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feat: introduce LookupKey and rounding schemes

Browse Source 
feat: implement data clustering using PHT

feat: implement interpolation

refactor: use named vector for DHT species definition and significant digits

data: remove unusable input scripts

data: move Phreeqc database to benchmark dir

refactor: rename dolomite benchmark directory

refactor: remove DHT prop type from input script
This commit is contained in:
Max Luebke 2023-04-25 17:38:58 +02:00
parent e62472237d
commit 0c2597d97f
47 changed files with 3003 additions and 1237 deletions
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2
CMake/POET_Scripts.cmake
View File

@ -9,7 +9,7 @@ macro(get_POET_version)
OUTPUT_VARIABLE POET_GIT_BRANCH
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(
COMMAND ${GIT_EXECUTABLE} describe --always
COMMAND ${GIT_EXECUTABLE} describe --tags --always
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE POET_GIT_VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE)

1
CMakeLists.txt
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@ -24,7 +24,6 @@ find_package(RRuntime REQUIRED)
add_subdirectory(src)
add_subdirectory(R_lib)
add_subdirectory(data)
add_subdirectory(app)
add_subdirectory(bench)

2
README.md
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@ -1,5 +1,5 @@
<!--
Time-stamp: "Last modified 2023-07-21 12:34:43 mluebke"
Time-stamp: "Last modified 2023-07-20 11:30:44 delucia"
-->
# POET

53
R_lib/kin_r_library.R
View File

@ -64,28 +64,33 @@ master_init <- function(setup) {
## calculated time step if store_result is TRUE and increments the
## iteration counter
master_iteration_end <- function(setup) {
iter <- setup$iter
## MDL Write on disk state_T and state_C after every iteration
## comprised in setup$out_save
if (setup$store_result) {
if (iter %in% setup$out_save) {
nameout <- paste0(fileout, "/iter_", sprintf("%03d", iter), ".rds")
info <- list(
tr_req_dt = as.integer(setup$req_dt)
# tr_allow_dt = setup$allowed_dt,
# tr_inniter = as.integer(setup$inniter)
)
saveRDS(list(
T = setup$state_T, C = setup$state_C,
simtime = as.integer(setup$simtime),
tr_info = info
), file = nameout)
msgm("results stored in <", nameout, ">")
iter <- setup$iter
## max digits for iterations
dgts <- as.integer(ceiling(log10(setup$iterations + 1)))
## string format to use in sprintf
fmt <- paste0("%0", dgts, "d")
## Write on disk state_T and state_C after every iteration
## comprised in setup$out_save
if (setup$store_result) {
if (iter %in% setup$out_save) {
nameout <- paste0(fileout, "/iter_", sprintf(fmt=fmt, iter), ".rds")
info <- list(
tr_req_dt = as.integer(setup$req_dt)
## tr_allow_dt = setup$allowed_dt,
## tr_inniter = as.integer(setup$inniter)
)
saveRDS(list(
T = setup$state_T, C = setup$state_C,
simtime = as.integer(setup$simtime),
tr_info = info
), file = nameout)
msgm("results stored in <", nameout, ">")
}
}
}
msgm("done iteration", iter, "/", setup$maxiter)
setup$iter <- setup$iter + 1
return(setup)
msgm("done iteration", iter, "/", setup$maxiter)
setup$iter <- setup$iter + 1
return(setup)
}
## function for the workers to compute chemistry through PHREEQC
@ -264,9 +269,9 @@ StoreSetup <- function(setup) {
if (dht_enabled) {
to_store$DHT <- list(
enabled = dht_enabled,
log = dht_log,
signif = dht_final_signif,
proptype = dht_final_proptype
log = dht_log
#signif = dht_final_signif,
#proptype = dht_final_proptype
)
} else {
to_store$DHT <- FALSE

90
app/poet.cpp
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@ -70,7 +70,7 @@ void writeFieldsToR(RInside &R, const Field &trans, const Field &chem) {
void set_chem_parameters(poet::ChemistryModule &chem, uint32_t wp_size,
const std::string &database_path) {
chem.SetErrorHandlerMode(1);
chem.SetComponentH2O(true);
chem.SetComponentH2O(false);
chem.SetRebalanceFraction(0.5);
chem.SetRebalanceByCell(true);
chem.UseSolutionDensityVolume(false);
@ -112,7 +112,6 @@ void set_chem_parameters(poet::ChemistryModule &chem, uint32_t wp_size,
}
inline double RunMasterLoop(SimParams &params, RInside &R,
ChemistryParams &chem_params,
const GridParams &g_params, uint32_t nxyz_master) {
DiffusionParams d_params{R};
@ -123,10 +122,11 @@ inline double RunMasterLoop(SimParams &params, RInside &R,
double sim_time = .0;
ChemistryModule chem(nxyz_master, params.getNumParams().wp_size,
MPI_COMM_WORLD);
set_chem_parameters(chem, nxyz_master, chem_params.database_path);
chem.RunInitFile(chem_params.input_script);
ChemistryModule chem(nxyz_master, params.getNumParams().wp_size, maxiter,
params.getChemParams(), MPI_COMM_WORLD);
set_chem_parameters(chem, nxyz_master, params.getChemParams().database_path);
chem.RunInitFile(params.getChemParams().input_script);
poet::ChemistryModule::SingleCMap init_df = DFToHashMap(d_params.initial_t);
chem.initializeField(diffusion.getField());
@ -135,27 +135,11 @@ inline double RunMasterLoop(SimParams &params, RInside &R,
chem.setProgressBarPrintout(true);
}
if (params.getNumParams().dht_enabled) {
chem.SetDHTEnabled(true, params.getNumParams().dht_size_per_process,
chem_params.dht_species);
if (!chem_params.dht_signif.empty()) {
chem.SetDHTSignifVector(chem_params.dht_signif);
}
if (!params.getDHTPropTypeVector().empty()) {
chem.SetDHTPropTypeVector(params.getDHTPropTypeVector());
}
if (!params.getDHTFile().empty()) {
chem.ReadDHTFile(params.getDHTFile());
}
if (params.getNumParams().dht_snaps > 0) {
chem.SetDHTSnaps(params.getNumParams().dht_snaps, params.getOutDir());
}
}
/* SIMULATION LOOP */
double dStartTime = MPI_Wtime();
double dSimTime{0};
for (uint32_t iter = 1; iter < maxiter + 1; iter++) {
double start_t = MPI_Wtime();
uint32_t tick = 0;
// cout << "CPP: Evaluating next time step" << endl;
// R.parseEvalQ("mysetup <- master_iteration_setup(mysetup)");
@ -203,7 +187,8 @@ inline double RunMasterLoop(SimParams &params, RInside &R,
<< endl;
// MPI_Barrier(MPI_COMM_WORLD);
double end_t = MPI_Wtime();
dSimTime += end_t - start_t;
} // END SIMULATION LOOP
R.parseEvalQ("profiling <- list()");
@ -232,23 +217,36 @@ inline double RunMasterLoop(SimParams &params, RInside &R,
// R["phreeqc_count"] = phreeqc_counts;
// R.parseEvalQ("profiling$phreeqc_count <- phreeqc_count");
if (params.getNumParams().dht_enabled) {
if (params.getChemParams().use_dht) {
R["dht_hits"] = Rcpp::wrap(chem.GetWorkerDHTHits());
R.parseEvalQ("profiling$dht_hits <- dht_hits");
R["dht_miss"] = Rcpp::wrap(chem.GetWorkerDHTMiss());
R.parseEvalQ("profiling$dht_miss <- dht_miss");
R["dht_evictions"] = Rcpp::wrap(chem.GetWorkerDHTEvictions());
R.parseEvalQ("profiling$dht_evictions <- dht_evictions");
R["dht_get_time"] = Rcpp::wrap(chem.GetWorkerDHTGetTimings());
R.parseEvalQ("profiling$dht_get_time <- dht_get_time");
R["dht_fill_time"] = Rcpp::wrap(chem.GetWorkerDHTFillTimings());
R.parseEvalQ("profiling$dht_fill_time <- dht_fill_time");
if (params.getChemParams().use_interp) {
R["interp_w"] = Rcpp::wrap(chem.GetWorkerInterpolationWriteTimings());
R.parseEvalQ("profiling$interp_write <- interp_w");
R["interp_r"] = Rcpp::wrap(chem.GetWorkerInterpolationReadTimings());
R.parseEvalQ("profiling$interp_read <- interp_r");
R["interp_g"] = Rcpp::wrap(chem.GetWorkerInterpolationGatherTimings());
R.parseEvalQ("profiling$interp_gather <- interp_g");
R["interp_fc"] =
Rcpp::wrap(chem.GetWorkerInterpolationFunctionCallTimings());
R.parseEvalQ("profiling$interp_function_calls <- interp_fc");
R["interp_calls"] = Rcpp::wrap(chem.GetWorkerInterpolationCalls());
R.parseEvalQ("profiling$interp_calls <- interp_calls");
R["interp_cached"] = Rcpp::wrap(chem.GetWorkerPHTCacheHits());
R.parseEvalQ("profiling$interp_cached <- interp_cached");
}
}
chem.MasterLoopBreak();
diffusion.end();
return MPI_Wtime() - dStartTime;
return dSimTime;
}
int main(int argc, char *argv[]) {
@ -268,19 +266,23 @@ int main(int argc, char *argv[]) {
if (world_rank > 0) {
{
uint32_t c_size;
MPI_Bcast(&c_size, 1, MPI_UINT32_T, 0, MPI_COMM_WORLD);
char *buffer = new char[c_size + 1];
MPI_Bcast(buffer, c_size, MPI_CHAR, 0, MPI_COMM_WORLD);
buffer[c_size] = '\0';
SimParams params(world_rank, world_size);
int pret = params.parseFromCmdl(argv, RInsidePOET::getInstance());
if (pret == poet::PARSER_ERROR) {
MPI_Finalize();
return EXIT_FAILURE;
} else if (pret == poet::PARSER_HELP) {
MPI_Finalize();
return EXIT_SUCCESS;
}
// ChemistryModule worker(nxyz, nxyz, MPI_COMM_WORLD);
ChemistryModule worker =
poet::ChemistryModule::createWorker(MPI_COMM_WORLD);
set_chem_parameters(worker, worker.GetWPSize(), std::string(buffer));
delete[] buffer;
ChemistryModule worker = poet::ChemistryModule::createWorker(
MPI_COMM_WORLD, params.getChemParams());
set_chem_parameters(worker, worker.GetWPSize(),
params.getChemParams().database_path);
worker.WorkerLoop();
}
@ -334,17 +336,9 @@ int main(int argc, char *argv[]) {
// MPI_Barrier(MPI_COMM_WORLD);
poet::ChemistryParams chem_params(R);
/* THIS IS EXECUTED BY THE MASTER */
std::string db_path = chem_params.database_path;
uint32_t c_size = db_path.size();
MPI_Bcast(&c_size, 1, MPI_UINT32_T, 0, MPI_COMM_WORLD);
MPI_Bcast(db_path.data(), c_size, MPI_CHAR, 0, MPI_COMM_WORLD);
uint32_t nxyz_master = (world_size == 1 ? g_params.total_n : 1);
dSimTime = RunMasterLoop(params, R, chem_params, g_params, nxyz_master);
dSimTime = RunMasterLoop(params, R, g_params, nxyz_master);
cout << "CPP: finished simulation loop" << endl;

2
bench/CMakeLists.txt
View File

@ -1,3 +1,3 @@
add_subdirectory(dolo_diffu_inner)
add_subdirectory(dolo)
add_subdirectory(surfex)
add_subdirectory(barite)

1
bench/barite/CMakeLists.txt
View File

@ -1,5 +1,6 @@
install(FILES
barite.R
barite_interp_eval.R
barite.pqi
db_barite.dat
DESTINATION

16
bench/barite/barite.R
View File

@ -115,16 +115,20 @@ diffusion <- list(
## # Needed when using DHT
dht_species <- names(init_diffu)
#dht_signif <- rep(15, length(dht_species))
dht_signif <- c(10, 10, 3, 5, 5, 5, 5)
dht_species <- c(
"H" = 10,
"O" = 10,
"Charge" = 3,
"Ba" = 5,
"Cl" = 5,
"S(6)" = 5,
"Sr" = 5
)
chemistry <- list(
database = database,
input_script = input_script,
dht_species = dht_species,
dht_signif = dht_signif
dht_species = dht_species
)
#################################################################

151
bench/barite/barite_interp_eval.R Normal file
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@ -0,0 +1,151 @@
## Time-stamp: "Last modified 2023-07-21 15:04:49 mluebke"
database <- normalizePath("../share/poet/bench/barite/db_barite.dat")
input_script <- normalizePath("../share/poet/bench/barite/barite.pqi")
#################################################################
## Section 1 ##
## Grid initialization ##
#################################################################
n <- 400
m <- 200
types <- c("scratch", "phreeqc", "rds")
init_cell <- list(
"H" = 110.0124,
"O" = 55.5087,
"Charge" = -1.217E-09,
"Ba" = 1.E-10,
"Cl" = 2.E-10,
"S" = 6.205E-4,
"Sr" = 6.205E-4,
"Barite" = 0.001,
"Celestite" = 1
)
grid <- list(
n_cells = c(n, m),
s_cells = c(n / 10, m / 10),
type = types[1],
init_cell = as.data.frame(init_cell, check.names = FALSE),
props = names(init_cell),
database = database,
input_script = input_script
)
##################################################################
## Section 2 ##
## Diffusion parameters and boundary conditions ##
##################################################################
## initial conditions
init_diffu <- list(
# "H" = 110.0124,
"H" = 0.00000028904,
# "O" = 55.5087,
"O" = 0.000000165205,
# "Charge" = -1.217E-09,
"Charge" = -3.337E-08,
"Ba" = 1.E-10,
"Cl" = 1.E-10,
"S(6)" = 6.205E-4,
"Sr" = 6.205E-4
)
injection_diff <- list(
list(
# "H" = 111.0124,
"H" = 0.0000002890408,
# "O" = 55.50622,
"O" = 0.00002014464,
# "Charge" = -3.337E-08,
"Charge" = -3.337000004885E-08,
"Ba" = 0.1,
"Cl" = 0.2,
"S(6)" = 0,
"Sr" = 0
)
)
## diffusion coefficients
alpha_diffu <- c(
"H" = 1E-06,
"O" = 1E-06,
"Charge" = 1E-06,
"Ba" = 1E-06,
"Cl" = 1E-06,
"S(6)" = 1E-06,
"Sr" = 1E-06
)
vecinj_inner <- list(
l1 = c(1, floor(n / 2), floor(m / 2))
## l2 = c(2,80,80),
## l3 = c(2,60,80)
)
boundary <- list(
# "N" = rep(1, n),
"N" = rep(0, n),
"E" = rep(0, n),
"S" = rep(0, n),
"W" = rep(0, n)
)
diffu_list <- names(alpha_diffu)
vecinj <- do.call(rbind.data.frame, injection_diff)
names(vecinj) <- names(init_diffu)
diffusion <- list(
init = as.data.frame(init_diffu, check.names = FALSE),
vecinj = vecinj,
vecinj_inner = vecinj_inner,
vecinj_index = boundary,
alpha = alpha_diffu
)
#################################################################
## Section 3 ##
## Chemistry module (Phreeqc) ##
#################################################################
## # Needed when using DHT
dht_species <- c(
"H" = 10,
"O" = 10,
"Charge" = 3,
"Ba" = 5,
"Cl" = 5,
"S(6)" = 5,
"Sr" = 5
)
chemistry <- list(
database = database,
input_script = input_script,
dht_species = dht_species
)
#################################################################
## Section 4 ##
## Putting all those things together ##
#################################################################
iterations <- 200
dt <- 250
setup <- list(
grid = grid,
diffusion = diffusion,
chemistry = chemistry,
iterations = iterations,
timesteps = rep(dt, iterations),
store_result = TRUE,
out_save = seq(1, iterations)
)

2
bench/dolo_diffu_inner/CMakeLists.txt → bench/dolo/CMakeLists.txt
View File

@ -2,6 +2,8 @@ install(FILES
dolo_diffu_inner.R
dolo_diffu_inner_large.R
dolo_inner.pqi
dolo_interp_long.R
phreeqc_kin.dat
DESTINATION
share/poet/bench/dolo
)

0
bench/dolo_diffu_inner/Eval.R → bench/dolo/Eval.R
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0
data/dol.pqi → bench/dolo/dol.pqi
View File

33
bench/dolo_diffu_inner/dolo_diffu_inner.R → bench/dolo/dolo_diffu_inner.R
View File

@ -1,6 +1,6 @@
## Time-stamp: "Last modified 2023-04-24 15:12:02 mluebke"
## Time-stamp: "Last modified 2023-07-28 16:57:40 mluebke"
database <- normalizePath("../share/poet/examples/phreeqc_kin.dat")
database <- normalizePath("../share/poet/bench/dolo/phreeqc_kin.dat")
input_script <- normalizePath("../share/poet/bench/dolo/dolo_inner.pqi")
#################################################################
@ -44,8 +44,8 @@ grid <- list(
## initial conditions
init_diffu <- list(
"H" = 0.000211313883539788,
"O" = 0.00398302904424952,
"H" = 110.683,
"O" = 55.3413,
"Charge" = -5.0822e-19,
"C(4)" = 1.2279E-4,
"Ca" = 1.2279E-4,
@ -67,8 +67,8 @@ alpha_diffu <- c(
## list of boundary conditions/inner nodes
vecinj_diffu <- list(
list(
"H" = 0.0001540445,
"O" = 0.002148006,
"H" = 110.683,
"O" = 55.3413,
"Charge" = 1.90431e-16,
"C(4)" = 0,
"Ca" = 0,
@ -76,8 +76,8 @@ vecinj_diffu <- list(
"Mg" = 0.001
),
list(
"H" = 0.0001610193,
"O" = 0.002386934,
"H" = 110.683,
"O" = 55.3413,
"Charge" = 1.90431e-16,
"C(4)" = 0,
"Ca" = 0.0,
@ -120,16 +120,21 @@ diffusion <- list(
## # Needed when using DHT
dht_species <- c("H", "O", "Charge", "C(4)", "Ca", "Cl", "Mg", "Calcite",
"Dolomite")
#dht_signif <- rep(15, length(dht_species))
dht_signif <- c(10, 10, 3, 5, 5, 5, 5, 5, 5)
dht_species <- c("H" = 10,
"O" = 10,
"Charge" = 3,
"C(4)" = 5,
"Ca" = 5,
"Cl" = 5,
"Mg" = 5,
"Calcite" = 5,
"Dolomite" =5
)
chemistry <- list(
database = database,
input_script = input_script,
dht_species = dht_species,
dht_signif = dht_signif
dht_species = dht_species
)
#################################################################

22
bench/dolo_diffu_inner/dolo_diffu_inner_large.R → bench/dolo/dolo_diffu_inner_large.R
View File

@ -1,6 +1,6 @@
## Time-stamp: "Last modified 2023-04-24 15:43:26 mluebke"
## Time-stamp: "Last modified 2023-07-28 16:57:40 mluebke"
database <- normalizePath("../share/poet/examples/phreeqc_kin.dat")
database <- normalizePath("../share/poet/bench/dolo/phreeqc_kin.dat")
input_script <- normalizePath("../share/poet/bench/dolo/dolo_inner.pqi")
#################################################################
@ -118,18 +118,22 @@ diffusion <- list(
## Chemistry module (Phreeqc) ##
#################################################################
## # Needed when using DHT
dht_species <- c("H", "O", "Charge", "C(4)", "Ca", "Cl", "Mg", "Calcite",
"Dolomite")
#dht_signif <- rep(15, length(dht_species))
dht_signif <- c(10, 10, 3, 5, 5, 5, 5, 5, 5)
dht_species <- c("H" = 10,
"O" = 10,
"Charge" = 3,
"C(4)" = 5,
"Ca" = 5,
"Cl" = 5,
"Mg" = 5,
"Calcite" = 5,
"Dolomite" =5
)
chemistry <- list(
database = database,
input_script = input_script,
dht_species = dht_species,
dht_signif = dht_signif
dht_species = dht_species
)
#################################################################

0
bench/dolo_diffu_inner/dolo_inner.pqi → bench/dolo/dolo_inner.pqi
View File

171
bench/dolo/dolo_interp_long.R Normal file
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@ -0,0 +1,171 @@
## Time-stamp: "Last modified 2023-08-01 18:34:47 mluebke"
database <- normalizePath("../share/poet/bench/dolo/phreeqc_kin.dat")
input_script <- normalizePath("../share/poet/bench/dolo/dolo_inner.pqi")
#################################################################
## Section 1 ##
## Grid initialization ##
#################################################################
n <- 400
m <- 200
types <- c("scratch", "phreeqc", "rds")
init_cell <- list(
"H" = 110.683,
"O" = 55.3413,
"Charge" = -5.0822e-19,
"C" = 1.2279E-4,
"Ca" = 1.2279E-4,
"Cl" = 0,
"Mg" = 0,
"O2g" = 0.499957,
"Calcite" = 2.07e-4,
"Dolomite" = 0
)
grid <- list(
n_cells = c(n, m),
s_cells = c(5, 2.5),
type = types[1],
init_cell = as.data.frame(init_cell, check.names = FALSE),
props = names(init_cell),
database = database,
input_script = input_script
)
##################################################################
## Section 2 ##
## Diffusion parameters and boundary conditions ##
##################################################################
## initial conditions
init_diffu <- list(
"H" = 1.110124E+02,
"O" = 5.550833E+01,
"Charge" = -1.216307659761E-09,
"C(4)" = 1.230067028174E-04,
"Ca" = 1.230067028174E-04,
"Cl" = 0,
"Mg" = 0
)
## diffusion coefficients
alpha_diffu <- c(
"H" = 1E-6,
"O" = 1E-6,
"Charge" = 1E-6,
"C(4)" = 1E-6,
"Ca" = 1E-6,
"Cl" = 1E-6,
"Mg" = 1E-6
)
## list of boundary conditions/inner nodes
vecinj_diffu <- list(
list(
"H" = 1.110124E+02,
"O" = 5.550796E+01,
"Charge" = -3.230390327801E-08,
"C(4)" = 0,
"Ca" = 0,
"Cl" = 0.002,
"Mg" = 0.001
),
list(
"H" = 110.683,
"O" = 55.3413,
"Charge" = 1.90431e-16,
"C(4)" = 0,
"Ca" = 0.0,
"Cl" = 0.004,
"Mg" = 0.002
),
init_diffu
)
vecinj_inner <- list(
l1 = c(1, floor(n / 2), floor(m / 2))
# l2 = c(2,1400,800),
# l3 = c(2,1600,800)
)
boundary <- list(
# "N" = c(1, rep(0, n-1)),
"N" = rep(3, n),
"E" = rep(3, m),
"S" = rep(3, n),
"W" = rep(3, m)
)
diffu_list <- names(alpha_diffu)
vecinj <- do.call(rbind.data.frame, vecinj_diffu)
names(vecinj) <- names(init_diffu)
diffusion <- list(
init = as.data.frame(init_diffu, check.names = FALSE),
vecinj = vecinj,
vecinj_inner = vecinj_inner,
vecinj_index = boundary,
alpha = alpha_diffu
)
#################################################################
## Section 3 ##
## Chemistry module (Phreeqc) ##
#################################################################
## # optional when using DHT
dht_species <- c(
"H" = 3,
"O" = 3,
"Charge" = 3,
"C(4)" = 6,
"Ca" = 6,
"Cl" = 3,
"Mg" = 5,
"Calcite" = 4,
"Dolomite" = 4
)
## # Optional when using Interpolation (example with less key species and custom
## # significant digits)
#pht_species <- c(
# "C(4)" = 3,
# "Ca" = 3,
# "Mg" = 2,
# "Calcite" = 2,
# "Dolomite" = 2
#)
chemistry <- list(
database = database,
input_script = input_script,
dht_species = dht_species
# pht_species = pht_species
)
#################################################################
## Section 4 ##
## Putting all those things together ##
#################################################################
iterations <- 20000
dt <- 200
setup <- list(
grid = grid,
diffusion = diffusion,
chemistry = chemistry,
iterations = iterations,
timesteps = rep(dt, iterations),
store_result = TRUE,
out_save = c(1, seq(50, iterations, by = 50))
)

