RcppEigen LLT resulted in a vector of NaN - eigen

I am trying the below RcppEigen function to solve a linear model. It compiled with no error but when I am applying it in R, it gave a vector of NaN values. I tried similar script with C++ without R and it worked perfectly. Any suggestions?
// [[Rcpp::depends(RcppEigen)]]
// [[Rcpp::plugins("cpp11")]]
#include <RcppEigen.h>
#include <Rcpp.h>
#include <Eigen/Dense>
using namespace std;
using namespace Eigen;
using namespace Rcpp;
// [[Rcpp::export]]
SEXP LLtSolve(const MatrixXd A, const MatrixXd b) {
LLT<MatrixXd> llt;
llt.compute(A);
return Rcpp::wrap(llt.solve(b));
}
An example R code:
library(Rcpp)
sourceCpp("Functions.cpp") # contains the previous LLtSolve function
n=1000
A=matrix(rnorm(n*n),nrow=n,ncol=n)
b=matrix(rnorm(n),nrow=n,ncol=1)
xxx=Sys.time()
f=LLtSolve(A,b)
Sys.time()-xxx
f[1:4]

Your code works if you reduce n. For example:
> set.seed(42)
> n=500
> A=matrix(rnorm(n*n),nrow=n,ncol=n)
> b=matrix(rnorm(n),nrow=n,ncol=1)
> f=LLtSolve(A,b)
> min(f)
[1] -1.40086e+300
> max(f)
[1] 1.757129e+300
However, the minimum and maximum values are already quite extreme. When you increase the problem size further, you will reach the point where the result is no longer representable as a double:
> .Machine$double.xmax
[1] 1.797693e+308
> .Machine$double.xmin
[1] 2.225074e-308
This is not the case for a sparse matrix, e.g.:
// [[Rcpp::depends(RcppEigen)]]
#include <RcppEigen.h>
#include <Eigen/SparseLU>
using namespace Eigen;
// [[Rcpp::export]]
MatrixXd SparseSolve(const SparseMatrix<double>& A, const MatrixXd& b) {
SparseLU<SparseMatrix<double> > solver;
solver.compute(A);
if(solver.info()!=Success) {
Rcpp::stop("decomposition failed");
}
MatrixXd x = solver.solve(b);
if(solver.info()!=Success) {
Rcpp::stop("solving failed");
}
return x;
}
/*** R
set.seed(42)
n <- 10000
A <- Matrix::rsparsematrix(n, n, density = 0.2)
b <- matrix(rnorm(n), nrow = n, ncol = 1)
system.time(f <- SparseSolve(A,b))
f[1:4]
*/
Result:
> set.seed(42)
> n <- 10000
> A <- Matrix::rsparsematrix(n, n, density = 0.2)
> b <- matrix(rnorm(n), nrow = n, ncol = 1)
> system.time(f <- SparseSolve(A,b))
user system elapsed
80.640 0.524 81.163
> f[1:4]
[1] -1.5994258 -0.6987579 1.3042338 0.1084376

Related

Rcpp Parallel or openmp for matrixvector product

I am trying to program the naive parallel version of Conjugate gradient, so I started with the simple Wikipedia algorithm, and I want to change the dot-products and MatrixVector products by their appropriate parallel version, The Rcppparallel documentation has the code for the dot-product using parallelReduce; I think I'm gonna use that version for my code, but I'm trying to make the MatrixVector multiplication, but I haven't achieved good results compared to R base (no parallel)
Some versions of parallel matrix multiplication: using OpenMP, Rcppparallel, serial version, a serial version with Armadillo, and the benchmark
// [[Rcpp::depends(RcppParallel)]]
#include <Rcpp.h>
#include <RcppParallel.h>
#include <numeric>
// #include <cstddef>
// #include <cstdio>
#include <iostream>
using namespace RcppParallel;
using namespace Rcpp;
struct InnerProduct : public Worker
{
// source vectors
const RVector<double> x;
const RVector<double> y;
// product that I have accumulated
double product;
// constructors
InnerProduct(const NumericVector x, const NumericVector y)
: x(x), y(y), product(0) {}
InnerProduct(const InnerProduct& innerProduct, Split)
: x(innerProduct.x), y(innerProduct.y), product(0) {}
// process just the elements of the range I've been asked to
void operator()(std::size_t begin, std::size_t end) {
product += std::inner_product(x.begin() + begin,
x.begin() + end,
y.begin() + begin,
0.0);
}
// join my value with that of another InnerProduct
