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cleanup of kin.cpp

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Max Lübke 2021-02-02 18:26:29 +01:00
parent 049120ae96
commit 33d35eafda
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3 changed files with 49 additions and 458 deletions
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src/kin.cpp
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@ -1,81 +1,19 @@
#include <ChemSim.h>
#include <Grid.h>
#include <RRuntime.h>
#include <Rcpp.h> #include <Rcpp.h>
#include <SimParams.h>
#include <TransportSim.h>
#include <cstring> #include <cstring>
#include <iostream> #include <iostream>
#include <string> #include <string>
#include <vector> #include <vector>
// #include "DHT.h" // MPI-DHT Implementation
// #include "argh.h" // Argument handler https://github.com/adishavit/argh
// BSD-licenced #include "dht_wrapper.h" #include "global_buffer.h"
#include <ChemSim.h>
#include <Grid.h>
#include <RRuntime.h>
#include <SimParams.h>
#include <TransportSim.h>
// #include "worker.h"
//#define DHT_SIZE_PER_PROCESS 1073741824
using namespace std; using namespace std;
using namespace poet; using namespace poet;
using namespace Rcpp; using namespace Rcpp;
// double *mpi_buffer;
// double *mpi_buffer_results;
// uint32_t work_package_size;
// #define WORK_PACKAGE_SIZE_DEFAULT 5
// bool store_result;
// std::set<std::string> paramList() {
// std::set<std::string> options;
// // global
// options.insert("work-package-size");
// // only DHT
// options.insert("dht-signif");
// options.insert("dht-strategy");
// options.insert("dht-size");
// options.insert("dht-snaps");
// options.insert("dht-file");
// return options;
// }
// std::set<std::string> flagList() {
// std::set<std::string> options;
// // global
// options.insert("ignore-result");
// // only DHT
// options.insert("dht");
// options.insert("dht-log");
// return options;
// }
// std::list<std::string> checkOptions(argh::parser cmdl) {
// std::list<std::string> retList;
// std::set<std::string> flist = flagList();
// std::set<std::string> plist = paramList();
// for (auto &flag : cmdl.flags()) {
// if (!(flist.find(flag) != flist.end())) retList.push_back(flag);
// }
// for (auto &param : cmdl.params()) {
// if (!(plist.find(param.first) != plist.end()))
// retList.push_back(param.first);
// }
// return retList;
// }
// typedef struct {
// char has_work;
// double *send_addr;
// } worker_struct;
int main(int argc, char *argv[]) { int main(int argc, char *argv[]) {
double sim_start, sim_b_transport, sim_a_transport, sim_b_chemistry, double sim_start, sim_b_transport, sim_a_transport, sim_b_chemistry,
sim_a_chemistry, sim_end; sim_a_chemistry, sim_end;
@ -84,10 +22,6 @@ int main(int argc, char *argv[]) {
double cummul_chemistry = 0.f; double cummul_chemistry = 0.f;
double cummul_master_seq = 0.f; double cummul_master_seq = 0.f;
// argh::parser cmdl(argv);
// int dht_significant_digits;
// cout << "CPP: Start Init (MPI)" << endl;
int world_size, world_rank; int world_size, world_rank;
MPI_Init(&argc, &argv); MPI_Init(&argc, &argv);
@ -97,7 +31,7 @@ int main(int argc, char *argv[]) {
MPI_Comm_rank(MPI_COMM_WORLD, &world_rank); MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
/*Create custom Communicator with all processes except 0 (the master) for DHT /*Create custom Communicator with all processes except 0 (the master) for DHT
* storage*/ * storage */
MPI_Comm dht_comm; MPI_Comm dht_comm;
if (world_rank == 0) { if (world_rank == 0) {
@ -105,80 +39,9 @@ int main(int argc, char *argv[]) {
} else { } else {
MPI_Comm_split(MPI_COMM_WORLD, 1, world_rank, &dht_comm); MPI_Comm_split(MPI_COMM_WORLD, 1, world_rank, &dht_comm);
} }
// cout << "Done";
// if (cmdl[{"help", "h"}]) {
// if (params.world_rank == 0) {
// cout << "Todo" << endl
// << "See README.md for further information." << endl;
// }
// MPI_Finalize();
// return EXIT_SUCCESS;
// }
// /*INIT is now done separately in an R file provided here as argument!*/
// if (!cmdl(2)) {
// if (params.world_rank == 0) {
// cerr << "ERROR. Kin needs 2 positional arguments: " << endl
// << "1) the R script defining your simulation and" << endl
// << "2) the directory prefix where to save results and profiling"
// << endl;
// }
// MPI_Finalize();
// return EXIT_FAILURE;
// }
// std::list<std::string> optionsError = checkOptions(cmdl);
// if (!optionsError.empty()) {
// if (params.world_rank == 0) {
// cerr << "Unrecognized option(s):\n" << endl;
// for (auto option : optionsError) {
// cerr << option << endl;
// }
// cerr << "\nMake sure to use available options. Exiting!" << endl;
// }
// MPI_Finalize();
// return EXIT_FAILURE;
// }
// /*Parse DHT arguments*/
// params.dht_enabled = cmdl["dht"];
// // cout << "CPP: DHT is " << ( dht_enabled ? "ON" : "OFF" ) << '\n';
// if (params.dht_enabled) {
// cmdl("dht-strategy", 0) >> params.dht_strategy;
// // cout << "CPP: DHT strategy is " << dht_strategy << endl;
// cmdl("dht-signif", 5) >> dht_significant_digits;
// // cout << "CPP: DHT significant digits = " << dht_significant_digits <<
// // endl;
// params.dht_log = !(cmdl["dht-nolog"]);
// // cout << "CPP: DHT logarithm before rounding: " << ( dht_logarithm ?