6
data/phreeqc_kin.dat → bench/dolo/phreeqc_kin.dat
View File

@ -2,7 +2,7 @@
### SURFACE and with the RATES for Calcite and Dolomite to use with
### RedModRphree
### Time-stamp: "Last modified 2018-05-06 14:36:23 delucia"
### Time-stamp: "Last modified 2023-05-23 10:35:56 mluebke"
# PHREEQC.DAT for calculating pressure dependence of reactions, with
# molal volumina of aqueous species and of minerals, and
@ -1276,9 +1276,9 @@ Calcite
110 logK25=-5.81
120 mech_c=(10^logK25)*(e^(-Ea/R*deltaT))
130 rate=mech_a+mech_c
## 140 IF SI("Calcite")<0 then moles=parm(1)*rate*(1-SR("Calcite")) # dissolution
140 IF (SI("Calcite")<0 AND M>0) then moles=parm(1)*rate*(1-SR("Calcite")) # dissolution
## 145 IF SI("Calcite")>0 then moles=parm(1)*M*rate*(-1+SR("Calcite")) # precipitation
150 moles=parm(1)*rate*(1-SR("Calcite")) # precipitation
## 150 moles=parm(1)*rate*(1-SR("Calcite")) # precipitation
200 save moles*time
-end

8
data/CMakeLists.txt
View File

@ -1,8 +0,0 @@
install(
FILES
SimDol2D_diffu.R
SimDol1D_diffu.R
phreeqc_kin.dat
dol.pqi
DESTINATION
share/poet/examples)

180
data/SimDol1D_diffu.R
View File

@ -1,180 +0,0 @@
#################################################################
## Section 1 ##
## Grid initialization ##
#################################################################
n <- 5
m <- 5
types <- c("scratch", "phreeqc", "rds")
# initsim <- c("SELECTED_OUTPUT", "-high_precision true",
# "-reset false",
# "USER_PUNCH",
# "-head C Ca Cl Mg pH pe O2g Calcite Dolomite",
# "10 PUNCH TOT(\"C\"), TOT(\"Ca\"), TOT(\"Cl\"), TOT(\"Mg\"), -LA(\"H+\"), -LA(\"e-\"), EQUI(\"O2g\"), EQUI(\"Calcite\"), EQUI(\"Dolomite\")",
# "SOLUTION 1",
# "units mol/kgw",
# "temp 25.0", "water 1",
# "pH 9.91 charge",
# "pe 4.0",
# "C 1.2279E-04",
# "Ca 1.2279E-04",
# "Cl 1E-12",
# "Mg 1E-12",
# "PURE 1",
# "O2g -0.6788 10.0",
# "Calcite 0.0 2.07E-3",
# "Dolomite 0.0 0.0",
# "END")
# needed if init type is set to "scratch"
# prop <- c("C", "Ca", "Cl", "Mg", "pH", "pe", "O2g", "Calcite", "Dolomite")
init_cell <- list(
"C" = 1.2279E-4,
"Ca" = 1.2279E-4,
"Cl" = 0,
"Mg" = 0,
"pH" = 9.91,
"pe" = 4,
"O2g" = 10,
"Calcite" = 2.07e-4,
"Dolomite" = 0
)
grid <- list(
n_cells = n,
s_cells = n,
type = types[1],
init_cell = as.data.frame(init_cell),
props = names(init_cell),
init_script = NULL
)
##################################################################
## Section 2 ##
## Diffusion parameters and boundary conditions ##
##################################################################
init_diffu <- c(
"C" = 1.2279E-4,
"Ca" = 1.2279E-4,
"Cl" = 0,
"Mg" = 0,
"pe" = 4,
"pH" = 7
)
alpha_diffu <- c(
"C" = 1E-4,
"Ca" = 1E-4,
"Cl" = 1E-4,
"Mg" = 1E-4,
"pe" = 1E-4,
"pH" = 1E-4
)
vecinj_diffu <- list(
list(
"C" = 0,
"Ca" = 0,
"Cl" = 0.002,
"Mg" = 0.001,
"pe" = 4,
"pH" = 9.91
)
)
boundary <- list(
"E" = 0,
"W" = 1
)
diffu_list <- names(alpha_diffu)
diffusion <- list(
init = init_diffu,
vecinj = do.call(rbind.data.frame, vecinj_diffu),
vecinj_index = boundary,
alpha = alpha_diffu
)
##################################################################
## Section 3 ##
## Phreeqc simulation ##
##################################################################
db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat",
package = "RedModRphree"
), is.db = TRUE)
phreeqc::phrLoadDatabaseString(db)
# NOTE: This won't be needed in the future either. Could also be done in a. pqi
# file
base <- c(
"SOLUTION 1",
"units mol/kgw",
"temp 25.0",
"water 1",
"pH 9.91 charge",
"pe 4.0",
"C 1.2279E-04",
"Ca 1.2279E-04",
"Mg 0.001",
"Cl 0.002",
"PURE 1",
"O2g -0.1675 10",
"KINETICS 1",
"-steps 100",
"-step_divide 100",
"-bad_step_max 2000",
"Calcite", "-m 0.000207",
"-parms 0.0032",
"Dolomite",
"-m 0.0",
"-parms 0.00032",
"END"
)
selout <- c(
"SELECTED_OUTPUT", "-high_precision true", "-reset false",
"-time", "-soln", "-temperature true", "-water true",
"-pH", "-pe", "-totals C Ca Cl Mg",
"-kinetic_reactants Calcite Dolomite", "-equilibrium O2g"
)
# Needed when using DHT
signif_vector <- c(7, 7, 7, 7, 7, 7, 7, 5, 5)
prop_type <- c("act", "act", "act", "act", "logact", "logact", "ignore", "act", "act")
prop <- names(init_cell)
iterations <- 500
setup <- list(
# bound = myboundmat,
base = base,
first = selout,
# initsim = initsim,
# Cf = 1,
grid = grid,
diffusion = diffusion,
prop = prop,
immobile = c(7, 8, 9),
kin = c(8, 9),
ann = list(O2g = -0.1675),
# phase = "FLUX1",
# density = "DEN1",
reduce = FALSE,
# snapshots = demodir, ## directory where we will read MUFITS SUM files
# gridfile = paste0(demodir, "/d2ascii.run.GRID.SUM")
# init = init,
# vecinj = vecinj,
# cinj = c(0,1),
# boundary = boundary,
# injections = FALSE,
iterations = iterations,
timesteps = rep(10, iterations)
)

213
data/SimDol2D_diffu.R
View File

@ -1,213 +0,0 @@
database <- normalizePath("../share/poet/examples/phreeqc_kin.dat")
input_script <- normalizePath("../share/poet/examples/dol.pqi")
#################################################################
## Section 1 ##
## Grid initialization ##
#################################################################
n <- 100
m <- 100
types <- c("scratch", "phreeqc", "rds")
# initsim <- c("SELECTED_OUTPUT", "-high_precision true",
# "-reset false",
# "USER_PUNCH",
# "-head C Ca Cl Mg pH pe O2g Calcite Dolomite",
# "10 PUNCH TOT(\"C\"), TOT(\"Ca\"), TOT(\"Cl\"), TOT(\"Mg\"), -LA(\"H+\"), -LA(\"e-\"), EQUI(\"O2g\"), EQUI(\"Calcite\"), EQUI(\"Dolomite\")",
# "SOLUTION 1",
# "units mol/kgw",
# "temp 25.0", "water 1",
# "pH 9.91 charge",
# "pe 4.0",
# "C 1.2279E-04",
# "Ca 1.2279E-04",
# "Cl 1E-12",
# "Mg 1E-12",
# "PURE 1",
# "O2g -0.6788 10.0",
# "Calcite 0.0 2.07E-3",
# "Dolomite 0.0 0.0",
# "END")
# needed if init type is set to "scratch"
# prop <- c("C", "Ca", "Cl", "Mg", "pH", "pe", "O2g", "Calcite", "Dolomite")
init_cell <- list(
"H" = 110.683,
"O" = 55.3413,
"Charge" = -5.0822e-19,
"C" = 1.2279E-4,
"Ca" = 1.2279E-4,
"Cl" = 0,
"Mg" = 0,
"O2g" = 0.499957,
"Calcite" = 2.07e-4,
"Dolomite" = 0
)
grid <- list(
n_cells = c(n, m),
s_cells = c(n, m),
type = types[1],
init_cell = as.data.frame(init_cell),
props = names(init_cell),
database = database,
input_script = input_script
)
##################################################################
## Section 2 ##
## Diffusion parameters and boundary conditions ##
##################################################################
init_diffu <- c(
"H" = 110.683,
"O" = 55.3413,
"Charge" = -5.0822e-19,
"C" = 1.2279E-4,
"Ca" = 1.2279E-4,
"Cl" = 0,
"Mg" = 0
)
alpha_diffu <- c(
"H" = 1E-4,
"O" = 1E-4,
"Charge" = 1E-4,
"C" = 1E-4,
"Ca" = 1E-4,
"Cl" = 1E-4,
"Mg" = 1E-4
)
vecinj_diffu <- list(
list(
"H" = 110.683,
"O" = 55.3413,
"Charge" = 1.90431e-16,
"C" = 0,
"Ca" = 0,
"Cl" = 0.002,
"Mg" = 0.001
)
)
#inner_index <- c(5, 15, 25)
#inner_vecinj_index <- rep(1, 3)
#
#vecinj_inner <- cbind(inner_index, inner_vecinj_index)
vecinj_inner <- list(
l1 = c(1,2,2)
)
boundary <- list(
"N" = rep(0, n),
"E" = rep(0, n),
"S" = rep(0, n),
"W" = rep(0, n)
)
diffu_list <- names(alpha_diffu)
diffusion <- list(
init = init_diffu,
vecinj = do.call(rbind.data.frame, vecinj_diffu),
vecinj_inner = vecinj_inner,
vecinj_index = boundary,
alpha = alpha_diffu
)
#################################################################
## Section 3 ##
## Chemitry module (Phreeqc) ##
#################################################################
# db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat",
# package = "RedModRphree"
# ), is.db = TRUE)
#
# phreeqc::phrLoadDatabaseString(db)
# NOTE: This won't be needed in the future either. Could also be done in a. pqi
# file
base <- c(
"SOLUTION 1",
"units mol/kgw",
"temp 25.0",
"water 1",
"pH 9.91 charge",
"pe 4.0",
"C 1.2279E-04",
"Ca 1.2279E-04",
"Mg 0.001",
"Cl 0.002",
"PURE 1",
"O2g -0.1675 10",
"KINETICS 1",
"-steps 100",
"-step_divide 100",
"-bad_step_max 2000",
"Calcite", "-m 0.000207",
"-parms 0.0032",
"Dolomite",
"-m 0.0",
"-parms 0.00032",
"END"
)
selout <- c(
"SELECTED_OUTPUT", "-high_precision true", "-reset false",
"-time", "-soln", "-temperature true", "-water true",
"-pH", "-pe", "-totals C Ca Cl Mg",
"-kinetic_reactants Calcite Dolomite", "-equilibrium O2g"
)
# Needed when using DHT
signif_vector <- c(10, 10, 10, 7, 7, 7, 7, 0, 5, 5)
prop_type <- c("", "", "", "act", "act", "act", "act", "ignore", "", "")
prop <- names(init_cell)
chemistry <- list(
database = database,
input_script = input_script
)
#################################################################
## Section 4 ##
## Putting all those things together ##
#################################################################
iterations <- 10
setup <- list(
# bound = myboundmat,
base = base,
first = selout,
# initsim = initsim,
# Cf = 1,
grid = grid,
diffusion = diffusion,
chemistry = chemistry,
prop = prop,
immobile = c(7, 8, 9),
kin = c(8, 9),
ann = list(O2g = -0.1675),
# phase = "FLUX1",
# density = "DEN1",
reduce = FALSE,
# snapshots = demodir, ## directory where we will read MUFITS SUM files
# gridfile = paste0(demodir, "/d2ascii.run.GRID.SUM")
# init = init,
# vecinj = vecinj,
# cinj = c(0,1),
# boundary = boundary,
# injections = FALSE,
iterations = iterations,
timesteps = rep(10, iterations)
)

13
data/SimDol2D_diffu.yaml
View File

@ -1,13 +0,0 @@
phreeqc:
RebalanceByCell: True
RebalanceFraction: 0.5
SolutionDensityVolume: False
PartitionUZSolids: False
Units:
Solution: "mg/L"
PPassamblage: "mol/L"
Exchange: "mol/L"
Surface: "mol/L"
GasPhase: "mol/L"
SSassemblage: "mol/L"
Kinetics: "mol/L"

2
ext/phreeqcrm

@ -1 +1 @@
Subproject commit ba5dc40af119da015d36d2554ecd558ef9da1eb6
Subproject commit 89f713b273cd5340b2e8169523da04c2d7ad89c9

126
include/poet/ChemistryModule.hpp
View File

@ -1,20 +1,23 @@
// Time-stamp: "Last modified 2023-07-21 12:35:23 mluebke"
// Time-stamp: "Last modified 2023-08-01 13:13:18 mluebke"
#ifndef CHEMISTRYMODULE_H_
#define CHEMISTRYMODULE_H_
#include "DHT_Wrapper.hpp"
#include "Field.hpp"
#include "Interpolation.hpp"
#include "IrmResult.h"
#include "PhreeqcRM.h"
#include "poet/DHT_Wrapper.hpp"
#include "SimParams.hpp"
#include "DataStructures.hpp"
#include <array>
#include <cstddef>
#include <cstdint>
#include <map>
#include <memory>
#include <mpi.h>
#include <string>
#include <unordered_map>
#include <vector>
namespace poet {
@ -39,7 +42,8 @@ public:
* \param wp_size Count of grid cells to fill each work package at maximum.
* \param communicator MPI communicator to distribute work in.
*/
ChemistryModule(uint32_t nxyz, uint32_t wp_size, MPI_Comm communicator);
ChemistryModule(uint32_t nxyz, uint32_t wp_size, std::uint32_t maxiter,
const ChemistryParams &chem_param, MPI_Comm communicator);
/**
* Deconstructor, which frees DHT data structure if used.
@ -86,7 +90,8 @@ public:
*
* \returns A worker instance with fixed work package size.
*/
static ChemistryModule createWorker(MPI_Comm communicator);
static ChemistryModule createWorker(MPI_Comm communicator,
const ChemistryParams &chem_param);
/**
* Default work package size.
@ -109,9 +114,9 @@ public:
* Enumerating DHT file options
*/
enum {
DHT_FILES_DISABLED = 0, //!< disabled file output
DHT_FILES_SIMEND, //!< only output of snapshot after simulation
DHT_FILES_ITEREND //!< output snapshots after each iteration
DHT_SNAPS_DISABLED = 0, //!< disabled file output
DHT_SNAPS_SIMEND, //!< only output of snapshot after simulation
DHT_SNAPS_ITEREND //!< output snapshots after each iteration
};
/**
@ -135,47 +140,6 @@ public:
*/
void MasterLoopBreak();
/**
* **Master only** Enables DHT usage for the workers.
*
* If called multiple times enabling the DHT, the current state of DHT will be
* overwritten with a new instance of the DHT.
*
* \param enable Enables or disables the usage of the DHT.
* \param size_mb Size in megabyte to allocate for the DHT if enabled.
* \param key_species Name of species to be used for key creation.
*/
void SetDHTEnabled(bool enable, uint32_t size_mb,
const std::vector<std::string> &key_species);
/**
* **Master only** Set DHT snapshots to specific mode.
*
* \param type DHT snapshot mode.
* \param out_dir Path to output DHT snapshots.
*/
void SetDHTSnaps(int type, const std::string &out_dir);
/**
* **Master only** Set the vector with significant digits to round before
* inserting into DHT.
*
* \param signif_vec Vector defining significant digit for each species. Order
* is defined by prop_type vector (ChemistryModule::GetPropNames).
*/
void SetDHTSignifVector(std::vector<uint32_t> &signif_vec);
/**
* **Master only** Set the DHT rounding type of each species. See
* DHT_PROP_TYPES enumemartion for explanation.
*
* \param proptype_vec Vector defining DHT prop type for each species.
*/
void SetDHTPropTypeVector(std::vector<uint32_t> proptype_vec);
/**
* **Master only** Load the state of the DHT from given file.
*
* \param input_file File to load data from.
*/
void ReadDHTFile(const std::string &input_file);
/**
* **Master only** Return count of grid cells.
*/
@ -237,13 +201,6 @@ public:
*/
std::vector<uint32_t> GetWorkerDHTHits() const;
/**
* **Master only** Collect and return DHT misses of all workers.
*
* \return Vector of all count of DHT misses.
*/
std::vector<uint32_t> GetWorkerDHTMiss() const;
/**
* **Master only** Collect and return DHT evictions of all workers.
*
@ -263,9 +220,29 @@ public:
*
* \param enabled True if print progressbar, false if not.
*/
void setProgressBarPrintout(bool enabled);
void setProgressBarPrintout(bool enabled) {
this->print_progessbar = enabled;
};
std::vector<uint32_t> GetWorkerInterpolationCalls() const;
std::vector<double> GetWorkerInterpolationWriteTimings() const;
std::vector<double> GetWorkerInterpolationReadTimings() const;
std::vector<double> GetWorkerInterpolationGatherTimings() const;
std::vector<double> GetWorkerInterpolationFunctionCallTimings() const;
std::vector<uint32_t> GetWorkerPHTCacheHits() const;
protected:
void initializeDHT(uint32_t size_mb,
const NamedVector<std::uint32_t> &key_species);
void setDHTSnapshots(int type, const std::string &out_dir);
void setDHTReadFile(const std::string &input_file);
void initializeInterp(std::uint32_t bucket_size, std::uint32_t size_mb,
std::uint32_t min_entries,
const NamedVector<std::uint32_t> &key_species);
enum {
CHEM_INIT,
CHEM_WP_SIZE,
@ -275,9 +252,11 @@ protected:
CHEM_DHT_PROP_TYPE_VEC,
CHEM_DHT_SNAPS,
CHEM_DHT_READ_FILE,
CHEM_IP_ENABLE,
CHEM_IP_MIN_ENTRIES,
CHEM_IP_SIGNIF_VEC,
CHEM_WORK_LOOP,
CHEM_PERF,
CHEM_PROGRESSBAR,
CHEM_BREAK_MAIN_LOOP
};
@ -288,11 +267,20 @@ protected:
WORKER_DHT_GET,
WORKER_DHT_FILL,
WORKER_IDLE,
WORKER_IP_WRITE,
WORKER_IP_READ,
WORKER_IP_GATHER,
WORKER_IP_FC,
WORKER_DHT_HITS,
WORKER_DHT_MISS,
WORKER_DHT_EVICTIONS
WORKER_DHT_EVICTIONS,
WORKER_PHT_CACHE_HITS,
WORKER_IP_CALLS
};
std::vector<uint32_t> interp_calls;
std::vector<uint32_t> dht_hits;
std::vector<uint32_t> dht_evictions;
struct worker_s {
double phreeqc_t = 0.;
double dht_get = 0.;
@ -347,8 +335,11 @@ protected:
void unshuffleField(const std::vector<double> &in_buffer,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count, std::vector<double> &out_field);
std::vector<std::uint32_t>
parseDHTSpeciesVec(const std::vector<std::string> &species_vec) const;
std::vector<std::int32_t>
parseDHTSpeciesVec(const NamedVector<std::uint32_t> &key_species,
const std::vector<std::string> &to_compare) const;
void BCastStringVec(std::vector<std::string> &io);
int comm_size, comm_rank;
MPI_Comm group_comm;
@ -358,11 +349,14 @@ protected:
uint32_t wp_size{CHEM_DEFAULT_WP_SIZE};
bool dht_enabled{false};
int dht_snaps_type{DHT_FILES_DISABLED};
int dht_snaps_type{DHT_SNAPS_DISABLED};
std::string dht_file_out_dir;
poet::DHT_Wrapper *dht = nullptr;
bool interp_enabled{false};
std::unique_ptr<poet::InterpolationModule> interp;
static constexpr uint32_t BUFFER_OFFSET = 5;
inline void ChemBCast(void *buf, int count, MPI_Datatype datatype) const {
@ -381,7 +375,9 @@ protected:
bool print_progessbar{false};
double chem_t = 0.;
std::uint32_t file_pad;
double chem_t{0.};
uint32_t n_cells = 0;
uint32_t prop_count = 0;
@ -391,6 +387,8 @@ protected:
static constexpr int MODULE_COUNT = 5;
const ChemistryParams &params;
std::array<std::uint32_t, MODULE_COUNT> speciesPerModule{};
};
} // namespace poet