void join(const InnerProduct& rhs) {
product += rhs.product;
}
};
struct MatrixMultiplication : public Worker
{
// source matrix
const RMatrix<double> A;
//source vector
const RVector<double> x;
// destination matrix
RMatrix<double> out;
// initialize with source and destination
MatrixMultiplication(const NumericMatrix A, const NumericVector x, NumericMatrix out)
: A(A), x(x), out(out) {}
// take the square root of the range of elements requested
void operator()(std::size_t begin, std::size_t end) {
for (std::size_t i = begin; i < end; i++) {
// rows we will operate on
//RMatrix<double>::Row rowi = A.row(i);
RMatrix<double>::Row rowi = A.row(i);
//double res = std::inner_product(rowi.begin(), rowi.end(), x.begin(), 0.0);
//Rcout << "res" << res << std::endl;
out(i,1) = std::inner_product(rowi.begin(), rowi.end(), x.begin(), 0.0);
//Rcout << "res" << out(i,1) << std::endl;
}
}
};
// [[Rcpp::export]]
double parallelInnerProduct(NumericVector x, NumericVector y) {
// declare the InnerProduct instance that takes a pointer to the vector data
InnerProduct innerProduct(x, y);
// call paralleReduce to start the work
parallelReduce(0, x.length(), innerProduct);
// return the computed product
return innerProduct.product;
}
//librar(Rbenchmark)
// [[Rcpp::export]]
NumericVector matrixXvectorRcppParallel(NumericMatrix A, NumericVector x) {
// // declare the InnerProduct instance that takes a pointer to the vector data
// InnerProduct innerProduct(x, y);
int nrows = A.nrow();
NumericVector out(nrows);
for(int i = 0; i< nrows;i++ )
{
out(i) = parallelInnerProduct(A(i,_),x);
}
// return the computed product
return out;
}
// [[Rcpp::export]]
arma::rowvec matrixXvectorParallel(arma::mat A, arma::colvec x){
arma::rowvec y = A.row(0)*0;
int filas = A.n_rows;
int columnas = A.n_cols;
#pragma omp parallel for
for(int j=0;j<columnas;j++)
{
//y(j) = A.row(j)*x(j))
y(j) = dotproduct(A.row(j),x);
}
return y;
}
arma::mat matrixXvector2(arma::mat A, arma::mat x){
//arma::rowvec y = A.row(0)*0;
//y=A*x;
return A*x;
}
arma::rowvec matrixXvectorParallel2(arma::mat A, arma::colvec x){
arma::rowvec y = A.row(0)*0;
int filas = A.n_rows;
int columnas = A.n_cols;
#pragma omp parallel for
for(int j = 0; j < columnas ; j++){
double result = 0;
for(int i = 0; i < filas; i++){
result += x(i)*A(j,i);
}
y(j) = result;
}
return y;
}
Benchmark
test replications elapsed relative user.self sys.self user.child sys.child
1 M %*% a 20 0.026 1.000 0.140 0.060 0 0
2 matrixXvector2(M, as.matrix(a)) 20 0.040 1.538 0.101 0.217 0 0
4 matrixXvectorParallel2(M, a) 20 0.063 2.423 0.481 0.000 0 0
3 matrixXvectorParallel(M, a) 20 0.146 5.615 0.745 0.398 0 0
5 matrixXvectorRcppParallel(M, a) 20 0.335 12.885 2.305 0.079 0 0
My last trial at the moment was using parallefor with Rcppparallel, but I'm getting memory errors and I dont have idea where the problem is
// [[Rcpp::export]]
NumericVector matrixXvectorRcppParallel2(NumericMatrix A, NumericVector x) {
// // declare the InnerProduct instance that takes a pointer to the vector data
int nrows = A.nrow();
NumericMatrix out(nrows,1); //allocar mempria de vector de salida
//crear worker
MatrixMultiplication matrixMultiplication(A, x, out);
parallelFor(0,A.nrow(),matrixMultiplication);
// return the computed product
return out;
}
What I notice is that when I check in my terminal using htop how the processors are working, I see in htop when I apply the conventional Matrix vector multiplication using R-base, that is using all the processors, so Does the matrix multiplication perform parallel by default? because in theory, only one processor should be working if is the serial version.
If someone knows which is the better path, OpenMP or Rcppparallel, or another way, that gives me better performance than the apparently serial version of R-base.
