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Merge pull request #6 from pablooliveira/test-datasets

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Test datasets
This commit is contained in:
François Coppens 2021-02-16 15:06:04 +01:00 committed by GitHub
commit f17a7a2c9b
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12 changed files with 2786 additions and 32 deletions
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6
.gitignore vendored
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@ -1,5 +1,7 @@
*.o *.o
*.mod *.mod
cppSherman-Morrison
fSherman-Morrison
.vscode .vscode
cMaponiA3_test
fMaponiA3_test
QMCChem_dataset_test

12
Helpers.hpp
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@ -119,3 +119,15 @@ T matDet(T **A, unsigned int M) {
} }
delete [] temp; delete [] temp;
} }
template<typename T>
bool is_identity(T *A, unsigned int M, double tolerance) {
for (unsigned int i = 0; i < M; i++) {
for (unsigned int j = 0; j < M; j++) {
if (i==j && fabs(A[i*M+j]-1) > tolerance) return false;
if (i!=j && fabs(A[i*M+j]) > tolerance) return false;
}
}
return true;
}

54
Makefile
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@ -1,44 +1,56 @@
## Used compilers ## Used compilers
CXX = icpc H5CXX = h5c++
FC = ifort CXX = clang++
FC = flang
## Compiler flags ## Compiler flags
CXXFLAGS = -O0 #-debug full -traceback CXXFLAGS = -O0
FFLAGS = -O0 #-debug full -traceback FFLAGS = -O0
# ARCH = -xCORE-AVX2
## Deps & objs for the C++ stuff ## Deps & objs for C++ cMaponiA3_test
cppDEPS = cppmain.cpp SM_MaponiA3.cpp SM_MaponiA3.hpp Helpers.hpp cMaponiA3_testDEP = cMaponiA3_test.cpp SM_MaponiA3.cpp SM_MaponiA3.hpp Helpers.hpp
cppOBJ = cppmain.o SM_MaponiA3.o cMaponiA3_testOBJ = cMaponiA3_test.o SM_MaponiA3.o
## Deps & objs for the Fortran stuff ## Deps & objs for Fortran fMaponiA3_test
fDEPS = fmain.f90 SM_MaponiA3_mod.f90 fMaponiA3_testDEP = fMaponiA3_test.f90 SM_MaponiA3_mod.f90
fOBJ = SM_MaponiA3.o SM_MaponiA3_mod.o fmain.o fMaponiA3_testOBJ = SM_MaponiA3.o SM_MaponiA3_mod.o fMaponiA3_test.o
fLIBS = -lstdc++ fMaponiA3_testLIB = -lstdc++
## Compile recipes for C++ stuff ## Deps & objs for Fortran QMCChem_dataset_test
%.o: %.cpp $(cppDEPS) QMCChem_dataset_testDEP = QMCChem_dataset_test.f90 SM_MaponiA3_mod.f90 Utils_mod.f90
QMCChem_dataset_testOBJ = SM_MaponiA3.o Utils_mod.o SM_MaponiA3_mod.o QMCChem_dataset_test.o
QMCChem_dataset_testLIB = -lstdc++
## Compile recipes for C++ cMaponiA3_test
%.o: %.cpp $(cMaponiA3_testDEP)
$(CXX) $(ARCH) $(CXXFLAGS) -c -o $@ $< $(CXX) $(ARCH) $(CXXFLAGS) -c -o $@ $<
## Compile recepies for Fortran stuff ## Compile recepies for Fortran fMaponiA3_test
%.o: %.f90 $(fDEPS) %.o: %.f90 $(fMaponiA3_testDEP)
$(FC) $(ARCH) $(FFLAGS) -c -o $@ $< $(FC) $(ARCH) $(FFLAGS) -c -o $@ $<
## Build tagets ## Build tagets
.PHONY: all clean distclean .PHONY: all clean distclean
all: cppSherman-Morrison fSherman-Morrison all: cMaponiA3_test fMaponiA3_test QMCChem_dataset_test tests/test
clean: clean:
@rm -vf *.o *.mod @rm -vf *.o *.mod
distclean: clean distclean: clean
@rm -vf cppSherman-Morrison fSherman-Morrison @rm -vf cMaponiA3_test fMaponiA3_test QMCChem_dataset_test
## Linking the C++ example program ## Linking the C++ example program
cppSherman-Morrison: $(cppOBJ) cMaponiA3_test: $(cMaponiA3_testOBJ)
$(CXX) $(ARCH) $(CXXFLAGS) -o $@ $^ $(CXX) $(ARCH) $(CXXFLAGS) -o $@ $^
## Linking Fortran example program calling the C++ function 'Sherman_Morrison()' ## Linking Fortran example program calling the C++ function 'Sherman_Morrison()'
fSherman-Morrison: $(fOBJ) fMaponiA3_test: $(fMaponiA3_testOBJ)
$(FC) $(ARCH) $(FFLAGS) $(fLIBS) -o $@ $^ $(FC) $(ARCH) $(FFLAGS) $(fMaponiA3_testLIB) -o $@ $^
## Linking Fortran example program calling the C++ function 'Sherman_Morrison()'
QMCChem_dataset_test: $(QMCChem_dataset_testOBJ)
$(FC) $(ARCH) $(FFLAGS) $(QMCChem_dataset_testLIB) -o $@ $^
tests/test: tests/test.cpp SM_MaponiA3.o
$(H5CXX) $(ARCH) $(CXXFLAGS) -o $@ $^

