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Remove unnecessary includes and update function signature

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This commit is contained in:
Max Luebke 2024-04-02 09:16:58 +00:00
parent a345191d5a
commit 53f68a2e56
4 changed files with 86 additions and 73 deletions
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37
R_lib/kin_r_library.R
View File

@ -67,33 +67,32 @@ master_init <- function(setup) {
## This function, called only by master, stores on disk the last
## calculated time step if store_result is TRUE and increments the
## iteration counter
master_iteration_end <- function(setup) {
master_iteration_end <- function(setup,iter) {
# iter <- setup$iter
# print(iter)
## max digits for iterations
iter <- 1
dgts <- as.integer(ceiling(log10(1)))
dgts <- as.integer(ceiling(log10(iter)))
## string format to use in sprintf
fmt <- paste0("%0", dgts, "d")
## Write on disk state_T and state_C after every iteration
## comprised in setup$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(1)
## 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(0),
tr_info = info
), file = nameout)
msgm("results stored in <", nameout, ">")
# }
# }
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(1)
## 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(0),
tr_info = info
), file = nameout)
msgm("results stored in <", nameout, ">")
}
}
msgm("done iteration", iter, "/", 1)
setup$iter <- setup$iter + 1
return(setup)

59
src/Chemistry/WorkerFunctions.cpp
View File

@ -281,7 +281,7 @@ void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package,
double dSimTime,
double dTimestep) {
// check if we actually need to start phreeqc
bool queued_cell = false;
std::map<int, std::vector<std::size_t>> zone_mapping;
for (std::size_t wp_id = 0; wp_id < work_package.size; wp_id++) {
if (work_package.mapping[wp_id] != CHEM_PQC) {
@ -289,9 +289,9 @@ void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package,
}
const auto &input = work_package.input[wp_id];
const auto &sol_id = input[0];
const auto pqc_id = input[0];
auto &phreeqc_instance = this->phreeqc_instances[sol_id];
auto &phreeqc_instance = this->phreeqc_instances[pqc_id];
work_package.output[wp_id] = work_package.input[wp_id];
work_package.input[wp_id].erase(work_package.input[wp_id].begin());
@ -304,38 +304,57 @@ void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package,
work_package.input[wp_id].end());
phreeqc_instance->queueCell(work_package.input[wp_id]);
queued_cell = true;
zone_mapping[pqc_id].push_back(wp_id);
}
if (!queued_cell) {
if (zone_mapping.empty()) {
return;
}
std::map<int, std::vector<std::size_t>> zone_mapping;
// run the phreeqc instances
for (const auto &[pqc_id, phreeqc_instance] : this->phreeqc_instances) {
if (zone_mapping.find(pqc_id) == zone_mapping.end()) {
for (const auto &[pqc_id, eval_cells] : zone_mapping) {
if (eval_cells.empty()) {
continue;
}
phreeqc_instance->runQueuedCells(dTimestep);
// remap the output to the work_package
this->phreeqc_instances[pqc_id]->runQueuedCells(dTimestep);
std::vector<std::vector<double>> pqc_out;
phreeqc_instance->dequeueCells(pqc_out);
this->phreeqc_instances[pqc_id]->dequeueCells(pqc_out);
std::size_t output_id = 0;
for (const auto &wp_id : zone_mapping[pqc_id]) {
for (std::size_t i = 0; i < eval_cells.size(); i++) {
std::size_t wp_id = eval_cells[i];
std::size_t output_index = 0;
for (std::size_t i = 1; i < work_package.output[wp_id].size(); i++) {
if (!(std::isnan(work_package.output[wp_id][i]))) {
work_package.output[wp_id][i] = pqc_out[output_id][output_index++];
for (std::size_t j = 1; j < work_package.output[wp_id].size(); j++) {
if (!(std::isnan(work_package.output[wp_id][j]))) {
work_package.output[wp_id][j] = pqc_out[i][output_index++];
}
}
output_id++;
}
}
// run the phreeqc instances
// for (const auto &[pqc_id, phreeqc_instance] : this->phreeqc_instances) {
// // if (zone_mapping.find(pqc_id) == zone_mapping.end()) {
// // continue;
// // }
// phreeqc_instance->runQueuedCells(dTimestep);
// // remap the output to the work_package
// std::vector<std::vector<double>> pqc_out;
// phreeqc_instance->dequeueCells(pqc_out);
// std::size_t output_id = 0;
// for (const auto &wp_id : zone_mapping[pqc_id]) {
// std::size_t output_index = 0;
// for (std::size_t i = 1; i < work_package.output[wp_id].size(); i++) {
// if (!(std::isnan(work_package.output[wp_id][i]))) {
// work_package.output[wp_id][i] = pqc_out[output_id][output_index++];
// }
// }
// output_id++;
// }
// }
}
void poet::ChemistryModule::WorkerPerfToMaster(int type,

2
src/Transport/DiffusionModule.cpp
View File

@ -35,8 +35,6 @@
#include "tug/Grid.hpp"
#include "tug/Simulation.hpp"
#include <iostream>
#include <ostream>
#include <string>
#include <vector>

