.0);
double max = tolerance+1;
while (max > tolerance && ++it < maxit) {
copyVector(e->as_vec, u->as_vec);
copyVector(u->as_vec, b->as_vec);
for (int color=0;color<2;++color) {
for (int i=1;i<u->cols-1;++i) {
#pragma omp parallel
{
int cnt=displ[get_thread()*2+color]+1;
for (int j=0;j<sizes[get_thread()*2+color];++j, ++cnt) {
u->data[i][cnt] += v->data[i][cnt-1];
u->data[i][cnt] += v->data[i][cnt+1];
u->data[i][cnt] += v->data[i-1][cnt];
u->data[i][cnt] += v->data[i+1][cnt];
u->data[i][cnt] /= 4.0;
v->data[i][cnt] = u->data[i][cnt];
}
}
}
}
axpy(e->as_vec, u->as_vec, -1.0);
max = sqrt(innerproduct(e->as_vec, e->as_vec));
}
printf("number of iterations %i %f\n", it, max);
freeMatrix(b);
freeMatrix(e);
freeMatrix(v);
free(sizes);
free(displ);
}
bool RosenbrockDaeDefinition::numericalJacVec(const Vec& v, Vec& Jv)
{
bool evalError=false;
real delFac=1.0e-5;
value(evalError);//sets Fcurrent
if (evalError)
return evalError;
else
{
//cek del = -delFac*v;
del = v;
scal(-delFac,del);
//end cek
correctArgument(del);//sets Flast to Fcurrent --
//remember correction is -del = delFac*v
value(evalError);
while (evalError)
{
std::cerr<<"cutting back on del in numerical jac vec"<<std::endl;
unCorrect();//sets Flast to Fcurrent
delFac*=0.1;
//cek del = -delFac*v;
del = v;
scal(-delFac,del);
//end cek
correctArgument(del);
value(evalError);//sets Fcurrent
}
//cek Jv = (Fcurrent - Flast)/delFac;
Jv = Fcurrent;
axpy(-1.0,Flast,Jv);
scal(delFac,Jv);
//end cek
unCorrect();
}
return evalError;
}