66
QMCChem_dataset_test.f90 Normal file
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@ -0,0 +1,66 @@
program QMCChem_dataset_test
use Sherman_Morrison, only : MaponiA3
use Utils, only : Read_dataset
use, intrinsic :: iso_c_binding, only : c_int, c_double
implicit none
integer :: i, j, col !! Iterators
integer :: cycle_id, dim, n_updates
integer(c_int), dimension(:), allocatable :: Updates_index
real(c_double), dimension(:,:), allocatable :: S, S_inv, Updates
call Read_dataset("test.dataset.dat", &
cycle_id, &
dim, &
n_updates, &
S, &
S_inv, &
Updates_index, &
Updates)
!! Write current S and S_inv to file for check in Octave
open(unit = 2000, file = "Slater_old.dat")
open(unit = 3000, file = "Slater_inv_old.dat")
do i=1,dim
do j=1,dim
write(2000,"(E23.15, 1X)", advance="no") S(i,j)
write(3000,"(E23.15, 1X)", advance="no") S_inv(i,j)
end do
write(2000,*)
write(3000,*)
end do
call flush(2000)
call flush(3000)
close(2000)
close(3000)
!! Send S, S_inv and Updates to MaponiA3 algo
call MaponiA3(S, S_inv, dim, n_updates, Updates, Updates_index)
!! Update S itself
do j=1,n_updates
do i=1,dim
col = Updates_index(j)
S(i,col) = S(i,col) + Updates(i,col)
end do
end do
!! Write new S and S_inv to file for check in Octave
open(unit = 2000, file = "Slater_new.dat")
open(unit = 3000, file = "Slater_inv_new.dat")
do i=1,dim
do j=1,dim
write(2000,"(E23.15, 1X)", advance="no") S(i,j)
write(3000,"(E23.15, 1X)", advance="no") S_inv(i,j)
end do
write(2000,*)
write(3000,*)
end do
call flush(2000)
call flush(3000)
close(2000)
close(3000)
deallocate(S, S_inv, Updates, Updates_index)
end program

