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Merge pull request #34 from fmgjcoppens/fix/slagel_splitting

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Various fixes
This commit is contained in:
François Coppens 2021-05-10 14:29:02 +02:00 committed by GitHub
commit 0984682bdf
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GPG Key ID: 4AEE18F83AFDEB23
16 changed files with 220 additions and 234 deletions
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7
Makefile
View File

@ -29,13 +29,12 @@ FLIBS = -lstdc++
## Includes and dependencies
INCLUDE = -I $(INC_DIR)/
DEPS_CXX = $(OBJ_DIR)/SM_MaponiA3.o \
$(OBJ_DIR)/SM_MaponiA3S.o \
DEPS_CXX = $(OBJ_DIR)/SM_Maponi.o \
$(OBJ_DIR)/SM_Standard.o \
$(OBJ_DIR)/SM_Helpers.o
DEPS_F = $(DEPS_CXX) \
$(OBJ_DIR)/SM_mod.o \
$(OBJ_DIR)/Helpers_mod.o
$(OBJ_DIR)/finterface_mod.o \
$(OBJ_DIR)/helpers_mod.o
## Directory structure
SRC_DIR := src

7
Makefile.verificarlo
View File

@ -16,13 +16,12 @@ CXXFLAGS = -O0 -g $(H5FLAGS)
FFLAGS = $(CXXFLAGS)
INCLUDE = -I $(INC_DIR)/
DEPS_CXX = $(OBJ_DIR)/SM_MaponiA3.o \
$(OBJ_DIR)/SM_MaponiA3S.o \
DEPS_CXX = $(OBJ_DIR)/SM_Maponi.o \
$(OBJ_DIR)/SM_Standard.o \
$(OBJ_DIR)/SM_Helpers.o
DEPS_F = $(DEPS_CXX) \
$(OBJ_DIR)/SM_mod.o \
$(OBJ_DIR)/Helpers_mod.o
$(OBJ_DIR)/finterface_mod.o \
$(OBJ_DIR)/helpers_mod.o
FLIBS = -lstdc++
SRC_DIR := src

50
include/SM_Helpers.hpp
View File

@ -127,3 +127,53 @@ template <typename T> bool is_identity(T *A, unsigned int M, double tolerance) {
}
return true;
}
template <typename T> T norm_max(T * A, unsigned int Dim) {
T res = 0;
for (unsigned int i = 0; i < Dim; i++) {
for (unsigned int j = 0; j < Dim; j++) {
T delta = A[i * Dim + j];
delta = fabs(delta);
if (delta > res) {
res = delta;
}
}
}
return res;
}
template <typename T> T norm_frobenius2(T * A, unsigned int Dim) {
T res = 0;
for (unsigned int i = 0; i < Dim; i++) {
for (unsigned int j = 0; j < Dim; j++) {
T delta = A[i * Dim + j];
res += delta*delta;
}
}
return res;
}
template <typename T> T residual_max(T * A, unsigned int Dim) {
T res = 0;
for (unsigned int i = 0; i < Dim; i++) {
for (unsigned int j = 0; j < Dim; j++) {
T delta = A[i * Dim + j] - (i == j);
delta = fabs(delta);
if (delta > res) {
res = delta;
}
}
}
return res;
}
template <typename T> T residual_frobenius2(T * A, unsigned int Dim) {
T res = 0;
for (unsigned int i = 0; i < Dim; i++) {
for (unsigned int j = 0; j < Dim; j++) {
T delta = A[i * Dim + j] - (i == j);
res += delta*delta;
}
}
return res;
}

8
include/SM_Maponi.hpp Normal file
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@ -0,0 +1,8 @@
// P. Maponi Algorithm 3
void MaponiA3(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index);
// P. Maponi Algorithm 3 with J. Slagel splitting
// http://hdl.handle.net/10919/52966
void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index);