51
include/poet/DHT.h
View File

@ -67,7 +67,7 @@
*/
typedef struct {
/** Count of writes to specific process this process did. */
int* writes_local;
int *writes_local;
/** Writes after last call of DHT_print_statistics. */
int old_writes;
/** How many read misses occur? */
@ -100,27 +100,36 @@ typedef struct {
/** Size of the MPI communicator respectively all participating processes. */
int comm_size;
/** Pointer to a hashfunction. */
uint64_t (*hash_func)(int, const void*);
uint64_t (*hash_func)(int, const void *);
/** Pre-allocated memory where a bucket can be received. */
void* recv_entry;
void *recv_entry;
/** Pre-allocated memory where a bucket to send can be stored. */
void* send_entry;
void *send_entry;
/** Allocated memory on which the MPI window was created. */
void* mem_alloc;
void *mem_alloc;
/** Count of read misses over all time. */
int read_misses;
/** Count of evictions over all time. */
int evictions;
/** Array of indeces where a bucket can be stored. */
uint64_t* index;
uint64_t *index;
/** Count of possible indeces. */
unsigned int index_count;
int (*accumulate_callback)(int, void *, int, void *);
#ifdef DHT_STATISTICS
/** Detailed statistics of the usage of the DHT. */
DHT_stats* stats;
DHT_stats *stats;
#endif
} DHT;
extern void DHT_set_accumulate_callback(DHT *table,
int (*callback_func)(int, void *, int,
void *));
extern int DHT_write_accumulate(DHT *table, const void *key, int send_size,
void *data, uint32_t *proc, uint32_t *index, int *callback_ret);
/**
* @brief Create a DHT.
*
@ -141,9 +150,9 @@ typedef struct {
* @return DHT* The returned value is the \a DHT-object which serves as a handle
* for all DHT operations. If an error occured NULL is returned.
*/
extern DHT* DHT_create(MPI_Comm comm, uint64_t size_per_process,
extern DHT *DHT_create(MPI_Comm comm, uint64_t size_per_process,
unsigned int data_size, unsigned int key_size,
uint64_t (*hash_func)(int, const void*));
uint64_t (*hash_func)(int, const void *));
/**
* @brief Write data into DHT.
@ -161,10 +170,14 @@ extern DHT* DHT_create(MPI_Comm comm, uint64_t size_per_process,
* @param table Pointer to the \a DHT-object.
* @param key Pointer to the key.
* @param data Pointer to the data.
* @param proc If not NULL, returns the process number written to.
* @param index If not NULL, returns the index of the bucket where the data was
* written to.
* @return int Returns either DHT_SUCCESS on success or correspondending error
* value on eviction or error.
*/
extern int DHT_write(DHT* table, void* key, void* data);
extern int DHT_write(DHT *table, void *key, void *data, uint32_t *proc,
uint32_t *index);
/**
* @brief Read data from DHT.
@ -187,8 +200,10 @@ extern int DHT_write(DHT* table, void* key, void* data);
* @return int Returns either DHT_SUCCESS on success or correspondending error
* value on read miss or error.
*/
extern int DHT_read(DHT* table, void* key, void* destination);
extern int DHT_read(DHT *table, const void *key, void *destination);
extern int DHT_read_location(DHT *table, uint32_t proc, uint32_t index,
void *destination);
/**
* @brief Write current state of DHT to file.
*
@ -203,7 +218,7 @@ extern int DHT_read(DHT* table, void* key, void* destination);
* @return int Returns DHT_SUCCESS on succes, DHT_FILE_IO_ERROR if file can't be
* opened/closed or DHT_WRITE_ERROR if file is not writable.
*/
extern int DHT_to_file(DHT* table, const char* filename);
extern int DHT_to_file(DHT *table, const char *filename);
/**
* @brief Read state of DHT from file.
@ -223,7 +238,7 @@ extern int DHT_to_file(DHT* table, const char* filename);
* file doesn't match expectation. This is possible if the data size or key size
* is different.
*/
extern int DHT_from_file(DHT* table, const char* filename);
extern int DHT_from_file(DHT *table, const char *filename);
/**
* @brief Free ressources of DHT.
@ -241,7 +256,7 @@ extern int DHT_from_file(DHT* table, const char* filename);
* @return int Returns either DHT_SUCCESS on success or DHT_MPI_ERROR on
* internal MPI error.
*/
extern int DHT_free(DHT* table, int* eviction_counter, int* readerror_counter);
extern int DHT_free(DHT *table, int *eviction_counter, int *readerror_counter);
/**
* @brief Prints a table with statistics about current use of DHT.
@ -267,7 +282,7 @@ extern int DHT_free(DHT* table, int* eviction_counter, int* readerror_counter);
* @return int Returns DHT_SUCCESS on success or DHT_MPI_ERROR on internal MPI
* error.
*/
extern int DHT_print_statistics(DHT* table);
extern int DHT_print_statistics(DHT *table);
/**
* @brief Determine destination rank and index.
@ -286,8 +301,8 @@ extern int DHT_print_statistics(DHT* table);
* @param index_count Count of possible indeces.
*/
static void determine_dest(uint64_t hash, int comm_size,
unsigned int table_size, unsigned int* dest_rank,
uint64_t* index, unsigned int index_count);
unsigned int table_size, unsigned int *dest_rank,
uint64_t *index, unsigned int index_count);
/**
* @brief Set the occupied flag.
@ -296,7 +311,7 @@ static void determine_dest(uint64_t hash, int comm_size,
*
* @param flag_byte First byte of a bucket.
*/
static void set_flag(char* flag_byte);
static void set_flag(char *flag_byte);
/**
* @brief Get the occupied flag.

2
include/poet/DHT_Types.hpp
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@ -2,7 +2,7 @@
#define DHT_TYPES_H_
namespace poet {
enum DHT_PROP_TYPES { DHT_TYPE_DEFAULT, DHT_TYPE_CHARGE, DHT_TYPE_IGNORE, DHT_TYPE_TOTAL };
enum DHT_PROP_TYPES { DHT_TYPE_DEFAULT, DHT_TYPE_CHARGE, DHT_TYPE_TOTAL };
}
#endif // DHT_TYPES_H_

121
include/poet/DHT_Wrapper.hpp
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@ -1,4 +1,4 @@
// Time-stamp: "Last modified 2023-04-24 16:23:42 mluebke"
// Time-stamp: "Last modified 2023-08-01 13:48:34 mluebke"
/*
** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
@ -23,10 +23,18 @@
#ifndef DHT_WRAPPER_H
#define DHT_WRAPPER_H
#include "DataStructures.hpp"
#include "LookupKey.hpp"
#include "poet/DHT_Types.hpp"
#include "poet/HashFunctions.hpp"
#include "poet/LookupKey.hpp"
#include "poet/Rounding.hpp"
#include <array>
#include <cstdint>
#include <limits>
#include <string>
#include <unordered_map>
#include <utility>
#include <vector>
extern "C" {
@ -37,35 +45,7 @@ extern "C" {
namespace poet {
struct DHT_SCNotation {
std::int8_t exp : 8;
std::int64_t significant : 56;
};
union DHT_Keyelement {
double fp_elemet;
DHT_SCNotation sc_notation;
};
using DHT_ResultObject = struct DHTResobj {
uint32_t length;
std::vector<std::vector<DHT_Keyelement>> keys;
std::vector<std::vector<double>> results;
std::vector<bool> needPhreeqc;
};
/**
* @brief Return user-defined md5sum
*
* This function will calculate a hashsum with the help of md5sum. Therefore the
* md5sum for a given key is calculated and divided into two 64-bit parts. These
* will be XORed and returned as the hash.
*
* @param key_size Size of key in bytes
* @param key Pointer to key
* @return uint64_t Hashsum as an unsigned 64-bit integer
*/
static uint64_t get_md5(int key_size, void *key);
using DHT_Location = std::pair<std::uint32_t, std::uint32_t>;
/**
* @brief C++-Wrapper around DHT implementation
@ -76,6 +56,20 @@ static uint64_t get_md5(int key_size, void *key);
*/
class DHT_Wrapper {
public:
using DHT_ResultObject = struct DHTResobj {
uint32_t length;
std::vector<LookupKey> keys;
std::vector<std::vector<double>> results;
std::vector<double> old_values;
std::vector<bool> needPhreeqc;
std::vector<DHT_Location> locations;
};
static constexpr std::int32_t DHT_KEY_INPUT_CUSTOM =
std::numeric_limits<std::int32_t>::min();
static constexpr int DHT_KEY_SIGNIF_DEFAULT = 5;
/**
* @brief Construct a new dht wrapper object
*
@ -91,8 +85,9 @@ public:
* for key creation.
* @param data_count Count of data entries
*/
DHT_Wrapper(MPI_Comm dht_comm, uint32_t dht_size,
const std::vector<std::uint32_t> &key_indices,
DHT_Wrapper(MPI_Comm dht_comm, std::uint64_t dht_size,
const NamedVector<std::uint32_t> &key_species,
const std::vector<std::int32_t> &key_indices,
uint32_t data_count);
/**
* @brief Destroy the dht wrapper object
@ -105,6 +100,9 @@ public:
*/
~DHT_Wrapper();
DHT_Wrapper &operator=(const DHT_Wrapper &) = delete;
DHT_Wrapper(const DHT_Wrapper &) = delete;
/**
* @brief Check if values of workpackage are stored in DHT
*
@ -123,7 +121,7 @@ public:
*/
auto checkDHT(int length, double dt, const std::vector<double> &work_package,
std::vector<std::uint32_t> &curr_mapping)
-> const poet::DHT_ResultObject &;
-> const DHT_ResultObject &;
/**
* @brief Write simulated values into DHT
@ -183,13 +181,6 @@ public:
*/
auto getHits() { return this->dht_hits; };
/**
* @brief Get the Misses object
*
* @return uint64_t Count of read misses
*/
auto getMisses() { return this->dht_miss; };
/**
* @brief Get the Evictions object
*
@ -197,32 +188,56 @@ public:
*/
auto getEvictions() { return this->dht_evictions; };
void SetSignifVector(std::vector<uint32_t> signif_vec);
void SetPropTypeVector(std::vector<uint32_t> prop_type_vec);
void setBaseTotals(const std::array<double, 2> &bt) {
this->base_totals = bt;
void resetCounter() {
this->dht_hits = 0;
this->dht_evictions = 0;
}
void SetSignifVector(std::vector<uint32_t> signif_vec);
auto getDataCount() { return this->data_count; }
auto getCommunicator() { return this->communicator; }
DHT *getDHT() { return this->dht_object; };
DHT_ResultObject &getDHTResults() { return this->dht_results; }
const auto &getKeyElements() const { return this->input_key_elements; }
const auto &getKeySpecies() const { return this->key_species; }
void setBaseTotals(double tot_h, double tot_o) {
this->base_totals = {tot_h, tot_o};
}
std::uint32_t getInputCount() const {
return this->input_key_elements.size();
}
std::uint32_t getOutputCount() const { return this->data_count; }
private:
uint32_t key_count;
uint32_t data_count;
DHT *dht_object;
MPI_Comm communicator;
std::vector<DHT_Keyelement> fuzzForDHT(int var_count, void *key, double dt);
LookupKey fuzzForDHT(int var_count, void *key, double dt);
std::vector<double>
outputToInputAndRates(const std::vector<double> &old_results,
const std::vector<double> &new_results);
std::vector<double>
inputAndRatesToOutput(const std::vector<double> &dht_data);
uint32_t dht_hits = 0;
uint32_t dht_miss = 0;
uint32_t dht_evictions = 0;
std::vector<uint32_t> dht_signif_vector;
std::vector<std::uint32_t> dht_prop_type_vector;
std::vector<std::uint32_t> input_key_elements;
NamedVector<std::uint32_t> key_species;
static constexpr int DHT_KEY_SIGNIF_DEFAULT = 5;
static constexpr int DHT_KEY_SIGNIF_TOTALS = 10;
static constexpr int DHT_KEY_SIGNIF_CHARGE = 3;
std::vector<std::uint32_t> dht_signif_vector;
std::vector<std::uint32_t> dht_prop_type_vector;
std::vector<std::int32_t> input_key_elements;
DHT_ResultObject dht_results;

35
include/poet/DataStructures.hpp Normal file
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@ -0,0 +1,35 @@
#ifndef DATASTRUCTURES_H_
#define DATASTRUCTURES_H_
#include <cstddef>
#include <string>
#include <utility>
#include <vector>
namespace poet {
template <typename value_type> class NamedVector {
public:
void insert(std::pair<std::string, value_type> to_insert) {
this->names.push_back(to_insert.first);
this->values.push_back(to_insert.second);
container_size++;
}
bool empty() const { return this->container_size == 0; }
std::size_t size() const { return this->container_size; }
value_type &operator[](std::size_t i) { return values[i]; }
const std::vector<std::string> &getNames() const { return this->names; }
const std::vector<value_type> &getValues() const { return this->values; }
private:
std::size_t container_size{0};
std::vector<std::string> names{};
std::vector<value_type> values{};
};
} // namespace poet
#endif // DATASTRUCTURES_H_

266
include/poet/Interpolation.hpp Normal file
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@ -0,0 +1,266 @@
// Time-stamp: "Last modified 2023-08-01 18:10:48 mluebke"
#ifndef INTERPOLATION_H_
#define INTERPOLATION_H_
#include "DHT.h"
#include "DHT_Wrapper.hpp"
#include "DataStructures.hpp"
#include "LookupKey.hpp"
#include "poet/DHT_Wrapper.hpp"
#include "poet/Rounding.hpp"
#include <cassert>
#include <iostream>
#include <list>
#include <memory>
#include <mpi.h>
#include <string>
#include <utility>
extern "C" {
#include "poet/DHT.h"
}
#include "poet/LookupKey.hpp"
#include <cstdint>
#include <functional>
#include <unordered_map>
#include <vector>
namespace poet {
class ProximityHashTable {
public:
using bucket_indicator = std::uint64_t;
ProximityHashTable(uint32_t key_size, uint32_t data_size,
uint32_t entry_count, uint32_t size_per_process,
MPI_Comm communicator);
~ProximityHashTable();
// delete assign and copy operator
ProximityHashTable &operator=(const ProximityHashTable *) = delete;
ProximityHashTable(const ProximityHashTable &) = delete;
struct PHT_Result {
std::uint32_t size;
std::vector<std::vector<double>> in_values;
std::vector<std::vector<double>> out_values;
std::uint32_t getSize() const {
std::uint32_t sum{0};
for (const auto &results : out_values) {
sum += results.size() * sizeof(double);
}
return sum;
}
};
void setSourceDHT(DHT *src) {
this->source_dht = src;
this->dht_key_count = src->key_size / sizeof(Lookup_Keyelement);
this->dht_data_count = src->data_size / sizeof(double);
this->dht_buffer.resize(src->data_size + src->key_size);
}
void writeLocationToPHT(LookupKey key, DHT_Location location);
const PHT_Result &query(const LookupKey &key,
const std::vector<std::uint32_t> &signif,
std::uint32_t min_entries_needed,
std::uint32_t input_count,
std::uint32_t output_count);
std::uint64_t getLocations(const LookupKey &key);
void getEntriesFromLocation(const PHT_Result &locations,
const std::vector<uint32_t> &signif);
void writeStats() { DHT_print_statistics(this->prox_ht); }
DHT *getDHTObject() { return this->prox_ht; }
auto getPHTWriteTime() const -> double { return this->pht_write_t; };
auto getPHTReadTime() const -> double { return this->pht_read_t; };
auto getDHTGatherTime() const -> double { return this->pht_gather_dht_t; };
auto getLocalCacheHits() const -> std::vector<std::uint32_t> {
return this->all_cache_hits;
}
void storeAndResetCounter() {
all_cache_hits.push_back(cache_hits);
cache_hits = 0;
}
#if POET_PHT_ADD
void incrementReadCounter(const LookupKey &key);
#endif
private:
enum { INTERP_CB_OK, INTERP_CB_FULL, INTERP_CB_ALREADY_IN };
static int PHT_callback_function(int in_data_size, void *in_data,
int out_data_size, void *out_data);
static std::vector<double> convertKeysFromDHT(Lookup_Keyelement *keys_in,
std::uint32_t key_size);
static bool similarityCheck(const LookupKey &fine, const LookupKey &coarse,
const std::vector<uint32_t> &signif);
char *bucket_store;
class Cache
: private std::unordered_map<LookupKey, PHT_Result, LookupKeyHasher> {
public:
void operator()(const LookupKey &key, const PHT_Result val);
std::pair<bool, PHT_Result> operator[](const LookupKey &key);
void flush() { this->clear(); }
protected:
private:
static constexpr std::int64_t MAX_CACHE_SIZE = 100E6;
std::int64_t free_mem{MAX_CACHE_SIZE};
std::list<LookupKey> lru_queue;
using lru_iterator = typename std::list<LookupKey>::iterator;
std::unordered_map<LookupKey, lru_iterator, LookupKeyHasher> keyfinder;
};
Cache localCache;
DHT *prox_ht;
std::uint32_t dht_evictions = 0;
DHT *source_dht = nullptr;
PHT_Result lookup_results;
std::vector<char> dht_buffer;
std::uint32_t dht_key_count;
std::uint32_t dht_data_count;
MPI_Comm communicator;
double pht_write_t = 0.;
double pht_read_t = 0.;
double pht_gather_dht_t = 0.;
std::uint32_t cache_hits{0};
std::vector<std::uint32_t> all_cache_hits{};
};
class InterpolationModule {
public:
using InterpFunction = std::vector<double> (*)(
const std::vector<std::int32_t> &, const std::vector<double> &,
const std::vector<std::vector<double>> &,
const std::vector<std::vector<double>> &);
InterpolationModule(std::uint32_t entries_per_bucket,
std::uint64_t size_per_process,
std::uint32_t min_entries_needed, DHT_Wrapper &dht,
const NamedVector<std::uint32_t> &interp_key_signifs,
const std::vector<std::int32_t> &dht_key_indices);
enum result_status { RES_OK, INSUFFICIENT_DATA, NOT_NEEDED };
struct InterpolationResult {
std::vector<std::vector<double>> results;
std::vector<result_status> status;
void ResultsToWP(std::vector<double> &currWP);
};
void setInterpolationFunction(InterpFunction func) {
this->f_interpolate = func;
}
void setMinEntriesNeeded(std::uint32_t entries) {
this->min_entries_needed = entries;
}
auto getMinEntriesNeeded() { return this->min_entries_needed; }
void writePairs(const DHT_Wrapper::DHT_ResultObject &in);
void tryInterpolation(DHT_Wrapper::DHT_ResultObject &dht_results,
std::vector<std::uint32_t> &curr_mapping);
void resultsToWP(std::vector<double> &work_package) const;
auto getPHTWriteTime() const { return pht->getPHTWriteTime(); };
auto getPHTReadTime() const { return pht->getPHTReadTime(); };
auto getDHTGatherTime() const { return pht->getDHTGatherTime(); };
auto getInterpolationTime() const { return this->interp_t; };
auto getInterpolationCount() const -> std::uint32_t {
return this->interpolations;
}
auto getPHTLocalCacheHits() const -> std::vector<std::uint32_t> {
return this->pht->getLocalCacheHits();
}
void resetCounter() {
this->interpolations = 0;
this->pht->storeAndResetCounter();
}
void writePHTStats() { this->pht->writeStats(); }
void dumpPHTState(const std::string &filename) {
DHT_to_file(this->pht->getDHTObject(), filename.c_str());
}
static constexpr std::uint32_t COARSE_DIFF = 2;
static constexpr std::uint32_t COARSE_SIGNIF_DEFAULT =
DHT_Wrapper::DHT_KEY_SIGNIF_DEFAULT - COARSE_DIFF;
private:
void initPHT(std::uint32_t key_count, std::uint32_t entries_per_bucket,
std::uint32_t size_per_process, MPI_Comm communicator);
static std::vector<double> dummy(const std::vector<std::int32_t> &,
const std::vector<double> &,
const std::vector<std::vector<double>> &,
const std::vector<std::vector<double>> &) {
return {};
}
double interp_t = 0.;
std::uint32_t interpolations{0};
InterpFunction f_interpolate = dummy;
std::uint32_t min_entries_needed = 5;
std::unique_ptr<ProximityHashTable> pht;
DHT_Wrapper &dht_instance;
NamedVector<std::uint32_t> key_signifs;
std::vector<std::int32_t> key_indices;
InterpolationResult interp_result;
PHT_Rounder rounder;
LookupKey roundKey(const LookupKey &in_key) {
LookupKey out_key;
for (std::uint32_t i = 0; i < key_indices.size(); i++) {
out_key.push_back(rounder.round(in_key[key_indices[i]], key_signifs[i]));
}
// timestep
out_key.push_back(in_key.back());
return out_key;
}
};
} // namespace poet
#endif // INTERPOLATION_H_

50
include/poet/LookupKey.hpp Normal file
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@ -0,0 +1,50 @@
// Time-stamp: "Last modified 2023-07-26 10:20:10 mluebke"
#ifndef LOOKUPKEY_H_
#define LOOKUPKEY_H_
#include "poet/HashFunctions.hpp"
#include <cstdint>
#include <cstring>
#include <vector>
namespace poet {
struct Lookup_SC_notation {
std::int8_t exp : 8;
std::int64_t significant : 56;
};
union Lookup_Keyelement {
double fp_element;
Lookup_SC_notation sc_notation;
bool operator==(const Lookup_Keyelement &other) const {
return std::memcmp(this, &other, sizeof(Lookup_Keyelement)) == 0 ? true
: false;
}
};
class LookupKey : public std::vector<Lookup_Keyelement> {
public:
explicit LookupKey(size_type count);
using std::vector<Lookup_Keyelement>::vector;
std::vector<double> to_double() const;
static Lookup_SC_notation round_from_double(const double in,
std::uint32_t signif);
static double to_double(const Lookup_SC_notation in);
};
struct LookupKeyHasher {
std::uint64_t operator()(const LookupKey &k) const {
const uint32_t key_size = k.size() * sizeof(Lookup_Keyelement);
return poet::Murmur2_64A(key_size, k.data());
}
};
} // namespace poet
#endif // LOOKUPKEY_H_