// "ON"
// // : "OFF" ) << endl;
// cmdl("dht-size", DHT_SIZE_PER_PROCESS) >> params.dht_size_per_process;
// // cout << "CPP: DHT size per process (Byte) = " << dht_size_per_process
// <<
// // endl;
// cmdl("dht-snaps", 0) >> params.dht_snaps;
// cmdl("dht-file") >> params.dht_file;
// }
// /*Parse work package size*/
// cmdl("work-package-size", WORK_PACKAGE_SIZE_DEFAULT) >> params.wp_size;
// /*Parse output options*/
// store_result = !cmdl["ignore-result"];
/* initialize R runtime */
RRuntime R(argc, argv); RRuntime R(argc, argv);
cout << "CPP: R Init (RInside) on process " << world_rank << endl;
// if local_rank == 0 then master else worker
// R["local_rank"] = params.world_rank;
/*Loading Dependencies*/ /*Loading Dependencies*/
std::string r_load_dependencies = std::string r_load_dependencies =
@ -188,8 +51,8 @@ int main(int argc, char *argv[]) {
"source('parallel_r_library.R');"; "source('parallel_r_library.R');";
R.parseEvalQ(r_load_dependencies); R.parseEvalQ(r_load_dependencies);
SimParams parser(world_rank, world_size); SimParams params(world_rank, world_size);
int pret = parser.parseFromCmdl(argv, R); int pret = params.parseFromCmdl(argv, R);
if (pret == PARSER_ERROR) { if (pret == PARSER_ERROR) {
MPI_Finalize(); MPI_Finalize();
@ -199,231 +62,81 @@ int main(int argc, char *argv[]) {
return EXIT_SUCCESS; return EXIT_SUCCESS;
} }
// parser.parseR(R); cout << "CPP: R Init (RInside) on process " << world_rank << endl;
// params = parser.getParams();
// if (params.world_rank == 0) {
// cout << "CPP: Complete results storage is " << (params.store_result ?
// "ON" : "OFF")
// << endl;
// cout << "CPP: Work Package Size: " << params.wp_size << endl;
// cout << "CPP: DHT is " << (params.dht_enabled ? "ON" : "OFF") << '\n';
// if (params.dht_enabled) {
// cout << "CPP: DHT strategy is " << params.dht_strategy << endl;
// // cout << "CPP: DHT key default digits (ignored if 'signif_vector' is
// "
// // "defined) = "
// // << dht_significant_digits << endl;
// cout << "CPP: DHT logarithm before rounding: "
// << (params.dht_log ? "ON" : "OFF") << endl;
// cout << "CPP: DHT size per process (Byte) = "
// << params.dht_size_per_process << endl;
// cout << "CPP: DHT save snapshots is " << params.dht_snaps << endl;
// cout << "CPP: DHT load file is " << params.dht_file << endl;
// }
// }
// std::string filesim;
// cmdl(1) >> filesim; // <- first positional argument
// R["filesim"] = wrap(filesim); // assign a char* (string) to 'filesim'
// R.parseEvalQ(
// "source(filesim)"); // eval the init string, ignoring any returns
// only rank 0 initializes goes through the whole initialization
bool dt_differ; bool dt_differ;
if (world_rank == 0) { if (world_rank == 0) {
// cmdl(2) >> params.out_dir; // <- second positional argument
// R["fileout"] =
// wrap(params.out_dir); // assign a char* (string) to 'fileout'
// Note: R::sim_init() checks if the directory already exists,
// if not it makes it
// pass the boolean "store_result" to the R process
// R["store_result"] = store_result;
// get timestep vector from grid_init function ... // get timestep vector from grid_init function ...