2
include/SM_MaponiA3.hpp
View File

@ -1,2 +0,0 @@
void MaponiA3(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index);

2
include/SM_MaponiA3S.hpp
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@ -1,2 +0,0 @@
void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index);

1
smvars.sh
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@ -45,6 +45,7 @@ case $ENV in
*)
echo "Unknown environment descriptor given."
echo "Usage: source smvars.sh {intel | llvm | vfc | gnu}"
echo "Usage: source smvars.sh {intel | llvm | vfc | gnu} [threshold]"
return 1
;;
esac

163
src/SM_MaponiA3S.cpp → src/SM_Maponi.cpp
View File

@ -1,17 +1,146 @@
// SM-MaponiA3_f.cpp
// SM_Maponi.cpp
// Algorithm 3 from P. Maponi,
// p. 283, doi:10.1016/j.laa.2006.07.007
#include "SM_MaponiA3S.hpp"
#include "SM_Maponi.hpp"
#include "SM_Helpers.hpp"
// #define DEBUG
void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index) {
void MaponiA3(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index) {
std::cerr << "Called MaponiA3 with " << N_updates << " updates" << std::endl;
/*
DECLARE AND INITIALISE ARRAYS
*/
unsigned int k, l, i, j, component;
unsigned int *p = new unsigned int[N_updates + 1]{0};
double alpha, beta;
double *Al = new double[Dim * Dim];
double *next = new double[Dim * Dim]{0};
double *last = Slater_inv, *tmp;
// Populate update-order vector
for (i = 0; i < N_updates; i++) {
p[i + 1] = i + 1;
}
// Declare auxiliary solution matrix ylk[N_updates][N_updates+1][Dim]
double ***ylk = new double **[N_updates];
for (l = 0; l < N_updates; l++) {
ylk[l] = new double *[N_updates + 1];
for (k = 0; k < N_updates + 1; k++) {
ylk[l][k] = new double[Dim + 1]{0};
}
}
/*
START ALGORITHM
*/
// Calculate the {y_{0,k}}
for (k = 1; k < N_updates + 1; k++) {
#ifdef DEBUG
std::cerr << "Compute y0k: " << std::endl;
std::cerr << "ylk[0][" << k << "][:]";
std::cerr << std::endl;
#endif
for (i = 1; i < Dim + 1; i++) {
for (j = 1; j < Dim + 1; j++) {
ylk[0][k][i] += Slater_inv[(i - 1) * Dim + (j - 1)] *
Updates[(k - 1) * Dim + (j - 1)];
}
}
#ifdef DEBUG
showVector(ylk[0][k], Dim, "");
#endif
}
// Calculate the {y_{l,k}} from the {y_{0,k}}
for (l = 0; l < N_updates; l++) {
#ifdef DEBUG
std::cerr << "In outer compute-ylk-loop: l = " << l << std::endl;
std::cerr << std::endl;
#endif
// For given l select intermediate update with largest break-down val
selectLargestDenominator(l, N_updates, Updates_index, p, ylk);
// Select component and comp. bd-condition.
component = Updates_index[p[l + 1] - 1];
beta = 1 + ylk[l][p[l + 1]][component];
#ifdef DEBUG
std::cerr << "p[l+1] = " << p[l + 1] << std::endl;
std::cerr << "component = " << component << std::endl;
std::cerr << "beta = 1 + ylk[" << l << "][" << p[l + 1] << "][" << component
<< "] = " << beta << std::endl;
std::cerr << std::endl;
#endif
if (fabs(beta) < threshold()) {
std::cerr << "Breakdown condition triggered at " << Updates_index[l]
<< std::endl;
}
double ibeta = 1.0 / beta;
// Compute intermediate update to Slater_inv
#ifdef DEBUG
std::cerr << "Compute intermediate update to Slater_inv" << std::endl;
std::cerr << "component = " << component << std::endl;
std::cerr << "beta = 1 + ylk[" << l << "][" << p[l + 1] << "][" << component
<< "]" << std::endl;
std::cerr << "ylk[l][p[k]][:] = ylk[" << l << "][" << p[l + 1] << "][:]"
<< std::endl;
std::cerr << std::endl;
#endif
for (i = 0; i < Dim; i++) {