The serial code for conjugte gradient at the moment
// [[Rcpp::export]]
arma::colvec ConjugateGradient(arma::mat A, arma::colvec xini, arma::colvec b, int num_iteraciones){
//arma::colvec xnew = xini*0 //inicializar en 0's
arma::colvec x= xini; //inicializar en 0's
arma::colvec rkold = b - A*xini;
arma::colvec rknew = b*0;
arma::colvec pk = rkold;
int k=0;
double alpha_k=0;
double betak=0;
double normak = 0.0;
for(k=0; k<num_iteraciones;k++){
Rcout << "iteracion numero " << k << std::endl;
alpha_k = sum(rkold.t() * rkold) / sum(pk.t()*A*pk); //sum de un elemento para realizar casting
(pk.t()*A*pk);
x = x+ alpha_k * pk;
rknew = rkold - alpha_k*A*pk;
normak = sum(rknew.t()*rknew);
if( normak < 0.000001){
break;
}
betak = sum(rknew.t()*rknew) / sum( rkold.t() * rkold );
//actualizar valores para siguiente iteracion
pk = rknew + betak*pk;
rkold = rknew;
}
return x;
}
I wasn't aware of the use of BLAS in R, thanks Hong Ooi and tim18, so the new benchmark using option(matprod="internal") and option(matprod="blas")
options(matprod = "internal")
res<-benchmark(M%*%a,matrixXvector2(M,as.matrix(a)),matrixXvectorParallel(M,a),matrixXvectorParallel2(M,a),matrixXvectorRcppParallel(M,a),order="relative",replications = 20)
res
test replications elapsed relative user.self sys.self user.child sys.child
2 matrixXvector2(M, as.matrix(a)) 20 0.043 1.000 0.107 0.228 0 0
4 matrixXvectorParallel2(M, a) 20 0.069 1.605 0.530 0.000 0 0
1 M %*% a 20 0.072 1.674 0.071 0.000 0 0
3 matrixXvectorParallel(M, a) 20 0.140 3.256 0.746 0.346 0 0
5 matrixXvectorRcppParallel(M, a) 20 0.343 7.977 2.272 0.175 0 0
options(matprod="blas")
options(matprod = "blas")
res<-benchmark(M%*%a,matrixXvector2(M,as.matrix(a)),matrixXvectorParallel(M,a),matrixXvectorParallel2(M,a),matrixXvectorRcppParallel(M,a),order="relative",replications = 20)
res
test replications elapsed relative user.self sys.self user.child sys.child
1 M %*% a 20 0.021 1.000 0.093 0.054 0 0
2 matrixXvector2(M, as.matrix(a)) 20 0.092 4.381 0.177 0.464 0 0
5 matrixXvectorRcppParallel(M, a) 20 0.328 15.619 2.143 0.109 0 0
4 matrixXvectorParallel2(M, a) 20 0.438 20.857 3.036 0.000 0 0
3 matrixXvectorParallel(M, a) 20 0.546 26.000 3.667 0.127 0 0
As you already found out, the base R matrix multiplication can be multi-threaded, if a multi-threaded BLAS implementation is used. This is the case for the rocker/* docker images, which typically use OpenBLAS.
In addition, (Rcpp)Armadillo already uses the BLAS library used by R (in this case multi-threaded OpenBLAS) as well as OpenMP. So your "serial" version is actually multi-threaded. You can verify this in htop with a large enough matrix as input.
BTW, what you are trying to do looks like premature optimization to me.

Dealing with matrices in CUDA: understanding basic concepts

I'm building a CUDA kernel to compute the numerical N*N jacobian of a function, using finite differences; in the example I provided, it is the square function (each entry of the vector is squared). The host coded allocates in linear memory, while I'm using a 2-dimensional indexing in the kernel.
My issue is that I haven't found a way to sum on the diagonal of the matrices cudaMalloc'ed. My attempt has been to use the statement threadIdx.x == blockIdx.x as a condition for the diagonal, but instead it evaluates to true only for them both at 0.