40
include/poet/RInsidePOET.hpp
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@ -1,7 +1,15 @@
#ifndef RPOET_H_
#define RPOET_H_
#include "DataStructures.hpp"
#include <RInside.h>
#include <Rcpp.h>
#include <cstddef>
#include <stdexcept>
#include <string>
#include <utility>
#include <vector>
class RInsidePOET : public RInside {
public:
@ -14,6 +22,38 @@ public:
RInsidePOET(RInsidePOET const &) = delete;
void operator=(RInsidePOET const &) = delete;
inline bool checkIfExists(const std::string &R_name,
const std::string &where) {
return Rcpp::as<bool>(
this->parseEval("'" + R_name + "' %in% names(" + where + ")"));
}
template <class T> inline T getSTL(const std::string &R_name) {
return Rcpp::as<T>(RInside::operator[](R_name));
}
template <typename value_type>
poet::NamedVector<value_type> wrapNamedVector(const std::string &R_name) {
std::size_t name_size = this->parseEval("length(names(" + R_name + "))");
if (name_size == 0) {
throw std::runtime_error("wrapNamedVector: " + R_name +
" is not a named vector!");
}
auto names = Rcpp::as<std::vector<std::string>>(
this->parseEval("names(" + R_name + ")"));
auto values = Rcpp::as<Rcpp::NumericVector>(this->parseEval(R_name));
poet::NamedVector<value_type> ret_map;
for (std::size_t i = 0; i < names.size(); i++) {
ret_map.insert(
std::make_pair(names[i], static_cast<value_type>(values[i])));
}
return ret_map;
}
private:
RInsidePOET() : RInside(){};
};

92
include/poet/Rounding.hpp Normal file
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@ -0,0 +1,92 @@
#ifndef ROUNDING_H_
#define ROUNDING_H_
#include "LookupKey.hpp"
#include <cmath>
#include <cstdint>
namespace poet {
constexpr std::int8_t AQUEOUS_EXP = -13;
template <typename Input, typename Output, typename ConvertTo = double>
class IRounding {
public:
virtual Output round(const Input &, std::uint32_t signif) = 0;
virtual ConvertTo convert(const Output &) = 0;
};
class DHT_Rounder {
public:
Lookup_Keyelement round(const double &value, std::uint32_t signif,
bool is_ho) {
std::int8_t exp =
static_cast<std::int8_t>(std::floor(std::log10(std::fabs(value))));
if (!is_ho) {
if (exp < AQUEOUS_EXP) {
return {.sc_notation = {0, 0}};
}
std::int8_t diff = exp - signif + 1;
if (diff < AQUEOUS_EXP) {
signif -= AQUEOUS_EXP - diff;
}
}
Lookup_Keyelement elem;
elem.sc_notation.exp = exp;
elem.sc_notation.significant =
static_cast<std::int64_t>(value * std::pow(10, signif - exp - 1));
return elem;
}
double convert(const Lookup_Keyelement &key_elem) {
std::int32_t normalized_exp = static_cast<std::int32_t>(
-std::log10(std::fabs(key_elem.sc_notation.significant)));
// add stored exponent to normalized exponent
normalized_exp += key_elem.sc_notation.exp;
// return significant times 10 to the power of exponent
return key_elem.sc_notation.significant * std::pow(10., normalized_exp);
}
};
class PHT_Rounder : public IRounding<Lookup_Keyelement, Lookup_Keyelement> {
public:
Lookup_Keyelement round(const Lookup_Keyelement &value,
std::uint32_t signif) {
Lookup_Keyelement new_val = value;
std::uint32_t diff_signif =
static_cast<std::uint32_t>(
std::ceil(std::log10(std::abs(value.sc_notation.significant)))) -
signif;
new_val.sc_notation.significant = static_cast<int64_t>(
value.sc_notation.significant / std::pow(10., diff_signif));
if (new_val.sc_notation.significant == 0) {
new_val.sc_notation.exp = 0;
}
return new_val;
}
double convert(const Lookup_Keyelement &key_elem) {
std::int32_t normalized_exp = static_cast<std::int32_t>(
-std::log10(std::fabs(key_elem.sc_notation.significant)));
// add stored exponent to normalized exponent
normalized_exp += key_elem.sc_notation.exp;
// return significant times 10 to the power of exponent
return key_elem.sc_notation.significant * std::pow(10., normalized_exp);
}
};
} // namespace poet
#endif // ROUNDING_H_

72
include/poet/SimParams.hpp
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@ -24,17 +24,20 @@
#include <cstdint>
#include <string>
#include <string_view>
#include <unordered_map>
#include <vector>
#include "DataStructures.hpp"
#include "RInsidePOET.hpp"
#include "argh.hpp" // Argument handler https://github.com/adishavit/argh
#include <RInside.h>
#include <Rcpp.h>
// BSD-licenced
/** Standard DHT Size. Defaults to 1 GB (1000 MB) */
constexpr uint32_t DHT_SIZE_PER_PROCESS_MB = 1E3;
constexpr uint32_t DHT_SIZE_PER_PROCESS_MB = 1.5E3;
/** Standard work package size */
#define WORK_PACKAGE_SIZE_DEFAULT 5
#define WORK_PACKAGE_SIZE_DEFAULT 32
namespace poet {
@ -70,6 +73,8 @@ typedef struct {
/** indicating whether the progress bar during chemistry simulation should be
* printed or not */
bool print_progressbar;
bool interp_enabled;
} t_simparams;
using GridParams = struct s_GridParams {
@ -101,13 +106,24 @@ using DiffusionParams = struct s_DiffusionParams {
s_DiffusionParams(RInside &R);
};
using ChemistryParams = struct s_ChemistryParams {
struct ChemistryParams {
std::string database_path;
std::string input_script;
std::vector<std::string> dht_species;
std::vector<std::uint32_t> dht_signif;
s_ChemistryParams(RInside &R);
bool use_dht;
std::uint64_t dht_size;
int dht_snaps;
std::string dht_file;
std::string dht_outdir;
NamedVector<std::uint32_t> dht_signifs;
bool use_interp;
std::uint64_t pht_size;
std::uint32_t pht_max_entries;
std::uint32_t interp_min_entries;
NamedVector<std::uint32_t> pht_signifs;
void initFromR(RInsidePOET &R);
};
/**
@ -159,7 +175,7 @@ public:
* @return int Returns with 0 if no error occured, otherwise value less than 0
* is returned.
*/
int parseFromCmdl(char *argv[], RInside &R);
int parseFromCmdl(char *argv[], RInsidePOET &R);
/**
* @brief Init std::vector values
@ -193,25 +209,10 @@ public:
*/
auto getDHTSignifVector() const { return this->dht_signif_vector; };
/**
* @brief Get the DHT_Prop_Type_Vector
*
* Returns a vector indicating of which type a variable of a grid cell is.
*
* @return std::vector<std::string> Vector if strings defining a type of a
* variable
*/
auto getDHTPropTypeVector() const { return this->dht_prop_type_vector; };
auto getPHTSignifVector() const { return this->pht_signif_vector; };
/**
* @brief Return name of DHT snapshot.
*
* Name of the DHT file which is used to initialize the DHT with a previously
* written snapshot.
*
* @return std::string Absolute paht to the DHT snapshot
*/
auto getDHTFile() const { return this->dht_file; };
auto getPHTBucketSize() const { return this->pht_bucket_size; };
auto getPHTMinEntriesNeeded() const { return this->pht_min_entries_needed; };
/**
* @brief Get the filesim name
@ -233,23 +234,30 @@ public:
*/
auto getOutDir() const { return this->out_dir; };
const auto &getChemParams() const { return chem_params; }
private:
std::list<std::string> validateOptions(argh::parser cmdl);
const std::set<std::string> flaglist{"ignore-result", "dht", "dht-nolog", "P",
"progress"};
const std::set<std::string> paramlist{"work-package-size", "dht-signif",
"dht-strategy", "dht-size",
"dht-snaps", "dht-file"};
const std::set<std::string> flaglist{
"ignore-result", "dht", "dht-nolog", "P", "progress", "interp"};
const std::set<std::string> paramlist{
"work-package-size", "dht-signif", "dht-strategy",
"dht-size", "dht-snaps", "dht-file",
"interp-size", "interp-min", "interp-bucket-entries"};
t_simparams simparams;
std::vector<uint32_t> dht_signif_vector;
std::vector<uint32_t> dht_prop_type_vector;
std::vector<uint32_t> pht_signif_vector;
uint32_t pht_bucket_size;
uint32_t pht_min_entries_needed;
std::string dht_file;
std::string filesim;
std::string out_dir;
ChemistryParams chem_params;
};
} // namespace poet
#endif // PARSER_H

9
src/CMakeLists.txt
View File

@ -2,9 +2,6 @@ file(GLOB_RECURSE poet_lib_SRC
CONFIGURE_DEPENDS
"*.cpp" "*.c")
find_library(MATH_LIBRARY m)
find_library(CRYPTO_LIBRARY crypto)
add_library(poet_lib ${poet_lib_SRC})
target_include_directories(poet_lib PUBLIC ${PROJECT_SOURCE_DIR}/include)
target_link_libraries(poet_lib PUBLIC
@ -20,3 +17,9 @@ option(POET_DHT_DEBUG "Build with DHT debug info" OFF)
if(POET_DHT_DEBUG)
target_compile_definitions(poet_lib PRIVATE DHT_STATISTICS)
endif()
option(POET_PHT_ADDITIONAL_INFO "Enables additional information in the PHT" OFF)
if (POET_PHT_ADDITIONAL_INFO)
target_compile_definitions(poet_lib PRIVATE POET_PHT_ADD)
endif()

406
src/ChemistryModule/ChemistryModule.cpp
View File

@ -1,20 +1,167 @@
#include "poet/ChemistryModule.hpp"
#include "PhreeqcRM.h"
#include "poet/DHT_Wrapper.hpp"
#include "poet/Interpolation.hpp"
#include <algorithm>
#include <cassert>
#include <cstddef>
#include <cstdint>
#include <map>
#include <memory>
#include <mpi.h>
#include <stdexcept>
#include <string>
#include <utility>
#include <vector>
constexpr uint32_t MB_FACTOR = 1E6;
std::vector<double>
inverseDistanceWeighting(const std::vector<std::int32_t> &to_calc,
const std::vector<double> &from,
const std::vector<std::vector<double>> &input,
const std::vector<std::vector<double>> &output) {
std::vector<double> results = from;
const std::uint32_t buffer_size = input.size() + 1;
double buffer[buffer_size];
double from_rescaled;
const std::uint32_t data_set_n = input.size();
double rescaled[to_calc.size()][data_set_n + 1];
double weights[data_set_n];
// rescaling over all key elements
for (int key_comp_i = 0; key_comp_i < to_calc.size(); key_comp_i++) {
const auto output_comp_i = to_calc[key_comp_i];
// rescale input between 0 and 1
for (int point_i = 0; point_i < data_set_n; point_i++) {
rescaled[key_comp_i][point_i] = input[point_i][key_comp_i];
}
rescaled[key_comp_i][data_set_n] = from[output_comp_i];
const double min = *std::min_element(rescaled[key_comp_i],
rescaled[key_comp_i] + data_set_n + 1);
const double max = *std::max_element(rescaled[key_comp_i],
rescaled[key_comp_i] + data_set_n + 1);
for (int point_i = 0; point_i < data_set_n; point_i++) {
rescaled[key_comp_i][point_i] =
((max - min) != 0
? (rescaled[key_comp_i][point_i] - min) / (max - min)
: 0);
}
rescaled[key_comp_i][data_set_n] =
((max - min) != 0 ? (from[output_comp_i] - min) / (max - min) : 0);
}
// calculate distances for each data set
double inv_sum = 0;
for (int point_i = 0; point_i < data_set_n; point_i++) {
double distance = 0;
for (int key_comp_i = 0; key_comp_i < to_calc.size(); key_comp_i++) {
distance += std::pow(
rescaled[key_comp_i][point_i] - rescaled[key_comp_i][data_set_n], 2);
}
weights[point_i] = 1 / std::sqrt(distance);
assert(!std::isnan(weights[point_i]));
inv_sum += weights[point_i];
}
assert(!std::isnan(inv_sum));
// actual interpolation
// bool has_h = false;
// bool has_o = false;
for (int key_comp_i = 0; key_comp_i < to_calc.size(); key_comp_i++) {
const auto output_comp_i = to_calc[key_comp_i];
double key_delta = 0;
// if (interp_i == 0) {
// has_h = true;
// }
// if (interp_i == 1) {
// has_o = true;
// }
for (int j = 0; j < data_set_n; j++) {
key_delta += weights[j] * input[j][key_comp_i];
}
key_delta /= inv_sum;
results[output_comp_i] = from[output_comp_i] + key_delta;
}
// if (!has_h) {
// double new_val = 0;
// for (int j = 0; j < data_set_n; j++) {
// new_val += weights[j] * output[j][0];
// }
// results[0] = new_val / inv_sum;
// }
// if (!has_h) {
// double new_val = 0;
// for (int j = 0; j < data_set_n; j++) {
// new_val += weights[j] * output[j][1];
// }
// results[1] = new_val / inv_sum;
// }
// for (std::uint32_t i = 0; i < to_calc.size(); i++) {
// const std::uint32_t interp_i = to_calc[i];
// // rescale input between 0 and 1
// for (int j = 0; j < input.size(); j++) {
// buffer[j] = input[j].at(i);
// }
// buffer[buffer_size - 1] = from[interp_i];
// const double min = *std::min_element(buffer, buffer + buffer_size);
// const double max = *std::max_element(buffer, buffer + buffer_size);
// for (int j = 0; j < input.size(); j++) {
// buffer[j] = ((max - min) != 0 ? (buffer[j] - min) / (max - min) : 1);
// }
// from_rescaled =
// ((max - min) != 0 ? (from[interp_i] - min) / (max - min) : 0);
// double inv_sum = 0;
// // calculate distances for each point
// for (int i = 0; i < input.size(); i++) {
// const double distance = std::pow(buffer[i] - from_rescaled, 2);
// buffer[i] = distance > 0 ? (1 / std::sqrt(distance)) : 0;
// inv_sum += buffer[i];
// }
// // calculate new values
// double new_val = 0;
// for (int i = 0; i < output.size(); i++) {
// new_val += buffer[i] * output[i][interp_i];
// }
// results[interp_i] = new_val / inv_sum;
// if (std::isnan(results[interp_i])) {
// std::cout << "nan with new_val = " << output[0][i] << std::endl;
// }
// }
return results;
}
poet::ChemistryModule::ChemistryModule(uint32_t nxyz, uint32_t wp_size,
std::uint32_t maxiter,
const ChemistryParams &chem_param,
MPI_Comm communicator)
: PhreeqcRM(nxyz, 1), group_comm(communicator), wp_size(wp_size) {
: PhreeqcRM(nxyz, 1), group_comm(communicator), wp_size(wp_size),
params(chem_param) {
MPI_Comm_size(communicator, &this->comm_size);
MPI_Comm_rank(communicator, &this->comm_rank);
@ -24,7 +171,10 @@ poet::ChemistryModule::ChemistryModule(uint32_t nxyz, uint32_t wp_size,
if (!is_sequential && is_master) {
MPI_Bcast(&wp_size, 1, MPI_UINT32_T, 0, this->group_comm);
MPI_Bcast(&maxiter, 1, MPI_UINT32_T, 0, this->group_comm);
}
this->file_pad = std::ceil(std::log10(maxiter + 1));
}
poet::ChemistryModule::~ChemistryModule() {
@ -34,11 +184,15 @@ poet::ChemistryModule::~ChemistryModule() {
}
poet::ChemistryModule
poet::ChemistryModule::createWorker(MPI_Comm communicator) {
poet::ChemistryModule::createWorker(MPI_Comm communicator,
const ChemistryParams &chem_param) {
uint32_t wp_size;
MPI_Bcast(&wp_size, 1, MPI_UINT32_T, 0, communicator);
return ChemistryModule(wp_size, wp_size, communicator);
std::uint32_t maxiter;
MPI_Bcast(&maxiter, 1, MPI_UINT32_T, 0, communicator);
return ChemistryModule(wp_size, wp_size, maxiter, chem_param, communicator);
}
void poet::ChemistryModule::RunInitFile(const std::string &input_script_path) {
@ -122,7 +276,9 @@ void poet::ChemistryModule::initializeField(const Field &trans_field) {
}
// now sort the new values
std::sort(new_solution_names.begin() + 4, new_solution_names.end());
std::sort(new_solution_names.begin() + 3, new_solution_names.end());
this->SetPOETSolutionNames(new_solution_names);
this->speciesPerModule[0] = new_solution_names.size();
// and append other processes than solutions
std::vector<std::string> new_prop_names = new_solution_names;
@ -133,8 +289,6 @@ void poet::ChemistryModule::initializeField(const Field &trans_field) {
this->prop_names = std::move(new_prop_names);
this->prop_count = prop_names.size();
this->SetPOETSolutionNames(new_solution_names);
if (is_master) {
this->n_cells = trans_field.GetRequestedVecSize();
chem_field = Field(n_cells);
@ -151,162 +305,186 @@ void poet::ChemistryModule::initializeField(const Field &trans_field) {
std::vector<std::vector<double>> initial_values;
for (int i = 0; i < phreeqc_init.size(); i++) {
for (const auto &vec : trans_field.As2DVector()) {
initial_values.push_back(vec);
}
this->base_totals = {initial_values.at(0).at(0),
initial_values.at(1).at(0)};
ChemBCast(base_totals.data(), 2, MPI_DOUBLE);
for (int i = speciesPerModule[0]; i < phreeqc_init.size(); i++) {
std::vector<double> init(n_cells, phreeqc_init[i]);
initial_values.push_back(std::move(init));
}
chem_field.InitFromVec(initial_values, prop_names);
} else {
ChemBCast(base_totals.data(), 2, MPI_DOUBLE);
}
if (this->params.use_dht || this->params.use_interp) {
initializeDHT(this->params.dht_size, this->params.dht_signifs);
setDHTSnapshots(this->params.dht_snaps, this->params.dht_outdir);
setDHTReadFile(this->params.dht_file);
this->dht_enabled = this->params.use_dht;
if (this->params.use_interp) {
initializeInterp(this->params.pht_max_entries, this->params.pht_size,
this->params.interp_min_entries,
this->params.pht_signifs);
this->interp_enabled = this->params.use_interp;
}
}
}
void poet::ChemistryModule::SetDHTEnabled(
bool enable, uint32_t size_mb,
const std::vector<std::string> &key_species) {
void poet::ChemistryModule::initializeDHT(
uint32_t size_mb, const NamedVector<std::uint32_t> &key_species) {
constexpr uint32_t MB_FACTOR = 1E6;
std::vector<std::uint32_t> key_inidices;
this->dht_enabled = true;
MPI_Comm dht_comm;
if (this->is_master) {
int ftype = CHEM_DHT_ENABLE;
PropagateFunctionType(ftype);
ChemBCast(&enable, 1, MPI_CXX_BOOL);
ChemBCast(&size_mb, 1, MPI_UINT32_T);
key_inidices = parseDHTSpeciesVec(key_species);
int vec_size = key_inidices.size();
ChemBCast(&vec_size, 1, MPI_INT);
ChemBCast(key_inidices.data(), key_inidices.size(), MPI_UINT32_T);
} else {
int vec_size;
ChemBCast(&vec_size, 1, MPI_INT);
key_inidices.resize(vec_size);
ChemBCast(key_inidices.data(), vec_size, MPI_UINT32_T);
MPI_Comm_split(this->group_comm, MPI_UNDEFINED, this->comm_rank, &dht_comm);
return;
}
this->dht_enabled = enable;
if (enable) {
MPI_Comm dht_comm;
if (this->is_master) {
MPI_Comm_split(this->group_comm, MPI_UNDEFINED, this->comm_rank,
&dht_comm);
return;
}
if (!this->is_master) {
MPI_Comm_split(this->group_comm, 1, this->comm_rank, &dht_comm);
auto map_copy = key_species;
if (key_species.empty()) {
const auto &all_species = this->prop_names;
for (std::size_t i = 0; i < all_species.size(); i++) {
map_copy.insert(std::make_pair(all_species[i],
DHT_Wrapper::DHT_KEY_SIGNIF_DEFAULT));
}
}
auto key_indices = parseDHTSpeciesVec(key_species, this->prop_names);
if (this->dht) {
delete this->dht;
}
const uint32_t dht_size = size_mb * MB_FACTOR;
const std::uint64_t dht_size = size_mb * MB_FACTOR;
this->dht =
new DHT_Wrapper(dht_comm, dht_size, key_inidices, this->prop_count);
// this->dht->setBaseTotals(this->base_totals);
this->dht = new DHT_Wrapper(dht_comm, dht_size, map_copy, key_indices,
this->prop_count);
this->dht->setBaseTotals(base_totals.at(0), base_totals.at(1));
}
}
inline std::vector<std::uint32_t> poet::ChemistryModule::parseDHTSpeciesVec(
const std::vector<std::string> &species_vec) const {
std::vector<uint32_t> species_indices;
inline std::vector<std::int32_t> poet::ChemistryModule::parseDHTSpeciesVec(
const NamedVector<std::uint32_t> &key_species,
const std::vector<std::string> &to_compare) const {
std::vector<int32_t> species_indices;
species_indices.reserve(key_species.size());
if (species_vec.empty()) {
species_indices.resize(this->prop_count);
int i = 0;
std::generate(species_indices.begin(), species_indices.end(),
[&] { return i++; });
return species_indices;
}
species_indices.reserve(species_vec.size());
for (const auto &name : species_vec) {
auto it = std::find(this->prop_names.begin(), this->prop_names.end(), name);
if (it == prop_names.end()) {
throw std::runtime_error(
"DHT species name was not found in prop name vector!");
for (const auto &species : key_species.getNames()) {
auto it = std::find(to_compare.begin(), to_compare.end(), species);
if (it == to_compare.end()) {
species_indices.push_back(DHT_Wrapper::DHT_KEY_INPUT_CUSTOM);
continue;
}
const std::uint32_t index = it - prop_names.begin();
const std::uint32_t index = it - to_compare.begin();
species_indices.push_back(index);
}
return species_indices;
}
void poet::ChemistryModule::SetDHTSnaps(int type, const std::string &out_dir) {
void poet::ChemistryModule::BCastStringVec(std::vector<std::string> &io) {
if (this->is_master) {
int ftype = CHEM_DHT_SNAPS;
PropagateFunctionType(ftype);
int vec_size = io.size();
ChemBCast(&vec_size, 1, MPI_INT);
int str_size = out_dir.size();
ChemBCast(&type, 1, MPI_INT);
ChemBCast(&str_size, 1, MPI_INT);
ChemBCast(const_cast<char *>(out_dir.data()), str_size, MPI_CHAR);
}
this->dht_snaps_type = type;
this->dht_file_out_dir = out_dir;
}
void poet::ChemistryModule::SetDHTSignifVector(
std::vector<uint32_t> &signif_vec) {
if (this->is_master) {
int ftype = CHEM_DHT_SIGNIF_VEC;
PropagateFunctionType(ftype);
int data_count = signif_vec.size();
ChemBCast(&data_count, 1, MPI_INT);
ChemBCast(signif_vec.data(), signif_vec.size(), MPI_UINT32_T);
return;
}
int data_count;
ChemBCast(&data_count, 1, MPI_INT);
signif_vec.resize(data_count);
ChemBCast(signif_vec.data(), data_count, MPI_UINT32_T);
this->dht->SetSignifVector(signif_vec);
}
void poet::ChemistryModule::SetDHTPropTypeVector(
std::vector<uint32_t> proptype_vec) {
if (this->is_master) {
if (proptype_vec.size() != this->prop_count) {
throw std::runtime_error("Prop type vector sizes mismatches prop count.");
for (const auto &value : io) {
int buf_size = value.size() + 1;
ChemBCast(&buf_size, 1, MPI_INT);
ChemBCast(const_cast<char *>(value.c_str()), buf_size, MPI_CHAR);
}
} else {
int vec_size;
ChemBCast(&vec_size, 1, MPI_INT);
int ftype = CHEM_DHT_PROP_TYPE_VEC;
PropagateFunctionType(ftype);
ChemBCast(proptype_vec.data(), proptype_vec.size(), MPI_UINT32_T);
io.resize(vec_size);
for (int i = 0; i < vec_size; i++) {
int buf_size;
ChemBCast(&buf_size, 1, MPI_INT);
char buf[buf_size];
ChemBCast(buf, buf_size, MPI_CHAR);
io[i] = std::string{buf};
}
}
}
void poet::ChemistryModule::setDHTSnapshots(int type,
const std::string &out_dir) {
if (this->is_master) {
return;
}
this->dht->SetPropTypeVector(proptype_vec);
this->dht_file_out_dir = out_dir;
this->dht_snaps_type = type;
}
void poet::ChemistryModule::ReadDHTFile(const std::string &input_file) {
void poet::ChemistryModule::setDHTReadFile(const std::string &input_file) {
if (this->is_master) {
int ftype = CHEM_DHT_READ_FILE;
PropagateFunctionType(ftype);
int str_size = input_file.size();
ChemBCast(&str_size, 1, MPI_INT);
ChemBCast(const_cast<char *>(input_file.data()), str_size, MPI_CHAR);
return;
}
if (!this->dht_enabled) {
throw std::runtime_error("DHT file cannot be read. DHT is not enabled.");
if (!input_file.empty()) {
WorkerReadDHTDump(input_file);
}
}
void poet::ChemistryModule::initializeInterp(
std::uint32_t bucket_size, std::uint32_t size_mb, std::uint32_t min_entries,
const NamedVector<std::uint32_t> &key_species) {
if (!this->is_master) {
WorkerReadDHTDump(input_file);
constexpr uint32_t MB_FACTOR = 1E6;
assert(this->dht);
this->interp_enabled = true;
auto map_copy = key_species;
if (key_species.empty()) {
map_copy = this->dht->getKeySpecies();
for (std::size_t i = 0; i < map_copy.size(); i++) {
const std::uint32_t signif =
map_copy[i] - (map_copy[i] > InterpolationModule::COARSE_DIFF
? InterpolationModule::COARSE_DIFF
: 0);
map_copy[i] = signif;
}
}
auto key_indices =
parseDHTSpeciesVec(key_species, dht->getKeySpecies().getNames());
if (this->interp) {
this->interp.reset();
}
const uint64_t pht_size = size_mb * MB_FACTOR;
interp = std::make_unique<poet::InterpolationModule>(
bucket_size, pht_size, min_entries, *(this->dht), map_copy,
key_indices);
interp->setInterpolationFunction(inverseDistanceWeighting);
}
}