for (j = 0; j < Dim; j++) {
Al[i * Dim + j] =
(i == j) - (j == component - 1) * ylk[l][p[l + 1]][i + 1] * ibeta;
}
}
matMul(Al, last, next, Dim);
tmp = next;
next = last;
last = tmp;
#ifdef DEBUG
showMatrix(last, Dim, "last");
#endif
// For given l != 0 compute the next {y_{l,k}}
for (k = l + 2; k < N_updates + 1; k++) {
alpha = ylk[l][p[k]][component] * ibeta;
#ifdef DEBUG
std::cerr << "Inside k-loop: k = " << k << std::endl;
std::cerr << "ylk[" << l + 1 << "][" << p[k] << "][:]" << std::endl;
std::cerr << std::endl;
#endif
for (i = 1; i < Dim + 1; i++) {
ylk[l + 1][p[k]][i] = ylk[l][p[k]][i] - alpha * ylk[l][p[l + 1]][i];
}
}
}
memcpy(Slater_inv, last, Dim * Dim * sizeof(double));
/*
CLEANUP MEMORY
*/
for (l = 0; l < N_updates; l++) {
for (k = 0; k < N_updates + 1; k++) {
delete[] ylk[l][k];
}
delete[] ylk[l];
}
delete[] Al, next, p, ylk;
}
void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index) {
std::cerr << "Called MaponiA3S with " << N_updates << " updates" << std::endl;
/*
DECLARE AND INITIALISE ARRAYS
*/
showVector(Updates_index, Dim, "Updates_index");
unsigned int k, l, i, j, component;
unsigned int *p = new unsigned int[N_updates + 1]{0};
double alpha, beta;
@ -40,7 +169,6 @@ void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
/*
START ALGORITHM
*/
showMatrix(Slater_inv, Dim, "S^{-1}");
// Calculate the y_{0,k} = S_0^{-1} u_k
for (k = 1; k < N_updates + 1; k++) {
@ -81,27 +209,17 @@ void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
std::cerr << std::endl;
#endif
if (fabs(beta) < threshold()) {
#ifdef DEBUG
std::cerr << "Breakdown condition triggered at l = " << l << " and component "<< component
std::cerr << "Breakdown condition triggered at " << Updates_index[l]
<< std::endl;
#endif
for (unsigned int i = 1; i < Dim + 1; i++) {
std::cout << "Let's split..." << std::endl;
ylk[l][p[l + 1]][i] *= 0.5;
// later_updates[later * Dim + i - 1] = ylk[l][p[l + 1]][i]; // Updates[l * Dim + i] * 0.5;
later_updates[later * Dim + i - 1] = Updates[l * Dim + i - 1] * 0.5;
}
later_index[later] = Updates_index[p[l + 1] - 1];
std::cout << "Later = " << later << std::endl;
later++;
std::cout << "Later = " << later << std::endl;
beta = 1 + ylk[l][p[l + 1]][component];
std::cout << "New beta is: " << beta << std::endl;
}
double ibeta = 1.0 / beta;
showVector(ylk[l][p[l + 1]], Dim+1, "");
showVector(later_updates+(Dim*0), Dim, "later_updateds");
// Compute intermediate update to Slater_inv
#ifdef DEBUG
@ -135,7 +253,6 @@ void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
for (i = 1; i < Dim + 1; i++) {
ylk[l + 1][p[k]][i] = ylk[l][p[k]][i] - alpha * ylk[l][p[l + 1]][i];
}
showVector(ylk[l + 1][p[k]], Dim+1, "");
}
}
memcpy(Slater_inv, last, Dim * Dim * sizeof(double));
@ -153,12 +270,18 @@ void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
delete[] Al, next, p, ylk;
if (later > 0) {
std::cerr << "Entering recursive loop with " << later << " updates" << std::endl;
std::cout << later_index[0] << std::endl;
MaponiA3S(Slater_inv, Dim, later, later_updates, later_index);
}
}
extern "C" {
void MaponiA3_f(double **linSlater_inv, unsigned int *Dim,
unsigned int *N_updates, double **linUpdates,
unsigned int **Updates_index) {
MaponiA3(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
}
}
extern "C" {
void MaponiA3S_f(double **linSlater_inv, unsigned int *Dim,
unsigned int *N_updates, double **linUpdates,