Here is the kernel and EDIT: I posted the whole code as an answer, based on the suggestions in the comments (the main() is basically the same, while the kernel is not)
template <typename T>
__global__ void jacobian_kernel (
T * J,
const T t0,
const T tn,
const T h,
const T * u0,
const T * un,
const T * un_old)
{
T cgamma = 2 - sqrtf(2);
const unsigned int t = threadIdx.x;
const unsigned int b = blockIdx.x;
const unsigned int tid = t + b * blockDim.x;
/*__shared__*/ T temp_sx[BLOCK_SIZE][BLOCK_SIZE];
/*__shared__*/ T temp_dx[BLOCK_SIZE][BLOCK_SIZE];
__shared__ T sm_temp_du[BLOCK_SIZE];
T* temp_du = &sm_temp_du[0];
if (tid < N )
{
temp_sx[b][t] = un[t];
temp_dx[b][t] = un[t];
if ( t == b )
{
if ( tn == t0 )
{
temp_du[t] = u0[t]*0.001;
temp_sx[b][t] += temp_du[t]; //(*)
temp_dx[b][t] -= temp_du[t];
temp_sx[b][t] += ( abs( temp_sx[b][t] ) < 10e-6 ? 0.1 : 0 );
temp_dx[b][t] += ( abs( temp_dx[b][t] ) < 10e-6 ? 0.1 : 0 );
temp_sx[b][t] = ( temp_sx[b][t] == 0 ? 0.1 : temp_sx[b][t] );
temp_dx[b][t] = ( temp_dx[b][t] == 0 ? 0.1 : temp_dx[b][t] );
}
else
{
temp_du[t] = MAX( un[t] - un_old[t], 10e-6 );
temp_sx[b][t] += temp_du[t];
temp_dx[b][t] -= temp_du[t];
}
}
__syncthreads();
//J = f(tn, un + du)
d_func(tn, (temp_sx[b]), (temp_sx[b]), 1.f);
d_func(tn, (temp_dx[b]), (temp_dx[b]), 1.f);
__syncthreads();
J[tid] = (temp_sx[b][t] - temp_dx[b][t]) * powf((2 * temp_du[t]), -1);
//J[tid]*= - h*cgamma/2;
//J[tid]+= ( t == b ? 1 : 0);
//J[tid] = temp_J[tid];
}
}
The general procedure for computing the jacobian is
Copy un into every row of temp_sx and temp_dx
Compute du as a 0.01 magnitude from u0
Sum du to the diagonal of temp_sx, subtract du from the diagonal of temp_dx
Compute the square function on each entry of temp_sx and temp_dx
Subtract them and divide every entry by 2*du
This procedure can be summarized with (f(un + du*e_i) - f(un - du*e_i))/2*du.
My problem is to sum du to the diagonal of the matrices of temp_sx and temp_dx like I tried in (*). How can I achieve that?
EDIT: Now calling 1D blocks and threads; in fact, .y axis wasn't used at all in the kernel. I'm calling the kernel with a fixed amount of shared memory
Note that in int main() I'm calling the kernel with
#define REAL sizeof(float)
#define N 32
#define BLOCK_SIZE 16
#define NUM_BLOCKS ((N*N + BLOCK_SIZE - 1)/ BLOCK_SIZE)
...
dim3 dimGrid(NUM_BLOCKS,);
dim3 dimBlock(BLOCK_SIZE);
size_t shm_size = N*N*REAL;
jacobian_kernel <<< dimGrid, dimBlock, size_t shm_size >>> (...);
So that I attempt to deal with block-splitting the function calls. In the kernel to sum on the diagonal I used if(threadIdx.x == blockIdx.x){...}. Why isn't this correct? I'm asking it because while debugging and making the code print the statement, It only evaluates true if they both are 0. Thus du[0] is the only numerical value and the matrix becomes nan. Note that this approach worked with the first code I built, where instead I called the kernel with
jacobian_kernel <<< N, N >>> (...)
So that when threadIdx.x == blockIdx.x the element is on the diagonal. This approach doesn't fit anymore though, since now I need to deal with larger N (possibly larger than 1024, which is the maximum number of threads per block).
What statement should I put there that works even if the matrices are split into blocks and threads?
Let me know if I should share some other info.
Here is how I managed to solve my problem, based on the suggestion in the comments on the answer. The example is compilable, provided you put helper_cuda.h and helper_string.h in the same directory or you add -I directive to the CUDA examples include path, installed along with the CUDA toolkit. The relevant changes are only in the kernel; there's a minor change in the main() though, since I was calling double the resources to execute the kernel, but the .y axis of the grid of thread blocks wasn't even used at all, so it didn't generate any error.