std::string master_init_code = "mysetup <- master_init(setup=setup)"; std::string master_init_code = "mysetup <- master_init(setup=setup)";
R.parseEval(master_init_code); R.parseEval(master_init_code);
dt_differ = R.parseEval("mysetup$dt_differ"); dt_differ = R.parseEval("mysetup$dt_differ");
// ... and broadcast it to every other rank unequal to 0
MPI_Bcast(&dt_differ, 1, MPI_C_BOOL, 0, MPI_COMM_WORLD); MPI_Bcast(&dt_differ, 1, MPI_C_BOOL, 0, MPI_COMM_WORLD);
} else { // workers will only read the setup DataFrame defined by input file }
/* workers will only read the setup DataFrame defined by input file */
else {
R.parseEval("mysetup <- setup"); R.parseEval("mysetup <- setup");
MPI_Bcast(&dt_differ, 1, MPI_C_BOOL, 0, MPI_COMM_WORLD); MPI_Bcast(&dt_differ, 1, MPI_C_BOOL, 0, MPI_COMM_WORLD);
} }
parser.setDtDiffer(dt_differ); params.setDtDiffer(dt_differ);
t_simparams params = parser.getNumParams();
if (world_rank == 0) {
cout << "CPP: R init done on process with rank " << params.world_rank
<< endl;
}
// initialize chemistry on all processes // initialize chemistry on all processes
std::string init_chemistry_code = "mysetup <- init_chemistry(setup=mysetup)"; std::string init_chemistry_code = "mysetup <- init_chemistry(setup=mysetup)";
R.parseEval(init_chemistry_code); R.parseEval(init_chemistry_code);
Grid grid(R); Grid grid(R);
// params.grid = &grid;
grid.init(); grid.init();
parser.initVectorParams(R, grid.getCols()); params.initVectorParams(R, grid.getCols());
/* Retrieve state_C from R context for MPI buffer generation */
// Rcpp::DataFrame state_C = R.parseEval("mysetup$state_C");
/* Init Parallel helper functions */
// R["n_procs"] = params.world_size - 1; /* worker count */
// R["work_package_size"] = params.wp_size;
// Removed additional field for ID in previous versions
// if (params.world_rank == 0) {
// mpi_buffer =
// (double *)calloc(grid.getRows() * grid.getCols(), sizeof(double));
// } else {
// mpi_buffer = (double *)calloc(
// (params.wp_size * (grid.getCols())) + BUFFER_OFFSET, sizeof(double));
// mpi_buffer_results =
// (double *)calloc(params.wp_size * (grid.getCols()), sizeof(double));
// }
// if (params.world_rank == 0) {
// cout << "CPP: parallel init completed (buffers allocated)!" << endl;
// }
// MDL: pass to R the DHT stuff (basically, only for storing of
// simulation parameters). These 2 variables are always defined:
// R["dht_enabled"] = params.dht_enabled;
// R["dht_log"] = params.dht_log;
// params.R = &R;
// if (params.dht_enabled) {
// // cout << "\nCreating DHT\n";
// // determine size of dht entries
// // int dht_data_size = grid.getCols() * sizeof(double);
// // int dht_key_size =
// // grid.getCols() * sizeof(double) + (params.dt_differ *
// // sizeof(double));
// // // // determine bucket count for preset memory usage
// // // // bucket size is key + value + 1 byte for status
// // int dht_buckets_per_process =
// // params.dht_size_per_process / (1 + dht_data_size + dht_key_size);
// // MDL : following code moved here from worker.cpp
// /*Load significance vector from R setup file (or set default)*/
// bool signif_vector_exists = R.parseEval("exists('signif_vector')");
// if (signif_vector_exists) {
// params.dht_signif_vector = as<std::vector<int>>(R["signif_vector"]);
// } else {
// params.dht_signif_vector.assign(grid.getCols(),
// params.dht_significant_digits);
// }
// /*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) {
// params.dht_prop_type_vector = as<std::vector<string>>(R["prop_type"]);
// } else {
// params.dht_prop_type_vector.assign(grid.getCols(), "act");