226
src/ChemistryModule/DHT_Wrapper.cpp
View File

@ -1,226 +0,0 @@
/*
** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
** Potsdam)
**
** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
**
** POET is free software; you can redistribute it and/or modify it under the
** terms of the GNU General Public License as published by the Free Software
** Foundation; either version 2 of the License, or (at your option) any later
** version.
**
** POET is distributed in the hope that it will be useful, but WITHOUT ANY
** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
**
** You should have received a copy of the GNU General Public License along with
** this program; if not, write to the Free Software Foundation, Inc., 51
** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include "poet/DHT_Wrapper.hpp"
#include "poet/DHT_Types.hpp"
#include "poet/HashFunctions.hpp"
#include <algorithm>
#include <cmath>
#include <cstddef>
#include <cstdint>
#include <cstring>
#include <iostream>
#include <math.h>
#include <stdexcept>
#include <vector>
using namespace poet;
using namespace std;
inline DHT_SCNotation round_key_element(double value, std::uint32_t signif) {
std::int8_t exp =
static_cast<std::int8_t>(std::floor(std::log10(std::fabs(value))));
std::int64_t significant =
static_cast<std::int64_t>(value * std::pow(10, signif - exp - 1));
DHT_SCNotation elem;
elem.exp = exp;
elem.significant = significant;
return elem;
}
DHT_Wrapper::DHT_Wrapper(MPI_Comm dht_comm, uint32_t dht_size,
const std::vector<std::uint32_t> &key_indices,
uint32_t data_count)
: key_count(key_indices.size()), data_count(data_count),
input_key_elements(key_indices) {
// initialize DHT object
uint32_t key_size = (key_count + 1) * sizeof(DHT_Keyelement);
uint32_t data_size = data_count * sizeof(double);
uint32_t buckets_per_process = dht_size / (1 + data_size + key_size);
dht_object = DHT_create(dht_comm, buckets_per_process, data_size, key_size,
&poet::Murmur2_64A);
this->dht_signif_vector.resize(key_size, DHT_KEY_SIGNIF_DEFAULT);
this->dht_signif_vector[0] = DHT_KEY_SIGNIF_TOTALS;
this->dht_signif_vector[1] = DHT_KEY_SIGNIF_TOTALS;
this->dht_signif_vector[2] = DHT_KEY_SIGNIF_CHARGE;
this->dht_prop_type_vector.resize(key_count, DHT_TYPE_DEFAULT);
this->dht_prop_type_vector[0] = DHT_TYPE_TOTAL;
this->dht_prop_type_vector[1] = DHT_TYPE_TOTAL;
this->dht_prop_type_vector[2] = DHT_TYPE_CHARGE;
}
DHT_Wrapper::~DHT_Wrapper() {
// free DHT
DHT_free(dht_object, NULL, NULL);
}
auto DHT_Wrapper::checkDHT(int length, double dt,
const std::vector<double> &work_package,
std::vector<std::uint32_t> &curr_mapping)
-> const poet::DHT_ResultObject & {
dht_results.length = length;
dht_results.keys.resize(length);
dht_results.results.resize(length);
dht_results.needPhreeqc.resize(length);
std::vector<std::uint32_t> new_mapping;
// loop over every grid cell contained in work package
for (int i = 0; i < length; i++) {
// point to current grid cell
void *key = (void *)&(work_package[i * this->data_count]);
auto &data = dht_results.results[i];
auto &key_vector = dht_results.keys[i];
data.resize(this->data_count);
key_vector = fuzzForDHT(this->key_count, key, dt);
// overwrite input with data from DHT, IF value is found in DHT
int res = DHT_read(this->dht_object, key_vector.data(), data.data());
switch (res) {
case DHT_SUCCESS:
dht_results.needPhreeqc[i] = false;
this->dht_hits++;
break;
case DHT_READ_MISS:
dht_results.needPhreeqc[i] = true;
new_mapping.push_back(curr_mapping[i]);
this->dht_miss++;
break;
}
}
curr_mapping = std::move(new_mapping);
return dht_results;
}
void DHT_Wrapper::fillDHT(int length, const std::vector<double> &work_package) {
// loop over every grid cell contained in work package
for (int i = 0; i < length; i++) {
// If true grid cell was simulated, needs to be inserted into dht
if (dht_results.needPhreeqc[i]) {
const auto &key = dht_results.keys[i];
void *data = (void *)&(work_package[i * this->data_count]);
// fuzz data (round, logarithm etc.)
// insert simulated data with fuzzed key into DHT
int res = DHT_write(this->dht_object, (void *)key.data(), data);
// if data was successfully written ...
if ((res != DHT_SUCCESS) && (res == DHT_WRITE_SUCCESS_WITH_EVICTION)) {
dht_evictions++;
}
}
}
}
void DHT_Wrapper::resultsToWP(std::vector<double> &work_package) {
for (int i = 0; i < dht_results.length; i++) {
if (!dht_results.needPhreeqc[i]) {
std::copy(dht_results.results[i].begin(), dht_results.results[i].end(),
work_package.begin() + (data_count * i));
}
}
}
int DHT_Wrapper::tableToFile(const char *filename) {
int res = DHT_to_file(dht_object, filename);
return res;
}
int DHT_Wrapper::fileToTable(const char *filename) {
int res = DHT_from_file(dht_object, filename);
if (res != DHT_SUCCESS)
return res;
#ifdef DHT_STATISTICS
DHT_print_statistics(dht_object);
#endif
return DHT_SUCCESS;
}
void DHT_Wrapper::printStatistics() {
int res;
res = DHT_print_statistics(dht_object);
if (res != DHT_SUCCESS) {
// MPI ERROR ... WHAT TO DO NOW?
// RUNNING CIRCLES WHILE SCREAMING
}
}
std::vector<DHT_Keyelement> DHT_Wrapper::fuzzForDHT(int var_count, void *key,
double dt) {
constexpr double zero_val = 10E-14;
std::vector<DHT_Keyelement> vecFuzz(var_count + 1);
std::memset(&vecFuzz[0], 0, sizeof(DHT_Keyelement) * var_count);
int totals_i = 0;
// introduce fuzzing to allow more hits in DHT
// loop over every variable of grid cell
for (std::uint32_t i = 0; i < input_key_elements.size(); i++) {
double curr_key = ((double *)key)[input_key_elements[i]];
if (curr_key != 0) {
if (curr_key < zero_val &&
this->dht_prop_type_vector[i] == DHT_TYPE_DEFAULT) {
continue;
}
if (this->dht_prop_type_vector[i] == DHT_TYPE_IGNORE) {
continue;
}
if (this->dht_prop_type_vector[i] == DHT_TYPE_TOTAL) {
curr_key -= base_totals[totals_i++];
}
vecFuzz[i].sc_notation = round_key_element(curr_key, dht_signif_vector[i]);
}
}
// if timestep differs over iterations set current current time step at the
// end of fuzzing buffer
vecFuzz[var_count].fp_elemet = dt;
return vecFuzz;
}
void poet::DHT_Wrapper::SetSignifVector(std::vector<uint32_t> signif_vec) {
if (signif_vec.size() != this->key_count) {
throw std::runtime_error(
"Significant vector size mismatches count of key elements.");
}
this->dht_signif_vector = signif_vec;
}
void poet::DHT_Wrapper::SetPropTypeVector(std::vector<uint32_t> prop_type_vec) {
if (prop_type_vec.size() != this->key_count) {
throw std::runtime_error(
"Prop type vector size mismatches count of key elements.");
}
this->dht_prop_type_vector = prop_type_vec;
}

153
src/ChemistryModule/MasterFunctions.cpp
View File

@ -2,6 +2,7 @@
#include "poet/ChemistryModule.hpp"
#include <algorithm>
#include <cstddef>
#include <cstdint>
#include <mpi.h>
#include <stdexcept>
@ -62,19 +63,136 @@ std::vector<double> poet::ChemistryModule::GetWorkerIdleTimings() const {
std::vector<uint32_t> poet::ChemistryModule::GetWorkerDHTHits() const {
int type = CHEM_PERF;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
return MasterGatherWorkerMetrics(WORKER_DHT_HITS);
}
std::vector<uint32_t> poet::ChemistryModule::GetWorkerDHTMiss() const {
int type = CHEM_PERF;
type = WORKER_DHT_HITS;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
return MasterGatherWorkerMetrics(WORKER_DHT_MISS);
MPI_Status probe;
MPI_Probe(MPI_ANY_SOURCE, WORKER_DHT_HITS, this->group_comm, &probe);
int count;
MPI_Get_count(&probe, MPI_UINT32_T, &count);
std::vector<uint32_t> ret(count);
MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, WORKER_DHT_HITS,
this->group_comm, NULL);
return ret;
}
std::vector<uint32_t> poet::ChemistryModule::GetWorkerDHTEvictions() const {
int type = CHEM_PERF;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
return MasterGatherWorkerMetrics(WORKER_DHT_EVICTIONS);
type = WORKER_DHT_EVICTIONS;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
MPI_Status probe;
MPI_Probe(MPI_ANY_SOURCE, WORKER_DHT_EVICTIONS, this->group_comm, &probe);
int count;
MPI_Get_count(&probe, MPI_UINT32_T, &count);
std::vector<uint32_t> ret(count);
MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, WORKER_DHT_EVICTIONS,
this->group_comm, NULL);
return ret;
}
std::vector<double>
poet::ChemistryModule::GetWorkerInterpolationWriteTimings() const {
int type = CHEM_PERF;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
return MasterGatherWorkerTimings(WORKER_IP_WRITE);
}
std::vector<double>
poet::ChemistryModule::GetWorkerInterpolationReadTimings() const {
int type = CHEM_PERF;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
return MasterGatherWorkerTimings(WORKER_IP_READ);
}
std::vector<double>
poet::ChemistryModule::GetWorkerInterpolationGatherTimings() const {
int type = CHEM_PERF;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
return MasterGatherWorkerTimings(WORKER_IP_GATHER);
}
std::vector<double>
poet::ChemistryModule::GetWorkerInterpolationFunctionCallTimings() const {
int type = CHEM_PERF;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
return MasterGatherWorkerTimings(WORKER_IP_FC);
}
std::vector<uint32_t>
poet::ChemistryModule::GetWorkerInterpolationCalls() const {
int type = CHEM_PERF;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
type = WORKER_IP_CALLS;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
MPI_Status probe;
MPI_Probe(MPI_ANY_SOURCE, WORKER_IP_CALLS, this->group_comm, &probe);
int count;
MPI_Get_count(&probe, MPI_UINT32_T, &count);
std::vector<uint32_t> ret(count);
MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, WORKER_IP_CALLS,
this->group_comm, NULL);
return ret;
}
std::vector<uint32_t> poet::ChemistryModule::GetWorkerPHTCacheHits() const {
int type = CHEM_PERF;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
type = WORKER_PHT_CACHE_HITS;
MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
MPI_Status probe;
MPI_Probe(MPI_ANY_SOURCE, type, this->group_comm, &probe);
int count;
MPI_Get_count(&probe, MPI_UINT32_T, &count);
std::vector<uint32_t> ret(count);
MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, type,
this->group_comm, NULL);
return ret;
}
inline std::vector<double> shuffleField(const std::vector<double> &in_field,
uint32_t size_per_prop,
uint32_t prop_count,
uint32_t wp_count) {
std::vector<double> out_buffer(in_field.size());
uint32_t write_i = 0;
for (uint32_t i = 0; i < wp_count; i++) {
for (uint32_t j = i; j < size_per_prop; j += wp_count) {
for (uint32_t k = 0; k < prop_count; k++) {
out_buffer[(write_i * prop_count) + k] =
in_field[(k * size_per_prop) + j];
}
write_i++;
}
}
return out_buffer;
}
inline void unshuffleField(const std::vector<double> &in_buffer,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count, std::vector<double> &out_field) {
uint32_t read_i = 0;
for (uint32_t i = 0; i < wp_count; i++) {
for (uint32_t j = i; j < size_per_prop; j += wp_count) {
for (uint32_t k = 0; k < prop_count; k++) {
out_field[(k * size_per_prop) + j] =
in_buffer[(read_i * prop_count) + k];
}
read_i++;
}
}
}
inline void printProgressbar(int count_pkgs, int n_wp, int barWidth = 70) {
@ -190,12 +308,15 @@ inline void poet::ChemistryModule::MasterRecvPkgs(worker_list_t &w_list,
}
void poet::ChemistryModule::RunCells() {
double start_t{MPI_Wtime()};
if (this->is_sequential) {
MasterRunSequential();
return;
}
MasterRunParallel();
double end_t{MPI_Wtime()};
this->chem_t += end_t - start_t;
}
void poet::ChemistryModule::MasterRunSequential() {
@ -211,7 +332,6 @@ void poet::ChemistryModule::MasterRunSequential() {
void poet::ChemistryModule::MasterRunParallel() {
/* declare most of the needed variables here */
double chem_a, chem_b;
double seq_a, seq_b, seq_c, seq_d;
double worker_chemistry_a, worker_chemistry_b;
double sim_e_chemistry, sim_f_chemistry;
@ -227,9 +347,6 @@ void poet::ChemistryModule::MasterRunParallel() {
double dt = this->PhreeqcRM::GetTimeStep();
static uint32_t iteration = 0;
/* start time measurement of whole chemistry simulation */
chem_a = MPI_Wtime();
/* start time measurement of sequential part */
seq_a = MPI_Wtime();
@ -308,8 +425,6 @@ void poet::ChemistryModule::MasterRunParallel() {
for (int i = 1; i < this->comm_size; i++) {
MPI_Send(NULL, 0, MPI_DOUBLE, i, LOOP_END, this->group_comm);
}
chem_b = MPI_Wtime();
this->chem_t += chem_b - chem_a;
this->simtime += dt;
iteration++;
@ -324,7 +439,8 @@ std::vector<uint32_t>
poet::ChemistryModule::CalculateWPSizesVector(uint32_t n_cells,
uint32_t wp_size) const {
bool mod_pkgs = (n_cells % wp_size) != 0;
uint32_t n_packages = (uint32_t)(n_cells / wp_size) + mod_pkgs;
uint32_t n_packages =
(uint32_t)(n_cells / wp_size) + static_cast<int>(mod_pkgs);
std::vector<uint32_t> wp_sizes_vector(n_packages, 0);
@ -334,12 +450,3 @@ poet::ChemistryModule::CalculateWPSizesVector(uint32_t n_cells,
return wp_sizes_vector;
}
void poet::ChemistryModule::setProgressBarPrintout(bool enabled) {
if (is_master) {
int type = CHEM_PROGRESSBAR;
ChemBCast(&type, 1, MPI_INT);
ChemBCast(&enabled, 1, MPI_CXX_BOOL);
}
this->print_progessbar = enabled;
}

21
src/ChemistryModule/SurrogateModels/CMakeLists.txt Normal file
View File

@ -0,0 +1,21 @@
file(GLOB surrogate_models_SRC
CONFIGURE_DEPENDS
"*.cpp" "*.c")
find_library(MATH_LIBRARY m)
add_library(surrogate_models ${surrogate_models_SRC})
target_include_directories(surrogate_models PUBLIC ${PROJECT_SOURCE_DIR}/include)
target_link_libraries(surrogate_models PUBLIC
MPI::MPI_CXX ${MATH_LIBRARY})
target_compile_definitions(surrogate_models PUBLIC OMPI_SKIP_MPICXX)
option(POET_PHT_ADDITIONAL_INFO "Enables additional information in the PHT" OFF)
if (POET_PHT_ADDITIONAL_INFO)
target_compile_definitions(surrogate_models PRIVATE POET_PHT_ADD)
endif()
if(POET_DHT_DEBUG)
target_compile_definitions(surrogate_models PRIVATE DHT_STATISTICS)
endif()

233
src/ChemistryModule/DHT.c → src/ChemistryModule/SurrogateModels/DHT.c
View File