142
src/SM_MaponiA3.cpp
View File

@ -1,142 +0,0 @@
// SM-MaponiA3_f.cpp
// Algorithm 3 from P. Maponi,
// p. 283, doi:10.1016/j.laa.2006.07.007
#include "SM_MaponiA3.hpp"
#include "SM_Helpers.hpp"
// #define DEBUG
void MaponiA3(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index) {
/*
DECLARE AND INITIALISE ARRAYS
*/
unsigned int k, l, i, j, component;
unsigned int *p = new unsigned int[N_updates + 1]{0};
double alpha, beta;
double *Al = new double[Dim * Dim];
double *next = new double[Dim * Dim]{0};
double *last = Slater_inv, *tmp;
// Populate update-order vector
for (i = 0; i < N_updates; i++) {
p[i + 1] = i + 1;
}
// Declare auxiliary solution matrix ylk[N_updates][N_updates+1][Dim]
double ***ylk = new double **[N_updates];
for (l = 0; l < N_updates; l++) {
ylk[l] = new double *[N_updates + 1];
for (k = 0; k < N_updates + 1; k++) {
ylk[l][k] = new double[Dim + 1]{0};
}
}
/*
START ALGORITHM
*/
// Calculate the {y_{0,k}}
for (k = 1; k < N_updates + 1; k++) {
#ifdef DEBUG
std::cout << "Compute y0k: " << std::endl;
std::cout << "ylk[0][" << k << "][:]";
std::cout << std::endl;
#endif
for (i = 1; i < Dim + 1; i++) {
for (j = 1; j < Dim + 1; j++) {
ylk[0][k][i] += Slater_inv[(i - 1) * Dim + (j - 1)] *
Updates[(k - 1) * Dim + (j - 1)];
}
}
#ifdef DEBUG
showVector(ylk[0][k], Dim, "");
#endif
}
// Calculate the {y_{l,k}} from the {y_{0,k}}
for (l = 0; l < N_updates; l++) {
#ifdef DEBUG
std::cout << "In outer compute-ylk-loop: l = " << l << std::endl;
std::cout << std::endl;
#endif
// For given l select intermediate update with largest break-down val
selectLargestDenominator(l, N_updates, Updates_index, p, ylk);
// Select component and comp. bd-condition.
component = Updates_index[p[l + 1] - 1];
beta = 1 + ylk[l][p[l + 1]][component];
#ifdef DEBUG
std::cout << "p[l+1] = " << p[l + 1] << std::endl;
std::cout << "component = " << component << std::endl;
std::cout << "beta = 1 + ylk[" << l << "][" << p[l + 1] << "][" << component
<< "] = " << beta << std::endl;
std::cout << std::endl;
#endif
if (fabs(beta) < threshold()) {
std::cerr << "Break-down occured." << std::endl;
}
double ibeta = 1.0 / beta;
// Compute intermediate update to Slater_inv
#ifdef DEBUG
std::cout << "Compute intermediate update to Slater_inv" << std::endl;
std::cout << "component = " << component << std::endl;
std::cout << "beta = 1 + ylk[" << l << "][" << p[l + 1] << "][" << component
<< "]" << std::endl;
std::cout << "ylk[l][p[k]][:] = ylk[" << l << "][" << p[l + 1] << "][:]"
<< std::endl;
std::cout << std::endl;
#endif
for (i = 0; i < Dim; i++) {
for (j = 0; j < Dim; j++) {
Al[i * Dim + j] =
(i == j) - (j == component - 1) * ylk[l][p[l + 1]][i + 1] * ibeta;
}
}
matMul(Al, last, next, Dim);
tmp = next;
next = last;
last = tmp;
#ifdef DEBUG
showMatrix(last, Dim, "last");
#endif
// For given l != 0 compute the next {y_{l,k}}
for (k = l + 2; k < N_updates + 1; k++) {
alpha = ylk[l][p[k]][component] * ibeta;
#ifdef DEBUG
std::cout << "Inside k-loop: k = " << k << std::endl;
std::cout << "ylk[" << l + 1 << "][" << p[k] << "][:]" << std::endl;
std::cout << std::endl;
#endif
for (i = 1; i < Dim + 1; i++) {
ylk[l + 1][p[k]][i] = ylk[l][p[k]][i] - alpha * ylk[l][p[l + 1]][i];
}
}
}
memcpy(Slater_inv, last, Dim * Dim * sizeof(double));
/*
CLEANUP MEMORY
*/
for (l = 0; l < N_updates; l++) {
for (k = 0; k < N_updates + 1; k++) {
delete[] ylk[l][k];
}
delete[] ylk[l];
}
delete[] Al, next, p, ylk;
}
extern "C" {
void MaponiA3_f(double **linSlater_inv, unsigned int *Dim,
unsigned int *N_updates, double **linUpdates,
unsigned int **Updates_index) {
MaponiA3(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
}
}