// }
// if (params.world_rank == 0) {
// // // print only on master, values are equal on all workes
// // cout << "CPP: dht_data_size: " << dht_data_size << "\n";
// // cout << "CPP: dht_key_size: " << dht_key_size << "\n";
// // cout << "CPP: dht_buckets_per_process: " << dht_buckets_per_process
// // << endl;
// // 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 = "
// << params.dht_significant_digits << endl;
// }
// // MDL: pass to R the DHT stuff. These variables exist
// // only if dht_enabled is true
// R["dht_final_signif"] = params.dht_signif_vector;
// R["dht_final_proptype"] = params.dht_prop_type_vector;
// }
// // if (params.dht_strategy == 0) {
// // if (params.world_rank != 0) {
// // dht_object = DHT_create(dht_comm, dht_buckets_per_process,
// // dht_data_size, dht_key_size, get_md5);
// // // storing for access from worker and callback functions
// // fuzzing_buffer = (double *)malloc(dht_key_size);
// // }
// // } else {
// // dht_object = DHT_create(MPI_COMM_WORLD, dht_buckets_per_process,
// // dht_data_size, dht_key_size, get_md5);
// // }
// // if (params.world_rank == 0) {
// // cout << "CPP: DHT successfully created!" << endl;
// // }
// }
// MDL: store all parameters // MDL: store all parameters
if (params.world_rank == 0) { if (world_rank == 0) {
cout << "CPP: Calling R Function to store calling parameters" << endl; cout << "CPP: Calling R Function to store calling parameters" << endl;
R.parseEvalQ("StoreSetup(setup=mysetup)"); R.parseEvalQ("StoreSetup(setup=mysetup)");
} }
if (world_rank == 0) {
cout << "CPP: Init done on process with rank " << world_rank << endl;
}
MPI_Barrier(MPI_COMM_WORLD); MPI_Barrier(MPI_COMM_WORLD);
if (params.world_rank == 0) { /* This is executed by the master */ /* THIS IS EXECUTED BY THE MASTER */
ChemMaster master(parser, R, grid); if (world_rank == 0) {
ChemMaster master(params, R, grid);
TransportSim trans(R); TransportSim trans(R);
Rcpp::NumericVector master_send;
Rcpp::NumericVector master_recv;
double *timings;
uint64_t *dht_perfs = NULL;
// a temporary send buffer
sim_start = MPI_Wtime(); sim_start = MPI_Wtime();
// Iteration Count is dynamic, retrieving value from R (is only needed by /* Iteration Count is dynamic, retrieving value from R (is only needed by
// master for the following loop) * master for the following loop) */
uint32_t maxiter = R.parseEval("mysetup$maxiter"); uint32_t maxiter = R.parseEval("mysetup$maxiter");
/*SIMULATION LOOP*/ /* SIMULATION LOOP */
for (uint32_t iter = 1; iter < maxiter + 1; iter++) { for (uint32_t iter = 1; iter < maxiter + 1; iter++) {
cout << "CPP: Evaluating next time step" << endl; cout << "CPP: Evaluating next time step" << endl;
R.parseEvalQ("mysetup <- master_iteration_setup(mysetup)"); R.parseEvalQ("mysetup <- master_iteration_setup(mysetup)");
/*displaying iteration number, with C++ and R iterator*/ /* displaying iteration number, with C++ and R iterator */
cout << "CPP: Going through iteration " << iter << endl; cout << "CPP: Going through iteration " << iter << endl;
cout << "CPP: R's $iter: " << ((uint32_t)(R.parseEval("mysetup$iter"))) cout << "CPP: R's $iter: " << ((uint32_t)(R.parseEval("mysetup$iter")))
<< ". Iteration" << endl; << ". Iteration" << endl;
cout << "CPP: Calling Advection" << endl; cout << "CPP: Calling Advection" << endl;
/* run transport */
trans.run(); trans.run();
// sim_b_transport = MPI_Wtime();
// R.parseEvalQ("mysetup <- master_advection(setup=mysetup)");
// sim_a_transport = MPI_Wtime();
// if (iter == 1) master.prepareSimulation();