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <math.h>
#include <assert.h>
#include <cuda.h>
#include <cuda_runtime.h>
#include "helper_cuda.h"
#include "helper_string.h"
#include <fstream>
#ifndef MAX
#define MAX(a,b) ((a > b) ? a : b)
#endif
#define REAL sizeof(float)
#define N 128
#define BLOCK_SIZE 128
#define NUM_BLOCKS ((N*N + BLOCK_SIZE - 1)/ BLOCK_SIZE)
template <typename T>
inline void printmatrix( T mat, int rows, int cols);
template <typename T>
__global__ void jacobian_kernel ( const T * A, T * J, const T t0, const T tn, const T h, const T * u0, const T * un, const T * un_old);
template<typename T>
__device__ void d_func(const T t, const T u[], T res[], const T h = 1);
template<typename T>
int main ()
{
float t0 = 0.; //float tn = 0.;
float h = 0.1;
float* u0 = (float*)malloc(REAL*N); for(int i = 0; i < N; ++i){u0[i] = i+1;}
float* un = (float*)malloc(REAL*N); memcpy(un, u0, REAL*N);
float* un_old = (float*)malloc(REAL*N); memcpy(un_old, u0, REAL*N);
float* J = (float*)malloc(REAL*N*N);
float* A = (float*)malloc(REAL*N*N); host_heat_matrix(A);
float *d_u0;
float *d_un;
float *d_un_old;
float *d_J;
float *d_A;
checkCudaErrors(cudaMalloc((void**)&d_u0, REAL*N)); //printf("1: %p\n", d_u0);
checkCudaErrors(cudaMalloc((void**)&d_un, REAL*N)); //printf("2: %p\n", d_un);
checkCudaErrors(cudaMalloc((void**)&d_un_old, REAL*N)); //printf("3: %p\n", d_un_old);
checkCudaErrors(cudaMalloc((void**)&d_J, REAL*N*N)); //printf("4: %p\n", d_J);
checkCudaErrors(cudaMalloc((void**)&d_A, REAL*N*N)); //printf("4: %p\n", d_J);
checkCudaErrors(cudaMemcpy(d_u0, u0, REAL*N, cudaMemcpyHostToDevice)); assert(d_u0 != NULL);
checkCudaErrors(cudaMemcpy(d_un, un, REAL*N, cudaMemcpyHostToDevice)); assert(d_un != NULL);
checkCudaErrors(cudaMemcpy(d_un_old, un_old, REAL*N, cudaMemcpyHostToDevice)); assert(d_un_old != NULL);
checkCudaErrors(cudaMemcpy(d_J, J, REAL*N*N, cudaMemcpyHostToDevice)); assert(d_J != NULL);
checkCudaErrors(cudaMemcpy(d_A, A, REAL*N*N, cudaMemcpyHostToDevice)); assert(d_A != NULL);
dim3 dimGrid(NUM_BLOCKS); std::cout << "NUM_BLOCKS \t" << dimGrid.x << "\n";
dim3 dimBlock(BLOCK_SIZE); std::cout << "BLOCK_SIZE \t" << dimBlock.x << "\n";
size_t shm_size = N*REAL; //std::cout << shm_size << "\n";
//HERE IS A RELEVANT CHANGE OF THE MAIN, SINCE I WAS CALLING
//THE KERNEL WITH A 2D GRID BUT WITHOUT USING THE .y AXIS,
//WHILE NOW THE GRID IS 1D
jacobian_kernel <<< dimGrid, dimBlock, shm_size >>> (d_A, d_J, t0, t0, h, d_u0, d_un, d_un_old);
checkCudaErrors(cudaMemcpy(J, d_J, REAL*N*N, cudaMemcpyDeviceToHost)); //printf("4: %p\n", d_J);
printmatrix( J, N, N);
checkCudaErrors(cudaDeviceReset());
free(u0);
free(un);
free(un_old);
free(J);
}
template <typename T>
__global__ void jacobian_kernel (
const T * A,
T * J,
const T t0,
const T tn,
const T h,
const T * u0,
const T * un,
const T * un_old)
{
T cgamma = 2 - sqrtf(2);
const unsigned int t = threadIdx.x;
const unsigned int b = blockIdx.x;
const unsigned int tid = t + b * blockDim.x;
/*__shared__*/ T temp_sx[BLOCK_SIZE][BLOCK_SIZE];
/*__shared__*/ T temp_dx[BLOCK_SIZE][BLOCK_SIZE];
__shared__ T sm_temp_du;
T* temp_du = &sm_temp_du;
//HERE IS A RELEVANT CHANGE (*)
if ( t < BLOCK_SIZE && b < NUM_BLOCKS )
{
temp_sx[b][t] = un[t]; //printf("temp_sx[%d] = %f\n", t,(temp_sx[b][t]));
temp_dx[b][t] = un[t];
//printf("t = %d, b = %d, t + b * blockDim.x = %d \n",t, b, tid);
//HERE IS A NOTE (**)
if ( t == b )
{
//printf("t = %d, b = %d \n",t, b);
if ( tn == t0 )
{
*temp_du = u0[t]*0.001;
temp_sx[b][t] += *temp_du;
temp_dx[b][t] -= *temp_du;
temp_sx[b][t] += ( abs( temp_sx[b][t] ) < 10e-6 ? 0.1 : 0 );
temp_dx[b][t] += ( abs( temp_dx[b][t] ) < 10e-6 ? 0.1 : 0 );
temp_sx[b][t] = ( temp_sx[b][t] == 0 ? 0.1 : temp_sx[b][t] );
temp_dx[b][t] = ( temp_dx[b][t] == 0 ? 0.1 : temp_dx[b][t] );
}
else
{
*temp_du = MAX( un[t] - un_old[t], 10e-6 );
temp_sx[b][t] += *temp_du;
temp_dx[b][t] -= *temp_du;
}
;
}
//printf("du[%d] %f\n", tid, (*temp_du));
__syncthreads();
//printf("temp_sx[%d][%d] = %f\n", b, t, temp_sx[b][t]);
//printf("temp_dx[%d][%d] = %f\n", b, t, temp_dx[b][t]);
//d_func(tn, (temp_sx[b]), (temp_sx[b]), 1.f);
//d_func(tn, (temp_dx[b]), (temp_dx[b]), 1.f);
matvec_dev( tn, A, (temp_sx[b]), (temp_sx[b]), N, N, 1.f );
matvec_dev( tn, A, (temp_dx[b]), (temp_dx[b]), N, N, 1.f );