9
SM_MaponiA3.cpp
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@ -28,7 +28,7 @@ void MaponiA3(double *Slater0, double *Slater_inv, unsigned int M,
} }
// Calculate all the y0k in M^2 multiplications instead of M^3 // Calculate all the y0k in M^2 multiplications instead of M^3
for (k = 1; k < M + 1; k++) { for (k = 1; k < N_updates + 1; k++) {
for (i = 1; i < M + 1; i++) { for (i = 1; i < M + 1; i++) {
ylk[0][k][i] = ylk[0][k][i] =
Slater_inv[(i - 1) * M + (i - 1)] * Updates[(i - 1) * M + (k - 1)]; Slater_inv[(i - 1) * M + (i - 1)] * Updates[(i - 1) * M + (k - 1)];
@ -92,10 +92,11 @@ void MaponiA3(double *Slater0, double *Slater_inv, unsigned int M,
} }
extern "C" { extern "C" {
void MaponiA3_f(double **linSlater0, double **linSlater_inv, unsigned int *Dim, void MaponiA3_f(double **linSlater0, double **linSlater_inv, unsigned int *Dim,
unsigned int *N_updates, double **linUpdates, unsigned int *N_updates, double **linUpdates,
unsigned int **Updates_index) { unsigned int **Updates_index) {
MaponiA3(*linSlater0, *linSlater_inv, *Dim, *N_updates, *linUpdates, MaponiA3(*linSlater0, *linSlater_inv, *Dim,
*N_updates, *linUpdates,
*Updates_index); *Updates_index);
} }
} }

47
Utils_mod.f90 Normal file
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@ -0,0 +1,47 @@
module Utils
implicit none
contains
subroutine Read_dataset(filename, cycle_id, dim, n_updates, &
S, S_inv, Updates_index, Updates)
use, intrinsic :: iso_c_binding, only : c_int, c_double
implicit none
character (len = *), intent(in) :: filename
integer, intent(inout) :: cycle_id, dim, n_updates
integer(c_int), allocatable, intent(inout) :: Updates_index(:)
real(c_double), allocatable, intent(inout) :: S(:,:), S_inv(:,:)
real(c_double), allocatable, intent(inout) :: Updates(:,:)
integer :: i, j
character (len = 32) :: ignore
!! Start of reading the dataset from file
open(unit = 1000, file = filename)
read(1000,*)
read(1000,*) ignore, cycle_id
read(1000,*) ignore, dim
read(1000,*) ignore,n_updates
allocate(Updates_index(n_updates), S(dim,dim), &
S_inv(dim,dim), Updates(dim,n_updates))
!! Read S and S_inv
read(1000,*)
do i=1,dim
do j=1,dim
read(1000,*) ignore, ignore, S(i,j), S_inv(i,j)
end do
end do
!! Read the updates Updates and Updates_index
do j=1,n_updates
read(1000,*) ignore, Updates_index(j)
do i=1,dim
read(1000,*) ignore, Updates(i,j)
end do
end do
read(1000,*) ignore
close(1000)
!! End of reading the dataset from file
end subroutine Read_dataset
end module Utils

0
cppmain.cpp → cMaponiA3_test.cpp
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1966
det.irp.f Normal file
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File diff suppressed because it is too large Load Diff

2
fmain.f90 → fMaponiA3_test.f90
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@ -10,7 +10,7 @@ program Interface_test
real(c_double), dimension(:,:), allocatable :: A0_inv real(c_double), dimension(:,:), allocatable :: A0_inv
dim = 3 dim = 3
N_updates = dim N_updates = 3
allocate(Ar_index(dim), A(dim,dim), A0(dim,dim), Ar(dim,dim), A0_inv(dim,dim)) allocate(Ar_index(dim), A(dim,dim), A0(dim,dim), Ar(dim,dim), A0_inv(dim,dim))
!! Initialize A with M=3 and fill acc. to Eq. (17) from paper !! Initialize A with M=3 and fill acc. to Eq. (17) from paper