cout << "CPP: Chemistry" << endl; cout << "CPP: Chemistry" << endl;
/*Fallback for sequential execution*/
if (params.world_size == 1) { /* Fallback for sequential execution */
if (world_size == 1) {
master.ChemSim::run(); master.ChemSim::run();
} else { }
/* otherwise run parallel */
else {
master.run(); master.run();
} }
@ -433,21 +146,11 @@ int main(int argc, char *argv[]) {
// store_result is TRUE) // store_result is TRUE)
R.parseEvalQ("mysetup <- master_iteration_end(setup=mysetup)"); R.parseEvalQ("mysetup <- master_iteration_end(setup=mysetup)");
// cummul_transport += trans.getTransportTime();
// cummul_chemistry += master.getChemistryTime();
cout << endl cout << endl
<< "CPP: End of *coupling* iteration " << iter << "/" << maxiter << "CPP: End of *coupling* iteration " << iter << "/" << maxiter
<< endl << endl
<< endl; << endl;
// master_send.push_back(master.getSendTime(), "it_" + to_string(iter));
// master_recv.push_back(master.getRecvTime(), "it_" + to_string(iter));
for (int i = 1; i < params.world_size; i++) {
MPI_Send(NULL, 0, MPI_DOUBLE, i, TAG_DHT_ITER, MPI_COMM_WORLD);
}
MPI_Barrier(MPI_COMM_WORLD); MPI_Barrier(MPI_COMM_WORLD);
} // END SIMULATION LOOP } // END SIMULATION LOOP
@ -465,147 +168,29 @@ int main(int argc, char *argv[]) {
trans.end(); trans.end();
if (params.world_size == 1) { if (world_size == 1) {
master.ChemSim::end(); master.ChemSim::end();
} else { } else {
master.end(); master.end();
} }
// Rcpp::NumericVector phreeqc_time;
// Rcpp::NumericVector dht_get_time;
// Rcpp::NumericVector dht_fill_time;
// Rcpp::IntegerVector phreeqc_counts;
// Rcpp::NumericVector idle_worker;
// int phreeqc_tmp;
// timings = (double *)calloc(3, sizeof(double));
// int dht_hits = 0;
// int dht_miss = 0;
// int dht_collision = 0;
// if (params.dht_enabled) {
// dht_hits = 0;
// dht_miss = 0;
// dht_collision = 0;
// dht_perfs = (uint64_t *)calloc(3, sizeof(uint64_t));
// }
// double idle_worker_tmp;
// for (int p = 0; p < params.world_size - 1; p++) {
// /* ATTENTION Worker p has rank p+1 */
// /* Send termination message to worker */
// MPI_Send(NULL, 0, MPI_DOUBLE, p + 1, TAG_FINISH, MPI_COMM_WORLD);
// MPI_Recv(timings, 3, MPI_DOUBLE, p + 1, TAG_TIMING, MPI_COMM_WORLD,
// MPI_STATUS_IGNORE);
// phreeqc_time.push_back(timings[0], "w" + to_string(p + 1));
// MPI_Recv(&phreeqc_tmp, 1, MPI_INT, p + 1, TAG_TIMING, MPI_COMM_WORLD,
// MPI_STATUS_IGNORE);
// phreeqc_counts.push_back(phreeqc_tmp, "w" + to_string(p + 1));
// MPI_Recv(&idle_worker_tmp, 1, MPI_DOUBLE, p + 1, TAG_TIMING,
// MPI_COMM_WORLD, MPI_STATUS_IGNORE);
// idle_worker.push_back(idle_worker_tmp, "w" + to_string(p + 1));
// if (params.dht_enabled) {
// dht_get_time.push_back(timings[1], "w" + to_string(p + 1));
// dht_fill_time.push_back(timings[2], "w" + to_string(p + 1));
// MPI_Recv(dht_perfs, 3, MPI_UNSIGNED_LONG_LONG, p + 1, TAG_DHT_PERF,
// MPI_COMM_WORLD, MPI_STATUS_IGNORE);
// dht_hits += dht_perfs[0];
// dht_miss += dht_perfs[1];
// dht_collision += dht_perfs[2];
// }
// }
// R.parseEvalQ("profiling <- list()");
// R["simtime"] = sim_end - sim_start;
// R.parseEvalQ("profiling$simtime <- simtime");
// R["simtime_transport"] = cummul_transport;
// R.parseEvalQ("profiling$simtime_transport <- simtime_transport");
// R["simtime_chemistry"] = cummul_chemistry;
// R.parseEvalQ("profiling$simtime_chemistry <- simtime_chemistry");
// R["simtime_workers"] = master.getWorkerTime();
// R.parseEvalQ("profiling$simtime_workers <- simtime_workers");
// R["simtime_chemistry_master"] = master.getChemMasterTime();
// R.parseEvalQ(