__syncthreads();
//printf("temp_sx_later[%d][%d] = %f\n", b, t, (temp_sx[b][t]));
//printf("temp_sx_later[%d][%d] - temp_dx_later[%d][%d] = %f\n", b,t,b,t, (temp_sx[b][t] - temp_dx[b][t]) / 2 * *temp_du);
//if (t == b ) printf( "2du[%d]^-1 = %f\n",t, powf((2 * *temp_du), -1));
J[tid] = (temp_sx[b][t] - temp_dx[b][t]) / (2 * *temp_du);
}
}
template<typename T>
__device__ void d_func(const T t, const T u[], T res[], const T h )
{
__shared__ float temp_u;
temp_u = u[threadIdx.x];
res[threadIdx.x] = h*powf( (temp_u), 2);
}
template <typename T>
inline void printmatrix( T mat, int rows, int cols)
{
std::ofstream matrix_out;
matrix_out.open( "heat_matrix.txt", std::ofstream::out);
for( int i = 0; i < rows; i++)
{
for( int j = 0; j <cols; j++)
{
double next = mat[i + N*j];
matrix_out << ( (next >= 0) ? " " : "") << next << " ";
}
matrix_out << "\n";
}
}
The relevant change is on (*). Before I used if (tid < N) which has two downsides:
First, it is wrong, since it should be tid < N*N, as my data is 2D, while tid is a global index which tracks all the data.
Even if I wrote tid < N*N, since I'm splitting the function calls into blocks, the t < BLOCK_SIZE && b < NUM_BLOCKS seems clearer to me in how the indexing is arranged in the code.
Moreover, the statement t == b in (**) is actually the right one to operate on the diagonal elements of the matrix. The fact that it was evaluated true only on 0 was because of my error right above.
Thanks for the suggestions!

Conditional reduction in CUDA

I need to sum about 100000 values stored in an array, but with conditions.
Is there a way to do that in CUDA to produce fast results?
Can anyone post a small code to do that?
I think that, to perform conditional reduction, you can directly introduce the condition as a multiplication by 0 (false) or 1 (true) to the addends. In other words, suppose that the condition you would like to meet is that the addends be smaller than 10.f. In this case, borrowing the first code at Optimizing Parallel Reduction in CUDA by M. Harris, then the above would mean
__global__ void reduce0(int *g_idata, int *g_odata) {
extern __shared__ int sdata[];
// each thread loads one element from global to shared mem
unsigned int tid = threadIdx.x;
unsigned int i = blockIdx.x*blockDim.x + threadIdx.x;
sdata[tid] = g_idata[i]*(g_data[i]<10.f);
__syncthreads();
// do reduction in shared mem
for(unsigned int s=1; s < blockDim.x; s *= 2) {
if (tid % (2*s) == 0) {
sdata[tid] += sdata[tid + s];
}
__syncthreads();
}
// write result for this block to global mem
if (tid == 0) g_odata[blockIdx.x] = sdata[0];
}
If you wish to use CUDA Thrust to perform conditional reduction, you can do the same by using thrust::transform_reduce. Alternatively, you can create a new vector d_b copying in that all the elements of d_a satisfying the predicate by thrust::copy_if and then applying thrust::reduce on d_b. I haven't checked which solution performs the best. Perhaps, the second solution will perform better on sparse arrays. Below is an example with an implementation of both the approaches.
#include <thrust/host_vector.h>
#include <thrust/device_vector.h>
#include <thrust/reduce.h>
#include <thrust/count.h>
#include <thrust/copy.h>
// --- Operator for the first approach
struct conditional_operator {
__host__ __device__ float operator()(const float a) const {
return a*(a<10.f);
}
};
// --- Operator for the second approach
struct is_smaller_than_10 {
__host__ __device__ bool operator()(const float a) const {
return (a<10.f);
}
};
void main(void)
{
int N = 20;
// --- Host side allocation and vector initialization
thrust::host_vector<float> h_a(N,1.f);
h_a[0] = 20.f;
h_a[1] = 20.f;
// --- Device side allocation and vector initialization
thrust::device_vector<float> d_a(h_a);
// --- First approach
float sum = thrust::transform_reduce(d_a.begin(), d_a.end(), conditional_operator(), 0.f, thrust::plus<float>());
printf("Result = %f\n",sum);
// --- Second approach
int N_prime = thrust::count_if(d_a.begin(), d_a.end(), is_smaller_than_10());
thrust::device_vector<float> d_b(N_prime);
thrust::copy_if(d_a.begin(), d_a.begin() + N, d_b.begin(), is_smaller_than_10());
sum = thrust::reduce(d_b.begin(), d_b.begin() + N_prime, 0.f);
printf("Result = %f\n",sum);
getchar();
}

How to partly sort arrays on CUDA?