@ -1,3 +1,4 @@
/// Time-stamp: "Last modified 2023-06-28 15:58:19 mluebke"
/*
** Copyright (C) 2017-2021 Max Luebke (University of Potsdam)
**
@ -15,10 +16,12 @@
** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include <mpi.h>
#include <poet/DHT.h>
#include <inttypes.h>
#include <math.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
@ -52,7 +55,8 @@ static int read_flag(char flag_byte) {
}
DHT *DHT_create(MPI_Comm comm, uint64_t size, unsigned int data_size,
unsigned int key_size, uint64_t (*hash_func)(int, const void *)) {
unsigned int key_size,
uint64_t (*hash_func)(int, const void *)) {
DHT *object;
MPI_Win window;
void *mem_alloc;
@ -61,17 +65,20 @@ DHT *DHT_create(MPI_Comm comm, uint64_t size, unsigned int data_size,
// calculate how much bytes for the index are needed to address count of
// buckets per process
index_bytes = (int)ceil(log2(size));
if (index_bytes % 8 != 0) index_bytes = index_bytes + (8 - (index_bytes % 8));
if (index_bytes % 8 != 0)
index_bytes = index_bytes + (8 - (index_bytes % 8));
// allocate memory for dht-object
object = (DHT *)malloc(sizeof(DHT));
if (object == NULL) return NULL;
if (object == NULL)
return NULL;
// every memory allocation has 1 additional byte for flags etc.
if (MPI_Alloc_mem(size * (1 + data_size + key_size), MPI_INFO_NULL,
&mem_alloc) != 0)
return NULL;
if (MPI_Comm_size(comm, &comm_size) != 0) return NULL;
if (MPI_Comm_size(comm, &comm_size) != 0)
return NULL;
// since MPI_Alloc_mem doesn't provide memory allocation with the memory set
// to zero, we're doing this here
@ -104,7 +111,8 @@ DHT *DHT_create(MPI_Comm comm, uint64_t size, unsigned int data_size,
DHT_stats *stats;
stats = (DHT_stats *)malloc(sizeof(DHT_stats));
if (stats == NULL) return NULL;
if (stats == NULL)
return NULL;
object->stats = stats;
object->stats->writes_local = (int *)calloc(comm_size, sizeof(int));
@ -118,7 +126,106 @@ DHT *DHT_create(MPI_Comm comm, uint64_t size, unsigned int data_size,
return object;
}
int DHT_write(DHT *table, void *send_key, void *send_data) {
void DHT_set_accumulate_callback(DHT *table,
int (*callback_func)(int, void *, int,
void *)) {
table->accumulate_callback = callback_func;
}
int DHT_write_accumulate(DHT *table, const void *send_key, int data_size,
void *send_data, uint32_t *proc, uint32_t *index,
int *callback_ret) {
unsigned int dest_rank, i;
int result = DHT_SUCCESS;
#ifdef DHT_STATISTICS
table->stats->w_access++;
#endif
// determine destination rank and index by hash of key
determine_dest(table->hash_func(table->key_size, send_key), table->comm_size,
table->table_size, &dest_rank, table->index,
table->index_count);
// concatenating key with data to write entry to DHT
set_flag((char *)table->send_entry);
memcpy((char *)table->send_entry + 1, (char *)send_key, table->key_size);
/* memcpy((char *)table->send_entry + table->key_size + 1, (char *)send_data,
*/
/* table->data_size); */
// locking window of target rank with exclusive lock
if (MPI_Win_lock(MPI_LOCK_EXCLUSIVE, dest_rank, 0, table->window) != 0)
return DHT_MPI_ERROR;
for (i = 0; i < table->index_count; i++) {
if (MPI_Get(table->recv_entry, 1 + table->data_size + table->key_size,
MPI_BYTE, dest_rank, table->index[i],
1 + table->data_size + table->key_size, MPI_BYTE,
table->window) != 0)
return DHT_MPI_ERROR;
if (MPI_Win_flush(dest_rank, table->window) != 0)
return DHT_MPI_ERROR;
// increment eviction counter if receiving key doesn't match sending key
// entry has write flag and last index is reached.
if (read_flag(*(char *)table->recv_entry)) {
if (memcmp(send_key, (char *)table->recv_entry + 1, table->key_size) !=
0) {
if (i == (table->index_count) - 1) {
table->evictions += 1;
#ifdef DHT_STATISTICS
table->stats->evictions += 1;
#endif
result = DHT_WRITE_SUCCESS_WITH_EVICTION;
break;
}
} else
break;
} else {
#ifdef DHT_STATISTICS
table->stats->writes_local[dest_rank]++;
#endif
break;
}
}
if (result == DHT_WRITE_SUCCESS_WITH_EVICTION) {
memset((char *)table->send_entry + 1 + table->key_size, '\0',
table->data_size);
} else {
memcpy((char *)table->send_entry + 1 + table->key_size,
(char *)table->recv_entry + 1 + table->key_size, table->data_size);
}
*callback_ret = table->accumulate_callback(
data_size, (char *)send_data, table->data_size,
(char *)table->send_entry + 1 + table->key_size);
// put data to DHT (with last selected index by value i)
if (*callback_ret == 0) {
if (MPI_Put(table->send_entry, 1 + table->data_size + table->key_size,
MPI_BYTE, dest_rank, table->index[i],
1 + table->data_size + table->key_size, MPI_BYTE,
table->window) != 0)
return DHT_MPI_ERROR;
}
// unlock window of target rank
if (MPI_Win_unlock(dest_rank, table->window) != 0)
return DHT_MPI_ERROR;
if (proc) {
*proc = dest_rank;
}
if (index) {
*index = table->index[i];
}
return result;
}
int DHT_write(DHT *table, void *send_key, void *send_data, uint32_t *proc,
uint32_t *index) {
unsigned int dest_rank, i;
int result = DHT_SUCCESS;
@ -146,7 +253,8 @@ int DHT_write(DHT *table, void *send_key, void *send_data) {
1 + table->data_size + table->key_size, MPI_BYTE,
table->window) != 0)
return DHT_MPI_ERROR;
if (MPI_Win_flush(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
if (MPI_Win_flush(dest_rank, table->window) != 0)
return DHT_MPI_ERROR;
// increment eviction counter if receiving key doesn't match sending key
// entry has write flag and last index is reached.
@ -178,12 +286,21 @@ int DHT_write(DHT *table, void *send_key, void *send_data) {
table->window) != 0)
return DHT_MPI_ERROR;
// unlock window of target rank
if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
if (MPI_Win_unlock(dest_rank, table->window) != 0)
return DHT_MPI_ERROR;
if (proc) {
*proc = dest_rank;
}
if (index) {
*index = table->index[i];
}
return result;
}
int DHT_read(DHT *table, void *send_key, void *destination) {
int DHT_read(DHT *table, const void *send_key, void *destination) {
unsigned int dest_rank, i;
#ifdef DHT_STATISTICS
@ -205,7 +322,8 @@ int DHT_read(DHT *table, void *send_key, void *destination) {
1 + table->data_size + table->key_size, MPI_BYTE,
table->window) != 0)
return DHT_MPI_ERROR;
if (MPI_Win_flush(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
if (MPI_Win_flush(dest_rank, table->window) != 0)
return DHT_MPI_ERROR;
// increment read error counter if write flag isn't set ...
if ((read_flag(*(char *)table->recv_entry)) == 0) {
@ -214,7 +332,8 @@ int DHT_read(DHT *table, void *send_key, void *destination) {
table->stats->read_misses += 1;
#endif
// unlock window and return
if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
if (MPI_Win_unlock(dest_rank, table->window) != 0)
return DHT_MPI_ERROR;
return DHT_READ_MISS;
}
@ -227,7 +346,8 @@ int DHT_read(DHT *table, void *send_key, void *destination) {
table->stats->read_misses += 1;
#endif
// unlock window an return
if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
if (MPI_Win_unlock(dest_rank, table->window) != 0)
return DHT_MPI_ERROR;
return DHT_READ_MISS;
}
} else
@ -235,7 +355,8 @@ int DHT_read(DHT *table, void *send_key, void *destination) {
}
// unlock window of target rank
if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
if (MPI_Win_unlock(dest_rank, table->window) != 0)
return DHT_MPI_ERROR;
// if matching key was found copy data into memory of passed pointer
memcpy((char *)destination, (char *)table->recv_entry + table->key_size + 1,
@ -244,6 +365,34 @@ int DHT_read(DHT *table, void *send_key, void *destination) {
return DHT_SUCCESS;
}
int DHT_read_location(DHT *table, uint32_t proc, uint32_t index,
void *destination) {
const uint32_t bucket_size = table->data_size + table->key_size + 1;
#ifdef DHT_STATISTICS
table->stats->r_access++;
#endif
// locking window of target rank with shared lock
if (MPI_Win_lock(MPI_LOCK_SHARED, proc, 0, table->window) != 0)
return DHT_MPI_ERROR;
// receive data
if (MPI_Get(table->recv_entry, bucket_size, MPI_BYTE, proc, index,
bucket_size, MPI_BYTE, table->window) != 0) {
return DHT_MPI_ERROR;
}
// unlock window of target rank
if (MPI_Win_unlock(proc, table->window) != 0)
return DHT_MPI_ERROR;
// if matching key was found copy data into memory of passed pointer
memcpy((char *)destination, (char *)table->recv_entry + 1 + table->key_size,
table->data_size);
return DHT_SUCCESS;
}
int DHT_to_file(DHT *table, const char *filename) {
// open file
MPI_File file;
@ -257,17 +406,15 @@ int DHT_to_file(DHT *table, const char *filename) {
// write header (key_size and data_size)
if (rank == 0) {
if (MPI_File_write(file, &table->key_size, 1, MPI_INT, MPI_STATUS_IGNORE) !=
0)
if (MPI_File_write_shared(file, &table->key_size, 1, MPI_INT,
MPI_STATUS_IGNORE) != 0)
return DHT_FILE_WRITE_ERROR;
if (MPI_File_write(file, &table->data_size, 1, MPI_INT,
MPI_STATUS_IGNORE) != 0)
if (MPI_File_write_shared(file, &table->data_size, 1, MPI_INT,
MPI_STATUS_IGNORE) != 0)
return DHT_FILE_WRITE_ERROR;
}
// seek file pointer behind header for all processes
if (MPI_File_seek_shared(file, DHT_FILEHEADER_SIZE, MPI_SEEK_SET) != 0)
return DHT_FILE_IO_ERROR;
MPI_Barrier(table->communicator);
char *ptr;
int bucket_size = table->key_size + table->data_size + 1;
@ -283,8 +430,12 @@ int DHT_to_file(DHT *table, const char *filename) {
return DHT_FILE_WRITE_ERROR;
}
}
MPI_Barrier(table->communicator);
// close file
if (MPI_File_close(&file) != 0) return DHT_FILE_IO_ERROR;
if (MPI_File_close(&file) != 0)
return DHT_FILE_IO_ERROR;
return DHT_SUCCESS;
}
@ -303,7 +454,8 @@ int DHT_from_file(DHT *table, const char *filename) {
return DHT_FILE_IO_ERROR;
// get file size
if (MPI_File_get_size(file, &f_size) != 0) return DHT_FILE_IO_ERROR;
if (MPI_File_get_size(file, &f_size) != 0)
return DHT_FILE_IO_ERROR;
MPI_Comm_rank(table->communicator, &rank);
@ -322,8 +474,10 @@ int DHT_from_file(DHT *table, const char *filename) {
return DHT_FILE_READ_ERROR;
// compare if written header data and key size matches current sizes
if (*(int *)buffer != table->key_size) return DHT_WRONG_FILE;
if (*(int *)(buffer + 4) != table->data_size) return DHT_WRONG_FILE;
if (*(int *)buffer != table->key_size)
return DHT_WRONG_FILE;
if (*(int *)(buffer + 4) != table->data_size)
return DHT_WRONG_FILE;
// set offset for each process
offset = bucket_size * table->comm_size;
@ -348,14 +502,16 @@ int DHT_from_file(DHT *table, const char *filename) {
// extract key and data and write to DHT
key = buffer;
data = (buffer + table->key_size);
if (DHT_write(table, key, data) == DHT_MPI_ERROR) return DHT_MPI_ERROR;
if (DHT_write(table, key, data, NULL, NULL) == DHT_MPI_ERROR)
return DHT_MPI_ERROR;
// increment current position
cur_pos += offset;
}
free(buffer);
if (MPI_File_close(&file) != 0) return DHT_FILE_IO_ERROR;
if (MPI_File_close(&file) != 0)
return DHT_FILE_IO_ERROR;
return DHT_SUCCESS;
}
@ -377,8 +533,10 @@ int DHT_free(DHT *table, int *eviction_counter, int *readerror_counter) {
return DHT_MPI_ERROR;
*readerror_counter = buf;
}
if (MPI_Win_free(&(table->window)) != 0) return DHT_MPI_ERROR;
if (MPI_Free_mem(table->mem_alloc) != 0) return DHT_MPI_ERROR;
if (MPI_Win_free(&(table->window)) != 0)
return DHT_MPI_ERROR;
if (MPI_Free_mem(table->mem_alloc) != 0)
return DHT_MPI_ERROR;
free(table->recv_entry);
free(table->send_entry);
free(table->index);
@ -407,7 +565,8 @@ int DHT_print_statistics(DHT *table) {
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
// obtaining all values from all processes in the communicator
if (rank == 0) read_misses = (int *)malloc(table->comm_size * sizeof(int));
if (rank == 0)
read_misses = (int *)malloc(table->comm_size * sizeof(int));
if (MPI_Gather(&table->stats->read_misses, 1, MPI_INT, read_misses, 1,
MPI_INT, 0, table->communicator) != 0)
return DHT_MPI_ERROR;
@ -416,7 +575,8 @@ int DHT_print_statistics(DHT *table) {
return DHT_MPI_ERROR;
table->stats->read_misses = 0;
if (rank == 0) evictions = (int *)malloc(table->comm_size * sizeof(int));
if (rank == 0)
evictions = (int *)malloc(table->comm_size * sizeof(int));
if (MPI_Gather(&table->stats->evictions, 1, MPI_INT, evictions, 1, MPI_INT, 0,
table->communicator) != 0)
return DHT_MPI_ERROR;
@ -425,7 +585,8 @@ int DHT_print_statistics(DHT *table) {
return DHT_MPI_ERROR;
table->stats->evictions = 0;
if (rank == 0) w_access = (int *)malloc(table->comm_size * sizeof(int));
if (rank == 0)
w_access = (int *)malloc(table->comm_size * sizeof(int));
if (MPI_Gather(&table->stats->w_access, 1, MPI_INT, w_access, 1, MPI_INT, 0,
table->communicator) != 0)
return DHT_MPI_ERROR;
@ -434,7 +595,8 @@ int DHT_print_statistics(DHT *table) {
return DHT_MPI_ERROR;
table->stats->w_access = 0;
if (rank == 0) r_access = (int *)malloc(table->comm_size * sizeof(int));
if (rank == 0)
r_access = (int *)malloc(table->comm_size * sizeof(int));
if (MPI_Gather(&table->stats->r_access, 1, MPI_INT, r_access, 1, MPI_INT, 0,
table->communicator) != 0)
return DHT_MPI_ERROR;
@ -443,13 +605,14 @@ int DHT_print_statistics(DHT *table) {
return DHT_MPI_ERROR;
table->stats->r_access = 0;
if (rank == 0) written_buckets = (int *)calloc(table->comm_size, sizeof(int));
if (rank == 0)
written_buckets = (int *)calloc(table->comm_size, sizeof(int));
if (MPI_Reduce(table->stats->writes_local, written_buckets, table->comm_size,
MPI_INT, MPI_SUM, 0, table->communicator) != 0)
return DHT_MPI_ERROR;
if (rank == 0) { // only process with rank 0 will print out results as a
// table
if (rank == 0) { // only process with rank 0 will print out results as a
// table
int sum_written_buckets = 0;
for (int i = 0; i < table->comm_size; i++) {

300
src/ChemistryModule/SurrogateModels/DHT_Wrapper.cpp Normal file
View File

@ -0,0 +1,300 @@
// Time-stamp: "Last modified 2023-08-01 13:41:57 mluebke"
/*
** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
** Potsdam)
**
** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
**
** POET is free software; you can redistribute it and/or modify it under the
** terms of the GNU General Public License as published by the Free Software
** Foundation; either version 2 of the License, or (at your option) any later
** version.
**
** POET is distributed in the hope that it will be useful, but WITHOUT ANY
** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
**
** You should have received a copy of the GNU General Public License along with
** this program; if not, write to the Free Software Foundation, Inc., 51
** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include "poet/DHT_Wrapper.hpp"
#include "poet/DHT_Types.hpp"
#include "poet/HashFunctions.hpp"
#include "poet/Interpolation.hpp"
#include "poet/LookupKey.hpp"
#include "poet/Rounding.hpp"
#include <algorithm>
#include <cmath>
#include <cstddef>
#include <cstdint>
#include <cstring>
#include <iostream>
#include <stdexcept>
#include <vector>
using namespace std;
namespace poet {
DHT_Wrapper::DHT_Wrapper(MPI_Comm dht_comm, std::uint64_t dht_size,
const NamedVector<std::uint32_t> &key_species,
const std::vector<std::int32_t> &key_indices,
uint32_t data_count)
: key_count(key_indices.size()), data_count(data_count),
input_key_elements(key_indices), communicator(dht_comm),
key_species(key_species) {
// initialize DHT object
// key size = count of key elements + timestep
uint32_t key_size = (key_count + 1) * sizeof(Lookup_Keyelement);
uint32_t data_size =
(data_count + input_key_elements.size()) * sizeof(double);
uint32_t buckets_per_process =
static_cast<std::uint32_t>(dht_size / (data_size + key_size));
dht_object = DHT_create(dht_comm, buckets_per_process, data_size, key_size,
&poet::Murmur2_64A);
dht_signif_vector = key_species.getValues();
// this->dht_signif_vector.resize(key_size, DHT_KEY_SIGNIF_DEFAULT);
this->dht_prop_type_vector.resize(key_count, DHT_TYPE_DEFAULT);
const auto key_names = key_species.getNames();
auto tot_h = std::find(key_names.begin(), key_names.end(), "H");
if (tot_h != key_names.end()) {
this->dht_prop_type_vector[tot_h - key_names.begin()] = DHT_TYPE_TOTAL;
}
auto tot_o = std::find(key_names.begin(), key_names.end(), "O");
if (tot_o != key_names.end()) {
this->dht_prop_type_vector[tot_o - key_names.begin()] = DHT_TYPE_TOTAL;
}
auto charge = std::find(key_names.begin(), key_names.end(), "Charge");
if (charge != key_names.end()) {
this->dht_prop_type_vector[charge - key_names.begin()] = DHT_TYPE_CHARGE;
}
}
DHT_Wrapper::~DHT_Wrapper() {
// free DHT
DHT_free(dht_object, NULL, NULL);
}
auto DHT_Wrapper::checkDHT(int length, double dt,
const std::vector<double> &work_package,
std::vector<std::uint32_t> &curr_mapping)
-> const DHT_ResultObject & {
dht_results.length = length;
dht_results.keys.resize(length);
dht_results.results.resize(length);
dht_results.needPhreeqc.resize(length);
std::vector<double> bucket_writer(this->data_count +
input_key_elements.size());
std::vector<std::uint32_t> new_mapping;
// loop over every grid cell contained in work package
for (int i = 0; i < length; i++) {
// point to current grid cell
void *key = (void *)&(work_package[i * this->data_count]);
auto &data = dht_results.results[i];
auto &key_vector = dht_results.keys[i];
// data.resize(this->data_count);
key_vector = fuzzForDHT(this->key_count, key, dt);
// overwrite input with data from DHT, IF value is found in DHT
int res =
DHT_read(this->dht_object, key_vector.data(), bucket_writer.data());
switch (res) {
case DHT_SUCCESS:
dht_results.results[i] = inputAndRatesToOutput(bucket_writer);
dht_results.needPhreeqc[i] = false;
this->dht_hits++;
break;
case DHT_READ_MISS:
dht_results.needPhreeqc[i] = true;
new_mapping.push_back(curr_mapping[i]);
dht_results.results[i] = std::vector<double>{
&work_package[i * this->data_count],
&work_package[i * this->data_count] + this->data_count};
// HACK: apply normalization to total H and O in results field of DHT
// dht_results.results[i][0] -= base_totals[0];
// dht_results.results[i][1] -= base_totals[1];
break;
}
}
curr_mapping = std::move(new_mapping);
dht_results.old_values = work_package;
return dht_results;
}
void DHT_Wrapper::fillDHT(int length, const std::vector<double> &work_package) {
// loop over every grid cell contained in work package
dht_results.locations.resize(length);
for (int i = 0; i < length; i++) {
// If true grid cell was simulated, needs to be inserted into dht
if (dht_results.needPhreeqc[i]) {
// check if calcite or dolomite is absent and present, resp.n and vice
// versa in input/output. If this is the case -> Do not write to DHT!
// HACK: hardcoded, should be fixed!
if ((dht_results.old_values[i * this->data_count + 7] == 0) !=
(work_package[i * this->data_count + 7] == 0)) {
dht_results.needPhreeqc[i] = false;
continue;
}
if ((dht_results.old_values[i * this->data_count + 9] == 0) !=
(work_package[i * this->data_count + 9] == 0)) {
dht_results.needPhreeqc[i] = false;
continue;
}
uint32_t proc, index;
const auto &key = dht_results.keys[i];
const auto curr_old_data = std::vector<double>(
dht_results.old_values.begin() + (i * this->data_count),
dht_results.old_values.begin() + ((i + 1) * this->data_count));
const auto curr_new_data = std::vector<double>(
work_package.begin() + (i * this->data_count),
work_package.begin() + ((i + 1) * this->data_count));
const auto data = outputToInputAndRates(curr_old_data, curr_new_data);
// void *data = (void *)&(work_package[i * this->data_count]);
// fuzz data (round, logarithm etc.)
// insert simulated data with fuzzed key into DHT
int res = DHT_write(this->dht_object, (void *)(key.data()),
const_cast<double *>(data.data()), &proc, &index);
dht_results.locations[i] = {proc, index};
// if data was successfully written ...
if ((res != DHT_SUCCESS) && (res == DHT_WRITE_SUCCESS_WITH_EVICTION)) {
dht_evictions++;
}
}
}
}
std::vector<double>
DHT_Wrapper::outputToInputAndRates(const std::vector<double> &old_results,
const std::vector<double> &new_results) {
const int prefix_size = this->input_key_elements.size();
std::vector<double> output(prefix_size + this->data_count);
std::copy(new_results.begin(), new_results.end(),
output.begin() + prefix_size);
for (int i = 0; i < prefix_size; i++) {
const int data_elem_i = input_key_elements[i];
output[i] = old_results[data_elem_i];
output[prefix_size + data_elem_i] -= old_results[data_elem_i];
}
return output;
}
std::vector<double>
DHT_Wrapper::inputAndRatesToOutput(const std::vector<double> &dht_data) {
const int prefix_size = this->input_key_elements.size();
std::vector<double> output{dht_data.begin() + prefix_size, dht_data.end()};
for (int i = 0; i < prefix_size; i++) {
const int data_elem_i = input_key_elements[i];
output[data_elem_i] += dht_data[i];
}
return output;
}
void DHT_Wrapper::resultsToWP(std::vector<double> &work_package) {
for (int i = 0; i < dht_results.length; i++) {
if (!dht_results.needPhreeqc[i]) {
std::copy(dht_results.results[i].begin(), dht_results.results[i].end(),
work_package.begin() + (data_count * i));
}
}
}
int DHT_Wrapper::tableToFile(const char *filename) {
int res = DHT_to_file(dht_object, filename);
return res;
}
int DHT_Wrapper::fileToTable(const char *filename) {
int res = DHT_from_file(dht_object, filename);
if (res != DHT_SUCCESS)
return res;
#ifdef DHT_STATISTICS
DHT_print_statistics(dht_object);
#endif
return DHT_SUCCESS;
}
void DHT_Wrapper::printStatistics() {
int res;
res = DHT_print_statistics(dht_object);
if (res != DHT_SUCCESS) {
// MPI ERROR ... WHAT TO DO NOW?
// RUNNING CIRCLES WHILE SCREAMING
}
}
LookupKey DHT_Wrapper::fuzzForDHT(int var_count, void *key, double dt) {
const auto c_zero_val = std::pow(10, AQUEOUS_EXP);
const Lookup_Keyelement dummy = {.0};
LookupKey vecFuzz(var_count + 1, dummy);
DHT_Rounder rounder;
int totals_i = 0;
// introduce fuzzing to allow more hits in DHT
// loop over every variable of grid cell
for (std::uint32_t i = 0; i < input_key_elements.size(); i++) {
if (input_key_elements[i] == DHT_KEY_INPUT_CUSTOM) {
continue;
}
double curr_key = ((double *)key)[input_key_elements[i]];
if (curr_key != 0) {
if (curr_key < c_zero_val &&
this->dht_prop_type_vector[i] == DHT_TYPE_DEFAULT) {
continue;
}
if (this->dht_prop_type_vector[i] == DHT_TYPE_TOTAL) {
curr_key -= base_totals[totals_i++];
}
vecFuzz[i] =
rounder.round(curr_key, dht_signif_vector[i],
this->dht_prop_type_vector[i] == DHT_TYPE_TOTAL);
}
}
// add timestep to the end of the key as double value
vecFuzz[var_count].fp_element = dt;
return vecFuzz;
}
void poet::DHT_Wrapper::SetSignifVector(std::vector<uint32_t> signif_vec) {
if (signif_vec.size() != this->key_count) {
throw std::runtime_error(
"Significant vector size mismatches count of key elements.");
}
this->dht_signif_vector = signif_vec;
}
} // namespace poet