7
src/SM_Standard.cpp
View File

@ -50,7 +50,7 @@ void SM1(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
// http://hdl.handle.net/10919/52966
void SM2(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index) {
std::cerr << "Called SM2 with updates " << N_updates << std::endl;
std::cerr << "Called SM2 with " << N_updates << " updates" << std::endl;
double C[Dim];
double D[Dim];
@ -110,7 +110,7 @@ void SM2(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
// Sherman Morrison, leaving zero denominators for later
void SM3(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index) {
std::cerr << "Called SM3 with updates " << N_updates << std::endl;
std::cerr << "Called SM3 with " << N_updates << " updates" << std::endl;
double C[Dim];
double D[Dim];
@ -176,7 +176,7 @@ void SM3(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
// Leave zero denominators for later (SM3), and when none are left then split (SM2)
void SM4(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
double *Updates, unsigned int *Updates_index) {
std::cerr << "Called SM4 with updates " << N_updates << std::endl;
std::cerr << "Called SM4 with " << N_updates << " updates" << std::endl;
double C[Dim];
double D[Dim];
@ -254,6 +254,7 @@ extern "C" {
unsigned int **Updates_index) {
SM3(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
}
void SM4_f(double **linSlater_inv, unsigned int *Dim,
unsigned int *N_updates, double **linUpdates,
unsigned int **Updates_index) {

0
src/SM_mod.f90 → src/finterface_mod.f90
View File

0
src/Helpers_mod.f90 → src/helpers_mod.f90
View File

2
tests/cMaponiA3_test_3x3_3.cpp
View File

@ -1,5 +1,5 @@
// main.cpp
#include "SM_MaponiA3.hpp"
#include "SM_Maponi.hpp"
#include "SM_Helpers.hpp"
int main() {

3
tests/run_test.sh
View File

@ -12,7 +12,8 @@ ALGO=$1
START=$2
STOP=$3
BLOCKSIZE=329
TOLERANCE=1e-3
#TOLERANCE=1e-3
TOLERANCE=$4
BLOCKS=$((STOP / BLOCKSIZE))
LEFT=$((STOP % BLOCKSIZE))