513
test.dataset.dat Normal file
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@ -0,0 +1,513 @@
#START_PACKET
#CYCLE_ID: 13
#SLATER_MATRIX_DIM: 21
#NUPDATES: 3
#SLATER_MATRIX: (i (outer), j (inner)), slater_matrix_alpha(i,j), ddet * slater_matrix_alpha_inv_det(i,j) / ddet
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(20,09) -0.206277355551720E+00 -0.190035138613005E+01
(20,10) -0.207551613450050E+00 0.118705706035607E+01
(20,11) 0.124761372804642E+00 0.218395870949059E+01
(20,12) 0.863072555512190E-02 -0.225848673886085E+01
(20,13) -0.714888703078032E-02 0.183569641575782E+01
(20,14) 0.456247404217720E-01 -0.103488813996630E+01
(20,15) -0.708496421575546E-01 -0.190399084333949E+00
(20,16) 0.107937427237630E-01 -0.149848769988273E+00
(20,17) -0.103561900556087E+00 0.263149954374569E+00
(20,18) 0.195673510432243E+00 0.226312056314707E+01
(20,19) -0.138991530984640E-01 -0.215379472713573E+00
(20,20) -0.738288741558790E-02 -0.717177684354636E+00
(20,21) 0.119809703901410E-01 0.395015106415659E+00
(21,01) -0.111714076995850E+01 -0.157006272972466E+01
(21,02) 0.136832118034363E+01 -0.165695410559176E+01
(21,03) 0.789960503578186E+00 -0.102464959222303E+01
(21,04) -0.136850726604462E+01 -0.197490477262258E+01
(21,05) -0.790138483047485E+00 -0.123963009795365E+01
(21,06) -0.111746346950531E+01 0.127940329351346E+01
(21,07) -0.158849164843559E+00 -0.115726516828563E-01
(21,08) 0.157852247357368E+00 0.278837130191972E+00
(21,09) 0.170709997415543E+00 0.100161817596371E+00
(21,10) 0.214689865708351E+00 -0.726523579353106E-01
(21,11) -0.167143829166889E-01 -0.678547976954667E-01
(21,12) -0.241510886698961E-01 0.377502144275716E-01
(21,13) -0.105082295835018E+00 -0.447407742013355E+00
(21,14) 0.101131219416857E-01 0.419175912148910E+00
(21,15) 0.525299832224846E-01 -0.233384037060628E+00
(21,16) -0.143686249852180E+00 -0.418753822037995E-02
(21,17) 0.132168933749199E+00 -0.856999606537821E-01
(21,18) -0.693865939974785E-01 -0.714580334063162E-02
(21,19) 0.104032047092915E+00 -0.161645225161624E-01
(21,20) 0.185707733035088E+00 -0.856160510487734E-02
(21,21) -0.296475943177938E-01 0.957054267749156E-01
#COL_UPDATE_INDEX: 12
#COL_UPDATE_COMP_(01): 0.102125488221645E+00
#COL_UPDATE_COMP_(02): 0.962643101811409E-01
#COL_UPDATE_COMP_(03): -0.180085301399231E-01
#COL_UPDATE_COMP_(04): -0.116052091121674E+00
#COL_UPDATE_COMP_(05): 0.100100971758366E-01
#COL_UPDATE_COMP_(06): 0.168905649334192E-01
#COL_UPDATE_COMP_(07): -0.168554261326790E-01
#COL_UPDATE_COMP_(08): 0.334977582097054E-01
#COL_UPDATE_COMP_(09): 0.775983557105064E-01
#COL_UPDATE_COMP_(10): -0.509594380855560E-01
#COL_UPDATE_COMP_(11): -0.110948169603944E-01
#COL_UPDATE_COMP_(12): -0.301160980015993E-01
#COL_UPDATE_COMP_(13): -0.210931494832039E+00
#COL_UPDATE_COMP_(14): -0.409047538414598E-02
#COL_UPDATE_COMP_(15): 0.239971160888672E+00
#COL_UPDATE_COMP_(16): -0.458180941641331E-01
#COL_UPDATE_COMP_(17): 0.231322161853313E-01
#COL_UPDATE_COMP_(18): -0.548814050853252E-01
#COL_UPDATE_COMP_(19): 0.185034181922674E-01
#COL_UPDATE_COMP_(20): -0.714888703078032E-02
#COL_UPDATE_COMP_(21): -0.105082295835018E+00
#COL_UPDATE_INDEX: 13
#COL_UPDATE_COMP_(01): -0.727039668709040E-02
#COL_UPDATE_COMP_(02): -0.329451821744442E-01
#COL_UPDATE_COMP_(03): 0.230633586645126E+00
#COL_UPDATE_COMP_(04): 0.322856456041336E-01
#COL_UPDATE_COMP_(05): 0.188164815306664E+00
#COL_UPDATE_COMP_(06): 0.976034477353096E-01
#COL_UPDATE_COMP_(07): 0.124376058578491E+00
#COL_UPDATE_COMP_(08): -0.241902604699135E+00
#COL_UPDATE_COMP_(09): -0.214029267430305E+00
#COL_UPDATE_COMP_(10): -0.164923388510942E-01
#COL_UPDATE_COMP_(11): -0.796175077557564E-01
#COL_UPDATE_COMP_(12): 0.552074126899242E-01
#COL_UPDATE_COMP_(13): 0.794003605842590E-01
#COL_UPDATE_COMP_(14): -0.999749153852463E-01
#COL_UPDATE_COMP_(15): 0.135955372825265E-01
#COL_UPDATE_COMP_(16): -0.876737236976624E-01
#COL_UPDATE_COMP_(17): 0.210409909486771E+00
#COL_UPDATE_COMP_(18): 0.177621953189373E-01
#COL_UPDATE_COMP_(19): -0.151124328374863E+00
#COL_UPDATE_COMP_(20): 0.247122272849083E+00
#COL_UPDATE_COMP_(21): -0.161797225475311E+00
#COL_UPDATE_INDEX: 21
#COL_UPDATE_COMP_(01): -0.817385390400887E-01
#COL_UPDATE_COMP_(02): 0.108162150718272E-02
#COL_UPDATE_COMP_(03): 0.693925749510527E-02
#COL_UPDATE_COMP_(04): 0.493063451722264E-02
#COL_UPDATE_COMP_(05): -0.334013439714909E-01
#COL_UPDATE_COMP_(06): 0.323923602700233E-01
#COL_UPDATE_COMP_(07): 0.120032556355000E+00
#COL_UPDATE_COMP_(08): -0.119067849591374E-01
#COL_UPDATE_COMP_(09): -0.334841385483742E-01
#COL_UPDATE_COMP_(10): 0.125436363741755E-01
#COL_UPDATE_COMP_(11): -0.145120620727539E+00
#COL_UPDATE_COMP_(12): -0.101416520774364E-01
#COL_UPDATE_COMP_(13): -0.723919421434402E-01
#COL_UPDATE_COMP_(14): 0.134314149618149E+00
#COL_UPDATE_COMP_(15): -0.125767393037677E-01
#COL_UPDATE_COMP_(16): 0.361425074515864E-03
#COL_UPDATE_COMP_(17): -0.351854860782623E-01
#COL_UPDATE_COMP_(18): -0.506495498120785E-01
#COL_UPDATE_COMP_(19): -0.291761625558138E-01
#COL_UPDATE_COMP_(20): -0.932136957999319E-03
#COL_UPDATE_COMP_(21): -0.500183776021004E-01
#END_PACKET