2
src/ChemistryModule/HashFunctions.cpp → src/ChemistryModule/SurrogateModels/HashFunctions.cpp
View File

@ -1,4 +1,4 @@
// Time-stamp: "Last modified 2023-04-24 16:56:18 mluebke"
// Time-stamp: "Last modified 2023-04-24 23:20:55 mluebke"
/*
**-----------------------------------------------------------------------------
** MurmurHash2 was written by Austin Appleby, and is placed in the public

197
src/ChemistryModule/SurrogateModels/InterpolationModule.cpp Normal file
View File

@ -0,0 +1,197 @@
// Time-stamp: "Last modified 2023-08-01 17:54:53 mluebke"
#include "poet/DHT_Wrapper.hpp"
#include "poet/HashFunctions.hpp"
#include "poet/Interpolation.hpp"
#include "poet/LookupKey.hpp"
#include "poet/Rounding.hpp"
#include <algorithm>
#include <array>
#include <cassert>
#include <cstddef>
#include <cstdint>
#include <functional>
#include <iterator>
#include <memory>
#include <mpi.h>
#include <string>
#include <utility>
#include <vector>
extern "C" {
#include "poet/DHT.h"
}
namespace poet {
InterpolationModule::InterpolationModule(
std::uint32_t entries_per_bucket, std::uint64_t size_per_process,
std::uint32_t min_entries_needed, DHT_Wrapper &dht,
const NamedVector<std::uint32_t> &interp_key_signifs,
const std::vector<std::int32_t> &dht_key_indices)
: dht_instance(dht), key_signifs(interp_key_signifs),
key_indices(dht_key_indices), min_entries_needed(min_entries_needed) {
initPHT(this->key_signifs.size(), entries_per_bucket, size_per_process,
dht.getCommunicator());
pht->setSourceDHT(dht.getDHT());
}
void InterpolationModule::initPHT(std::uint32_t key_count,
std::uint32_t entries_per_bucket,
std::uint32_t size_per_process,
MPI_Comm communicator) {
uint32_t key_size = key_count * sizeof(Lookup_Keyelement) + sizeof(double);
uint32_t data_size = sizeof(DHT_Location);
pht = std::make_unique<ProximityHashTable>(
key_size, data_size, entries_per_bucket, size_per_process, communicator);
}
void InterpolationModule::writePairs(const DHT_Wrapper::DHT_ResultObject &in) {
for (int i = 0; i < in.length; i++) {
if (in.needPhreeqc[i]) {
const auto coarse_key = roundKey(in.keys[i]);
pht->writeLocationToPHT(coarse_key, in.locations[i]);
}
}
}
void InterpolationModule::tryInterpolation(
DHT_Wrapper::DHT_ResultObject &dht_results,
std::vector<std::uint32_t> &curr_mapping) {
interp_result.status.resize(dht_results.length, NOT_NEEDED);
interp_result.results.resize(dht_results.length, {});
for (int i = 0; i < dht_results.length; i++) {
if (!dht_results.needPhreeqc[i]) {
interp_result.status[i] = NOT_NEEDED;
continue;
}
auto pht_result =
pht->query(roundKey(dht_results.keys[i]), this->key_signifs.getValues(),
this->min_entries_needed, dht_instance.getInputCount(),
dht_instance.getOutputCount());
int pht_i = 0;
while (pht_i < pht_result.size) {
if (pht_result.size < this->min_entries_needed) {
break;
}
auto in_it = pht_result.in_values.begin() + pht_i;
auto out_it = pht_result.out_values.begin() + pht_i;
bool same_sig_calcite = (pht_result.in_values[pht_i][7] == 0) ==
(dht_results.results[i][7] == 0);
bool same_sig_dolomite = (pht_result.in_values[pht_i][8] == 0) ==
(dht_results.results[i][9] == 0);
if (!same_sig_calcite || !same_sig_dolomite) {
pht_result.size -= 1;
pht_result.in_values.erase(in_it);
pht_result.out_values.erase(out_it);
continue;
}
pht_i += 1;
}
if (pht_result.size < this->min_entries_needed) {
interp_result.status[i] = INSUFFICIENT_DATA;
continue;
}
#ifdef POET_PHT_ADD
this->pht->incrementReadCounter(roundKey(dht_results.keys[i]));
#endif
double start_fc = MPI_Wtime();
// mean water
// double mean_water = 0;
// for (int out_i = 0; out_i < pht_result.size; out_i++) {
// mean_water += pht_result.out_values[out_i][0];
// }
// mean_water /= pht_result.size;
auto calcMassBalance = [](const std::vector<double> &input) {
double C, Ca, Mg;
C = input[3] + input[7] + 2 * input[9];
Ca = input[4] + input[7] + input[9];
Mg = input[6] + input[9];
return std::array<double, 3>{C, Ca, Mg};
};
auto mass_in = calcMassBalance(dht_results.results[i]);
const auto DHT_inputElements = dht_instance.getKeyElements();
// HACK: transform input elements to uint, as there shall no any user
// defined key species present yet
// std::vector<std::uint32_t> interp_inputElements;
// std::transform(DHT_inputElements.begin(), DHT_inputElements.end(),
// interp_inputElements.begin(), [](std::int32_t x) {
// if (x < 0) {
// x = 0;
// }
// return x;
// });
interp_result.results[i] =
f_interpolate(dht_instance.getKeyElements(), dht_results.results[i],
pht_result.in_values, pht_result.out_values);
auto mass_out = calcMassBalance(interp_result.results[i]);
double diff[3];
std::transform(mass_in.begin(), mass_in.end(), mass_out.begin(), diff,
std::minus<>());
bool exceeding = false;
for (const auto comp : diff) {
if (std::abs(comp) > 1e-10) {
exceeding = true;
break;
}
}
if (exceeding) {
interp_result.status[i] = INSUFFICIENT_DATA;
continue;
}
if (interp_result.results[i][7] < 0 || interp_result.results[i][9] < 0) {
interp_result.status[i] = INSUFFICIENT_DATA;
continue;
}
// interp_result.results[i][0] = mean_water;
this->interp_t += MPI_Wtime() - start_fc;
this->interpolations++;
curr_mapping.erase(std::remove(curr_mapping.begin(), curr_mapping.end(), i),
curr_mapping.end());
dht_results.needPhreeqc[i] = false;
interp_result.status[i] = RES_OK;
}
}
void InterpolationModule::resultsToWP(std::vector<double> &work_package) const {
for (uint32_t i = 0; i < interp_result.status.size(); i++) {
if (interp_result.status[i] == RES_OK) {
const std::size_t length =
interp_result.results[i].end() - interp_result.results[i].begin();
std::copy(interp_result.results[i].begin(),
interp_result.results[i].end(),
work_package.begin() + (length * i));
}
}
}
} // namespace poet

275
src/ChemistryModule/SurrogateModels/ProximityHashTable.cpp Normal file
View File

@ -0,0 +1,275 @@
// Time-stamp: "Last modified 2023-08-01 17:11:42 mluebke"
#include "poet/DHT_Wrapper.hpp"
#include "poet/HashFunctions.hpp"
#include "poet/Interpolation.hpp"
#include "poet/LookupKey.hpp"
#include "poet/Rounding.hpp"
#include <cassert>
#include <cstddef>
#include <cstdint>
#include <iostream>
#include <memory>
#include <unordered_set>
#include <vector>
extern "C" {
#include "poet/DHT.h"
}
namespace poet {
ProximityHashTable::ProximityHashTable(uint32_t key_size, uint32_t data_size,
uint32_t entry_count,
uint32_t size_per_process,
MPI_Comm communicator_)
: communicator(communicator_) {
data_size *= entry_count;
data_size += sizeof(bucket_indicator);
#ifdef POET_PHT_ADD
data_size += sizeof(std::uint64_t);
#endif
bucket_store = new char[data_size];
uint32_t buckets_per_process =
static_cast<std::uint32_t>(size_per_process / (data_size + key_size));
this->prox_ht = DHT_create(communicator, buckets_per_process, data_size,
key_size, &poet::Murmur2_64A);
DHT_set_accumulate_callback(this->prox_ht, PHT_callback_function);
}
ProximityHashTable::~ProximityHashTable() {
delete[] bucket_store;
if (prox_ht) {
DHT_free(prox_ht, NULL, NULL);
}
}
int ProximityHashTable::PHT_callback_function(int in_data_size, void *in_data,
int out_data_size,
void *out_data) {
const int max_elements_per_bucket =
static_cast<int>((out_data_size - sizeof(bucket_indicator)
#ifdef POET_PHT_ADD
- sizeof(std::uint64_t)
#endif
) /
in_data_size);
DHT_Location *input = reinterpret_cast<DHT_Location *>(in_data);
bucket_indicator *occupied_buckets =
reinterpret_cast<bucket_indicator *>(out_data);
DHT_Location *pairs = reinterpret_cast<DHT_Location *>(occupied_buckets + 1);
if (*occupied_buckets == max_elements_per_bucket) {
return INTERP_CB_FULL;
}
for (bucket_indicator i = 0; i < *occupied_buckets; i++) {
if (pairs[i] == *input) {
return INTERP_CB_ALREADY_IN;
}
}
pairs[(*occupied_buckets)++] = *input;
return INTERP_CB_OK;
}
void ProximityHashTable::writeLocationToPHT(LookupKey key,
DHT_Location location) {
double start = MPI_Wtime();
// if (localCache[key].first) {
// return;
// }
int ret_val;
int status = DHT_write_accumulate(prox_ht, key.data(), sizeof(location),
&location, NULL, NULL, &ret_val);
if (status == DHT_WRITE_SUCCESS_WITH_EVICTION) {
this->dht_evictions++;
}
// if (ret_val == INTERP_CB_FULL) {
// localCache(key, {});
// }
this->pht_write_t += MPI_Wtime() - start;
}
const ProximityHashTable::PHT_Result &ProximityHashTable::query(
const LookupKey &key, const std::vector<std::uint32_t> &signif,
std::uint32_t min_entries_needed, std::uint32_t input_count,
std::uint32_t output_count) {
double start_r = MPI_Wtime();
const auto cache_ret = localCache[key];
if (cache_ret.first) {
cache_hits++;
return (lookup_results = cache_ret.second);
}
int res = DHT_read(prox_ht, key.data(), bucket_store);
this->pht_read_t += MPI_Wtime() - start_r;
if (res != DHT_SUCCESS) {
this->lookup_results.size = 0;
return lookup_results;
}
auto *bucket_element_count =
reinterpret_cast<bucket_indicator *>(bucket_store);
auto *bucket_elements =
reinterpret_cast<DHT_Location *>(bucket_element_count + 1);
if (*bucket_element_count < min_entries_needed) {
this->lookup_results.size = 0;
return lookup_results;
}
lookup_results.size = *bucket_element_count;
auto locations = std::vector<DHT_Location>(
bucket_elements, bucket_elements + *(bucket_element_count));
lookup_results.in_values.clear();
lookup_results.in_values.reserve(*bucket_element_count);
lookup_results.out_values.clear();
lookup_results.out_values.reserve(*bucket_element_count);
for (const auto &loc : locations) {
double start_g = MPI_Wtime();
DHT_read_location(source_dht, loc.first, loc.second, dht_buffer.data());
this->pht_gather_dht_t += MPI_Wtime() - start_g;
auto *buffer = reinterpret_cast<double *>(dht_buffer.data());
lookup_results.in_values.push_back(
std::vector<double>(buffer, buffer + input_count));
buffer += input_count;
lookup_results.out_values.push_back(
std::vector<double>(buffer, buffer + output_count));
// if (!similarityCheck(check_key, key, signif)) {
// // TODO: original stored location in PHT was overwritten in DHT.
// Need to
// // handle this!
// lookup_results.size--;
// if (lookup_results.size < min_entries_needed) {
// lookup_results.size = 0;
// break;
// }
// continue;
// }
// auto input = convertKeysFromDHT(buffer_start, dht_key_count);
// // remove timestep from the key
// input.pop_back();
// lookup_results.in_keys.push_back(input);
// auto *data = reinterpret_cast<double *>(buffer + dht_key_count);
// lookup_results.out_values.push_back(
// std::vector<double>(data, data + dht_data_count));
}
if (lookup_results.size != 0) {
localCache(key, lookup_results);
}
return lookup_results;
}
inline bool
ProximityHashTable::similarityCheck(const LookupKey &fine,
const LookupKey &coarse,
const std::vector<uint32_t> &signif) {
PHT_Rounder rounder;
for (int i = 0; i < signif.size(); i++) {
if (!(rounder.round(fine[i], signif[i]) == coarse[i])) {
return false;
}
}
return true;
}
inline std::vector<double>
ProximityHashTable::convertKeysFromDHT(Lookup_Keyelement *keys_in,
std::uint32_t key_size) {
std::vector<double> output(key_size);
DHT_Rounder rounder;
for (int i = 0; i < key_size; i++) {
output[i] = rounder.convert(keys_in[i]);
}
return output;
}
void ProximityHashTable::Cache::operator()(const LookupKey &key,
const PHT_Result val) {
const auto elemIt = this->find(key);
if (elemIt == this->end()) {
if (this->free_mem < 0) {
const LookupKey &to_del = this->lru_queue.back();
const auto elem_d = this->find(to_del);
this->free_mem += elem_d->second.getSize();
this->erase(to_del);
this->keyfinder.erase(to_del);
this->lru_queue.pop_back();
}
this->insert({key, val});
this->lru_queue.emplace_front(key);
this->keyfinder[key] = lru_queue.begin();
this->free_mem -= val.getSize();
return;
}
elemIt->second = val;
}
std::pair<bool, ProximityHashTable::PHT_Result>
ProximityHashTable::Cache::operator[](const LookupKey &key) {
const auto elemIt = this->find(key);
if (elemIt == this->end()) {
return {false, {}};
}
this->lru_queue.splice(lru_queue.begin(), lru_queue, this->keyfinder[key]);
return {true, elemIt->second};
}
#ifdef POET_PHT_ADD
static int PHT_increment_counter(int in_data_size, void *in_data,
int out_data_size, void *out_data) {
char *start = reinterpret_cast<char *>(out_data);
std::uint64_t *counter = reinterpret_cast<std::uint64_t *>(
start + out_data_size - sizeof(std::uint64_t));
*counter += 1;
return 0;
}
void ProximityHashTable::incrementReadCounter(const LookupKey &key) {
auto *old_func_ptr = this->prox_ht->accumulate_callback;
DHT_set_accumulate_callback(prox_ht, PHT_increment_counter);
int ret, dummy;
DHT_write_accumulate(prox_ht, key.data(), 0, NULL, NULL, NULL, &ret);
DHT_set_accumulate_callback(prox_ht, old_func_ptr);
}
#endif
} // namespace poet

293
src/ChemistryModule/WorkerFunctions.cpp
View File

@ -1,10 +1,13 @@
// Time-stamp: "Last modified 2023-07-12 12:56:17 mluebke"
// Time-stamp: "Last modified 2023-08-01 17:22:20 mluebke"
#include "IrmResult.h"
#include "poet/ChemistryModule.hpp"
#include "poet/DHT_Wrapper.hpp"
#include "poet/Interpolation.hpp"
#include <algorithm>
#include <bits/stdint-uintn.h>
#include <cassert>
#include <cmath>
#include <cstddef>
#include <cstdint>
#include <iomanip>
@ -15,6 +18,147 @@
#include <string>
#include <vector>
namespace poet {
//std::vector<double>
//inverseDistanceWeighting(const std::vector<std::int32_t> &to_calc,
// const std::vector<double> &from,
// const std::vector<std::vector<double>> &input,
// const std::vector<std::vector<double>> &output) {
// std::vector<double> results = from;
//
// const std::uint32_t buffer_size = input.size() + 1;
// double buffer[buffer_size];
// double from_rescaled;
//
// const std::uint32_t data_set_n = input.size();
// double rescaled[to_calc.size()][data_set_n + 1];
// double weights[data_set_n];
//
// // rescaling over all key elements
// for (int key_comp_i = 0; key_comp_i < to_calc.size(); key_comp_i++) {
// const auto output_comp_i = to_calc[key_comp_i];
//
// // rescale input between 0 and 1
// for (int point_i = 0; point_i < data_set_n; point_i++) {
// rescaled[key_comp_i][point_i] = input[point_i][key_comp_i];
// }
//
// rescaled[key_comp_i][data_set_n] = from[output_comp_i];
//
// const double min = *std::min_element(rescaled[key_comp_i],
// rescaled[key_comp_i] + data_set_n + 1);
// const double max = *std::max_element(rescaled[key_comp_i],
// rescaled[key_comp_i] + data_set_n + 1);
//
// for (int point_i = 0; point_i < data_set_n; point_i++) {
// rescaled[key_comp_i][point_i] =
// ((max - min) != 0
// ? (rescaled[key_comp_i][point_i] - min) / (max - min)
// : 0);
// }
// rescaled[key_comp_i][data_set_n] =
// ((max - min) != 0 ? (from[output_comp_i] - min) / (max - min) : 0);
// }
//
// // calculate distances for each data set
// double inv_sum = 0;
// for (int point_i = 0; point_i < data_set_n; point_i++) {
// double distance = 0;
// for (int key_comp_i = 0; key_comp_i < to_calc.size(); key_comp_i++) {
// distance += std::pow(
// rescaled[key_comp_i][point_i] - rescaled[key_comp_i][data_set_n], 2);
// }
// weights[point_i] = 1 / std::sqrt(distance);
// assert(!std::isnan(weights[point_i]));
// inv_sum += weights[point_i];
// }
//
// assert(!std::isnan(inv_sum));
//
// // actual interpolation
// // bool has_h = false;
// // bool has_o = false;
//
// for (int key_comp_i = 0; key_comp_i < to_calc.size(); key_comp_i++) {
// const auto output_comp_i = to_calc[key_comp_i];
// double key_delta = 0;
//
// // if (interp_i == 0) {
// // has_h = true;
// // }
//
// // if (interp_i == 1) {
// // has_o = true;
// // }
//
// for (int j = 0; j < data_set_n; j++) {
// key_delta += weights[j] * input[j][key_comp_i];
// }
//
// key_delta /= inv_sum;
//
// results[output_comp_i] = from[output_comp_i] + key_delta;
// }
//
// // if (!has_h) {
// // double new_val = 0;
// // for (int j = 0; j < data_set_n; j++) {
// // new_val += weights[j] * output[j][0];
// // }
// // results[0] = new_val / inv_sum;
// // }
//
// // if (!has_h) {
// // double new_val = 0;
// // for (int j = 0; j < data_set_n; j++) {
// // new_val += weights[j] * output[j][1];
// // }
// // results[1] = new_val / inv_sum;
// // }
//
// // for (std::uint32_t i = 0; i < to_calc.size(); i++) {
// // const std::uint32_t interp_i = to_calc[i];
//
// // // rescale input between 0 and 1
// // for (int j = 0; j < input.size(); j++) {
// // buffer[j] = input[j].at(i);
// // }
//
// // buffer[buffer_size - 1] = from[interp_i];
//
// // const double min = *std::min_element(buffer, buffer + buffer_size);
// // const double max = *std::max_element(buffer, buffer + buffer_size);
//
// // for (int j = 0; j < input.size(); j++) {
// // buffer[j] = ((max - min) != 0 ? (buffer[j] - min) / (max - min) : 1);
// // }
// // from_rescaled =
// // ((max - min) != 0 ? (from[interp_i] - min) / (max - min) : 0);
//
// // double inv_sum = 0;
//
// // // calculate distances for each point
// // for (int i = 0; i < input.size(); i++) {
// // const double distance = std::pow(buffer[i] - from_rescaled, 2);
//
// // buffer[i] = distance > 0 ? (1 / std::sqrt(distance)) : 0;
// // inv_sum += buffer[i];
// // }
// // // calculate new values
// // double new_val = 0;
// // for (int i = 0; i < output.size(); i++) {
// // new_val += buffer[i] * output[i][interp_i];
// // }
// // results[interp_i] = new_val / inv_sum;
// // if (std::isnan(results[interp_i])) {
// // std::cout << "nan with new_val = " << output[0][i] << std::endl;
// // }
// // }
//
// return results;
//}
inline std::string get_string(int root, MPI_Comm communicator) {
int count;
MPI_Bcast(&count, 1, MPI_INT, root, communicator);
@ -52,43 +196,6 @@ void poet::ChemistryModule::WorkerLoop() {
initializeField(dummy);
break;
}
case CHEM_DHT_ENABLE: {
bool enable;
ChemBCast(&enable, 1, MPI_CXX_BOOL);
uint32_t size_mb;
ChemBCast(&size_mb, 1, MPI_UINT32_T);
std::vector<std::string> name_dummy;
SetDHTEnabled(enable, size_mb, name_dummy);
break;
}
case CHEM_DHT_SIGNIF_VEC: {
std::vector<uint32_t> input_vec;
SetDHTSignifVector(input_vec);
break;
}
case CHEM_DHT_PROP_TYPE_VEC: {
std::vector<uint32_t> input_vec(this->prop_count);
ChemBCast(input_vec.data(), this->prop_count, MPI_UINT32_T);
SetDHTPropTypeVector(input_vec);
break;
}
case CHEM_DHT_SNAPS: {
int type;
ChemBCast(&type, 1, MPI_INT);
SetDHTSnaps(type, get_string(0, this->group_comm));
break;
}
case CHEM_DHT_READ_FILE: {
ReadDHTFile(get_string(0, this->group_comm));
break;
}
case CHEM_WORK_LOOP: {
WorkerProcessPkgs(timings, iteration);
break;
@ -103,12 +210,6 @@ void poet::ChemistryModule::WorkerLoop() {
WorkerMetricsToMaster(type);
break;
}
case CHEM_PROGRESSBAR: {
bool enable;
ChemBCast(&enable, 1, MPI_CXX_BOOL);
setProgressBarPrintout(enable);
break;
}
case CHEM_BREAK_MAIN_LOOP: {
WorkerPostSim(iteration);
loop = false;
@ -211,7 +312,9 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status,
dht->checkDHT(local_work_package_size, dt, vecCurrWP, vecMappingWP);
dht_get_end = MPI_Wtime();
// DHT_Results.ResultsToMapping(vecMappingWP);
if (interp_enabled) {
interp->tryInterpolation(dht->getDHTResults(), vecMappingWP);
}
}
phreeqc_time_start = MPI_Wtime();
@ -225,6 +328,9 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status,
if (dht_enabled) {
dht->resultsToWP(vecCurrWP);
if (interp_enabled) {
interp->resultsToWP(vecCurrWP);
}
}
/* send results to master */
@ -238,6 +344,10 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status,
dht->fillDHT(local_work_package_size, vecCurrWP);
dht_fill_end = MPI_Wtime();
if (interp_enabled) {
interp->writePairs(dht->getDHTResults());
}
timings.dht_get += dht_get_end - dht_get_start;
timings.dht_fill += dht_fill_end - dht_fill_start;
}
@ -252,23 +362,44 @@ void poet::ChemistryModule::WorkerPostIter(MPI_Status &prope_status,
MPI_Recv(NULL, 0, MPI_DOUBLE, 0, LOOP_END, this->group_comm,
MPI_STATUS_IGNORE);
if (this->dht_enabled) {
this->dht->printStatistics();
dht_hits.push_back(dht->getHits());
dht_evictions.push_back(dht->getEvictions());
dht->resetCounter();
if (this->dht_snaps_type == DHT_FILES_ITEREND) {
if (this->interp_enabled) {
interp_calls.push_back(interp->getInterpolationCount());
interp->resetCounter();
interp->writePHTStats();
}
if (this->dht_snaps_type == DHT_SNAPS_ITEREND) {
WorkerWriteDHTDump(iteration);
if (this->interp_enabled) {
std::stringstream out;
out << this->dht_file_out_dir << "/iter_" << std::setfill('0')
<< std::setw(this->file_pad) << iteration << ".pht";
interp->dumpPHTState(out.str());
}
}
}
}
void poet::ChemistryModule::WorkerPostSim(uint32_t iteration) {
if (this->dht_enabled && this->dht_snaps_type == DHT_FILES_SIMEND) {
if (this->dht_enabled && this->dht_snaps_type == DHT_SNAPS_SIMEND) {
WorkerWriteDHTDump(iteration);
if (this->interp_enabled) {
std::stringstream out;
out << this->dht_file_out_dir << "/iter_" << std::setfill('0')
<< std::setw(this->file_pad) << iteration << ".pht";
interp->dumpPHTState(out.str());
}
}
}
void poet::ChemistryModule::WorkerWriteDHTDump(uint32_t iteration) {
std::stringstream out;
out << this->dht_file_out_dir << "/iter_" << std::setfill('0') << std::setw(3)
<< iteration << ".dht";
out << this->dht_file_out_dir << "/iter_" << std::setfill('0')
<< std::setw(this->file_pad) << iteration << ".dht";
int res = dht->tableToFile(out.str().c_str());
if (res != DHT_SUCCESS && this->comm_rank == 2)
std::cerr
@ -355,6 +486,26 @@ void poet::ChemistryModule::WorkerPerfToMaster(int type,
this->group_comm);
break;
}
case WORKER_IP_WRITE: {
double val = interp->getPHTWriteTime();
MPI_Gather(&val, 1, MPI_DOUBLE, NULL, 1, MPI_DOUBLE, 0, this->group_comm);
break;
}
case WORKER_IP_READ: {
double val = interp->getPHTReadTime();
MPI_Gather(&val, 1, MPI_DOUBLE, NULL, 1, MPI_DOUBLE, 0, this->group_comm);
break;
}
case WORKER_IP_GATHER: {
double val = interp->getDHTGatherTime();
MPI_Gather(&val, 1, MPI_DOUBLE, NULL, 1, MPI_DOUBLE, 0, this->group_comm);
break;
}
case WORKER_IP_FC: {
double val = interp->getInterpolationTime();
MPI_Gather(&val, 1, MPI_DOUBLE, NULL, 1, MPI_DOUBLE, 0, this->group_comm);
break;
}
default: {
throw std::runtime_error("Unknown perf type in master's message.");
}
@ -362,24 +513,46 @@ void poet::ChemistryModule::WorkerPerfToMaster(int type,
}
void poet::ChemistryModule::WorkerMetricsToMaster(int type) {
uint32_t value;
MPI_Comm worker_comm = dht->getCommunicator();
int worker_rank;
MPI_Comm_rank(worker_comm, &worker_rank);
MPI_Comm &group_comm = this->group_comm;
auto reduce_and_send = [&worker_rank, &worker_comm, &group_comm](
std::vector<std::uint32_t> &send_buffer, int tag) {
std::vector<uint32_t> to_master(send_buffer.size());
MPI_Reduce(send_buffer.data(), to_master.data(), send_buffer.size(),
MPI_UINT32_T, MPI_SUM, 0, worker_comm);
if (worker_rank == 0) {
MPI_Send(to_master.data(), to_master.size(), MPI_UINT32_T, 0, tag,
group_comm);
}
};
switch (type) {
case WORKER_DHT_HITS: {
value = dht->getHits();
break;
}
case WORKER_DHT_MISS: {
value = dht->getMisses();
reduce_and_send(dht_hits, WORKER_DHT_HITS);
break;
}
case WORKER_DHT_EVICTIONS: {
value = dht->getEvictions();
reduce_and_send(dht_evictions, WORKER_DHT_EVICTIONS);
break;
}
case WORKER_IP_CALLS: {
reduce_and_send(interp_calls, WORKER_IP_CALLS);
return;
}
case WORKER_PHT_CACHE_HITS: {
std::vector<std::uint32_t> input = this->interp->getPHTLocalCacheHits();
reduce_and_send(input, WORKER_PHT_CACHE_HITS);
return;
}
default: {
throw std::runtime_error("Unknown perf type in master's message.");
}
}
MPI_Gather(&value, 1, MPI_UINT32_T, NULL, 1, MPI_UINT32_T, 0,
this->group_comm);
}
} // namespace poet