Problem
Provided I have two arrays:
const int N = 1000000;
float A[N];
myStruct *B[N];
The numbers in A can be positive or negative (e.g. A[N]={3,2,-1,0,5,-2}), how can I make the array A partly sorted (all positive values first, not need to be sorted, then negative values)(e.g. A[N]={3,2,5,0,-1,-2} or A[N]={5,2,3,0,-2,-1}) on the GPU? The array B should be changed according to A (A is keys, B is values).
Since the scale of A,B can be very large, I think the sort algorithm should be implemented on GPU (especially on CUDA, because I use this platform). Surely I know thrust::sort_by_key can do this work, but it does muck extra work since I do not need the array A&B to be sorted entirely.
Has anyone come across this kind of problem?
Thrust example
thrust::sort_by_key(thrust::device_ptr<float> (A),
thrust::device_ptr<float> ( A + N ),
thrust::device_ptr<myStruct> ( B ),
thrust::greater<float>() );
Thrust's documentation on Github is not up-to-date. As #JaredHoberock said, thrust::partition is the way to go since it now supports stencils. You may need to get a copy from the Github repository:
git clone git://github.com/thrust/thrust.git
Then run scons doc in the Thrust folder to get an updated documentation, and use these updated Thrust sources when compiling your code (nvcc -I/path/to/thrust ...). With the new stencil partition, you can do:
#include <thrust/partition.h>
#include <thrust/execution_policy.h>
#include <thrust/iterator/zip_iterator.h>
#include <thrust/tuple.h>
struct is_positive
{
__host__ __device__
bool operator()(const int &x)
{
return x >= 0;
}
};
thrust::partition(thrust::host, // if you want to test on the host
thrust::make_zip_iterator(thrust::make_tuple(keyVec.begin(), valVec.begin())),
thrust::make_zip_iterator(thrust::make_tuple(keyVec.end(), valVec.end())),
keyVec.begin(),
is_positive());
This returns:
Before:
keyVec = 0 -1 2 -3 4 -5 6 -7 8 -9
valVec = 0 1 2 3 4 5 6 7 8 9
After:
keyVec = 0 2 4 6 8 -5 -3 -7 -1 -9
valVec = 0 2 4 6 8 5 3 7 1 9
Note that the 2 partitions are not necessarily sorted. Also, the order may differ between the original vectors and the partitions. If this is important to you, you can use thrust::stable_partition:
stable_partition differs from partition in that stable_partition is
guaranteed to preserve relative order. That is, if x and y are
elements in [first, last), such that pred(x) == pred(y), and if x
precedes y, then it will still be true after stable_partition that x
precedes y.
If you want a complete example, here it is:
#include <thrust/host_vector.h>
#include <thrust/device_vector.h>
#include <thrust/partition.h>
#include <thrust/iterator/zip_iterator.h>
#include <thrust/tuple.h>
struct is_positive
{
__host__ __device__
bool operator()(const int &x)
{
return x >= 0;
}
};
void print_vec(const thrust::host_vector<int>& v)
{
for(size_t i = 0; i < v.size(); i++)
std::cout << " " << v[i];
std::cout << "\n";
}
int main ()
{
const int N = 10;
thrust::host_vector<int> keyVec(N);
thrust::host_vector<int> valVec(N);
int sign = 1;
for(int i = 0; i < N; ++i)
{
keyVec[i] = sign * i;
valVec[i] = i;
sign *= -1;
}
// Copy host to device
thrust::device_vector<int> d_keyVec = keyVec;
thrust::device_vector<int> d_valVec = valVec;
std::cout << "Before:\n keyVec = ";
print_vec(keyVec);
std::cout << " valVec = ";
print_vec(valVec);
// Partition key-val on device
thrust::partition(thrust::make_zip_iterator(thrust::make_tuple(d_keyVec.begin(), d_valVec.begin())),
thrust::make_zip_iterator(thrust::make_tuple(d_keyVec.end(), d_valVec.end())),
d_keyVec.begin(),
is_positive());
// Copy result back to host
keyVec = d_keyVec;
valVec = d_valVec;
std::cout << "After:\n keyVec = ";
print_vec(keyVec);
std::cout << " valVec = ";
print_vec(valVec);
}
UPDATE
I made a quick comparison with the thrust::sort_by_key version, and the thrust::partition implementation does seem to be faster (which is what we could naturally expect). Here is what I obtain on NVIDIA Visual Profiler, with N = 1024 * 1024, with the sort version on the left, and the partition version on the right. You may want to do the same kind of tests on your own.