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import h5py
import numpy as np
from parse import parse
def rl(rf):
return " ".join(rf.readline().split())
with h5py.File('datasets.hdf5', 'w') as f:
with open('dataset.dat', 'r') as rf:
while(1):
line = rl(rf)
if not line or not line.startswith('#START_PACKET'):
break
cycle_id = parse('#CYCLE_ID: {:d}', rl(rf))[0]
slater_matrix_dim = parse('#SLATER_MATRIX_DIM: {:d}', rl(rf))[0]
nupdates = parse('#NUPDATES: {:d}', rl(rf))[0]
assert(rf.readline().startswith('#SLATER_MATRIX'))
# Read matrices
slater_matrix = np.zeros((slater_matrix_dim,slater_matrix_dim))
slater_inverse = np.zeros((slater_matrix_dim,slater_matrix_dim))
for i in range(slater_matrix_dim*slater_matrix_dim):
res = parse('({i:d},{j:d}) {sla:e} {inv:e}', rl(rf))
slater_matrix[res['i']-1, res['j']-1] = res['sla']
slater_inverse[res['i']-1, res['j']-1] = res['inv']
# Read updates
col_update_index = np.zeros(nupdates, dtype='i')
updates = np.zeros((nupdates, slater_matrix_dim))
for n in range(nupdates):
col_update_index[n] = parse('#COL_UPDATE_INDEX: {:d}', rl(rf))[0]
for i in range(slater_matrix_dim):
res = parse('#COL_UPDATE_COMP_({i:d}): {x:e}', rl(rf))
updates[n][res['i']-1] = res['x']
assert(rf.readline().startswith('#END_PACKET'))
rf.readline()
cycle = f.create_group('cycle_{}'.format(cycle_id))
cycle.create_dataset("slater_matrix_dim", data=slater_matrix_dim)
cycle.create_dataset("nupdates", data=nupdates)
cycle.create_dataset("slater_matrix", data=slater_matrix, compression='gzip')
cycle.create_dataset("slater_inverse", data=slater_inverse, compression='gzip')
cycle.create_dataset("col_update_index", data=col_update_index)
cycle.create_dataset("updates", data=updates, compression='gzip')