115
src/SimParams.cpp
View File

@ -82,20 +82,20 @@ poet::DiffusionParams::s_DiffusionParams(RInside &R) {
Rcpp::as<Rcpp::DataFrame>(R.parseEval("mysetup$diffusion$vecinj_index"));
}
poet::ChemistryParams::s_ChemistryParams(RInside &R) {
void poet::ChemistryParams::initFromR(RInsidePOET &R) {
this->database_path =
Rcpp::as<std::string>(R.parseEval("mysetup$chemistry$database"));
this->input_script =
Rcpp::as<std::string>(R.parseEval("mysetup$chemistry$input_script"));
if (Rcpp::as<bool>(
R.parseEval("'dht_species' %in% names(mysetup$chemistry)"))) {
this->dht_species = Rcpp::as<std::vector<std::string>>(
R.parseEval("mysetup$chemistry$dht_species"));
if (R.checkIfExists("dht_species", "mysetup$chemistry")) {
this->dht_signifs =
R.wrapNamedVector<std::uint32_t>("mysetup$chemistry$dht_species");
}
if (Rcpp::as<bool>(
R.parseEval("'dht_signif' %in% names(mysetup$chemistry)"))) {
this->dht_signif = Rcpp::as<std::vector<std::uint32_t>>(
R.parseEval("mysetup$chemistry$dht_signif"));
if (R.checkIfExists("pht_species", "mysetup$chemistry")) {
this->pht_signifs =
R.wrapNamedVector<std::uint32_t>("mysetup$chemistry$pht_species");
}
}
@ -104,7 +104,7 @@ SimParams::SimParams(int world_rank_, int world_size_) {
this->simparams.world_size = world_size_;
}
int SimParams::parseFromCmdl(char *argv[], RInside &R) {
int SimParams::parseFromCmdl(char *argv[], RInsidePOET &R) {
// initialize argh object
argh::parser cmdl(argv);
@ -144,32 +144,26 @@ int SimParams::parseFromCmdl(char *argv[], RInside &R) {
simparams.print_progressbar = cmdl[{"P", "progress"}];
/*Parse DHT arguments*/
simparams.dht_enabled = cmdl["dht"];
chem_params.use_dht = cmdl["dht"];
// cout << "CPP: DHT is " << ( dht_enabled ? "ON" : "OFF" ) << '\n';
if (simparams.dht_enabled) {
cmdl("dht-strategy", 0) >> simparams.dht_strategy;
// cout << "CPP: DHT strategy is " << dht_strategy << endl;
cmdl("dht-signif", 5) >> simparams.dht_significant_digits;
// cout << "CPP: DHT significant digits = " << dht_significant_digits <<
// endl;
simparams.dht_log = !(cmdl["dht-nolog"]);
// cout << "CPP: DHT logarithm before rounding: " << ( dht_logarithm ? "ON"
// : "OFF" ) << endl;
cmdl("dht-size", DHT_SIZE_PER_PROCESS_MB) >> simparams.dht_size_per_process;
if (chem_params.use_dht) {
cmdl("dht-size", DHT_SIZE_PER_PROCESS_MB) >> chem_params.dht_size;
// cout << "CPP: DHT size per process (Byte) = " << dht_size_per_process <<
// endl;
cmdl("dht-snaps", 0) >> simparams.dht_snaps;
cmdl("dht-snaps", 0) >> chem_params.dht_snaps;
cmdl("dht-file") >> dht_file;
cmdl("dht-file") >> chem_params.dht_file;
}
/*Parse work package size*/
cmdl("work-package-size", WORK_PACKAGE_SIZE_DEFAULT) >> simparams.wp_size;
chem_params.use_interp = cmdl["interp"];
cmdl("interp-size", 100) >> chem_params.pht_size;
cmdl("interp-min", 5) >> chem_params.interp_min_entries;
cmdl("interp-bucket-entries", 20) >> chem_params.pht_max_entries;
/*Parse output options*/
simparams.store_result = !cmdl["ignore-result"];
@ -177,25 +171,27 @@ int SimParams::parseFromCmdl(char *argv[], RInside &R) {
cout << "CPP: Complete results storage is "
<< (simparams.store_result ? "ON" : "OFF") << endl;
cout << "CPP: Work Package Size: " << simparams.wp_size << endl;
cout << "CPP: DHT is " << (simparams.dht_enabled ? "ON" : "OFF") << '\n';
cout << "CPP: DHT is " << (chem_params.use_dht ? "ON" : "OFF") << '\n';
if (simparams.dht_enabled) {
if (chem_params.use_dht) {
cout << "CPP: DHT strategy is " << simparams.dht_strategy << endl;
cout << "CPP: DHT key default digits (ignored if 'signif_vector' is "
"defined) = "
<< simparams.dht_significant_digits << endl;
cout << "CPP: DHT logarithm before rounding: "
<< (simparams.dht_log ? "ON" : "OFF") << endl;
cout << "CPP: DHT size per process (Byte) = "
<< simparams.dht_size_per_process << endl;
cout << "CPP: DHT save snapshots is " << simparams.dht_snaps << endl;
cout << "CPP: DHT load file is " << dht_file << endl;
cout << "CPP: DHT size per process (Byte) = " << chem_params.dht_size
<< endl;
cout << "CPP: DHT save snapshots is " << chem_params.dht_snaps << endl;
cout << "CPP: DHT load file is " << chem_params.dht_file << endl;
}
}
cmdl(1) >> filesim;
cmdl(2) >> out_dir;
chem_params.dht_outdir = out_dir;
/* distribute information to R runtime */
// if local_rank == 0 then master else worker
R["local_rank"] = simparams.world_rank;
@ -210,65 +206,20 @@ int SimParams::parseFromCmdl(char *argv[], RInside &R) {
// work package size
R["work_package_size"] = simparams.wp_size;
// dht enabled?
R["dht_enabled"] = simparams.dht_enabled;
R["dht_enabled"] = chem_params.use_dht;
// log before rounding?
R["dht_log"] = simparams.dht_log;
// eval the init string, ignoring any returns
R.parseEvalQ("source(filesim)");
R.parseEvalQ("mysetup <- setup");
this->chem_params.initFromR(R);
return poet::PARSER_OK;
}
void SimParams::initVectorParams(RInside &R) {
if (simparams.dht_enabled) {
/*Load significance vector from R setup file (or set default)*/
bool signif_vector_exists = R.parseEval("exists('signif_vector')");
if (signif_vector_exists) {
dht_signif_vector = as<std::vector<uint32_t>>(R["signif_vector"]);
}
/*Load property type vector from R setup file (or set default)*/
bool prop_type_vector_exists = R.parseEval("exists('prop_type')");
if (prop_type_vector_exists) {
std::vector<std::string> prop_type_R =
as<std::vector<string>>(R["prop_type"]);
this->dht_prop_type_vector.clear();
this->dht_prop_type_vector.reserve(prop_type_R.size());
for (const auto &type : prop_type_R) {
if (type == "act") {
this->dht_prop_type_vector.push_back(DHT_TYPE_CHARGE);
continue;
}
if (type == "ignore") {
this->dht_prop_type_vector.push_back(DHT_TYPE_IGNORE);
continue;
}
this->dht_prop_type_vector.push_back(DHT_TYPE_DEFAULT);
}
}
if (simparams.world_rank == 0) {
// MDL: new output on signif_vector and prop_type
if (signif_vector_exists) {
cout << "CPP: using problem-specific rounding digits: " << endl;
R.parseEval("print(data.frame(prop=prop, type=prop_type, "
"digits=signif_vector))");
} else {
cout << "CPP: using DHT default rounding digits = "
<< simparams.dht_significant_digits << endl;
}
// MDL: pass to R the DHT stuff. These variables exist
// only if dht_enabled is true
R["dht_final_signif"] = dht_signif_vector;
R["dht_final_proptype"] = dht_prop_type_vector;
}
}
}
void SimParams::initVectorParams(RInside &R) {}
std::list<std::string> SimParams::validateOptions(argh::parser cmdl) {
/* store all unknown parameters here */

79
test/testRounding.cpp Normal file
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@ -0,0 +1,79 @@
#include <doctest/doctest.h>
#include "poet/Rounding.hpp"
TEST_CASE("Rounding") {
constexpr int signif = 3;
poet::DHT_Rounder rounder;
SUBCASE("+exp - +sig") {
double input = 1.2345;
auto rounded = rounder.round(input, signif, false);
CHECK_EQ(rounded.sc_notation.significant, 123);
CHECK_EQ(rounded.sc_notation.exp, 0);
}
SUBCASE("+exp - -sig") {
double input = -1.2345;
auto rounded = rounder.round(input, signif, false);
CHECK_EQ(rounded.sc_notation.significant, -123);
CHECK_EQ(rounded.sc_notation.exp, 0);
}
SUBCASE("-exp - +sig") {
double input = 1.23456789E-5;
auto rounded = rounder.round(input, signif, false);
CHECK_EQ(rounded.sc_notation.significant, 123);
CHECK_EQ(rounded.sc_notation.exp, -5);
}
SUBCASE("-exp - -sig") {
double input = -1.23456789E-5;
auto rounded = rounder.round(input, signif, false);
CHECK_EQ(rounded.sc_notation.significant, -123);
CHECK_EQ(rounded.sc_notation.exp, -5);
}
SUBCASE("-exp - +sig (exceeding aqueous minimum)") {
double input = 1.23456789E-14;
auto rounded = rounder.round(input, signif, false);
CHECK_EQ(rounded.sc_notation.significant, 0);
CHECK_EQ(rounded.sc_notation.exp, 0);
}
SUBCASE("-exp - -sig (exceeding aqueous minimum)") {
double input = -1.23456789E-14;
auto rounded = rounder.round(input, signif, false);
CHECK_EQ(rounded.sc_notation.significant, 0);
CHECK_EQ(rounded.sc_notation.exp, 0);
}
SUBCASE("-exp - +sig (diff exceeds aqueous minimum)") {
double input = 1.23456789E-13;
auto rounded = rounder.round(input, signif, false);
CHECK_EQ(rounded.sc_notation.significant, 1);
CHECK_EQ(rounded.sc_notation.exp, -13);
}
SUBCASE("-exp - -sig (diff exceeds aqueous minimum)") {
double input = -1.23456789E-13;
auto rounded = rounder.round(input, signif, false);
CHECK_EQ(rounded.sc_notation.significant, -1);
CHECK_EQ(rounded.sc_notation.exp, -13);
}
SUBCASE("-exp - +sig (diff exceeds aqueous minimum - but H or O)") {
double input = 1.23456789E-13;
auto rounded = rounder.round(input, signif, true);
CHECK_EQ(rounded.sc_notation.significant, 123);
CHECK_EQ(rounded.sc_notation.exp, -13);
}
SUBCASE("-exp - -sig (diff exceeds aqueous minimum - but H or O)") {
double input = -1.23456789E-13;
auto rounded = rounder.round(input, signif, true);
CHECK_EQ(rounded.sc_notation.significant, -123);
CHECK_EQ(rounded.sc_notation.exp, -13);
}
}

95
util/data_evaluation/RFun_Eval.R
View File

@ -1,10 +1,11 @@
## Simple library of functions to assess and visualize the results of the coupled simulations
## Time-stamp: "Last modified 2023-04-24 16:09:55 mluebke"
## Time-stamp: "Last modified 2023-05-29 13:51:21 mluebke"
require(RedModRphree)
require(Rmufits) ## essentially for PlotCartCellData
require(Rcpp)
require(stringr)
curdir <- dirname(sys.frame(1)$ofile) ##path.expand(".")
@ -16,13 +17,18 @@ ConvertDHTKey <- function(value) {
rcpp_key_convert(value)
}
ConvertToUInt64 <- function(double_data) {
rcpp_uint64_convert(double_data)
}
## function which reads all simulation results in a given directory
ReadRTSims <- function(dir) {
files_full <- list.files(dir, pattern="iter.*rds", full.names=TRUE)
files_name <- list.files(dir, pattern="iter.*rds", full.names=FALSE)
res <- lapply(files_full, readRDS)
names(res) <- gsub(".rds","",files_name, fixed=TRUE)
return(res)
return(res[str_sort(names(res), numeric = TRUE)])
}
## function which reads all successive DHT stored in a given directory
@ -68,6 +74,61 @@ ReadDHT <- function(file, new_scheme = TRUE) {
return(res)
}
## function which reads all successive DHT stored in a given directory
ReadAllPHT <- function(dir, with_info = FALSE) {
files_full <- list.files(dir, pattern="iter.*pht", full.names=TRUE)
files_name <- list.files(dir, pattern="iter.*pht", full.names=FALSE)
res <- lapply(files_full, ReadPHT, with_info = with_info)
names(res) <- gsub(".pht","",files_name, fixed=TRUE)
return(res)
}
## function which reads one .dht file and gives a matrix
ReadPHT <- function(file, with_info = FALSE) {
conn <- file(file, "rb") ## open for reading in binary mode
if (!isSeekable(conn))
stop("Connection not seekable")
## we first reposition ourselves to the end of the file...
tmp <- seek(conn, where=0, origin = "end")
## ... and then back to the origin so to store the length in bytes
flen <- seek(conn, where=0, origin = "start")
## we read the first 2 integers (4 bytes each) containing dimensions in bytes
dims <- readBin(conn, what="integer", n=2)
## compute dimensions of the data
tots <- sum(dims)
ncol <- tots/8
nrow <- (flen - 8)/tots ## 8 here is 2*sizeof("int")
buff <- readBin(conn, what="double", n=ncol*nrow)
## close connection
close(conn)
res <- matrix(buff, nrow=nrow, ncol=ncol, byrow=TRUE)
nkeys <- dims[1] / 8
keys <- res[, 1:nkeys - 1]
timesteps <- res[, nkeys]
conv <- apply(keys, 2, ConvertDHTKey)
#res[, 1:nkeys - 1] <- conv
ndata <- dims[2] / 8
fill_rate <- ConvertToUInt64(res[, nkeys + 1])
buff <- c(conv, timesteps, fill_rate)
if (with_info) {
ndata <- dims[2]/8
visit_count <- ConvertToUInt64(res[, nkeys + ndata])
buff <- c(buff, visit_count)
}
res <- matrix(buff, nrow = nrow, byrow = FALSE)
return(res)
}
## Scatter plots of each variable in the iteration
PlotScatter <- function(sam1, sam2, which=NULL, labs=c("NO DHT", "DHT"), pch=".", cols=3, ...) {
if ((!is.data.frame(sam1)) & ("T" %in% names(sam1)))
@ -228,3 +289,33 @@ Plot2DCellData <- function (data, grid, nx, ny, contour = TRUE,
}
invisible(pp)
}
PlotAsMP4 <- function(data, nx, ny, to_plot, out_dir, name,
contour = FALSE, scale = FALSE, framerate = 30) {
sort_data <- data[str_sort(names(data), numeric = TRUE)]
plot_data <- lapply(sort_data, function(x) x$C[[to_plot]])
pad_size <- ceiling(log10(length(plot_data)))
dir.create(out_dir, showWarnings = FALSE)
output_files <- paste0(out_dir, "/", name, "_%0", pad_size, "d.png")
output_mp4 <- paste0(out_dir, "/", name, ".mp4")
png(output_files,
width = 297, height = 210, units = "mm",
res = 100
)
for (i in 1:length(plot_data)) {
Rmufits::PlotCartCellData(plot_data[[i]], nx = nx, ny = ny, contour = contour, scale = scale)
}
dev.off()
ffmpeg_command <- paste(
"ffmpeg -framerate", framerate, "-i", output_files,
"-c:v libx264 -crf 22", output_mp4
)
unlink(output_mp4)
system(ffmpeg_command)
}

13
util/data_evaluation/interpret_keys.cpp
View File

@ -35,3 +35,16 @@ std::vector<double> rcpp_key_convert(std::vector<double> input) {
return output;
}
// [[Rcpp::export]]
std::vector<std::uint64_t> rcpp_uint64_convert(std::vector<double> input) {
std::vector<std::uint64_t> output;
output.reserve(input.size());
for (double &value : input) {
std::uint64_t *as_int = reinterpret_cast<std::uint64_t *>(&value);
output.push_back(*as_int);
}
return output;
}