32
tests/test_h5.cpp
View File

@ -1,39 +1,15 @@
#include "hdf5/serial/hdf5.h"
#include "hdf5/serial/H5Cpp.h"
#include "SM_MaponiA3.hpp"
#include "SM_MaponiA3S.hpp"
#include "SM_Maponi.hpp"
#include "SM_Standard.hpp"
#include "SM_Helpers.hpp"
using namespace H5;
#define DEBUG
// #define DEBUG
const H5std_string FILE_NAME( "dataset.hdf5" );
double residual_max(double * A, unsigned int Dim) {
double max = 0.0;
for (unsigned int i = 0; i < Dim; i++) {
for (unsigned int j = 0; j < Dim; j++) {
double delta = (A[i * Dim + j] - (i == j));
delta = abs(delta);
if (delta > max) max = delta;
}
}
return max;
}
double residual2(double * A, unsigned int Dim) {
double res = 0.0;
for (unsigned int i = 0; i < Dim; i++) {
for (unsigned int j = 0; j < Dim; j++) {
double delta = (A[i * Dim + j] - (i == j));
res += delta*delta;
}
}
return res;
}
void read_int(H5File file, std::string key, unsigned int * data) {
DataSet ds = file.openDataSet(key);
ds.read(data, PredType::STD_U32LE);
@ -92,8 +68,6 @@ int test_cycle(H5File file, int cycle, std::string version, double tolerance) {
showMatrix(u, dim, "Updates");
#endif
if (version == "maponia3") {
MaponiA3(slater_inverse, dim, nupdates, u, col_update_index);
} else if (version == "maponia3s") {
@ -124,7 +98,7 @@ int test_cycle(H5File file, int cycle, std::string version, double tolerance) {
bool ok = is_identity(res, dim, tolerance);
double res_max = residual_max(res, dim);
double res2 = residual2(res, dim);
double res2 = residual_frobenius2(res, dim);
std::cout << "Residual = " << version << " " << cycle << " " << res_max << " " << res2 << std::endl;
#ifdef DEBUG

28
tests/vfc_test_h5.cpp
View File

@ -11,7 +11,7 @@
#include <sstream>
#include "SM_MaponiA3.hpp"
#include "SM_Maponi.hpp"
#include "SM_Standard.hpp"
#include "SM_Helpers.hpp"
#include "vfc_probe.h"
@ -21,29 +21,6 @@ using namespace H5;
const H5std_string FILE_NAME( "datasets/ci_dataset.hdf5" );
double residual_max(double * A, unsigned int Dim) {
double max = 0.0;
for (unsigned int i = 0; i < Dim; i++) {
for (unsigned int j = 0; j < Dim; j++) {
double delta = (A[i * Dim + j] - (i == j));
delta = abs(delta);
if (delta > max) max = delta;
}
}
return max;
}
double residual2(double * A, unsigned int Dim) {
double res = 0.0;
for (unsigned int i = 0; i < Dim; i++) {
for (unsigned int j = 0; j < Dim; j++) {
double delta = (A[i * Dim + j] - (i == j));
res += delta*delta;
}
}
return res;
}
void read_int(H5File file, std::string key, unsigned int * data) {
DataSet ds = file.openDataSet(key);
ds.read(data, PredType::STD_U32LE);
@ -56,7 +33,6 @@ void read_double(H5File file, std::string key, double * data) {
ds.close();
}
/* Return a vector containing all cycles to execute by reading a data file */
std::vector<int> get_cycles_list(std::string path) {
std::ifstream file_stream(path);
@ -157,7 +133,7 @@ int test_cycle(H5File file, int cycle, std::string version, vfc_probes * probes)
bool ok = is_identity(res, dim, 1e-3);
double res_max = residual_max(res, dim);
double res2 = residual2(res, dim);
double res2 = residual_frobenius2(res, dim);
#ifdef DEBUG
showMatrix(res, dim, "Result");