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#include <iostream>
#include <string>
#include "hdf5/serial/hdf5.h"
#include "H5Cpp.h"
#include "../SM_MaponiA3.hpp"
#include "../Helpers.hpp"
using namespace H5;
#define DEBUG 1
const H5std_string FILE_NAME( "datasets.hdf5" );
void read_int(H5File file, std::string key, unsigned int * data) {
DataSet ds = file.openDataSet(key);
ds.read(data, PredType::STD_U32LE);
ds.close();
}
void read_double(H5File file, std::string key, double * data) {
DataSet ds = file.openDataSet(key);
ds.read(data, PredType::IEEE_F64LE);
ds.close();
}
int test_cycle(H5File file, int cycle) {
/* Read the data */
std::string group = "cycle_" + std::to_string(cycle);
unsigned int dim, nupdates;
read_int(file, group + "/slater_matrix_dim", &dim);
read_int(file, group + "/nupdates", &nupdates);
double * slater_matrix = new double[dim*dim];
read_double(file, group + "/slater_matrix", slater_matrix);
double * slater_inverse = new double[dim*dim];
read_double(file, group + "/slater_inverse", slater_inverse);
unsigned int * col_update_index = new unsigned int[nupdates];
read_int(file, group + "/col_update_index", col_update_index);
double * updates = new double[nupdates*dim];
read_double(file, group + "/updates", updates);
/* Test */
#ifdef DEBUG
showMatrix(slater_matrix, dim, "Slater");
#endif
MaponiA3(slater_matrix, slater_inverse, dim, nupdates, updates, col_update_index);
#ifdef DEBUG
showMatrix(slater_inverse, dim, "Inverse");
#endif
double * res = matMul(slater_matrix, slater_inverse, dim);
bool ok = is_identity(res, dim, 1.0e-8);
#ifdef DEBUG
showMatrix(res, dim, "Result");
#endif
delete [] res, updates, col_update_index, slater_matrix, slater_inverse;
return ok;
}
int main(int argc, char **argv) {
if (argc != 2) {
std::cerr << "usage: ./test_dataset <cycle>" << std::endl;
return 1;
}
int cycle = std::stoi(argv[1]);
H5File file(FILE_NAME, H5F_ACC_RDONLY);
bool ok = test_cycle(file, 21);
if (ok) {
std::cerr << "ok -- cycle " << std::to_string(cycle) << std::endl;
} else {
std::cerr << "failed -- cycle " << std::to_string(cycle) << std::endl;
}
return ok;
}