How about this?:
Count how many positive numbers to determine the inflexion point
Evenly divide each side of the inflexion point into groups (negative-groups are all same length but different length to positive-groups. these groups are the memory chunks for the results)
Use one kernel call (one thread) per chunk pair
Each kernel swaps any out-of-place elements in the input groups into the desired output groups. You will need to flag any chunks that have more swaps than the maximum so that you can fix them during subsequent iterations.
Repeat until done
Memory traffic is swaps only (from original element position, to sorted position). I don't know if this algorithm sounds like anything already defined...
You should be able to achieve this in thrust simply with a modification of your comparison operator:
struct my_compare
{
__device__ __host__ bool operator()(const float x, const float y) const
{
return !((x<0.0f) && (y>0.0f));
}
};
thrust::sort_by_key(thrust::device_ptr<float> (A),
thrust::device_ptr<float> ( A + N ),
thrust::device_ptr<myStruct> ( B ),
my_compare() );

Decimal to Irrational fraction approximation

I have implemented an algorithm for floating point decimal to rational fraction approximation (example: 0.333 -> 1/3) and now I wonder, is there a way to find an irrational number which satisfies the condition. For example, given the input 0.282842712474 I want the result to be sqrt(2)/5 and not 431827/1526739 which my algorithm produces. The only condition is that the first digits of the result (converted back to floating point) should be the digits of the input, the rest doesn't matter. Thanks in advance!
I came up with solution, that from given set of possible denominators and nominators finds best approximation of given number.
For example this set can contain all numbers that can be created by:
1 <= radicand <= 100000
1 <= root_index <= 20
If set has N elements, than this solution finds best approximation in O(N log N).
In this solution X represents denominator and Y nominator.
sort numbers from set
for each number X from set:
using binary find smallest Y such that Y/X >= input_number
compare Y/X with currently best approximation of input_number
I couldn't resist and I implemented it:
#include <cstdio>
#include <vector>
#include <algorithm>
#include <cmath>
using namespace std;
struct Number {
// number value
double value;
// number representation
int root_index;
int radicand;
Number(){}
Number(double value, int root_index, int radicand)
: value(value), root_index(root_index), radicand(radicand) {}
bool operator < (const Number& rhs) const {
// in case of equal numbers, i want smaller radicand first
if (fabs(value - rhs.value) < 1e-12) return radicand < rhs.radicand;
return value < rhs.value;
}
void print() const {
if (value - (int)value < 1e-12) printf("%.0f", value);
else printf("sqrt_%d(%d)",root_index, radicand);
}
};
std::vector<Number> numbers;
double best_result = 1e100;
Number best_numerator;
Number best_denominator;
double input;
void compare_approximpation(const Number& numerator, const Number& denominator) {
double value = numerator.value / denominator.value;
if (fabs(value - input) < fabs(best_result - input)) {
best_result = value;
best_numerator = numerator;
best_denominator = denominator;
}
}
int main() {
const int NUMBER_LIMIT = 100000;
const int ROOT_LIMIT = 20;
// only numbers created by this loops will be used
// as numerator and denominator
for(int i=1; i<=ROOT_LIMIT; i++) {
for(int j=1; j<=NUMBER_LIMIT; j++) {
double value = pow(j, 1.0 /i);
numbers.push_back(Number(value, i, j));
}
}
sort(numbers.begin(), numbers.end());
scanf("%lf",&input);
int numerator_index = 0;
for(int denominator_index=0; denominator_index<numbers.size(); denominator_index++) {
// you were interested only in integral denominators
if (numbers[denominator_index].root_index == 1) {
// i use simple sweeping technique instead of binary search (its faster)
while(numerator_index < numbers.size() && numbers[numerator_index].root_index &&
numbers[numerator_index].value / numbers[denominator_index].value <= input) {
numerator_index++;
}
// comparing approximations
compare_approximpation(numbers[numerator_index], numbers[denominator_index]);
if (numerator_index > 0) {
compare_approximpation(numbers[numerator_index - 1], numbers[denominator_index]);
}
}
}
printf("Best approximation %.12lf = ", best_numerator.value / best_denominator.value);
best_numerator.print();
printf(" / ");
best_denominator.print();
printf("\n");
}

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