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fixed damn source_R

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This commit is contained in:
Marco De Lucia 2024-09-12 16:15:21 +02:00
parent 91cf9658d2
commit 1e14ba6d69
1 changed files with 32 additions and 32 deletions
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64
src/poet.cpp
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@ -225,15 +225,15 @@ ParseRet parseInitValues(char **argv, RuntimeParameters &params) {
params.init_params = init_params_;
global_rt_setup = std::make_unique<Rcpp::List>();
*global_rt_setup = source(runtime_file, Rcpp::Named("local", true));
*global_rt_setup = source_R(runtime_file, Rcpp::Named("local", true));
*global_rt_setup = global_rt_setup->operator[]("value");
// MDL add "out_ext" for output format to R setup
(*global_rt_setup)["out_ext"] = params.out_ext;
params.timesteps =
Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("timesteps"));
} catch (const std::exception &e) {
ERRMSG("Error while parsing R scripts: " + std::string(e.what()));
return ParseRet::PARSER_ERROR;
@ -250,7 +250,7 @@ void call_master_iter_end(RInside &R, const Field &trans, const Field &chem) {
R.parseEval(std::string("state_T <- setNames(data.frame(matrix(TMP, nrow=" +
std::to_string(trans.GetRequestedVecSize()) +
")), TMP_PROPS)"));
R["TMP"] = Rcpp::wrap(chem.AsVector());
R["TMP_PROPS"] = Rcpp::wrap(chem.GetProps());
R.parseEval(std::string("state_C <- setNames(data.frame(matrix(TMP, nrow=" +
@ -264,16 +264,16 @@ void call_master_iter_end(RInside &R, const Field &trans, const Field &chem) {
static Rcpp::List RunMasterLoop(RInsidePOET &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) */
uint32_t maxiter = params.timesteps.size();
if (params.print_progressbar) {
chem.setProgressBarPrintout(true);
}
R["TMP_PROPS"] = Rcpp::wrap(chem.getField().GetProps());
/* SIMULATION LOOP */
double dSimTime{0};
for (uint32_t iter = 1; iter < maxiter + 1; iter++) {
@ -302,7 +302,7 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
std::to_string(chem.getField().GetRequestedVecSize()) + ")), TMP_PROPS)"));
R.parseEval("predictors <- predictors[ai_surrogate_species]");
// Apply preprocessing
// Apply preprocessing
MSG("AI Preprocessing");
R.parseEval("predictors_scaled <- preprocess(predictors)");
@ -317,7 +317,7 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
// Validate prediction and write valid predictions to chem field
MSG("AI Validate");
R.parseEval("validity_vector <- validate_predictions(predictors, aipreds)");
MSG("AI Marking accepted");
chem.set_ai_surrogate_validity_vector(R.parseEval("validity_vector"));
@ -327,13 +327,13 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
validity_vector)");
MSG("AI Set Field");
Field predictions_field = Field(R.parseEval("nrow(predictors)"),
Field predictions_field = Field(R.parseEval("nrow(predictors)"),
RTempField,
R.parseEval("colnames(predictors)"));
MSG("AI Update");
chem.getField().update(predictions_field);
double ai_end_t = MPI_Wtime();
double ai_end_t = MPI_Wtime();
R["ai_prediction_time"] = ai_end_t - ai_start_t;
}
@ -348,7 +348,7 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
"targets <- setNames(data.frame(matrix(TMP, nrow=" +
std::to_string(chem.getField().GetRequestedVecSize()) + ")), TMP_PROPS)"));
R.parseEval("targets <- targets[ai_surrogate_species]");
// TODO: Check how to get the correct columns
R.parseEval("target_scaled <- preprocess(targets)");
@ -465,19 +465,19 @@ std::vector<std::string> getSpeciesNames(const Field &&field, int root,
int main(int argc, char *argv[]) {
int world_size;
MPI_Init(&argc, &argv);
{
MPI_Comm_size(MPI_COMM_WORLD, &world_size);
MPI_Comm_rank(MPI_COMM_WORLD, &MY_RANK);
RInsidePOET &R = RInsidePOET::getInstance();
if (MY_RANK == 0) {
MSG("Running POET version " + std::string(poet_version));
}
init_global_functions(R);
@ -491,19 +491,19 @@ int main(int argc, char *argv[]) {
case ParseRet::PARSER_OK:
break;
}
InitialList init_list(R);
init_list.importList(run_params.init_params, MY_RANK != 0);
MSG("RInside initialized on process " + std::to_string(MY_RANK));
std::cout << std::flush;
MPI_Barrier(MPI_COMM_WORLD);
ChemistryModule chemistry(run_params.work_package_size,
init_list.getChemistryInit(), MPI_COMM_WORLD);
const ChemistryModule::SurrogateSetup surr_setup = {
getSpeciesNames(init_list.getInitialGrid(), 0, MPI_COMM_WORLD),
@ -541,28 +541,28 @@ int main(int argc, char *argv[]) {
R["ai_surrogate_species"] = init_list.getChemistryInit().dht_species.getNames();
const std::string ai_surrogate_input_script = init_list.getChemistryInit().ai_surrogate_input_script;
MSG("AI: sourcing user-provided script");
R.parseEvalQ(ai_surrogate_input_script);
MSG("AI: initialize AI model");
R.parseEval("model <- initiate_model()");
R.parseEval("gpu_info()");
}
MSG("Init done on process with rank " + std::to_string(MY_RANK));
// MPI_Barrier(MPI_COMM_WORLD);
DiffusionModule diffusion(init_list.getDiffusionInit(),
init_list.getInitialGrid());
chemistry.masterSetField(init_list.getInitialGrid());
Rcpp::List profiling = RunMasterLoop(R, run_params, diffusion, chemistry);
MSG("finished simulation loop");
R["profiling"] = profiling;
R["setup"] = *global_rt_setup;
R["setup$out_ext"] = run_params.out_ext;
@ -571,7 +571,7 @@ int main(int argc, char *argv[]) {
r_vis_code =
"SaveRObj(x = profiling, path = paste0(out_dir, '/timings.', setup$out_ext));";
R.parseEval(r_vis_code);
MSG("Done! Results are stored as R objects into <" + run_params.out_dir +
"/timings." + run_params.out_ext);
}