61
src/poet.cpp
View File

@ -276,8 +276,9 @@ ParseRet parseInitValues(char **argv, RInsidePOET &R,
// chem.LoadDatabase(database_path);
// }
static double RunMasterLoop(RInside &R, const RuntimeParameters &params,
DiffusionModule &diffusion, ChemistryModule &chem) {
static Rcpp::List RunMasterLoop(RInside &R, const RuntimeParameters &params,
DiffusionModule &diffusion,
ChemistryModule &chem) {
/* Iteration Count is dynamic, retrieving value from R (is only needed by
* master for the following loop) */
@ -333,7 +334,9 @@ static double RunMasterLoop(RInside &R, const RuntimeParameters &params,
chem.simulate(dt);
writeFieldsToR(R, diffusion.getField(), chem.GetField());
// diffusion.getField().update(chem.GetField());
// R["store_result"] = true;
// R.parseEval("mysetup$store_result <- TRUE");
diffusion.getField().update(chem.GetField());
R["req_dt"] = dt;
R["simtime"] = (sim_time += dt);
@ -341,11 +344,13 @@ static double RunMasterLoop(RInside &R, const RuntimeParameters &params,
R.parseEval("mysetup$req_dt <- req_dt");
R.parseEval("mysetup$simtime <- simtime");
R["iter"] = iter;
// MDL master_iteration_end just writes on disk state_T and
// state_C after every iteration if the cmdline option
// --ignore-results is not given (and thus the R variable
// store_result is TRUE)
R.parseEval("mysetup <- master_iteration_end(setup=mysetup)");
R.parseEval("mysetup <- master_iteration_end(setup=mysetup, iter)");
MSG("End of *coupling* iteration " + std::to_string(iter) + "/" +
std::to_string(maxiter));
@ -356,31 +361,21 @@ static double RunMasterLoop(RInside &R, const RuntimeParameters &params,
dSimTime += end_t - start_t;
} // END SIMULATION LOOP
// R.parseEvalQ("profiling <- list()");
Rcpp::List chem_profiling;
chem_profiling["simtime"] = chem.GetChemistryTime();
chem_profiling["loop"] = chem.GetMasterLoopTime();
chem_profiling["sequential"] = chem.GetMasterSequentialTime();
chem_profiling["idle_master"] = chem.GetMasterIdleTime();
chem_profiling["idle_worker"] = Rcpp::wrap(chem.GetWorkerIdleTimings());
chem_profiling["phreeqc_time"] = Rcpp::wrap(chem.GetWorkerPhreeqcTimings());
// R["simtime_chemistry"] = chem.GetChemistryTime();
// R.parseEvalQ("profiling$simtime_chemistry <- simtime_chemistry");
Rcpp::List diffusion_profiling;
diffusion_profiling["simtime"] = diffusion.getTransportTime();
// R["chemistry_loop"] = chem.GetMasterLoopTime();
// R.parseEvalQ("profiling$chemistry_loop <- chemistry_loop");
// R["chemistry_sequential"] = chem.GetMasterSequentialTime();
// R.parseEvalQ("profiling$simtime_sequential <- chemistry_sequential");
// R["idle_master"] = chem.GetMasterIdleTime();
// R.parseEvalQ("profiling$idle_master <- idle_master");
// R["idle_worker"] = Rcpp::wrap(chem.GetWorkerIdleTimings());
// R.parseEvalQ("profiling$idle_worker <- idle_worker");
// R["phreeqc_time"] = Rcpp::wrap(chem.GetWorkerPhreeqcTimings());
// R.parseEvalQ("profiling$phreeqc <- phreeqc_time");
// R["simtime_transport"] = diffusion.getTransportTime();
// R.parseEvalQ("profiling$simtime_transport <- simtime_transport");
// R["phreeqc_count"] = phreeqc_counts;
// R.parseEvalQ("profiling$phreeqc_count <- phreeqc_count");
Rcpp::List profiling;
profiling["simtime"] = dSimTime;
profiling["chemistry"] = chem_profiling;
profiling["diffusion"] = diffusion_profiling;
// if (params.getChemParams().use_dht) {
// R["dht_hits"] = Rcpp::wrap(chem.GetWorkerDHTHits());
@ -411,7 +406,7 @@ static double RunMasterLoop(RInside &R, const RuntimeParameters &params,
chem.MasterLoopBreak();
return dSimTime;
return profiling;
}
int main(int argc, char *argv[]) {
@ -492,7 +487,7 @@ int main(int argc, char *argv[]) {
chemistry.masterSetField(init_list.getInitialGrid());
dSimTime = RunMasterLoop(R, run_params, diffusion, chemistry);
Rcpp::List profiling = RunMasterLoop(R, run_params, diffusion, chemistry);
MSG("finished simulation loop");
@ -501,9 +496,11 @@ int main(int argc, char *argv[]) {
// R["simtime"] = dSimTime;
// R.parseEvalQ("profiling$simtime <- simtime");
// string r_vis_code;
// r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));";
// R.parseEval(r_vis_code);
R["profiling"] = profiling;
string r_vis_code;
r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));";
R.parseEval(r_vis_code);
// MSG("Done! Results are stored as R objects into <" + run_params.getOutDir()
// +