// "profiling$simtime_chemistry_master <- simtime_chemistry_master");
// R["seq_master"] = cummul_master_seq;
// R.parseEvalQ("profiling$seq_master <- seq_master");
// // R["master_send"] = master_send;
// // R.parseEvalQ("profiling$master_send <- master_send");
// // R["master_recv"] = master_recv;
// // R.parseEvalQ("profiling$master_recv <- master_recv");
// R["idle_master"] = master.getIdleTime();
// R.parseEvalQ("profiling$idle_master <- idle_master");
// R["idle_worker"] = idle_worker;
// R.parseEvalQ("profiling$idle_worker <- idle_worker");
// R["phreeqc_time"] = phreeqc_time;
// R.parseEvalQ("profiling$phreeqc <- phreeqc_time");
// R["phreeqc_count"] = phreeqc_counts;
// R.parseEvalQ("profiling$phreeqc_count <- phreeqc_count");
// if (params.dht_enabled) {
// R["dht_hits"] = dht_hits;
// R.parseEvalQ("profiling$dht_hits <- dht_hits");
// R["dht_miss"] = dht_miss;
// R.parseEvalQ("profiling$dht_miss <- dht_miss");
// R["dht_collision"] = dht_collision;
// R.parseEvalQ("profiling$dht_collisions <- dht_collision");
// R["dht_get_time"] = dht_get_time;
// R.parseEvalQ("profiling$dht_get_time <- dht_get_time");
// R["dht_fill_time"] = dht_fill_time;
// R.parseEvalQ("profiling$dht_fill_time <- dht_fill_time");
// }
// free(timings);
// if (params.dht_enabled) free(dht_perfs);
string r_vis_code; string r_vis_code;
r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));"; r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));";
R.parseEval(r_vis_code); R.parseEval(r_vis_code);
cout << "CPP: Done! Results are stored as R objects into <" cout << "CPP: Done! Results are stored as R objects into <"
<< parser.getOutDir() << "/timings.rds>" << endl; << params.getOutDir() << "/timings.rds>" << endl;
/*exporting results and profiling data*/ }
/* THIS IS EXECUTED BY THE WORKERS */
// std::string r_vis_code; else {
// r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));"; ChemWorker worker(params, R, grid, dht_comm);
// R.parseEval(r_vis_code);
} else { /*This is executed by the workers*/
ChemWorker worker(parser, R, grid, dht_comm);
// worker.prepareSimulation(dht_comm);
worker.loop(); worker.loop();
} }
cout << "CPP: finished, cleanup of process " << params.world_rank << endl; cout << "CPP: finished, cleanup of process " << world_rank << endl;
// if (params.dht_enabled) {
// if (params.dht_strategy == 0) {
// if (params.world_rank != 0) {
// DHT_free(dht_object, NULL, NULL);
// }
// } else {
// DHT_free(dht_object, NULL, NULL);
// }
// }
// free(mpi_buffer);
MPI_Finalize(); MPI_Finalize();
if (params.world_rank == 0) { if (world_rank == 0) {
cout << "CPP: done, bye!" << endl; cout << "CPP: done, bye!" << endl;
} }

5
src/model/ChemMaster.cpp
View File

@ -125,6 +125,11 @@ void ChemMaster::run() {
/* end time measurement of whole chemistry simulation */ /* end time measurement of whole chemistry simulation */
chem_b = MPI_Wtime(); chem_b = MPI_Wtime();
chem_t += chem_b - chem_a; chem_t += chem_b - chem_a;
/* advise workers to end chemistry iteration */
for (int i = 1; i < world_size; i++) {
MPI_Send(NULL, 0, MPI_DOUBLE, i, TAG_DHT_ITER, MPI_COMM_WORLD);
}
} }
void ChemMaster::sendPkgs(int &pkg_to_send, int &count_pkgs, void ChemMaster::sendPkgs(int &pkg_to_send, int &count_pkgs,

3
src/util/SimParams.h
View File

@ -4,7 +4,8 @@
#include <string> #include <string>
#include "RRuntime.h" #include "RRuntime.h"
#include "argh.h" #include "argh.h" // Argument handler https://github.com/adishavit/argh
// BSD-licenced
/** Return value if no error occured */ /** Return value if no error occured */
#define PARSER_OK 0 #define PARSER_OK 0